# command:# Prefix for input files set to /projects/kestrel/users/karplus/burial/undertaker/spots/ # command:# ReadVDW initial.radii # command:Reading spots from dunbrack-925-wet-6.5.spot. Read prototypes from /projects/kestrel/users/karplus/burial/undertaker/spots/../normalize_prototypes/prototypes # command:# reading histogram from smoothed-dunbrack-925-wet-6.5.hist # command:Reading spots from dunbrack-925-dry-12.spot. Read prototypes from /projects/kestrel/users/karplus/burial/undertaker/spots/../normalize_prototypes/prototypes # command:# reading histogram from smoothed-dunbrack-925-dry-12.hist # command:Setting costs from histograms # command:# Prefix for input files set to /projects/kestrel/users/karplus/burial/undertaker/atoms-inputs/ # command:# reading dunbrack-925.atoms.gz # After reading dunbrack-925.atoms.gz have 925 chains in training database # command:# fragment library contains # type length num_fragments num_indexes_used # n-terminus 1 849 20 (100%) # n-terminus 2 842 253 (63.25%) # middle 1 205367 20 (100%) # middle 2 203845 400 (100%) # middle 3 202366 7929 (99.1125%) # middle 4 200913 88584 (55.365%) # c-terminus 1 862 20 (100%) # c-terminus 2 216 148 (37%) # ss-bonds 650 # command:# Reading rotamer library from dunbrack-925.rot # command:# Score parameters set to # sidechain_weight 1 # clash_penalty 30 nats/clash # ss_bond_bonus 30 # known_ss_bond_bonus 0 # chain_break_penalty 50 nats/Angstrom # wet_spot_weight 2 # dry_spot_weight 50 # command:# Prefix for input files set to # command:Created new target T0106 from ../T0106.seq # command:# Will now start reporting scores to t106-6.5w-12d.rdb # command:# created fragments for T0106 from 1boeA-T0106-local.index # command:# created fragments for T0106 from 1klo-T0106-local.index # command:# created fragments for T0106 from T0106-1c4eA-local.index # command:# created fragments for T0106 from 1by2-T0106-local.index # command:# created fragments for T0106 from 1qatB-T0106-local.index # command:# created fragments for T0106 from T0106-1dec-local.index # command:# created fragments for T0106 from 1c2aA-T0106-local.index # command:# created fragments for T0106 from T0106-1ayj-local.index # command:# created fragments for T0106 from T0106-1eaiC-local.index # command:# created fragments for T0106 from 1c4eA-T0106-local.index # command:# created fragments for T0106 from T0106-1boeA-local.index # command:# created fragments for T0106 from T0106-1klo-local.index # command:# created fragments for T0106 from 1eaiC-T0106-local.index # command:# created fragments for T0106 from T0106-1c2aA-local.index # command:# created fragments for T0106 from T0106-1qatB-local.index # command:# naming current conformation t106-rand # command:# command:# Will do 10 iterations of optimization # best score in initial pool at pool[39] 355.762 bits/residue, 202 clashes 5.53366 breaks # optimizing backbone with 50 conformations in pool # doing 6 generations, with 300 new conformations in each generation. # keep at most 20 conformations from old pool # generation 1: best score 349.547 bits/residue, 192 clashes 5.53366 breaks # Cumulative usage by method: ## InsertFragment 7 ## ReduceClash 4 ## CrossOver 2 ## CrossAndInsert 12 ## TwoFragment 11 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 2 ## InsertAlignment 5 ## ReduceBreak 4 # generation 2: best score 339.807 bits/residue, 57 clashes 5.53366 breaks # Cumulative usage by method: ## InsertFragment 21 ## ReduceClash 11 ## CrossOver 3 ## CrossAndInsert 24 ## TwoFragment 19 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 2 ## InsertAlignment 7 ## ReduceBreak 4 # generation 3: best score 326.855 bits/residue, 70 clashes 5.53366 breaks # Cumulative usage by method: ## InsertFragment 32 ## ReduceClash 18 ## CrossOver 4 ## CrossAndInsert 36 ## TwoFragment 23 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 4 ## InsertAlignment 9 ## ReduceBreak 4 # generation 4: best score 325.248 bits/residue, 69 clashes 5.53366 breaks # Cumulative usage by method: ## InsertFragment 46 ## ReduceClash 21 ## CrossOver 6 ## CrossAndInsert 46 ## TwoFragment 31 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 4 ## InsertAlignment 11 ## ReduceBreak 4 # generation 5: best score 324.01 bits/residue, 87 clashes 5.53366 breaks # Cumulative usage by method: ## InsertFragment 60 ## ReduceClash 22 ## CrossOver 7 ## CrossAndInsert 57 ## TwoFragment 33 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 4 ## InsertAlignment 14 ## ReduceBreak 4 # generation 6: best score 321.317 bits/residue, 69 clashes 5.53366 breaks # Cumulative usage by method: ## InsertFragment 72 ## ReduceClash 24 ## CrossOver 11 ## CrossAndInsert 67 ## TwoFragment 35 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 6 ## InsertAlignment 14 ## ReduceBreak 4 # best score in initial pool at pool[32] 379.766 bits/residue, 139 clashes 20.6417 breaks # optimizing backbone with 50 conformations in pool # doing 6 generations, with 300 new conformations in each generation. # keep at most 20 conformations from old pool # generation 1: best score 355.033 bits/residue, 63 clashes 17.688 breaks # Cumulative usage by method: ## InsertFragment 8 ## ReduceClash 6 ## CrossOver 1 ## CrossAndInsert 14 ## TwoFragment 7 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 1 ## InsertAlignment 6 ## ReduceBreak 3 # generation 2: best score 353.7 bits/residue, 93 clashes 8.24019 breaks # Cumulative usage by method: ## InsertFragment 15 ## ReduceClash 13 ## CrossOver 2 ## CrossAndInsert 25 ## TwoFragment 17 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 2 ## InsertAlignment 10 ## ReduceBreak 7 # generation 3: best score 340.018 bits/residue, 72 clashes 13.3931 breaks # Cumulative usage by method: ## InsertFragment 24 ## ReduceClash 19 ## CrossOver 3 ## CrossAndInsert 37 ## TwoFragment 22 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 4 ## InsertAlignment 12 ## ReduceBreak 8 # generation 4: best score 339.242 bits/residue, 72 clashes 13.3931 breaks # Cumulative usage by method: ## InsertFragment 27 ## ReduceClash 25 ## CrossOver 4 ## CrossAndInsert 54 ## TwoFragment 25 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 4 ## InsertAlignment 13 ## ReduceBreak 13 # generation 5: best score 330.545 bits/residue, 70 clashes 0 breaks # Cumulative usage by method: ## InsertFragment 35 ## ReduceClash 31 ## CrossOver 5 ## CrossAndInsert 68 ## TwoFragment 29 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 4 ## InsertAlignment 14 ## ReduceBreak 16 # generation 6: best score 326.063 bits/residue, 92 clashes # Cumulative usage by method: ## InsertFragment 45 ## ReduceClash 34 ## CrossOver 7 ## CrossAndInsert 82 ## TwoFragment 30 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 5 ## InsertAlignment 14 ## ReduceBreak 19 # best score in initial pool at pool[44] 377.903 bits/residue, 107 clashes 32.8762 breaks # optimizing backbone with 50 conformations in pool # doing 6 generations, with 300 new conformations in each generation. # keep at most 20 conformations from old pool # generation 1: best score 367.507 bits/residue, 191 clashes 29.9381 breaks # Cumulative usage by method: ## InsertFragment 8 ## ReduceClash 6 ## CrossOver 1 ## CrossAndInsert 7 ## TwoFragment 9 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 1 ## InsertAlignment 6 ## ReduceBreak 7 # generation 2: best score 354.14 bits/residue, 118 clashes 15.0815 breaks # Cumulative usage by method: ## InsertFragment 18 ## ReduceClash 12 ## CrossOver 2 ## CrossAndInsert 14 ## TwoFragment 22 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 3 ## InsertAlignment 8 ## ReduceBreak 10 # generation 3: best score 342.576 bits/residue, 77 clashes 19.7886 breaks # Cumulative usage by method: ## InsertFragment 26 ## ReduceClash 21 ## CrossOver 4 ## CrossAndInsert 24 ## TwoFragment 29 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 4 ## InsertAlignment 10 ## ReduceBreak 14 # generation 4: best score 330.166 bits/residue, 83 clashes 19.7886 breaks # Cumulative usage by method: ## InsertFragment 37 ## ReduceClash 27 ## CrossOver 10 ## CrossAndInsert 36 ## TwoFragment 35 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 4 ## InsertAlignment 10 ## ReduceBreak 15 # generation 5: best score 318.612 bits/residue, 63 clashes 19.7886 breaks # Cumulative usage by method: ## InsertFragment 53 ## ReduceClash 38 ## CrossOver 12 ## CrossAndInsert 42 ## TwoFragment 38 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 5 ## InsertAlignment 13 ## ReduceBreak 15 # generation 6: best score 313.652 bits/residue, 78 clashes 19.7886 breaks # Cumulative usage by method: ## InsertFragment 71 ## ReduceClash 48 ## CrossOver 18 ## CrossAndInsert 47 ## TwoFragment 43 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 6 ## InsertAlignment 13 ## ReduceBreak 15 # best score in initial pool at pool[14] 368.998 bits/residue, 187 clashes 28.8486 breaks # optimizing backbone with 50 conformations in pool # doing 6 generations, with 300 new conformations in each generation. # keep at most 20 conformations from old pool # generation 1: best score 352.788 bits/residue, 147 clashes 26.7204 breaks # Cumulative usage by method: ## InsertFragment 8 ## ReduceClash 6 ## CrossOver 1 ## CrossAndInsert 10 ## TwoFragment 9 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 1 ## InsertAlignment 8 ## ReduceBreak 3 # generation 2: best score 346.504 bits/residue, 116 clashes 39.4804 breaks # Cumulative usage by method: ## InsertFragment 17 ## ReduceClash 16 ## CrossOver 1 ## CrossAndInsert 22 ## TwoFragment 14 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 1 ## InsertAlignment 13 ## ReduceBreak 7 # generation 3: best score 342.28 bits/residue, 95 clashes 36.6347 breaks # Cumulative usage by method: ## InsertFragment 27 ## ReduceClash 27 ## CrossOver 1 ## CrossAndInsert 34 ## TwoFragment 18 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 1 ## InsertAlignment 15 ## ReduceBreak 11 # generation 4: best score 321.36 bits/residue, 41 clashes 0 breaks # Cumulative usage by method: ## InsertFragment 33 ## ReduceClash 42 ## CrossOver 3 ## CrossAndInsert 46 ## TwoFragment 23 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 1 ## InsertAlignment 17 ## ReduceBreak 13 # generation 5: best score 317.902 bits/residue, 55 clashes # Cumulative usage by method: ## InsertFragment 39 ## ReduceClash 59 ## CrossOver 3 ## CrossAndInsert 58 ## TwoFragment 27 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 2 ## InsertAlignment 17 ## ReduceBreak 14 # generation 6: best score 313.529 bits/residue, 74 clashes # Cumulative usage by method: ## InsertFragment 49 ## ReduceClash 68 ## CrossOver 5 ## CrossAndInsert 70 ## TwoFragment 31 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 3 ## InsertAlignment 18 ## ReduceBreak 14 # best score in initial pool at pool[26] 376.364 bits/residue, 106 clashes 0 breaks # optimizing backbone with 50 conformations in pool # doing 6 generations, with 300 new conformations in each generation. # keep at most 20 conformations from old pool # generation 1: best score 359.769 bits/residue, 121 clashes 12.9602 breaks # Cumulative usage by method: ## InsertFragment 9 ## ReduceClash 6 ## CrossOver 0 ## CrossAndInsert 9 ## TwoFragment 11 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 1 ## InsertAlignment 7 ## ReduceBreak 2 # generation 2: best score 351.125 bits/residue, 96 clashes 12.8325 breaks # Cumulative usage by method: ## InsertFragment 20 ## ReduceClash 16 ## CrossOver 0 ## CrossAndInsert 15 ## TwoFragment 17 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 5 ## InsertAlignment 9 ## ReduceBreak 6 # generation 3: best score 339.43 bits/residue, 73 clashes 9.52076 breaks # Cumulative usage by method: ## InsertFragment 32 ## ReduceClash 25 ## CrossOver 0 ## CrossAndInsert 24 ## TwoFragment 23 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 6 ## InsertAlignment 10 ## ReduceBreak 10 # generation 4: best score 333.525 bits/residue, 111 clashes 8.68474 breaks # Cumulative usage by method: ## InsertFragment 45 ## ReduceClash 35 ## CrossOver 0 ## CrossAndInsert 36 ## TwoFragment 25 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 8 ## InsertAlignment 10 ## ReduceBreak 11 # generation 5: best score 324.231 bits/residue, 72 clashes 12.3176 breaks # Cumulative usage by method: ## InsertFragment 59 ## ReduceClash 40 ## CrossOver 0 ## CrossAndInsert 44 ## TwoFragment 27 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 8 ## InsertAlignment 10 ## ReduceBreak 12 # generation 6: best score 308.291 bits/residue, 68 clashes 12.3176 breaks # Cumulative usage by method: ## InsertFragment 68 ## ReduceClash 50 ## CrossOver 1 ## CrossAndInsert 56 ## TwoFragment 30 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 8 ## InsertAlignment 10 ## ReduceBreak 14 # best score in initial pool at pool[46] 375.444 bits/residue, 196 clashes 11.6751 breaks # optimizing backbone with 50 conformations in pool # doing 6 generations, with 300 new conformations in each generation. # keep at most 20 conformations from old pool # generation 1: best score 354.96 bits/residue, 129 clashes 32.6069 breaks # Cumulative usage by method: ## InsertFragment 14 ## ReduceClash 9 ## CrossOver 0 ## CrossAndInsert 7 ## TwoFragment 4 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 5 ## InsertAlignment 3 ## ReduceBreak 2 # generation 2: best score 345.913 bits/residue, 89 clashes 32.6069 breaks # Cumulative usage by method: ## InsertFragment 25 ## ReduceClash 21 ## CrossOver 0 ## CrossAndInsert 15 ## TwoFragment 9 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 10 ## InsertAlignment 4 ## ReduceBreak 4 # generation 3: best score 342.002 bits/residue, 107 clashes 12.3994 breaks # Cumulative usage by method: ## InsertFragment 36 ## ReduceClash 36 ## CrossOver 0 ## CrossAndInsert 23 ## TwoFragment 11 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 14 ## InsertAlignment 4 ## ReduceBreak 6 # generation 4: best score 333.511 bits/residue, 96 clashes 13.9631 breaks # Cumulative usage by method: ## InsertFragment 51 ## ReduceClash 48 ## CrossOver 0 ## CrossAndInsert 32 ## TwoFragment 11 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 19 ## InsertAlignment 4 ## ReduceBreak 6 # generation 5: best score 325.187 bits/residue, 51 clashes 5.64334 breaks # Cumulative usage by method: ## InsertFragment 69 ## ReduceClash 55 ## CrossOver 0 ## CrossAndInsert 44 ## TwoFragment 12 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 23 ## InsertAlignment 5 ## ReduceBreak 8 # generation 6: best score 325.187 bits/residue, 51 clashes 5.64334 breaks # Cumulative usage by method: ## InsertFragment 86 ## ReduceClash 63 ## CrossOver 0 ## CrossAndInsert 49 ## TwoFragment 16 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 25 ## InsertAlignment 5 ## ReduceBreak 8 # best score in initial pool at pool[16] 381.913 bits/residue, 94 clashes 0 breaks # optimizing backbone with 50 conformations in pool # doing 6 generations, with 300 new conformations in each generation. # keep at most 20 conformations from old pool # generation 1: best score 362.479 bits/residue, 116 clashes 0 breaks # Cumulative usage by method: ## InsertFragment 10 ## ReduceClash 13 ## CrossOver 1 ## CrossAndInsert 9 ## TwoFragment 8 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 0 ## InsertAlignment 4 ## ReduceBreak 1 # generation 2: best score 357.759 bits/residue, 120 clashes 0 breaks # Cumulative usage by method: ## InsertFragment 19 ## ReduceClash 29 ## CrossOver 1 ## CrossAndInsert 18 ## TwoFragment 16 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 1 ## InsertAlignment 6 ## ReduceBreak 1 # generation 3: best score 343.244 bits/residue, 129 clashes 30.2585 breaks # Cumulative usage by method: ## InsertFragment 35 ## ReduceClash 36 ## CrossOver 1 ## CrossAndInsert 27 ## TwoFragment 21 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 1 ## InsertAlignment 8 ## ReduceBreak 2 # generation 4: best score 340.528 bits/residue, 95 clashes 30.2585 breaks # Cumulative usage by method: ## InsertFragment 56 ## ReduceClash 44 ## CrossOver 1 ## CrossAndInsert 36 ## TwoFragment 25 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 1 ## InsertAlignment 10 ## ReduceBreak 2 # generation 5: best score 334.077 bits/residue, 93 clashes 30.4332 breaks # Cumulative usage by method: ## InsertFragment 72 ## ReduceClash 56 ## CrossOver 2 ## CrossAndInsert 41 ## TwoFragment 28 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 1 ## InsertAlignment 10 ## ReduceBreak 2 # generation 6: best score 334.077 bits/residue, 93 clashes 30.4332 breaks # Cumulative usage by method: ## InsertFragment 87 ## ReduceClash 64 ## CrossOver 3 ## CrossAndInsert 46 ## TwoFragment 29 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 1 ## InsertAlignment 11 ## ReduceBreak 2 # best score in initial pool at pool[7] 359.034 bits/residue, 164 clashes 14.8512 breaks # optimizing backbone with 50 conformations in pool # doing 6 generations, with 300 new conformations in each generation. # keep at most 20 conformations from old pool # generation 1: best score 348.987 bits/residue, 55 clashes 28.8263 breaks # Cumulative usage by method: ## InsertFragment 7 ## ReduceClash 10 ## CrossOver 2 ## CrossAndInsert 7 ## TwoFragment 7 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 3 ## InsertAlignment 3 ## ReduceBreak 7 # generation 2: best score 341.577 bits/residue, 37 clashes 28.8263 breaks # Cumulative usage by method: ## InsertFragment 13 ## ReduceClash 23 ## CrossOver 4 ## CrossAndInsert 13 ## TwoFragment 14 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 5 ## InsertAlignment 5 ## ReduceBreak 13 # generation 3: best score 336.505 bits/residue, 35 clashes 11.0729 breaks # Cumulative usage by method: ## InsertFragment 26 ## ReduceClash 34 ## CrossOver 6 ## CrossAndInsert 19 ## TwoFragment 16 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 6 ## InsertAlignment 6 ## ReduceBreak 17 # generation 4: best score 331.474 bits/residue, 29 clashes 25.5045 breaks # Cumulative usage by method: ## InsertFragment 36 ## ReduceClash 49 ## CrossOver 12 ## CrossAndInsert 22 ## TwoFragment 19 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 6 ## InsertAlignment 9 ## ReduceBreak 17 # generation 5: best score 325.716 bits/residue, 58 clashes 7.7094 breaks # Cumulative usage by method: ## InsertFragment 47 ## ReduceClash 61 ## CrossOver 15 ## CrossAndInsert 31 ## TwoFragment 19 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 7 ## InsertAlignment 9 ## ReduceBreak 19 # generation 6: best score 317.782 bits/residue, 59 clashes 8.06537 breaks # Cumulative usage by method: ## InsertFragment 58 ## ReduceClash 69 ## CrossOver 20 ## CrossAndInsert 38 ## TwoFragment 21 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 8 ## InsertAlignment 9 ## ReduceBreak 20 # best score in initial pool at pool[5] 376.364 bits/residue, 179 clashes 31.6621 breaks # optimizing backbone with 50 conformations in pool # doing 6 generations, with 300 new conformations in each generation. # keep at most 20 conformations from old pool # generation 1: best score 364.004 bits/residue, 137 clashes 31.6621 breaks # Cumulative usage by method: ## InsertFragment 9 ## ReduceClash 10 ## CrossOver 1 ## CrossAndInsert 10 ## TwoFragment 6 ## InsertSSBond 1 ## OneRotamer 0 ## ClashingRotamer 1 ## InsertAlignment 3 ## ReduceBreak 4 # generation 2: best score 356.044 bits/residue, 124 clashes 25.634 breaks # Cumulative usage by method: ## InsertFragment 20 ## ReduceClash 14 ## CrossOver 2 ## CrossAndInsert 18 ## TwoFragment 11 ## InsertSSBond 1 ## OneRotamer 0 ## ClashingRotamer 5 ## InsertAlignment 4 ## ReduceBreak 10 # generation 3: best score 352.5 bits/residue, 91 clashes 32.6451 breaks # Cumulative usage by method: ## InsertFragment 30 ## ReduceClash 22 ## CrossOver 4 ## CrossAndInsert 27 ## TwoFragment 14 ## InsertSSBond 1 ## OneRotamer 0 ## ClashingRotamer 6 ## InsertAlignment 7 ## ReduceBreak 11 # generation 4: best score 345.699 bits/residue, 104 clashes 25.1287 breaks # Cumulative usage by method: ## InsertFragment 46 ## ReduceClash 27 ## CrossOver 7 ## CrossAndInsert 34 ## TwoFragment 16 ## InsertSSBond 1 ## OneRotamer 0 ## ClashingRotamer 6 ## InsertAlignment 10 ## ReduceBreak 14 # generation 5: best score 341.268 bits/residue, 92 clashes 25.1287 breaks # Cumulative usage by method: ## InsertFragment 57 ## ReduceClash 32 ## CrossOver 13 ## CrossAndInsert 38 ## TwoFragment 20 ## InsertSSBond 1 ## OneRotamer 0 ## ClashingRotamer 8 ## InsertAlignment 10 ## ReduceBreak 19 # generation 6: best score 331.499 bits/residue, 61 clashes 25.1287 breaks # Cumulative usage by method: ## InsertFragment 68 ## ReduceClash 40 ## CrossOver 18 ## CrossAndInsert 44 ## TwoFragment 21 ## InsertSSBond 1 ## OneRotamer 0 ## ClashingRotamer 8 ## InsertAlignment 13 ## ReduceBreak 21 # best score in initial pool at pool[45] 361.21 bits/residue, 63 clashes 31.6115 breaks # optimizing backbone with 50 conformations in pool # doing 6 generations, with 300 new conformations in each generation. # keep at most 20 conformations from old pool # generation 1: best score 356.806 bits/residue, 117 clashes 12.0395 breaks # Cumulative usage by method: ## InsertFragment 8 ## ReduceClash 7 ## CrossOver 0 ## CrossAndInsert 7 ## TwoFragment 8 ## InsertSSBond 1 ## OneRotamer 0 ## ClashingRotamer 3 ## InsertAlignment 4 ## ReduceBreak 8 # generation 2: best score 349.105 bits/residue, 74 clashes 31.6115 breaks # Cumulative usage by method: ## InsertFragment 19 ## ReduceClash 11 ## CrossOver 0 ## CrossAndInsert 15 ## TwoFragment 15 ## InsertSSBond 2 ## OneRotamer 0 ## ClashingRotamer 4 ## InsertAlignment 7 ## ReduceBreak 14 # generation 3: best score 333.421 bits/residue, 76 clashes 18.2075 breaks # Cumulative usage by method: ## InsertFragment 27 ## ReduceClash 18 ## CrossOver 0 ## CrossAndInsert 25 ## TwoFragment 21 ## InsertSSBond 3 ## OneRotamer 0 ## ClashingRotamer 6 ## InsertAlignment 7 ## ReduceBreak 21 # generation 4: best score 330.969 bits/residue, 81 clashes 18.2075 breaks # Cumulative usage by method: ## InsertFragment 39 ## ReduceClash 24 ## CrossOver 0 ## CrossAndInsert 34 ## TwoFragment 27 ## InsertSSBond 3 ## OneRotamer 0 ## ClashingRotamer 9 ## InsertAlignment 7 ## ReduceBreak 24 # generation 5: best score 325.651 bits/residue, 78 clashes 18.2075 breaks # Cumulative usage by method: ## InsertFragment 53 ## ReduceClash 31 ## CrossOver 1 ## CrossAndInsert 46 ## TwoFragment 31 ## InsertSSBond 3 ## OneRotamer 0 ## ClashingRotamer 10 ## InsertAlignment 8 ## ReduceBreak 27 # generation 6: best score 323.443 bits/residue, 48 clashes 18.2075 breaks # Cumulative usage by method: ## InsertFragment 65 ## ReduceClash 35 ## CrossOver 2 ## CrossAndInsert 56 ## TwoFragment 31 ## InsertSSBond 3 ## OneRotamer 0 ## ClashingRotamer 11 ## InsertAlignment 8 ## ReduceBreak 29 # best score in super_pool at pool[4] 308.291 bits/residue, 68 clashes 12.3176 breaks # optimizing backbone with 50 conformations in pool # doing 6 generations, with 300 new conformations in each generation. # keep at most 20 conformations from old pool # generation 1: best score 303.339 bits/residue, 65 clashes 7.89934 breaks # Cumulative usage by method: ## InsertFragment 12 ## ReduceClash 9 ## CrossOver 0 ## CrossAndInsert 6 ## TwoFragment 4 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 6 ## InsertAlignment 1 ## ReduceBreak 2 # generation 2: best score 300.683 bits/residue, 91 clashes 7.89934 breaks # Cumulative usage by method: ## InsertFragment 28 ## ReduceClash 13 ## CrossOver 0 ## CrossAndInsert 13 ## TwoFragment 6 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 11 ## InsertAlignment 1 ## ReduceBreak 6 # generation 3: best score 300.683 bits/residue, 91 clashes 7.89934 breaks # Cumulative usage by method: ## InsertFragment 44 ## ReduceClash 17 ## CrossOver 0 ## CrossAndInsert 20 ## TwoFragment 7 ## InsertSSBond 1 ## OneRotamer 0 ## ClashingRotamer 15 ## InsertAlignment 1 ## ReduceBreak 7 # generation 4: best score 296.68 bits/residue, 70 clashes 12.3176 breaks # Cumulative usage by method: ## InsertFragment 60 ## ReduceClash 19 ## CrossOver 0 ## CrossAndInsert 27 ## TwoFragment 8 ## InsertSSBond 1 ## OneRotamer 0 ## ClashingRotamer 16 ## InsertAlignment 1 ## ReduceBreak 10 # generation 5: best score 293.702 bits/residue, 81 clashes 7.89934 breaks # Cumulative usage by method: ## InsertFragment 81 ## ReduceClash 22 ## CrossOver 0 ## CrossAndInsert 38 ## TwoFragment 9 ## InsertSSBond 1 ## OneRotamer 0 ## ClashingRotamer 16 ## InsertAlignment 1 ## ReduceBreak 10 # generation 6: best score 290.33 bits/residue, 69 clashes 7.89934 breaks # Cumulative usage by method: ## InsertFragment 99 ## ReduceClash 25 ## CrossOver 0 ## CrossAndInsert 45 ## TwoFragment 10 ## InsertSSBond 1 ## OneRotamer 0 ## ClashingRotamer 16 ## InsertAlignment 1 ## ReduceBreak 11 # command:# naming current conformation t106-opt # command:# command:# ScwrlConform produces command scwrl -i /projects/compbio/tmp/to_scwrl_1860801111.pdb -s /projects/compbio/tmp/to_scwrl_1860801111.seq -o /projects/compbio/tmp/from_scwrl_1860801111.pdb > /projects/compbio/tmp/scwrl.log # conformation set from SCWRL output # command:# naming current conformation t106-opt-scwrl # command:# command:# ScoreConform t106-rand 406.696 bits/residue, 176 clashes t106-opt at pool[1] 290.33 bits/residue, 69 clashes 7.89934 breaks t106-opt-scwrl at pool[2] 278.735 bits/residue, 44 clashes 7.89934 breaks # command: