##### Testing testOptimizeHelicesCommandWithLengths #####
Oct 19, 2010 2:04:33 PM rnadesign.designapp.OptimizeBasepairsCommand <init>
INFO: Creating OptimizeBasepairsCommand object
Oct 19, 2010 2:04:33 PM rnadesign.rnamodel.RnaPdbRnaviewReader readBundle
INFO: Launching command: /home/bas2/bindewae/spvs_projects/nanotiler/develop/nanotiler_05022009/bin/addrnaview /tmp/nanotiler46585.pdb n
Status of read reference bases: 

4
G C A U 
Status of read reference base pairs: 

Number of defined base pairs: 0

Status of read reference junctions and kissing loops: 

No junction data defined.
No kissing loop data defined.
Oct 19, 2010 2:04:34 PM rnadesign.designapp.LoadJunctionsCommand executeWithoutUndo
INFO: Starting to read junctions using a minimum stem-length cutoff of 3
Oct 19, 2010 2:04:34 PM rnadesign.rnamodel.StrandJunctionDBTools parsePdbFilesToDB
INFO: Processing file : /home/bas2/bindewae/spvs_projects/nanotiler/develop/nanotiler_05022009/test/fixtures/2J00.rnaview.pdb_j3_A-G1064_A-C1107_A-G1187_filt_rnaview.pdb
Oct 19, 2010 2:04:34 PM rnadesign.rnamodel.StrandJunctionDBTools parsePdbFilesToDB
INFO: NOT randomizing orientation of object tree: PdbImport
Oct 19, 2010 2:04:34 PM rnadesign.rnamodel.StrandJunctionDBTools parsePdbFilesToDB
INFO: Generated 3 stems using a minimum length cutoff 3
Oct 19, 2010 2:04:34 PM rnadesign.rnamodel.StrandJunctionDBTools parsePdbFilesToDB
INFO: StrandJunctionDBTools: Generating junctions from 3 stems.
Oct 19, 2010 2:04:36 PM rnadesign.rnamodel.StrandJunctionDBTools parsePdbFilesToDB
INFO: Number of junctions in pdb: 1
Oct 19, 2010 2:04:36 PM tools3d.objects3d.SimpleObject3D setFilename
INFO: object filename = 2J00a
Oct 19, 2010 2:04:36 PM rnadesign.rnamodel.StrandJunctionDBTools parsePdbFilesToDB
INFO: Number of kissing loops in pdb: 0
Status of read reference bases: 

4
G C A U 
Status of read reference base pairs: 

Number of defined base pairs: 0

Status of read reference junctions and kissing loops: 

Number of loaded junctions of order 3 : 1
Number of loaded kissing loops: 0
Oct 19, 2010 2:04:36 PM tools3d.objects3d.SimpleObject3D setFilename
INFO: object filename = 2J00a
Oct 19, 2010 2:04:37 PM tools3d.objects3d.SimpleObject3D setFilename
INFO: object filename = 2J00a
Oct 19, 2010 2:04:37 PM tools3d.objects3d.SimpleObject3D setFilename
INFO: object filename = 2J00a
Oct 19, 2010 2:04:37 PM rnadesign.designapp.TreeCommand executeWithoutUndo
INFO: Using name: null
root 1 3 Object3D   0.000   0.000   0.000
root.j1 1.1 6 StrandJunction3D   0.000   0.000   0.000
root.j1.A_1_B_10 1.1.1 1 BranchDescriptor3D  -1.658  -8.312  14.875
root.j1.A_1_B_10.coordinate-system 1.1.1.1 3 CoordinateSystem3D  -1.658  -8.312  14.875
root.j1.A_1_B_10.coordinate-system.x 1.1.1.1.1 0 Object3D  -0.703  -8.037  14.980
root.j1.A_1_B_10.coordinate-system.y 1.1.1.1.2 0 Object3D  -1.934  -7.603  15.524
root.j1.A_1_B_10.coordinate-system.z 1.1.1.1.3 0 Object3D  -1.554  -8.961  15.628
root.j1.A_1-9_1 1.1.2 9 RnaStrand   4.116   1.298   7.038
root.j1.A_1-9_1.U1 1.1.2.1 20 Nucleotide3D  -3.103  -0.014  15.761
root.j1.A_1-9_1.C2 1.1.2.2 20 Nucleotide3D   1.109   2.305  14.205
root.j1.A_1-9_1.G3 1.1.2.3 23 Nucleotide3D   0.980   3.531  10.385
root.j1.A_1-9_1.U4 1.1.2.4 20 Nucleotide3D  -2.846   5.013   5.325
root.j1.A_1-9_1.C5 1.1.2.5 20 Nucleotide3D   2.263   6.218   6.487
root.j1.A_1-9_1.A6 1.1.2.6 22 Nucleotide3D   5.731   5.040   3.061
root.j1.A_1-9_1.G7 1.1.2.7 23 Nucleotide3D   9.023   0.907   2.659
root.j1.A_1-9_1.C8 1.1.2.8 20 Nucleotide3D  10.942  -3.625   3.656
root.j1.A_1-9_1.U9 1.1.2.9 20 Nucleotide3D  12.942  -7.695   1.804
root.j1.B_1-10_1 1.1.3 10 RnaStrand  -4.869   1.179   3.977
root.j1.B_1-10_1.G1 1.1.3.1 23 Nucleotide3D -11.627  15.753  -4.574
root.j1.B_1-10_1.G2 1.1.3.2 23 Nucleotide3D -13.266  12.214  -1.325
root.j1.B_1-10_1.G3 1.1.3.3 23 Nucleotide3D -13.856   7.031  -0.204
root.j1.B_1-10_1.A4 1.1.3.4 22 Nucleotide3D -12.580   2.685   0.266
root.j1.B_1-10_1.C5 1.1.3.5 20 Nucleotide3D  -9.143   0.476   1.384
root.j1.B_1-10_1.G6 1.1.3.6 23 Nucleotide3D  -5.407  -0.520   6.051
root.j1.B_1-10_1.A7 1.1.3.7 22 Nucleotide3D   2.525  -3.797   4.828
root.j1.B_1-10_1.C8 1.1.3.8 20 Nucleotide3D   5.329  -7.732   6.611
root.j1.B_1-10_1.G9 1.1.3.9 23 Nucleotide3D   4.861  -7.762  10.814
root.j1.B_1-10_1.U10 1.1.3.10 20 Nucleotide3D   4.477  -6.560  15.919
root.j1.C_1_A_9 1.1.4 1 BranchDescriptor3D  15.928  -3.068  -3.557
root.j1.C_1_A_9.coordinate-system 1.1.4.1 3 CoordinateSystem3D  15.928  -3.068  -3.557
root.j1.C_1_A_9.coordinate-system.x 1.1.4.1.1 0 Object3D  15.590  -3.695  -2.854
root.j1.C_1_A_9.coordinate-system.y 1.1.4.1.2 0 Object3D  15.835  -3.789  -4.244
root.j1.C_1_A_9.coordinate-system.z 1.1.4.1.3 0 Object3D  16.864  -3.366  -3.371
root.j1.C_1-11_1 1.1.5 11 RnaStrand  -3.242  -0.063  -6.865
root.j1.C_1-11_1.A1 1.1.5.1 22 Nucleotide3D  11.625  -7.563  -9.362
root.j1.C_1-11_1.G2 1.1.5.2 23 Nucleotide3D   7.659  -8.040  -5.894
root.j1.C_1-11_1.C3 1.1.5.3 20 Nucleotide3D   4.204  -6.879  -3.086
root.j1.C_1-11_1.G4 1.1.5.4 23 Nucleotide3D   2.981  -1.876  -1.780
root.j1.C_1-11_1.C5 1.1.5.5 20 Nucleotide3D   1.509   2.125  -3.501
root.j1.C_1-11_1.A6 1.1.5.6 22 Nucleotide3D  -0.966   3.447  -6.854
root.j1.C_1-11_1.A7 1.1.5.7 22 Nucleotide3D  -4.277   2.738  -9.641
root.j1.C_1-11_1.C8 1.1.5.8 20 Nucleotide3D  -8.296   0.698 -11.123
root.j1.C_1-11_1.C9 1.1.5.9 20 Nucleotide3D -13.161   1.692  -9.528
root.j1.C_1-11_1.C10 1.1.5.10 20 Nucleotide3D -17.313   4.213  -7.849
root.j1.C_1-11_1.C11 1.1.5.11 20 Nucleotide3D -19.627   8.755  -6.899
root.j1.B_1_C_11 1.1.6 1 BranchDescriptor3D -14.270  11.380 -11.318
root.j1.B_1_C_11.coordinate-system 1.1.6.1 3 CoordinateSystem3D -14.270  11.380 -11.318
root.j1.B_1_C_11.coordinate-system.x 1.1.6.1.1 0 Object3D -15.038  11.041 -10.775
root.j1.B_1_C_11.coordinate-system.y 1.1.6.1.2 0 Object3D -14.251  12.217 -10.770
root.j1.B_1_C_11.coordinate-system.z 1.1.6.1.3 0 Object3D -14.910  11.811 -11.954
root.j2 1.2 6 StrandJunction3D 100.000   0.000   0.000
root.j2.A_1_B_10 1.2.1 1 BranchDescriptor3D  98.342  -8.312  14.875
root.j2.A_1_B_10.coordinate-system 1.2.1.1 3 CoordinateSystem3D  98.342  -8.312  14.875
root.j2.A_1_B_10.coordinate-system.x 1.2.1.1.1 0 Object3D  99.297  -8.037  14.980
root.j2.A_1_B_10.coordinate-system.y 1.2.1.1.2 0 Object3D  98.066  -7.603  15.524
root.j2.A_1_B_10.coordinate-system.z 1.2.1.1.3 0 Object3D  98.446  -8.961  15.628
root.j2.A_1-9_2 1.2.2 9 RnaStrand 104.116   1.298   7.038
root.j2.A_1-9_2.U1 1.2.2.1 20 Nucleotide3D  96.897  -0.014  15.761
root.j2.A_1-9_2.C2 1.2.2.2 20 Nucleotide3D 101.109   2.305  14.205
root.j2.A_1-9_2.G3 1.2.2.3 23 Nucleotide3D 100.980   3.531  10.385
root.j2.A_1-9_2.U4 1.2.2.4 20 Nucleotide3D  97.154   5.013   5.325
root.j2.A_1-9_2.C5 1.2.2.5 20 Nucleotide3D 102.263   6.218   6.487
root.j2.A_1-9_2.A6 1.2.2.6 22 Nucleotide3D 105.731   5.040   3.061
root.j2.A_1-9_2.G7 1.2.2.7 23 Nucleotide3D 109.023   0.907   2.659
root.j2.A_1-9_2.C8 1.2.2.8 20 Nucleotide3D 110.942  -3.625   3.656
root.j2.A_1-9_2.U9 1.2.2.9 20 Nucleotide3D 112.942  -7.695   1.804
root.j2.B_1-10_2 1.2.3 10 RnaStrand  95.131   1.179   3.977
root.j2.B_1-10_2.G1 1.2.3.1 23 Nucleotide3D  88.373  15.753  -4.574
root.j2.B_1-10_2.G2 1.2.3.2 23 Nucleotide3D  86.734  12.214  -1.325
root.j2.B_1-10_2.G3 1.2.3.3 23 Nucleotide3D  86.144   7.031  -0.204
root.j2.B_1-10_2.A4 1.2.3.4 22 Nucleotide3D  87.420   2.685   0.266
root.j2.B_1-10_2.C5 1.2.3.5 20 Nucleotide3D  90.857   0.476   1.384
root.j2.B_1-10_2.G6 1.2.3.6 23 Nucleotide3D  94.593  -0.520   6.051
root.j2.B_1-10_2.A7 1.2.3.7 22 Nucleotide3D 102.525  -3.797   4.828
root.j2.B_1-10_2.C8 1.2.3.8 20 Nucleotide3D 105.329  -7.732   6.611
root.j2.B_1-10_2.G9 1.2.3.9 23 Nucleotide3D 104.861  -7.762  10.814
root.j2.B_1-10_2.U10 1.2.3.10 20 Nucleotide3D 104.477  -6.560  15.919
root.j2.C_1_A_9 1.2.4 1 BranchDescriptor3D 115.928  -3.068  -3.557
root.j2.C_1_A_9.coordinate-system 1.2.4.1 3 CoordinateSystem3D 115.928  -3.068  -3.557
root.j2.C_1_A_9.coordinate-system.x 1.2.4.1.1 0 Object3D 115.590  -3.695  -2.854
root.j2.C_1_A_9.coordinate-system.y 1.2.4.1.2 0 Object3D 115.835  -3.789  -4.244
root.j2.C_1_A_9.coordinate-system.z 1.2.4.1.3 0 Object3D 116.864  -3.366  -3.371
root.j2.C_1-11_2 1.2.5 11 RnaStrand  96.758  -0.063  -6.865
root.j2.C_1-11_2.A1 1.2.5.1 22 Nucleotide3D 111.625  -7.563  -9.362
root.j2.C_1-11_2.G2 1.2.5.2 23 Nucleotide3D 107.659  -8.040  -5.894
root.j2.C_1-11_2.C3 1.2.5.3 20 Nucleotide3D 104.204  -6.879  -3.086
root.j2.C_1-11_2.G4 1.2.5.4 23 Nucleotide3D 102.981  -1.876  -1.780
root.j2.C_1-11_2.C5 1.2.5.5 20 Nucleotide3D 101.509   2.125  -3.501
root.j2.C_1-11_2.A6 1.2.5.6 22 Nucleotide3D  99.034   3.447  -6.854
root.j2.C_1-11_2.A7 1.2.5.7 22 Nucleotide3D  95.723   2.738  -9.641
root.j2.C_1-11_2.C8 1.2.5.8 20 Nucleotide3D  91.704   0.698 -11.123
root.j2.C_1-11_2.C9 1.2.5.9 20 Nucleotide3D  86.839   1.692  -9.528
root.j2.C_1-11_2.C10 1.2.5.10 20 Nucleotide3D  82.687   4.213  -7.849
root.j2.C_1-11_2.C11 1.2.5.11 20 Nucleotide3D  80.373   8.755  -6.899
root.j2.B_1_C_11 1.2.6 1 BranchDescriptor3D  85.730  11.380 -11.318
root.j2.B_1_C_11.coordinate-system 1.2.6.1 3 CoordinateSystem3D  85.730  11.380 -11.318
root.j2.B_1_C_11.coordinate-system.x 1.2.6.1.1 0 Object3D  84.962  11.041 -10.775
root.j2.B_1_C_11.coordinate-system.y 1.2.6.1.2 0 Object3D  85.749  12.217 -10.770
root.j2.B_1_C_11.coordinate-system.z 1.2.6.1.3 0 Object3D  85.090  11.811 -11.954
root.j3 1.3 6 StrandJunction3D   0.000 100.000   0.000
root.j3.A_1_B_10 1.3.1 1 BranchDescriptor3D  -1.658  91.688  14.875
root.j3.A_1_B_10.coordinate-system 1.3.1.1 3 CoordinateSystem3D  -1.658  91.688  14.875
root.j3.A_1_B_10.coordinate-system.x 1.3.1.1.1 0 Object3D  -0.703  91.963  14.980
root.j3.A_1_B_10.coordinate-system.y 1.3.1.1.2 0 Object3D  -1.934  92.397  15.524
root.j3.A_1_B_10.coordinate-system.z 1.3.1.1.3 0 Object3D  -1.554  91.039  15.628
root.j3.A_1-9_3 1.3.2 9 RnaStrand   4.116 101.298   7.038
root.j3.A_1-9_3.U1 1.3.2.1 20 Nucleotide3D  -3.103  99.986  15.761
root.j3.A_1-9_3.C2 1.3.2.2 20 Nucleotide3D   1.109 102.305  14.205
root.j3.A_1-9_3.G3 1.3.2.3 23 Nucleotide3D   0.980 103.531  10.385
root.j3.A_1-9_3.U4 1.3.2.4 20 Nucleotide3D  -2.846 105.013   5.325
root.j3.A_1-9_3.C5 1.3.2.5 20 Nucleotide3D   2.263 106.218   6.487
root.j3.A_1-9_3.A6 1.3.2.6 22 Nucleotide3D   5.731 105.040   3.061
root.j3.A_1-9_3.G7 1.3.2.7 23 Nucleotide3D   9.023 100.907   2.659
root.j3.A_1-9_3.C8 1.3.2.8 20 Nucleotide3D  10.942  96.375   3.656
root.j3.A_1-9_3.U9 1.3.2.9 20 Nucleotide3D  12.942  92.305   1.804
root.j3.B_1-10_3 1.3.3 10 RnaStrand  -4.869 101.179   3.977
root.j3.B_1-10_3.G1 1.3.3.1 23 Nucleotide3D -11.627 115.753  -4.574
root.j3.B_1-10_3.G2 1.3.3.2 23 Nucleotide3D -13.266 112.214  -1.325
root.j3.B_1-10_3.G3 1.3.3.3 23 Nucleotide3D -13.856 107.031  -0.204
root.j3.B_1-10_3.A4 1.3.3.4 22 Nucleotide3D -12.580 102.685   0.266
root.j3.B_1-10_3.C5 1.3.3.5 20 Nucleotide3D  -9.143 100.476   1.384
root.j3.B_1-10_3.G6 1.3.3.6 23 Nucleotide3D  -5.407  99.480   6.051
root.j3.B_1-10_3.A7 1.3.3.7 22 Nucleotide3D   2.525  96.203   4.828
root.j3.B_1-10_3.C8 1.3.3.8 20 Nucleotide3D   5.329  92.268   6.611
root.j3.B_1-10_3.G9 1.3.3.9 23 Nucleotide3D   4.861  92.238  10.814
root.j3.B_1-10_3.U10 1.3.3.10 20 Nucleotide3D   4.477  93.440  15.919
root.j3.C_1_A_9 1.3.4 1 BranchDescriptor3D  15.928  96.932  -3.557
root.j3.C_1_A_9.coordinate-system 1.3.4.1 3 CoordinateSystem3D  15.928  96.932  -3.557
root.j3.C_1_A_9.coordinate-system.x 1.3.4.1.1 0 Object3D  15.590  96.305  -2.854
root.j3.C_1_A_9.coordinate-system.y 1.3.4.1.2 0 Object3D  15.835  96.211  -4.244
root.j3.C_1_A_9.coordinate-system.z 1.3.4.1.3 0 Object3D  16.864  96.634  -3.371
root.j3.C_1-11_3 1.3.5 11 RnaStrand  -3.242  99.937  -6.865
root.j3.C_1-11_3.A1 1.3.5.1 22 Nucleotide3D  11.625  92.437  -9.362
root.j3.C_1-11_3.G2 1.3.5.2 23 Nucleotide3D   7.659  91.960  -5.894
root.j3.C_1-11_3.C3 1.3.5.3 20 Nucleotide3D   4.204  93.121  -3.086
root.j3.C_1-11_3.G4 1.3.5.4 23 Nucleotide3D   2.981  98.124  -1.780
root.j3.C_1-11_3.C5 1.3.5.5 20 Nucleotide3D   1.509 102.125  -3.501
root.j3.C_1-11_3.A6 1.3.5.6 22 Nucleotide3D  -0.966 103.447  -6.854
root.j3.C_1-11_3.A7 1.3.5.7 22 Nucleotide3D  -4.277 102.738  -9.641
root.j3.C_1-11_3.C8 1.3.5.8 20 Nucleotide3D  -8.296 100.698 -11.123
root.j3.C_1-11_3.C9 1.3.5.9 20 Nucleotide3D -13.161 101.692  -9.528
root.j3.C_1-11_3.C10 1.3.5.10 20 Nucleotide3D -17.313 104.213  -7.849
root.j3.C_1-11_3.C11 1.3.5.11 20 Nucleotide3D -19.627 108.755  -6.899
root.j3.B_1_C_11 1.3.6 1 BranchDescriptor3D -14.270 111.380 -11.318
root.j3.B_1_C_11.coordinate-system 1.3.6.1 3 CoordinateSystem3D -14.270 111.380 -11.318
root.j3.B_1_C_11.coordinate-system.x 1.3.6.1.1 0 Object3D -15.038 111.041 -10.775
root.j3.B_1_C_11.coordinate-system.y 1.3.6.1.2 0 Object3D -14.251 112.217 -10.770
root.j3.B_1_C_11.coordinate-system.z 1.3.6.1.3 0 Object3D -14.910 111.811 -11.954
Number of generated child nodes of root after importing 3 junctions: 3
Setting first constraint...
Setting second constraint...
Oct 19, 2010 2:04:38 PM rnadesign.rnacontrol.SimpleLinkController toPrettyString
INFO: Starting toPrettyString(null)
LinkCount 2
1 Link root.j1.A_1_B_10 root.j2.C_1_A_9 helix-constraint bpmin=5 bpmax=5 rms=3.0 name=null
2 Link root.j2.A_1_B_10 root.j3.C_1_A_9 helix-constraint bpmin=5 bpmax=5 rms=3.0 name=null

Optimizing helices before closing circle (two-stages: later a ring closing constraint is set and the structure is again optimized
Starting to optimize helices!
All objects with constraints are considered movable.
Number of parent objects that are moved as one block: 3
Starting controller.optimizeHelices!
Oct 19, 2010 2:04:38 PM rnadesign.rnacontrol.Object3DGraphController optimizeHelices
INFO: Starting optimizeHelices...
Oct 19, 2010 2:04:38 PM rnadesign.rnamodel.HelixOptimizer findSuitableParentObject
INFO: Suitable parent object of root.j1.A_1_B_10 is: root.j1
Oct 19, 2010 2:04:38 PM rnadesign.rnamodel.HelixOptimizer findSuitableParentObject
INFO: Suitable parent object of root.j2.C_1_A_9 is: root.j2
Oct 19, 2010 2:04:38 PM rnadesign.rnamodel.HelixOptimizer findSuitableParentObject
INFO: Suitable parent object of root.j1.A_1_B_10 is: root.j1
Oct 19, 2010 2:04:38 PM rnadesign.rnamodel.HelixOptimizer findSuitableParentObject
INFO: Suitable parent object of root.j2.A_1_B_10 is: root.j2
Oct 19, 2010 2:04:38 PM rnadesign.rnamodel.HelixOptimizer findSuitableParentObject
INFO: Suitable parent object of root.j1.A_1_B_10 is: root.j1
Oct 19, 2010 2:04:38 PM rnadesign.rnamodel.HelixOptimizer findSuitableParentObject
INFO: Suitable parent object of root.j3.C_1_A_9 is: root.j3
Oct 19, 2010 2:04:38 PM rnadesign.rnamodel.HelixOptimizer findSuitableParentObject
INFO: Suitable parent object of root.j2.C_1_A_9 is: root.j2
Oct 19, 2010 2:04:38 PM rnadesign.rnamodel.HelixOptimizer findSuitableParentObject
INFO: Suitable parent object of root.j2.A_1_B_10 is: root.j2
Oct 19, 2010 2:04:38 PM rnadesign.rnamodel.HelixOptimizer findSuitableParentObject
INFO: Suitable parent object of root.j2.C_1_A_9 is: root.j2
Oct 19, 2010 2:04:38 PM rnadesign.rnamodel.HelixOptimizer findSuitableParentObject
INFO: Suitable parent object of root.j3.C_1_A_9 is: root.j3
Oct 19, 2010 2:04:38 PM rnadesign.rnamodel.HelixOptimizer findSuitableParentObject
INFO: Suitable parent object of root.j2.A_1_B_10 is: root.j2
Oct 19, 2010 2:04:38 PM rnadesign.rnamodel.HelixOptimizer findSuitableParentObject
INFO: Suitable parent object of root.j3.C_1_A_9 is: root.j3
Oct 19, 2010 2:04:38 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Starting helix optimization! Number of found helix constraints: 2 Number of found distance constraints: 0 error limit0.1 initial error limit: 1.0E15 keep-first-fixed: false
Oct 19, 2010 2:04:38 PM rnadesign.rnamodel.HelixOptimizer findSuitableParentObject
INFO: Suitable parent object of root.j1.A_1_B_10 is: root.j1
Oct 19, 2010 2:04:38 PM rnadesign.rnamodel.HelixOptimizer findSuitableParentObject
INFO: Suitable parent object of root.j2.C_1_A_9 is: root.j2
Oct 19, 2010 2:04:38 PM rnadesign.rnamodel.HelixOptimizer findSuitableParentObject
INFO: Suitable parent object of root.j2.A_1_B_10 is: root.j2
Oct 19, 2010 2:04:38 PM rnadesign.rnamodel.HelixOptimizer findSuitableParentObject
INFO: Suitable parent object of root.j3.C_1_A_9 is: root.j3
Oct 19, 2010 2:04:38 PM rnadesign.rnamodel.HelixOptimizer applyEndPointHelixConstraint
INFO: Perfectly matched (swapped) helix constraint: (Link SimpleHelixConstraintLink root.j2.C_1_A_9 root.j1.A_1_B_10 )

Oct 19, 2010 2:04:38 PM rnadesign.rnamodel.HelixOptimizer applyEndPointHelixConstraint
INFO: Perfectly matched helix constraint: (Link null root.j2.A_1_B_10 root.j3.C_1_A_9 )

Oct 19, 2010 2:04:38 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 3.0175985100399864E-24 at iteration 1 using kt 10.0
Oct 19, 2010 2:04:38 PM rnadesign.rnamodel.HelixOptimizer findSuitableParentObject
INFO: Suitable parent object of root.j1.A_1_B_10 is: root.j1
Oct 19, 2010 2:04:38 PM rnadesign.rnamodel.HelixOptimizer findSuitableParentObject
INFO: Suitable parent object of root.j2.C_1_A_9 is: root.j2
Oct 19, 2010 2:04:38 PM rnadesign.rnamodel.HelixOptimizer findSuitableParentObject
INFO: Suitable parent object of root.j2.A_1_B_10 is: root.j2
Oct 19, 2010 2:04:38 PM rnadesign.rnamodel.HelixOptimizer findSuitableParentObject
INFO: Suitable parent object of root.j3.C_1_A_9 is: root.j3
Oct 19, 2010 2:04:38 PM rnadesign.rnacontrol.Object3DGraphController optimizeHelices
INFO: Finished optimizeHelices...
Finished controller.optimizeHelices!
Helix optimization finished! Result:
{number_steps=1, final_score=3.0175985100399864E-24, start_score=41794.62821514973}
Setting third constraint...
Optimizing helices
Starting to optimize helices!
All objects with constraints are considered movable.
Number of parent objects that are moved as one block: 3
Starting controller.optimizeHelices!
Oct 19, 2010 2:04:38 PM rnadesign.rnacontrol.Object3DGraphController optimizeHelices
INFO: Starting optimizeHelices...
Oct 19, 2010 2:04:38 PM rnadesign.rnamodel.HelixOptimizer findSuitableParentObject
INFO: Suitable parent object of root.j1.A_1_B_10 is: root.j1
Oct 19, 2010 2:04:38 PM rnadesign.rnamodel.HelixOptimizer findSuitableParentObject
INFO: Suitable parent object of root.j2.C_1_A_9 is: root.j2
Oct 19, 2010 2:04:38 PM rnadesign.rnamodel.HelixOptimizer findSuitableParentObject
INFO: Suitable parent object of root.j1.A_1_B_10 is: root.j1
Oct 19, 2010 2:04:38 PM rnadesign.rnamodel.HelixOptimizer findSuitableParentObject
INFO: Suitable parent object of root.j2.A_1_B_10 is: root.j2
Oct 19, 2010 2:04:38 PM rnadesign.rnamodel.HelixOptimizer findSuitableParentObject
INFO: Suitable parent object of root.j1.A_1_B_10 is: root.j1
Oct 19, 2010 2:04:38 PM rnadesign.rnamodel.HelixOptimizer findSuitableParentObject
INFO: Suitable parent object of root.j3.C_1_A_9 is: root.j3
Oct 19, 2010 2:04:38 PM rnadesign.rnamodel.HelixOptimizer findSuitableParentObject
INFO: Suitable parent object of root.j1.A_1_B_10 is: root.j1
Oct 19, 2010 2:04:38 PM rnadesign.rnamodel.HelixOptimizer findSuitableParentObject
INFO: Suitable parent object of root.j3.A_1_B_10 is: root.j3
Oct 19, 2010 2:04:38 PM rnadesign.rnamodel.HelixOptimizer findSuitableParentObject
INFO: Suitable parent object of root.j1.A_1_B_10 is: root.j1
Oct 19, 2010 2:04:38 PM rnadesign.rnamodel.HelixOptimizer findSuitableParentObject
INFO: Suitable parent object of root.j1.C_1_A_9 is: root.j1
Oct 19, 2010 2:04:38 PM rnadesign.rnamodel.HelixOptimizer findSuitableParentObject
INFO: Suitable parent object of root.j2.C_1_A_9 is: root.j2
Oct 19, 2010 2:04:38 PM rnadesign.rnamodel.HelixOptimizer findSuitableParentObject
INFO: Suitable parent object of root.j2.A_1_B_10 is: root.j2
Oct 19, 2010 2:04:38 PM rnadesign.rnamodel.HelixOptimizer findSuitableParentObject
INFO: Suitable parent object of root.j2.C_1_A_9 is: root.j2
Oct 19, 2010 2:04:38 PM rnadesign.rnamodel.HelixOptimizer findSuitableParentObject
INFO: Suitable parent object of root.j3.C_1_A_9 is: root.j3
Oct 19, 2010 2:04:38 PM rnadesign.rnamodel.HelixOptimizer findSuitableParentObject
INFO: Suitable parent object of root.j2.C_1_A_9 is: root.j2
Oct 19, 2010 2:04:38 PM rnadesign.rnamodel.HelixOptimizer findSuitableParentObject
INFO: Suitable parent object of root.j3.A_1_B_10 is: root.j3
Oct 19, 2010 2:04:38 PM rnadesign.rnamodel.HelixOptimizer findSuitableParentObject
INFO: Suitable parent object of root.j2.C_1_A_9 is: root.j2
Oct 19, 2010 2:04:38 PM rnadesign.rnamodel.HelixOptimizer findSuitableParentObject
INFO: Suitable parent object of root.j1.C_1_A_9 is: root.j1
Oct 19, 2010 2:04:38 PM rnadesign.rnamodel.HelixOptimizer findSuitableParentObject
INFO: Suitable parent object of root.j2.A_1_B_10 is: root.j2
Oct 19, 2010 2:04:38 PM rnadesign.rnamodel.HelixOptimizer findSuitableParentObject
INFO: Suitable parent object of root.j3.C_1_A_9 is: root.j3
Oct 19, 2010 2:04:38 PM rnadesign.rnamodel.HelixOptimizer findSuitableParentObject
INFO: Suitable parent object of root.j2.A_1_B_10 is: root.j2
Oct 19, 2010 2:04:38 PM rnadesign.rnamodel.HelixOptimizer findSuitableParentObject
INFO: Suitable parent object of root.j3.A_1_B_10 is: root.j3
Oct 19, 2010 2:04:38 PM rnadesign.rnamodel.HelixOptimizer findSuitableParentObject
INFO: Suitable parent object of root.j2.A_1_B_10 is: root.j2
Oct 19, 2010 2:04:38 PM rnadesign.rnamodel.HelixOptimizer findSuitableParentObject
INFO: Suitable parent object of root.j1.C_1_A_9 is: root.j1
Oct 19, 2010 2:04:38 PM rnadesign.rnamodel.HelixOptimizer findSuitableParentObject
INFO: Suitable parent object of root.j3.C_1_A_9 is: root.j3
Oct 19, 2010 2:04:38 PM rnadesign.rnamodel.HelixOptimizer findSuitableParentObject
INFO: Suitable parent object of root.j3.A_1_B_10 is: root.j3
Oct 19, 2010 2:04:38 PM rnadesign.rnamodel.HelixOptimizer findSuitableParentObject
INFO: Suitable parent object of root.j3.C_1_A_9 is: root.j3
Oct 19, 2010 2:04:38 PM rnadesign.rnamodel.HelixOptimizer findSuitableParentObject
INFO: Suitable parent object of root.j1.C_1_A_9 is: root.j1
Oct 19, 2010 2:04:38 PM rnadesign.rnamodel.HelixOptimizer findSuitableParentObject
INFO: Suitable parent object of root.j3.A_1_B_10 is: root.j3
Oct 19, 2010 2:04:38 PM rnadesign.rnamodel.HelixOptimizer findSuitableParentObject
INFO: Suitable parent object of root.j1.C_1_A_9 is: root.j1
Oct 19, 2010 2:04:38 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Starting helix optimization! Number of found helix constraints: 3 Number of found distance constraints: 0 error limit8.0 initial error limit: 1.0E15 keep-first-fixed: true
Oct 19, 2010 2:04:38 PM rnadesign.rnamodel.HelixOptimizer findSuitableParentObject
INFO: Suitable parent object of root.j1.A_1_B_10 is: root.j1
Oct 19, 2010 2:04:38 PM rnadesign.rnamodel.HelixOptimizer findSuitableParentObject
INFO: Suitable parent object of root.j2.C_1_A_9 is: root.j2
Oct 19, 2010 2:04:38 PM rnadesign.rnamodel.HelixOptimizer findSuitableParentObject
INFO: Suitable parent object of root.j2.A_1_B_10 is: root.j2
Oct 19, 2010 2:04:38 PM rnadesign.rnamodel.HelixOptimizer findSuitableParentObject
INFO: Suitable parent object of root.j3.C_1_A_9 is: root.j3
Oct 19, 2010 2:04:38 PM rnadesign.rnamodel.HelixOptimizer findSuitableParentObject
INFO: Suitable parent object of root.j3.A_1_B_10 is: root.j3
Oct 19, 2010 2:04:38 PM rnadesign.rnamodel.HelixOptimizer findSuitableParentObject
INFO: Suitable parent object of root.j1.C_1_A_9 is: root.j1
Oct 19, 2010 2:04:38 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 643.0708491674376 at iteration 1 using kt 100.0
Currently best helix constraint lengths: 
5 5 5 Oct 19, 2010 2:04:38 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 1 Best score so far: 643.0708491674376 . Using annealing factor: 1.0 kt: 100.0 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:04:38 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 639.8436052416098 at iteration 2 using kt 100.0
Currently best helix constraint lengths: 
5 5 5 Oct 19, 2010 2:04:38 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 635.1966558043263 at iteration 11 using kt 100.0
Currently best helix constraint lengths: 
5 5 5 Oct 19, 2010 2:04:38 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 631.4059108389596 at iteration 14 using kt 100.0
Currently best helix constraint lengths: 
5 5 5 Oct 19, 2010 2:04:38 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 627.3750510226257 at iteration 15 using kt 100.0
Currently best helix constraint lengths: 
5 5 5 Oct 19, 2010 2:04:38 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 625.2480803286973 at iteration 16 using kt 100.0
Currently best helix constraint lengths: 
5 5 5 Oct 19, 2010 2:04:38 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 609.2786016302728 at iteration 17 using kt 100.0
Currently best helix constraint lengths: 
5 5 5 Oct 19, 2010 2:04:39 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 580.9479758141164 at iteration 108 using kt 100.0
Currently best helix constraint lengths: 
5 5 5 Oct 19, 2010 2:04:39 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 579.3227153205628 at iteration 109 using kt 100.0
Currently best helix constraint lengths: 
5 5 5 Oct 19, 2010 2:04:39 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 569.0187009301512 at iteration 111 using kt 100.0
Currently best helix constraint lengths: 
5 5 5 Oct 19, 2010 2:04:39 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 555.654659570919 at iteration 112 using kt 100.0
Currently best helix constraint lengths: 
5 5 5 Oct 19, 2010 2:04:39 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 539.2704100780836 at iteration 113 using kt 100.0
Currently best helix constraint lengths: 
5 5 5 Oct 19, 2010 2:04:39 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 533.8950853462899 at iteration 121 using kt 100.0
Currently best helix constraint lengths: 
5 5 5 Oct 19, 2010 2:04:39 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 525.5163917751365 at iteration 122 using kt 100.0
Currently best helix constraint lengths: 
5 5 5 Oct 19, 2010 2:04:39 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 510.0225161993112 at iteration 138 using kt 100.0
Currently best helix constraint lengths: 
5 5 5 Oct 19, 2010 2:04:39 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 509.21241013948134 at iteration 139 using kt 100.0
Currently best helix constraint lengths: 
5 5 5 Oct 19, 2010 2:04:39 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 504.64097479943325 at iteration 140 using kt 100.0
Currently best helix constraint lengths: 
5 5 5 Oct 19, 2010 2:04:39 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 490.35049512609066 at iteration 142 using kt 100.0
Currently best helix constraint lengths: 
5 5 5 Oct 19, 2010 2:04:39 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 484.81839619167243 at iteration 230 using kt 100.0
Currently best helix constraint lengths: 
5 5 5 Oct 19, 2010 2:04:39 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 477.126766557372 at iteration 231 using kt 100.0
Currently best helix constraint lengths: 
5 5 5 Oct 19, 2010 2:04:39 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 470.4293026860128 at iteration 236 using kt 100.0
Currently best helix constraint lengths: 
5 5 5 Oct 19, 2010 2:04:39 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 469.932086929764 at iteration 243 using kt 100.0
Currently best helix constraint lengths: 
5 5 5 Oct 19, 2010 2:04:39 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 465.92884278958326 at iteration 244 using kt 100.0
Currently best helix constraint lengths: 
5 5 5 Oct 19, 2010 2:04:39 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 461.5626193546867 at iteration 245 using kt 100.0
Currently best helix constraint lengths: 
5 5 5 Oct 19, 2010 2:04:39 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 452.48834067812396 at iteration 246 using kt 100.0
Currently best helix constraint lengths: 
5 5 5 Oct 19, 2010 2:04:39 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 437.0163990553688 at iteration 260 using kt 100.0
Currently best helix constraint lengths: 
5 5 5 Oct 19, 2010 2:04:39 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 425.47309132926245 at iteration 261 using kt 100.0
Currently best helix constraint lengths: 
5 5 5 Oct 19, 2010 2:04:39 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 408.34392681777837 at iteration 281 using kt 100.0
Currently best helix constraint lengths: 
5 5 5 Oct 19, 2010 2:04:39 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 407.5697888734949 at iteration 472 using kt 100.0
Currently best helix constraint lengths: 
5 5 5 Oct 19, 2010 2:04:39 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 392.34690447245634 at iteration 473 using kt 100.0
Currently best helix constraint lengths: 
5 5 5 Oct 19, 2010 2:04:39 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 378.7683915719058 at iteration 476 using kt 100.0
Currently best helix constraint lengths: 
5 5 5 Oct 19, 2010 2:04:39 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 377.3952332895901 at iteration 482 using kt 100.0
Currently best helix constraint lengths: 
5 5 5 Oct 19, 2010 2:04:39 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 374.34584576948725 at iteration 483 using kt 100.0
Currently best helix constraint lengths: 
5 5 5 Oct 19, 2010 2:04:39 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 370.3456552538879 at iteration 1024 using kt 100.0
Currently best helix constraint lengths: 
5 5 5 Oct 19, 2010 2:04:39 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 358.6723264627947 at iteration 1082 using kt 100.0
Currently best helix constraint lengths: 
5 5 5 Oct 19, 2010 2:04:39 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 348.6856345427134 at iteration 1085 using kt 100.0
Currently best helix constraint lengths: 
5 5 5 Oct 19, 2010 2:04:39 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 343.09741763542416 at iteration 1153 using kt 100.0
Currently best helix constraint lengths: 
5 5 5 Oct 19, 2010 2:04:39 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 334.7989166696101 at iteration 1621 using kt 100.0
Currently best helix constraint lengths: 
5 5 5 Oct 19, 2010 2:04:39 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 329.5265102812327 at iteration 1626 using kt 100.0
Currently best helix constraint lengths: 
5 5 5 Oct 19, 2010 2:04:39 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 329.19431653612867 at iteration 1627 using kt 100.0
Currently best helix constraint lengths: 
5 5 5 Oct 19, 2010 2:04:39 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 329.1578288118454 at iteration 1632 using kt 100.0
Currently best helix constraint lengths: 
5 5 5 Oct 19, 2010 2:04:39 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 327.27675414110723 at iteration 1633 using kt 100.0
Currently best helix constraint lengths: 
5 5 5 Oct 19, 2010 2:04:39 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 324.4471040527227 at iteration 1634 using kt 100.0
Currently best helix constraint lengths: 
5 5 5 Oct 19, 2010 2:04:39 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 318.4981823086497 at iteration 1652 using kt 100.0
Currently best helix constraint lengths: 
5 5 5 Oct 19, 2010 2:04:39 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 313.4371171917756 at iteration 1688 using kt 100.0
Currently best helix constraint lengths: 
5 5 5 Oct 19, 2010 2:04:39 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 312.7041391911848 at iteration 1689 using kt 100.0
Currently best helix constraint lengths: 
5 5 5 Oct 19, 2010 2:04:39 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 311.5000305623279 at iteration 1690 using kt 100.0
Currently best helix constraint lengths: 
5 5 5 Oct 19, 2010 2:04:39 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 307.6891974155971 at iteration 1693 using kt 100.0
Currently best helix constraint lengths: 
5 5 5 Oct 19, 2010 2:04:40 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 306.20151841865874 at iteration 1707 using kt 100.0
Currently best helix constraint lengths: 
5 5 5 Oct 19, 2010 2:04:40 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 303.39785988582776 at iteration 2260 using kt 100.0
Currently best helix constraint lengths: 
5 5 5 Oct 19, 2010 2:04:40 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 298.19746034362146 at iteration 2261 using kt 100.0
Currently best helix constraint lengths: 
5 5 5 Oct 19, 2010 2:04:40 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 297.29587234702035 at iteration 3985 using kt 100.0
Currently best helix constraint lengths: 
5 5 5 Oct 19, 2010 2:04:40 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 297.13333423818307 at iteration 3989 using kt 100.0
Currently best helix constraint lengths: 
5 5 5 Oct 19, 2010 2:04:40 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 292.86113294073544 at iteration 3991 using kt 100.0
Currently best helix constraint lengths: 
5 5 5 Oct 19, 2010 2:04:40 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 291.65850844988677 at iteration 3992 using kt 100.0
Currently best helix constraint lengths: 
5 5 5 Oct 19, 2010 2:04:40 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 291.2506262865614 at iteration 3994 using kt 100.0
Currently best helix constraint lengths: 
5 5 5 Oct 19, 2010 2:04:40 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 286.4466012189156 at iteration 3996 using kt 100.0
Currently best helix constraint lengths: 
5 5 5 Oct 19, 2010 2:04:41 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 285.32064647935795 at iteration 4552 using kt 100.0
Currently best helix constraint lengths: 
5 5 5 Oct 19, 2010 2:04:41 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 279.5887817494944 at iteration 4553 using kt 100.0
Currently best helix constraint lengths: 
5 5 5 Oct 19, 2010 2:04:41 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 264.80365304112536 at iteration 4578 using kt 100.0
Currently best helix constraint lengths: 
5 5 5 Oct 19, 2010 2:04:41 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 264.4860003140301 at iteration 4579 using kt 100.0
Currently best helix constraint lengths: 
5 5 5 Oct 19, 2010 2:04:41 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 248.77392274514906 at iteration 4584 using kt 100.0
Currently best helix constraint lengths: 
5 5 5 Oct 19, 2010 2:04:41 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 233.3841849402894 at iteration 4585 using kt 100.0
Currently best helix constraint lengths: 
5 5 5 Oct 19, 2010 2:04:41 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 231.81205368272805 at iteration 4594 using kt 100.0
Currently best helix constraint lengths: 
5 5 5 Oct 19, 2010 2:04:41 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 226.99225740511343 at iteration 4595 using kt 100.0
Currently best helix constraint lengths: 
5 5 5 Oct 19, 2010 2:04:41 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 226.23730330277937 at iteration 4596 using kt 100.0
Currently best helix constraint lengths: 
5 5 5 Oct 19, 2010 2:04:41 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 223.3202029515404 at iteration 4598 using kt 100.0
Currently best helix constraint lengths: 
5 5 5 Oct 19, 2010 2:04:41 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 220.59826616929732 at iteration 5140 using kt 100.0
Currently best helix constraint lengths: 
5 5 5 Oct 19, 2010 2:04:41 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 219.54924007340077 at iteration 5234 using kt 100.0
Currently best helix constraint lengths: 
5 5 5 Oct 19, 2010 2:04:41 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 219.16284270751962 at iteration 5268 using kt 100.0
Currently best helix constraint lengths: 
5 5 5 Oct 19, 2010 2:04:41 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 218.77420885029997 at iteration 5273 using kt 100.0
Currently best helix constraint lengths: 
5 5 5 Oct 19, 2010 2:04:41 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 213.16094529001566 at iteration 5274 using kt 100.0
Currently best helix constraint lengths: 
5 5 5 Oct 19, 2010 2:04:41 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 205.88884432960336 at iteration 5275 using kt 100.0
Currently best helix constraint lengths: 
5 5 5 Oct 19, 2010 2:04:41 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 205.7216321285856 at iteration 5279 using kt 100.0
Currently best helix constraint lengths: 
5 5 5 Oct 19, 2010 2:04:41 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 205.3509698930476 at iteration 5281 using kt 100.0
Currently best helix constraint lengths: 
5 5 5 Oct 19, 2010 2:04:41 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 201.97636807675764 at iteration 5282 using kt 100.0
Currently best helix constraint lengths: 
5 5 5 Oct 19, 2010 2:04:42 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 10001 Best score so far: 201.97636807675764 . Using annealing factor: 0.985 kt: 98.5 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:04:42 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 198.233399467902 at iteration 10228 using kt 98.5
Currently best helix constraint lengths: 
5 5 5 Oct 19, 2010 2:04:42 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 196.47631652502884 at iteration 10261 using kt 98.5
Currently best helix constraint lengths: 
5 5 5 Oct 19, 2010 2:04:42 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 193.7755444490689 at iteration 10266 using kt 98.5
Currently best helix constraint lengths: 
5 5 5 Oct 19, 2010 2:04:42 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 193.20898443048605 at iteration 10279 using kt 98.5
Currently best helix constraint lengths: 
5 5 5 Oct 19, 2010 2:04:42 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 189.87067804442466 at iteration 10280 using kt 98.5
Currently best helix constraint lengths: 
5 5 5 Oct 19, 2010 2:04:44 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 20001 Best score so far: 189.87067804442466 . Using annealing factor: 0.970225 kt: 97.0225 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:04:47 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 30001 Best score so far: 189.87067804442466 . Using annealing factor: 0.9556716249999999 kt: 95.5671625 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:04:49 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 40001 Best score so far: 189.87067804442466 . Using annealing factor: 0.941336550625 kt: 94.1336550625 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:04:52 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Mutating helix constraints!
Oct 19, 2010 2:04:52 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 50000 Best score so far: 189.87067804442466 . Using annealing factor: 0.9272165023656249 kt: 92.7216502365625 coordinate system multipliers: 1.0 1.0 1.0  MUTATING HELIX LENGTHS: 
5 ( 5 ) 5 ( 5 ) 5 ( 5 ) Modified helix constraint lengths: 4 5 5 
Oct 19, 2010 2:04:52 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 50001 Best score so far: 189.87067804442466 . Using annealing factor: 0.9272165023656249 kt: 92.7216502365625 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:04:55 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 60001 Best score so far: 189.87067804442466 . Using annealing factor: 0.9133082548301406 kt: 91.33082548301405 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:04:57 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 70001 Best score so far: 189.87067804442466 . Using annealing factor: 0.8996086310076884 kt: 89.96086310076883 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:04:58 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 189.0747339682796 at iteration 72837 using kt 89.96086310076883
Currently best helix constraint lengths: 
5 5 5 Oct 19, 2010 2:04:58 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 187.63105861336118 at iteration 72842 using kt 89.96086310076883
Currently best helix constraint lengths: 
5 5 5 Oct 19, 2010 2:04:58 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 183.74643771582058 at iteration 72843 using kt 89.96086310076883
Currently best helix constraint lengths: 
5 5 5 Oct 19, 2010 2:04:58 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 180.61107546529337 at iteration 72844 using kt 89.96086310076883
Currently best helix constraint lengths: 
5 5 5 Oct 19, 2010 2:04:58 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 178.60971226020317 at iteration 72846 using kt 89.96086310076883
Currently best helix constraint lengths: 
5 5 5 Oct 19, 2010 2:04:58 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 178.4683155249228 at iteration 72847 using kt 89.96086310076883
Currently best helix constraint lengths: 
5 5 5 Oct 19, 2010 2:04:58 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 178.05164765510457 at iteration 72849 using kt 89.96086310076883
Currently best helix constraint lengths: 
5 5 5 Oct 19, 2010 2:04:58 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 175.17429465782777 at iteration 73973 using kt 89.96086310076883
Currently best helix constraint lengths: 
5 5 5 Oct 19, 2010 2:04:58 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 173.19404396896803 at iteration 74397 using kt 89.96086310076883
Currently best helix constraint lengths: 
5 5 5 Oct 19, 2010 2:04:59 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 168.97174309279467 at iteration 76909 using kt 89.96086310076883
Currently best helix constraint lengths: 
5 5 5 Oct 19, 2010 2:04:59 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 163.48719736556885 at iteration 76911 using kt 89.96086310076883
Currently best helix constraint lengths: 
5 5 5 Oct 19, 2010 2:04:59 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 161.94400540798284 at iteration 76913 using kt 89.96086310076883
Currently best helix constraint lengths: 
5 5 5 Oct 19, 2010 2:04:59 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 158.71725959408298 at iteration 76916 using kt 89.96086310076883
Currently best helix constraint lengths: 
5 5 5 Oct 19, 2010 2:04:59 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 158.38570160288933 at iteration 77433 using kt 89.96086310076883
Currently best helix constraint lengths: 
5 5 5 Oct 19, 2010 2:04:59 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 156.42257602470346 at iteration 77434 using kt 89.96086310076883
Currently best helix constraint lengths: 
5 5 5 Oct 19, 2010 2:04:59 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 153.91724730891139 at iteration 77435 using kt 89.96086310076883
Currently best helix constraint lengths: 
5 5 5 Oct 19, 2010 2:04:59 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 150.47805157007434 at iteration 77437 using kt 89.96086310076883
Currently best helix constraint lengths: 
5 5 5 Oct 19, 2010 2:04:59 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 149.84808231470936 at iteration 77438 using kt 89.96086310076883
Currently best helix constraint lengths: 
5 5 5 Oct 19, 2010 2:04:59 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 145.89647906213216 at iteration 77441 using kt 89.96086310076883
Currently best helix constraint lengths: 
5 5 5 Oct 19, 2010 2:05:00 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 80001 Best score so far: 145.89647906213216 . Using annealing factor: 0.8861145015425731 kt: 88.61145015425731 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:05:02 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 90001 Best score so far: 145.89647906213216 . Using annealing factor: 0.8728227840194345 kt: 87.28227840194344 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:05:03 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 144.81844323875725 at iteration 92061 using kt 87.28227840194344
Currently best helix constraint lengths: 
5 5 5 Oct 19, 2010 2:05:03 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 139.427997487239 at iteration 92091 using kt 87.28227840194344
Currently best helix constraint lengths: 
5 5 5 Oct 19, 2010 2:05:05 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Mutating helix constraints!
Oct 19, 2010 2:05:05 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 100000 Best score so far: 139.427997487239 . Using annealing factor: 0.859730442259143 kt: 85.9730442259143 coordinate system multipliers: 1.0 1.0 1.0  MUTATING HELIX LENGTHS: 
5 ( 5 ) 5 ( 5 ) 5 ( 5 ) Modified helix constraint lengths: 6 5 4 
Oct 19, 2010 2:05:05 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 100001 Best score so far: 139.427997487239 . Using annealing factor: 0.859730442259143 kt: 85.9730442259143 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:05:07 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 110001 Best score so far: 139.427997487239 . Using annealing factor: 0.8468344856252558 kt: 84.68344856252557 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:05:10 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 120001 Best score so far: 139.427997487239 . Using annealing factor: 0.834131968340877 kt: 83.4131968340877 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:05:12 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 130001 Best score so far: 139.427997487239 . Using annealing factor: 0.8216199888157638 kt: 82.16199888157638 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:05:15 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 140001 Best score so far: 139.427997487239 . Using annealing factor: 0.8092956889835273 kt: 80.92956889835273 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:05:17 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Mutating helix constraints!
Oct 19, 2010 2:05:17 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 150000 Best score so far: 139.427997487239 . Using annealing factor: 0.7971562536487744 kt: 79.71562536487744 coordinate system multipliers: 1.0 1.0 1.0  MUTATING HELIX LENGTHS: 
5 ( 5 ) 5 ( 5 ) 5 ( 5 ) Modified helix constraint lengths: 4 4 4 
Oct 19, 2010 2:05:17 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 150001 Best score so far: 139.427997487239 . Using annealing factor: 0.7971562536487744 kt: 79.71562536487744 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:05:20 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 160001 Best score so far: 139.427997487239 . Using annealing factor: 0.7851989098440428 kt: 78.51989098440428 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:05:22 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 170001 Best score so far: 139.427997487239 . Using annealing factor: 0.7734209261963821 kt: 77.34209261963821 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:05:25 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 180001 Best score so far: 139.427997487239 . Using annealing factor: 0.7618196123034364 kt: 76.18196123034365 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:05:27 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 190001 Best score so far: 139.427997487239 . Using annealing factor: 0.7503923181188848 kt: 75.03923181188848 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:05:30 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Mutating helix constraints!
Oct 19, 2010 2:05:30 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 200000 Best score so far: 139.427997487239 . Using annealing factor: 0.7391364333471016 kt: 73.91364333471016 coordinate system multipliers: 1.0 1.0 1.0  MUTATING HELIX LENGTHS: 
5 ( 5 ) 5 ( 5 ) 5 ( 5 ) Modified helix constraint lengths: 6 5 4 
Oct 19, 2010 2:05:30 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 200001 Best score so far: 139.427997487239 . Using annealing factor: 0.7391364333471016 kt: 73.91364333471016 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:05:33 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 210001 Best score so far: 139.427997487239 . Using annealing factor: 0.728049386846895 kt: 72.8049386846895 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:05:35 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 220001 Best score so far: 139.427997487239 . Using annealing factor: 0.7171286460441916 kt: 71.71286460441915 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:05:38 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 230001 Best score so far: 139.427997487239 . Using annealing factor: 0.7063717163535287 kt: 70.63717163535287 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:05:40 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 240001 Best score so far: 139.427997487239 . Using annealing factor: 0.6957761406082257 kt: 69.57761406082257 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:05:43 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Mutating helix constraints!
Oct 19, 2010 2:05:43 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 250000 Best score so far: 139.427997487239 . Using annealing factor: 0.6853394984991024 kt: 68.53394984991024 coordinate system multipliers: 1.0 1.0 1.0  MUTATING HELIX LENGTHS: 
5 ( 5 ) 5 ( 5 ) 5 ( 5 ) Modified helix constraint lengths: 7 4 4 
Oct 19, 2010 2:05:43 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 250001 Best score so far: 139.427997487239 . Using annealing factor: 0.6853394984991024 kt: 68.53394984991024 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:05:45 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 260001 Best score so far: 139.427997487239 . Using annealing factor: 0.6750594060216157 kt: 67.50594060216157 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:05:48 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 270001 Best score so far: 139.427997487239 . Using annealing factor: 0.6649335149312916 kt: 66.49335149312915 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:05:50 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 280001 Best score so far: 139.427997487239 . Using annealing factor: 0.6549595122073222 kt: 65.49595122073222 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:05:53 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 290001 Best score so far: 139.427997487239 . Using annealing factor: 0.6451351195242123 kt: 64.51351195242123 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:05:55 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Mutating helix constraints!
Oct 19, 2010 2:05:55 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 300000 Best score so far: 139.427997487239 . Using annealing factor: 0.6354580927313491 kt: 63.545809273134914 coordinate system multipliers: 1.0 1.0 1.0  MUTATING HELIX LENGTHS: 
6 ( 5 ) 5 ( 5 ) 4 ( 5 ) Modified helix constraint lengths: 8 5 3 
Oct 19, 2010 2:05:55 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 300001 Best score so far: 139.427997487239 . Using annealing factor: 0.6354580927313491 kt: 63.545809273134914 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:05:58 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 310001 Best score so far: 139.427997487239 . Using annealing factor: 0.6259262213403789 kt: 62.59262213403789 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:06:00 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 320001 Best score so far: 139.427997487239 . Using annealing factor: 0.6165373280202732 kt: 61.653732802027314 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:06:03 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 330001 Best score so far: 139.427997487239 . Using annealing factor: 0.6072892680999691 kt: 60.728926809996906 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:06:06 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 340001 Best score so far: 139.427997487239 . Using annealing factor: 0.5981799290784695 kt: 59.81799290784695 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:06:08 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Mutating helix constraints!
Oct 19, 2010 2:06:08 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 350000 Best score so far: 139.427997487239 . Using annealing factor: 0.5892072301422925 kt: 58.920723014229246 coordinate system multipliers: 1.0 1.0 1.0  MUTATING HELIX LENGTHS: 
7 ( 5 ) 4 ( 5 ) 4 ( 5 ) Oct 19, 2010 2:06:08 PM rnadesign.rnamodel.HelixOptimizer mutateHelixLengths
WARNING: No helix lengths were modified!
Oct 19, 2010 2:06:08 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 350001 Best score so far: 139.427997487239 . Using annealing factor: 0.5892072301422925 kt: 58.920723014229246 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:06:11 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 360001 Best score so far: 139.427997487239 . Using annealing factor: 0.5803691216901581 kt: 58.03691216901581 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:06:13 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 370001 Best score so far: 139.427997487239 . Using annealing factor: 0.5716635848648057 kt: 57.166358486480576 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:06:16 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 380001 Best score so far: 139.427997487239 . Using annealing factor: 0.5630886310918336 kt: 56.30886310918336 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:06:18 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 390001 Best score so far: 139.427997487239 . Using annealing factor: 0.5546423016254561 kt: 55.46423016254561 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:06:21 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Mutating helix constraints!
Oct 19, 2010 2:06:21 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 400000 Best score so far: 139.427997487239 . Using annealing factor: 0.5463226671010742 kt: 54.63226671010742 coordinate system multipliers: 1.0 1.0 1.0  MUTATING HELIX LENGTHS: 
7 ( 5 ) 4 ( 5 ) 4 ( 5 ) Modified helix constraint lengths: 6 4 3 
Oct 19, 2010 2:06:21 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 400001 Best score so far: 139.427997487239 . Using annealing factor: 0.5463226671010742 kt: 54.63226671010742 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:06:23 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 410001 Best score so far: 139.427997487239 . Using annealing factor: 0.5381278270945582 kt: 53.81278270945582 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:06:26 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 420001 Best score so far: 139.427997487239 . Using annealing factor: 0.5300559096881398 kt: 53.005590968813976 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:06:28 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 430001 Best score so far: 139.427997487239 . Using annealing factor: 0.5221050710428177 kt: 52.21050710428177 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:06:31 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 440001 Best score so far: 139.427997487239 . Using annealing factor: 0.5142734949771754 kt: 51.42734949771754 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:06:33 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Mutating helix constraints!
Oct 19, 2010 2:06:33 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 450000 Best score so far: 139.427997487239 . Using annealing factor: 0.5065593925525178 kt: 50.65593925525178 coordinate system multipliers: 1.0 1.0 1.0  MUTATING HELIX LENGTHS: 
7 ( 5 ) 4 ( 5 ) 4 ( 5 ) Modified helix constraint lengths: 6 5 3 
Oct 19, 2010 2:06:33 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 450001 Best score so far: 139.427997487239 . Using annealing factor: 0.5065593925525178 kt: 50.65593925525178 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:06:36 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 460001 Best score so far: 139.427997487239 . Using annealing factor: 0.49896100166422996 kt: 49.896100166423 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:06:38 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 470001 Best score so far: 139.427997487239 . Using annealing factor: 0.4914765866392665 kt: 49.14765866392665 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:06:41 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 480001 Best score so far: 139.427997487239 . Using annealing factor: 0.48410443783967755 kt: 48.41044378396776 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:06:44 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 490001 Best score so far: 139.427997487239 . Using annealing factor: 0.47684287127208236 kt: 47.684287127208236 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:06:46 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Mutating helix constraints!
Oct 19, 2010 2:06:46 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 500000 Best score so far: 139.427997487239 . Using annealing factor: 0.4696902282030011 kt: 46.96902282030011 coordinate system multipliers: 1.0 1.0 1.0  MUTATING HELIX LENGTHS: 
6 ( 5 ) 4 ( 5 ) 3 ( 5 ) Modified helix constraint lengths: 7 6 2 
Oct 19, 2010 2:06:46 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 500001 Best score so far: 139.427997487239 . Using annealing factor: 0.4696902282030011 kt: 46.96902282030011 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:06:49 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 510001 Best score so far: 139.427997487239 . Using annealing factor: 0.4626448747799561 kt: 46.26448747799561 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:06:51 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 520001 Best score so far: 139.427997487239 . Using annealing factor: 0.45570520165825673 kt: 45.57052016582567 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:06:54 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 530001 Best score so far: 139.427997487239 . Using annealing factor: 0.4488696236333829 kt: 44.88696236333829 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:06:56 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 540001 Best score so far: 139.427997487239 . Using annealing factor: 0.44213657927888217 kt: 44.213657927888214 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:06:59 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Mutating helix constraints!
Oct 19, 2010 2:06:59 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 550000 Best score so far: 139.427997487239 . Using annealing factor: 0.4355045305896989 kt: 43.55045305896989 coordinate system multipliers: 1.0 1.0 1.0  MUTATING HELIX LENGTHS: 
6 ( 5 ) 5 ( 5 ) 3 ( 5 ) Modified helix constraint lengths: 7 6 3 
Oct 19, 2010 2:06:59 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 550001 Best score so far: 139.427997487239 . Using annealing factor: 0.4355045305896989 kt: 43.55045305896989 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:07:01 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 560001 Best score so far: 139.427997487239 . Using annealing factor: 0.4289719626308534 kt: 42.89719626308534 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:07:04 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 570001 Best score so far: 139.427997487239 . Using annealing factor: 0.4225373831913906 kt: 42.25373831913906 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:07:06 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 580001 Best score so far: 139.427997487239 . Using annealing factor: 0.41619932244351976 kt: 41.61993224435198 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:07:09 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 590001 Best score so far: 139.427997487239 . Using annealing factor: 0.4099563326068669 kt: 40.995633260686695 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:07:12 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Mutating helix constraints!
Oct 19, 2010 2:07:12 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 600000 Best score so far: 139.427997487239 . Using annealing factor: 0.4038069876177639 kt: 40.38069876177639 coordinate system multipliers: 1.0 1.0 1.0  MUTATING HELIX LENGTHS: 
6 ( 5 ) 5 ( 5 ) 3 ( 5 ) Modified helix constraint lengths: 6 4 2 
Oct 19, 2010 2:07:12 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 600001 Best score so far: 139.427997487239 . Using annealing factor: 0.4038069876177639 kt: 40.38069876177639 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:07:14 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 610001 Best score so far: 139.427997487239 . Using annealing factor: 0.39774988280349743 kt: 39.774988280349746 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:07:17 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 620001 Best score so far: 139.427997487239 . Using annealing factor: 0.391783634561445 kt: 39.1783634561445 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:07:19 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 630001 Best score so far: 139.427997487239 . Using annealing factor: 0.3859068800430233 kt: 38.59068800430233 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:07:22 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 640001 Best score so far: 139.427997487239 . Using annealing factor: 0.380118276842378 kt: 38.0118276842378 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:07:24 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Mutating helix constraints!
Oct 19, 2010 2:07:24 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 650000 Best score so far: 139.427997487239 . Using annealing factor: 0.3744165026897423 kt: 37.44165026897423 coordinate system multipliers: 1.0 1.0 1.0  MUTATING HELIX LENGTHS: 
6 ( 5 ) 5 ( 5 ) 3 ( 5 ) Modified helix constraint lengths: 7 4 3 
Oct 19, 2010 2:07:24 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 650001 Best score so far: 139.427997487239 . Using annealing factor: 0.3744165026897423 kt: 37.44165026897423 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:07:27 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 660001 Best score so far: 139.427997487239 . Using annealing factor: 0.3688002551493962 kt: 36.88002551493962 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:07:29 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 670001 Best score so far: 139.427997487239 . Using annealing factor: 0.36326825132215523 kt: 36.326825132215525 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:07:32 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 680001 Best score so far: 139.427997487239 . Using annealing factor: 0.35781922755232287 kt: 35.78192275523229 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:07:34 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 690001 Best score so far: 139.427997487239 . Using annealing factor: 0.35245193913903805 kt: 35.245193913903805 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:07:37 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Mutating helix constraints!
Oct 19, 2010 2:07:37 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 700000 Best score so far: 139.427997487239 . Using annealing factor: 0.3471651600519524 kt: 34.71651600519524 coordinate system multipliers: 1.0 1.0 1.0  MUTATING HELIX LENGTHS: 
6 ( 5 ) 5 ( 5 ) 3 ( 5 ) Modified helix constraint lengths: 7 6 3 
Oct 19, 2010 2:07:37 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 700001 Best score so far: 139.427997487239 . Using annealing factor: 0.3471651600519524 kt: 34.71651600519524 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:07:39 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 710001 Best score so far: 139.427997487239 . Using annealing factor: 0.34195768265117316 kt: 34.195768265117316 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:07:42 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 720001 Best score so far: 139.427997487239 . Using annealing factor: 0.33682831741140556 kt: 33.682831741140554 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:07:45 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 730001 Best score so far: 139.427997487239 . Using annealing factor: 0.33177589265023444 kt: 33.17758926502344 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:07:47 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 740001 Best score so far: 139.427997487239 . Using annealing factor: 0.32679925426048095 kt: 32.679925426048094 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:07:50 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Mutating helix constraints!
Oct 19, 2010 2:07:50 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 750000 Best score so far: 139.427997487239 . Using annealing factor: 0.3218972654465737 kt: 32.18972654465737 coordinate system multipliers: 1.0 1.0 1.0  MUTATING HELIX LENGTHS: 
6 ( 5 ) 5 ( 5 ) 3 ( 5 ) Oct 19, 2010 2:07:50 PM rnadesign.rnamodel.HelixOptimizer mutateHelixLengths
WARNING: No helix lengths were modified!
Oct 19, 2010 2:07:50 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 750001 Best score so far: 139.427997487239 . Using annealing factor: 0.3218972654465737 kt: 32.18972654465737 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:07:52 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 760001 Best score so far: 139.427997487239 . Using annealing factor: 0.3170688064648751 kt: 31.706880646487512 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:07:55 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 770001 Best score so far: 139.427997487239 . Using annealing factor: 0.312312774367902 kt: 31.2312774367902 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:07:57 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 780001 Best score so far: 139.427997487239 . Using annealing factor: 0.30762808275238346 kt: 30.762808275238346 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:08:00 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 790001 Best score so far: 139.427997487239 . Using annealing factor: 0.3030136615110977 kt: 30.30136615110977 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:08:02 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Mutating helix constraints!
Oct 19, 2010 2:08:02 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 800000 Best score so far: 139.427997487239 . Using annealing factor: 0.29846845658843124 kt: 29.846845658843122 coordinate system multipliers: 1.0 1.0 1.0  MUTATING HELIX LENGTHS: 
6 ( 5 ) 5 ( 5 ) 3 ( 5 ) Modified helix constraint lengths: 6 4 4 
Oct 19, 2010 2:08:02 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 800001 Best score so far: 139.427997487239 . Using annealing factor: 0.29846845658843124 kt: 29.846845658843122 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:08:05 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 810001 Best score so far: 139.427997487239 . Using annealing factor: 0.29399142973960474 kt: 29.399142973960473 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:08:07 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 820001 Best score so far: 139.427997487239 . Using annealing factor: 0.2895815582935107 kt: 28.958155829351067 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:08:10 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 830001 Best score so far: 139.427997487239 . Using annealing factor: 0.28523783491910804 kt: 28.523783491910805 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:08:12 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 840001 Best score so far: 139.427997487239 . Using annealing factor: 0.2809592673953214 kt: 28.09592673953214 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:08:15 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Mutating helix constraints!
Oct 19, 2010 2:08:15 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 850000 Best score so far: 139.427997487239 . Using annealing factor: 0.27674487838439155 kt: 27.674487838439155 coordinate system multipliers: 1.0 1.0 1.0  MUTATING HELIX LENGTHS: 
6 ( 5 ) 5 ( 5 ) 3 ( 5 ) Oct 19, 2010 2:08:15 PM rnadesign.rnamodel.HelixOptimizer mutateHelixLengths
WARNING: No helix lengths were modified!
Oct 19, 2010 2:08:15 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 850001 Best score so far: 139.427997487239 . Using annealing factor: 0.27674487838439155 kt: 27.674487838439155 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:08:18 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 860001 Best score so far: 139.427997487239 . Using annealing factor: 0.2725937052086257 kt: 27.259370520862568 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:08:20 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 870001 Best score so far: 139.427997487239 . Using annealing factor: 0.2685047996304963 kt: 26.85047996304963 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:08:23 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 880001 Best score so far: 139.427997487239 . Using annealing factor: 0.26447722763603887 kt: 26.44772276360389 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:08:25 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 890001 Best score so far: 139.427997487239 . Using annealing factor: 0.2605100692214983 kt: 26.051006922149828 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:08:28 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Mutating helix constraints!
Oct 19, 2010 2:08:28 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 900000 Best score so far: 139.427997487239 . Using annealing factor: 0.2566024181831758 kt: 25.66024181831758 coordinate system multipliers: 1.0 1.0 1.0  MUTATING HELIX LENGTHS: 
6 ( 5 ) 4 ( 5 ) 4 ( 5 ) Modified helix constraint lengths: 6 3 3 
Oct 19, 2010 2:08:28 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 900001 Best score so far: 139.427997487239 . Using annealing factor: 0.2566024181831758 kt: 25.66024181831758 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:08:30 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 910001 Best score so far: 139.427997487239 . Using annealing factor: 0.2527533819104281 kt: 25.275338191042813 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:08:33 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 920001 Best score so far: 139.427997487239 . Using annealing factor: 0.2489620811817717 kt: 24.89620811817717 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:08:35 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 930001 Best score so far: 139.427997487239 . Using annealing factor: 0.24522764996404514 kt: 24.522764996404515 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:08:38 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 940001 Best score so far: 139.427997487239 . Using annealing factor: 0.24154923521458446 kt: 24.154923521458446 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:08:40 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Mutating helix constraints!
Oct 19, 2010 2:08:40 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 950000 Best score so far: 139.427997487239 . Using annealing factor: 0.2379259966863657 kt: 23.79259966863657 coordinate system multipliers: 1.0 1.0 1.0  MUTATING HELIX LENGTHS: 
6 ( 5 ) 4 ( 5 ) 4 ( 5 ) Modified helix constraint lengths: 5 4 5 
Oct 19, 2010 2:08:40 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 950001 Best score so far: 139.427997487239 . Using annealing factor: 0.2379259966863657 kt: 23.79259966863657 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:08:43 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 960001 Best score so far: 139.427997487239 . Using annealing factor: 0.23435710673607021 kt: 23.435710673607023 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:08:45 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 970001 Best score so far: 139.427997487239 . Using annealing factor: 0.23084175013502914 kt: 23.084175013502914 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:08:48 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 980001 Best score so far: 139.427997487239 . Using annealing factor: 0.22737912388300371 kt: 22.737912388300373 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:08:50 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 990001 Best score so far: 139.427997487239 . Using annealing factor: 0.22396843702475866 kt: 22.396843702475866 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:08:53 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Mutating helix constraints!
Oct 19, 2010 2:08:53 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 1000000 Best score so far: 139.427997487239 . Using annealing factor: 0.22060891046938727 kt: 22.06089104693873 coordinate system multipliers: 1.0 1.0 1.0  MUTATING HELIX LENGTHS: 
6 ( 5 ) 4 ( 5 ) 4 ( 5 ) Modified helix constraint lengths: 6 3 6 
Oct 19, 2010 2:08:53 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 1000001 Best score so far: 139.427997487239 . Using annealing factor: 0.22060891046938727 kt: 22.06089104693873 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:08:55 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 1010001 Best score so far: 139.427997487239 . Using annealing factor: 0.21729977681234647 kt: 21.729977681234647 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:08:58 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 1020001 Best score so far: 139.427997487239 . Using annealing factor: 0.21404028016016124 kt: 21.404028016016124 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:09:01 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 1030001 Best score so far: 139.427997487239 . Using annealing factor: 0.21082967595775884 kt: 21.082967595775884 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:09:03 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 1040001 Best score so far: 139.427997487239 . Using annealing factor: 0.20766723081839245 kt: 20.766723081839245 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:09:06 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Mutating helix constraints!
Oct 19, 2010 2:09:06 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 1050000 Best score so far: 139.427997487239 . Using annealing factor: 0.20455222235611656 kt: 20.455222235611657 coordinate system multipliers: 1.0 1.0 1.0  MUTATING HELIX LENGTHS: 
5 ( 5 ) 4 ( 5 ) 5 ( 5 ) Modified helix constraint lengths: 7 4 6 
Oct 19, 2010 2:09:06 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 1050001 Best score so far: 139.427997487239 . Using annealing factor: 0.20455222235611656 kt: 20.455222235611657 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:09:08 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 1060001 Best score so far: 139.427997487239 . Using annealing factor: 0.2014839390207748 kt: 20.14839390207748 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:09:11 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 1070001 Best score so far: 139.427997487239 . Using annealing factor: 0.19846167993546318 kt: 19.846167993546317 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:09:13 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 1080001 Best score so far: 139.427997487239 . Using annealing factor: 0.19548475473643123 kt: 19.548475473643123 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:09:16 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 1090001 Best score so far: 139.427997487239 . Using annealing factor: 0.19255248341538475 kt: 19.255248341538476 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:09:18 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Mutating helix constraints!
Oct 19, 2010 2:09:18 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 1100000 Best score so far: 139.427997487239 . Using annealing factor: 0.18966419616415398 kt: 18.966419616415397 coordinate system multipliers: 1.0 1.0 1.0  MUTATING HELIX LENGTHS: 
6 ( 5 ) 3 ( 5 ) 6 ( 5 ) Modified helix constraint lengths: 7 4 6 
Oct 19, 2010 2:09:18 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 1100001 Best score so far: 139.427997487239 . Using annealing factor: 0.18966419616415398 kt: 18.966419616415397 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:09:21 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 1110001 Best score so far: 139.427997487239 . Using annealing factor: 0.18681923322169167 kt: 18.681923322169165 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:09:24 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 1120001 Best score so far: 139.427997487239 . Using annealing factor: 0.1840169447233663 kt: 18.40169447233663 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:09:26 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 1130001 Best score so far: 139.427997487239 . Using annealing factor: 0.1812566905525158 kt: 18.12566905525158 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:09:29 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 1140001 Best score so far: 139.427997487239 . Using annealing factor: 0.17853784019422805 kt: 17.853784019422804 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:09:31 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Mutating helix constraints!
Oct 19, 2010 2:09:31 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 1150000 Best score so far: 139.427997487239 . Using annealing factor: 0.17585977259131463 kt: 17.585977259131464 coordinate system multipliers: 1.0 1.0 1.0  MUTATING HELIX LENGTHS: 
6 ( 5 ) 3 ( 5 ) 6 ( 5 ) Modified helix constraint lengths: 6 3 5 
Oct 19, 2010 2:09:31 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 1150001 Best score so far: 139.427997487239 . Using annealing factor: 0.17585977259131463 kt: 17.585977259131464 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:09:34 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 1160001 Best score so far: 139.427997487239 . Using annealing factor: 0.17322187600244493 kt: 17.322187600244494 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:09:36 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 1170001 Best score so far: 139.427997487239 . Using annealing factor: 0.17062354786240824 kt: 17.062354786240824 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:09:39 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 1180001 Best score so far: 139.427997487239 . Using annealing factor: 0.16806419464447211 kt: 16.806419464447213 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:09:41 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 1190001 Best score so far: 139.427997487239 . Using annealing factor: 0.16554323172480503 kt: 16.554323172480505 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:09:44 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Mutating helix constraints!
Oct 19, 2010 2:09:44 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 1200000 Best score so far: 139.427997487239 . Using annealing factor: 0.16306008324893295 kt: 16.306008324893295 coordinate system multipliers: 1.0 1.0 1.0  MUTATING HELIX LENGTHS: 
7 ( 5 ) 4 ( 5 ) 6 ( 5 ) Modified helix constraint lengths: 8 3 5 
Oct 19, 2010 2:09:44 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 1200001 Best score so far: 139.427997487239 . Using annealing factor: 0.16306008324893295 kt: 16.306008324893295 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:09:46 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 1210001 Best score so far: 139.427997487239 . Using annealing factor: 0.16061418200019895 kt: 16.061418200019894 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:09:49 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 1220001 Best score so far: 139.427997487239 . Using annealing factor: 0.15820496927019598 kt: 15.820496927019597 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:09:51 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 1230001 Best score so far: 139.427997487239 . Using annealing factor: 0.15583189473114303 kt: 15.583189473114304 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:09:54 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 1240001 Best score so far: 139.427997487239 . Using annealing factor: 0.15349441631017588 kt: 15.349441631017587 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:09:57 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Mutating helix constraints!
Oct 19, 2010 2:09:57 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 1250000 Best score so far: 139.427997487239 . Using annealing factor: 0.15119200006552325 kt: 15.119200006552324 coordinate system multipliers: 1.0 1.0 1.0  MUTATING HELIX LENGTHS: 
7 ( 5 ) 4 ( 5 ) 6 ( 5 ) Modified helix constraint lengths: 8 4 7 
Oct 19, 2010 2:09:57 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 1250001 Best score so far: 139.427997487239 . Using annealing factor: 0.15119200006552325 kt: 15.119200006552324 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:09:59 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 1260001 Best score so far: 139.427997487239 . Using annealing factor: 0.1489241200645404 kt: 14.89241200645404 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:10:02 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 1270001 Best score so far: 139.427997487239 . Using annealing factor: 0.1466902582635723 kt: 14.66902582635723 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:10:04 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 1280001 Best score so far: 139.427997487239 . Using annealing factor: 0.1444899043896187 kt: 14.44899043896187 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:10:07 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 1290001 Best score so far: 139.427997487239 . Using annealing factor: 0.1423225558237744 kt: 14.23225558237744 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:10:09 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Mutating helix constraints!
Oct 19, 2010 2:10:09 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 1300000 Best score so far: 139.427997487239 . Using annealing factor: 0.14018771748641778 kt: 14.018771748641779 coordinate system multipliers: 1.0 1.0 1.0  MUTATING HELIX LENGTHS: 
7 ( 5 ) 4 ( 5 ) 6 ( 5 ) Modified helix constraint lengths: 8 5 6 
Oct 19, 2010 2:10:09 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 1300001 Best score so far: 139.427997487239 . Using annealing factor: 0.14018771748641778 kt: 14.018771748641779 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:10:12 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 1310001 Best score so far: 139.427997487239 . Using annealing factor: 0.13808490172412152 kt: 13.808490172412153 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:10:14 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 1320001 Best score so far: 139.427997487239 . Using annealing factor: 0.1360136281982597 kt: 13.60136281982597 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:10:17 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 1330001 Best score so far: 139.427997487239 . Using annealing factor: 0.13397342377528582 kt: 13.397342377528581 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:10:19 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 1340001 Best score so far: 139.427997487239 . Using annealing factor: 0.1319638224186565 kt: 13.196382241865651 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:10:22 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Mutating helix constraints!
Oct 19, 2010 2:10:22 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 1350000 Best score so far: 139.427997487239 . Using annealing factor: 0.12998436508237665 kt: 12.998436508237665 coordinate system multipliers: 1.0 1.0 1.0  MUTATING HELIX LENGTHS: 
7 ( 5 ) 4 ( 5 ) 6 ( 5 ) Modified helix constraint lengths: 7 5 7 
Oct 19, 2010 2:10:22 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 1350001 Best score so far: 139.427997487239 . Using annealing factor: 0.12998436508237665 kt: 12.998436508237665 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:10:25 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 1360001 Best score so far: 139.427997487239 . Using annealing factor: 0.12803459960614103 kt: 12.803459960614102 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:10:25 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 139.30164008578345 at iteration 1362185 using kt 12.803459960614102
Currently best helix constraint lengths: 
7 5 7 Oct 19, 2010 2:10:25 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 139.0401732669182 at iteration 1363153 using kt 12.803459960614102
Currently best helix constraint lengths: 
7 5 7 Oct 19, 2010 2:10:25 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 139.01381059872045 at iteration 1363154 using kt 12.803459960614102
Currently best helix constraint lengths: 
7 5 7 Oct 19, 2010 2:10:27 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 1370001 Best score so far: 139.01381059872045 . Using annealing factor: 0.1261140806120489 kt: 12.61140806120489 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:10:30 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 1380001 Best score so far: 139.01381059872045 . Using annealing factor: 0.12422236940286815 kt: 12.422236940286815 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:10:32 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 1390001 Best score so far: 139.01381059872045 . Using annealing factor: 0.12235903386182513 kt: 12.235903386182514 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:10:35 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Mutating helix constraints!
Oct 19, 2010 2:10:35 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 1400000 Best score so far: 139.01381059872045 . Using annealing factor: 0.12052364835389776 kt: 12.052364835389776 coordinate system multipliers: 1.0 1.0 1.0  MUTATING HELIX LENGTHS: 
7 ( 7 ) 4 ( 5 ) 6 ( 7 ) Oct 19, 2010 2:10:35 PM rnadesign.rnamodel.HelixOptimizer mutateHelixLengths
WARNING: No helix lengths were modified!
Oct 19, 2010 2:10:35 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 1400001 Best score so far: 139.01381059872045 . Using annealing factor: 0.12052364835389776 kt: 12.052364835389776 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:10:37 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 1410001 Best score so far: 139.01381059872045 . Using annealing factor: 0.11871579362858929 kt: 11.87157936285893 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:10:40 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 1420001 Best score so far: 139.01381059872045 . Using annealing factor: 0.11693505672416045 kt: 11.693505672416045 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:10:42 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 1430001 Best score so far: 139.01381059872045 . Using annealing factor: 0.11518103087329803 kt: 11.518103087329804 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:10:45 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 1440001 Best score so far: 139.01381059872045 . Using annealing factor: 0.11345331541019857 kt: 11.345331541019856 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:10:47 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Mutating helix constraints!
Oct 19, 2010 2:10:47 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 1450000 Best score so far: 139.01381059872045 . Using annealing factor: 0.1117515156790456 kt: 11.175151567904559 coordinate system multipliers: 1.0 1.0 1.0  MUTATING HELIX LENGTHS: 
7 ( 7 ) 5 ( 5 ) 7 ( 7 ) Modified helix constraint lengths: 6 5 7 
Oct 19, 2010 2:10:47 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 1450001 Best score so far: 139.01381059872045 . Using annealing factor: 0.1117515156790456 kt: 11.175151567904559 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:10:47 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 138.97275442108895 at iteration 1450036 using kt 11.175151567904559
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:10:47 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 138.56770699062915 at iteration 1450041 using kt 11.175151567904559
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:10:47 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 138.41010215122634 at iteration 1450043 using kt 11.175151567904559
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:10:47 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 138.33419460325104 at iteration 1450048 using kt 11.175151567904559
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:10:47 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 138.2259671508297 at iteration 1450049 using kt 11.175151567904559
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:10:47 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 137.70893915341765 at iteration 1450053 using kt 11.175151567904559
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:10:47 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 137.24422058975534 at iteration 1450214 using kt 11.175151567904559
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:10:47 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 136.84953799142062 at iteration 1450216 using kt 11.175151567904559
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:10:47 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 136.70555450586468 at iteration 1450226 using kt 11.175151567904559
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:10:47 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 136.68501418145024 at iteration 1450227 using kt 11.175151567904559
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:10:47 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 136.63985874270293 at iteration 1450229 using kt 11.175151567904559
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:10:47 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 136.56335350580596 at iteration 1450231 using kt 11.175151567904559
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:10:47 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 136.55363800878513 at iteration 1450255 using kt 11.175151567904559
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:10:47 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 136.52622180446855 at iteration 1450285 using kt 11.175151567904559
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:10:47 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 136.393261015817 at iteration 1450286 using kt 11.175151567904559
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:10:47 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 136.36066458151691 at iteration 1450383 using kt 11.175151567904559
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:10:47 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 135.99094390153442 at iteration 1450385 using kt 11.175151567904559
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:10:47 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 135.7133823360989 at iteration 1450386 using kt 11.175151567904559
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:10:47 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 135.3588828900708 at iteration 1450387 using kt 11.175151567904559
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:10:47 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 134.99744861001543 at iteration 1450390 using kt 11.175151567904559
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:10:47 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 134.84272163786423 at iteration 1450392 using kt 11.175151567904559
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:10:47 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 134.58245677153303 at iteration 1450393 using kt 11.175151567904559
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:10:47 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 134.55703738598314 at iteration 1450395 using kt 11.175151567904559
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:10:47 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 134.4949239101779 at iteration 1450405 using kt 11.175151567904559
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:10:47 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 134.1347970251264 at iteration 1450413 using kt 11.175151567904559
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:10:47 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 134.00353546587115 at iteration 1450415 using kt 11.175151567904559
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:10:47 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 133.5254730701971 at iteration 1450416 using kt 11.175151567904559
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:10:47 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 133.44392109794174 at iteration 1450421 using kt 11.175151567904559
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:10:47 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 133.39628088336835 at iteration 1450422 using kt 11.175151567904559
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:10:47 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 132.65921889116683 at iteration 1450424 using kt 11.175151567904559
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:10:47 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 132.61927872541122 at iteration 1450425 using kt 11.175151567904559
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:10:47 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 132.2635398754817 at iteration 1450426 using kt 11.175151567904559
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:10:47 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 132.24730596980552 at iteration 1450440 using kt 11.175151567904559
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:10:47 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 131.92826191347274 at iteration 1450447 using kt 11.175151567904559
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:10:47 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 131.84519537418353 at iteration 1450448 using kt 11.175151567904559
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:10:47 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 131.70819445245533 at iteration 1450510 using kt 11.175151567904559
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:10:47 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 131.66869285909448 at iteration 1450514 using kt 11.175151567904559
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:10:48 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 131.49548241688183 at iteration 1451271 using kt 11.175151567904559
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:10:48 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 131.40130703991423 at iteration 1451275 using kt 11.175151567904559
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:10:48 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 130.9204036204461 at iteration 1451276 using kt 11.175151567904559
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:10:48 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 130.75044622934814 at iteration 1452735 using kt 11.175151567904559
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:10:48 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 130.71823837833543 at iteration 1452746 using kt 11.175151567904559
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:10:48 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 130.39445594097975 at iteration 1452747 using kt 11.175151567904559
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:10:48 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 129.96970806430164 at iteration 1453327 using kt 11.175151567904559
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:10:48 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 129.9572124991919 at iteration 1453328 using kt 11.175151567904559
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:10:48 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 129.940190828518 at iteration 1453343 using kt 11.175151567904559
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:10:48 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 129.9122220799457 at iteration 1454022 using kt 11.175151567904559
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:10:48 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 129.83881961531677 at iteration 1454023 using kt 11.175151567904559
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:10:48 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 129.5690771357696 at iteration 1454037 using kt 11.175151567904559
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:10:48 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 129.31874285076532 at iteration 1454040 using kt 11.175151567904559
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:10:48 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 129.15085690330153 at iteration 1454041 using kt 11.175151567904559
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:10:48 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 129.11438120703136 at iteration 1454042 using kt 11.175151567904559
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:10:48 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 128.91705401051001 at iteration 1454043 using kt 11.175151567904559
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:10:48 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 128.89290152862776 at iteration 1454057 using kt 11.175151567904559
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:10:48 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 128.80149628409748 at iteration 1454097 using kt 11.175151567904559
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:10:48 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 128.1465049225911 at iteration 1454101 using kt 11.175151567904559
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:10:48 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 128.10390634898667 at iteration 1454108 using kt 11.175151567904559
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:10:48 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 127.9721846651781 at iteration 1454109 using kt 11.175151567904559
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:10:48 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 127.88409444579521 at iteration 1454111 using kt 11.175151567904559
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:10:48 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 127.66252073727452 at iteration 1454112 using kt 11.175151567904559
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:10:48 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 127.34384250601371 at iteration 1454125 using kt 11.175151567904559
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:10:48 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 126.55704252390717 at iteration 1454126 using kt 11.175151567904559
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:10:48 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 126.24028888445268 at iteration 1454127 using kt 11.175151567904559
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:10:48 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 126.12226711279567 at iteration 1454132 using kt 11.175151567904559
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:10:48 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 125.69632017125865 at iteration 1454133 using kt 11.175151567904559
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:10:48 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 124.80503428858904 at iteration 1454134 using kt 11.175151567904559
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:10:49 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 124.10089763421149 at iteration 1455235 using kt 11.175151567904559
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:10:49 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 123.30202099033681 at iteration 1455236 using kt 11.175151567904559
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:10:49 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 123.0904814379953 at iteration 1455240 using kt 11.175151567904559
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:10:49 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 123.01102620644473 at iteration 1455650 using kt 11.175151567904559
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:10:49 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 122.81884695029886 at iteration 1455651 using kt 11.175151567904559
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:10:49 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 122.79272485327462 at iteration 1455652 using kt 11.175151567904559
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:10:49 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 122.69953887499153 at iteration 1455759 using kt 11.175151567904559
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:10:49 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 122.43249110378486 at iteration 1455760 using kt 11.175151567904559
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:10:49 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 121.30528950370652 at iteration 1455762 using kt 11.175151567904559
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:10:49 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 121.05491820734116 at iteration 1455763 using kt 11.175151567904559
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:10:49 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 120.692656801264 at iteration 1455800 using kt 11.175151567904559
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:10:49 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 119.9902469262483 at iteration 1455806 using kt 11.175151567904559
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:10:49 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 118.92504949223144 at iteration 1455807 using kt 11.175151567904559
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:10:49 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 118.24765789077682 at iteration 1455808 using kt 11.175151567904559
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:10:49 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 117.53499765634928 at iteration 1456896 using kt 11.175151567904559
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:10:49 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 117.42684175289409 at iteration 1456897 using kt 11.175151567904559
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:10:49 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 116.31532901404346 at iteration 1456898 using kt 11.175151567904559
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:10:49 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 115.47811343527995 at iteration 1456899 using kt 11.175151567904559
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:10:49 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 115.33603254759939 at iteration 1456949 using kt 11.175151567904559
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:10:49 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 114.82321488014665 at iteration 1456998 using kt 11.175151567904559
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:10:49 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 113.35846671640084 at iteration 1457002 using kt 11.175151567904559
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:10:49 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 113.06229195118792 at iteration 1458069 using kt 11.175151567904559
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:10:49 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 112.9850298303725 at iteration 1458080 using kt 11.175151567904559
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:10:49 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 112.89144867503876 at iteration 1458081 using kt 11.175151567904559
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:10:50 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 1460001 Best score so far: 112.89144867503876 . Using annealing factor: 0.1100752429438599 kt: 11.00752429438599 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:10:50 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 112.66727863294695 at iteration 1460848 using kt 11.00752429438599
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:10:50 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 112.19437243544732 at iteration 1460849 using kt 11.00752429438599
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:10:50 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 111.83974332384257 at iteration 1460850 using kt 11.00752429438599
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:10:50 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 111.46937272269437 at iteration 1461061 using kt 11.00752429438599
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:10:50 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 111.2459250697853 at iteration 1461062 using kt 11.00752429438599
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:10:50 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 111.22608727853898 at iteration 1461063 using kt 11.00752429438599
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:10:50 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 110.94996429308192 at iteration 1461069 using kt 11.00752429438599
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:10:50 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 110.8291866628677 at iteration 1461078 using kt 11.00752429438599
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:10:50 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 110.74906220874735 at iteration 1461082 using kt 11.00752429438599
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:10:50 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 110.3136269381329 at iteration 1461083 using kt 11.00752429438599
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:10:50 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 110.28973961349001 at iteration 1461084 using kt 11.00752429438599
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:10:50 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 110.0117820446192 at iteration 1461097 using kt 11.00752429438599
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:10:50 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 109.13875226120487 at iteration 1461112 using kt 11.00752429438599
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:10:50 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 109.10702479308777 at iteration 1461113 using kt 11.00752429438599
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:10:50 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 108.95648287549777 at iteration 1461114 using kt 11.00752429438599
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:10:50 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 108.26294022877346 at iteration 1461115 using kt 11.00752429438599
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:10:50 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 108.17259567436086 at iteration 1461129 using kt 11.00752429438599
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:10:50 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 107.71690644948919 at iteration 1461138 using kt 11.00752429438599
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:10:50 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 107.59294726924432 at iteration 1461139 using kt 11.00752429438599
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:10:50 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 107.4595142612961 at iteration 1461173 using kt 11.00752429438599
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:10:50 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 107.43756019515246 at iteration 1461175 using kt 11.00752429438599
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:10:50 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 107.16462996396575 at iteration 1461187 using kt 11.00752429438599
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:10:50 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 107.0823060408245 at iteration 1461188 using kt 11.00752429438599
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:10:50 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 106.87759246964637 at iteration 1461193 using kt 11.00752429438599
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:10:50 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 106.65996995267146 at iteration 1461703 using kt 11.00752429438599
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:10:50 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 106.42177571434723 at iteration 1461704 using kt 11.00752429438599
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:10:50 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 106.06227832856244 at iteration 1461721 using kt 11.00752429438599
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:10:50 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 105.99729899071099 at iteration 1461722 using kt 11.00752429438599
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:10:50 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 105.44023928485788 at iteration 1462133 using kt 11.00752429438599
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:10:50 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 105.41437042964145 at iteration 1462138 using kt 11.00752429438599
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:10:50 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 105.23499579468836 at iteration 1462140 using kt 11.00752429438599
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:10:50 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 105.20035546662012 at iteration 1462141 using kt 11.00752429438599
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:10:51 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 105.18659784782807 at iteration 1462742 using kt 11.00752429438599
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:10:51 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 105.16392780641871 at iteration 1462750 using kt 11.00752429438599
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:10:51 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 105.04942758791705 at iteration 1462751 using kt 11.00752429438599
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:10:51 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 103.3310289526305 at iteration 1462752 using kt 11.00752429438599
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:10:51 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 103.23974863850867 at iteration 1462756 using kt 11.00752429438599
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:10:52 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 1470001 Best score so far: 103.23974863850867 . Using annealing factor: 0.108424114299702 kt: 10.8424114299702 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:10:55 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 1480001 Best score so far: 103.23974863850867 . Using annealing factor: 0.10679775258520648 kt: 10.679775258520648 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:10:56 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 102.73618968751808 at iteration 1482878 using kt 10.679775258520648
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:10:56 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 102.6650862955036 at iteration 1482879 using kt 10.679775258520648
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:10:56 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 102.58154958493739 at iteration 1482880 using kt 10.679775258520648
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:10:56 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 102.55182040473713 at iteration 1482881 using kt 10.679775258520648
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:10:56 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 102.29070952301126 at iteration 1482883 using kt 10.679775258520648
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:10:56 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 102.03309033141699 at iteration 1482884 using kt 10.679775258520648
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:10:56 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 101.86994105509154 at iteration 1482885 using kt 10.679775258520648
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:10:56 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 101.76419985736413 at iteration 1482921 using kt 10.679775258520648
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:10:56 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 101.66098888936227 at iteration 1482928 using kt 10.679775258520648
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:10:56 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 101.34128882879787 at iteration 1482929 using kt 10.679775258520648
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:10:56 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 101.09974313580392 at iteration 1482934 using kt 10.679775258520648
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:10:56 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 101.07029661494695 at iteration 1482942 using kt 10.679775258520648
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:10:56 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 101.02462845473671 at iteration 1482943 using kt 10.679775258520648
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:10:56 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 100.81879397831389 at iteration 1482946 using kt 10.679775258520648
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:10:56 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 100.21139209978601 at iteration 1483021 using kt 10.679775258520648
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:10:56 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 100.03216599324077 at iteration 1483022 using kt 10.679775258520648
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:10:56 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 99.9330846395925 at iteration 1483023 using kt 10.679775258520648
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:10:56 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 99.85880188306521 at iteration 1483032 using kt 10.679775258520648
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:10:56 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 99.83676958431849 at iteration 1483033 using kt 10.679775258520648
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:10:56 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 99.78025935251573 at iteration 1483036 using kt 10.679775258520648
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:10:56 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 99.64805062779146 at iteration 1483040 using kt 10.679775258520648
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:10:56 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 98.96036917383509 at iteration 1485624 using kt 10.679775258520648
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:10:56 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 98.86242260813108 at iteration 1485631 using kt 10.679775258520648
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:10:56 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 98.68232054231851 at iteration 1485632 using kt 10.679775258520648
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:10:56 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 98.27645080124375 at iteration 1485634 using kt 10.679775258520648
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:10:56 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 98.123143003521 at iteration 1485635 using kt 10.679775258520648
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:10:56 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 97.53508663963652 at iteration 1485636 using kt 10.679775258520648
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:10:56 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 96.83190413077284 at iteration 1485642 using kt 10.679775258520648
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:10:56 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 96.78406284703237 at iteration 1485644 using kt 10.679775258520648
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:10:56 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 96.60310980592953 at iteration 1485645 using kt 10.679775258520648
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:10:56 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 96.4966155560933 at iteration 1485649 using kt 10.679775258520648
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:10:56 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 96.40182723079653 at iteration 1485651 using kt 10.679775258520648
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:10:56 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 96.03612077715024 at iteration 1485657 using kt 10.679775258520648
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:10:56 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 95.9425186791422 at iteration 1485660 using kt 10.679775258520648
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:10:56 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 95.58366825180086 at iteration 1485819 using kt 10.679775258520648
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:10:56 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 95.25111999960214 at iteration 1485996 using kt 10.679775258520648
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:10:56 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 95.23168434349319 at iteration 1486013 using kt 10.679775258520648
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:10:56 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 95.21870922032113 at iteration 1486014 using kt 10.679775258520648
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:10:56 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 94.88787245379987 at iteration 1486015 using kt 10.679775258520648
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:10:56 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 94.6354661064847 at iteration 1486016 using kt 10.679775258520648
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:10:56 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 94.3917714173914 at iteration 1486018 using kt 10.679775258520648
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:10:56 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 93.97220809615189 at iteration 1486019 using kt 10.679775258520648
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:10:56 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 93.66140277317157 at iteration 1486020 using kt 10.679775258520648
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:10:56 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 93.610757266697 at iteration 1486022 using kt 10.679775258520648
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:10:56 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 93.52862129631811 at iteration 1486023 using kt 10.679775258520648
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:10:56 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 93.51641980319218 at iteration 1486024 using kt 10.679775258520648
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:10:57 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 92.88200362574919 at iteration 1486473 using kt 10.679775258520648
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:10:57 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 92.42521615373029 at iteration 1486476 using kt 10.679775258520648
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:10:57 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 92.38939882294137 at iteration 1486477 using kt 10.679775258520648
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:10:57 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 92.27538748338262 at iteration 1486481 using kt 10.679775258520648
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:10:57 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 92.03286600423023 at iteration 1486484 using kt 10.679775258520648
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:10:57 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 91.47913765467234 at iteration 1486485 using kt 10.679775258520648
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:10:57 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 91.16434159787377 at iteration 1486486 using kt 10.679775258520648
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:10:57 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 90.86455924308562 at iteration 1486488 using kt 10.679775258520648
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:10:57 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 90.80322014784497 at iteration 1487036 using kt 10.679775258520648
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:10:57 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 90.49987170625651 at iteration 1487055 using kt 10.679775258520648
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:10:57 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 89.9558484498136 at iteration 1487058 using kt 10.679775258520648
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:10:57 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 88.95805101590224 at iteration 1487059 using kt 10.679775258520648
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:10:57 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 88.76403994469858 at iteration 1487060 using kt 10.679775258520648
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:10:57 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 88.57240654328035 at iteration 1487061 using kt 10.679775258520648
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:10:57 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 88.5267728098209 at iteration 1487192 using kt 10.679775258520648
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:10:57 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 88.45527962154733 at iteration 1487199 using kt 10.679775258520648
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:10:57 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 88.45216557915971 at iteration 1487221 using kt 10.679775258520648
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:10:57 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 87.85840157148527 at iteration 1489211 using kt 10.679775258520648
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:10:57 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 87.81343794461722 at iteration 1489212 using kt 10.679775258520648
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:10:57 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 87.27988262394905 at iteration 1489333 using kt 10.679775258520648
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:10:57 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 86.86695586602184 at iteration 1489412 using kt 10.679775258520648
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:10:57 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 86.82061239926574 at iteration 1489417 using kt 10.679775258520648
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:10:57 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 86.40370866583169 at iteration 1489428 using kt 10.679775258520648
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:10:57 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 85.98270191218144 at iteration 1489433 using kt 10.679775258520648
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:10:57 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 85.7355116450651 at iteration 1489435 using kt 10.679775258520648
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:10:57 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 85.34126121924854 at iteration 1489436 using kt 10.679775258520648
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:10:57 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 85.07504306323659 at iteration 1489443 using kt 10.679775258520648
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:10:57 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 85.01881845057707 at iteration 1489444 using kt 10.679775258520648
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:10:57 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 84.73358059617172 at iteration 1489445 using kt 10.679775258520648
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:10:57 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 84.6147615066399 at iteration 1489446 using kt 10.679775258520648
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:10:57 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 84.56474260334451 at iteration 1489447 using kt 10.679775258520648
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:10:57 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 83.72155456243307 at iteration 1489448 using kt 10.679775258520648
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:10:58 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 1490001 Best score so far: 83.72155456243307 . Using annealing factor: 0.10519578629642837 kt: 10.519578629642837 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:11:00 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 83.49109910471236 at iteration 1499313 using kt 10.519578629642837
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:11:00 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 82.67615088968698 at iteration 1499314 using kt 10.519578629642837
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:11:00 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 82.31074434215967 at iteration 1499315 using kt 10.519578629642837
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:11:00 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 81.88145106762848 at iteration 1499316 using kt 10.519578629642837
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:11:00 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 81.46298063853854 at iteration 1499317 using kt 10.519578629642837
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:11:00 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Mutating helix constraints!
Oct 19, 2010 2:11:00 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 1500000 Best score so far: 81.46298063853854 . Using annealing factor: 0.10361784950198194 kt: 10.361784950198194 coordinate system multipliers: 1.0 1.0 1.0  MUTATING HELIX LENGTHS: 
7 ( 6 ) 5 ( 5 ) 7 ( 7 ) Modified helix constraint lengths: 7 5 8 
Oct 19, 2010 2:11:00 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 1500001 Best score so far: 81.46298063853854 . Using annealing factor: 0.10361784950198194 kt: 10.361784950198194 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:11:00 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 80.25645833467583 at iteration 1500605 using kt 10.361784950198194
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:11:00 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 80.05147648969341 at iteration 1500606 using kt 10.361784950198194
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:11:00 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 79.7514553308472 at iteration 1500658 using kt 10.361784950198194
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:11:00 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 79.7488202978504 at iteration 1500689 using kt 10.361784950198194
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:11:00 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 79.23533190117804 at iteration 1500690 using kt 10.361784950198194
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:11:00 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 79.2080351339039 at iteration 1500702 using kt 10.361784950198194
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:11:01 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 79.1513104385715 at iteration 1503130 using kt 10.361784950198194
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:11:01 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 78.71888864427092 at iteration 1503131 using kt 10.361784950198194
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:11:01 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 78.59634753506204 at iteration 1503132 using kt 10.361784950198194
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:11:03 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 1510001 Best score so far: 78.59634753506204 . Using annealing factor: 0.10206358175945221 kt: 10.20635817594522 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:11:05 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 1520001 Best score so far: 78.59634753506204 . Using annealing factor: 0.10053262803306043 kt: 10.053262803306042 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:11:08 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 1530001 Best score so far: 78.59634753506204 . Using annealing factor: 0.09902463861256453 kt: 9.902463861256452 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:11:10 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 1540001 Best score so far: 78.59634753506204 . Using annealing factor: 0.09753926903337605 kt: 9.753926903337605 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:11:13 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Mutating helix constraints!
Oct 19, 2010 2:11:13 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 1550000 Best score so far: 78.59634753506204 . Using annealing factor: 0.0960761799978754 kt: 9.607617999787541 coordinate system multipliers: 1.0 1.0 1.0  MUTATING HELIX LENGTHS: 
6 ( 6 ) 5 ( 5 ) 7 ( 7 ) Modified helix constraint lengths: 5 5 7 
Oct 19, 2010 2:11:13 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 1550001 Best score so far: 78.59634753506204 . Using annealing factor: 0.0960761799978754 kt: 9.607617999787541 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:11:15 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 1560001 Best score so far: 78.59634753506204 . Using annealing factor: 0.09463503729790729 kt: 9.463503729790729 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:11:18 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 1570001 Best score so far: 78.59634753506204 . Using annealing factor: 0.09321551173843867 kt: 9.321551173843867 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:11:21 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 1580001 Best score so far: 78.59634753506204 . Using annealing factor: 0.09181727906236209 kt: 9.181727906236208 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:11:22 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 78.42833622069077 at iteration 1584445 using kt 9.181727906236208
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:11:22 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 78.18216245302737 at iteration 1584446 using kt 9.181727906236208
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:11:22 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 77.77614213694181 at iteration 1584447 using kt 9.181727906236208
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:11:22 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 77.07278898938063 at iteration 1584448 using kt 9.181727906236208
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:11:22 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 77.04119117336751 at iteration 1584450 using kt 9.181727906236208
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:11:22 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 76.92952265294633 at iteration 1584458 using kt 9.181727906236208
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:11:22 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 75.72881975952998 at iteration 1584460 using kt 9.181727906236208
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:11:22 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 75.71706402235537 at iteration 1584462 using kt 9.181727906236208
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:11:22 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 75.56101883880447 at iteration 1584645 using kt 9.181727906236208
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:11:22 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 75.52310046071506 at iteration 1584647 using kt 9.181727906236208
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:11:22 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 75.06576327756179 at iteration 1584669 using kt 9.181727906236208
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:11:22 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 74.95382112814207 at iteration 1584725 using kt 9.181727906236208
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:11:22 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 74.77154240688793 at iteration 1584729 using kt 9.181727906236208
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:11:22 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 74.64165051020296 at iteration 1584734 using kt 9.181727906236208
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:11:22 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 74.56320724334527 at iteration 1584738 using kt 9.181727906236208
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:11:22 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 74.36575592511439 at iteration 1584744 using kt 9.181727906236208
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:11:22 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 74.03019443021847 at iteration 1584745 using kt 9.181727906236208
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:11:22 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 73.98558679175983 at iteration 1584759 using kt 9.181727906236208
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:11:22 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 73.73793919123199 at iteration 1584760 using kt 9.181727906236208
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:11:22 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 73.5673584104096 at iteration 1585830 using kt 9.181727906236208
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:11:22 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 73.50380629906927 at iteration 1585832 using kt 9.181727906236208
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:11:22 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 72.99311023035784 at iteration 1585833 using kt 9.181727906236208
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:11:22 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 72.77031940827646 at iteration 1585834 using kt 9.181727906236208
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:11:22 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 72.65513034494484 at iteration 1585835 using kt 9.181727906236208
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:11:22 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 72.18024274208705 at iteration 1585836 using kt 9.181727906236208
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:11:22 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 71.68415351176235 at iteration 1586245 using kt 9.181727906236208
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:11:22 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 71.63656796580484 at iteration 1586246 using kt 9.181727906236208
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:11:22 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 71.63414598736586 at iteration 1586248 using kt 9.181727906236208
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:11:22 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 71.60074643080246 at iteration 1586249 using kt 9.181727906236208
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:11:23 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 71.51123041002175 at iteration 1586367 using kt 9.181727906236208
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:11:23 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 71.10235382635342 at iteration 1586370 using kt 9.181727906236208
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:11:23 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 70.98041123831986 at iteration 1586374 using kt 9.181727906236208
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:11:23 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 70.96489385514548 at iteration 1586375 using kt 9.181727906236208
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:11:23 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 70.87919718312376 at iteration 1586376 using kt 9.181727906236208
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:11:23 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 70.56012401278596 at iteration 1586377 using kt 9.181727906236208
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:11:23 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 70.44085808362598 at iteration 1586379 using kt 9.181727906236208
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:11:23 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 70.10289315344393 at iteration 1586380 using kt 9.181727906236208
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:11:23 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 70.08974362467126 at iteration 1586381 using kt 9.181727906236208
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:11:23 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 70.00279737842621 at iteration 1586489 using kt 9.181727906236208
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:11:23 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 69.97912150969712 at iteration 1586490 using kt 9.181727906236208
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:11:23 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 69.90599402043901 at iteration 1586494 using kt 9.181727906236208
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:11:23 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 69.60003371491887 at iteration 1586498 using kt 9.181727906236208
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:11:23 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 69.4480300764101 at iteration 1586508 using kt 9.181727906236208
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:11:23 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 69.18642136821342 at iteration 1586514 using kt 9.181727906236208
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:11:23 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 69.10395292184313 at iteration 1586549 using kt 9.181727906236208
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:11:23 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 69.05218627878655 at iteration 1586552 using kt 9.181727906236208
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:11:23 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 68.90436417358687 at iteration 1586553 using kt 9.181727906236208
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:11:23 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 68.52196215394324 at iteration 1586561 using kt 9.181727906236208
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:11:23 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 68.10848454934516 at iteration 1586562 using kt 9.181727906236208
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:11:23 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 67.99324197388687 at iteration 1586564 using kt 9.181727906236208
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:11:23 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 67.97107185290038 at iteration 1586565 using kt 9.181727906236208
Currently best helix constraint lengths: 
6 5 7 Oct 19, 2010 2:11:24 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 1590001 Best score so far: 67.97107185290038 . Using annealing factor: 0.09044001987642666 kt: 9.044001987642666 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:11:26 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Mutating helix constraints!
Oct 19, 2010 2:11:26 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 1600000 Best score so far: 67.97107185290038 . Using annealing factor: 0.08908341957828025 kt: 8.908341957828025 coordinate system multipliers: 1.0 1.0 1.0  MUTATING HELIX LENGTHS: 
6 ( 6 ) 5 ( 5 ) 7 ( 7 ) Modified helix constraint lengths: 6 6 7 
Oct 19, 2010 2:11:26 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 1600001 Best score so far: 67.97107185290038 . Using annealing factor: 0.08908341957828025 kt: 8.908341957828025 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:11:29 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 1610001 Best score so far: 67.97107185290038 . Using annealing factor: 0.08774716828460605 kt: 8.774716828460605 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:11:31 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 1620001 Best score so far: 67.97107185290038 . Using annealing factor: 0.08643096076033696 kt: 8.643096076033697 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:11:34 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 1630001 Best score so far: 67.97107185290038 . Using annealing factor: 0.0851344963489319 kt: 8.51344963489319 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:11:37 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 1640001 Best score so far: 67.97107185290038 . Using annealing factor: 0.08385747890369792 kt: 8.385747890369792 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:11:39 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Mutating helix constraints!
Oct 19, 2010 2:11:39 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 1650000 Best score so far: 67.97107185290038 . Using annealing factor: 0.08259961672014246 kt: 8.259961672014246 coordinate system multipliers: 1.0 1.0 1.0  MUTATING HELIX LENGTHS: 
6 ( 6 ) 5 ( 5 ) 7 ( 7 ) Modified helix constraint lengths: 5 6 8 
Oct 19, 2010 2:11:39 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 1650001 Best score so far: 67.97107185290038 . Using annealing factor: 0.08259961672014246 kt: 8.259961672014246 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:11:42 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 1660001 Best score so far: 67.97107185290038 . Using annealing factor: 0.08136062246934031 kt: 8.136062246934031 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:11:45 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 1670001 Best score so far: 67.97107185290038 . Using annealing factor: 0.08014021313230021 kt: 8.014021313230021 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:11:46 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 67.83582412939433 at iteration 1673954 using kt 8.014021313230021
Currently best helix constraint lengths: 
6 6 7 Oct 19, 2010 2:11:46 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 67.66858524857716 at iteration 1673955 using kt 8.014021313230021
Currently best helix constraint lengths: 
6 6 7 Oct 19, 2010 2:11:46 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 67.5950898808746 at iteration 1673963 using kt 8.014021313230021
Currently best helix constraint lengths: 
6 6 7 Oct 19, 2010 2:11:46 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 67.48962384349906 at iteration 1673964 using kt 8.014021313230021
Currently best helix constraint lengths: 
6 6 7 Oct 19, 2010 2:11:46 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 67.45705933248769 at iteration 1673965 using kt 8.014021313230021
Currently best helix constraint lengths: 
6 6 7 Oct 19, 2010 2:11:46 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 66.96043427946812 at iteration 1673966 using kt 8.014021313230021
Currently best helix constraint lengths: 
6 6 7 Oct 19, 2010 2:11:46 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 66.74863685527816 at iteration 1673967 using kt 8.014021313230021
Currently best helix constraint lengths: 
6 6 7 Oct 19, 2010 2:11:46 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 66.68072438044092 at iteration 1673972 using kt 8.014021313230021
Currently best helix constraint lengths: 
6 6 7 Oct 19, 2010 2:11:46 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 66.64930013923691 at iteration 1673973 using kt 8.014021313230021
Currently best helix constraint lengths: 
6 6 7 Oct 19, 2010 2:11:46 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 66.50809545267734 at iteration 1673976 using kt 8.014021313230021
Currently best helix constraint lengths: 
6 6 7 Oct 19, 2010 2:11:46 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 66.37615069310921 at iteration 1673977 using kt 8.014021313230021
Currently best helix constraint lengths: 
6 6 7 Oct 19, 2010 2:11:46 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 66.28000294666737 at iteration 1673988 using kt 8.014021313230021
Currently best helix constraint lengths: 
6 6 7 Oct 19, 2010 2:11:46 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 66.1603910884247 at iteration 1673989 using kt 8.014021313230021
Currently best helix constraint lengths: 
6 6 7 Oct 19, 2010 2:11:46 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 65.94418179069544 at iteration 1673993 using kt 8.014021313230021
Currently best helix constraint lengths: 
6 6 7 Oct 19, 2010 2:11:46 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 65.81097297668589 at iteration 1673994 using kt 8.014021313230021
Currently best helix constraint lengths: 
6 6 7 Oct 19, 2010 2:11:46 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 65.60687585098569 at iteration 1674001 using kt 8.014021313230021
Currently best helix constraint lengths: 
6 6 7 Oct 19, 2010 2:11:46 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 65.35998341425909 at iteration 1674008 using kt 8.014021313230021
Currently best helix constraint lengths: 
6 6 7 Oct 19, 2010 2:11:46 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 65.35157963086158 at iteration 1674009 using kt 8.014021313230021
Currently best helix constraint lengths: 
6 6 7 Oct 19, 2010 2:11:46 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 65.33638877441109 at iteration 1674096 using kt 8.014021313230021
Currently best helix constraint lengths: 
6 6 7 Oct 19, 2010 2:11:46 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 64.86682324941277 at iteration 1674123 using kt 8.014021313230021
Currently best helix constraint lengths: 
6 6 7 Oct 19, 2010 2:11:46 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 64.62637453193634 at iteration 1674345 using kt 8.014021313230021
Currently best helix constraint lengths: 
6 6 7 Oct 19, 2010 2:11:46 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 64.29818109159402 at iteration 1674346 using kt 8.014021313230021
Currently best helix constraint lengths: 
6 6 7 Oct 19, 2010 2:11:46 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 63.36003100381187 at iteration 1674347 using kt 8.014021313230021
Currently best helix constraint lengths: 
6 6 7 Oct 19, 2010 2:11:46 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 63.162859466759876 at iteration 1674350 using kt 8.014021313230021
Currently best helix constraint lengths: 
6 6 7 Oct 19, 2010 2:11:47 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 1680001 Best score so far: 63.162859466759876 . Using annealing factor: 0.0789381099353157 kt: 7.893810993531571 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:11:50 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 1690001 Best score so far: 63.162859466759876 . Using annealing factor: 0.07775403828628596 kt: 7.775403828628597 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:11:53 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Mutating helix constraints!
Oct 19, 2010 2:11:53 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 1700000 Best score so far: 63.162859466759876 . Using annealing factor: 0.07658772771199168 kt: 7.658772771199168 coordinate system multipliers: 1.0 1.0 1.0  MUTATING HELIX LENGTHS: 
6 ( 6 ) 6 ( 6 ) 7 ( 7 ) Modified helix constraint lengths: 5 7 7 
Oct 19, 2010 2:11:53 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 1700001 Best score so far: 63.162859466759876 . Using annealing factor: 0.07658772771199168 kt: 7.658772771199168 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:11:56 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 1710001 Best score so far: 63.162859466759876 . Using annealing factor: 0.0754389117963118 kt: 7.5438911796311805 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:11:58 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 1720001 Best score so far: 63.162859466759876 . Using annealing factor: 0.07430732811936712 kt: 7.4307328119367115 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:12:01 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 1730001 Best score so far: 63.162859466759876 . Using annealing factor: 0.07319271819757661 kt: 7.319271819757661 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:12:04 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 1740001 Best score so far: 63.162859466759876 . Using annealing factor: 0.07209482742461297 kt: 7.209482742461297 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:12:06 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Mutating helix constraints!
Oct 19, 2010 2:12:06 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 1750000 Best score so far: 63.162859466759876 . Using annealing factor: 0.07101340501324377 kt: 7.101340501324377 coordinate system multipliers: 1.0 1.0 1.0  MUTATING HELIX LENGTHS: 
6 ( 6 ) 6 ( 6 ) 7 ( 7 ) Modified helix constraint lengths: 6 5 6 
Oct 19, 2010 2:12:06 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 1750001 Best score so far: 63.162859466759876 . Using annealing factor: 0.07101340501324377 kt: 7.101340501324377 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:12:07 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 62.86103009785853 at iteration 1754423 using kt 7.101340501324377
Currently best helix constraint lengths: 
6 5 6 Oct 19, 2010 2:12:07 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 62.489575087209644 at iteration 1754428 using kt 7.101340501324377
Currently best helix constraint lengths: 
6 5 6 Oct 19, 2010 2:12:07 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 61.874785621863474 at iteration 1754430 using kt 7.101340501324377
Currently best helix constraint lengths: 
6 5 6 Oct 19, 2010 2:12:07 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 60.68703485751718 at iteration 1754441 using kt 7.101340501324377
Currently best helix constraint lengths: 
6 5 6 Oct 19, 2010 2:12:07 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 60.56783445459726 at iteration 1754442 using kt 7.101340501324377
Currently best helix constraint lengths: 
6 5 6 Oct 19, 2010 2:12:07 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 60.26344365754589 at iteration 1754444 using kt 7.101340501324377
Currently best helix constraint lengths: 
6 5 6 Oct 19, 2010 2:12:07 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 60.022937949569666 at iteration 1754446 using kt 7.101340501324377
Currently best helix constraint lengths: 
6 5 6 Oct 19, 2010 2:12:07 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 59.89562114200082 at iteration 1754447 using kt 7.101340501324377
Currently best helix constraint lengths: 
6 5 6 Oct 19, 2010 2:12:07 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 59.72523465046386 at iteration 1754523 using kt 7.101340501324377
Currently best helix constraint lengths: 
6 5 6 Oct 19, 2010 2:12:07 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 59.41779737902134 at iteration 1754549 using kt 7.101340501324377
Currently best helix constraint lengths: 
6 5 6 Oct 19, 2010 2:12:07 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 59.34164053157846 at iteration 1754550 using kt 7.101340501324377
Currently best helix constraint lengths: 
6 5 6 Oct 19, 2010 2:12:07 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 59.16207942859326 at iteration 1754551 using kt 7.101340501324377
Currently best helix constraint lengths: 
6 5 6 Oct 19, 2010 2:12:07 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 58.85191718186579 at iteration 1754552 using kt 7.101340501324377
Currently best helix constraint lengths: 
6 5 6 Oct 19, 2010 2:12:07 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 58.541200358103474 at iteration 1754560 using kt 7.101340501324377
Currently best helix constraint lengths: 
6 5 6 Oct 19, 2010 2:12:07 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 58.311324928403 at iteration 1754561 using kt 7.101340501324377
Currently best helix constraint lengths: 
6 5 6 Oct 19, 2010 2:12:07 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 58.10288825258132 at iteration 1754562 using kt 7.101340501324377
Currently best helix constraint lengths: 
6 5 6 Oct 19, 2010 2:12:07 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 58.03060411927596 at iteration 1754565 using kt 7.101340501324377
Currently best helix constraint lengths: 
6 5 6 Oct 19, 2010 2:12:07 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 58.000181980115144 at iteration 1754566 using kt 7.101340501324377
Currently best helix constraint lengths: 
6 5 6 Oct 19, 2010 2:12:07 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 57.963548142023384 at iteration 1754567 using kt 7.101340501324377
Currently best helix constraint lengths: 
6 5 6 Oct 19, 2010 2:12:07 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 57.79813608025806 at iteration 1754571 using kt 7.101340501324377
Currently best helix constraint lengths: 
6 5 6 Oct 19, 2010 2:12:07 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 57.59098591768471 at iteration 1754576 using kt 7.101340501324377
Currently best helix constraint lengths: 
6 5 6 Oct 19, 2010 2:12:07 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 57.13993341118263 at iteration 1754579 using kt 7.101340501324377
Currently best helix constraint lengths: 
6 5 6 Oct 19, 2010 2:12:07 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 57.09851785962468 at iteration 1754580 using kt 7.101340501324377
Currently best helix constraint lengths: 
6 5 6 Oct 19, 2010 2:12:07 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 57.078748268435795 at iteration 1754581 using kt 7.101340501324377
Currently best helix constraint lengths: 
6 5 6 Oct 19, 2010 2:12:07 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 57.036011966902336 at iteration 1754602 using kt 7.101340501324377
Currently best helix constraint lengths: 
6 5 6 Oct 19, 2010 2:12:07 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 56.85723780110306 at iteration 1754603 using kt 7.101340501324377
Currently best helix constraint lengths: 
6 5 6 Oct 19, 2010 2:12:07 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 56.83190528896224 at iteration 1754604 using kt 7.101340501324377
Currently best helix constraint lengths: 
6 5 6 Oct 19, 2010 2:12:07 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 56.73519304131351 at iteration 1754606 using kt 7.101340501324377
Currently best helix constraint lengths: 
6 5 6 Oct 19, 2010 2:12:07 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 56.60004796563254 at iteration 1754607 using kt 7.101340501324377
Currently best helix constraint lengths: 
6 5 6 Oct 19, 2010 2:12:07 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 56.33345477215241 at iteration 1754608 using kt 7.101340501324377
Currently best helix constraint lengths: 
6 5 6 Oct 19, 2010 2:12:07 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 56.09787360404724 at iteration 1754610 using kt 7.101340501324377
Currently best helix constraint lengths: 
6 5 6 Oct 19, 2010 2:12:07 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 55.67155710242588 at iteration 1754617 using kt 7.101340501324377
Currently best helix constraint lengths: 
6 5 6 Oct 19, 2010 2:12:07 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 55.45049470640545 at iteration 1754621 using kt 7.101340501324377
Currently best helix constraint lengths: 
6 5 6 Oct 19, 2010 2:12:07 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 55.365432349517214 at iteration 1754623 using kt 7.101340501324377
Currently best helix constraint lengths: 
6 5 6 Oct 19, 2010 2:12:07 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 55.15612565012847 at iteration 1754626 using kt 7.101340501324377
Currently best helix constraint lengths: 
6 5 6 Oct 19, 2010 2:12:07 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 54.781033534675885 at iteration 1754630 using kt 7.101340501324377
Currently best helix constraint lengths: 
6 5 6 Oct 19, 2010 2:12:07 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 54.7441569219885 at iteration 1754681 using kt 7.101340501324377
Currently best helix constraint lengths: 
6 5 6 Oct 19, 2010 2:12:07 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 54.685112232507564 at iteration 1754685 using kt 7.101340501324377
Currently best helix constraint lengths: 
6 5 6 Oct 19, 2010 2:12:07 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 54.45807927539788 at iteration 1754688 using kt 7.101340501324377
Currently best helix constraint lengths: 
6 5 6 Oct 19, 2010 2:12:07 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 54.29929295509318 at iteration 1754690 using kt 7.101340501324377
Currently best helix constraint lengths: 
6 5 6 Oct 19, 2010 2:12:07 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 54.084537997839846 at iteration 1754691 using kt 7.101340501324377
Currently best helix constraint lengths: 
6 5 6 Oct 19, 2010 2:12:09 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 1760001 Best score so far: 54.084537997839846 . Using annealing factor: 0.06994820393804511 kt: 6.9948203938045115 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:12:10 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 53.8369799528264 at iteration 1763050 using kt 6.9948203938045115
Currently best helix constraint lengths: 
6 5 6 Oct 19, 2010 2:12:10 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 53.524263821107425 at iteration 1763051 using kt 6.9948203938045115
Currently best helix constraint lengths: 
6 5 6 Oct 19, 2010 2:12:12 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 53.51332506418082 at iteration 1769930 using kt 6.9948203938045115
Currently best helix constraint lengths: 
6 5 6 Oct 19, 2010 2:12:12 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 53.156823575642456 at iteration 1769931 using kt 6.9948203938045115
Currently best helix constraint lengths: 
6 5 6 Oct 19, 2010 2:12:12 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 52.91144229675638 at iteration 1769933 using kt 6.9948203938045115
Currently best helix constraint lengths: 
6 5 6 Oct 19, 2010 2:12:12 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 52.87795175537133 at iteration 1769934 using kt 6.9948203938045115
Currently best helix constraint lengths: 
6 5 6 Oct 19, 2010 2:12:12 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 52.80015969458859 at iteration 1769935 using kt 6.9948203938045115
Currently best helix constraint lengths: 
6 5 6 Oct 19, 2010 2:12:12 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 1770001 Best score so far: 52.80015969458859 . Using annealing factor: 0.06889898087897443 kt: 6.889898087897444 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:12:12 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 52.301447380995626 at iteration 1770387 using kt 6.889898087897444
Currently best helix constraint lengths: 
6 5 6 Oct 19, 2010 2:12:12 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 51.765971199709114 at iteration 1770388 using kt 6.889898087897444
Currently best helix constraint lengths: 
6 5 6 Oct 19, 2010 2:12:12 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 51.66749691126494 at iteration 1770389 using kt 6.889898087897444
Currently best helix constraint lengths: 
6 5 6 Oct 19, 2010 2:12:12 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 51.546592636013855 at iteration 1770391 using kt 6.889898087897444
Currently best helix constraint lengths: 
6 5 6 Oct 19, 2010 2:12:12 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 51.38575423690713 at iteration 1770395 using kt 6.889898087897444
Currently best helix constraint lengths: 
6 5 6 Oct 19, 2010 2:12:12 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 51.294158617460084 at iteration 1770396 using kt 6.889898087897444
Currently best helix constraint lengths: 
6 5 6 Oct 19, 2010 2:12:12 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 51.26581826592045 at iteration 1770409 using kt 6.889898087897444
Currently best helix constraint lengths: 
6 5 6 Oct 19, 2010 2:12:12 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 51.21383878669731 at iteration 1770410 using kt 6.889898087897444
Currently best helix constraint lengths: 
6 5 6 Oct 19, 2010 2:12:12 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 51.21154313077221 at iteration 1770418 using kt 6.889898087897444
Currently best helix constraint lengths: 
6 5 6 Oct 19, 2010 2:12:12 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 51.09597925820291 at iteration 1770454 using kt 6.889898087897444
Currently best helix constraint lengths: 
6 5 6 Oct 19, 2010 2:12:12 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 51.02444611209013 at iteration 1770486 using kt 6.889898087897444
Currently best helix constraint lengths: 
6 5 6 Oct 19, 2010 2:12:12 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 50.940493554993 at iteration 1770487 using kt 6.889898087897444
Currently best helix constraint lengths: 
6 5 6 Oct 19, 2010 2:12:12 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 50.76067549963581 at iteration 1770541 using kt 6.889898087897444
Currently best helix constraint lengths: 
6 5 6 Oct 19, 2010 2:12:12 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 50.59602738972539 at iteration 1770544 using kt 6.889898087897444
Currently best helix constraint lengths: 
6 5 6 Oct 19, 2010 2:12:12 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 50.47714401185445 at iteration 1770546 using kt 6.889898087897444
Currently best helix constraint lengths: 
6 5 6 Oct 19, 2010 2:12:12 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 50.35312196639748 at iteration 1770547 using kt 6.889898087897444
Currently best helix constraint lengths: 
6 5 6 Oct 19, 2010 2:12:12 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 49.09018434154538 at iteration 1770548 using kt 6.889898087897444
Currently best helix constraint lengths: 
6 5 6 Oct 19, 2010 2:12:13 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 49.04346827552274 at iteration 1774064 using kt 6.889898087897444
Currently best helix constraint lengths: 
6 5 6 Oct 19, 2010 2:12:13 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 48.34637152533102 at iteration 1774065 using kt 6.889898087897444
Currently best helix constraint lengths: 
6 5 6 Oct 19, 2010 2:12:13 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 48.31790134448574 at iteration 1774082 using kt 6.889898087897444
Currently best helix constraint lengths: 
6 5 6 Oct 19, 2010 2:12:13 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 48.30886641611686 at iteration 1774083 using kt 6.889898087897444
Currently best helix constraint lengths: 
6 5 6 Oct 19, 2010 2:12:13 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 48.06683475074913 at iteration 1774085 using kt 6.889898087897444
Currently best helix constraint lengths: 
6 5 6 Oct 19, 2010 2:12:14 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 1780001 Best score so far: 48.06683475074913 . Using annealing factor: 0.06786549616578982 kt: 6.7865496165789825 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:12:17 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 1790001 Best score so far: 48.06683475074913 . Using annealing factor: 0.06684751372330297 kt: 6.684751372330297 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:12:20 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Mutating helix constraints!
Oct 19, 2010 2:12:20 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 1800000 Best score so far: 48.06683475074913 . Using annealing factor: 0.06584480101745342 kt: 6.584480101745342 coordinate system multipliers: 1.0 1.0 1.0  MUTATING HELIX LENGTHS: 
6 ( 6 ) 6 ( 5 ) 7 ( 6 ) Modified helix constraint lengths: 7 4 5 
Oct 19, 2010 2:12:20 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 1800001 Best score so far: 48.06683475074913 . Using annealing factor: 0.06584480101745342 kt: 6.584480101745342 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:12:22 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 1810001 Best score so far: 48.06683475074913 . Using annealing factor: 0.06485712900219162 kt: 6.485712900219162 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:12:25 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 1820001 Best score so far: 48.06683475074913 . Using annealing factor: 0.06388427206715874 kt: 6.388427206715875 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:12:28 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 1830001 Best score so far: 48.06683475074913 . Using annealing factor: 0.06292600798615136 kt: 6.292600798615136 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:12:31 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 1840001 Best score so far: 48.06683475074913 . Using annealing factor: 0.06198211786635909 kt: 6.198211786635909 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:12:33 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Mutating helix constraints!
Oct 19, 2010 2:12:33 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 1850000 Best score so far: 48.06683475074913 . Using annealing factor: 0.061052386098363706 kt: 6.105238609836371 coordinate system multipliers: 1.0 1.0 1.0  MUTATING HELIX LENGTHS: 
6 ( 6 ) 5 ( 5 ) 6 ( 6 ) Modified helix constraint lengths: 6 6 6 
Oct 19, 2010 2:12:33 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 1850001 Best score so far: 48.06683475074913 . Using annealing factor: 0.061052386098363706 kt: 6.105238609836371 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:12:33 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 48.030115908265216 at iteration 1850409 using kt 6.105238609836371
Currently best helix constraint lengths: 
6 6 6 Oct 19, 2010 2:12:33 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 48.00104013823692 at iteration 1850411 using kt 6.105238609836371
Currently best helix constraint lengths: 
6 6 6 Oct 19, 2010 2:12:33 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 47.82802547693663 at iteration 1850453 using kt 6.105238609836371
Currently best helix constraint lengths: 
6 6 6 Oct 19, 2010 2:12:33 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 47.73744849171118 at iteration 1850538 using kt 6.105238609836371
Currently best helix constraint lengths: 
6 6 6 Oct 19, 2010 2:12:33 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 47.657561317290345 at iteration 1850541 using kt 6.105238609836371
Currently best helix constraint lengths: 
6 6 6 Oct 19, 2010 2:12:33 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 47.52244529048747 at iteration 1850542 using kt 6.105238609836371
Currently best helix constraint lengths: 
6 6 6 Oct 19, 2010 2:12:33 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 47.411718835162326 at iteration 1850554 using kt 6.105238609836371
Currently best helix constraint lengths: 
6 6 6 Oct 19, 2010 2:12:33 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 47.373117894989605 at iteration 1850634 using kt 6.105238609836371
Currently best helix constraint lengths: 
6 6 6 Oct 19, 2010 2:12:33 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 47.286883660117866 at iteration 1850635 using kt 6.105238609836371
Currently best helix constraint lengths: 
6 6 6 Oct 19, 2010 2:12:33 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 47.240380662669615 at iteration 1850644 using kt 6.105238609836371
Currently best helix constraint lengths: 
6 6 6 Oct 19, 2010 2:12:33 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 47.140634804645714 at iteration 1850657 using kt 6.105238609836371
Currently best helix constraint lengths: 
6 6 6 Oct 19, 2010 2:12:33 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 47.063559953989596 at iteration 1850658 using kt 6.105238609836371
Currently best helix constraint lengths: 
6 6 6 Oct 19, 2010 2:12:33 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 47.04720730939507 at iteration 1850659 using kt 6.105238609836371
Currently best helix constraint lengths: 
6 6 6 Oct 19, 2010 2:12:33 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 46.703582264084545 at iteration 1850696 using kt 6.105238609836371
Currently best helix constraint lengths: 
6 6 6 Oct 19, 2010 2:12:33 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 46.496888699151654 at iteration 1850697 using kt 6.105238609836371
Currently best helix constraint lengths: 
6 6 6 Oct 19, 2010 2:12:33 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 46.494422940208864 at iteration 1850698 using kt 6.105238609836371
Currently best helix constraint lengths: 
6 6 6 Oct 19, 2010 2:12:33 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 46.344728691846285 at iteration 1850699 using kt 6.105238609836371
Currently best helix constraint lengths: 
6 6 6 Oct 19, 2010 2:12:33 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 46.227391765600956 at iteration 1850700 using kt 6.105238609836371
Currently best helix constraint lengths: 
6 6 6 Oct 19, 2010 2:12:36 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 46.22123841188226 at iteration 1858759 using kt 6.105238609836371
Currently best helix constraint lengths: 
6 6 6 Oct 19, 2010 2:12:36 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 46.19542402540287 at iteration 1858763 using kt 6.105238609836371
Currently best helix constraint lengths: 
6 6 6 Oct 19, 2010 2:12:36 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 45.9830867366912 at iteration 1858811 using kt 6.105238609836371
Currently best helix constraint lengths: 
6 6 6 Oct 19, 2010 2:12:36 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 45.50741516003524 at iteration 1858820 using kt 6.105238609836371
Currently best helix constraint lengths: 
6 6 6 Oct 19, 2010 2:12:36 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 45.46701068717195 at iteration 1858821 using kt 6.105238609836371
Currently best helix constraint lengths: 
6 6 6 Oct 19, 2010 2:12:36 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 45.44583270834302 at iteration 1858823 using kt 6.105238609836371
Currently best helix constraint lengths: 
6 6 6 Oct 19, 2010 2:12:36 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 45.27235932206344 at iteration 1858843 using kt 6.105238609836371
Currently best helix constraint lengths: 
6 6 6 Oct 19, 2010 2:12:36 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 45.1935634588357 at iteration 1858844 using kt 6.105238609836371
Currently best helix constraint lengths: 
6 6 6 Oct 19, 2010 2:12:36 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 1860001 Best score so far: 45.1935634588357 . Using annealing factor: 0.06013660030688825 kt: 6.013660030688825 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:12:39 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 1870001 Best score so far: 45.1935634588357 . Using annealing factor: 0.05923455130228492 kt: 5.923455130228493 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:12:41 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 1880001 Best score so far: 45.1935634588357 . Using annealing factor: 0.05834603303275065 kt: 5.834603303275065 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:12:43 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 45.147298530107406 at iteration 1888173 using kt 5.834603303275065
Currently best helix constraint lengths: 
6 6 6 Oct 19, 2010 2:12:43 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 45.02402942316338 at iteration 1888197 using kt 5.834603303275065
Currently best helix constraint lengths: 
6 6 6 Oct 19, 2010 2:12:43 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 44.9563883906319 at iteration 1888199 using kt 5.834603303275065
Currently best helix constraint lengths: 
6 6 6 Oct 19, 2010 2:12:43 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 44.84547530372663 at iteration 1888230 using kt 5.834603303275065
Currently best helix constraint lengths: 
6 6 6 Oct 19, 2010 2:12:43 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 44.76816241648721 at iteration 1888233 using kt 5.834603303275065
Currently best helix constraint lengths: 
6 6 6 Oct 19, 2010 2:12:44 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 44.68279044772474 at iteration 1889322 using kt 5.834603303275065
Currently best helix constraint lengths: 
6 6 6 Oct 19, 2010 2:12:44 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 44.54449724653615 at iteration 1889323 using kt 5.834603303275065
Currently best helix constraint lengths: 
6 6 6 Oct 19, 2010 2:12:44 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 44.495561731314595 at iteration 1889325 using kt 5.834603303275065
Currently best helix constraint lengths: 
6 6 6 Oct 19, 2010 2:12:44 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 44.44951432075975 at iteration 1889326 using kt 5.834603303275065
Currently best helix constraint lengths: 
6 6 6 Oct 19, 2010 2:12:44 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 44.37351183821546 at iteration 1889455 using kt 5.834603303275065
Currently best helix constraint lengths: 
6 6 6 Oct 19, 2010 2:12:44 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 44.228906342375495 at iteration 1889511 using kt 5.834603303275065
Currently best helix constraint lengths: 
6 6 6 Oct 19, 2010 2:12:44 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 44.22280992773416 at iteration 1889520 using kt 5.834603303275065
Currently best helix constraint lengths: 
6 6 6 Oct 19, 2010 2:12:44 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 44.180538402941295 at iteration 1889521 using kt 5.834603303275065
Currently best helix constraint lengths: 
6 6 6 Oct 19, 2010 2:12:44 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 44.156813288285406 at iteration 1889532 using kt 5.834603303275065
Currently best helix constraint lengths: 
6 6 6 Oct 19, 2010 2:12:44 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 44.11240351341584 at iteration 1889533 using kt 5.834603303275065
Currently best helix constraint lengths: 
6 6 6 Oct 19, 2010 2:12:44 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 44.07984125347812 at iteration 1889535 using kt 5.834603303275065
Currently best helix constraint lengths: 
6 6 6 Oct 19, 2010 2:12:44 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 44.01807051740624 at iteration 1889536 using kt 5.834603303275065
Currently best helix constraint lengths: 
6 6 6 Oct 19, 2010 2:12:44 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 43.95213437704907 at iteration 1889540 using kt 5.834603303275065
Currently best helix constraint lengths: 
6 6 6 Oct 19, 2010 2:12:44 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 43.8780371384903 at iteration 1889541 using kt 5.834603303275065
Currently best helix constraint lengths: 
6 6 6 Oct 19, 2010 2:12:44 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 43.87197131196584 at iteration 1889547 using kt 5.834603303275065
Currently best helix constraint lengths: 
6 6 6 Oct 19, 2010 2:12:44 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 43.87191636431899 at iteration 1889591 using kt 5.834603303275065
Currently best helix constraint lengths: 
6 6 6 Oct 19, 2010 2:12:44 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 43.83928448512307 at iteration 1889592 using kt 5.834603303275065
Currently best helix constraint lengths: 
6 6 6 Oct 19, 2010 2:12:44 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 43.691208947654374 at iteration 1889593 using kt 5.834603303275065
Currently best helix constraint lengths: 
6 6 6 Oct 19, 2010 2:12:44 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 43.65508706282113 at iteration 1889596 using kt 5.834603303275065
Currently best helix constraint lengths: 
6 6 6 Oct 19, 2010 2:12:44 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 43.621336276999045 at iteration 1889599 using kt 5.834603303275065
Currently best helix constraint lengths: 
6 6 6 Oct 19, 2010 2:12:44 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 43.61836968867499 at iteration 1889621 using kt 5.834603303275065
Currently best helix constraint lengths: 
6 6 6 Oct 19, 2010 2:12:44 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 43.5365039602722 at iteration 1889622 using kt 5.834603303275065
Currently best helix constraint lengths: 
6 6 6 Oct 19, 2010 2:12:44 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 43.43949020778216 at iteration 1889623 using kt 5.834603303275065
Currently best helix constraint lengths: 
6 6 6 Oct 19, 2010 2:12:44 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 43.40693783480792 at iteration 1889664 using kt 5.834603303275065
Currently best helix constraint lengths: 
6 6 6 Oct 19, 2010 2:12:44 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 43.30322961751794 at iteration 1889665 using kt 5.834603303275065
Currently best helix constraint lengths: 
6 6 6 Oct 19, 2010 2:12:44 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 43.27192550981678 at iteration 1889666 using kt 5.834603303275065
Currently best helix constraint lengths: 
6 6 6 Oct 19, 2010 2:12:44 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 43.22247228098884 at iteration 1889667 using kt 5.834603303275065
Currently best helix constraint lengths: 
6 6 6 Oct 19, 2010 2:12:44 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 43.194455595325806 at iteration 1889668 using kt 5.834603303275065
Currently best helix constraint lengths: 
6 6 6 Oct 19, 2010 2:12:44 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 43.168662399498245 at iteration 1889669 using kt 5.834603303275065
Currently best helix constraint lengths: 
6 6 6 Oct 19, 2010 2:12:44 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 43.14780315836633 at iteration 1889670 using kt 5.834603303275065
Currently best helix constraint lengths: 
6 6 6 Oct 19, 2010 2:12:44 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 1890001 Best score so far: 43.14780315836633 . Using annealing factor: 0.05747084253725939 kt: 5.747084253725939 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:12:46 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 43.13750587814216 at iteration 1897193 using kt 5.747084253725939
Currently best helix constraint lengths: 
6 6 6 Oct 19, 2010 2:12:46 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 43.13144887092851 at iteration 1897683 using kt 5.747084253725939
Currently best helix constraint lengths: 
6 6 6 Oct 19, 2010 2:12:46 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 43.08518512175049 at iteration 1897687 using kt 5.747084253725939
Currently best helix constraint lengths: 
6 6 6 Oct 19, 2010 2:12:46 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 42.99138865325179 at iteration 1897695 using kt 5.747084253725939
Currently best helix constraint lengths: 
6 6 6 Oct 19, 2010 2:12:46 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 42.95137851982763 at iteration 1897696 using kt 5.747084253725939
Currently best helix constraint lengths: 
6 6 6 Oct 19, 2010 2:12:46 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 42.92394727600694 at iteration 1897697 using kt 5.747084253725939
Currently best helix constraint lengths: 
6 6 6 Oct 19, 2010 2:12:46 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 42.9156018044776 at iteration 1897699 using kt 5.747084253725939
Currently best helix constraint lengths: 
6 6 6 Oct 19, 2010 2:12:46 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 42.888678157523884 at iteration 1897700 using kt 5.747084253725939
Currently best helix constraint lengths: 
6 6 6 Oct 19, 2010 2:12:46 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 42.80888864115423 at iteration 1897702 using kt 5.747084253725939
Currently best helix constraint lengths: 
6 6 6 Oct 19, 2010 2:12:46 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 42.78902146104658 at iteration 1897708 using kt 5.747084253725939
Currently best helix constraint lengths: 
6 6 6 Oct 19, 2010 2:12:46 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 42.71073530923821 at iteration 1897751 using kt 5.747084253725939
Currently best helix constraint lengths: 
6 6 6 Oct 19, 2010 2:12:47 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Mutating helix constraints!
Oct 19, 2010 2:12:47 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 1900000 Best score so far: 42.71073530923821 . Using annealing factor: 0.0566087798992005 kt: 5.66087798992005 coordinate system multipliers: 1.0 1.0 1.0  MUTATING HELIX LENGTHS: 
6 ( 6 ) 5 ( 6 ) 6 ( 6 ) Oct 19, 2010 2:12:47 PM rnadesign.rnamodel.HelixOptimizer mutateHelixLengths
WARNING: No helix lengths were modified!
Oct 19, 2010 2:12:47 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 1900001 Best score so far: 42.71073530923821 . Using annealing factor: 0.0566087798992005 kt: 5.66087798992005 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:12:48 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 42.46324574095716 at iteration 1905937 using kt 5.66087798992005
Currently best helix constraint lengths: 
6 6 6 Oct 19, 2010 2:12:48 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 42.052856109189946 at iteration 1905938 using kt 5.66087798992005
Currently best helix constraint lengths: 
6 6 6 Oct 19, 2010 2:12:48 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 41.96894531894155 at iteration 1905939 using kt 5.66087798992005
Currently best helix constraint lengths: 
6 6 6 Oct 19, 2010 2:12:48 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 41.86468091129419 at iteration 1905940 using kt 5.66087798992005
Currently best helix constraint lengths: 
6 6 6 Oct 19, 2010 2:12:48 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 41.77378480521974 at iteration 1905941 using kt 5.66087798992005
Currently best helix constraint lengths: 
6 6 6 Oct 19, 2010 2:12:48 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 41.58759820094507 at iteration 1905942 using kt 5.66087798992005
Currently best helix constraint lengths: 
6 6 6 Oct 19, 2010 2:12:48 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 41.56024554772063 at iteration 1905946 using kt 5.66087798992005
Currently best helix constraint lengths: 
6 6 6 Oct 19, 2010 2:12:48 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 41.185002378848964 at iteration 1905983 using kt 5.66087798992005
Currently best helix constraint lengths: 
6 6 6 Oct 19, 2010 2:12:48 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 41.066885258562195 at iteration 1906043 using kt 5.66087798992005
Currently best helix constraint lengths: 
6 6 6 Oct 19, 2010 2:12:48 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 41.03278507896559 at iteration 1906044 using kt 5.66087798992005
Currently best helix constraint lengths: 
6 6 6 Oct 19, 2010 2:12:48 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 40.87914663609557 at iteration 1906045 using kt 5.66087798992005
Currently best helix constraint lengths: 
6 6 6 Oct 19, 2010 2:12:48 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 40.64410632513534 at iteration 1906046 using kt 5.66087798992005
Currently best helix constraint lengths: 
6 6 6 Oct 19, 2010 2:12:48 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 40.33303629531957 at iteration 1906047 using kt 5.66087798992005
Currently best helix constraint lengths: 
6 6 6 Oct 19, 2010 2:12:48 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 40.312166424818045 at iteration 1906050 using kt 5.66087798992005
Currently best helix constraint lengths: 
6 6 6 Oct 19, 2010 2:12:48 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 40.09933851739428 at iteration 1906057 using kt 5.66087798992005
Currently best helix constraint lengths: 
6 6 6 Oct 19, 2010 2:12:48 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 40.08543671680009 at iteration 1906059 using kt 5.66087798992005
Currently best helix constraint lengths: 
6 6 6 Oct 19, 2010 2:12:48 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 39.99013126278922 at iteration 1906061 using kt 5.66087798992005
Currently best helix constraint lengths: 
6 6 6 Oct 19, 2010 2:12:48 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 39.94574167112802 at iteration 1906069 using kt 5.66087798992005
Currently best helix constraint lengths: 
6 6 6 Oct 19, 2010 2:12:48 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 39.833344823032334 at iteration 1906072 using kt 5.66087798992005
Currently best helix constraint lengths: 
6 6 6 Oct 19, 2010 2:12:48 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 39.80323121884976 at iteration 1906075 using kt 5.66087798992005
Currently best helix constraint lengths: 
6 6 6 Oct 19, 2010 2:12:48 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 39.77567145401409 at iteration 1906076 using kt 5.66087798992005
Currently best helix constraint lengths: 
6 6 6 Oct 19, 2010 2:12:48 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 39.75913302055983 at iteration 1906077 using kt 5.66087798992005
Currently best helix constraint lengths: 
6 6 6 Oct 19, 2010 2:12:48 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 39.75473287649262 at iteration 1906083 using kt 5.66087798992005
Currently best helix constraint lengths: 
6 6 6 Oct 19, 2010 2:12:48 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 39.731820250325775 at iteration 1906084 using kt 5.66087798992005
Currently best helix constraint lengths: 
6 6 6 Oct 19, 2010 2:12:48 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 39.7150965440716 at iteration 1906130 using kt 5.66087798992005
Currently best helix constraint lengths: 
6 6 6 Oct 19, 2010 2:12:48 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 39.70235796601102 at iteration 1906167 using kt 5.66087798992005
Currently best helix constraint lengths: 
6 6 6 Oct 19, 2010 2:12:48 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 39.65867114048778 at iteration 1906280 using kt 5.66087798992005
Currently best helix constraint lengths: 
6 6 6 Oct 19, 2010 2:12:48 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 39.492246880985235 at iteration 1906281 using kt 5.66087798992005
Currently best helix constraint lengths: 
6 6 6 Oct 19, 2010 2:12:48 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 39.419700923574084 at iteration 1906283 using kt 5.66087798992005
Currently best helix constraint lengths: 
6 6 6 Oct 19, 2010 2:12:49 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 1910001 Best score so far: 39.419700923574084 . Using annealing factor: 0.05575964820071249 kt: 5.575964820071249 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:12:52 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 1920001 Best score so far: 39.419700923574084 . Using annealing factor: 0.0549232534777018 kt: 5.49232534777018 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:12:53 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 39.37345858836082 at iteration 1923902 using kt 5.49232534777018
Currently best helix constraint lengths: 
6 6 6 Oct 19, 2010 2:12:53 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 39.32308197221168 at iteration 1923903 using kt 5.49232534777018
Currently best helix constraint lengths: 
6 6 6 Oct 19, 2010 2:12:53 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 39.30522665421121 at iteration 1923904 using kt 5.49232534777018
Currently best helix constraint lengths: 
6 6 6 Oct 19, 2010 2:12:53 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 39.3043494398468 at iteration 1923912 using kt 5.49232534777018
Currently best helix constraint lengths: 
6 6 6 Oct 19, 2010 2:12:53 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 39.22337400465442 at iteration 1923913 using kt 5.49232534777018
Currently best helix constraint lengths: 
6 6 6 Oct 19, 2010 2:12:53 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 39.1504747884952 at iteration 1923940 using kt 5.49232534777018
Currently best helix constraint lengths: 
6 6 6 Oct 19, 2010 2:12:53 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 39.14175835447242 at iteration 1923944 using kt 5.49232534777018
Currently best helix constraint lengths: 
6 6 6 Oct 19, 2010 2:12:53 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 39.003038168119346 at iteration 1923945 using kt 5.49232534777018
Currently best helix constraint lengths: 
6 6 6 Oct 19, 2010 2:12:53 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 38.96976756428904 at iteration 1923946 using kt 5.49232534777018
Currently best helix constraint lengths: 
6 6 6 Oct 19, 2010 2:12:53 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 38.74146411791931 at iteration 1923951 using kt 5.49232534777018
Currently best helix constraint lengths: 
6 6 6 Oct 19, 2010 2:12:53 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 38.66354038466005 at iteration 1923952 using kt 5.49232534777018
Currently best helix constraint lengths: 
6 6 6 Oct 19, 2010 2:12:53 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 38.65613798302843 at iteration 1923990 using kt 5.49232534777018
Currently best helix constraint lengths: 
6 6 6 Oct 19, 2010 2:12:53 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 38.60632716237069 at iteration 1924011 using kt 5.49232534777018
Currently best helix constraint lengths: 
6 6 6 Oct 19, 2010 2:12:53 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 38.575003914190866 at iteration 1924012 using kt 5.49232534777018
Currently best helix constraint lengths: 
6 6 6 Oct 19, 2010 2:12:53 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 38.44713415969646 at iteration 1924013 using kt 5.49232534777018
Currently best helix constraint lengths: 
6 6 6 Oct 19, 2010 2:12:53 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 38.39651831578915 at iteration 1924014 using kt 5.49232534777018
Currently best helix constraint lengths: 
6 6 6 Oct 19, 2010 2:12:53 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 38.30908322653718 at iteration 1924016 using kt 5.49232534777018
Currently best helix constraint lengths: 
6 6 6 Oct 19, 2010 2:12:53 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 38.273409223420195 at iteration 1924071 using kt 5.49232534777018
Currently best helix constraint lengths: 
6 6 6 Oct 19, 2010 2:12:53 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 38.25839775780625 at iteration 1924072 using kt 5.49232534777018
Currently best helix constraint lengths: 
6 6 6 Oct 19, 2010 2:12:53 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 38.258132811635285 at iteration 1924073 using kt 5.49232534777018
Currently best helix constraint lengths: 
6 6 6 Oct 19, 2010 2:12:53 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 38.24874369716369 at iteration 1924074 using kt 5.49232534777018
Currently best helix constraint lengths: 
6 6 6 Oct 19, 2010 2:12:53 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 38.19746933584044 at iteration 1924076 using kt 5.49232534777018
Currently best helix constraint lengths: 
6 6 6 Oct 19, 2010 2:12:53 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 38.19492471450167 at iteration 1924077 using kt 5.49232534777018
Currently best helix constraint lengths: 
6 6 6 Oct 19, 2010 2:12:53 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 38.1560031648101 at iteration 1924079 using kt 5.49232534777018
Currently best helix constraint lengths: 
6 6 6 Oct 19, 2010 2:12:53 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 37.91664347591509 at iteration 1924241 using kt 5.49232534777018
Currently best helix constraint lengths: 
6 6 6 Oct 19, 2010 2:12:53 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 37.85790424281355 at iteration 1924250 using kt 5.49232534777018
Currently best helix constraint lengths: 
6 6 6 Oct 19, 2010 2:12:53 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 37.85106186699918 at iteration 1924251 using kt 5.49232534777018
Currently best helix constraint lengths: 
6 6 6 Oct 19, 2010 2:12:53 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 37.78553512449432 at iteration 1924252 using kt 5.49232534777018
Currently best helix constraint lengths: 
6 6 6 Oct 19, 2010 2:12:53 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 37.7196452611161 at iteration 1924253 using kt 5.49232534777018
Currently best helix constraint lengths: 
6 6 6 Oct 19, 2010 2:12:53 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 37.6998934875904 at iteration 1924254 using kt 5.49232534777018
Currently best helix constraint lengths: 
6 6 6 Oct 19, 2010 2:12:53 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 37.655470459054015 at iteration 1924255 using kt 5.49232534777018
Currently best helix constraint lengths: 
6 6 6 Oct 19, 2010 2:12:53 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 37.51021509924777 at iteration 1924256 using kt 5.49232534777018
Currently best helix constraint lengths: 
6 6 6 Oct 19, 2010 2:12:53 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 37.40898256890814 at iteration 1924257 using kt 5.49232534777018
Currently best helix constraint lengths: 
6 6 6 Oct 19, 2010 2:12:53 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 37.3146067368249 at iteration 1924261 using kt 5.49232534777018
Currently best helix constraint lengths: 
6 6 6 Oct 19, 2010 2:12:53 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 37.297463057335 at iteration 1924262 using kt 5.49232534777018
Currently best helix constraint lengths: 
6 6 6 Oct 19, 2010 2:12:53 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 37.256121763707974 at iteration 1924264 using kt 5.49232534777018
Currently best helix constraint lengths: 
6 6 6 Oct 19, 2010 2:12:53 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 37.2097467954614 at iteration 1924268 using kt 5.49232534777018
Currently best helix constraint lengths: 
6 6 6 Oct 19, 2010 2:12:53 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 37.196885915001495 at iteration 1924269 using kt 5.49232534777018
Currently best helix constraint lengths: 
6 6 6 Oct 19, 2010 2:12:53 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 37.18135086662787 at iteration 1924270 using kt 5.49232534777018
Currently best helix constraint lengths: 
6 6 6 Oct 19, 2010 2:12:53 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 37.15281464306277 at iteration 1924271 using kt 5.49232534777018
Currently best helix constraint lengths: 
6 6 6 Oct 19, 2010 2:12:53 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 37.080759469445184 at iteration 1924275 using kt 5.49232534777018
Currently best helix constraint lengths: 
6 6 6 Oct 19, 2010 2:12:53 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 36.996909991198294 at iteration 1924278 using kt 5.49232534777018
Currently best helix constraint lengths: 
6 6 6 Oct 19, 2010 2:12:53 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 36.959074882389594 at iteration 1924279 using kt 5.49232534777018
Currently best helix constraint lengths: 
6 6 6 Oct 19, 2010 2:12:53 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 36.926795449511154 at iteration 1924280 using kt 5.49232534777018
Currently best helix constraint lengths: 
6 6 6 Oct 19, 2010 2:12:53 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 36.87844914311104 at iteration 1924545 using kt 5.49232534777018
Currently best helix constraint lengths: 
6 6 6 Oct 19, 2010 2:12:53 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 36.874743207471 at iteration 1924546 using kt 5.49232534777018
Currently best helix constraint lengths: 
6 6 6 Oct 19, 2010 2:12:53 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 36.84313008997934 at iteration 1924547 using kt 5.49232534777018
Currently best helix constraint lengths: 
6 6 6 Oct 19, 2010 2:12:53 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 36.83423540180574 at iteration 1924552 using kt 5.49232534777018
Currently best helix constraint lengths: 
6 6 6 Oct 19, 2010 2:12:53 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 36.77503374049019 at iteration 1924553 using kt 5.49232534777018
Currently best helix constraint lengths: 
6 6 6 Oct 19, 2010 2:12:53 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 36.764624789175926 at iteration 1924554 using kt 5.49232534777018
Currently best helix constraint lengths: 
6 6 6 Oct 19, 2010 2:12:54 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 36.704678903150665 at iteration 1926868 using kt 5.49232534777018
Currently best helix constraint lengths: 
6 6 6 Oct 19, 2010 2:12:54 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 36.59687129279342 at iteration 1926869 using kt 5.49232534777018
Currently best helix constraint lengths: 
6 6 6 Oct 19, 2010 2:12:54 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 36.36250467016525 at iteration 1926870 using kt 5.49232534777018
Currently best helix constraint lengths: 
6 6 6 Oct 19, 2010 2:12:54 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 36.189200684636326 at iteration 1926883 using kt 5.49232534777018
Currently best helix constraint lengths: 
6 6 6 Oct 19, 2010 2:12:54 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 36.1611057018208 at iteration 1926886 using kt 5.49232534777018
Currently best helix constraint lengths: 
6 6 6 Oct 19, 2010 2:12:54 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 36.0364080267819 at iteration 1926890 using kt 5.49232534777018
Currently best helix constraint lengths: 
6 6 6 Oct 19, 2010 2:12:54 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 36.00623269647224 at iteration 1926896 using kt 5.49232534777018
Currently best helix constraint lengths: 
6 6 6 Oct 19, 2010 2:12:54 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 35.99748310437428 at iteration 1926901 using kt 5.49232534777018
Currently best helix constraint lengths: 
6 6 6 Oct 19, 2010 2:12:54 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 35.90943997148249 at iteration 1926913 using kt 5.49232534777018
Currently best helix constraint lengths: 
6 6 6 Oct 19, 2010 2:12:54 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 35.88312064142899 at iteration 1926914 using kt 5.49232534777018
Currently best helix constraint lengths: 
6 6 6 Oct 19, 2010 2:12:54 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 35.57548423994228 at iteration 1926915 using kt 5.49232534777018
Currently best helix constraint lengths: 
6 6 6 Oct 19, 2010 2:12:54 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: New best score found: 35.44431972342052 at iteration 1926920 using kt 5.49232534777018
Currently best helix constraint lengths: 
6 6 6 Oct 19, 2010 2:12:55 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 1930001 Best score so far: 35.44431972342052 . Using annealing factor: 0.05409940467553627 kt: 5.409940467553627 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:12:57 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 1940001 Best score so far: 35.44431972342052 . Using annealing factor: 0.05328791360540323 kt: 5.328791360540323 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:13:00 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Mutating helix constraints!
Oct 19, 2010 2:13:00 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 1950000 Best score so far: 35.44431972342052 . Using annealing factor: 0.05248859490132218 kt: 5.248859490132219 coordinate system multipliers: 1.0 1.0 1.0  MUTATING HELIX LENGTHS: 
6 ( 6 ) 6 ( 6 ) 6 ( 6 ) Modified helix constraint lengths: 5 6 5 
Oct 19, 2010 2:13:00 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 1950001 Best score so far: 35.44431972342052 . Using annealing factor: 0.05248859490132218 kt: 5.248859490132219 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:13:03 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 1960001 Best score so far: 35.44431972342052 . Using annealing factor: 0.05170126597780235 kt: 5.170126597780235 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:13:06 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 1970001 Best score so far: 35.44431972342052 . Using annealing factor: 0.05092574698813531 kt: 5.092574698813531 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:13:08 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 1980001 Best score so far: 35.44431972342052 . Using annealing factor: 0.05016186078331328 kt: 5.0161860783313275 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:13:11 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 1990001 Best score so far: 35.44431972342052 . Using annealing factor: 0.04940943287156358 kt: 4.940943287156358 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:13:14 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Mutating helix constraints!
Oct 19, 2010 2:13:14 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 2000000 Best score so far: 35.44431972342052 . Using annealing factor: 0.048668291378490124 kt: 4.866829137849012 coordinate system multipliers: 1.0 1.0 1.0  MUTATING HELIX LENGTHS: 
6 ( 6 ) 6 ( 6 ) 6 ( 6 ) Modified helix constraint lengths: 6 7 6 
Oct 19, 2010 2:13:14 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 2000001 Best score so far: 35.44431972342052 . Using annealing factor: 0.048668291378490124 kt: 4.866829137849012 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:13:16 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 2010001 Best score so far: 35.44431972342052 . Using annealing factor: 0.04793826700781277 kt: 4.793826700781277 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:13:19 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 2020001 Best score so far: 35.44431972342052 . Using annealing factor: 0.04721919300269558 kt: 4.721919300269558 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:13:22 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 2030001 Best score so far: 35.44431972342052 . Using annealing factor: 0.04651090510765515 kt: 4.651090510765514 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:13:24 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 2040001 Best score so far: 35.44431972342052 . Using annealing factor: 0.04581324153104032 kt: 4.581324153104032 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:13:27 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Mutating helix constraints!
Oct 19, 2010 2:13:27 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 2050000 Best score so far: 35.44431972342052 . Using annealing factor: 0.04512604290807472 kt: 4.512604290807472 coordinate system multipliers: 1.0 1.0 1.0  MUTATING HELIX LENGTHS: 
6 ( 6 ) 6 ( 6 ) 6 ( 6 ) Modified helix constraint lengths: 6 7 5 
Oct 19, 2010 2:13:27 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 2050001 Best score so far: 35.44431972342052 . Using annealing factor: 0.04512604290807472 kt: 4.512604290807472 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:13:30 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 2060001 Best score so far: 35.44431972342052 . Using annealing factor: 0.04444915226445359 kt: 4.444915226445359 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:13:33 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 2070001 Best score so far: 35.44431972342052 . Using annealing factor: 0.04378241498048679 kt: 4.378241498048679 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:13:35 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 2080001 Best score so far: 35.44431972342052 . Using annealing factor: 0.04312567875577948 kt: 4.312567875577948 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:13:38 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 2090001 Best score so far: 35.44431972342052 . Using annealing factor: 0.04247879357444279 kt: 4.24787935744428 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:13:41 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Mutating helix constraints!
Oct 19, 2010 2:13:41 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 2100000 Best score so far: 35.44431972342052 . Using annealing factor: 0.04184161167082615 kt: 4.184161167082615 coordinate system multipliers: 1.0 1.0 1.0  MUTATING HELIX LENGTHS: 
6 ( 6 ) 6 ( 6 ) 6 ( 6 ) Modified helix constraint lengths: 5 6 5 
Oct 19, 2010 2:13:41 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 2100001 Best score so far: 35.44431972342052 . Using annealing factor: 0.04184161167082615 kt: 4.184161167082615 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:13:43 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 2110001 Best score so far: 35.44431972342052 . Using annealing factor: 0.04121398749576376 kt: 4.121398749576375 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:13:46 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 2120001 Best score so far: 35.44431972342052 . Using annealing factor: 0.0405957776833273 kt: 4.05957776833273 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:13:49 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 2130001 Best score so far: 35.44431972342052 . Using annealing factor: 0.03998684101807739 kt: 3.998684101807739 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:13:51 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 2140001 Best score so far: 35.44431972342052 . Using annealing factor: 0.03938703840280623 kt: 3.938703840280623 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:13:54 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Mutating helix constraints!
Oct 19, 2010 2:13:54 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 2150000 Best score so far: 35.44431972342052 . Using annealing factor: 0.038796232826764136 kt: 3.8796232826764134 coordinate system multipliers: 1.0 1.0 1.0  MUTATING HELIX LENGTHS: 
6 ( 6 ) 6 ( 6 ) 6 ( 6 ) Modified helix constraint lengths: 6 6 7 
Oct 19, 2010 2:13:54 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 2150001 Best score so far: 35.44431972342052 . Using annealing factor: 0.038796232826764136 kt: 3.8796232826764134 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:13:57 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 2160001 Best score so far: 35.44431972342052 . Using annealing factor: 0.038214289334362675 kt: 3.8214289334362674 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:13:59 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 2170001 Best score so far: 35.44431972342052 . Using annealing factor: 0.03764107499434723 kt: 3.7641074994347234 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:14:02 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 2180001 Best score so far: 35.44431972342052 . Using annealing factor: 0.03707645886943202 kt: 3.707645886943202 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:14:05 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 2190001 Best score so far: 35.44431972342052 . Using annealing factor: 0.03652031198639054 kt: 3.6520311986390537 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:14:07 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Mutating helix constraints!
Oct 19, 2010 2:14:07 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 2200000 Best score so far: 35.44431972342052 . Using annealing factor: 0.03597250730659468 kt: 3.597250730659468 coordinate system multipliers: 1.0 1.0 1.0  MUTATING HELIX LENGTHS: 
6 ( 6 ) 6 ( 6 ) 6 ( 6 ) Oct 19, 2010 2:14:07 PM rnadesign.rnamodel.HelixOptimizer mutateHelixLengths
WARNING: No helix lengths were modified!
Oct 19, 2010 2:14:07 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 2200001 Best score so far: 35.44431972342052 . Using annealing factor: 0.03597250730659468 kt: 3.597250730659468 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:14:10 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 2210001 Best score so far: 35.44431972342052 . Using annealing factor: 0.03543291969699576 kt: 3.543291969699576 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:14:13 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 2220001 Best score so far: 35.44431972342052 . Using annealing factor: 0.03490142590154083 kt: 3.4901425901540826 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:14:16 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 2230001 Best score so far: 35.44431972342052 . Using annealing factor: 0.03437790451301771 kt: 3.437790451301771 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:14:18 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 2240001 Best score so far: 35.44431972342052 . Using annealing factor: 0.03386223594532245 kt: 3.386223594532245 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:14:21 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Mutating helix constraints!
Oct 19, 2010 2:14:21 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 2250000 Best score so far: 35.44431972342052 . Using annealing factor: 0.03335430240614261 kt: 3.3354302406142606 coordinate system multipliers: 1.0 1.0 1.0  MUTATING HELIX LENGTHS: 
6 ( 6 ) 6 ( 6 ) 6 ( 6 ) Modified helix constraint lengths: 5 6 6 
Oct 19, 2010 2:14:21 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 2250001 Best score so far: 35.44431972342052 . Using annealing factor: 0.03335430240614261 kt: 3.3354302406142606 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:14:24 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 2260001 Best score so far: 35.44431972342052 . Using annealing factor: 0.03285398787005047 kt: 3.285398787005047 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:14:26 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 2270001 Best score so far: 35.44431972342052 . Using annealing factor: 0.032361178051999714 kt: 3.2361178051999713 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:14:29 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 2280001 Best score so far: 35.44431972342052 . Using annealing factor: 0.03187576038121972 kt: 3.1875760381219718 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:14:32 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 2290001 Best score so far: 35.44431972342052 . Using annealing factor: 0.03139762397550142 kt: 3.1397623975501423 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:14:34 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Mutating helix constraints!
Oct 19, 2010 2:14:34 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 2300000 Best score so far: 35.44431972342052 . Using annealing factor: 0.0309266596158689 kt: 3.09266596158689 coordinate system multipliers: 1.0 1.0 1.0  MUTATING HELIX LENGTHS: 
6 ( 6 ) 6 ( 6 ) 6 ( 6 ) Modified helix constraint lengths: 5 7 5 
Oct 19, 2010 2:14:34 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 2300001 Best score so far: 35.44431972342052 . Using annealing factor: 0.0309266596158689 kt: 3.09266596158689 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:14:37 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 2310001 Best score so far: 35.44431972342052 . Using annealing factor: 0.030462759721630865 kt: 3.0462759721630865 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:14:40 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 2320001 Best score so far: 35.44431972342052 . Using annealing factor: 0.030005818325806403 kt: 3.0005818325806404 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:14:42 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 2330001 Best score so far: 35.44431972342052 . Using annealing factor: 0.029555731050919305 kt: 2.9555731050919305 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:14:45 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 2340001 Best score so far: 35.44431972342052 . Using annealing factor: 0.029112395085155514 kt: 2.9112395085155516 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:14:48 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Mutating helix constraints!
Oct 19, 2010 2:14:48 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 2350000 Best score so far: 35.44431972342052 . Using annealing factor: 0.028675709158878182 kt: 2.867570915887818 coordinate system multipliers: 1.0 1.0 1.0  MUTATING HELIX LENGTHS: 
6 ( 6 ) 6 ( 6 ) 6 ( 6 ) Oct 19, 2010 2:14:48 PM rnadesign.rnamodel.HelixOptimizer mutateHelixLengths
WARNING: No helix lengths were modified!
Oct 19, 2010 2:14:48 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 2350001 Best score so far: 35.44431972342052 . Using annealing factor: 0.028675709158878182 kt: 2.867570915887818 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:14:51 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 2360001 Best score so far: 35.44431972342052 . Using annealing factor: 0.02824557352149501 kt: 2.824557352149501 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:14:53 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 2370001 Best score so far: 35.44431972342052 . Using annealing factor: 0.027821889918672585 kt: 2.7821889918672587 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:14:56 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 2380001 Best score so far: 35.44431972342052 . Using annealing factor: 0.027404561569892495 kt: 2.7404561569892496 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:14:59 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 2390001 Best score so far: 35.44431972342052 . Using annealing factor: 0.026993493146344107 kt: 2.6993493146344107 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:15:01 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Mutating helix constraints!
Oct 19, 2010 2:15:01 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 2400000 Best score so far: 35.44431972342052 . Using annealing factor: 0.026588590749148943 kt: 2.6588590749148944 coordinate system multipliers: 1.0 1.0 1.0  MUTATING HELIX LENGTHS: 
6 ( 6 ) 6 ( 6 ) 6 ( 6 ) Modified helix constraint lengths: 6 5 6 
Oct 19, 2010 2:15:01 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 2400001 Best score so far: 35.44431972342052 . Using annealing factor: 0.026588590749148943 kt: 2.6588590749148944 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:15:04 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 2410001 Best score so far: 35.44431972342052 . Using annealing factor: 0.02618976188791171 kt: 2.6189761887911707 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:15:07 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 2420001 Best score so far: 35.44431972342052 . Using annealing factor: 0.025796915459593034 kt: 2.5796915459593035 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:15:09 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 2430001 Best score so far: 35.44431972342052 . Using annealing factor: 0.02540996172769914 kt: 2.5409961727699137 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:15:12 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 2440001 Best score so far: 35.44431972342052 . Using annealing factor: 0.02502881230178365 kt: 2.502881230178365 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:15:15 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Mutating helix constraints!
Oct 19, 2010 2:15:15 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 2450000 Best score so far: 35.44431972342052 . Using annealing factor: 0.024653380117256894 kt: 2.4653380117256893 coordinate system multipliers: 1.0 1.0 1.0  MUTATING HELIX LENGTHS: 
6 ( 6 ) 6 ( 6 ) 6 ( 6 ) Modified helix constraint lengths: 6 6 7 
Oct 19, 2010 2:15:15 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 2450001 Best score so far: 35.44431972342052 . Using annealing factor: 0.024653380117256894 kt: 2.4653380117256893 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:15:17 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 2460001 Best score so far: 35.44431972342052 . Using annealing factor: 0.024283579415498042 kt: 2.428357941549804 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:15:20 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 2470001 Best score so far: 35.44431972342052 . Using annealing factor: 0.02391932572426557 kt: 2.391932572426557 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:15:23 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 2480001 Best score so far: 35.44431972342052 . Using annealing factor: 0.023560535838401585 kt: 2.3560535838401586 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:15:26 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 2490001 Best score so far: 35.44431972342052 . Using annealing factor: 0.023207127800825563 kt: 2.320712780082556 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:15:29 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Mutating helix constraints!
Oct 19, 2010 2:15:29 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 2500000 Best score so far: 35.44431972342052 . Using annealing factor: 0.02285902088381318 kt: 2.285902088381318 coordinate system multipliers: 1.0 1.0 1.0  MUTATING HELIX LENGTHS: 
6 ( 6 ) 6 ( 6 ) 6 ( 6 ) Modified helix constraint lengths: 6 7 5 
Oct 19, 2010 2:15:29 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 2500001 Best score so far: 35.44431972342052 . Using annealing factor: 0.02285902088381318 kt: 2.285902088381318 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:15:31 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 2510001 Best score so far: 35.44431972342052 . Using annealing factor: 0.02251613557055598 kt: 2.251613557055598 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:15:34 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 2520001 Best score so far: 35.44431972342052 . Using annealing factor: 0.02217839353699764 kt: 2.217839353699764 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:15:37 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 2530001 Best score so far: 35.44431972342052 . Using annealing factor: 0.021845717633942677 kt: 2.184571763394268 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:15:40 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 2540001 Best score so far: 35.44431972342052 . Using annealing factor: 0.021518031869433536 kt: 2.1518031869433534 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:15:42 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Mutating helix constraints!
Oct 19, 2010 2:15:42 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 2550000 Best score so far: 35.44431972342052 . Using annealing factor: 0.021195261391392033 kt: 2.1195261391392033 coordinate system multipliers: 1.0 1.0 1.0  MUTATING HELIX LENGTHS: 
6 ( 6 ) 6 ( 6 ) 6 ( 6 ) Modified helix constraint lengths: 6 5 7 
Oct 19, 2010 2:15:42 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 2550001 Best score so far: 35.44431972342052 . Using annealing factor: 0.021195261391392033 kt: 2.1195261391392033 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:15:45 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 2560001 Best score so far: 35.44431972342052 . Using annealing factor: 0.020877332470521152 kt: 2.0877332470521153 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:15:48 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 2570001 Best score so far: 35.44431972342052 . Using annealing factor: 0.020564172483463334 kt: 2.0564172483463334 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:15:51 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 2580001 Best score so far: 35.44431972342052 . Using annealing factor: 0.020255709896211383 kt: 2.0255709896211385 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:15:54 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 2590001 Best score so far: 35.44431972342052 . Using annealing factor: 0.019951874247768214 kt: 1.9951874247768213 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:15:56 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Mutating helix constraints!
Oct 19, 2010 2:15:56 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 2600000 Best score so far: 35.44431972342052 . Using annealing factor: 0.019652596134051688 kt: 1.9652596134051687 coordinate system multipliers: 1.0 1.0 1.0  MUTATING HELIX LENGTHS: 
6 ( 6 ) 6 ( 6 ) 6 ( 6 ) Modified helix constraint lengths: 6 6 5 
Oct 19, 2010 2:15:56 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 2600001 Best score so far: 35.44431972342052 . Using annealing factor: 0.019652596134051688 kt: 1.9652596134051687 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:15:59 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 2610001 Best score so far: 35.44431972342052 . Using annealing factor: 0.019357807192040912 kt: 1.9357807192040912 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:16:02 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 2620001 Best score so far: 35.44431972342052 . Using annealing factor: 0.019067440084160298 kt: 1.9067440084160299 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:16:05 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 2630001 Best score so far: 35.44431972342052 . Using annealing factor: 0.018781428482897895 kt: 1.8781428482897895 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:16:07 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 2640001 Best score so far: 35.44431972342052 . Using annealing factor: 0.018499707055654426 kt: 1.8499707055654426 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:16:10 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Mutating helix constraints!
Oct 19, 2010 2:16:10 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 2650000 Best score so far: 35.44431972342052 . Using annealing factor: 0.01822221144981961 kt: 1.822221144981961 coordinate system multipliers: 1.0 1.0 1.0  MUTATING HELIX LENGTHS: 
6 ( 6 ) 6 ( 6 ) 6 ( 6 ) Oct 19, 2010 2:16:10 PM rnadesign.rnamodel.HelixOptimizer mutateHelixLengths
WARNING: No helix lengths were modified!
Oct 19, 2010 2:16:10 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 2650001 Best score so far: 35.44431972342052 . Using annealing factor: 0.01822221144981961 kt: 1.822221144981961 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:16:13 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 2660001 Best score so far: 35.44431972342052 . Using annealing factor: 0.017948878278072317 kt: 1.7948878278072318 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:16:16 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 2670001 Best score so far: 35.44431972342052 . Using annealing factor: 0.01767964510390123 kt: 1.767964510390123 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:16:19 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 2680001 Best score so far: 35.44431972342052 . Using annealing factor: 0.01741445042734271 kt: 1.7414450427342711 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:16:21 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 2690001 Best score so far: 35.44431972342052 . Using annealing factor: 0.01715323367093257 kt: 1.715323367093257 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:16:24 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Mutating helix constraints!
Oct 19, 2010 2:16:24 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 2700000 Best score so far: 35.44431972342052 . Using annealing factor: 0.016895935165868584 kt: 1.6895935165868583 coordinate system multipliers: 1.0 1.0 1.0  MUTATING HELIX LENGTHS: 
6 ( 6 ) 6 ( 6 ) 6 ( 6 ) Modified helix constraint lengths: 5 6 6 
Oct 19, 2010 2:16:24 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 2700001 Best score so far: 35.44431972342052 . Using annealing factor: 0.016895935165868584 kt: 1.6895935165868583 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:16:27 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 2710001 Best score so far: 35.44431972342052 . Using annealing factor: 0.016642496138380553 kt: 1.6642496138380554 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:16:30 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 2720001 Best score so far: 35.44431972342052 . Using annealing factor: 0.016392858696304843 kt: 1.6392858696304844 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:16:33 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 2730001 Best score so far: 35.44431972342052 . Using annealing factor: 0.01614696581586027 kt: 1.614696581586027 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:16:36 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 2740001 Best score so far: 35.44431972342052 . Using annealing factor: 0.01590476132862237 kt: 1.590476132862237 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:16:38 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Mutating helix constraints!
Oct 19, 2010 2:16:38 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 2750000 Best score so far: 35.44431972342052 . Using annealing factor: 0.01566618990869303 kt: 1.5666189908693031 coordinate system multipliers: 1.0 1.0 1.0  MUTATING HELIX LENGTHS: 
6 ( 6 ) 6 ( 6 ) 6 ( 6 ) Modified helix constraint lengths: 6 5 7 
Oct 19, 2010 2:16:38 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 2750001 Best score so far: 35.44431972342052 . Using annealing factor: 0.01566618990869303 kt: 1.5666189908693031 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:16:41 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 2760001 Best score so far: 35.44431972342052 . Using annealing factor: 0.015431197060062636 kt: 1.5431197060062636 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:16:44 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 2770001 Best score so far: 35.44431972342052 . Using annealing factor: 0.015199729104161695 kt: 1.5199729104161694 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:16:47 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 2780001 Best score so far: 35.44431972342052 . Using annealing factor: 0.01497173316759927 kt: 1.497173316759927 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:16:50 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 2790001 Best score so far: 35.44431972342052 . Using annealing factor: 0.014747157170085281 kt: 1.474715717008528 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:16:52 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Mutating helix constraints!
Oct 19, 2010 2:16:52 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 2800000 Best score so far: 35.44431972342052 . Using annealing factor: 0.014525949812534002 kt: 1.4525949812534003 coordinate system multipliers: 1.0 1.0 1.0  MUTATING HELIX LENGTHS: 
6 ( 6 ) 6 ( 6 ) 6 ( 6 ) Modified helix constraint lengths: 5 7 5 
Oct 19, 2010 2:16:52 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 2800001 Best score so far: 35.44431972342052 . Using annealing factor: 0.014525949812534002 kt: 1.4525949812534003 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:16:55 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 2810001 Best score so far: 35.44431972342052 . Using annealing factor: 0.014308060565345991 kt: 1.4308060565345992 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:16:58 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 2820001 Best score so far: 35.44431972342052 . Using annealing factor: 0.0140934396568658 kt: 1.40934396568658 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:17:01 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 2830001 Best score so far: 35.44431972342052 . Using annealing factor: 0.013882038062012814 kt: 1.3882038062012814 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:17:04 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 2840001 Best score so far: 35.44431972342052 . Using annealing factor: 0.013673807491082622 kt: 1.3673807491082621 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:17:06 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Mutating helix constraints!
Oct 19, 2010 2:17:06 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 2850000 Best score so far: 35.44431972342052 . Using annealing factor: 0.013468700378716381 kt: 1.346870037871638 coordinate system multipliers: 1.0 1.0 1.0  MUTATING HELIX LENGTHS: 
6 ( 6 ) 6 ( 6 ) 6 ( 6 ) Modified helix constraint lengths: 6 5 5 
Oct 19, 2010 2:17:06 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 2850001 Best score so far: 35.44431972342052 . Using annealing factor: 0.013468700378716381 kt: 1.346870037871638 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:17:09 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 2860001 Best score so far: 35.44431972342052 . Using annealing factor: 0.013266669873035637 kt: 1.3266669873035637 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:17:12 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 2870001 Best score so far: 35.44431972342052 . Using annealing factor: 0.013067669824940101 kt: 1.30676698249401 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:17:15 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 2880001 Best score so far: 35.44431972342052 . Using annealing factor: 0.012871654777566001 kt: 1.2871654777566002 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:17:18 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 2890001 Best score so far: 35.44431972342052 . Using annealing factor: 0.012678579955902509 kt: 1.267857995590251 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:17:21 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Mutating helix constraints!
Oct 19, 2010 2:17:21 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 2900000 Best score so far: 35.44431972342052 . Using annealing factor: 0.012488401256563971 kt: 1.248840125656397 coordinate system multipliers: 1.0 1.0 1.0  MUTATING HELIX LENGTHS: 
6 ( 6 ) 6 ( 6 ) 6 ( 6 ) Modified helix constraint lengths: 6 6 5 
Oct 19, 2010 2:17:21 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 2900001 Best score so far: 35.44431972342052 . Using annealing factor: 0.012488401256563971 kt: 1.248840125656397 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:17:23 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 2910001 Best score so far: 35.44431972342052 . Using annealing factor: 0.012301075237715512 kt: 1.2301075237715513 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:17:26 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 2920001 Best score so far: 35.44431972342052 . Using annealing factor: 0.012116559109149778 kt: 1.2116559109149778 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:17:29 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 2930001 Best score so far: 35.44431972342052 . Using annealing factor: 0.011934810722512533 kt: 1.1934810722512532 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:17:32 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 2940001 Best score so far: 35.44431972342052 . Using annealing factor: 0.011755788561674845 kt: 1.1755788561674845 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:17:35 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Mutating helix constraints!
Oct 19, 2010 2:17:35 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 2950000 Best score so far: 35.44431972342052 . Using annealing factor: 0.011579451733249722 kt: 1.1579451733249722 coordinate system multipliers: 1.0 1.0 1.0  MUTATING HELIX LENGTHS: 
6 ( 6 ) 6 ( 6 ) 6 ( 6 ) Modified helix constraint lengths: 5 7 5 
Oct 19, 2010 2:17:35 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 2950001 Best score so far: 35.44431972342052 . Using annealing factor: 0.011579451733249722 kt: 1.1579451733249722 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:17:37 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 2960001 Best score so far: 35.44431972342052 . Using annealing factor: 0.011405759957250974 kt: 1.1405759957250974 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:17:40 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 2970001 Best score so far: 35.44431972342052 . Using annealing factor: 0.01123467355789221 kt: 1.123467355789221 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:17:43 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 2980001 Best score so far: 35.44431972342052 . Using annealing factor: 0.011066153454523827 kt: 1.1066153454523826 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:17:46 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 2990001 Best score so far: 35.44431972342052 . Using annealing factor: 0.01090016115270597 kt: 1.090016115270597 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:17:48 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Mutating helix constraints!
Oct 19, 2010 2:17:48 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 3000000 Best score so far: 35.44431972342052 . Using annealing factor: 0.010736658735415381 kt: 1.073665873541538 coordinate system multipliers: 1.0 1.0 1.0  MUTATING HELIX LENGTHS: 
6 ( 6 ) 6 ( 6 ) 6 ( 6 ) Oct 19, 2010 2:17:48 PM rnadesign.rnamodel.HelixOptimizer mutateHelixLengths
WARNING: No helix lengths were modified!
Oct 19, 2010 2:17:48 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 3000001 Best score so far: 35.44431972342052 . Using annealing factor: 0.010736658735415381 kt: 1.073665873541538 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:17:51 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 3010001 Best score so far: 35.44431972342052 . Using annealing factor: 0.01057560885438415 kt: 1.057560885438415 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:17:54 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 3020001 Best score so far: 35.44431972342052 . Using annealing factor: 0.010416974721568387 kt: 1.0416974721568388 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:17:57 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 3030001 Best score so far: 35.44431972342052 . Using annealing factor: 0.010260720100744861 kt: 1.0260720100744862 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:18:00 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 3040001 Best score so far: 35.44431972342052 . Using annealing factor: 0.010106809299233688 kt: 1.0106809299233688 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:18:02 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Mutating helix constraints!
Oct 19, 2010 2:18:02 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 3050000 Best score so far: 35.44431972342052 . Using annealing factor: 0.009955207159745183 kt: 0.9955207159745183 coordinate system multipliers: 1.0 1.0 1.0  MUTATING HELIX LENGTHS: 
6 ( 6 ) 6 ( 6 ) 6 ( 6 ) Modified helix constraint lengths: 7 5 6 
Oct 19, 2010 2:18:02 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 3050001 Best score so far: 35.44431972342052 . Using annealing factor: 0.009955207159745183 kt: 0.9955207159745183 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:18:05 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 3060001 Best score so far: 35.44431972342052 . Using annealing factor: 0.009805879052349005 kt: 0.9805879052349006 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:18:08 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 3070001 Best score so far: 35.44431972342052 . Using annealing factor: 0.009658790866563769 kt: 0.9658790866563769 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:18:11 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 3080001 Best score so far: 35.44431972342052 . Using annealing factor: 0.009513909003565312 kt: 0.9513909003565312 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:18:14 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 3090001 Best score so far: 35.44431972342052 . Using annealing factor: 0.009371200368511834 kt: 0.9371200368511834 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:18:16 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Mutating helix constraints!
Oct 19, 2010 2:18:16 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 3100000 Best score so far: 35.44431972342052 . Using annealing factor: 0.009230632362984156 kt: 0.9230632362984156 coordinate system multipliers: 1.0 1.0 1.0  MUTATING HELIX LENGTHS: 
6 ( 6 ) 6 ( 6 ) 6 ( 6 ) Oct 19, 2010 2:18:16 PM rnadesign.rnamodel.HelixOptimizer mutateHelixLengths
WARNING: No helix lengths were modified!
Oct 19, 2010 2:18:16 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 3100001 Best score so far: 35.44431972342052 . Using annealing factor: 0.009230632362984156 kt: 0.9230632362984156 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:18:19 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 3110001 Best score so far: 35.44431972342052 . Using annealing factor: 0.009092172877539393 kt: 0.9092172877539393 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:18:22 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 3120001 Best score so far: 35.44431972342052 . Using annealing factor: 0.008955790284376302 kt: 0.8955790284376302 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:18:25 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 3130001 Best score so far: 35.44431972342052 . Using annealing factor: 0.008821453430110657 kt: 0.8821453430110657 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:18:28 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 3140001 Best score so far: 35.44431972342052 . Using annealing factor: 0.008689131628658997 kt: 0.8689131628658997 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:18:30 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Mutating helix constraints!
Oct 19, 2010 2:18:30 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 3150000 Best score so far: 35.44431972342052 . Using annealing factor: 0.008558794654229112 kt: 0.8558794654229112 coordinate system multipliers: 1.0 1.0 1.0  MUTATING HELIX LENGTHS: 
6 ( 6 ) 6 ( 6 ) 6 ( 6 ) Modified helix constraint lengths: 7 6 7 
Oct 19, 2010 2:18:30 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 3150001 Best score so far: 35.44431972342052 . Using annealing factor: 0.008558794654229112 kt: 0.8558794654229112 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:18:33 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 3160001 Best score so far: 35.44431972342052 . Using annealing factor: 0.008430412734415676 kt: 0.8430412734415675 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:18:36 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 3170001 Best score so far: 35.44431972342052 . Using annealing factor: 0.00830395654339944 kt: 0.830395654339944 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:18:39 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 3180001 Best score so far: 35.44431972342052 . Using annealing factor: 0.008179397195248449 kt: 0.8179397195248449 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:18:42 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 3190001 Best score so far: 35.44431972342052 . Using annealing factor: 0.008056706237319721 kt: 0.8056706237319722 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:18:44 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Mutating helix constraints!
Oct 19, 2010 2:18:44 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 3200000 Best score so far: 35.44431972342052 . Using annealing factor: 0.007935855643759926 kt: 0.7935855643759926 coordinate system multipliers: 1.0 1.0 1.0  MUTATING HELIX LENGTHS: 
6 ( 6 ) 6 ( 6 ) 6 ( 6 ) Modified helix constraint lengths: 7 5 6 
Oct 19, 2010 2:18:44 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 3200001 Best score so far: 35.44431972342052 . Using annealing factor: 0.007935855643759926 kt: 0.7935855643759926 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:18:47 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 3210001 Best score so far: 35.44431972342052 . Using annealing factor: 0.007816817809103527 kt: 0.7816817809103528 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:18:50 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 3220001 Best score so far: 35.44431972342052 . Using annealing factor: 0.007699565541966974 kt: 0.7699565541966974 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:18:53 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 3230001 Best score so far: 35.44431972342052 . Using annealing factor: 0.007584072058837469 kt: 0.7584072058837469 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:18:56 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 3240001 Best score so far: 35.44431972342052 . Using annealing factor: 0.007470310977954907 kt: 0.7470310977954907 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:18:58 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Mutating helix constraints!
Oct 19, 2010 2:18:58 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 3250000 Best score so far: 35.44431972342052 . Using annealing factor: 0.007358256313285583 kt: 0.7358256313285583 coordinate system multipliers: 1.0 1.0 1.0  MUTATING HELIX LENGTHS: 
6 ( 6 ) 6 ( 6 ) 6 ( 6 ) Modified helix constraint lengths: 6 7 5 
Oct 19, 2010 2:18:58 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 3250001 Best score so far: 35.44431972342052 . Using annealing factor: 0.007358256313285583 kt: 0.7358256313285583 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:19:01 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 3260001 Best score so far: 35.44431972342052 . Using annealing factor: 0.007247882468586299 kt: 0.7247882468586299 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:19:04 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 3270001 Best score so far: 35.44431972342052 . Using annealing factor: 0.007139164231557505 kt: 0.7139164231557504 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:19:07 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 3280001 Best score so far: 35.44431972342052 . Using annealing factor: 0.007032076768084142 kt: 0.7032076768084142 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:19:09 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 3290001 Best score so far: 35.44431972342052 . Using annealing factor: 0.0069265956165628795 kt: 0.692659561656288 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:19:12 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Mutating helix constraints!
Oct 19, 2010 2:19:12 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 3300000 Best score so far: 35.44431972342052 . Using annealing factor: 0.006822696682314436 kt: 0.6822696682314436 coordinate system multipliers: 1.0 1.0 1.0  MUTATING HELIX LENGTHS: 
6 ( 6 ) 6 ( 6 ) 6 ( 6 ) Oct 19, 2010 2:19:12 PM rnadesign.rnamodel.HelixOptimizer mutateHelixLengths
WARNING: No helix lengths were modified!
Oct 19, 2010 2:19:12 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 3300001 Best score so far: 35.44431972342052 . Using annealing factor: 0.006822696682314436 kt: 0.6822696682314436 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:19:15 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 3310001 Best score so far: 35.44431972342052 . Using annealing factor: 0.00672035623207972 kt: 0.672035623207972 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:19:18 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 3320001 Best score so far: 35.44431972342052 . Using annealing factor: 0.006619550888598524 kt: 0.6619550888598524 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:19:21 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 3330001 Best score so far: 35.44431972342052 . Using annealing factor: 0.006520257625269546 kt: 0.6520257625269545 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:19:24 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 3340001 Best score so far: 35.44431972342052 . Using annealing factor: 0.006422453760890503 kt: 0.6422453760890503 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:19:27 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Mutating helix constraints!
Oct 19, 2010 2:19:27 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 3350000 Best score so far: 35.44431972342052 . Using annealing factor: 0.0063261169544771454 kt: 0.6326116954477146 coordinate system multipliers: 1.0 1.0 1.0  MUTATING HELIX LENGTHS: 
6 ( 6 ) 6 ( 6 ) 6 ( 6 ) Modified helix constraint lengths: 5 6 6 
Oct 19, 2010 2:19:27 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 3350001 Best score so far: 35.44431972342052 . Using annealing factor: 0.0063261169544771454 kt: 0.6326116954477146 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:19:30 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 3360001 Best score so far: 35.44431972342052 . Using annealing factor: 0.0062312252001599875 kt: 0.6231225200159988 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:19:33 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 3370001 Best score so far: 35.44431972342052 . Using annealing factor: 0.006137756822157588 kt: 0.6137756822157588 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:19:35 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 3380001 Best score so far: 35.44431972342052 . Using annealing factor: 0.006045690469825224 kt: 0.6045690469825225 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:19:38 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 3390001 Best score so far: 35.44431972342052 . Using annealing factor: 0.005955005112777845 kt: 0.5955005112777846 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:19:41 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Mutating helix constraints!
Oct 19, 2010 2:19:41 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 3400000 Best score so far: 35.44431972342052 . Using annealing factor: 0.005865680036086178 kt: 0.5865680036086178 coordinate system multipliers: 1.0 1.0 1.0  MUTATING HELIX LENGTHS: 
6 ( 6 ) 6 ( 6 ) 6 ( 6 ) Modified helix constraint lengths: 6 5 6 
Oct 19, 2010 2:19:41 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 3400001 Best score so far: 35.44431972342052 . Using annealing factor: 0.005865680036086178 kt: 0.5865680036086178 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:19:44 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 3410001 Best score so far: 35.44431972342052 . Using annealing factor: 0.005777694835544885 kt: 0.5777694835544885 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:19:47 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 3420001 Best score so far: 35.44431972342052 . Using annealing factor: 0.005691029413011712 kt: 0.5691029413011712 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:19:50 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 3430001 Best score so far: 35.44431972342052 . Using annealing factor: 0.0056056639718165355 kt: 0.5605663971816536 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:19:53 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 3440001 Best score so far: 35.44431972342052 . Using annealing factor: 0.005521579012239288 kt: 0.5521579012239288 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:19:56 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Mutating helix constraints!
Oct 19, 2010 2:19:56 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 3450000 Best score so far: 35.44431972342052 . Using annealing factor: 0.0054387553270556985 kt: 0.5438755327055699 coordinate system multipliers: 1.0 1.0 1.0  MUTATING HELIX LENGTHS: 
6 ( 6 ) 6 ( 6 ) 6 ( 6 ) Modified helix constraint lengths: 5 7 5 
Oct 19, 2010 2:19:56 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 3450001 Best score so far: 35.44431972342052 . Using annealing factor: 0.0054387553270556985 kt: 0.5438755327055699 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:19:59 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 3460001 Best score so far: 35.44431972342052 . Using annealing factor: 0.0053571739971498625 kt: 0.5357173997149862 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:20:01 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 3470001 Best score so far: 35.44431972342052 . Using annealing factor: 0.005276816387192615 kt: 0.5276816387192615 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:20:04 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 3480001 Best score so far: 35.44431972342052 . Using annealing factor: 0.005197664141384725 kt: 0.5197664141384726 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:20:07 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 3490001 Best score so far: 35.44431972342052 . Using annealing factor: 0.0051196991792639545 kt: 0.5119699179263955 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:20:10 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Mutating helix constraints!
Oct 19, 2010 2:20:10 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 3500000 Best score so far: 35.44431972342052 . Using annealing factor: 0.005042903691574995 kt: 0.5042903691574995 coordinate system multipliers: 1.0 1.0 1.0  MUTATING HELIX LENGTHS: 
6 ( 6 ) 6 ( 6 ) 6 ( 6 ) Oct 19, 2010 2:20:10 PM rnadesign.rnamodel.HelixOptimizer mutateHelixLengths
WARNING: No helix lengths were modified!
Oct 19, 2010 2:20:10 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 3500001 Best score so far: 35.44431972342052 . Using annealing factor: 0.005042903691574995 kt: 0.5042903691574995 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:20:13 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 3510001 Best score so far: 35.44431972342052 . Using annealing factor: 0.004967260136201371 kt: 0.4967260136201371 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:20:16 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 3520001 Best score so far: 35.44431972342052 . Using annealing factor: 0.00489275123415835 kt: 0.48927512341583496 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:20:18 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 3530001 Best score so far: 35.44431972342052 . Using annealing factor: 0.004819359965645974 kt: 0.4819359965645974 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:20:21 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 3540001 Best score so far: 35.44431972342052 . Using annealing factor: 0.004747069566161285 kt: 0.4747069566161285 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:20:24 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Mutating helix constraints!
Oct 19, 2010 2:20:24 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 3550000 Best score so far: 35.44431972342052 . Using annealing factor: 0.004675863522668865 kt: 0.46758635226688655 coordinate system multipliers: 1.0 1.0 1.0  MUTATING HELIX LENGTHS: 
6 ( 6 ) 6 ( 6 ) 6 ( 6 ) Modified helix constraint lengths: 5 5 7 
Oct 19, 2010 2:20:24 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 3550001 Best score so far: 35.44431972342052 . Using annealing factor: 0.004675863522668865 kt: 0.46758635226688655 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:20:27 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 3560001 Best score so far: 35.44431972342052 . Using annealing factor: 0.004605725569828832 kt: 0.46057255698288324 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:20:30 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 3570001 Best score so far: 35.44431972342052 . Using annealing factor: 0.0045366396862814 kt: 0.45366396862814 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:20:33 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 3580001 Best score so far: 35.44431972342052 . Using annealing factor: 0.0044685900909871784 kt: 0.44685900909871784 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:20:36 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 3590001 Best score so far: 35.44431972342052 . Using annealing factor: 0.004401561239622371 kt: 0.4401561239622371 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:20:38 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Mutating helix constraints!
Oct 19, 2010 2:20:38 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 3600000 Best score so far: 35.44431972342052 . Using annealing factor: 0.004335537821028035 kt: 0.4335537821028035 coordinate system multipliers: 1.0 1.0 1.0  MUTATING HELIX LENGTHS: 
6 ( 6 ) 6 ( 6 ) 6 ( 6 ) Modified helix constraint lengths: 6 6 5 
Oct 19, 2010 2:20:38 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 3600001 Best score so far: 35.44431972342052 . Using annealing factor: 0.004335537821028035 kt: 0.4335537821028035 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:20:41 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 3610001 Best score so far: 35.44431972342052 . Using annealing factor: 0.0042705047537126145 kt: 0.42705047537126145 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:20:44 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 3620001 Best score so far: 35.44431972342052 . Using annealing factor: 0.004206447182406926 kt: 0.4206447182406926 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:20:47 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 3630001 Best score so far: 35.44431972342052 . Using annealing factor: 0.004143350474670821 kt: 0.41433504746708216 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:20:50 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 3640001 Best score so far: 35.44431972342052 . Using annealing factor: 0.004081200217550759 kt: 0.4081200217550759 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:20:53 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Mutating helix constraints!
Oct 19, 2010 2:20:53 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 3650000 Best score so far: 35.44431972342052 . Using annealing factor: 0.0040199822142874975 kt: 0.40199822142874975 coordinate system multipliers: 1.0 1.0 1.0  MUTATING HELIX LENGTHS: 
6 ( 6 ) 6 ( 6 ) 6 ( 6 ) Modified helix constraint lengths: 7 6 7 
Oct 19, 2010 2:20:53 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 3650001 Best score so far: 35.44431972342052 . Using annealing factor: 0.0040199822142874975 kt: 0.40199822142874975 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:20:56 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 3660001 Best score so far: 35.44431972342052 . Using annealing factor: 0.003959682481073186 kt: 0.39596824810731857 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:20:58 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 3670001 Best score so far: 35.44431972342052 . Using annealing factor: 0.0039002872438570874 kt: 0.39002872438570874 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:21:01 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 3680001 Best score so far: 35.44431972342052 . Using annealing factor: 0.003841782935199231 kt: 0.3841782935199231 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:21:04 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 3690001 Best score so far: 35.44431972342052 . Using annealing factor: 0.0037841561911712424 kt: 0.37841561911712424 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:21:07 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Mutating helix constraints!
Oct 19, 2010 2:21:07 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 3700000 Best score so far: 35.44431972342052 . Using annealing factor: 0.0037273938483036737 kt: 0.3727393848303674 coordinate system multipliers: 1.0 1.0 1.0  MUTATING HELIX LENGTHS: 
6 ( 6 ) 6 ( 6 ) 6 ( 6 ) Modified helix constraint lengths: 5 6 7 
Oct 19, 2010 2:21:07 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 3700001 Best score so far: 35.44431972342052 . Using annealing factor: 0.0037273938483036737 kt: 0.3727393848303674 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:21:10 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 3710001 Best score so far: 35.44431972342052 . Using annealing factor: 0.0036714829405791187 kt: 0.3671482940579119 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:21:13 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 3720001 Best score so far: 35.44431972342052 . Using annealing factor: 0.0036164106964704317 kt: 0.3616410696470432 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:21:16 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 3730001 Best score so far: 35.44431972342052 . Using annealing factor: 0.0035621645360233755 kt: 0.35621645360233756 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:21:18 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 3740001 Best score so far: 35.44431972342052 . Using annealing factor: 0.0035087320679830247 kt: 0.3508732067983025 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:21:21 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Mutating helix constraints!
Oct 19, 2010 2:21:21 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 3750000 Best score so far: 35.44431972342052 . Using annealing factor: 0.003456101086963279 kt: 0.3456101086963279 coordinate system multipliers: 1.0 1.0 1.0  MUTATING HELIX LENGTHS: 
6 ( 6 ) 6 ( 6 ) 6 ( 6 ) Modified helix constraint lengths: 7 6 5 
Oct 19, 2010 2:21:21 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 3750001 Best score so far: 35.44431972342052 . Using annealing factor: 0.003456101086963279 kt: 0.3456101086963279 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:21:24 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 3760001 Best score so far: 35.44431972342052 . Using annealing factor: 0.00340425957065883 kt: 0.34042595706588297 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:21:27 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 3770001 Best score so far: 35.44431972342052 . Using annealing factor: 0.0033531956770989474 kt: 0.33531956770989474 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:21:30 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 3780001 Best score so far: 35.44431972342052 . Using annealing factor: 0.003302897741942463 kt: 0.3302897741942463 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:21:33 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 3790001 Best score so far: 35.44431972342052 . Using annealing factor: 0.003253354275813326 kt: 0.3253354275813326 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:21:35 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Mutating helix constraints!
Oct 19, 2010 2:21:35 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 3800000 Best score so far: 35.44431972342052 . Using annealing factor: 0.0032045539616761265 kt: 0.32045539616761265 coordinate system multipliers: 1.0 1.0 1.0  MUTATING HELIX LENGTHS: 
6 ( 6 ) 6 ( 6 ) 6 ( 6 ) Modified helix constraint lengths: 5 6 6 
Oct 19, 2010 2:21:35 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 3800001 Best score so far: 35.44431972342052 . Using annealing factor: 0.0032045539616761265 kt: 0.32045539616761265 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:21:38 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 3810001 Best score so far: 35.44431972342052 . Using annealing factor: 0.0031564856522509842 kt: 0.31564856522509843 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:21:41 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 3820001 Best score so far: 35.44431972342052 . Using annealing factor: 0.0031091383674672194 kt: 0.31091383674672196 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:21:44 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 3830001 Best score so far: 35.44431972342052 . Using annealing factor: 0.0030625012919552113 kt: 0.30625012919552114 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:21:47 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 3840001 Best score so far: 35.44431972342052 . Using annealing factor: 0.003016563772575883 kt: 0.3016563772575883 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:21:50 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Mutating helix constraints!
Oct 19, 2010 2:21:50 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 3850000 Best score so far: 35.44431972342052 . Using annealing factor: 0.0029713153159872446 kt: 0.29713153159872446 coordinate system multipliers: 1.0 1.0 1.0  MUTATING HELIX LENGTHS: 
6 ( 6 ) 6 ( 6 ) 6 ( 6 ) Modified helix constraint lengths: 7 6 6 
Oct 19, 2010 2:21:50 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 3850001 Best score so far: 35.44431972342052 . Using annealing factor: 0.0029713153159872446 kt: 0.29713153159872446 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:21:53 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 3860001 Best score so far: 35.44431972342052 . Using annealing factor: 0.002926745586247436 kt: 0.2926745586247436 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:21:56 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 3870001 Best score so far: 35.44431972342052 . Using annealing factor: 0.0028828444024537247 kt: 0.2882844402453725 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:21:59 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 3880001 Best score so far: 35.44431972342052 . Using annealing factor: 0.0028396017364169185 kt: 0.28396017364169185 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:22:01 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 3890001 Best score so far: 35.44431972342052 . Using annealing factor: 0.002797007710370665 kt: 0.2797007710370665 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:22:04 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Mutating helix constraints!
Oct 19, 2010 2:22:04 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 3900000 Best score so far: 35.44431972342052 . Using annealing factor: 0.0027550525947151044 kt: 0.27550525947151044 coordinate system multipliers: 1.0 1.0 1.0  MUTATING HELIX LENGTHS: 
6 ( 6 ) 6 ( 6 ) 6 ( 6 ) Modified helix constraint lengths: 6 5 7 
Oct 19, 2010 2:22:04 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 3900001 Best score so far: 35.44431972342052 . Using annealing factor: 0.0027550525947151044 kt: 0.27550525947151044 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:22:07 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 3910001 Best score so far: 35.44431972342052 . Using annealing factor: 0.002713726805794378 kt: 0.2713726805794378 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:22:10 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 3920001 Best score so far: 35.44431972342052 . Using annealing factor: 0.0026730209037074625 kt: 0.26730209037074626 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:22:13 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 3930001 Best score so far: 35.44431972342052 . Using annealing factor: 0.0026329255901518505 kt: 0.26329255901518506 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:22:16 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 3940001 Best score so far: 35.44431972342052 . Using annealing factor: 0.002593431706299573 kt: 0.25934317062995726 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:22:19 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Mutating helix constraints!
Oct 19, 2010 2:22:19 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 3950000 Best score so far: 35.44431972342052 . Using annealing factor: 0.002554530230705079 kt: 0.2554530230705079 coordinate system multipliers: 1.0 1.0 1.0  MUTATING HELIX LENGTHS: 
6 ( 6 ) 6 ( 6 ) 6 ( 6 ) Modified helix constraint lengths: 5 6 5 
Oct 19, 2010 2:22:19 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 3950001 Best score so far: 35.44431972342052 . Using annealing factor: 0.002554530230705079 kt: 0.2554530230705079 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:22:22 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 3960001 Best score so far: 35.44431972342052 . Using annealing factor: 0.002516212277244503 kt: 0.2516212277244503 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:22:25 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 3970001 Best score so far: 35.44431972342052 . Using annealing factor: 0.002478469093085835 kt: 0.24784690930858352 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:22:28 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 3980001 Best score so far: 35.44431972342052 . Using annealing factor: 0.0024412920566895474 kt: 0.24412920566895474 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:22:30 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 3990001 Best score so far: 35.44431972342052 . Using annealing factor: 0.0024046726758392045 kt: 0.24046726758392045 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:22:33 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Mutating helix constraints!
Oct 19, 2010 2:22:33 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 4000000 Best score so far: 35.44431972342052 . Using annealing factor: 0.002368602585701616 kt: 0.2368602585701616 coordinate system multipliers: 1.0 1.0 1.0  MUTATING HELIX LENGTHS: 
6 ( 6 ) 6 ( 6 ) 6 ( 6 ) Modified helix constraint lengths: 6 6 5 
Oct 19, 2010 2:22:33 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 4000001 Best score so far: 35.44431972342052 . Using annealing factor: 0.002368602585701616 kt: 0.2368602585701616 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:22:36 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 4010001 Best score so far: 35.44431972342052 . Using annealing factor: 0.002333073546916092 kt: 0.2333073546916092 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:22:39 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 4020001 Best score so far: 35.44431972342052 . Using annealing factor: 0.0022980774437123506 kt: 0.22980774437123508 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:22:42 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 4030001 Best score so far: 35.44431972342052 . Using annealing factor: 0.0022636062820566654 kt: 0.22636062820566655 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:22:45 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 4040001 Best score so far: 35.44431972342052 . Using annealing factor: 0.002229652187825815 kt: 0.22296521878258152 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:22:48 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Mutating helix constraints!
Oct 19, 2010 2:22:48 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 4050000 Best score so far: 35.44431972342052 . Using annealing factor: 0.002196207405008428 kt: 0.21962074050084282 coordinate system multipliers: 1.0 1.0 1.0  MUTATING HELIX LENGTHS: 
6 ( 6 ) 6 ( 6 ) 6 ( 6 ) Modified helix constraint lengths: 5 7 6 
Oct 19, 2010 2:22:48 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 4050001 Best score so far: 35.44431972342052 . Using annealing factor: 0.002196207405008428 kt: 0.21962074050084282 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:22:51 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 4060001 Best score so far: 35.44431972342052 . Using annealing factor: 0.0021632642939333016 kt: 0.21632642939333016 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:22:54 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 4070001 Best score so far: 35.44431972342052 . Using annealing factor: 0.0021308153295243023 kt: 0.21308153295243024 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:22:56 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 4080001 Best score so far: 35.44431972342052 . Using annealing factor: 0.0020988530995814376 kt: 0.20988530995814375 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:22:59 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 4090001 Best score so far: 35.44431972342052 . Using annealing factor: 0.0020673703030877157 kt: 0.20673703030877158 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:23:02 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Mutating helix constraints!
Oct 19, 2010 2:23:02 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 4100000 Best score so far: 35.44431972342052 . Using annealing factor: 0.0020363597485414 kt: 0.20363597485414 coordinate system multipliers: 1.0 1.0 1.0  MUTATING HELIX LENGTHS: 
6 ( 6 ) 6 ( 6 ) 6 ( 6 ) Oct 19, 2010 2:23:02 PM rnadesign.rnamodel.HelixOptimizer mutateHelixLengths
WARNING: No helix lengths were modified!
Oct 19, 2010 2:23:02 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 4100001 Best score so far: 35.44431972342052 . Using annealing factor: 0.0020363597485414 kt: 0.20363597485414 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:23:05 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 4110001 Best score so far: 35.44431972342052 . Using annealing factor: 0.002005814352313279 kt: 0.2005814352313279 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:23:08 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 4120001 Best score so far: 35.44431972342052 . Using annealing factor: 0.00197572713702858 kt: 0.197572713702858 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:23:11 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 4130001 Best score so far: 35.44431972342052 . Using annealing factor: 0.0019460912299731513 kt: 0.19460912299731511 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:23:14 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 4140001 Best score so far: 35.44431972342052 . Using annealing factor: 0.0019168998615235538 kt: 0.19168998615235538 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:23:17 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Mutating helix constraints!
Oct 19, 2010 2:23:17 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 4150000 Best score so far: 35.44431972342052 . Using annealing factor: 0.0018881463636007006 kt: 0.18881463636007007 coordinate system multipliers: 1.0 1.0 1.0  MUTATING HELIX LENGTHS: 
6 ( 6 ) 6 ( 6 ) 6 ( 6 ) Modified helix constraint lengths: 6 5 7 
Oct 19, 2010 2:23:17 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 4150001 Best score so far: 35.44431972342052 . Using annealing factor: 0.0018881463636007006 kt: 0.18881463636007007 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:23:20 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 4160001 Best score so far: 35.44431972342052 . Using annealing factor: 0.00185982416814669 kt: 0.185982416814669 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:23:22 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 4170001 Best score so far: 35.44431972342052 . Using annealing factor: 0.0018319268056244896 kt: 0.18319268056244897 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:23:25 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 4180001 Best score so far: 35.44431972342052 . Using annealing factor: 0.0018044479035401223 kt: 0.18044479035401223 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:23:28 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 4190001 Best score so far: 35.44431972342052 . Using annealing factor: 0.0017773811849870205 kt: 0.17773811849870205 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:23:31 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Mutating helix constraints!
Oct 19, 2010 2:23:31 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 4200000 Best score so far: 35.44431972342052 . Using annealing factor: 0.001750720467212215 kt: 0.1750720467212215 coordinate system multipliers: 1.0 1.0 1.0  MUTATING HELIX LENGTHS: 
6 ( 6 ) 6 ( 6 ) 6 ( 6 ) Modified helix constraint lengths: 5 6 7 
Oct 19, 2010 2:23:31 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 4200001 Best score so far: 35.44431972342052 . Using annealing factor: 0.001750720467212215 kt: 0.1750720467212215 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:23:34 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 4210001 Best score so far: 35.44431972342052 . Using annealing factor: 0.0017244596602040319 kt: 0.17244596602040319 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:23:37 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 4220001 Best score so far: 35.44431972342052 . Using annealing factor: 0.0016985927653009713 kt: 0.16985927653009714 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:23:40 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 4230001 Best score so far: 35.44431972342052 . Using annealing factor: 0.0016731138738214568 kt: 0.16731138738214568 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:23:43 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 4240001 Best score so far: 35.44431972342052 . Using annealing factor: 0.0016480171657141348 kt: 0.1648017165714135 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:23:45 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Mutating helix constraints!
Oct 19, 2010 2:23:45 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 4250000 Best score so far: 35.44431972342052 . Using annealing factor: 0.0016232969082284228 kt: 0.16232969082284227 coordinate system multipliers: 1.0 1.0 1.0  MUTATING HELIX LENGTHS: 
6 ( 6 ) 6 ( 6 ) 6 ( 6 ) Modified helix constraint lengths: 5 7 5 
Oct 19, 2010 2:23:45 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 4250001 Best score so far: 35.44431972342052 . Using annealing factor: 0.0016232969082284228 kt: 0.16232969082284227 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:23:48 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 4260001 Best score so far: 35.44431972342052 . Using annealing factor: 0.0015989474546049965 kt: 0.15989474546049964 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:23:51 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 4270001 Best score so far: 35.44431972342052 . Using annealing factor: 0.0015749632427859215 kt: 0.15749632427859214 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:23:54 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 4280001 Best score so far: 35.44431972342052 . Using annealing factor: 0.0015513387941441326 kt: 0.15513387941441326 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:23:57 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 4290001 Best score so far: 35.44431972342052 . Using annealing factor: 0.0015280687122319705 kt: 0.15280687122319705 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:24:00 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Mutating helix constraints!
Oct 19, 2010 2:24:00 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 4300000 Best score so far: 35.44431972342052 . Using annealing factor: 0.0015051476815484911 kt: 0.1505147681548491 coordinate system multipliers: 1.0 1.0 1.0  MUTATING HELIX LENGTHS: 
6 ( 6 ) 6 ( 6 ) 6 ( 6 ) Modified helix constraint lengths: 7 6 6 
Oct 19, 2010 2:24:00 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 4300001 Best score so far: 35.44431972342052 . Using annealing factor: 0.0015051476815484911 kt: 0.1505147681548491 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:24:03 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 4310001 Best score so far: 35.44431972342052 . Using annealing factor: 0.0014825704663252637 kt: 0.14825704663252637 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:24:06 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 4320001 Best score so far: 35.44431972342052 . Using annealing factor: 0.0014603319093303847 kt: 0.14603319093303846 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:24:09 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 4330001 Best score so far: 35.44431972342052 . Using annealing factor: 0.0014384269306904288 kt: 0.14384269306904288 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:24:12 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 4340001 Best score so far: 35.44431972342052 . Using annealing factor: 0.0014168505267300724 kt: 0.14168505267300724 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:24:14 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Mutating helix constraints!
Oct 19, 2010 2:24:14 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 4350000 Best score so far: 35.44431972342052 . Using annealing factor: 0.0013955977688291214 kt: 0.13955977688291213 coordinate system multipliers: 1.0 1.0 1.0  MUTATING HELIX LENGTHS: 
6 ( 6 ) 6 ( 6 ) 6 ( 6 ) Modified helix constraint lengths: 6 5 6 
Oct 19, 2010 2:24:14 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 4350001 Best score so far: 35.44431972342052 . Using annealing factor: 0.0013955977688291214 kt: 0.13955977688291213 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:24:17 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 4360001 Best score so far: 35.44431972342052 . Using annealing factor: 0.0013746638022966845 kt: 0.13746638022966845 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:24:20 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 4370001 Best score so far: 35.44431972342052 . Using annealing factor: 0.0013540438452622342 kt: 0.13540438452622341 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:24:23 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 4380001 Best score so far: 35.44431972342052 . Using annealing factor: 0.0013337331875833006 kt: 0.13337331875833006 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:24:26 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 4390001 Best score so far: 35.44431972342052 . Using annealing factor: 0.0013137271897695512 kt: 0.13137271897695513 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:24:29 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Mutating helix constraints!
Oct 19, 2010 2:24:29 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 4400000 Best score so far: 35.44431972342052 . Using annealing factor: 0.0012940212819230077 kt: 0.12940212819230076 coordinate system multipliers: 1.0 1.0 1.0  MUTATING HELIX LENGTHS: 
6 ( 6 ) 6 ( 6 ) 6 ( 6 ) Modified helix constraint lengths: 7 7 6 
Oct 19, 2010 2:24:29 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 4400001 Best score so far: 35.44431972342052 . Using annealing factor: 0.0012940212819230077 kt: 0.12940212819230076 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:24:32 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 4410001 Best score so far: 35.44431972342052 . Using annealing factor: 0.0012746109626941627 kt: 0.12746109626941626 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:24:34 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 4420001 Best score so far: 35.44431972342052 . Using annealing factor: 0.0012554917982537503 kt: 0.12554917982537503 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:24:37 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 4430001 Best score so far: 35.44431972342052 . Using annealing factor: 0.001236659421279944 kt: 0.12366594212799441 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:24:40 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 4440001 Best score so far: 35.44431972342052 . Using annealing factor: 0.0012181095299607448 kt: 0.12181095299607447 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:24:43 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Mutating helix constraints!
Oct 19, 2010 2:24:43 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 4450000 Best score so far: 35.44431972342052 . Using annealing factor: 0.0011998378870113336 kt: 0.11998378870113335 coordinate system multipliers: 1.0 1.0 1.0  MUTATING HELIX LENGTHS: 
6 ( 6 ) 6 ( 6 ) 6 ( 6 ) Modified helix constraint lengths: 7 5 6 
Oct 19, 2010 2:24:43 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 4450001 Best score so far: 35.44431972342052 . Using annealing factor: 0.0011998378870113336 kt: 0.11998378870113335 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:24:46 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 4460001 Best score so far: 35.44431972342052 . Using annealing factor: 0.0011818403187061636 kt: 0.11818403187061637 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:24:49 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 4470001 Best score so far: 35.44431972342052 . Using annealing factor: 0.0011641127139255711 kt: 0.11641127139255711 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:24:52 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 4480001 Best score so far: 35.44431972342052 . Using annealing factor: 0.0011466510232166875 kt: 0.11466510232166875 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:24:54 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 4490001 Best score so far: 35.44431972342052 . Using annealing factor: 0.0011294512578684372 kt: 0.11294512578684372 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:24:57 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Mutating helix constraints!
Oct 19, 2010 2:24:57 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 4500000 Best score so far: 35.44431972342052 . Using annealing factor: 0.0011125094890004107 kt: 0.11125094890004107 coordinate system multipliers: 1.0 1.0 1.0  MUTATING HELIX LENGTHS: 
6 ( 6 ) 6 ( 6 ) 6 ( 6 ) Modified helix constraint lengths: 7 5 6 
Oct 19, 2010 2:24:57 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 4500001 Best score so far: 35.44431972342052 . Using annealing factor: 0.0011125094890004107 kt: 0.11125094890004107 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:25:00 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 4510001 Best score so far: 35.44431972342052 . Using annealing factor: 0.0010958218466654045 kt: 0.10958218466654045 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:25:03 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 4520001 Best score so far: 35.44431972342052 . Using annealing factor: 0.0010793845189654234 kt: 0.10793845189654235 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:25:06 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 4530001 Best score so far: 35.44431972342052 . Using annealing factor: 0.0010631937511809421 kt: 0.10631937511809421 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:25:09 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 4540001 Best score so far: 35.44431972342052 . Using annealing factor: 0.001047245844913228 kt: 0.1047245844913228 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:25:11 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Mutating helix constraints!
Oct 19, 2010 2:25:11 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 4550000 Best score so far: 35.44431972342052 . Using annealing factor: 0.0010315371572395295 kt: 0.10315371572395295 coordinate system multipliers: 1.0 1.0 1.0  MUTATING HELIX LENGTHS: 
6 ( 6 ) 6 ( 6 ) 6 ( 6 ) Modified helix constraint lengths: 5 7 7 
Oct 19, 2010 2:25:11 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 4550001 Best score so far: 35.44431972342052 . Using annealing factor: 0.0010315371572395295 kt: 0.10315371572395295 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:25:14 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 4560001 Best score so far: 35.44431972342052 . Using annealing factor: 0.0010160640998809365 kt: 0.10160640998809366 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:25:17 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 4570001 Best score so far: 35.44431972342052 . Using annealing factor: 0.0010008231383827225 kt: 0.10008231383827225 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:25:20 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 4580001 Best score so far: 35.44431972342052 . Using annealing factor: 9.858107913069817E-4 kt: 0.09858107913069816 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:25:23 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 4590001 Best score so far: 35.44431972342052 . Using annealing factor: 9.710236294373769E-4 kt: 0.0971023629437377 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:25:26 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Mutating helix constraints!
Oct 19, 2010 2:25:26 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 4600000 Best score so far: 35.44431972342052 . Using annealing factor: 9.564582749958162E-4 kt: 0.09564582749958163 coordinate system multipliers: 1.0 1.0 1.0  MUTATING HELIX LENGTHS: 
6 ( 6 ) 6 ( 6 ) 6 ( 6 ) Modified helix constraint lengths: 6 5 6 
Oct 19, 2010 2:25:26 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 4600001 Best score so far: 35.44431972342052 . Using annealing factor: 9.564582749958162E-4 kt: 0.09564582749958163 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:25:29 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 4610001 Best score so far: 35.44431972342052 . Using annealing factor: 9.42111400870879E-4 kt: 0.09421114008708789 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:25:32 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 4620001 Best score so far: 35.44431972342052 . Using annealing factor: 9.279797298578158E-4 kt: 0.09279797298578157 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:25:34 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 4630001 Best score so far: 35.44431972342052 . Using annealing factor: 9.140600339099485E-4 kt: 0.09140600339099485 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:25:37 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 4640001 Best score so far: 35.44431972342052 . Using annealing factor: 9.003491334012993E-4 kt: 0.09003491334012993 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:25:40 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Mutating helix constraints!
Oct 19, 2010 2:25:40 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 4650000 Best score so far: 35.44431972342052 . Using annealing factor: 8.868438964002797E-4 kt: 0.08868438964002798 coordinate system multipliers: 1.0 1.0 1.0  MUTATING HELIX LENGTHS: 
6 ( 6 ) 6 ( 6 ) 6 ( 6 ) Modified helix constraint lengths: 7 6 7 
Oct 19, 2010 2:25:40 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 4650001 Best score so far: 35.44431972342052 . Using annealing factor: 8.868438964002797E-4 kt: 0.08868438964002798 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:25:43 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 4660001 Best score so far: 35.44431972342052 . Using annealing factor: 8.735412379542756E-4 kt: 0.08735412379542756 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:25:46 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 4670001 Best score so far: 35.44431972342052 . Using annealing factor: 8.604381193849614E-4 kt: 0.08604381193849614 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:25:49 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 4680001 Best score so far: 35.44431972342052 . Using annealing factor: 8.47531547594187E-4 kt: 0.0847531547594187 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:25:52 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 4690001 Best score so far: 35.44431972342052 . Using annealing factor: 8.348185743802742E-4 kt: 0.08348185743802743 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:25:54 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Mutating helix constraints!
Oct 19, 2010 2:25:54 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 4700000 Best score so far: 35.44431972342052 . Using annealing factor: 8.222962957645701E-4 kt: 0.082229629576457 coordinate system multipliers: 1.0 1.0 1.0  MUTATING HELIX LENGTHS: 
6 ( 6 ) 6 ( 6 ) 6 ( 6 ) Modified helix constraint lengths: 6 7 6 
Oct 19, 2010 2:25:54 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 4700001 Best score so far: 35.44431972342052 . Using annealing factor: 8.222962957645701E-4 kt: 0.082229629576457 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:25:57 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 4710001 Best score so far: 35.44431972342052 . Using annealing factor: 8.099618513281014E-4 kt: 0.08099618513281015 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:26:00 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 4720001 Best score so far: 35.44431972342052 . Using annealing factor: 7.978124235581799E-4 kt: 0.07978124235581799 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:26:03 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 4730001 Best score so far: 35.44431972342052 . Using annealing factor: 7.858452372048072E-4 kt: 0.07858452372048072 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:26:06 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 4740001 Best score so far: 35.44431972342052 . Using annealing factor: 7.740575586467351E-4 kt: 0.0774057558646735 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:26:09 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Mutating helix constraints!
Oct 19, 2010 2:26:09 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 4750000 Best score so far: 35.44431972342052 . Using annealing factor: 7.62446695267034E-4 kt: 0.0762446695267034 coordinate system multipliers: 1.0 1.0 1.0  MUTATING HELIX LENGTHS: 
6 ( 6 ) 6 ( 6 ) 6 ( 6 ) Modified helix constraint lengths: 5 7 6 
Oct 19, 2010 2:26:09 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 4750001 Best score so far: 35.44431972342052 . Using annealing factor: 7.62446695267034E-4 kt: 0.0762446695267034 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:26:12 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 4760001 Best score so far: 35.44431972342052 . Using annealing factor: 7.510099948380285E-4 kt: 0.07510099948380286 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:26:14 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 4770001 Best score so far: 35.44431972342052 . Using annealing factor: 7.397448449154581E-4 kt: 0.07397448449154581 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:26:17 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 4780001 Best score so far: 35.44431972342052 . Using annealing factor: 7.286486722417262E-4 kt: 0.07286486722417262 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:26:20 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 4790001 Best score so far: 35.44431972342052 . Using annealing factor: 7.177189421581003E-4 kt: 0.07177189421581004 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:26:23 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Mutating helix constraints!
Oct 19, 2010 2:26:23 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 4800000 Best score so far: 35.44431972342052 . Using annealing factor: 7.069531580257288E-4 kt: 0.07069531580257288 coordinate system multipliers: 1.0 1.0 1.0  MUTATING HELIX LENGTHS: 
6 ( 6 ) 6 ( 6 ) 6 ( 6 ) Modified helix constraint lengths: 6 6 5 
Oct 19, 2010 2:26:23 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 4800001 Best score so far: 35.44431972342052 . Using annealing factor: 7.069531580257288E-4 kt: 0.07069531580257288 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:26:26 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 4810001 Best score so far: 35.44431972342052 . Using annealing factor: 6.963488606553428E-4 kt: 0.06963488606553428 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:26:29 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 4820001 Best score so far: 35.44431972342052 . Using annealing factor: 6.859036277455128E-4 kt: 0.06859036277455127 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:26:32 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 4830001 Best score so far: 35.44431972342052 . Using annealing factor: 6.756150733293301E-4 kt: 0.06756150733293301 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:26:35 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 4840001 Best score so far: 35.44431972342052 . Using annealing factor: 6.6548084722939E-4 kt: 0.06654808472293901 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:26:38 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Mutating helix constraints!
Oct 19, 2010 2:26:38 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 4850000 Best score so far: 35.44431972342052 . Using annealing factor: 6.554986345209493E-4 kt: 0.06554986345209493 coordinate system multipliers: 1.0 1.0 1.0  MUTATING HELIX LENGTHS: 
6 ( 6 ) 6 ( 6 ) 6 ( 6 ) Modified helix constraint lengths: 7 6 6 
Oct 19, 2010 2:26:38 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 4850001 Best score so far: 35.44431972342052 . Using annealing factor: 6.554986345209493E-4 kt: 0.06554986345209493 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:26:41 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 4860001 Best score so far: 35.44431972342052 . Using annealing factor: 6.456661550031349E-4 kt: 0.06456661550031349 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:26:44 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 4870001 Best score so far: 35.44431972342052 . Using annealing factor: 6.359811626780879E-4 kt: 0.06359811626780879 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:26:46 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 4880001 Best score so far: 35.44431972342052 . Using annealing factor: 6.264414452379166E-4 kt: 0.06264414452379166 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:26:49 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 4890001 Best score so far: 35.44431972342052 . Using annealing factor: 6.170448235593479E-4 kt: 0.06170448235593479 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:26:52 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Mutating helix constraints!
Oct 19, 2010 2:26:52 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 4900000 Best score so far: 35.44431972342052 . Using annealing factor: 6.077891512059577E-4 kt: 0.060778915120595765 coordinate system multipliers: 1.0 1.0 1.0  MUTATING HELIX LENGTHS: 
6 ( 6 ) 6 ( 6 ) 6 ( 6 ) Modified helix constraint lengths: 6 5 6 
Oct 19, 2010 2:26:52 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 4900001 Best score so far: 35.44431972342052 . Using annealing factor: 6.077891512059577E-4 kt: 0.060778915120595765 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:26:55 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 4910001 Best score so far: 35.44431972342052 . Using annealing factor: 5.986723139378683E-4 kt: 0.05986723139378683 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:26:58 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 4920001 Best score so far: 35.44431972342052 . Using annealing factor: 5.896922292288002E-4 kt: 0.05896922292288002 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:27:01 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 4930001 Best score so far: 35.44431972342052 . Using annealing factor: 5.808468457903682E-4 kt: 0.058084684579036816 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:27:04 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 4940001 Best score so far: 35.44431972342052 . Using annealing factor: 5.721341431035126E-4 kt: 0.05721341431035126 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:27:07 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Mutating helix constraints!
Oct 19, 2010 2:27:07 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 4950000 Best score so far: 35.44431972342052 . Using annealing factor: 5.635521309569599E-4 kt: 0.056355213095695994 coordinate system multipliers: 1.0 1.0 1.0  MUTATING HELIX LENGTHS: 
6 ( 6 ) 6 ( 6 ) 6 ( 6 ) Modified helix constraint lengths: 5 6 6 
Oct 19, 2010 2:27:07 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 4950001 Best score so far: 35.44431972342052 . Using annealing factor: 5.635521309569599E-4 kt: 0.056355213095695994 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:27:10 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 4960001 Best score so far: 35.44431972342052 . Using annealing factor: 5.550988489926056E-4 kt: 0.05550988489926056 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:27:13 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 4970001 Best score so far: 35.44431972342052 . Using annealing factor: 5.467723662577165E-4 kt: 0.05467723662577165 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:27:15 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 4980001 Best score so far: 35.44431972342052 . Using annealing factor: 5.385707807638507E-4 kt: 0.053857078076385075 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:27:18 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 4990001 Best score so far: 35.44431972342052 . Using annealing factor: 5.304922190523929E-4 kt: 0.05304922190523929 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:27:21 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Mutating helix constraints!
Oct 19, 2010 2:27:21 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 5000000 Best score so far: 35.44431972342052 . Using annealing factor: 5.22534835766607E-4 kt: 0.0522534835766607 coordinate system multipliers: 1.0 1.0 1.0  MUTATING HELIX LENGTHS: 
6 ( 6 ) 6 ( 6 ) 6 ( 6 ) Modified helix constraint lengths: 5 7 7 
Oct 19, 2010 2:27:21 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 5000001 Best score so far: 35.44431972342052 . Using annealing factor: 5.22534835766607E-4 kt: 0.0522534835766607 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:27:24 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 5010001 Best score so far: 35.44431972342052 . Using annealing factor: 5.14696813230108E-4 kt: 0.051469681323010795 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:27:27 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 5020001 Best score so far: 35.44431972342052 . Using annealing factor: 5.069763610316563E-4 kt: 0.05069763610316563 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:27:30 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 5030001 Best score so far: 35.44431972342052 . Using annealing factor: 4.993717156161814E-4 kt: 0.04993717156161814 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:27:33 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 5040001 Best score so far: 35.44431972342052 . Using annealing factor: 4.918811398819387E-4 kt: 0.04918811398819387 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:27:36 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Mutating helix constraints!
Oct 19, 2010 2:27:36 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 5050000 Best score so far: 35.44431972342052 . Using annealing factor: 4.845029227837096E-4 kt: 0.048450292278370964 coordinate system multipliers: 1.0 1.0 1.0  MUTATING HELIX LENGTHS: 
6 ( 6 ) 6 ( 6 ) 6 ( 6 ) Modified helix constraint lengths: 5 6 6 
Oct 19, 2010 2:27:36 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 5050001 Best score so far: 35.44431972342052 . Using annealing factor: 4.845029227837096E-4 kt: 0.048450292278370964 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:27:39 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 5060001 Best score so far: 35.44431972342052 . Using annealing factor: 4.77235378941954E-4 kt: 0.0477235378941954 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:27:42 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 5070001 Best score so far: 35.44431972342052 . Using annealing factor: 4.700768482578247E-4 kt: 0.04700768482578247 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:27:44 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 5080001 Best score so far: 35.44431972342052 . Using annealing factor: 4.630256955339573E-4 kt: 0.04630256955339573 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:27:47 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 5090001 Best score so far: 35.44431972342052 . Using annealing factor: 4.5608031010094794E-4 kt: 0.04560803101009479 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:27:50 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Mutating helix constraints!
Oct 19, 2010 2:27:50 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 5100000 Best score so far: 35.44431972342052 . Using annealing factor: 4.4923910544943373E-4 kt: 0.04492391054494337 coordinate system multipliers: 1.0 1.0 1.0  MUTATING HELIX LENGTHS: 
6 ( 6 ) 6 ( 6 ) 6 ( 6 ) Modified helix constraint lengths: 6 5 6 
Oct 19, 2010 2:27:50 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 5100001 Best score so far: 35.44431972342052 . Using annealing factor: 4.4923910544943373E-4 kt: 0.04492391054494337 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:27:53 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 5110001 Best score so far: 35.44431972342052 . Using annealing factor: 4.425005188676922E-4 kt: 0.04425005188676922 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:27:56 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 5120001 Best score so far: 35.44431972342052 . Using annealing factor: 4.358630110846768E-4 kt: 0.04358630110846768 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:27:59 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 5130001 Best score so far: 35.44431972342052 . Using annealing factor: 4.293250659184066E-4 kt: 0.04293250659184066 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:28:02 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 5140001 Best score so far: 35.44431972342052 . Using annealing factor: 4.228851899296305E-4 kt: 0.04228851899296305 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:28:05 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Mutating helix constraints!
Oct 19, 2010 2:28:05 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 5150000 Best score so far: 35.44431972342052 . Using annealing factor: 4.165419120806861E-4 kt: 0.04165419120806861 coordinate system multipliers: 1.0 1.0 1.0  MUTATING HELIX LENGTHS: 
6 ( 6 ) 6 ( 6 ) 6 ( 6 ) Modified helix constraint lengths: 6 5 6 
Oct 19, 2010 2:28:05 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 5150001 Best score so far: 35.44431972342052 . Using annealing factor: 4.165419120806861E-4 kt: 0.04165419120806861 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:28:08 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 5160001 Best score so far: 35.44431972342052 . Using annealing factor: 4.1029378339947577E-4 kt: 0.041029378339947575 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:28:10 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 5170001 Best score so far: 35.44431972342052 . Using annealing factor: 4.0413937664848364E-4 kt: 0.04041393766484837 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:28:13 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 5180001 Best score so far: 35.44431972342052 . Using annealing factor: 3.980772859987564E-4 kt: 0.03980772859987564 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:28:16 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 5190001 Best score so far: 35.44431972342052 . Using annealing factor: 3.92106126708775E-4 kt: 0.0392106126708775 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:28:19 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Mutating helix constraints!
Oct 19, 2010 2:28:19 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 5200000 Best score so far: 35.44431972342052 . Using annealing factor: 3.862245348081434E-4 kt: 0.03862245348081434 coordinate system multipliers: 1.0 1.0 1.0  MUTATING HELIX LENGTHS: 
6 ( 6 ) 6 ( 6 ) 6 ( 6 ) Modified helix constraint lengths: 7 6 6 
Oct 19, 2010 2:28:19 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 5200001 Best score so far: 35.44431972342052 . Using annealing factor: 3.862245348081434E-4 kt: 0.03862245348081434 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:28:22 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 5210001 Best score so far: 35.44431972342052 . Using annealing factor: 3.804311667860213E-4 kt: 0.03804311667860213 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:28:25 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 5220001 Best score so far: 35.44431972342052 . Using annealing factor: 3.747246992842309E-4 kt: 0.03747246992842309 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:28:28 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 5230001 Best score so far: 35.44431972342052 . Using annealing factor: 3.6910382879496746E-4 kt: 0.036910382879496745 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:28:31 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 5240001 Best score so far: 35.44431972342052 . Using annealing factor: 3.635672713630429E-4 kt: 0.03635672713630429 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:28:33 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Mutating helix constraints!
Oct 19, 2010 2:28:33 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 5250000 Best score so far: 35.44431972342052 . Using annealing factor: 3.581137622925973E-4 kt: 0.03581137622925973 coordinate system multipliers: 1.0 1.0 1.0  MUTATING HELIX LENGTHS: 
6 ( 6 ) 6 ( 6 ) 6 ( 6 ) Modified helix constraint lengths: 6 6 7 
Oct 19, 2010 2:28:33 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 5250001 Best score so far: 35.44431972342052 . Using annealing factor: 3.581137622925973E-4 kt: 0.03581137622925973 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:28:36 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 5260001 Best score so far: 35.44431972342052 . Using annealing factor: 3.527420558582083E-4 kt: 0.03527420558582083 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:28:39 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 5270001 Best score so far: 35.44431972342052 . Using annealing factor: 3.474509250203352E-4 kt: 0.03474509250203352 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:28:42 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 5280001 Best score so far: 35.44431972342052 . Using annealing factor: 3.4223916114503014E-4 kt: 0.03422391611450301 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:28:45 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 5290001 Best score so far: 35.44431972342052 . Using annealing factor: 3.371055737278547E-4 kt: 0.03371055737278547 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:28:48 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Mutating helix constraints!
Oct 19, 2010 2:28:48 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 5300000 Best score so far: 35.44431972342052 . Using annealing factor: 3.3204899012193685E-4 kt: 0.03320489901219369 coordinate system multipliers: 1.0 1.0 1.0  MUTATING HELIX LENGTHS: 
6 ( 6 ) 6 ( 6 ) 6 ( 6 ) Oct 19, 2010 2:28:48 PM rnadesign.rnamodel.HelixOptimizer mutateHelixLengths
WARNING: No helix lengths were modified!
Oct 19, 2010 2:28:48 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 5300001 Best score so far: 35.44431972342052 . Using annealing factor: 3.3204899012193685E-4 kt: 0.03320489901219369 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:28:51 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 5310001 Best score so far: 35.44431972342052 . Using annealing factor: 3.270682552701078E-4 kt: 0.03270682552701078 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:28:54 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 5320001 Best score so far: 35.44431972342052 . Using annealing factor: 3.221622314410562E-4 kt: 0.03221622314410562 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:28:57 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 5330001 Best score so far: 35.44431972342052 . Using annealing factor: 3.1732979796944035E-4 kt: 0.03173297979694403 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:29:00 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 5340001 Best score so far: 35.44431972342052 . Using annealing factor: 3.1256985099989876E-4 kt: 0.03125698509998988 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:29:03 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Mutating helix constraints!
Oct 19, 2010 2:29:03 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 5350000 Best score so far: 35.44431972342052 . Using annealing factor: 3.0788130323490027E-4 kt: 0.030788130323490027 coordinate system multipliers: 1.0 1.0 1.0  MUTATING HELIX LENGTHS: 
6 ( 6 ) 6 ( 6 ) 6 ( 6 ) Modified helix constraint lengths: 6 7 6 
Oct 19, 2010 2:29:03 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 5350001 Best score so far: 35.44431972342052 . Using annealing factor: 3.0788130323490027E-4 kt: 0.030788130323490027 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:29:05 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 5360001 Best score so far: 35.44431972342052 . Using annealing factor: 3.0326308368637674E-4 kt: 0.030326308368637676 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:29:08 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 5370001 Best score so far: 35.44431972342052 . Using annealing factor: 2.987141374310811E-4 kt: 0.02987141374310811 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:29:11 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 5380001 Best score so far: 35.44431972342052 . Using annealing factor: 2.942334253696149E-4 kt: 0.029423342536961487 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:29:14 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 5390001 Best score so far: 35.44431972342052 . Using annealing factor: 2.8981992398907066E-4 kt: 0.028981992398907065 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:29:17 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Mutating helix constraints!
Oct 19, 2010 2:29:17 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 5400000 Best score so far: 35.44431972342052 . Using annealing factor: 2.8547262512923456E-4 kt: 0.028547262512923458 coordinate system multipliers: 1.0 1.0 1.0  MUTATING HELIX LENGTHS: 
6 ( 6 ) 6 ( 6 ) 6 ( 6 ) Modified helix constraint lengths: 5 5 7 
Oct 19, 2010 2:29:17 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 5400001 Best score so far: 35.44431972342052 . Using annealing factor: 2.8547262512923456E-4 kt: 0.028547262512923458 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:29:20 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 5410001 Best score so far: 35.44431972342052 . Using annealing factor: 2.8119053575229605E-4 kt: 0.028119053575229605 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:29:23 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 5420001 Best score so far: 35.44431972342052 . Using annealing factor: 2.769726777160116E-4 kt: 0.027697267771601163 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:29:26 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 5430001 Best score so far: 35.44431972342052 . Using annealing factor: 2.728180875502714E-4 kt: 0.027281808755027143 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:29:29 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 5440001 Best score so far: 35.44431972342052 . Using annealing factor: 2.6872581623701736E-4 kt: 0.026872581623701736 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:29:31 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Mutating helix constraints!
Oct 19, 2010 2:29:31 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 5450000 Best score so far: 35.44431972342052 . Using annealing factor: 2.646949289934621E-4 kt: 0.026469492899346213 coordinate system multipliers: 1.0 1.0 1.0  MUTATING HELIX LENGTHS: 
6 ( 6 ) 6 ( 6 ) 6 ( 6 ) Modified helix constraint lengths: 6 6 7 
Oct 19, 2010 2:29:31 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 5450001 Best score so far: 35.44431972342052 . Using annealing factor: 2.646949289934621E-4 kt: 0.026469492899346213 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:29:34 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 5460001 Best score so far: 35.44431972342052 . Using annealing factor: 2.607245050585602E-4 kt: 0.026072450505856017 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:29:37 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 5470001 Best score so far: 35.44431972342052 . Using annealing factor: 2.5681363748268176E-4 kt: 0.025681363748268175 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:29:40 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 5480001 Best score so far: 35.44431972342052 . Using annealing factor: 2.529614329204415E-4 kt: 0.025296143292044153 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:29:43 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 5490001 Best score so far: 35.44431972342052 . Using annealing factor: 2.491670114266349E-4 kt: 0.024916701142663488 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:29:46 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Mutating helix constraints!
Oct 19, 2010 2:29:46 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 5500000 Best score so far: 35.44431972342052 . Using annealing factor: 2.4542950625523535E-4 kt: 0.024542950625523537 coordinate system multipliers: 1.0 1.0 1.0  MUTATING HELIX LENGTHS: 
6 ( 6 ) 6 ( 6 ) 6 ( 6 ) Modified helix constraint lengths: 7 6 6 
Oct 19, 2010 2:29:46 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 5500001 Best score so far: 35.44431972342052 . Using annealing factor: 2.4542950625523535E-4 kt: 0.024542950625523537 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:29:49 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 5510001 Best score so far: 35.44431972342052 . Using annealing factor: 2.4174806366140684E-4 kt: 0.024174806366140684 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:29:52 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 5520001 Best score so far: 35.44431972342052 . Using annealing factor: 2.3812184270648572E-4 kt: 0.023812184270648573 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:29:55 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 5530001 Best score so far: 35.44431972342052 . Using annealing factor: 2.3455001506588843E-4 kt: 0.023455001506588843 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:29:58 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 5540001 Best score so far: 35.44431972342052 . Using annealing factor: 2.310317648399001E-4 kt: 0.02310317648399001 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:30:00 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Mutating helix constraints!
Oct 19, 2010 2:30:00 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 5550000 Best score so far: 35.44431972342052 . Using annealing factor: 2.2756628836730162E-4 kt: 0.022756628836730162 coordinate system multipliers: 1.0 1.0 1.0  MUTATING HELIX LENGTHS: 
6 ( 6 ) 6 ( 6 ) 6 ( 6 ) Modified helix constraint lengths: 6 5 6 
Oct 19, 2010 2:30:00 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 5550001 Best score so far: 35.44431972342052 . Using annealing factor: 2.2756628836730162E-4 kt: 0.022756628836730162 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:30:03 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 5560001 Best score so far: 35.44431972342052 . Using annealing factor: 2.241527940417921E-4 kt: 0.02241527940417921 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:30:06 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 5570001 Best score so far: 35.44431972342052 . Using annealing factor: 2.207905021311652E-4 kt: 0.02207905021311652 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:30:09 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 5580001 Best score so far: 35.44431972342052 . Using annealing factor: 2.1747864459919773E-4 kt: 0.021747864459919775 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:30:12 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 5590001 Best score so far: 35.44431972342052 . Using annealing factor: 2.1421646493020974E-4 kt: 0.021421646493020974 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:30:15 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Mutating helix constraints!
Oct 19, 2010 2:30:15 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 5600000 Best score so far: 35.44431972342052 . Using annealing factor: 2.1100321795625658E-4 kt: 0.021100321795625657 coordinate system multipliers: 1.0 1.0 1.0  MUTATING HELIX LENGTHS: 
6 ( 6 ) 6 ( 6 ) 6 ( 6 ) Modified helix constraint lengths: 5 6 5 
Oct 19, 2010 2:30:15 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 5600001 Best score so far: 35.44431972342052 . Using annealing factor: 2.1100321795625658E-4 kt: 0.021100321795625657 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:30:18 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 5610001 Best score so far: 35.44431972342052 . Using annealing factor: 2.0783816968691275E-4 kt: 0.020783816968691277 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:30:21 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 5620001 Best score so far: 35.44431972342052 . Using annealing factor: 2.0472059714160906E-4 kt: 0.020472059714160905 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:30:24 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 5630001 Best score so far: 35.44431972342052 . Using annealing factor: 2.0164978818448492E-4 kt: 0.020164978818448493 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:30:26 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 5640001 Best score so far: 35.44431972342052 . Using annealing factor: 1.9862504136171764E-4 kt: 0.019862504136171764 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:30:29 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Mutating helix constraints!
Oct 19, 2010 2:30:29 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 5650000 Best score so far: 35.44431972342052 . Using annealing factor: 1.956456657412919E-4 kt: 0.019564566574129187 coordinate system multipliers: 1.0 1.0 1.0  MUTATING HELIX LENGTHS: 
6 ( 6 ) 6 ( 6 ) 6 ( 6 ) Modified helix constraint lengths: 6 7 5 
Oct 19, 2010 2:30:29 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 5650001 Best score so far: 35.44431972342052 . Using annealing factor: 1.956456657412919E-4 kt: 0.019564566574129187 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:30:32 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 5660001 Best score so far: 35.44431972342052 . Using annealing factor: 1.9271098075517249E-4 kt: 0.01927109807551725 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:30:35 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 5670001 Best score so far: 35.44431972342052 . Using annealing factor: 1.898203160438449E-4 kt: 0.01898203160438449 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:30:38 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 5680001 Best score so far: 35.44431972342052 . Using annealing factor: 1.8697301130318723E-4 kt: 0.018697301130318724 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:30:41 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 5690001 Best score so far: 35.44431972342052 . Using annealing factor: 1.8416841613363942E-4 kt: 0.018416841613363943 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:30:44 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Mutating helix constraints!
Oct 19, 2010 2:30:44 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 5700000 Best score so far: 35.44431972342052 . Using annealing factor: 1.8140588989163482E-4 kt: 0.018140588989163483 coordinate system multipliers: 1.0 1.0 1.0  MUTATING HELIX LENGTHS: 
6 ( 6 ) 6 ( 6 ) 6 ( 6 ) Modified helix constraint lengths: 5 6 6 
Oct 19, 2010 2:30:44 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 5700001 Best score so far: 35.44431972342052 . Using annealing factor: 1.8140588989163482E-4 kt: 0.018140588989163483 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:30:47 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 5710001 Best score so far: 35.44431972342052 . Using annealing factor: 1.7868480154326028E-4 kt: 0.01786848015432603 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:30:50 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 5720001 Best score so far: 35.44431972342052 . Using annealing factor: 1.7600452952011138E-4 kt: 0.01760045295201114 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:30:52 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 5730001 Best score so far: 35.44431972342052 . Using annealing factor: 1.733644615773097E-4 kt: 0.01733644615773097 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:30:55 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 5740001 Best score so far: 35.44431972342052 . Using annealing factor: 1.7076399465365007E-4 kt: 0.017076399465365006 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:30:58 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Mutating helix constraints!
Oct 19, 2010 2:30:58 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 5750000 Best score so far: 35.44431972342052 . Using annealing factor: 1.682025347338453E-4 kt: 0.01682025347338453 coordinate system multipliers: 1.0 1.0 1.0  MUTATING HELIX LENGTHS: 
6 ( 6 ) 6 ( 6 ) 6 ( 6 ) Modified helix constraint lengths: 6 6 5 
Oct 19, 2010 2:30:58 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 5750001 Best score so far: 35.44431972342052 . Using annealing factor: 1.682025347338453E-4 kt: 0.01682025347338453 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:31:01 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 5760001 Best score so far: 35.44431972342052 . Using annealing factor: 1.6567949671283765E-4 kt: 0.016567949671283763 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:31:04 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 5770001 Best score so far: 35.44431972342052 . Using annealing factor: 1.6319430426214507E-4 kt: 0.016319430426214507 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:31:07 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 5780001 Best score so far: 35.44431972342052 . Using annealing factor: 1.607463896982129E-4 kt: 0.01607463896982129 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:31:10 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 5790001 Best score so far: 35.44431972342052 . Using annealing factor: 1.583351938527397E-4 kt: 0.01583351938527397 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:31:13 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Mutating helix constraints!
Oct 19, 2010 2:31:13 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 5800000 Best score so far: 35.44431972342052 . Using annealing factor: 1.559601659449486E-4 kt: 0.01559601659449486 coordinate system multipliers: 1.0 1.0 1.0  MUTATING HELIX LENGTHS: 
6 ( 6 ) 6 ( 6 ) 6 ( 6 ) Modified helix constraint lengths: 5 6 5 
Oct 19, 2010 2:31:13 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 5800001 Best score so far: 35.44431972342052 . Using annealing factor: 1.559601659449486E-4 kt: 0.01559601659449486 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:31:16 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 5810001 Best score so far: 35.44431972342052 . Using annealing factor: 1.5362076345577436E-4 kt: 0.015362076345577435 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:31:19 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 5820001 Best score so far: 35.44431972342052 . Using annealing factor: 1.5131645200393775E-4 kt: 0.015131645200393775 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:31:21 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 5830001 Best score so far: 35.44431972342052 . Using annealing factor: 1.4904670522387868E-4 kt: 0.014904670522387867 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:31:24 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 5840001 Best score so far: 35.44431972342052 . Using annealing factor: 1.468110046455205E-4 kt: 0.014681100464552049 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:31:27 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Mutating helix constraints!
Oct 19, 2010 2:31:27 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 5850000 Best score so far: 35.44431972342052 . Using annealing factor: 1.4460883957583768E-4 kt: 0.014460883957583768 coordinate system multipliers: 1.0 1.0 1.0  MUTATING HELIX LENGTHS: 
6 ( 6 ) 6 ( 6 ) 6 ( 6 ) Modified helix constraint lengths: 5 6 5 
Oct 19, 2010 2:31:27 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 5850001 Best score so far: 35.44431972342052 . Using annealing factor: 1.4460883957583768E-4 kt: 0.014460883957583768 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:31:30 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 5860001 Best score so far: 35.44431972342052 . Using annealing factor: 1.4243970698220011E-4 kt: 0.014243970698220011 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:31:33 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 5870001 Best score so far: 35.44431972342052 . Using annealing factor: 1.403031113774671E-4 kt: 0.01403031113774671 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:31:36 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 5880001 Best score so far: 35.44431972342052 . Using annealing factor: 1.381985647068051E-4 kt: 0.01381985647068051 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:31:39 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 5890001 Best score so far: 35.44431972342052 . Using annealing factor: 1.3612558623620302E-4 kt: 0.013612558623620302 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:31:42 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Mutating helix constraints!
Oct 19, 2010 2:31:42 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 5900000 Best score so far: 35.44431972342052 . Using annealing factor: 1.3408370244265998E-4 kt: 0.013408370244265999 coordinate system multipliers: 1.0 1.0 1.0  MUTATING HELIX LENGTHS: 
6 ( 6 ) 6 ( 6 ) 6 ( 6 ) Modified helix constraint lengths: 6 7 7 
Oct 19, 2010 2:31:42 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 5900001 Best score so far: 35.44431972342052 . Using annealing factor: 1.3408370244265998E-4 kt: 0.013408370244265999 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:31:45 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 5910001 Best score so far: 35.44431972342052 . Using annealing factor: 1.320724469060201E-4 kt: 0.01320724469060201 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:31:48 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 5920001 Best score so far: 35.44431972342052 . Using annealing factor: 1.3009136020242977E-4 kt: 0.013009136020242977 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:31:50 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 5930001 Best score so far: 35.44431972342052 . Using annealing factor: 1.2813998979939334E-4 kt: 0.012813998979939335 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:31:53 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 5940001 Best score so far: 35.44431972342052 . Using annealing factor: 1.2621788995240244E-4 kt: 0.012621788995240243 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:31:56 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Mutating helix constraints!
Oct 19, 2010 2:31:56 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 5950000 Best score so far: 35.44431972342052 . Using annealing factor: 1.2432462160311638E-4 kt: 0.012432462160311637 coordinate system multipliers: 1.0 1.0 1.0  MUTATING HELIX LENGTHS: 
6 ( 6 ) 6 ( 6 ) 6 ( 6 ) Modified helix constraint lengths: 6 6 5 
Oct 19, 2010 2:31:56 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 5950001 Best score so far: 35.44431972342052 . Using annealing factor: 1.2432462160311638E-4 kt: 0.012432462160311637 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:31:59 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 5960001 Best score so far: 35.44431972342052 . Using annealing factor: 1.2245975227906963E-4 kt: 0.012245975227906963 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:32:02 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 5970001 Best score so far: 35.44431972342052 . Using annealing factor: 1.2062285599488359E-4 kt: 0.012062285599488359 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:32:05 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 5980001 Best score so far: 35.44431972342052 . Using annealing factor: 1.1881351315496034E-4 kt: 0.011881351315496034 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:32:08 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 5990001 Best score so far: 35.44431972342052 . Using annealing factor: 1.1703131045763593E-4 kt: 0.011703131045763593 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:32:11 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Mutating helix constraints!
Oct 19, 2010 2:32:11 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 6000000 Best score so far: 35.44431972342052 . Using annealing factor: 1.152758408007714E-4 kt: 0.01152758408007714 coordinate system multipliers: 1.0 1.0 1.0  MUTATING HELIX LENGTHS: 
6 ( 6 ) 6 ( 6 ) 6 ( 6 ) Modified helix constraint lengths: 6 6 7 
Oct 19, 2010 2:32:11 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 6000001 Best score so far: 35.44431972342052 . Using annealing factor: 1.152758408007714E-4 kt: 0.01152758408007714 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:32:14 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 6010001 Best score so far: 35.44431972342052 . Using annealing factor: 1.1354670318875983E-4 kt: 0.011354670318875982 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:32:17 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 6020001 Best score so far: 35.44431972342052 . Using annealing factor: 1.1184350264092842E-4 kt: 0.011184350264092842 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:32:19 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 6030001 Best score so far: 35.44431972342052 . Using annealing factor: 1.101658501013145E-4 kt: 0.01101658501013145 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:32:22 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 6040001 Best score so far: 35.44431972342052 . Using annealing factor: 1.0851336234979478E-4 kt: 0.010851336234979478 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:32:25 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Mutating helix constraints!
Oct 19, 2010 2:32:25 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 6050000 Best score so far: 35.44431972342052 . Using annealing factor: 1.0688566191454785E-4 kt: 0.010688566191454784 coordinate system multipliers: 1.0 1.0 1.0  MUTATING HELIX LENGTHS: 
6 ( 6 ) 6 ( 6 ) 6 ( 6 ) Oct 19, 2010 2:32:25 PM rnadesign.rnamodel.HelixOptimizer mutateHelixLengths
WARNING: No helix lengths were modified!
Oct 19, 2010 2:32:25 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 6050001 Best score so far: 35.44431972342052 . Using annealing factor: 1.0688566191454785E-4 kt: 0.010688566191454784 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:32:28 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 6060001 Best score so far: 35.44431972342052 . Using annealing factor: 1.0528237698582962E-4 kt: 0.010528237698582962 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:32:31 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 6070001 Best score so far: 35.44431972342052 . Using annealing factor: 1.0370314133104219E-4 kt: 0.010370314133104219 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:32:34 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 6080001 Best score so far: 35.44431972342052 . Using annealing factor: 1.0214759421107655E-4 kt: 0.010214759421107656 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:32:37 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 6090001 Best score so far: 35.44431972342052 . Using annealing factor: 1.006153802979104E-4 kt: 0.01006153802979104 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:32:40 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Mutating helix constraints!
Oct 19, 2010 2:32:40 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 6100000 Best score so far: 35.44431972342052 . Using annealing factor: 9.910614959344174E-5 kt: 0.009910614959344173 coordinate system multipliers: 1.0 1.0 1.0  MUTATING HELIX LENGTHS: 
6 ( 6 ) 6 ( 6 ) 6 ( 6 ) Modified helix constraint lengths: 6 6 7 
Oct 19, 2010 2:32:40 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 6100001 Best score so far: 35.44431972342052 . Using annealing factor: 9.910614959344174E-5 kt: 0.009910614959344173 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:32:43 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 6110001 Best score so far: 35.44431972342052 . Using annealing factor: 9.761955734954012E-5 kt: 0.009761955734954012 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:32:45 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 6120001 Best score so far: 35.44431972342052 . Using annealing factor: 9.615526398929702E-5 kt: 0.009615526398929703 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:32:48 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 6130001 Best score so far: 35.44431972342052 . Using annealing factor: 9.471293502945756E-5 kt: 0.009471293502945757 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:32:51 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 6140001 Best score so far: 35.44431972342052 . Using annealing factor: 9.32922410040157E-5 kt: 0.00932922410040157 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:32:54 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Mutating helix constraints!
Oct 19, 2010 2:32:54 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 6150000 Best score so far: 35.44431972342052 . Using annealing factor: 9.189285738895545E-5 kt: 0.009189285738895546 coordinate system multipliers: 1.0 1.0 1.0  MUTATING HELIX LENGTHS: 
6 ( 6 ) 6 ( 6 ) 6 ( 6 ) Modified helix constraint lengths: 5 7 7 
Oct 19, 2010 2:32:54 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 6150001 Best score so far: 35.44431972342052 . Using annealing factor: 9.189285738895545E-5 kt: 0.009189285738895546 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:32:57 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 6160001 Best score so far: 35.44431972342052 . Using annealing factor: 9.051446452812112E-5 kt: 0.009051446452812112 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:33:00 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 6170001 Best score so far: 35.44431972342052 . Using annealing factor: 8.91567475601993E-5 kt: 0.00891567475601993 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:33:03 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 6180001 Best score so far: 35.44431972342052 . Using annealing factor: 8.781939634679632E-5 kt: 0.008781939634679633 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:33:06 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 6190001 Best score so far: 35.44431972342052 . Using annealing factor: 8.650210540159437E-5 kt: 0.008650210540159436 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:33:09 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Mutating helix constraints!
Oct 19, 2010 2:33:09 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 6200000 Best score so far: 35.44431972342052 . Using annealing factor: 8.520457382057045E-5 kt: 0.008520457382057044 coordinate system multipliers: 1.0 1.0 1.0  MUTATING HELIX LENGTHS: 
6 ( 6 ) 6 ( 6 ) 6 ( 6 ) Modified helix constraint lengths: 6 7 7 
Oct 19, 2010 2:33:09 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 6200001 Best score so far: 35.44431972342052 . Using annealing factor: 8.520457382057045E-5 kt: 0.008520457382057044 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:33:11 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 6210001 Best score so far: 35.44431972342052 . Using annealing factor: 8.392650521326189E-5 kt: 0.008392650521326189 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:33:14 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 6220001 Best score so far: 35.44431972342052 . Using annealing factor: 8.266760763506297E-5 kt: 0.008266760763506296 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:33:17 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 6230001 Best score so far: 35.44431972342052 . Using annealing factor: 8.142759352053702E-5 kt: 0.008142759352053702 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:33:20 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 6240001 Best score so far: 35.44431972342052 . Using annealing factor: 8.020617961772896E-5 kt: 0.008020617961772896 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:33:23 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Mutating helix constraints!
Oct 19, 2010 2:33:23 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 6250000 Best score so far: 35.44431972342052 . Using annealing factor: 7.900308692346303E-5 kt: 0.007900308692346304 coordinate system multipliers: 1.0 1.0 1.0  MUTATING HELIX LENGTHS: 
6 ( 6 ) 6 ( 6 ) 6 ( 6 ) Modified helix constraint lengths: 6 6 7 
Oct 19, 2010 2:33:23 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 6250001 Best score so far: 35.44431972342052 . Using annealing factor: 7.900308692346303E-5 kt: 0.007900308692346304 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:33:26 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 6260001 Best score so far: 35.44431972342052 . Using annealing factor: 7.781804061961109E-5 kt: 0.007781804061961109 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:33:29 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 6270001 Best score so far: 35.44431972342052 . Using annealing factor: 7.665077001031692E-5 kt: 0.007665077001031692 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:33:32 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 6280001 Best score so far: 35.44431972342052 . Using annealing factor: 7.550100846016216E-5 kt: 0.007550100846016216 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:33:34 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 6290001 Best score so far: 35.44431972342052 . Using annealing factor: 7.436849333325972E-5 kt: 0.007436849333325972 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:33:37 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Mutating helix constraints!
Oct 19, 2010 2:33:37 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 6300000 Best score so far: 35.44431972342052 . Using annealing factor: 7.325296593326084E-5 kt: 0.007325296593326084 coordinate system multipliers: 1.0 1.0 1.0  MUTATING HELIX LENGTHS: 
6 ( 6 ) 6 ( 6 ) 6 ( 6 ) Modified helix constraint lengths: 5 7 7 
Oct 19, 2010 2:33:37 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 6300001 Best score so far: 35.44431972342052 . Using annealing factor: 7.325296593326084E-5 kt: 0.007325296593326084 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:33:40 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 6310001 Best score so far: 35.44431972342052 . Using annealing factor: 7.215417144426192E-5 kt: 0.0072154171444261915 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:33:43 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 6320001 Best score so far: 35.44431972342052 . Using annealing factor: 7.107185887259799E-5 kt: 0.007107185887259799 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:33:46 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 6330001 Best score so far: 35.44431972342052 . Using annealing factor: 7.000578098950902E-5 kt: 0.007000578098950902 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:33:49 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 6340001 Best score so far: 35.44431972342052 . Using annealing factor: 6.895569427466638E-5 kt: 0.006895569427466638 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:33:52 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Mutating helix constraints!
Oct 19, 2010 2:33:52 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 6350000 Best score so far: 35.44431972342052 . Using annealing factor: 6.792135886054638E-5 kt: 0.006792135886054638 coordinate system multipliers: 1.0 1.0 1.0  MUTATING HELIX LENGTHS: 
6 ( 6 ) 6 ( 6 ) 6 ( 6 ) Modified helix constraint lengths: 7 5 5 
Oct 19, 2010 2:33:52 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 6350001 Best score so far: 35.44431972342052 . Using annealing factor: 6.792135886054638E-5 kt: 0.006792135886054638 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:33:55 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 6360001 Best score so far: 35.44431972342052 . Using annealing factor: 6.690253847763819E-5 kt: 0.0066902538477638185 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:33:58 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 6370001 Best score so far: 35.44431972342052 . Using annealing factor: 6.589900040047361E-5 kt: 0.006589900040047361 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:34:01 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 6380001 Best score so far: 35.44431972342052 . Using annealing factor: 6.491051539446651E-5 kt: 0.006491051539446651 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:34:03 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 6390001 Best score so far: 35.44431972342052 . Using annealing factor: 6.393685766354951E-5 kt: 0.0063936857663549505 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:34:06 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Mutating helix constraints!
Oct 19, 2010 2:34:06 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 6400000 Best score so far: 35.44431972342052 . Using annealing factor: 6.297780479859626E-5 kt: 0.006297780479859626 coordinate system multipliers: 1.0 1.0 1.0  MUTATING HELIX LENGTHS: 
6 ( 6 ) 6 ( 6 ) 6 ( 6 ) Modified helix constraint lengths: 6 6 5 
Oct 19, 2010 2:34:06 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 6400001 Best score so far: 35.44431972342052 . Using annealing factor: 6.297780479859626E-5 kt: 0.006297780479859626 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:34:09 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 6410001 Best score so far: 35.44431972342052 . Using annealing factor: 6.203313772661732E-5 kt: 0.006203313772661733 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:34:12 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 6420001 Best score so far: 35.44431972342052 . Using annealing factor: 6.110264066071807E-5 kt: 0.006110264066071807 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:34:15 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 6430001 Best score so far: 35.44431972342052 . Using annealing factor: 6.0186101050807285E-5 kt: 0.006018610105080729 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:34:18 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 6440001 Best score so far: 35.44431972342052 . Using annealing factor: 5.928330953504518E-5 kt: 0.005928330953504518 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:34:21 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Mutating helix constraints!
Oct 19, 2010 2:34:21 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 6450000 Best score so far: 35.44431972342052 . Using annealing factor: 5.8394059892019496E-5 kt: 0.005839405989201949 coordinate system multipliers: 1.0 1.0 1.0  MUTATING HELIX LENGTHS: 
6 ( 6 ) 6 ( 6 ) 6 ( 6 ) Modified helix constraint lengths: 5 6 7 
Oct 19, 2010 2:34:21 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 6450001 Best score so far: 35.44431972342052 . Using annealing factor: 5.8394059892019496E-5 kt: 0.005839405989201949 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:34:24 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 6460001 Best score so far: 35.44431972342052 . Using annealing factor: 5.7518148993639204E-5 kt: 0.00575181489936392 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:34:27 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 6470001 Best score so far: 35.44431972342052 . Using annealing factor: 5.6655376758734615E-5 kt: 0.005665537675873461 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:34:30 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 6480001 Best score so far: 35.44431972342052 . Using annealing factor: 5.58055461073536E-5 kt: 0.00558055461073536 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:34:33 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 6490001 Best score so far: 35.44431972342052 . Using annealing factor: 5.4968462915743294E-5 kt: 0.0054968462915743295 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:34:35 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Mutating helix constraints!
Oct 19, 2010 2:34:35 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 6500000 Best score so far: 35.44431972342052 . Using annealing factor: 5.414393597200714E-5 kt: 0.005414393597200714 coordinate system multipliers: 1.0 1.0 1.0  MUTATING HELIX LENGTHS: 
6 ( 6 ) 6 ( 6 ) 6 ( 6 ) Oct 19, 2010 2:34:35 PM rnadesign.rnamodel.HelixOptimizer mutateHelixLengths
WARNING: No helix lengths were modified!
Oct 19, 2010 2:34:35 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 6500001 Best score so far: 35.44431972342052 . Using annealing factor: 5.414393597200714E-5 kt: 0.005414393597200714 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:34:38 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 6510001 Best score so far: 35.44431972342052 . Using annealing factor: 5.333177693242703E-5 kt: 0.005333177693242703 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:34:41 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 6520001 Best score so far: 35.44431972342052 . Using annealing factor: 5.253180027844063E-5 kt: 0.0052531800278440635 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:34:44 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 6530001 Best score so far: 35.44431972342052 . Using annealing factor: 5.174382327426402E-5 kt: 0.005174382327426402 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:34:47 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 6540001 Best score so far: 35.44431972342052 . Using annealing factor: 5.0967665925150053E-5 kt: 0.005096766592515005 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:34:50 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Mutating helix constraints!
Oct 19, 2010 2:34:50 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 6550000 Best score so far: 35.44431972342052 . Using annealing factor: 5.0203150936272805E-5 kt: 0.00502031509362728 coordinate system multipliers: 1.0 1.0 1.0  MUTATING HELIX LENGTHS: 
6 ( 6 ) 6 ( 6 ) 6 ( 6 ) Oct 19, 2010 2:34:50 PM rnadesign.rnamodel.HelixOptimizer mutateHelixLengths
WARNING: No helix lengths were modified!
Oct 19, 2010 2:34:50 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 6550001 Best score so far: 35.44431972342052 . Using annealing factor: 5.0203150936272805E-5 kt: 0.00502031509362728 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:34:53 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 6560001 Best score so far: 35.44431972342052 . Using annealing factor: 4.9450103672228716E-5 kt: 0.004945010367222872 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:34:56 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 6570001 Best score so far: 35.44431972342052 . Using annealing factor: 4.870835211714528E-5 kt: 0.004870835211714527 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:34:58 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 6580001 Best score so far: 35.44431972342052 . Using annealing factor: 4.7977726835388105E-5 kt: 0.00479777268353881 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:35:01 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 6590001 Best score so far: 35.44431972342052 . Using annealing factor: 4.725806093285728E-5 kt: 0.004725806093285728 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:35:04 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Mutating helix constraints!
Oct 19, 2010 2:35:04 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 6600000 Best score so far: 35.44431972342052 . Using annealing factor: 4.654919001886442E-5 kt: 0.004654919001886442 coordinate system multipliers: 1.0 1.0 1.0  MUTATING HELIX LENGTHS: 
6 ( 6 ) 6 ( 6 ) 6 ( 6 ) Modified helix constraint lengths: 5 7 7 
Oct 19, 2010 2:35:04 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 6600001 Best score so far: 35.44431972342052 . Using annealing factor: 4.654919001886442E-5 kt: 0.004654919001886442 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:35:07 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 6610001 Best score so far: 35.44431972342052 . Using annealing factor: 4.585095216858145E-5 kt: 0.004585095216858145 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:35:10 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 6620001 Best score so far: 35.44431972342052 . Using annealing factor: 4.516318788605273E-5 kt: 0.004516318788605273 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:35:13 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 6630001 Best score so far: 35.44431972342052 . Using annealing factor: 4.4485740067761934E-5 kt: 0.004448574006776194 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:35:16 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 6640001 Best score so far: 35.44431972342052 . Using annealing factor: 4.381845396674551E-5 kt: 0.0043818453966745505 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:35:19 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Mutating helix constraints!
Oct 19, 2010 2:35:19 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 6650000 Best score so far: 35.44431972342052 . Using annealing factor: 4.316117715724432E-5 kt: 0.004316117715724432 coordinate system multipliers: 1.0 1.0 1.0  MUTATING HELIX LENGTHS: 
6 ( 6 ) 6 ( 6 ) 6 ( 6 ) Modified helix constraint lengths: 5 7 6 
Oct 19, 2010 2:35:19 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 6650001 Best score so far: 35.44431972342052 . Using annealing factor: 4.316117715724432E-5 kt: 0.004316117715724432 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:35:22 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 6660001 Best score so far: 35.44431972342052 . Using annealing factor: 4.251375949988566E-5 kt: 0.004251375949988566 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:35:24 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 6670001 Best score so far: 35.44431972342052 . Using annealing factor: 4.1876053107387374E-5 kt: 0.004187605310738737 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:35:27 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 6680001 Best score so far: 35.44431972342052 . Using annealing factor: 4.1247912310776566E-5 kt: 0.004124791231077656 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:35:30 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 6690001 Best score so far: 35.44431972342052 . Using annealing factor: 4.062919362611492E-5 kt: 0.004062919362611492 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:35:33 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Mutating helix constraints!
Oct 19, 2010 2:35:33 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 6700000 Best score so far: 35.44431972342052 . Using annealing factor: 4.0019755721723194E-5 kt: 0.00400197557217232 coordinate system multipliers: 1.0 1.0 1.0  MUTATING HELIX LENGTHS: 
6 ( 6 ) 6 ( 6 ) 6 ( 6 ) Modified helix constraint lengths: 5 5 5 
Oct 19, 2010 2:35:33 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 6700001 Best score so far: 35.44431972342052 . Using annealing factor: 4.0019755721723194E-5 kt: 0.00400197557217232 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:35:36 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 6710001 Best score so far: 35.44431972342052 . Using annealing factor: 3.941945938589734E-5 kt: 0.003941945938589734 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:35:39 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 6720001 Best score so far: 35.44431972342052 . Using annealing factor: 3.882816749510888E-5 kt: 0.003882816749510888 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:35:42 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 6730001 Best score so far: 35.44431972342052 . Using annealing factor: 3.8245744982682244E-5 kt: 0.0038245744982682243 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:35:45 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 6740001 Best score so far: 35.44431972342052 . Using annealing factor: 3.767205880794201E-5 kt: 0.003767205880794201 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:35:48 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Mutating helix constraints!
Oct 19, 2010 2:35:48 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 6750000 Best score so far: 35.44431972342052 . Using annealing factor: 3.710697792582288E-5 kt: 0.003710697792582288 coordinate system multipliers: 1.0 1.0 1.0  MUTATING HELIX LENGTHS: 
6 ( 6 ) 6 ( 6 ) 6 ( 6 ) Modified helix constraint lengths: 6 6 5 
Oct 19, 2010 2:35:48 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 6750001 Best score so far: 35.44431972342052 . Using annealing factor: 3.710697792582288E-5 kt: 0.003710697792582288 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:35:50 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 6760001 Best score so far: 35.44431972342052 . Using annealing factor: 3.655037325693554E-5 kt: 0.003655037325693554 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:35:53 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 6770001 Best score so far: 35.44431972342052 . Using annealing factor: 3.6002117658081505E-5 kt: 0.0036002117658081503 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:35:56 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 6780001 Best score so far: 35.44431972342052 . Using annealing factor: 3.546208589321028E-5 kt: 0.003546208589321028 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:35:59 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 6790001 Best score so far: 35.44431972342052 . Using annealing factor: 3.4930154604812127E-5 kt: 0.0034930154604812125 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:36:02 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Mutating helix constraints!
Oct 19, 2010 2:36:02 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 6800000 Best score so far: 35.44431972342052 . Using annealing factor: 3.4406202285739946E-5 kt: 0.0034406202285739945 coordinate system multipliers: 1.0 1.0 1.0  MUTATING HELIX LENGTHS: 
6 ( 6 ) 6 ( 6 ) 6 ( 6 ) Modified helix constraint lengths: 7 7 5 
Oct 19, 2010 2:36:02 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 6800001 Best score so far: 35.44431972342052 . Using annealing factor: 3.4406202285739946E-5 kt: 0.0034406202285739945 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:36:05 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 6810001 Best score so far: 35.44431972342052 . Using annealing factor: 3.389010925145385E-5 kt: 0.003389010925145385 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:36:08 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 6820001 Best score so far: 35.44431972342052 . Using annealing factor: 3.338175761268204E-5 kt: 0.003338175761268204 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:36:11 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 6830001 Best score so far: 35.44431972342052 . Using annealing factor: 3.28810312484918E-5 kt: 0.00328810312484918 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:36:14 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 6840001 Best score so far: 35.44431972342052 . Using annealing factor: 3.2387815779764426E-5 kt: 0.003238781577976443 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:36:17 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Mutating helix constraints!
Oct 19, 2010 2:36:17 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 6850000 Best score so far: 35.44431972342052 . Using annealing factor: 3.190199854306796E-5 kt: 0.0031901998543067958 coordinate system multipliers: 1.0 1.0 1.0  MUTATING HELIX LENGTHS: 
6 ( 6 ) 6 ( 6 ) 6 ( 6 ) Modified helix constraint lengths: 5 6 6 
Oct 19, 2010 2:36:17 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 6850001 Best score so far: 35.44431972342052 . Using annealing factor: 3.190199854306796E-5 kt: 0.0031901998543067958 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:36:19 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 6860001 Best score so far: 35.44431972342052 . Using annealing factor: 3.1423468564921944E-5 kt: 0.0031423468564921943 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:36:22 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 6870001 Best score so far: 35.44431972342052 . Using annealing factor: 3.095211653644811E-5 kt: 0.003095211653644811 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:36:25 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 6880001 Best score so far: 35.44431972342052 . Using annealing factor: 3.048783478840139E-5 kt: 0.003048783478840139 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:36:28 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 6890001 Best score so far: 35.44431972342052 . Using annealing factor: 3.003051726657537E-5 kt: 0.003003051726657537 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:36:31 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Mutating helix constraints!
Oct 19, 2010 2:36:31 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 6900000 Best score so far: 35.44431972342052 . Using annealing factor: 2.9580059507576738E-5 kt: 0.0029580059507576736 coordinate system multipliers: 1.0 1.0 1.0  MUTATING HELIX LENGTHS: 
6 ( 6 ) 6 ( 6 ) 6 ( 6 ) Modified helix constraint lengths: 5 7 5 
Oct 19, 2010 2:36:31 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 6900001 Best score so far: 35.44431972342052 . Using annealing factor: 2.9580059507576738E-5 kt: 0.0029580059507576736 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:36:34 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 6910001 Best score so far: 35.44431972342052 . Using annealing factor: 2.9136358614963087E-5 kt: 0.0029136358614963087 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:36:37 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 6920001 Best score so far: 35.44431972342052 . Using annealing factor: 2.869931323573864E-5 kt: 0.002869931323573864 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:36:40 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 6930001 Best score so far: 35.44431972342052 . Using annealing factor: 2.826882353720256E-5 kt: 0.002826882353720256 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:36:43 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 6940001 Best score so far: 35.44431972342052 . Using annealing factor: 2.7844791184144522E-5 kt: 0.002784479118414452 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:36:45 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Mutating helix constraints!
Oct 19, 2010 2:36:45 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 6950000 Best score so far: 35.44431972342052 . Using annealing factor: 2.7427119316382353E-5 kt: 0.0027427119316382354 coordinate system multipliers: 1.0 1.0 1.0  MUTATING HELIX LENGTHS: 
6 ( 6 ) 6 ( 6 ) 6 ( 6 ) Modified helix constraint lengths: 6 6 5 
Oct 19, 2010 2:36:45 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 6950001 Best score so far: 35.44431972342052 . Using annealing factor: 2.7427119316382353E-5 kt: 0.0027427119316382354 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:36:48 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 6960001 Best score so far: 35.44431972342052 . Using annealing factor: 2.701571252663662E-5 kt: 0.002701571252663662 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:36:51 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 6970001 Best score so far: 35.44431972342052 . Using annealing factor: 2.661047683873707E-5 kt: 0.002661047683873707 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:36:54 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 6980001 Best score so far: 35.44431972342052 . Using annealing factor: 2.621131968615601E-5 kt: 0.002621131968615601 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:36:57 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 6990001 Best score so far: 35.44431972342052 . Using annealing factor: 2.581814989086367E-5 kt: 0.002581814989086367 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:37:00 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Mutating helix constraints!
Oct 19, 2010 2:37:00 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 7000000 Best score so far: 35.44431972342052 . Using annealing factor: 2.5430877642500716E-5 kt: 0.0025430877642500715 coordinate system multipliers: 1.0 1.0 1.0  MUTATING HELIX LENGTHS: 
6 ( 6 ) 6 ( 6 ) 6 ( 6 ) Modified helix constraint lengths: 7 5 5 
Oct 19, 2010 2:37:00 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 7000001 Best score so far: 35.44431972342052 . Using annealing factor: 2.5430877642500716E-5 kt: 0.0025430877642500715 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:37:03 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 7010001 Best score so far: 35.44431972342052 . Using annealing factor: 2.5049414477863205E-5 kt: 0.0025049414477863203 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:37:06 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 7020001 Best score so far: 35.44431972342052 . Using annealing factor: 2.4673673260695257E-5 kt: 0.002467367326069526 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:37:09 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 7030001 Best score so far: 35.44431972342052 . Using annealing factor: 2.4303568161784826E-5 kt: 0.0024303568161784827 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:37:11 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 7040001 Best score so far: 35.44431972342052 . Using annealing factor: 2.3939014639358054E-5 kt: 0.0023939014639358055 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:37:14 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Mutating helix constraints!
Oct 19, 2010 2:37:14 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 7050000 Best score so far: 35.44431972342052 . Using annealing factor: 2.3579929419767682E-5 kt: 0.002357992941976768 coordinate system multipliers: 1.0 1.0 1.0  MUTATING HELIX LENGTHS: 
6 ( 6 ) 6 ( 6 ) 6 ( 6 ) Modified helix constraint lengths: 7 6 6 
Oct 19, 2010 2:37:14 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 7050001 Best score so far: 35.44431972342052 . Using annealing factor: 2.3579929419767682E-5 kt: 0.002357992941976768 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:37:17 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 7060001 Best score so far: 35.44431972342052 . Using annealing factor: 2.322623047847117E-5 kt: 0.0023226230478471167 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:37:20 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 7070001 Best score so far: 35.44431972342052 . Using annealing factor: 2.2877837021294098E-5 kt: 0.0022877837021294096 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:37:23 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 7080001 Best score so far: 35.44431972342052 . Using annealing factor: 2.2534669465974686E-5 kt: 0.002253466946597469 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:37:26 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 7090001 Best score so far: 35.44431972342052 . Using annealing factor: 2.2196649423985067E-5 kt: 0.0022196649423985066 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:37:29 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Mutating helix constraints!
Oct 19, 2010 2:37:29 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 7100000 Best score so far: 35.44431972342052 . Using annealing factor: 2.186369968262529E-5 kt: 0.0021863699682625293 coordinate system multipliers: 1.0 1.0 1.0  MUTATING HELIX LENGTHS: 
6 ( 6 ) 6 ( 6 ) 6 ( 6 ) Modified helix constraint lengths: 7 7 7 
Oct 19, 2010 2:37:29 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 7100001 Best score so far: 35.44431972342052 . Using annealing factor: 2.186369968262529E-5 kt: 0.0021863699682625293 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:37:32 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 7110001 Best score so far: 35.44431972342052 . Using annealing factor: 2.1535744187385912E-5 kt: 0.0021535744187385912 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:37:34 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 7120001 Best score so far: 35.44431972342052 . Using annealing factor: 2.1212708024575122E-5 kt: 0.002121270802457512 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:37:37 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 7130001 Best score so far: 35.44431972342052 . Using annealing factor: 2.0894517404206495E-5 kt: 0.0020894517404206497 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:37:40 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 7140001 Best score so far: 35.44431972342052 . Using annealing factor: 2.0581099643143398E-5 kt: 0.00205810996431434 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:37:43 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Mutating helix constraints!
Oct 19, 2010 2:37:43 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 7150000 Best score so far: 35.44431972342052 . Using annealing factor: 2.0272383148496246E-5 kt: 0.0020272383148496245 coordinate system multipliers: 1.0 1.0 1.0  MUTATING HELIX LENGTHS: 
6 ( 6 ) 6 ( 6 ) 6 ( 6 ) Modified helix constraint lengths: 6 6 7 
Oct 19, 2010 2:37:43 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 7150001 Best score so far: 35.44431972342052 . Using annealing factor: 2.0272383148496246E-5 kt: 0.0020272383148496245 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:37:46 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 7160001 Best score so far: 35.44431972342052 . Using annealing factor: 1.9968297401268803E-5 kt: 0.0019968297401268802 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:37:49 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 7170001 Best score so far: 35.44431972342052 . Using annealing factor: 1.966877294024977E-5 kt: 0.0019668772940249772 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:37:52 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 7180001 Best score so far: 35.44431972342052 . Using annealing factor: 1.9373741346146024E-5 kt: 0.0019373741346146024 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:37:55 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 7190001 Best score so far: 35.44431972342052 . Using annealing factor: 1.9083135225953834E-5 kt: 0.0019083135225953834 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:37:58 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Mutating helix constraints!
Oct 19, 2010 2:37:58 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 7200000 Best score so far: 35.44431972342052 . Using annealing factor: 1.8796888197564526E-5 kt: 0.0018796888197564526 coordinate system multipliers: 1.0 1.0 1.0  MUTATING HELIX LENGTHS: 
6 ( 6 ) 6 ( 6 ) 6 ( 6 ) Modified helix constraint lengths: 6 5 6 
Oct 19, 2010 2:37:58 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 7200001 Best score so far: 35.44431972342052 . Using annealing factor: 1.8796888197564526E-5 kt: 0.0018796888197564526 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:38:00 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 7210001 Best score so far: 35.44431972342052 . Using annealing factor: 1.851493487460106E-5 kt: 0.0018514934874601058 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:38:03 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 7220001 Best score so far: 35.44431972342052 . Using annealing factor: 1.823721085148204E-5 kt: 0.0018237210851482042 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:38:06 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 7230001 Best score so far: 35.44431972342052 . Using annealing factor: 1.796365268870981E-5 kt: 0.0017963652688709809 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:38:09 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 7240001 Best score so far: 35.44431972342052 . Using annealing factor: 1.7694197898379162E-5 kt: 0.0017694197898379161 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:38:12 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Mutating helix constraints!
Oct 19, 2010 2:38:12 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 7250000 Best score so far: 35.44431972342052 . Using annealing factor: 1.7428784929903474E-5 kt: 0.0017428784929903473 coordinate system multipliers: 1.0 1.0 1.0  MUTATING HELIX LENGTHS: 
6 ( 6 ) 6 ( 6 ) 6 ( 6 ) Modified helix constraint lengths: 6 5 7 
Oct 19, 2010 2:38:12 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 7250001 Best score so far: 35.44431972342052 . Using annealing factor: 1.7428784929903474E-5 kt: 0.0017428784929903473 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:38:15 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 7260001 Best score so far: 35.44431972342052 . Using annealing factor: 1.7167353155954923E-5 kt: 0.0017167353155954923 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:38:18 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 7270001 Best score so far: 35.44431972342052 . Using annealing factor: 1.6909842858615598E-5 kt: 0.0016909842858615599 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:38:21 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 7280001 Best score so far: 35.44431972342052 . Using annealing factor: 1.6656195215736366E-5 kt: 0.0016656195215736366 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:38:24 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 7290001 Best score so far: 35.44431972342052 . Using annealing factor: 1.6406352287500317E-5 kt: 0.0016406352287500318 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:38:26 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Mutating helix constraints!
Oct 19, 2010 2:38:26 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 7300000 Best score so far: 35.44431972342052 . Using annealing factor: 1.6160257003187813E-5 kt: 0.0016160257003187814 coordinate system multipliers: 1.0 1.0 1.0  MUTATING HELIX LENGTHS: 
6 ( 6 ) 6 ( 6 ) 6 ( 6 ) Modified helix constraint lengths: 6 5 7 
Oct 19, 2010 2:38:26 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 7300001 Best score so far: 35.44431972342052 . Using annealing factor: 1.6160257003187813E-5 kt: 0.0016160257003187814 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:38:29 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 7310001 Best score so far: 35.44431972342052 . Using annealing factor: 1.5917853148139995E-5 kt: 0.0015917853148139994 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:38:32 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 7320001 Best score so far: 35.44431972342052 . Using annealing factor: 1.5679085350917896E-5 kt: 0.0015679085350917895 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:38:35 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 7330001 Best score so far: 35.44431972342052 . Using annealing factor: 1.544389907065413E-5 kt: 0.001544389907065413 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:38:38 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 7340001 Best score so far: 35.44431972342052 . Using annealing factor: 1.5212240584594314E-5 kt: 0.0015212240584594314 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:38:41 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Mutating helix constraints!
Oct 19, 2010 2:38:41 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 7350000 Best score so far: 35.44431972342052 . Using annealing factor: 1.49840569758254E-5 kt: 0.00149840569758254 coordinate system multipliers: 1.0 1.0 1.0  MUTATING HELIX LENGTHS: 
6 ( 6 ) 6 ( 6 ) 6 ( 6 ) Modified helix constraint lengths: 6 5 6 
Oct 19, 2010 2:38:41 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 7350001 Best score so far: 35.44431972342052 . Using annealing factor: 1.49840569758254E-5 kt: 0.00149840569758254 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:38:44 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 7360001 Best score so far: 35.44431972342052 . Using annealing factor: 1.475929612118802E-5 kt: 0.001475929612118802 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:38:47 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 7370001 Best score so far: 35.44431972342052 . Using annealing factor: 1.4537906679370199E-5 kt: 0.0014537906679370199 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:38:50 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 7380001 Best score so far: 35.44431972342052 . Using annealing factor: 1.4319838079179646E-5 kt: 0.0014319838079179647 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:38:52 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 7390001 Best score so far: 35.44431972342052 . Using annealing factor: 1.4105040507991951E-5 kt: 0.001410504050799195 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:38:55 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Mutating helix constraints!
Oct 19, 2010 2:38:55 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 7400000 Best score so far: 35.44431972342052 . Using annealing factor: 1.389346490037207E-5 kt: 0.001389346490037207 coordinate system multipliers: 1.0 1.0 1.0  MUTATING HELIX LENGTHS: 
6 ( 6 ) 6 ( 6 ) 6 ( 6 ) Modified helix constraint lengths: 5 5 5 
Oct 19, 2010 2:38:55 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 7400001 Best score so far: 35.44431972342052 . Using annealing factor: 1.389346490037207E-5 kt: 0.001389346490037207 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:38:58 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 7410001 Best score so far: 35.44431972342052 . Using annealing factor: 1.368506292686649E-5 kt: 0.001368506292686649 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:39:01 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 7420001 Best score so far: 35.44431972342052 . Using annealing factor: 1.3479786982963493E-5 kt: 0.0013479786982963492 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:39:04 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 7430001 Best score so far: 35.44431972342052 . Using annealing factor: 1.327759017821904E-5 kt: 0.0013277590178219039 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:39:07 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 7440001 Best score so far: 35.44431972342052 . Using annealing factor: 1.3078426325545754E-5 kt: 0.0013078426325545754 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:39:10 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Mutating helix constraints!
Oct 19, 2010 2:39:10 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 7450000 Best score so far: 35.44431972342052 . Using annealing factor: 1.2882249930662568E-5 kt: 0.0012882249930662568 coordinate system multipliers: 1.0 1.0 1.0  MUTATING HELIX LENGTHS: 
6 ( 6 ) 6 ( 6 ) 6 ( 6 ) Modified helix constraint lengths: 7 7 6 
Oct 19, 2010 2:39:10 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 7450001 Best score so far: 35.44431972342052 . Using annealing factor: 1.2882249930662568E-5 kt: 0.0012882249930662568 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:39:13 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 7460001 Best score so far: 35.44431972342052 . Using annealing factor: 1.2689016181702628E-5 kt: 0.0012689016181702628 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:39:16 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 7470001 Best score so far: 35.44431972342052 . Using annealing factor: 1.249868093897709E-5 kt: 0.001249868093897709 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:39:18 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 7480001 Best score so far: 35.44431972342052 . Using annealing factor: 1.2311200724892433E-5 kt: 0.0012311200724892432 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:39:21 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 7490001 Best score so far: 35.44431972342052 . Using annealing factor: 1.2126532714019046E-5 kt: 0.0012126532714019046 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:39:24 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Mutating helix constraints!
Oct 19, 2010 2:39:24 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 7500000 Best score so far: 35.44431972342052 . Using annealing factor: 1.194463472330876E-5 kt: 0.001194463472330876 coordinate system multipliers: 1.0 1.0 1.0  MUTATING HELIX LENGTHS: 
6 ( 6 ) 6 ( 6 ) 6 ( 6 ) Modified helix constraint lengths: 7 7 5 
Oct 19, 2010 2:39:24 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 7500001 Best score so far: 35.44431972342052 . Using annealing factor: 1.194463472330876E-5 kt: 0.001194463472330876 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:39:27 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 7510001 Best score so far: 35.44431972342052 . Using annealing factor: 1.1765465202459128E-5 kt: 0.0011765465202459129 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:39:30 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 7520001 Best score so far: 35.44431972342052 . Using annealing factor: 1.158898322442224E-5 kt: 0.001158898322442224 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:39:33 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 7530001 Best score so far: 35.44431972342052 . Using annealing factor: 1.1415148476055908E-5 kt: 0.0011415148476055907 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:39:36 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 7540001 Best score so far: 35.44431972342052 . Using annealing factor: 1.1243921248915068E-5 kt: 0.0011243921248915067 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:39:39 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Mutating helix constraints!
Oct 19, 2010 2:39:39 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 7550000 Best score so far: 35.44431972342052 . Using annealing factor: 1.1075262430181344E-5 kt: 0.0011075262430181344 coordinate system multipliers: 1.0 1.0 1.0  MUTATING HELIX LENGTHS: 
6 ( 6 ) 6 ( 6 ) 6 ( 6 ) Modified helix constraint lengths: 6 7 7 
Oct 19, 2010 2:39:39 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 7550001 Best score so far: 35.44431972342052 . Using annealing factor: 1.1075262430181344E-5 kt: 0.0011075262430181344 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:39:42 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 7560001 Best score so far: 35.44431972342052 . Using annealing factor: 1.0909133493728623E-5 kt: 0.0010909133493728622 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:39:44 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 7570001 Best score so far: 35.44431972342052 . Using annealing factor: 1.0745496491322692E-5 kt: 0.0010745496491322692 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:39:47 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 7580001 Best score so far: 35.44431972342052 . Using annealing factor: 1.0584314043952853E-5 kt: 0.0010584314043952854 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:39:50 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 7590001 Best score so far: 35.44431972342052 . Using annealing factor: 1.042554933329356E-5 kt: 0.0010425549333293559 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:39:53 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Mutating helix constraints!
Oct 19, 2010 2:39:53 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 7600000 Best score so far: 35.44431972342052 . Using annealing factor: 1.0269166093294155E-5 kt: 0.0010269166093294156 coordinate system multipliers: 1.0 1.0 1.0  MUTATING HELIX LENGTHS: 
6 ( 6 ) 6 ( 6 ) 6 ( 6 ) Modified helix constraint lengths: 6 5 7 
Oct 19, 2010 2:39:53 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 7600001 Best score so far: 35.44431972342052 . Using annealing factor: 1.0269166093294155E-5 kt: 0.0010269166093294156 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:39:56 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 7610001 Best score so far: 35.44431972342052 . Using annealing factor: 1.0115128601894744E-5 kt: 0.0010115128601894743 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:39:59 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 7620001 Best score so far: 35.44431972342052 . Using annealing factor: 9.963401672866322E-6 kt: 9.96340167286632E-4 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:40:02 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 7630001 Best score so far: 35.44431972342052 . Using annealing factor: 9.813950647773326E-6 kt: 9.813950647773327E-4 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:40:05 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 7640001 Best score so far: 35.44431972342052 . Using annealing factor: 9.666741388056727E-6 kt: 9.666741388056727E-4 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:40:08 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Mutating helix constraints!
Oct 19, 2010 2:40:08 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 7650000 Best score so far: 35.44431972342052 . Using annealing factor: 9.521740267235876E-6 kt: 9.521740267235876E-4 coordinate system multipliers: 1.0 1.0 1.0  MUTATING HELIX LENGTHS: 
6 ( 6 ) 6 ( 6 ) 6 ( 6 ) Modified helix constraint lengths: 7 7 7 
Oct 19, 2010 2:40:08 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 7650001 Best score so far: 35.44431972342052 . Using annealing factor: 9.521740267235876E-6 kt: 9.521740267235876E-4 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:40:10 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 7660001 Best score so far: 35.44431972342052 . Using annealing factor: 9.378914163227338E-6 kt: 9.378914163227337E-4 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:40:13 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 7670001 Best score so far: 35.44431972342052 . Using annealing factor: 9.238230450778928E-6 kt: 9.238230450778929E-4 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:40:16 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 7680001 Best score so far: 35.44431972342052 . Using annealing factor: 9.099656994017243E-6 kt: 9.099656994017242E-4 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:40:19 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 7690001 Best score so far: 35.44431972342052 . Using annealing factor: 8.963162139106984E-6 kt: 8.963162139106985E-4 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:40:22 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Mutating helix constraints!
Oct 19, 2010 2:40:22 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 7700000 Best score so far: 35.44431972342052 . Using annealing factor: 8.82871470702038E-6 kt: 8.82871470702038E-4 coordinate system multipliers: 1.0 1.0 1.0  MUTATING HELIX LENGTHS: 
6 ( 6 ) 6 ( 6 ) 6 ( 6 ) Oct 19, 2010 2:40:22 PM rnadesign.rnamodel.HelixOptimizer mutateHelixLengths
WARNING: No helix lengths were modified!
Oct 19, 2010 2:40:22 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 7700001 Best score so far: 35.44431972342052 . Using annealing factor: 8.82871470702038E-6 kt: 8.82871470702038E-4 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:40:25 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 7710001 Best score so far: 35.44431972342052 . Using annealing factor: 8.696283986415075E-6 kt: 8.696283986415075E-4 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:40:28 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 7720001 Best score so far: 35.44431972342052 . Using annealing factor: 8.565839726618849E-6 kt: 8.565839726618849E-4 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:40:31 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 7730001 Best score so far: 35.44431972342052 . Using annealing factor: 8.437352130719566E-6 kt: 8.437352130719566E-4 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:40:33 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 7740001 Best score so far: 35.44431972342052 . Using annealing factor: 8.310791848758772E-6 kt: 8.310791848758773E-4 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:40:36 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Mutating helix constraints!
Oct 19, 2010 2:40:36 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 7750000 Best score so far: 35.44431972342052 . Using annealing factor: 8.18612997102739E-6 kt: 8.186129971027391E-4 coordinate system multipliers: 1.0 1.0 1.0  MUTATING HELIX LENGTHS: 
6 ( 6 ) 6 ( 6 ) 6 ( 6 ) Oct 19, 2010 2:40:36 PM rnadesign.rnamodel.HelixOptimizer mutateHelixLengths
WARNING: No helix lengths were modified!
Oct 19, 2010 2:40:36 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 7750001 Best score so far: 35.44431972342052 . Using annealing factor: 8.18612997102739E-6 kt: 8.186129971027391E-4 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:40:39 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 7760001 Best score so far: 35.44431972342052 . Using annealing factor: 8.063338021461979E-6 kt: 8.063338021461979E-4 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:40:42 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 7770001 Best score so far: 35.44431972342052 . Using annealing factor: 7.942387951140049E-6 kt: 7.942387951140049E-4 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:40:45 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 7780001 Best score so far: 35.44431972342052 . Using annealing factor: 7.823252131872949E-6 kt: 7.823252131872949E-4 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:40:48 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 7790001 Best score so far: 35.44431972342052 . Using annealing factor: 7.705903349894853E-6 kt: 7.705903349894853E-4 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:40:51 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Mutating helix constraints!
Oct 19, 2010 2:40:51 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 7800000 Best score so far: 35.44431972342052 . Using annealing factor: 7.590314799646431E-6 kt: 7.590314799646431E-4 coordinate system multipliers: 1.0 1.0 1.0  MUTATING HELIX LENGTHS: 
6 ( 6 ) 6 ( 6 ) 6 ( 6 ) Oct 19, 2010 2:40:51 PM rnadesign.rnamodel.HelixOptimizer mutateHelixLengths
WARNING: No helix lengths were modified!
Oct 19, 2010 2:40:51 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 7800001 Best score so far: 35.44431972342052 . Using annealing factor: 7.590314799646431E-6 kt: 7.590314799646431E-4 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:40:54 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 7810001 Best score so far: 35.44431972342052 . Using annealing factor: 7.4764600776517345E-6 kt: 7.476460077651734E-4 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:40:57 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 7820001 Best score so far: 35.44431972342052 . Using annealing factor: 7.364313176486959E-6 kt: 7.364313176486958E-4 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:41:00 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 7830001 Best score so far: 35.44431972342052 . Using annealing factor: 7.253848478839654E-6 kt: 7.253848478839654E-4 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:41:02 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 7840001 Best score so far: 35.44431972342052 . Using annealing factor: 7.145040751657059E-6 kt: 7.145040751657059E-4 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:41:05 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Mutating helix constraints!
Oct 19, 2010 2:41:05 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 7850000 Best score so far: 35.44431972342052 . Using annealing factor: 7.037865140382203E-6 kt: 7.037865140382203E-4 coordinate system multipliers: 1.0 1.0 1.0  MUTATING HELIX LENGTHS: 
6 ( 6 ) 6 ( 6 ) 6 ( 6 ) Modified helix constraint lengths: 5 7 5 
Oct 19, 2010 2:41:05 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 7850001 Best score so far: 35.44431972342052 . Using annealing factor: 7.037865140382203E-6 kt: 7.037865140382203E-4 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:41:08 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 7860001 Best score so far: 35.44431972342052 . Using annealing factor: 6.9322971632764695E-6 kt: 6.93229716327647E-4 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:41:11 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 7870001 Best score so far: 35.44431972342052 . Using annealing factor: 6.828312705827323E-6 kt: 6.828312705827323E-4 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:41:14 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 7880001 Best score so far: 35.44431972342052 . Using annealing factor: 6.7258880152399124E-6 kt: 6.725888015239913E-4 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:41:17 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 7890001 Best score so far: 35.44431972342052 . Using annealing factor: 6.624999695011314E-6 kt: 6.624999695011314E-4 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:41:20 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Mutating helix constraints!
Oct 19, 2010 2:41:20 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 7900000 Best score so far: 35.44431972342052 . Using annealing factor: 6.525624699586144E-6 kt: 6.525624699586144E-4 coordinate system multipliers: 1.0 1.0 1.0  MUTATING HELIX LENGTHS: 
6 ( 6 ) 6 ( 6 ) 6 ( 6 ) Modified helix constraint lengths: 5 5 6 
Oct 19, 2010 2:41:20 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 7900001 Best score so far: 35.44431972342052 . Using annealing factor: 6.525624699586144E-6 kt: 6.525624699586144E-4 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:41:23 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 7910001 Best score so far: 35.44431972342052 . Using annealing factor: 6.4277403290923515E-6 kt: 6.427740329092352E-4 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:41:26 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 7920001 Best score so far: 35.44431972342052 . Using annealing factor: 6.331324224155966E-6 kt: 6.331324224155967E-4 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:41:28 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 7930001 Best score so far: 35.44431972342052 . Using annealing factor: 6.236354360793627E-6 kt: 6.236354360793627E-4 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:41:31 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 7940001 Best score so far: 35.44431972342052 . Using annealing factor: 6.1428090453817226E-6 kt: 6.142809045381723E-4 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:41:34 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Mutating helix constraints!
Oct 19, 2010 2:41:34 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 7950000 Best score so far: 35.44431972342052 . Using annealing factor: 6.0506669097009965E-6 kt: 6.050666909700996E-4 coordinate system multipliers: 1.0 1.0 1.0  MUTATING HELIX LENGTHS: 
6 ( 6 ) 6 ( 6 ) 6 ( 6 ) Modified helix constraint lengths: 5 5 6 
Oct 19, 2010 2:41:34 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 7950001 Best score so far: 35.44431972342052 . Using annealing factor: 6.0506669097009965E-6 kt: 6.050666909700996E-4 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:41:37 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 7960001 Best score so far: 35.44431972342052 . Using annealing factor: 5.959906906055482E-6 kt: 5.959906906055482E-4 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:41:40 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 7970001 Best score so far: 35.44431972342052 . Using annealing factor: 5.870508302464649E-6 kt: 5.870508302464649E-4 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:41:43 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 7980001 Best score so far: 35.44431972342052 . Using annealing factor: 5.78245067792768E-6 kt: 5.782450677927679E-4 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:41:46 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 7990001 Best score so far: 35.44431972342052 . Using annealing factor: 5.695713917758764E-6 kt: 5.695713917758764E-4 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:41:49 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Mutating helix constraints!
Oct 19, 2010 2:41:49 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 8000000 Best score so far: 35.44431972342052 . Using annealing factor: 5.610278208992382E-6 kt: 5.610278208992382E-4 coordinate system multipliers: 1.0 1.0 1.0  MUTATING HELIX LENGTHS: 
6 ( 6 ) 6 ( 6 ) 6 ( 6 ) Modified helix constraint lengths: 7 7 5 
Oct 19, 2010 2:41:49 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 8000001 Best score so far: 35.44431972342052 . Using annealing factor: 5.610278208992382E-6 kt: 5.610278208992382E-4 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:41:52 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 8010001 Best score so far: 35.44431972342052 . Using annealing factor: 5.526124035857497E-6 kt: 5.526124035857496E-4 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:41:55 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 8020001 Best score so far: 35.44431972342052 . Using annealing factor: 5.443232175319635E-6 kt: 5.443232175319635E-4 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:41:57 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 8030001 Best score so far: 35.44431972342052 . Using annealing factor: 5.36158369268984E-6 kt: 5.36158369268984E-4 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:42:00 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 8040001 Best score so far: 35.44431972342052 . Using annealing factor: 5.281159937299492E-6 kt: 5.281159937299492E-4 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:42:03 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Mutating helix constraints!
Oct 19, 2010 2:42:03 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 8050000 Best score so far: 35.44431972342052 . Using annealing factor: 5.20194253824E-6 kt: 5.20194253824E-4 coordinate system multipliers: 1.0 1.0 1.0  MUTATING HELIX LENGTHS: 
6 ( 6 ) 6 ( 6 ) 6 ( 6 ) Modified helix constraint lengths: 6 5 6 
Oct 19, 2010 2:42:03 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 8050001 Best score so far: 35.44431972342052 . Using annealing factor: 5.20194253824E-6 kt: 5.20194253824E-4 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:42:06 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 8060001 Best score so far: 35.44431972342052 . Using annealing factor: 5.123913400166399E-6 kt: 5.123913400166399E-4 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:42:09 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 8070001 Best score so far: 35.44431972342052 . Using annealing factor: 5.047054699163904E-6 kt: 5.047054699163903E-4 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:42:12 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 8080001 Best score so far: 35.44431972342052 . Using annealing factor: 4.971348878676445E-6 kt: 4.971348878676445E-4 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:42:15 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 8090001 Best score so far: 35.44431972342052 . Using annealing factor: 4.896778645496298E-6 kt: 4.896778645496298E-4 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:42:17 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Mutating helix constraints!
Oct 19, 2010 2:42:17 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 8100000 Best score so far: 35.44431972342052 . Using annealing factor: 4.823326965813853E-6 kt: 4.823326965813853E-4 coordinate system multipliers: 1.0 1.0 1.0  MUTATING HELIX LENGTHS: 
6 ( 6 ) 6 ( 6 ) 6 ( 6 ) Modified helix constraint lengths: 6 6 7 
Oct 19, 2010 2:42:17 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 8100001 Best score so far: 35.44431972342052 . Using annealing factor: 4.823326965813853E-6 kt: 4.823326965813853E-4 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:42:20 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 8110001 Best score so far: 35.44431972342052 . Using annealing factor: 4.750977061326646E-6 kt: 4.750977061326646E-4 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:42:23 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 8120001 Best score so far: 35.44431972342052 . Using annealing factor: 4.679712405406746E-6 kt: 4.6797124054067464E-4 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:42:26 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 8130001 Best score so far: 35.44431972342052 . Using annealing factor: 4.609516719325645E-6 kt: 4.609516719325645E-4 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:42:29 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 8140001 Best score so far: 35.44431972342052 . Using annealing factor: 4.54037396853576E-6 kt: 4.5403739685357606E-4 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:42:32 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Mutating helix constraints!
Oct 19, 2010 2:42:32 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 8150000 Best score so far: 35.44431972342052 . Using annealing factor: 4.472268359007724E-6 kt: 4.472268359007724E-4 coordinate system multipliers: 1.0 1.0 1.0  MUTATING HELIX LENGTHS: 
6 ( 6 ) 6 ( 6 ) 6 ( 6 ) Modified helix constraint lengths: 7 6 6 
Oct 19, 2010 2:42:32 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 8150001 Best score so far: 35.44431972342052 . Using annealing factor: 4.472268359007724E-6 kt: 4.472268359007724E-4 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:42:35 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 8160001 Best score so far: 35.44431972342052 . Using annealing factor: 4.405184333622608E-6 kt: 4.405184333622608E-4 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:42:38 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 8170001 Best score so far: 35.44431972342052 . Using annealing factor: 4.339106568618269E-6 kt: 4.3391065686182684E-4 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:42:40 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 8180001 Best score so far: 35.44431972342052 . Using annealing factor: 4.274019970088995E-6 kt: 4.274019970088995E-4 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:42:43 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 8190001 Best score so far: 35.44431972342052 . Using annealing factor: 4.209909670537659E-6 kt: 4.209909670537659E-4 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:42:46 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Mutating helix constraints!
Oct 19, 2010 2:42:46 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 8200000 Best score so far: 35.44431972342052 . Using annealing factor: 4.1467610254795945E-6 kt: 4.1467610254795943E-4 coordinate system multipliers: 1.0 1.0 1.0  MUTATING HELIX LENGTHS: 
6 ( 6 ) 6 ( 6 ) 6 ( 6 ) Oct 19, 2010 2:42:46 PM rnadesign.rnamodel.HelixOptimizer mutateHelixLengths
WARNING: No helix lengths were modified!
Oct 19, 2010 2:42:46 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 8200001 Best score so far: 35.44431972342052 . Using annealing factor: 4.1467610254795945E-6 kt: 4.1467610254795943E-4 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:42:49 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 8210001 Best score so far: 35.44431972342052 . Using annealing factor: 4.084559610097401E-6 kt: 4.0845596100974005E-4 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:42:52 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 8220001 Best score so far: 35.44431972342052 . Using annealing factor: 4.023291215945939E-6 kt: 4.023291215945939E-4 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:42:55 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 8230001 Best score so far: 35.44431972342052 . Using annealing factor: 3.96294184770675E-6 kt: 3.9629418477067505E-4 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:42:58 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 8240001 Best score so far: 35.44431972342052 . Using annealing factor: 3.903497719991149E-6 kt: 3.903497719991149E-4 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:43:01 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Mutating helix constraints!
Oct 19, 2010 2:43:01 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 8250000 Best score so far: 35.44431972342052 . Using annealing factor: 3.8449452541912815E-6 kt: 3.8449452541912816E-4 coordinate system multipliers: 1.0 1.0 1.0  MUTATING HELIX LENGTHS: 
6 ( 6 ) 6 ( 6 ) 6 ( 6 ) Modified helix constraint lengths: 6 7 6 
Oct 19, 2010 2:43:01 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 8250001 Best score so far: 35.44431972342052 . Using annealing factor: 3.8449452541912815E-6 kt: 3.8449452541912816E-4 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:43:04 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 8260001 Best score so far: 35.44431972342052 . Using annealing factor: 3.7872710753784123E-6 kt: 3.7872710753784124E-4 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:43:06 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 8270001 Best score so far: 35.44431972342052 . Using annealing factor: 3.7304620092477362E-6 kt: 3.730462009247736E-4 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:43:09 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 8280001 Best score so far: 35.44431972342052 . Using annealing factor: 3.67450507910902E-6 kt: 3.67450507910902E-4 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:43:12 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 8290001 Best score so far: 35.44431972342052 . Using annealing factor: 3.619387502922385E-6 kt: 3.6193875029223846E-4 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:43:15 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Mutating helix constraints!
Oct 19, 2010 2:43:15 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 8300000 Best score so far: 35.44431972342052 . Using annealing factor: 3.565096690378549E-6 kt: 3.5650966903785487E-4 coordinate system multipliers: 1.0 1.0 1.0  MUTATING HELIX LENGTHS: 
6 ( 6 ) 6 ( 6 ) 6 ( 6 ) Modified helix constraint lengths: 6 5 7 
Oct 19, 2010 2:43:15 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 8300001 Best score so far: 35.44431972342052 . Using annealing factor: 3.565096690378549E-6 kt: 3.5650966903785487E-4 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:43:18 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 8310001 Best score so far: 35.44431972342052 . Using annealing factor: 3.5116202400228704E-6 kt: 3.5116202400228705E-4 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:43:21 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 8320001 Best score so far: 35.44431972342052 . Using annealing factor: 3.4589459364225274E-6 kt: 3.458945936422527E-4 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:43:24 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 8330001 Best score so far: 35.44431972342052 . Using annealing factor: 3.4070617473761896E-6 kt: 3.4070617473761893E-4 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:43:27 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 8340001 Best score so far: 35.44431972342052 . Using annealing factor: 3.3559558211655465E-6 kt: 3.3559558211655467E-4 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:43:30 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Mutating helix constraints!
Oct 19, 2010 2:43:30 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 8350000 Best score so far: 35.44431972342052 . Using annealing factor: 3.3056164838480633E-6 kt: 3.3056164838480634E-4 coordinate system multipliers: 1.0 1.0 1.0  MUTATING HELIX LENGTHS: 
6 ( 6 ) 6 ( 6 ) 6 ( 6 ) Modified helix constraint lengths: 5 6 5 
Oct 19, 2010 2:43:30 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 8350001 Best score so far: 35.44431972342052 . Using annealing factor: 3.3056164838480633E-6 kt: 3.3056164838480634E-4 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:43:32 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 8360001 Best score so far: 35.44431972342052 . Using annealing factor: 3.2560322365903424E-6 kt: 3.2560322365903427E-4 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:43:35 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 8370001 Best score so far: 35.44431972342052 . Using annealing factor: 3.2071917530414873E-6 kt: 3.207191753041487E-4 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:43:38 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 8380001 Best score so far: 35.44431972342052 . Using annealing factor: 3.159083876745865E-6 kt: 3.159083876745865E-4 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:43:41 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 8390001 Best score so far: 35.44431972342052 . Using annealing factor: 3.111697618594677E-6 kt: 3.111697618594677E-4 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:43:44 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Mutating helix constraints!
Oct 19, 2010 2:43:44 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 8400000 Best score so far: 35.44431972342052 . Using annealing factor: 3.065022154315757E-6 kt: 3.065022154315757E-4 coordinate system multipliers: 1.0 1.0 1.0  MUTATING HELIX LENGTHS: 
6 ( 6 ) 6 ( 6 ) 6 ( 6 ) Modified helix constraint lengths: 5 5 6 
Oct 19, 2010 2:43:44 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 8400001 Best score so far: 35.44431972342052 . Using annealing factor: 3.065022154315757E-6 kt: 3.065022154315757E-4 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:43:47 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 8410001 Best score so far: 35.44431972342052 . Using annealing factor: 3.0190468220010203E-6 kt: 3.0190468220010205E-4 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:43:50 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 8420001 Best score so far: 35.44431972342052 . Using annealing factor: 2.973761119671005E-6 kt: 2.973761119671005E-4 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:43:52 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 8430001 Best score so far: 35.44431972342052 . Using annealing factor: 2.9291547028759397E-6 kt: 2.9291547028759395E-4 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:43:55 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 8440001 Best score so far: 35.44431972342052 . Using annealing factor: 2.8852173823328006E-6 kt: 2.885217382332801E-4 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:43:58 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Mutating helix constraints!
Oct 19, 2010 2:43:58 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 8450000 Best score so far: 35.44431972342052 . Using annealing factor: 2.8419391215978085E-6 kt: 2.8419391215978084E-4 coordinate system multipliers: 1.0 1.0 1.0  MUTATING HELIX LENGTHS: 
6 ( 6 ) 6 ( 6 ) 6 ( 6 ) Modified helix constraint lengths: 7 6 6 
Oct 19, 2010 2:43:58 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 8450001 Best score so far: 35.44431972342052 . Using annealing factor: 2.8419391215978085E-6 kt: 2.8419391215978084E-4 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:44:01 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 8460001 Best score so far: 35.44431972342052 . Using annealing factor: 2.7993100347738415E-6 kt: 2.7993100347738415E-4 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:44:04 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 8470001 Best score so far: 35.44431972342052 . Using annealing factor: 2.757320384252234E-6 kt: 2.757320384252234E-4 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:44:07 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 8480001 Best score so far: 35.44431972342052 . Using annealing factor: 2.7159605784884503E-6 kt: 2.7159605784884505E-4 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:44:10 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 8490001 Best score so far: 35.44431972342052 . Using annealing factor: 2.6752211698111233E-6 kt: 2.675221169811123E-4 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:44:13 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Mutating helix constraints!
Oct 19, 2010 2:44:13 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 8500000 Best score so far: 35.44431972342052 . Using annealing factor: 2.6350928522639565E-6 kt: 2.6350928522639566E-4 coordinate system multipliers: 1.0 1.0 1.0  MUTATING HELIX LENGTHS: 
6 ( 6 ) 6 ( 6 ) 6 ( 6 ) Modified helix constraint lengths: 5 7 7 
Oct 19, 2010 2:44:13 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 8500001 Best score so far: 35.44431972342052 . Using annealing factor: 2.6350928522639565E-6 kt: 2.6350928522639566E-4 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:44:16 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 8510001 Best score so far: 35.44431972342052 . Using annealing factor: 2.5955664594799972E-6 kt: 2.595566459479997E-4 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:44:19 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 8520001 Best score so far: 35.44431972342052 . Using annealing factor: 2.556632962587797E-6 kt: 2.556632962587797E-4 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:44:21 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 8530001 Best score so far: 35.44431972342052 . Using annealing factor: 2.5182834681489802E-6 kt: 2.5182834681489804E-4 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:44:24 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 8540001 Best score so far: 35.44431972342052 . Using annealing factor: 2.4805092161267455E-6 kt: 2.4805092161267456E-4 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:44:27 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Mutating helix constraints!
Oct 19, 2010 2:44:27 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 8550000 Best score so far: 35.44431972342052 . Using annealing factor: 2.443301577884844E-6 kt: 2.4433015778848444E-4 coordinate system multipliers: 1.0 1.0 1.0  MUTATING HELIX LENGTHS: 
6 ( 6 ) 6 ( 6 ) 6 ( 6 ) Oct 19, 2010 2:44:27 PM rnadesign.rnamodel.HelixOptimizer mutateHelixLengths
WARNING: No helix lengths were modified!
Oct 19, 2010 2:44:27 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 8550001 Best score so far: 35.44431972342052 . Using annealing factor: 2.443301577884844E-6 kt: 2.4433015778848444E-4 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:44:30 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 8560001 Best score so far: 35.44431972342052 . Using annealing factor: 2.4066520542165716E-6 kt: 2.4066520542165716E-4 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:44:33 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 8570001 Best score so far: 35.44431972342052 . Using annealing factor: 2.370552273403323E-6 kt: 2.370552273403323E-4 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:44:36 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 8580001 Best score so far: 35.44431972342052 . Using annealing factor: 2.3349939893022732E-6 kt: 2.3349939893022733E-4 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:44:39 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 8590001 Best score so far: 35.44431972342052 . Using annealing factor: 2.299969079462739E-6 kt: 2.2999690794627388E-4 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:44:42 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Mutating helix constraints!
Oct 19, 2010 2:44:42 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 8600000 Best score so far: 35.44431972342052 . Using annealing factor: 2.265469543270798E-6 kt: 2.265469543270798E-4 coordinate system multipliers: 1.0 1.0 1.0  MUTATING HELIX LENGTHS: 
6 ( 6 ) 6 ( 6 ) 6 ( 6 ) Modified helix constraint lengths: 6 6 7 
Oct 19, 2010 2:44:42 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 8600001 Best score so far: 35.44431972342052 . Using annealing factor: 2.265469543270798E-6 kt: 2.265469543270798E-4 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:44:45 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 8610001 Best score so far: 35.44431972342052 . Using annealing factor: 2.2314875001217357E-6 kt: 2.2314875001217357E-4 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:44:48 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 8620001 Best score so far: 35.44431972342052 . Using annealing factor: 2.1980151876199096E-6 kt: 2.1980151876199096E-4 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:44:50 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 8630001 Best score so far: 35.44431972342052 . Using annealing factor: 2.165044959805611E-6 kt: 2.165044959805611E-4 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:44:53 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 8640001 Best score so far: 35.44431972342052 . Using annealing factor: 2.132569285408527E-6 kt: 2.132569285408527E-4 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:44:56 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Mutating helix constraints!
Oct 19, 2010 2:44:56 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 8650000 Best score so far: 35.44431972342052 . Using annealing factor: 2.100580746127399E-6 kt: 2.100580746127399E-4 coordinate system multipliers: 1.0 1.0 1.0  MUTATING HELIX LENGTHS: 
6 ( 6 ) 6 ( 6 ) 6 ( 6 ) Modified helix constraint lengths: 6 6 7 
Oct 19, 2010 2:44:56 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 8650001 Best score so far: 35.44431972342052 . Using annealing factor: 2.100580746127399E-6 kt: 2.100580746127399E-4 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:44:59 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 8660001 Best score so far: 35.44431972342052 . Using annealing factor: 2.069072034935488E-6 kt: 2.069072034935488E-4 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:45:02 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 8670001 Best score so far: 35.44431972342052 . Using annealing factor: 2.0380359544114556E-6 kt: 2.0380359544114557E-4 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:45:05 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 8680001 Best score so far: 35.44431972342052 . Using annealing factor: 2.007465415095284E-6 kt: 2.0074654150952837E-4 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:45:08 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 8690001 Best score so far: 35.44431972342052 . Using annealing factor: 1.9773534338688545E-6 kt: 1.9773534338688546E-4 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:45:11 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Mutating helix constraints!
Oct 19, 2010 2:45:11 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 8700000 Best score so far: 35.44431972342052 . Using annealing factor: 1.9476931323608217E-6 kt: 1.9476931323608216E-4 coordinate system multipliers: 1.0 1.0 1.0  MUTATING HELIX LENGTHS: 
6 ( 6 ) 6 ( 6 ) 6 ( 6 ) Modified helix constraint lengths: 5 7 6 
Oct 19, 2010 2:45:11 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 8700001 Best score so far: 35.44431972342052 . Using annealing factor: 1.9476931323608217E-6 kt: 1.9476931323608216E-4 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:45:14 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 8710001 Best score so far: 35.44431972342052 . Using annealing factor: 1.9184777353754094E-6 kt: 1.9184777353754094E-4 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:45:17 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 8720001 Best score so far: 35.44431972342052 . Using annealing factor: 1.8897005693447781E-6 kt: 1.889700569344778E-4 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:45:19 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 8730001 Best score so far: 35.44431972342052 . Using annealing factor: 1.8613550608046065E-6 kt: 1.8613550608046064E-4 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:45:22 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 8740001 Best score so far: 35.44431972342052 . Using annealing factor: 1.8334347348925374E-6 kt: 1.8334347348925373E-4 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:45:25 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Mutating helix constraints!
Oct 19, 2010 2:45:25 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 8750000 Best score so far: 35.44431972342052 . Using annealing factor: 1.8059332138691492E-6 kt: 1.8059332138691494E-4 coordinate system multipliers: 1.0 1.0 1.0  MUTATING HELIX LENGTHS: 
6 ( 6 ) 6 ( 6 ) 6 ( 6 ) Modified helix constraint lengths: 7 7 5 
Oct 19, 2010 2:45:25 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 8750001 Best score so far: 35.44431972342052 . Using annealing factor: 1.8059332138691492E-6 kt: 1.8059332138691494E-4 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:45:28 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 8760001 Best score so far: 35.44431972342052 . Using annealing factor: 1.778844215661112E-6 kt: 1.778844215661112E-4 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:45:31 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 8770001 Best score so far: 35.44431972342052 . Using annealing factor: 1.7521615524261952E-6 kt: 1.7521615524261952E-4 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:45:34 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 8780001 Best score so far: 35.44431972342052 . Using annealing factor: 1.7258791291398022E-6 kt: 1.7258791291398023E-4 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:45:37 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 8790001 Best score so far: 35.44431972342052 . Using annealing factor: 1.6999909422027054E-6 kt: 1.6999909422027053E-4 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:45:39 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Mutating helix constraints!
Oct 19, 2010 2:45:39 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 8800000 Best score so far: 35.44431972342052 . Using annealing factor: 1.6744910780696647E-6 kt: 1.6744910780696647E-4 coordinate system multipliers: 1.0 1.0 1.0  MUTATING HELIX LENGTHS: 
6 ( 6 ) 6 ( 6 ) 6 ( 6 ) Modified helix constraint lengths: 6 5 7 
Oct 19, 2010 2:45:39 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 8800001 Best score so far: 35.44431972342052 . Using annealing factor: 1.6744910780696647E-6 kt: 1.6744910780696647E-4 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:45:42 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 8810001 Best score so far: 35.44431972342052 . Using annealing factor: 1.6493737118986197E-6 kt: 1.6493737118986198E-4 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:45:45 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 8820001 Best score so far: 35.44431972342052 . Using annealing factor: 1.6246331062201404E-6 kt: 1.6246331062201404E-4 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:45:48 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 8830001 Best score so far: 35.44431972342052 . Using annealing factor: 1.6002636096268382E-6 kt: 1.6002636096268383E-4 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:45:51 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 8840001 Best score so far: 35.44431972342052 . Using annealing factor: 1.5762596554824356E-6 kt: 1.5762596554824357E-4 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:45:54 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Mutating helix constraints!
Oct 19, 2010 2:45:54 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 8850000 Best score so far: 35.44431972342052 . Using annealing factor: 1.552615760650199E-6 kt: 1.552615760650199E-4 coordinate system multipliers: 1.0 1.0 1.0  MUTATING HELIX LENGTHS: 
6 ( 6 ) 6 ( 6 ) 6 ( 6 ) Modified helix constraint lengths: 5 5 6 
Oct 19, 2010 2:45:54 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 8850001 Best score so far: 35.44431972342052 . Using annealing factor: 1.552615760650199E-6 kt: 1.552615760650199E-4 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:45:57 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 8860001 Best score so far: 35.44431972342052 . Using annealing factor: 1.529326524240446E-6 kt: 1.529326524240446E-4 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:46:00 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 8870001 Best score so far: 35.44431972342052 . Using annealing factor: 1.5063866263768393E-6 kt: 1.5063866263768393E-4 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:46:03 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 8880001 Best score so far: 35.44431972342052 . Using annealing factor: 1.4837908269811867E-6 kt: 1.4837908269811867E-4 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:46:06 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 8890001 Best score so far: 35.44431972342052 . Using annealing factor: 1.4615339645764689E-6 kt: 1.461533964576469E-4 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:46:08 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Mutating helix constraints!
Oct 19, 2010 2:46:08 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 8900000 Best score so far: 35.44431972342052 . Using annealing factor: 1.439610955107822E-6 kt: 1.4396109551078218E-4 coordinate system multipliers: 1.0 1.0 1.0  MUTATING HELIX LENGTHS: 
6 ( 6 ) 6 ( 6 ) 6 ( 6 ) Modified helix constraint lengths: 7 7 6 
Oct 19, 2010 2:46:08 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 8900001 Best score so far: 35.44431972342052 . Using annealing factor: 1.439610955107822E-6 kt: 1.4396109551078218E-4 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:46:11 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 8910001 Best score so far: 35.44431972342052 . Using annealing factor: 1.4180167907812044E-6 kt: 1.4180167907812044E-4 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:46:14 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 8920001 Best score so far: 35.44431972342052 . Using annealing factor: 1.3967465389194864E-6 kt: 1.3967465389194865E-4 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:46:17 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 8930001 Best score so far: 35.44431972342052 . Using annealing factor: 1.3757953408356942E-6 kt: 1.3757953408356942E-4 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:46:20 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 8940001 Best score so far: 35.44431972342052 . Using annealing factor: 1.3551584107231587E-6 kt: 1.3551584107231586E-4 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:46:23 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Mutating helix constraints!
Oct 19, 2010 2:46:23 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 8950000 Best score so far: 35.44431972342052 . Using annealing factor: 1.3348310345623113E-6 kt: 1.3348310345623113E-4 coordinate system multipliers: 1.0 1.0 1.0  MUTATING HELIX LENGTHS: 
6 ( 6 ) 6 ( 6 ) 6 ( 6 ) Modified helix constraint lengths: 6 6 7 
Oct 19, 2010 2:46:23 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 8950001 Best score so far: 35.44431972342052 . Using annealing factor: 1.3348310345623113E-6 kt: 1.3348310345623113E-4 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:46:26 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 8960001 Best score so far: 35.44431972342052 . Using annealing factor: 1.3148085690438765E-6 kt: 1.3148085690438765E-4 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:46:29 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 8970001 Best score so far: 35.44431972342052 . Using annealing factor: 1.2950864405082185E-6 kt: 1.2950864405082186E-4 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:46:32 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 8980001 Best score so far: 35.44431972342052 . Using annealing factor: 1.2756601439005951E-6 kt: 1.275660143900595E-4 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:46:34 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 8990001 Best score so far: 35.44431972342052 . Using annealing factor: 1.2565252417420861E-6 kt: 1.2565252417420862E-4 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:46:37 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Mutating helix constraints!
Oct 19, 2010 2:46:37 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 9000000 Best score so far: 35.44431972342052 . Using annealing factor: 1.2376773631159548E-6 kt: 1.2376773631159549E-4 coordinate system multipliers: 1.0 1.0 1.0  MUTATING HELIX LENGTHS: 
6 ( 6 ) 6 ( 6 ) 6 ( 6 ) Modified helix constraint lengths: 6 6 5 
Oct 19, 2010 2:46:37 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 9000001 Best score so far: 35.44431972342052 . Using annealing factor: 1.2376773631159548E-6 kt: 1.2376773631159549E-4 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:46:40 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 9010001 Best score so far: 35.44431972342052 . Using annealing factor: 1.2191122026692156E-6 kt: 1.2191122026692157E-4 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:46:43 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 9020001 Best score so far: 35.44431972342052 . Using annealing factor: 1.2008255196291773E-6 kt: 1.2008255196291773E-4 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:46:46 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 9030001 Best score so far: 35.44431972342052 . Using annealing factor: 1.1828131368347397E-6 kt: 1.1828131368347397E-4 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:46:49 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 9040001 Best score so far: 35.44431972342052 . Using annealing factor: 1.1650709397822184E-6 kt: 1.1650709397822184E-4 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:46:52 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Mutating helix constraints!
Oct 19, 2010 2:46:52 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 9050000 Best score so far: 35.44431972342052 . Using annealing factor: 1.147594875685485E-6 kt: 1.1475948756854851E-4 coordinate system multipliers: 1.0 1.0 1.0  MUTATING HELIX LENGTHS: 
6 ( 6 ) 6 ( 6 ) 6 ( 6 ) Modified helix constraint lengths: 5 5 6 
Oct 19, 2010 2:46:52 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 9050001 Best score so far: 35.44431972342052 . Using annealing factor: 1.147594875685485E-6 kt: 1.1475948756854851E-4 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:46:55 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 9060001 Best score so far: 35.44431972342052 . Using annealing factor: 1.130380952550203E-6 kt: 1.1303809525502029E-4 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:46:58 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 9070001 Best score so far: 35.44431972342052 . Using annealing factor: 1.1134252382619499E-6 kt: 1.1134252382619499E-4 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:47:00 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 9080001 Best score so far: 35.44431972342052 . Using annealing factor: 1.0967238596880206E-6 kt: 1.0967238596880206E-4 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:47:03 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 9090001 Best score so far: 35.44431972342052 . Using annealing factor: 1.0802730017927003E-6 kt: 1.0802730017927003E-4 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:47:06 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Mutating helix constraints!
Oct 19, 2010 2:47:06 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 9100000 Best score so far: 35.44431972342052 . Using annealing factor: 1.0640689067658097E-6 kt: 1.0640689067658096E-4 coordinate system multipliers: 1.0 1.0 1.0  MUTATING HELIX LENGTHS: 
6 ( 6 ) 6 ( 6 ) 6 ( 6 ) Modified helix constraint lengths: 5 6 5 
Oct 19, 2010 2:47:06 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 9100001 Best score so far: 35.44431972342052 . Using annealing factor: 1.0640689067658097E-6 kt: 1.0640689067658096E-4 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:47:09 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 9110001 Best score so far: 35.44431972342052 . Using annealing factor: 1.0481078731643225E-6 kt: 1.0481078731643226E-4 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:47:12 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 9120001 Best score so far: 35.44431972342052 . Using annealing factor: 1.0323862550668576E-6 kt: 1.0323862550668577E-4 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:47:15 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 9130001 Best score so far: 35.44431972342052 . Using annealing factor: 1.016900461240855E-6 kt: 1.0169004612408549E-4 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:47:18 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 9140001 Best score so far: 35.44431972342052 . Using annealing factor: 1.001646954322242E-6 kt: 1.001646954322242E-4 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:47:21 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Mutating helix constraints!
Oct 19, 2010 2:47:21 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 9150000 Best score so far: 35.44431972342052 . Using annealing factor: 9.866222500074084E-7 kt: 9.866222500074084E-5 coordinate system multipliers: 1.0 1.0 1.0  MUTATING HELIX LENGTHS: 
6 ( 6 ) 6 ( 6 ) 6 ( 6 ) Modified helix constraint lengths: 5 5 6 
Oct 19, 2010 2:47:21 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 9150001 Best score so far: 35.44431972342052 . Using annealing factor: 9.866222500074084E-7 kt: 9.866222500074084E-5 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:47:24 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 9160001 Best score so far: 35.44431972342052 . Using annealing factor: 9.718229162572973E-7 kt: 9.718229162572973E-5 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:47:26 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 9170001 Best score so far: 35.44431972342052 . Using annealing factor: 9.572455725134378E-7 kt: 9.572455725134378E-5 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:47:29 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 9180001 Best score so far: 35.44431972342052 . Using annealing factor: 9.428868889257362E-7 kt: 9.428868889257362E-5 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:47:32 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 9190001 Best score so far: 35.44431972342052 . Using annealing factor: 9.287435855918501E-7 kt: 9.287435855918501E-5 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:47:35 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Mutating helix constraints!
Oct 19, 2010 2:47:35 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 9200000 Best score so far: 35.44431972342052 . Using annealing factor: 9.148124318079723E-7 kt: 9.148124318079724E-5 coordinate system multipliers: 1.0 1.0 1.0  MUTATING HELIX LENGTHS: 
6 ( 6 ) 6 ( 6 ) 6 ( 6 ) Oct 19, 2010 2:47:35 PM rnadesign.rnamodel.HelixOptimizer mutateHelixLengths
WARNING: No helix lengths were modified!
Oct 19, 2010 2:47:35 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 9200001 Best score so far: 35.44431972342052 . Using annealing factor: 9.148124318079723E-7 kt: 9.148124318079724E-5 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:47:38 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 9210001 Best score so far: 35.44431972342052 . Using annealing factor: 9.010902453308528E-7 kt: 9.010902453308528E-5 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:47:41 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 9220001 Best score so far: 35.44431972342052 . Using annealing factor: 8.8757389165089E-7 kt: 8.8757389165089E-5 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:47:44 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 9230001 Best score so far: 35.44431972342052 . Using annealing factor: 8.742602832761266E-7 kt: 8.742602832761266E-5 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:47:47 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 9240001 Best score so far: 35.44431972342052 . Using annealing factor: 8.611463790269847E-7 kt: 8.611463790269847E-5 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:47:50 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Mutating helix constraints!
Oct 19, 2010 2:47:50 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 9250000 Best score so far: 35.44431972342052 . Using annealing factor: 8.482291833415799E-7 kt: 8.482291833415798E-5 coordinate system multipliers: 1.0 1.0 1.0  MUTATING HELIX LENGTHS: 
6 ( 6 ) 6 ( 6 ) 6 ( 6 ) Modified helix constraint lengths: 5 6 6 
Oct 19, 2010 2:47:50 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 9250001 Best score so far: 35.44431972342052 . Using annealing factor: 8.482291833415799E-7 kt: 8.482291833415798E-5 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:47:52 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 9260001 Best score so far: 35.44431972342052 . Using annealing factor: 8.355057455914562E-7 kt: 8.355057455914562E-5 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:47:55 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 9270001 Best score so far: 35.44431972342052 . Using annealing factor: 8.229731594075844E-7 kt: 8.229731594075843E-5 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:47:58 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 9280001 Best score so far: 35.44431972342052 . Using annealing factor: 8.106285620164705E-7 kt: 8.106285620164705E-5 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:48:01 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 9290001 Best score so far: 35.44431972342052 . Using annealing factor: 7.984691335862235E-7 kt: 7.984691335862234E-5 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:48:04 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Mutating helix constraints!
Oct 19, 2010 2:48:04 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 9300000 Best score so far: 35.44431972342052 . Using annealing factor: 7.864920965824302E-7 kt: 7.864920965824302E-5 coordinate system multipliers: 1.0 1.0 1.0  MUTATING HELIX LENGTHS: 
6 ( 6 ) 6 ( 6 ) 6 ( 6 ) Modified helix constraint lengths: 5 7 5 
Oct 19, 2010 2:48:04 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 9300001 Best score so far: 35.44431972342052 . Using annealing factor: 7.864920965824302E-7 kt: 7.864920965824302E-5 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:48:07 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 9310001 Best score so far: 35.44431972342052 . Using annealing factor: 7.746947151336937E-7 kt: 7.746947151336938E-5 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:48:10 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 9320001 Best score so far: 35.44431972342052 . Using annealing factor: 7.630742944066882E-7 kt: 7.630742944066883E-5 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:48:13 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 9330001 Best score so far: 35.44431972342052 . Using annealing factor: 7.51628179990588E-7 kt: 7.51628179990588E-5 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:48:16 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 9340001 Best score so far: 35.44431972342052 . Using annealing factor: 7.40353757290729E-7 kt: 7.40353757290729E-5 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:48:19 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Mutating helix constraints!
Oct 19, 2010 2:48:19 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 9350000 Best score so far: 35.44431972342052 . Using annealing factor: 7.292484509313681E-7 kt: 7.292484509313681E-5 coordinate system multipliers: 1.0 1.0 1.0  MUTATING HELIX LENGTHS: 
6 ( 6 ) 6 ( 6 ) 6 ( 6 ) Modified helix constraint lengths: 7 7 7 
Oct 19, 2010 2:48:19 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 9350001 Best score so far: 35.44431972342052 . Using annealing factor: 7.292484509313681E-7 kt: 7.292484509313681E-5 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:48:21 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 9360001 Best score so far: 35.44431972342052 . Using annealing factor: 7.183097241673976E-7 kt: 7.183097241673976E-5 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:48:24 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 9370001 Best score so far: 35.44431972342052 . Using annealing factor: 7.075350783048866E-7 kt: 7.075350783048866E-5 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:48:27 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 9380001 Best score so far: 35.44431972342052 . Using annealing factor: 6.969220521303133E-7 kt: 6.969220521303132E-5 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:48:30 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 9390001 Best score so far: 35.44431972342052 . Using annealing factor: 6.864682213483586E-7 kt: 6.864682213483587E-5 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:48:33 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Mutating helix constraints!
Oct 19, 2010 2:48:33 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 9400000 Best score so far: 35.44431972342052 . Using annealing factor: 6.761711980281333E-7 kt: 6.761711980281333E-5 coordinate system multipliers: 1.0 1.0 1.0  MUTATING HELIX LENGTHS: 
6 ( 6 ) 6 ( 6 ) 6 ( 6 ) Modified helix constraint lengths: 5 6 6 
Oct 19, 2010 2:48:33 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 9400001 Best score so far: 35.44431972342052 . Using annealing factor: 6.761711980281333E-7 kt: 6.761711980281333E-5 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:48:36 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 9410001 Best score so far: 35.44431972342052 . Using annealing factor: 6.660286300577113E-7 kt: 6.660286300577113E-5 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:48:39 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 9420001 Best score so far: 35.44431972342052 . Using annealing factor: 6.560382006068456E-7 kt: 6.560382006068455E-5 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:48:42 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 9430001 Best score so far: 35.44431972342052 . Using annealing factor: 6.461976275977429E-7 kt: 6.461976275977429E-5 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:48:45 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 9440001 Best score so far: 35.44431972342052 . Using annealing factor: 6.365046631837768E-7 kt: 6.365046631837767E-5 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:48:47 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Mutating helix constraints!
Oct 19, 2010 2:48:47 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 9450000 Best score so far: 35.44431972342052 . Using annealing factor: 6.2695709323602E-7 kt: 6.269570932360201E-5 coordinate system multipliers: 1.0 1.0 1.0  MUTATING HELIX LENGTHS: 
6 ( 6 ) 6 ( 6 ) 6 ( 6 ) Modified helix constraint lengths: 6 7 7 
Oct 19, 2010 2:48:47 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 9450001 Best score so far: 35.44431972342052 . Using annealing factor: 6.2695709323602E-7 kt: 6.269570932360201E-5 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:48:50 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 9460001 Best score so far: 35.44431972342052 . Using annealing factor: 6.175527368374798E-7 kt: 6.175527368374798E-5 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:48:53 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 9470001 Best score so far: 35.44431972342052 . Using annealing factor: 6.082894457849176E-7 kt: 6.082894457849176E-5 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:48:56 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 9480001 Best score so far: 35.44431972342052 . Using annealing factor: 5.991651040981438E-7 kt: 5.9916510409814376E-5 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:48:59 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 9490001 Best score so far: 35.44431972342052 . Using annealing factor: 5.901776275366716E-7 kt: 5.901776275366716E-5 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:49:02 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Mutating helix constraints!
Oct 19, 2010 2:49:02 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 9500000 Best score so far: 35.44431972342052 . Using annealing factor: 5.813249631236216E-7 kt: 5.813249631236216E-5 coordinate system multipliers: 1.0 1.0 1.0  MUTATING HELIX LENGTHS: 
6 ( 6 ) 6 ( 6 ) 6 ( 6 ) Modified helix constraint lengths: 7 7 5 
Oct 19, 2010 2:49:02 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 9500001 Best score so far: 35.44431972342052 . Using annealing factor: 5.813249631236216E-7 kt: 5.813249631236216E-5 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:49:05 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 9510001 Best score so far: 35.44431972342052 . Using annealing factor: 5.726050886767672E-7 kt: 5.726050886767672E-5 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:49:08 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 9520001 Best score so far: 35.44431972342052 . Using annealing factor: 5.640160123466157E-7 kt: 5.640160123466157E-5 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:49:11 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 9530001 Best score so far: 35.44431972342052 . Using annealing factor: 5.555557721614164E-7 kt: 5.5555577216141643E-5 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:49:13 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 9540001 Best score so far: 35.44431972342052 . Using annealing factor: 5.472224355789952E-7 kt: 5.472224355789952E-5 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:49:16 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Mutating helix constraints!
Oct 19, 2010 2:49:16 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 9550000 Best score so far: 35.44431972342052 . Using annealing factor: 5.390140990453103E-7 kt: 5.390140990453103E-5 coordinate system multipliers: 1.0 1.0 1.0  MUTATING HELIX LENGTHS: 
6 ( 6 ) 6 ( 6 ) 6 ( 6 ) Modified helix constraint lengths: 5 7 6 
Oct 19, 2010 2:49:16 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 9550001 Best score so far: 35.44431972342052 . Using annealing factor: 5.390140990453103E-7 kt: 5.390140990453103E-5 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:49:19 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 9560001 Best score so far: 35.44431972342052 . Using annealing factor: 5.309288875596306E-7 kt: 5.3092888755963056E-5 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:49:22 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 9570001 Best score so far: 35.44431972342052 . Using annealing factor: 5.229649542462361E-7 kt: 5.229649542462361E-5 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:49:25 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 9580001 Best score so far: 35.44431972342052 . Using annealing factor: 5.151204799325425E-7 kt: 5.151204799325425E-5 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:49:28 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 9590001 Best score so far: 35.44431972342052 . Using annealing factor: 5.073936727335544E-7 kt: 5.0739367273355435E-5 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:49:31 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Mutating helix constraints!
Oct 19, 2010 2:49:31 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 9600000 Best score so far: 35.44431972342052 . Using annealing factor: 4.997827676425511E-7 kt: 4.9978276764255104E-5 coordinate system multipliers: 1.0 1.0 1.0  MUTATING HELIX LENGTHS: 
6 ( 6 ) 6 ( 6 ) 6 ( 6 ) Modified helix constraint lengths: 7 6 7 
Oct 19, 2010 2:49:31 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 9600001 Best score so far: 35.44431972342052 . Using annealing factor: 4.997827676425511E-7 kt: 4.9978276764255104E-5 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:49:34 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 9610001 Best score so far: 35.44431972342052 . Using annealing factor: 4.922860261279128E-7 kt: 4.922860261279128E-5 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:49:37 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 9620001 Best score so far: 35.44431972342052 . Using annealing factor: 4.849017357359941E-7 kt: 4.849017357359941E-5 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:49:39 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 9630001 Best score so far: 35.44431972342052 . Using annealing factor: 4.776282096999542E-7 kt: 4.776282096999542E-5 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:49:42 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 9640001 Best score so far: 35.44431972342052 . Using annealing factor: 4.7046378655445486E-7 kt: 4.704637865544549E-5 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:49:45 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Mutating helix constraints!
Oct 19, 2010 2:49:45 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 9650000 Best score so far: 35.44431972342052 . Using annealing factor: 4.634068297561381E-7 kt: 4.634068297561381E-5 coordinate system multipliers: 1.0 1.0 1.0  MUTATING HELIX LENGTHS: 
6 ( 6 ) 6 ( 6 ) 6 ( 6 ) Modified helix constraint lengths: 6 6 7 
Oct 19, 2010 2:49:45 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 9650001 Best score so far: 35.44431972342052 . Using annealing factor: 4.634068297561381E-7 kt: 4.634068297561381E-5 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:49:48 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 9660001 Best score so far: 35.44431972342052 . Using annealing factor: 4.5645572730979596E-7 kt: 4.564557273097959E-5 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:49:51 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 9670001 Best score so far: 35.44431972342052 . Using annealing factor: 4.49608891400149E-7 kt: 4.49608891400149E-5 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:49:54 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 9680001 Best score so far: 35.44431972342052 . Using annealing factor: 4.428647580291468E-7 kt: 4.428647580291468E-5 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:49:57 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 9690001 Best score so far: 35.44431972342052 . Using annealing factor: 4.3622178665870956E-7 kt: 4.3622178665870954E-5 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:49:59 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Mutating helix constraints!
Oct 19, 2010 2:49:59 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 9700000 Best score so far: 35.44431972342052 . Using annealing factor: 4.2967845985882893E-7 kt: 4.296784598588289E-5 coordinate system multipliers: 1.0 1.0 1.0  MUTATING HELIX LENGTHS: 
6 ( 6 ) 6 ( 6 ) 6 ( 6 ) Modified helix constraint lengths: 6 5 6 
Oct 19, 2010 2:49:59 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 9700001 Best score so far: 35.44431972342052 . Using annealing factor: 4.2967845985882893E-7 kt: 4.296784598588289E-5 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:50:02 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 9710001 Best score so far: 35.44431972342052 . Using annealing factor: 4.232332829609465E-7 kt: 4.232332829609465E-5 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:50:05 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 9720001 Best score so far: 35.44431972342052 . Using annealing factor: 4.168847837165323E-7 kt: 4.1688478371653235E-5 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:50:08 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 9730001 Best score so far: 35.44431972342052 . Using annealing factor: 4.106315119607843E-7 kt: 4.1063151196078426E-5 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:50:11 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 9740001 Best score so far: 35.44431972342052 . Using annealing factor: 4.0447203928137255E-7 kt: 4.0447203928137256E-5 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:50:14 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Mutating helix constraints!
Oct 19, 2010 2:50:14 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 9750000 Best score so far: 35.44431972342052 . Using annealing factor: 3.9840495869215197E-7 kt: 3.9840495869215194E-5 coordinate system multipliers: 1.0 1.0 1.0  MUTATING HELIX LENGTHS: 
6 ( 6 ) 6 ( 6 ) 6 ( 6 ) Modified helix constraint lengths: 5 7 7 
Oct 19, 2010 2:50:14 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 9750001 Best score so far: 35.44431972342052 . Using annealing factor: 3.9840495869215197E-7 kt: 3.9840495869215194E-5 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:50:17 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 9760001 Best score so far: 35.44431972342052 . Using annealing factor: 3.9242888431176964E-7 kt: 3.924288843117696E-5 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:50:20 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 9770001 Best score so far: 35.44431972342052 . Using annealing factor: 3.865424510470931E-7 kt: 3.865424510470931E-5 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:50:23 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 9780001 Best score so far: 35.44431972342052 . Using annealing factor: 3.807443142813867E-7 kt: 3.807443142813867E-5 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:50:25 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 9790001 Best score so far: 35.44431972342052 . Using annealing factor: 3.750331495671659E-7 kt: 3.750331495671659E-5 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:50:28 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Mutating helix constraints!
Oct 19, 2010 2:50:28 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 9800000 Best score so far: 35.44431972342052 . Using annealing factor: 3.694076523236584E-7 kt: 3.694076523236584E-5 coordinate system multipliers: 1.0 1.0 1.0  MUTATING HELIX LENGTHS: 
6 ( 6 ) 6 ( 6 ) 6 ( 6 ) Modified helix constraint lengths: 6 7 6 
Oct 19, 2010 2:50:28 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 9800001 Best score so far: 35.44431972342052 . Using annealing factor: 3.694076523236584E-7 kt: 3.694076523236584E-5 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:50:31 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 9810001 Best score so far: 35.44431972342052 . Using annealing factor: 3.6386653753880356E-7 kt: 3.6386653753880356E-5 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:50:34 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 9820001 Best score so far: 35.44431972342052 . Using annealing factor: 3.584085394757215E-7 kt: 3.584085394757215E-5 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:50:37 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 9830001 Best score so far: 35.44431972342052 . Using annealing factor: 3.5303241138358564E-7 kt: 3.5303241138358566E-5 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:50:40 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 9840001 Best score so far: 35.44431972342052 . Using annealing factor: 3.4773692521283183E-7 kt: 3.4773692521283185E-5 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:50:43 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Mutating helix constraints!
Oct 19, 2010 2:50:43 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 9850000 Best score so far: 35.44431972342052 . Using annealing factor: 3.425208713346394E-7 kt: 3.425208713346394E-5 coordinate system multipliers: 1.0 1.0 1.0  MUTATING HELIX LENGTHS: 
6 ( 6 ) 6 ( 6 ) 6 ( 6 ) Modified helix constraint lengths: 7 6 7 
Oct 19, 2010 2:50:43 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 9850001 Best score so far: 35.44431972342052 . Using annealing factor: 3.425208713346394E-7 kt: 3.425208713346394E-5 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:50:46 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 9860001 Best score so far: 35.44431972342052 . Using annealing factor: 3.3738305826461976E-7 kt: 3.3738305826461975E-5 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:50:49 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 9870001 Best score so far: 35.44431972342052 . Using annealing factor: 3.3232231239065045E-7 kt: 3.323223123906504E-5 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:50:52 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 9880001 Best score so far: 35.44431972342052 . Using annealing factor: 3.2733747770479073E-7 kt: 3.2733747770479075E-5 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:50:54 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 9890001 Best score so far: 35.44431972342052 . Using annealing factor: 3.2242741553921885E-7 kt: 3.2242741553921886E-5 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:50:57 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Mutating helix constraints!
Oct 19, 2010 2:50:57 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 9900000 Best score so far: 35.44431972342052 . Using annealing factor: 3.1759100430613053E-7 kt: 3.175910043061305E-5 coordinate system multipliers: 1.0 1.0 1.0  MUTATING HELIX LENGTHS: 
6 ( 6 ) 6 ( 6 ) 6 ( 6 ) Oct 19, 2010 2:50:57 PM rnadesign.rnamodel.HelixOptimizer mutateHelixLengths
WARNING: No helix lengths were modified!
Oct 19, 2010 2:50:57 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 9900001 Best score so far: 35.44431972342052 . Using annealing factor: 3.1759100430613053E-7 kt: 3.175910043061305E-5 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:51:00 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 9910001 Best score so far: 35.44431972342052 . Using annealing factor: 3.128271392415386E-7 kt: 3.128271392415386E-5 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:51:03 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 9920001 Best score so far: 35.44431972342052 . Using annealing factor: 3.081347321529155E-7 kt: 3.081347321529155E-5 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:51:06 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 9930001 Best score so far: 35.44431972342052 . Using annealing factor: 3.0351271117062175E-7 kt: 3.0351271117062175E-5 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:51:09 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 9940001 Best score so far: 35.44431972342052 . Using annealing factor: 2.9896002050306244E-7 kt: 2.9896002050306244E-5 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:51:12 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Mutating helix constraints!
Oct 19, 2010 2:51:12 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 9950000 Best score so far: 35.44431972342052 . Using annealing factor: 2.944756201955165E-7 kt: 2.944756201955165E-5 coordinate system multipliers: 1.0 1.0 1.0  MUTATING HELIX LENGTHS: 
6 ( 6 ) 6 ( 6 ) 6 ( 6 ) Modified helix constraint lengths: 7 7 5 
Oct 19, 2010 2:51:12 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 9950001 Best score so far: 35.44431972342052 . Using annealing factor: 2.944756201955165E-7 kt: 2.944756201955165E-5 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:51:15 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 9960001 Best score so far: 35.44431972342052 . Using annealing factor: 2.9005848589258373E-7 kt: 2.9005848589258372E-5 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:51:17 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 9970001 Best score so far: 35.44431972342052 . Using annealing factor: 2.85707608604195E-7 kt: 2.8570760860419498E-5 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:51:20 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 9980001 Best score so far: 35.44431972342052 . Using annealing factor: 2.8142199447513204E-7 kt: 2.8142199447513202E-5 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:51:23 PM rnadesign.rnamodel.HelixOptimizer optimize
INFO: Iteration: 9990001 Best score so far: 35.44431972342052 . Using annealing factor: 2.772006645580051E-7 kt: 2.7720066455800507E-5 coordinate system multipliers: 1.0 1.0 1.0 
Oct 19, 2010 2:51:26 PM rnadesign.rnamodel.HelixOptimizer findSuitableParentObject
INFO: Suitable parent object of root.j1.A_1_B_10 is: root.j1
Oct 19, 2010 2:51:26 PM rnadesign.rnamodel.HelixOptimizer findSuitableParentObject
INFO: Suitable parent object of root.j1.C_1_A_9 is: root.j1
Oct 19, 2010 2:51:26 PM rnadesign.rnamodel.HelixOptimizer findSuitableParentObject
INFO: Suitable parent object of root.j2.C_1_A_9 is: root.j2
Oct 19, 2010 2:51:26 PM rnadesign.rnamodel.HelixOptimizer findSuitableParentObject
INFO: Suitable parent object of root.j2.A_1_B_10 is: root.j2
Oct 19, 2010 2:51:26 PM rnadesign.rnamodel.HelixOptimizer findSuitableParentObject
INFO: Suitable parent object of root.j3.C_1_A_9 is: root.j3
Oct 19, 2010 2:51:26 PM rnadesign.rnamodel.HelixOptimizer findSuitableParentObject
INFO: Suitable parent object of root.j3.A_1_B_10 is: root.j3
Oct 19, 2010 2:51:27 PM rnadesign.rnacontrol.Object3DGraphController optimizeHelices
INFO: Finished optimizeHelices...
Finished controller.optimizeHelices!
Helix optimization finished! Result:
{number_steps=10000001, final_score=35.44431972342052, start_score=653.5227622829735, generated_helices=h_root_j1_A_1_B_10_root_j2_C_1_A_9_root;h_root_j2_A_1_B_10_root_j3_C_1_A_9_root;h_root_j3_A_1_B_10_root_j1_C_1_A_9_root}
##### Finished testing testOptimizeHelicesCommandWithLengths #####

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NanoTilerTests
Total tests run: 1, Failures: 0, Skips: 0
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