# 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 1 # chain_break_penalty 50 nats/Angstrom # wet_spot_weight 2 # dry_spot_weight 50 # command:# Will now start reporting scores to t106-6.5w-12d.rdb # command:# Prefix for input files set to # command:Created new target T0106 from ../T0106.seq # 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:# created fragments for T0106 from T0106-1txb-local.index # command:# created fragments for T0106 from 1txb-T0106-local.index # command:# created fragments for T0106 from 1lpbA-T0106-local.index # command:# SSbond between 2 and 10 # command:# SSbond between 56 and 63 # command:# SSbond between 79 and 86 # command:# SSbond between 103 and 114 # command:# SSbond between 47 and 75 # command:# naming current conformation t106-2-10-rand # command:# Will do 10 iterations of optimization # best score in initial pool at pool[41] 364.726 bits/residue, 42 clashes 13.9624 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 356.829 bits/residue, 65 clashes 13.9624 breaks # Cumulative usage by method: ## InsertFragment 5 ## ReduceClash 4 ## CrossOver 0 ## CrossAndInsert 9 ## TwoFragment 12 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 4 ## InsertAlignment 6 ## ReduceBreak 6 # generation 2: best score 345.396 bits/residue, 15 clashes 0 breaks # Cumulative usage by method: ## InsertFragment 10 ## ReduceClash 9 ## CrossOver 1 ## CrossAndInsert 20 ## TwoFragment 18 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 12 ## InsertAlignment 10 ## ReduceBreak 11 # generation 3: best score 340.012 bits/residue, 10 clashes # Cumulative usage by method: ## InsertFragment 15 ## ReduceClash 11 ## CrossOver 1 ## CrossAndInsert 37 ## TwoFragment 26 ## InsertSSBond 1 ## OneRotamer 0 ## ClashingRotamer 22 ## InsertAlignment 12 ## ReduceBreak 12 # generation 4: best score 337.096 bits/residue, 27 clashes # Cumulative usage by method: ## InsertFragment 17 ## ReduceClash 15 ## CrossOver 1 ## CrossAndInsert 50 ## TwoFragment 31 ## InsertSSBond 1 ## OneRotamer 0 ## ClashingRotamer 39 ## InsertAlignment 13 ## ReduceBreak 12 # generation 5: best score 334.4 bits/residue, 35 clashes # Cumulative usage by method: ## InsertFragment 22 ## ReduceClash 19 ## CrossOver 1 ## CrossAndInsert 60 ## TwoFragment 35 ## InsertSSBond 3 ## OneRotamer 0 ## ClashingRotamer 50 ## InsertAlignment 16 ## ReduceBreak 12 # generation 6: best score 328.523 bits/residue, 13 clashes 0 breaks # Cumulative usage by method: ## InsertFragment 30 ## ReduceClash 24 ## CrossOver 1 ## CrossAndInsert 72 ## TwoFragment 37 ## InsertSSBond 3 ## OneRotamer 0 ## ClashingRotamer 62 ## InsertAlignment 17 ## ReduceBreak 12 # best score in initial pool at pool[29] 386.275 bits/residue, 103 clashes 30.4725 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 349.38 bits/residue, 75 clashes 22.3712 breaks # Cumulative usage by method: ## InsertFragment 7 ## ReduceClash 6 ## CrossOver 2 ## CrossAndInsert 8 ## TwoFragment 9 ## InsertSSBond 2 ## OneRotamer 0 ## ClashingRotamer 0 ## InsertAlignment 5 ## ReduceBreak 7 # generation 2: best score 346.03 bits/residue, 71 clashes 21.7731 breaks # Cumulative usage by method: ## InsertFragment 13 ## ReduceClash 12 ## CrossOver 3 ## CrossAndInsert 17 ## TwoFragment 21 ## InsertSSBond 2 ## OneRotamer 0 ## ClashingRotamer 3 ## InsertAlignment 8 ## ReduceBreak 12 # generation 3: best score 342.295 bits/residue, 95 clashes 8.22064 breaks # Cumulative usage by method: ## InsertFragment 21 ## ReduceClash 19 ## CrossOver 3 ## CrossAndInsert 28 ## TwoFragment 28 ## InsertSSBond 2 ## OneRotamer 0 ## ClashingRotamer 3 ## InsertAlignment 9 ## ReduceBreak 17 # generation 4: best score 331.398 bits/residue, 73 clashes 5.57062 breaks # Cumulative usage by method: ## InsertFragment 35 ## ReduceClash 23 ## CrossOver 6 ## CrossAndInsert 36 ## TwoFragment 33 ## InsertSSBond 3 ## OneRotamer 0 ## ClashingRotamer 3 ## InsertAlignment 9 ## ReduceBreak 19 # generation 5: best score 328.751 bits/residue, 72 clashes 5.57062 breaks # Cumulative usage by method: ## InsertFragment 49 ## ReduceClash 27 ## CrossOver 10 ## CrossAndInsert 44 ## TwoFragment 39 ## InsertSSBond 3 ## OneRotamer 0 ## ClashingRotamer 3 ## InsertAlignment 9 ## ReduceBreak 20 # generation 6: best score 325.371 bits/residue, 72 clashes 5.57062 breaks # Cumulative usage by method: ## InsertFragment 65 ## ReduceClash 28 ## CrossOver 13 ## CrossAndInsert 54 ## TwoFragment 41 ## InsertSSBond 3 ## OneRotamer 0 ## ClashingRotamer 3 ## InsertAlignment 9 ## ReduceBreak 20 # best score in initial pool at pool[1] 384.053 bits/residue, 90 clashes # 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 359.826 bits/residue, 66 clashes 0 breaks # Cumulative usage by method: ## InsertFragment 13 ## ReduceClash 6 ## CrossOver 0 ## CrossAndInsert 9 ## TwoFragment 10 ## InsertSSBond 1 ## OneRotamer 0 ## ClashingRotamer 1 ## InsertAlignment 6 ## ReduceBreak 1 # generation 2: best score 353.257 bits/residue, 81 clashes # Cumulative usage by method: ## InsertFragment 23 ## ReduceClash 13 ## CrossOver 0 ## CrossAndInsert 21 ## TwoFragment 18 ## InsertSSBond 1 ## OneRotamer 0 ## ClashingRotamer 1 ## InsertAlignment 15 ## ReduceBreak 1 # generation 3: best score 342.731 bits/residue, 67 clashes 14.7738 breaks # Cumulative usage by method: ## InsertFragment 36 ## ReduceClash 23 ## CrossOver 0 ## CrossAndInsert 33 ## TwoFragment 23 ## InsertSSBond 1 ## OneRotamer 0 ## ClashingRotamer 1 ## InsertAlignment 18 ## ReduceBreak 1 # generation 4: best score 336.609 bits/residue, 48 clashes # Cumulative usage by method: ## InsertFragment 46 ## ReduceClash 39 ## CrossOver 0 ## CrossAndInsert 41 ## TwoFragment 27 ## InsertSSBond 2 ## OneRotamer 0 ## ClashingRotamer 1 ## InsertAlignment 24 ## ReduceBreak 1 # generation 5: best score 335.051 bits/residue, 60 clashes # Cumulative usage by method: ## InsertFragment 60 ## ReduceClash 50 ## CrossOver 1 ## CrossAndInsert 46 ## TwoFragment 32 ## InsertSSBond 2 ## OneRotamer 0 ## ClashingRotamer 1 ## InsertAlignment 26 ## ReduceBreak 1 # generation 6: best score 322.83 bits/residue, 34 clashes # Cumulative usage by method: ## InsertFragment 67 ## ReduceClash 61 ## CrossOver 1 ## CrossAndInsert 56 ## TwoFragment 34 ## InsertSSBond 2 ## OneRotamer 0 ## ClashingRotamer 1 ## InsertAlignment 27 ## ReduceBreak 1 # best score in initial pool at pool[12] 381.798 bits/residue, 99 clashes 30.5434 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 376.647 bits/residue, 40 clashes 19.9365 breaks # Cumulative usage by method: ## InsertFragment 4 ## ReduceClash 4 ## CrossOver 1 ## CrossAndInsert 10 ## TwoFragment 9 ## InsertSSBond 5 ## OneRotamer 0 ## ClashingRotamer 5 ## InsertAlignment 4 ## ReduceBreak 4 # generation 2: best score 362.307 bits/residue, 155 clashes 8.03813 breaks # Cumulative usage by method: ## InsertFragment 10 ## ReduceClash 12 ## CrossOver 2 ## CrossAndInsert 23 ## TwoFragment 11 ## InsertSSBond 5 ## OneRotamer 0 ## ClashingRotamer 10 ## InsertAlignment 6 ## ReduceBreak 9 # generation 3: best score 354.625 bits/residue, 91 clashes 10.6835 breaks # Cumulative usage by method: ## InsertFragment 16 ## ReduceClash 24 ## CrossOver 2 ## CrossAndInsert 35 ## TwoFragment 20 ## InsertSSBond 5 ## OneRotamer 0 ## ClashingRotamer 13 ## InsertAlignment 9 ## ReduceBreak 9 # generation 4: best score 345.763 bits/residue, 49 clashes 12.2197 breaks # Cumulative usage by method: ## InsertFragment 19 ## ReduceClash 29 ## CrossOver 3 ## CrossAndInsert 55 ## TwoFragment 27 ## InsertSSBond 6 ## OneRotamer 0 ## ClashingRotamer 18 ## InsertAlignment 9 ## ReduceBreak 10 # generation 5: best score 340.735 bits/residue, 112 clashes 8.03813 breaks # Cumulative usage by method: ## InsertFragment 30 ## ReduceClash 35 ## CrossOver 4 ## CrossAndInsert 70 ## TwoFragment 30 ## InsertSSBond 7 ## OneRotamer 0 ## ClashingRotamer 21 ## InsertAlignment 9 ## ReduceBreak 10 # generation 6: best score 337.465 bits/residue, 76 clashes 14.7401 breaks # Cumulative usage by method: ## InsertFragment 37 ## ReduceClash 46 ## CrossOver 4 ## CrossAndInsert 81 ## TwoFragment 33 ## InsertSSBond 7 ## OneRotamer 0 ## ClashingRotamer 25 ## InsertAlignment 11 ## ReduceBreak 11 # best score in initial pool at pool[33] 391.823 bits/residue, 120 clashes 29.6215 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 377.755 bits/residue, 50 clashes 29.6215 breaks # Cumulative usage by method: ## InsertFragment 8 ## ReduceClash 13 ## CrossOver 0 ## CrossAndInsert 3 ## TwoFragment 7 ## InsertSSBond 2 ## OneRotamer 0 ## ClashingRotamer 6 ## InsertAlignment 5 ## ReduceBreak 3 # generation 2: best score 367.401 bits/residue, 86 clashes 37.6188 breaks # Cumulative usage by method: ## InsertFragment 15 ## ReduceClash 31 ## CrossOver 0 ## CrossAndInsert 9 ## TwoFragment 10 ## InsertSSBond 4 ## OneRotamer 0 ## ClashingRotamer 17 ## InsertAlignment 7 ## ReduceBreak 3 # generation 3: best score 357.585 bits/residue, 74 clashes 29.8077 breaks # Cumulative usage by method: ## InsertFragment 25 ## ReduceClash 48 ## CrossOver 0 ## CrossAndInsert 18 ## TwoFragment 19 ## InsertSSBond 4 ## OneRotamer 0 ## ClashingRotamer 20 ## InsertAlignment 7 ## ReduceBreak 3 # generation 4: best score 352.131 bits/residue, 73 clashes 29.6215 breaks # Cumulative usage by method: ## InsertFragment 37 ## ReduceClash 55 ## CrossOver 0 ## CrossAndInsert 25 ## TwoFragment 26 ## InsertSSBond 4 ## OneRotamer 0 ## ClashingRotamer 30 ## InsertAlignment 9 ## ReduceBreak 3 # generation 5: best score 340.749 bits/residue, 78 clashes 29.8077 breaks # Cumulative usage by method: ## InsertFragment 50 ## ReduceClash 65 ## CrossOver 0 ## CrossAndInsert 33 ## TwoFragment 30 ## InsertSSBond 4 ## OneRotamer 0 ## ClashingRotamer 38 ## InsertAlignment 9 ## ReduceBreak 3 # generation 6: best score 333.886 bits/residue, 69 clashes 29.8077 breaks # Cumulative usage by method: ## InsertFragment 63 ## ReduceClash 74 ## CrossOver 0 ## CrossAndInsert 39 ## TwoFragment 32 ## InsertSSBond 4 ## OneRotamer 0 ## ClashingRotamer 50 ## InsertAlignment 9 ## ReduceBreak 3 # best score in initial pool at pool[12] 375.63 bits/residue, 130 clashes 11.2058 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 362.555 bits/residue, 94 clashes 11.2058 breaks # Cumulative usage by method: ## InsertFragment 7 ## ReduceClash 6 ## CrossOver 0 ## CrossAndInsert 13 ## TwoFragment 6 ## InsertSSBond 2 ## OneRotamer 0 ## ClashingRotamer 6 ## InsertAlignment 3 ## ReduceBreak 4 # generation 2: best score 355.134 bits/residue, 102 clashes 11.2058 breaks # Cumulative usage by method: ## InsertFragment 17 ## ReduceClash 15 ## CrossOver 0 ## CrossAndInsert 21 ## TwoFragment 11 ## InsertSSBond 2 ## OneRotamer 0 ## ClashingRotamer 9 ## InsertAlignment 7 ## ReduceBreak 8 # generation 3: best score 346.133 bits/residue, 90 clashes 4.43014 breaks # Cumulative usage by method: ## InsertFragment 33 ## ReduceClash 25 ## CrossOver 1 ## CrossAndInsert 29 ## TwoFragment 15 ## InsertSSBond 2 ## OneRotamer 0 ## ClashingRotamer 9 ## InsertAlignment 10 ## ReduceBreak 8 # generation 4: best score 345.571 bits/residue, 47 clashes 12.1917 breaks # Cumulative usage by method: ## InsertFragment 45 ## ReduceClash 34 ## CrossOver 2 ## CrossAndInsert 37 ## TwoFragment 21 ## InsertSSBond 2 ## OneRotamer 0 ## ClashingRotamer 10 ## InsertAlignment 10 ## ReduceBreak 11 # generation 5: best score 339.54 bits/residue, 53 clashes 12.1917 breaks # Cumulative usage by method: ## InsertFragment 59 ## ReduceClash 40 ## CrossOver 2 ## CrossAndInsert 48 ## TwoFragment 26 ## InsertSSBond 2 ## OneRotamer 0 ## ClashingRotamer 10 ## InsertAlignment 10 ## ReduceBreak 11 # generation 6: best score 328.453 bits/residue, 40 clashes 12.1917 breaks # Cumulative usage by method: ## InsertFragment 73 ## ReduceClash 45 ## CrossOver 3 ## CrossAndInsert 64 ## TwoFragment 28 ## InsertSSBond 2 ## OneRotamer 0 ## ClashingRotamer 11 ## InsertAlignment 10 ## ReduceBreak 12 # best score in initial pool at pool[26] 368.261 bits/residue, 48 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 360.478 bits/residue, 71 clashes 0 breaks # Cumulative usage by method: ## InsertFragment 7 ## ReduceClash 9 ## CrossOver 0 ## CrossAndInsert 10 ## TwoFragment 5 ## InsertSSBond 4 ## OneRotamer 0 ## ClashingRotamer 1 ## InsertAlignment 4 ## ReduceBreak 3 # generation 2: best score 345.099 bits/residue, 80 clashes 0 breaks # Cumulative usage by method: ## InsertFragment 13 ## ReduceClash 21 ## CrossOver 0 ## CrossAndInsert 24 ## TwoFragment 13 ## InsertSSBond 6 ## OneRotamer 0 ## ClashingRotamer 2 ## InsertAlignment 5 ## ReduceBreak 4 # generation 3: best score 345.086 bits/residue, 81 clashes # Cumulative usage by method: ## InsertFragment 20 ## ReduceClash 30 ## CrossOver 0 ## CrossAndInsert 42 ## TwoFragment 21 ## InsertSSBond 9 ## OneRotamer 0 ## ClashingRotamer 2 ## InsertAlignment 5 ## ReduceBreak 5 # generation 4: best score 338.967 bits/residue, 74 clashes # Cumulative usage by method: ## InsertFragment 35 ## ReduceClash 35 ## CrossOver 0 ## CrossAndInsert 56 ## TwoFragment 25 ## InsertSSBond 11 ## OneRotamer 0 ## ClashingRotamer 2 ## InsertAlignment 6 ## ReduceBreak 6 # generation 5: best score 334.697 bits/residue, 74 clashes # Cumulative usage by method: ## InsertFragment 42 ## ReduceClash 42 ## CrossOver 0 ## CrossAndInsert 75 ## TwoFragment 29 ## InsertSSBond 11 ## OneRotamer 0 ## ClashingRotamer 2 ## InsertAlignment 7 ## ReduceBreak 6 # generation 6: best score 329.604 bits/residue, 76 clashes # Cumulative usage by method: ## InsertFragment 52 ## ReduceClash 50 ## CrossOver 0 ## CrossAndInsert 92 ## TwoFragment 30 ## InsertSSBond 11 ## OneRotamer 0 ## ClashingRotamer 3 ## InsertAlignment 7 ## ReduceBreak 6 # best score in initial pool at pool[48] 394.338 bits/residue, 130 clashes 34.1616 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 367.16 bits/residue, 97 clashes 44.9442 breaks # Cumulative usage by method: ## InsertFragment 12 ## ReduceClash 6 ## CrossOver 1 ## CrossAndInsert 5 ## TwoFragment 4 ## InsertSSBond 2 ## OneRotamer 0 ## ClashingRotamer 2 ## InsertAlignment 5 ## ReduceBreak 7 # generation 2: best score 362.741 bits/residue, 97 clashes 39.5633 breaks # Cumulative usage by method: ## InsertFragment 23 ## ReduceClash 18 ## CrossOver 2 ## CrossAndInsert 12 ## TwoFragment 7 ## InsertSSBond 3 ## OneRotamer 0 ## ClashingRotamer 5 ## InsertAlignment 7 ## ReduceBreak 14 # generation 3: best score 358.017 bits/residue, 61 clashes 42.6418 breaks # Cumulative usage by method: ## InsertFragment 30 ## ReduceClash 31 ## CrossOver 4 ## CrossAndInsert 22 ## TwoFragment 9 ## InsertSSBond 4 ## OneRotamer 0 ## ClashingRotamer 5 ## InsertAlignment 9 ## ReduceBreak 18 # generation 4: best score 339.306 bits/residue, 52 clashes 4.50979 breaks # Cumulative usage by method: ## InsertFragment 38 ## ReduceClash 45 ## CrossOver 6 ## CrossAndInsert 34 ## TwoFragment 9 ## InsertSSBond 5 ## OneRotamer 0 ## ClashingRotamer 5 ## InsertAlignment 10 ## ReduceBreak 21 # generation 5: best score 335.362 bits/residue, 52 clashes 4.50979 breaks # Cumulative usage by method: ## InsertFragment 49 ## ReduceClash 62 ## CrossOver 8 ## CrossAndInsert 41 ## TwoFragment 13 ## InsertSSBond 6 ## OneRotamer 0 ## ClashingRotamer 8 ## InsertAlignment 10 ## ReduceBreak 21 # generation 6: best score 323.919 bits/residue, 48 clashes 0 breaks # Cumulative usage by method: ## InsertFragment 63 ## ReduceClash 71 ## CrossOver 11 ## CrossAndInsert 48 ## TwoFragment 16 ## InsertSSBond 7 ## OneRotamer 0 ## ClashingRotamer 9 ## InsertAlignment 11 ## ReduceBreak 22 # best score in initial pool at pool[3] 360.334 bits/residue, 99 clashes 25.4232 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 352.149 bits/residue, 65 clashes 17.522 breaks # Cumulative usage by method: ## InsertFragment 10 ## ReduceClash 11 ## CrossOver 0 ## CrossAndInsert 8 ## TwoFragment 8 ## InsertSSBond 1 ## OneRotamer 0 ## ClashingRotamer 2 ## InsertAlignment 6 ## ReduceBreak 1 # generation 2: best score 346.741 bits/residue, 53 clashes 17.522 breaks # Cumulative usage by method: ## InsertFragment 22 ## ReduceClash 25 ## CrossOver 1 ## CrossAndInsert 15 ## TwoFragment 12 ## InsertSSBond 3 ## OneRotamer 0 ## ClashingRotamer 3 ## InsertAlignment 8 ## ReduceBreak 1 # generation 3: best score 344.887 bits/residue, 56 clashes 17.522 breaks # Cumulative usage by method: ## InsertFragment 36 ## ReduceClash 32 ## CrossOver 1 ## CrossAndInsert 23 ## TwoFragment 17 ## InsertSSBond 3 ## OneRotamer 0 ## ClashingRotamer 4 ## InsertAlignment 9 ## ReduceBreak 2 # generation 4: best score 344.887 bits/residue, 56 clashes 17.522 breaks # Cumulative usage by method: ## InsertFragment 52 ## ReduceClash 44 ## CrossOver 2 ## CrossAndInsert 26 ## TwoFragment 19 ## InsertSSBond 3 ## OneRotamer 0 ## ClashingRotamer 5 ## InsertAlignment 9 ## ReduceBreak 3 # generation 5: best score 341.345 bits/residue, 47 clashes 17.522 breaks # Cumulative usage by method: ## InsertFragment 65 ## ReduceClash 53 ## CrossOver 2 ## CrossAndInsert 27 ## TwoFragment 21 ## InsertSSBond 3 ## OneRotamer 0 ## ClashingRotamer 10 ## InsertAlignment 9 ## ReduceBreak 3 # generation 6: best score 339.546 bits/residue, 24 clashes 17.522 breaks # Cumulative usage by method: ## InsertFragment 80 ## ReduceClash 60 ## CrossOver 2 ## CrossAndInsert 31 ## TwoFragment 21 ## InsertSSBond 4 ## OneRotamer 0 ## ClashingRotamer 13 ## InsertAlignment 9 ## ReduceBreak 3 # best score in initial pool at pool[22] 375.36 bits/residue, 60 clashes 12.2197 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 368.432 bits/residue, 58 clashes 12.2197 breaks # Cumulative usage by method: ## InsertFragment 7 ## ReduceClash 6 ## CrossOver 0 ## CrossAndInsert 10 ## TwoFragment 10 ## InsertSSBond 3 ## OneRotamer 0 ## ClashingRotamer 1 ## InsertAlignment 6 ## ReduceBreak 5 # generation 2: best score 354.538 bits/residue, 66 clashes 11.6447 breaks # Cumulative usage by method: ## InsertFragment 14 ## ReduceClash 11 ## CrossOver 0 ## CrossAndInsert 21 ## TwoFragment 21 ## InsertSSBond 3 ## OneRotamer 0 ## ClashingRotamer 2 ## InsertAlignment 14 ## ReduceBreak 9 # generation 3: best score 348.225 bits/residue, 84 clashes 12.2197 breaks # Cumulative usage by method: ## InsertFragment 23 ## ReduceClash 17 ## CrossOver 0 ## CrossAndInsert 38 ## TwoFragment 31 ## InsertSSBond 4 ## OneRotamer 0 ## ClashingRotamer 3 ## InsertAlignment 16 ## ReduceBreak 9 # generation 4: best score 334.092 bits/residue, 66 clashes 4.96331 breaks # Cumulative usage by method: ## InsertFragment 38 ## ReduceClash 32 ## CrossOver 0 ## CrossAndInsert 45 ## TwoFragment 34 ## InsertSSBond 5 ## OneRotamer 0 ## ClashingRotamer 3 ## InsertAlignment 18 ## ReduceBreak 9 # generation 5: best score 333.672 bits/residue, 65 clashes 4.96331 breaks # Cumulative usage by method: ## InsertFragment 50 ## ReduceClash 40 ## CrossOver 0 ## CrossAndInsert 52 ## TwoFragment 39 ## InsertSSBond 5 ## OneRotamer 0 ## ClashingRotamer 4 ## InsertAlignment 21 ## ReduceBreak 11 # generation 6: best score 332.289 bits/residue, 63 clashes 5.25815 breaks # Cumulative usage by method: ## InsertFragment 59 ## ReduceClash 51 ## CrossOver 1 ## CrossAndInsert 60 ## TwoFragment 43 ## InsertSSBond 5 ## OneRotamer 0 ## ClashingRotamer 7 ## InsertAlignment 21 ## ReduceBreak 11 # best score in super_pool at pool[2] 322.83 bits/residue, 34 clashes # 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 319.456 bits/residue, 38 clashes # Cumulative usage by method: ## InsertFragment 13 ## ReduceClash 7 ## CrossOver 0 ## CrossAndInsert 10 ## TwoFragment 7 ## InsertSSBond 2 ## OneRotamer 0 ## ClashingRotamer 0 ## InsertAlignment 0 ## ReduceBreak 2 # generation 2: best score 315.386 bits/residue, 37 clashes # Cumulative usage by method: ## InsertFragment 26 ## ReduceClash 11 ## CrossOver 0 ## CrossAndInsert 21 ## TwoFragment 9 ## InsertSSBond 2 ## OneRotamer 0 ## ClashingRotamer 0 ## InsertAlignment 1 ## ReduceBreak 2 # generation 3: best score 314.742 bits/residue, 37 clashes # Cumulative usage by method: ## InsertFragment 44 ## ReduceClash 13 ## CrossOver 0 ## CrossAndInsert 26 ## TwoFragment 12 ## InsertSSBond 3 ## OneRotamer 0 ## ClashingRotamer 0 ## InsertAlignment 2 ## ReduceBreak 2 # generation 4: best score 313.982 bits/residue, 38 clashes # Cumulative usage by method: ## InsertFragment 58 ## ReduceClash 17 ## CrossOver 2 ## CrossAndInsert 34 ## TwoFragment 14 ## InsertSSBond 3 ## OneRotamer 0 ## ClashingRotamer 0 ## InsertAlignment 2 ## ReduceBreak 2 # generation 5: best score 309.315 bits/residue, 34 clashes # Cumulative usage by method: ## InsertFragment 69 ## ReduceClash 23 ## CrossOver 6 ## CrossAndInsert 45 ## TwoFragment 16 ## InsertSSBond 3 ## OneRotamer 0 ## ClashingRotamer 0 ## InsertAlignment 2 ## ReduceBreak 2 # generation 6: best score 308.505 bits/residue, 54 clashes # Cumulative usage by method: ## InsertFragment 90 ## ReduceClash 25 ## CrossOver 9 ## CrossAndInsert 48 ## TwoFragment 16 ## InsertSSBond 3 ## OneRotamer 0 ## ClashingRotamer 0 ## InsertAlignment 3 ## ReduceBreak 2 # command:# naming current conformation t106-2-10-opt # command:# command:# ScwrlConform produces command scwrl -i /projects/compbio/tmp/to_scwrl_2055695202.pdb -s /projects/compbio/tmp/to_scwrl_2055695202.seq -o /projects/compbio/tmp/from_scwrl_2055695202.pdb > /projects/compbio/tmp/scwrl.log # conformation set from SCWRL output # command:# naming current conformation t106-2-10-opt-scwrl # command:# command:# command:# ScoreConform t106-2-10-rand 406.696 bits/residue, 176 clashes t106-2-10-opt at pool[1] 311.005 bits/residue, 54 clashes t106-2-10-opt-scwrl at pool[2] 312.864 bits/residue, 36 clashes # command: