# 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 0.5 # clash_penalty 30 nats/clash # ss_bond_bonus 3 # known_ss_bond_bonus 0.1 # chain_break_penalty 30 nats/Angstrom # wet_spot_weight 3 # dry_spot_weight 40 # command:# Prefix for input files set to # command:Created new target T0113 from T0113.seq # command:# Prefix for output files set to undertaker-out/ # command:# Will now start reporting scores to undertaker-out/t113-6.5w-12d.rdb # command:# created fragments for T0113 from T0113-2hsdA.index # command:# naming current conformation t113-rand # command:# command:# created conformation for T0113 by applying fragments # command:# naming current conformation t113-2hsdA # command:# command:# Will do 8 iterations of optimization # best score in initial pool 241.494 bits/residue, 145 clashes 30.5253 breaks # optimizing backbone with 50 conformations in pool # doing 7 generations, with 200 new conformations in each generation. # keep at most 20 conformations from old pool # generation 1: best score 240.031 bits/residue, 128 clashes 34.991 breaks # Cumulative usage by method: ## InsertFragment 1 ## ReduceClash 4 ## CrossOver 0 ## CrossAndInsert 9 ## TwoFragment 5 ## InsertSSBond 2 ## OneRotamer 0 ## ClashingRotamer 2 ## InsertAlignment 24 ## ReduceBreak 1 # generation 2: best score 238.176 bits/residue, 122 clashes 32.0518 breaks # Cumulative usage by method: ## InsertFragment 6 ## ReduceClash 6 ## CrossOver 1 ## CrossAndInsert 9 ## TwoFragment 5 ## InsertSSBond 2 ## OneRotamer 0 ## ClashingRotamer 4 ## InsertAlignment 58 ## ReduceBreak 1 # generation 3: best score 238.173 bits/residue, 122 clashes 32.0526 breaks # Cumulative usage by method: ## InsertFragment 7 ## ReduceClash 6 ## CrossOver 1 ## CrossAndInsert 9 ## TwoFragment 5 ## InsertSSBond 2 ## OneRotamer 0 ## ClashingRotamer 4 ## InsertAlignment 97 ## ReduceBreak 1 # generation 4: best score 234.954 bits/residue, 90 clashes 38.9368 breaks # Cumulative usage by method: ## InsertFragment 9 ## ReduceClash 7 ## CrossOver 1 ## CrossAndInsert 9 ## TwoFragment 5 ## InsertSSBond 2 ## OneRotamer 0 ## ClashingRotamer 4 ## InsertAlignment 135 ## ReduceBreak 2 # generation 5: best score 234.928 bits/residue, 90 clashes 38.936 breaks # Cumulative usage by method: ## InsertFragment 10 ## ReduceClash 7 ## CrossOver 1 ## CrossAndInsert 10 ## TwoFragment 5 ## InsertSSBond 2 ## OneRotamer 0 ## ClashingRotamer 5 ## InsertAlignment 175 ## ReduceBreak 2 # generation 6: best score 234.923 bits/residue, 90 clashes 38.9724 breaks # Cumulative usage by method: ## InsertFragment 10 ## ReduceClash 8 ## CrossOver 1 ## CrossAndInsert 10 ## TwoFragment 6 ## InsertSSBond 2 ## OneRotamer 0 ## ClashingRotamer 5 ## InsertAlignment 213 ## ReduceBreak 2 # generation 7: best score 232.955 bits/residue, 73 clashes 38.9367 breaks # Cumulative usage by method: ## InsertFragment 11 ## ReduceClash 8 ## CrossOver 1 ## CrossAndInsert 10 ## TwoFragment 6 ## InsertSSBond 2 ## OneRotamer 0 ## ClashingRotamer 8 ## InsertAlignment 241 ## ReduceBreak 2 # best score in initial pool 241.494 bits/residue, 145 clashes 30.5253 breaks # optimizing backbone with 50 conformations in pool # doing 7 generations, with 200 new conformations in each generation. # keep at most 20 conformations from old pool # generation 1: best score 240.241 bits/residue, 129 clashes 35.0071 breaks # Cumulative usage by method: ## InsertFragment 4 ## ReduceClash 7 ## CrossOver 1 ## CrossAndInsert 2 ## TwoFragment 4 ## InsertSSBond 1 ## OneRotamer 0 ## ClashingRotamer 4 ## InsertAlignment 22 ## ReduceBreak 2 # generation 2: best score 238.465 bits/residue, 118 clashes 36.779 breaks # Cumulative usage by method: ## InsertFragment 6 ## ReduceClash 10 ## CrossOver 1 ## CrossAndInsert 3 ## TwoFragment 4 ## InsertSSBond 1 ## OneRotamer 0 ## ClashingRotamer 4 ## InsertAlignment 59 ## ReduceBreak 3 # generation 3: best score 237.298 bits/residue, 107 clashes 32.5947 breaks # Cumulative usage by method: ## InsertFragment 6 ## ReduceClash 12 ## CrossOver 1 ## CrossAndInsert 3 ## TwoFragment 4 ## InsertSSBond 1 ## OneRotamer 0 ## ClashingRotamer 4 ## InsertAlignment 97 ## ReduceBreak 3 # generation 4: best score 236.552 bits/residue, 94 clashes 42.1629 breaks # Cumulative usage by method: ## InsertFragment 6 ## ReduceClash 14 ## CrossOver 2 ## CrossAndInsert 4 ## TwoFragment 4 ## InsertSSBond 1 ## OneRotamer 0 ## ClashingRotamer 4 ## InsertAlignment 134 ## ReduceBreak 4 # generation 5: best score 234.398 bits/residue, 102 clashes 28.4826 breaks # Cumulative usage by method: ## InsertFragment 7 ## ReduceClash 18 ## CrossOver 2 ## CrossAndInsert 4 ## TwoFragment 4 ## InsertSSBond 1 ## OneRotamer 0 ## ClashingRotamer 5 ## InsertAlignment 169 ## ReduceBreak 4 # generation 6: best score 230.048 bits/residue, 52 clashes 41.0107 breaks # Cumulative usage by method: ## InsertFragment 8 ## ReduceClash 21 ## CrossOver 3 ## CrossAndInsert 5 ## TwoFragment 4 ## InsertSSBond 1 ## OneRotamer 0 ## ClashingRotamer 6 ## InsertAlignment 205 ## ReduceBreak 4 # generation 7: best score 230.048 bits/residue, 52 clashes 41.0107 breaks # Cumulative usage by method: ## InsertFragment 9 ## ReduceClash 27 ## CrossOver 3 ## CrossAndInsert 6 ## TwoFragment 4 ## InsertSSBond 1 ## OneRotamer 0 ## ClashingRotamer 6 ## InsertAlignment 236 ## ReduceBreak 4 # best score in initial pool 241.494 bits/residue, 145 clashes 30.5253 breaks # optimizing backbone with 50 conformations in pool # doing 7 generations, with 200 new conformations in each generation. # keep at most 20 conformations from old pool # generation 1: best score 241.494 bits/residue, 145 clashes 30.5253 breaks # Cumulative usage by method: ## InsertFragment 1 ## ReduceClash 5 ## CrossOver 2 ## CrossAndInsert 8 ## TwoFragment 8 ## InsertSSBond 2 ## OneRotamer 0 ## ClashingRotamer 2 ## InsertAlignment 15 ## ReduceBreak 4 # generation 2: best score 236.802 bits/residue, 109 clashes 36.22 breaks # Cumulative usage by method: ## InsertFragment 1 ## ReduceClash 10 ## CrossOver 2 ## CrossAndInsert 10 ## TwoFragment 8 ## InsertSSBond 2 ## OneRotamer 0 ## ClashingRotamer 5 ## InsertAlignment 49 ## ReduceBreak 4 # generation 3: best score 236.708 bits/residue, 108 clashes 36.2205 breaks # Cumulative usage by method: ## InsertFragment 2 ## ReduceClash 14 ## CrossOver 2 ## CrossAndInsert 10 ## TwoFragment 9 ## InsertSSBond 2 ## OneRotamer 0 ## ClashingRotamer 5 ## InsertAlignment 82 ## ReduceBreak 5 # generation 4: best score 234.583 bits/residue, 88 clashes 45.5658 breaks # Cumulative usage by method: ## InsertFragment 2 ## ReduceClash 18 ## CrossOver 2 ## CrossAndInsert 10 ## TwoFragment 9 ## InsertSSBond 2 ## OneRotamer 0 ## ClashingRotamer 5 ## InsertAlignment 118 ## ReduceBreak 5 # generation 5: best score 233.911 bits/residue, 89 clashes 41.9483 breaks # Cumulative usage by method: ## InsertFragment 3 ## ReduceClash 23 ## CrossOver 3 ## CrossAndInsert 10 ## TwoFragment 9 ## InsertSSBond 2 ## OneRotamer 0 ## ClashingRotamer 5 ## InsertAlignment 148 ## ReduceBreak 7 # generation 6: best score 232.294 bits/residue, 78 clashes 43.3024 breaks # Cumulative usage by method: ## InsertFragment 3 ## ReduceClash 26 ## CrossOver 3 ## CrossAndInsert 11 ## TwoFragment 9 ## InsertSSBond 2 ## OneRotamer 0 ## ClashingRotamer 5 ## InsertAlignment 182 ## ReduceBreak 7 # generation 7: best score 232.199 bits/residue, 87 clashes 38.5818 breaks # Cumulative usage by method: ## InsertFragment 3 ## ReduceClash 30 ## CrossOver 6 ## CrossAndInsert 12 ## TwoFragment 9 ## InsertSSBond 2 ## OneRotamer 0 ## ClashingRotamer 5 ## InsertAlignment 211 ## ReduceBreak 7 # best score in initial pool 241.494 bits/residue, 145 clashes 30.5253 breaks # optimizing backbone with 50 conformations in pool # doing 7 generations, with 200 new conformations in each generation. # keep at most 20 conformations from old pool # generation 1: best score 237.55 bits/residue, 105 clashes 37.6105 breaks # Cumulative usage by method: ## InsertFragment 6 ## ReduceClash 6 ## CrossOver 0 ## CrossAndInsert 6 ## TwoFragment 2 ## InsertSSBond 1 ## OneRotamer 0 ## ClashingRotamer 1 ## InsertAlignment 23 ## ReduceBreak 3 # generation 2: best score 236.967 bits/residue, 90 clashes 43.8573 breaks # Cumulative usage by method: ## InsertFragment 7 ## ReduceClash 12 ## CrossOver 0 ## CrossAndInsert 6 ## TwoFragment 3 ## InsertSSBond 1 ## OneRotamer 0 ## ClashingRotamer 1 ## InsertAlignment 58 ## ReduceBreak 5 # generation 3: best score 236.367 bits/residue, 89 clashes 43.587 breaks # Cumulative usage by method: ## InsertFragment 10 ## ReduceClash 13 ## CrossOver 1 ## CrossAndInsert 6 ## TwoFragment 3 ## InsertSSBond 1 ## OneRotamer 0 ## ClashingRotamer 1 ## InsertAlignment 93 ## ReduceBreak 5 # generation 4: best score 234.594 bits/residue, 89 clashes 37.1276 breaks # Cumulative usage by method: ## InsertFragment 11 ## ReduceClash 15 ## CrossOver 1 ## CrossAndInsert 7 ## TwoFragment 4 ## InsertSSBond 1 ## OneRotamer 0 ## ClashingRotamer 1 ## InsertAlignment 125 ## ReduceBreak 6 # generation 5: best score 232.753 bits/residue, 76 clashes 38.4969 breaks # Cumulative usage by method: ## InsertFragment 14 ## ReduceClash 16 ## CrossOver 1 ## CrossAndInsert 9 ## TwoFragment 5 ## InsertSSBond 1 ## OneRotamer 0 ## ClashingRotamer 1 ## InsertAlignment 152 ## ReduceBreak 6 # generation 6: best score 232.328 bits/residue, 76 clashes 36.9789 breaks # Cumulative usage by method: ## InsertFragment 15 ## ReduceClash 17 ## CrossOver 3 ## CrossAndInsert 9 ## TwoFragment 6 ## InsertSSBond 1 ## OneRotamer 0 ## ClashingRotamer 1 ## InsertAlignment 181 ## ReduceBreak 6 # generation 7: best score 232.288 bits/residue, 76 clashes 37.073 breaks # Cumulative usage by method: ## InsertFragment 17 ## ReduceClash 19 ## CrossOver 4 ## CrossAndInsert 9 ## TwoFragment 6 ## InsertSSBond 1 ## OneRotamer 0 ## ClashingRotamer 1 ## InsertAlignment 207 ## ReduceBreak 6 # best score in initial pool 241.494 bits/residue, 145 clashes 30.5253 breaks # optimizing backbone with 50 conformations in pool # doing 7 generations, with 200 new conformations in each generation. # keep at most 20 conformations from old pool # generation 1: best score 237.878 bits/residue, 113 clashes 36.8955 breaks # Cumulative usage by method: ## InsertFragment 1 ## ReduceClash 2 ## CrossOver 0 ## CrossAndInsert 4 ## TwoFragment 7 ## InsertSSBond 2 ## OneRotamer 0 ## ClashingRotamer 1 ## InsertAlignment 28 ## ReduceBreak 2 # generation 2: best score 232.906 bits/residue, 85 clashes 35.3422 breaks # Cumulative usage by method: ## InsertFragment 1 ## ReduceClash 8 ## CrossOver 0 ## CrossAndInsert 6 ## TwoFragment 7 ## InsertSSBond 2 ## OneRotamer 0 ## ClashingRotamer 1 ## InsertAlignment 64 ## ReduceBreak 2 # generation 3: best score 232.467 bits/residue, 82 clashes 35.8047 breaks # Cumulative usage by method: ## InsertFragment 1 ## ReduceClash 10 ## CrossOver 0 ## CrossAndInsert 6 ## TwoFragment 7 ## InsertSSBond 2 ## OneRotamer 0 ## ClashingRotamer 1 ## InsertAlignment 109 ## ReduceBreak 2 # generation 4: best score 232.178 bits/residue, 76 clashes 40.3042 breaks # Cumulative usage by method: ## InsertFragment 2 ## ReduceClash 11 ## CrossOver 1 ## CrossAndInsert 7 ## TwoFragment 7 ## InsertSSBond 2 ## OneRotamer 0 ## ClashingRotamer 1 ## InsertAlignment 149 ## ReduceBreak 2 # generation 5: best score 230.947 bits/residue, 69 clashes 37.1026 breaks # Cumulative usage by method: ## InsertFragment 2 ## ReduceClash 14 ## CrossOver 1 ## CrossAndInsert 7 ## TwoFragment 7 ## InsertSSBond 2 ## OneRotamer 0 ## ClashingRotamer 2 ## InsertAlignment 185 ## ReduceBreak 2 # generation 6: best score 230.578 bits/residue, 69 clashes 34.1816 breaks # Cumulative usage by method: ## InsertFragment 2 ## ReduceClash 16 ## CrossOver 2 ## CrossAndInsert 7 ## TwoFragment 7 ## InsertSSBond 2 ## OneRotamer 0 ## ClashingRotamer 2 ## InsertAlignment 215 ## ReduceBreak 2 # generation 7: best score 230.077 bits/residue, 65 clashes 37.8742 breaks # Cumulative usage by method: ## InsertFragment 2 ## ReduceClash 16 ## CrossOver 3 ## CrossAndInsert 7 ## TwoFragment 7 ## InsertSSBond 2 ## OneRotamer 0 ## ClashingRotamer 2 ## InsertAlignment 251 ## ReduceBreak 2 # best score in initial pool 241.494 bits/residue, 145 clashes 30.5253 breaks # optimizing backbone with 50 conformations in pool # doing 7 generations, with 200 new conformations in each generation. # keep at most 20 conformations from old pool # generation 1: best score 237.635 bits/residue, 125 clashes 25.6625 breaks # Cumulative usage by method: ## InsertFragment 5 ## ReduceClash 5 ## CrossOver 1 ## CrossAndInsert 10 ## TwoFragment 7 ## InsertSSBond 2 ## OneRotamer 0 ## ClashingRotamer 1 ## InsertAlignment 14 ## ReduceBreak 2 # generation 2: best score 236.143 bits/residue, 116 clashes 28.6662 breaks # Cumulative usage by method: ## InsertFragment 9 ## ReduceClash 7 ## CrossOver 2 ## CrossAndInsert 11 ## TwoFragment 8 ## InsertSSBond 2 ## OneRotamer 0 ## ClashingRotamer 2 ## InsertAlignment 46 ## ReduceBreak 4 # generation 3: best score 233.826 bits/residue, 96 clashes 27.8552 breaks # Cumulative usage by method: ## InsertFragment 12 ## ReduceClash 14 ## CrossOver 5 ## CrossAndInsert 13 ## TwoFragment 8 ## InsertSSBond 2 ## OneRotamer 0 ## ClashingRotamer 3 ## InsertAlignment 73 ## ReduceBreak 4 # generation 4: best score 232.397 bits/residue, 66 clashes 44.5147 breaks # Cumulative usage by method: ## InsertFragment 12 ## ReduceClash 18 ## CrossOver 5 ## CrossAndInsert 13 ## TwoFragment 9 ## InsertSSBond 2 ## OneRotamer 0 ## ClashingRotamer 3 ## InsertAlignment 107 ## ReduceBreak 4 # generation 5: best score 231.791 bits/residue, 80 clashes 31.9452 breaks # Cumulative usage by method: ## InsertFragment 14 ## ReduceClash 19 ## CrossOver 10 ## CrossAndInsert 13 ## TwoFragment 11 ## InsertSSBond 2 ## OneRotamer 0 ## ClashingRotamer 3 ## InsertAlignment 139 ## ReduceBreak 4 # generation 6: best score 231.348 bits/residue, 82 clashes 29.783 breaks # Cumulative usage by method: ## InsertFragment 16 ## ReduceClash 24 ## CrossOver 12 ## CrossAndInsert 14 ## TwoFragment 11 ## InsertSSBond 2 ## OneRotamer 0 ## ClashingRotamer 3 ## InsertAlignment 164 ## ReduceBreak 4 # generation 7: best score 231.348 bits/residue, 82 clashes 29.783 breaks # Cumulative usage by method: ## InsertFragment 19 ## ReduceClash 26 ## CrossOver 14 ## CrossAndInsert 14 ## TwoFragment 12 ## InsertSSBond 2 ## OneRotamer 0 ## ClashingRotamer 4 ## InsertAlignment 184 ## ReduceBreak 5 # best score in initial pool 241.494 bits/residue, 145 clashes 30.5253 breaks # optimizing backbone with 50 conformations in pool # doing 7 generations, with 200 new conformations in each generation. # keep at most 20 conformations from old pool # generation 1: best score 241.485 bits/residue, 145 clashes 30.5256 breaks # Cumulative usage by method: ## InsertFragment 2 ## ReduceClash 3 ## CrossOver 0 ## CrossAndInsert 5 ## TwoFragment 6 ## InsertSSBond 1 ## OneRotamer 0 ## ClashingRotamer 2 ## InsertAlignment 22 ## ReduceBreak 5 # generation 2: best score 237.543 bits/residue, 112 clashes 39.5006 breaks # Cumulative usage by method: ## InsertFragment 4 ## ReduceClash 7 ## CrossOver 0 ## CrossAndInsert 9 ## TwoFragment 8 ## InsertSSBond 1 ## OneRotamer 0 ## ClashingRotamer 2 ## InsertAlignment 53 ## ReduceBreak 5 # generation 3: best score 231.307 bits/residue, 59 clashes 40.493 breaks # Cumulative usage by method: ## InsertFragment 4 ## ReduceClash 17 ## CrossOver 0 ## CrossAndInsert 9 ## TwoFragment 8 ## InsertSSBond 1 ## OneRotamer 0 ## ClashingRotamer 2 ## InsertAlignment 81 ## ReduceBreak 6 # generation 4: best score 231.26 bits/residue, 61 clashes 38.3583 breaks # Cumulative usage by method: ## InsertFragment 8 ## ReduceClash 21 ## CrossOver 0 ## CrossAndInsert 9 ## TwoFragment 8 ## InsertSSBond 1 ## OneRotamer 0 ## ClashingRotamer 2 ## InsertAlignment 112 ## ReduceBreak 6 # generation 5: best score 230.104 bits/residue, 60 clashes 37.6951 breaks # Cumulative usage by method: ## InsertFragment 11 ## ReduceClash 26 ## CrossOver 0 ## CrossAndInsert 9 ## TwoFragment 8 ## InsertSSBond 1 ## OneRotamer 0 ## ClashingRotamer 3 ## InsertAlignment 138 ## ReduceBreak 7 # generation 6: best score 230.104 bits/residue, 60 clashes 37.6951 breaks # Cumulative usage by method: ## InsertFragment 11 ## ReduceClash 27 ## CrossOver 0 ## CrossAndInsert 10 ## TwoFragment 8 ## InsertSSBond 1 ## OneRotamer 0 ## ClashingRotamer 4 ## InsertAlignment 165 ## ReduceBreak 7 # generation 7: best score 229.883 bits/residue, 45 clashes 44.4175 breaks # Cumulative usage by method: ## InsertFragment 12 ## ReduceClash 28 ## CrossOver 1 ## CrossAndInsert 10 ## TwoFragment 9 ## InsertSSBond 1 ## OneRotamer 0 ## ClashingRotamer 5 ## InsertAlignment 190 ## ReduceBreak 7 # best score in initial pool 241.494 bits/residue, 145 clashes 30.5253 breaks # optimizing backbone with 50 conformations in pool # doing 7 generations, with 200 new conformations in each generation. # keep at most 20 conformations from old pool # generation 1: best score 232.844 bits/residue, 88 clashes 27.2647 breaks # Cumulative usage by method: ## InsertFragment 6 ## ReduceClash 4 ## CrossOver 0 ## CrossAndInsert 3 ## TwoFragment 4 ## InsertSSBond 2 ## OneRotamer 0 ## ClashingRotamer 2 ## InsertAlignment 19 ## ReduceBreak 6 # generation 2: best score 232.832 bits/residue, 88 clashes 27.2518 breaks # Cumulative usage by method: ## InsertFragment 7 ## ReduceClash 8 ## CrossOver 0 ## CrossAndInsert 5 ## TwoFragment 5 ## InsertSSBond 2 ## OneRotamer 0 ## ClashingRotamer 6 ## InsertAlignment 51 ## ReduceBreak 6 # generation 3: best score 232.832 bits/residue, 88 clashes 27.2518 breaks # Cumulative usage by method: ## InsertFragment 8 ## ReduceClash 10 ## CrossOver 0 ## CrossAndInsert 5 ## TwoFragment 6 ## InsertSSBond 2 ## OneRotamer 0 ## ClashingRotamer 11 ## InsertAlignment 79 ## ReduceBreak 6 # generation 4: best score 229.807 bits/residue, 69 clashes 27.1813 breaks # Cumulative usage by method: ## InsertFragment 12 ## ReduceClash 14 ## CrossOver 0 ## CrossAndInsert 5 ## TwoFragment 6 ## InsertSSBond 2 ## OneRotamer 0 ## ClashingRotamer 12 ## InsertAlignment 99 ## ReduceBreak 7 # generation 5: best score 229.807 bits/residue, 69 clashes 27.1813 breaks # Cumulative usage by method: ## InsertFragment 13 ## ReduceClash 19 ## CrossOver 0 ## CrossAndInsert 7 ## TwoFragment 7 ## InsertSSBond 2 ## OneRotamer 0 ## ClashingRotamer 13 ## InsertAlignment 119 ## ReduceBreak 7 # generation 6: best score 229.807 bits/residue, 69 clashes 27.1813 breaks # Cumulative usage by method: ## InsertFragment 15 ## ReduceClash 23 ## CrossOver 1 ## CrossAndInsert 7 ## TwoFragment 7 ## InsertSSBond 2 ## OneRotamer 0 ## ClashingRotamer 15 ## InsertAlignment 140 ## ReduceBreak 7 # generation 7: best score 228.267 bits/residue, 48 clashes 32.0044 breaks # Cumulative usage by method: ## InsertFragment 16 ## ReduceClash 23 ## CrossOver 1 ## CrossAndInsert 9 ## TwoFragment 9 ## InsertSSBond 2 ## OneRotamer 0 ## ClashingRotamer 18 ## InsertAlignment 162 ## ReduceBreak 7 # best score in super_pool at pool[7] 228.267 bits/residue, 48 clashes 32.0044 breaks # optimizing backbone with 50 conformations in pool # doing 7 generations, with 200 new conformations in each generation. # keep at most 20 conformations from old pool # generation 1: best score 228.267 bits/residue, 48 clashes 32.0044 breaks # Cumulative usage by method: ## InsertFragment 3 ## ReduceClash 6 ## CrossOver 0 ## CrossAndInsert 5 ## TwoFragment 2 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 4 ## InsertAlignment 19 ## ReduceBreak 2 # generation 2: best score 228.267 bits/residue, 48 clashes 32.0044 breaks # Cumulative usage by method: ## InsertFragment 7 ## ReduceClash 11 ## CrossOver 0 ## CrossAndInsert 5 ## TwoFragment 3 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 10 ## InsertAlignment 32 ## ReduceBreak 4 # generation 3: best score 228.267 bits/residue, 48 clashes 32.0044 breaks # Cumulative usage by method: ## InsertFragment 9 ## ReduceClash 15 ## CrossOver 0 ## CrossAndInsert 6 ## TwoFragment 4 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 15 ## InsertAlignment 46 ## ReduceBreak 7 # generation 4: best score 228.267 bits/residue, 48 clashes 32.0044 breaks # Cumulative usage by method: ## InsertFragment 10 ## ReduceClash 20 ## CrossOver 0 ## CrossAndInsert 8 ## TwoFragment 5 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 25 ## InsertAlignment 57 ## ReduceBreak 7 # generation 5: best score 228.267 bits/residue, 48 clashes 32.0044 breaks # Cumulative usage by method: ## InsertFragment 13 ## ReduceClash 26 ## CrossOver 0 ## CrossAndInsert 9 ## TwoFragment 5 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 35 ## InsertAlignment 66 ## ReduceBreak 8 # generation 6: best score 227.037 bits/residue, 43 clashes 25.0754 breaks # Cumulative usage by method: ## InsertFragment 16 ## ReduceClash 34 ## CrossOver 0 ## CrossAndInsert 10 ## TwoFragment 6 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 46 ## InsertAlignment 72 ## ReduceBreak 8 # generation 7: best score 227.037 bits/residue, 43 clashes 25.0754 breaks # Cumulative usage by method: ## InsertFragment 18 ## ReduceClash 41 ## CrossOver 2 ## CrossAndInsert 12 ## TwoFragment 6 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 54 ## InsertAlignment 81 ## ReduceBreak 8 # command:# naming current conformation t113-opt # command:# command:# Optimizing rotamers with 30 blocks of 100 conformations # P(change) = 0.9 * 0.9^ iter # P(new) = 0.5 * 0.95^ iter # P(neighbor) = 0.5 * 0.95^ iter # P(archetype) = 0.9 * 0.9^ iter # P(best_residue) = 0.9 * 0.9^ iter # clash penalty 30 nats/clash # ss_bond bonus 3 # sidechain weight 0.5 # best score from archetype iter: 227.037 bits/residue, 43 clashes, rmsd= 0 # best score after iter 1 227.037 bits/residue, 43 clashes, rmsd= 0 # best score after iter 2 227.037 bits/residue, 43 clashes, rmsd= 0 # best score after iter 3 227.037 bits/residue, 43 clashes, rmsd= 0 # best score after iter 4 227.037 bits/residue, 43 clashes, rmsd= 0 # best score after iter 5 226.311 bits/residue, 41 clashes, rmsd= 0 # best score after iter 6 226.116 bits/residue, 40 clashes, rmsd= 0 # best score after iter 7 225.837 bits/residue, 58 clashes, rmsd= 0 # best score after iter 8 223.679 bits/residue, 25 clashes, rmsd= 0 # best score after iter 9 223.015 bits/residue, 51 clashes, rmsd= 0 # best score after iter 10 223.015 bits/residue, 51 clashes, rmsd= 0 # best score after iter 11 222.758 bits/residue, 45 clashes, rmsd= 0 # best score after iter 12 222.758 bits/residue, 45 clashes, rmsd= 0 # best score after iter 13 222.758 bits/residue, 45 clashes, rmsd= 0 # best score after iter 14 222.758 bits/residue, 45 clashes, rmsd= 0 # best score after iter 15 221.95 bits/residue, 40 clashes, rmsd= 0 # best score after iter 16 221.95 bits/residue, 40 clashes, rmsd= 0 # best score after iter 17 221.95 bits/residue, 40 clashes, rmsd= 0 # best score after iter 18 221.679 bits/residue, 41 clashes, rmsd= 0 # best score after iter 19 221.061 bits/residue, 43 clashes, rmsd= 0 # best score after iter 20 221.061 bits/residue, 43 clashes, rmsd= 0 # best score after iter 21 220.096 bits/residue, 38 clashes, rmsd= 0 # best score after iter 22 219.346 bits/residue, 32 clashes, rmsd= 0 # best score after iter 23 219.346 bits/residue, 32 clashes, rmsd= 0 # best score after iter 24 218.753 bits/residue, 31 clashes, rmsd= 0 # best score after iter 25 217.467 bits/residue, 26 clashes, rmsd= 0 # best score after iter 26 217.467 bits/residue, 26 clashes, rmsd= 0 # best score after iter 27 217.467 bits/residue, 26 clashes, rmsd= 0 # best score after iter 28 217.467 bits/residue, 26 clashes, rmsd= 0 # best score after iter 29 217.467 bits/residue, 26 clashes, rmsd= 0 # command:# naming current conformation t113-opt-rot # command:# command:# Will now start reporting scores to undertaker-out/t113-6.5w-12d-rot.rdb # command:# Score parameters set to # sidechain_weight 1.5 # clash_penalty 30 nats/clash # ss_bond_bonus 3 # known_ss_bond_bonus 0.1 # chain_break_penalty 30 nats/Angstrom # wet_spot_weight 1 # dry_spot_weight 2 # command:# Optimizing rotamers with 20 blocks of 100 conformations # P(change) = 0.9 * 0.9^ iter # P(new) = 0.5 * 0.95^ iter # P(neighbor) = 0.5 * 0.95^ iter # P(archetype) = 0.9 * 0.9^ iter # P(best_residue) = 0.9 * 0.9^ iter # clash penalty 30 nats/clash # ss_bond bonus 3 # sidechain weight 1.5 # best score from archetype iter: 20.8029 bits/residue, 26 clashes, rmsd= 0 # best score after iter 1 17.7835 bits/residue, 23 clashes, rmsd= 0 # best score after iter 2 16.109 bits/residue, 33 clashes, rmsd= 0 # best score after iter 3 15.5314 bits/residue, 31 clashes, rmsd= 0 # best score after iter 4 15.5314 bits/residue, 31 clashes, rmsd= 0 # best score after iter 5 15.5314 bits/residue, 31 clashes, rmsd= 0 # best score after iter 6 15.5314 bits/residue, 31 clashes, rmsd= 0 # best score after iter 7 15.5314 bits/residue, 31 clashes, rmsd= 0 # best score after iter 8 15.5314 bits/residue, 31 clashes, rmsd= 0 # best score after iter 9 15.5314 bits/residue, 31 clashes, rmsd= 0 # best score after iter 10 15.4068 bits/residue, 32 clashes, rmsd= 0 # best score after iter 11 15.4005 bits/residue, 32 clashes, rmsd= 0 # best score after iter 12 15.4005 bits/residue, 32 clashes, rmsd= 0 # best score after iter 13 15.339 bits/residue, 32 clashes, rmsd= 0 # best score after iter 14 15.3137 bits/residue, 32 clashes, rmsd= 0 # best score after iter 15 15.2742 bits/residue, 32 clashes, rmsd= 0 # best score after iter 16 15.2586 bits/residue, 32 clashes, rmsd= 0 # best score after iter 17 15.2532 bits/residue, 32 clashes, rmsd= 0 # best score after iter 18 15.2464 bits/residue, 32 clashes, rmsd= 0 # best score after iter 19 15.245 bits/residue, 32 clashes, rmsd= 0 # command:# naming current conformation t113-opt-rot-rot # command:# command:# ScwrlConform produces command scwrl -i /projects/compbio/tmp/to_scwrl_1212980632.pdb -s /projects/compbio/tmp/to_scwrl_1212980632.seq -o /projects/compbio/tmp/from_scwrl_1212980632.pdb > /projects/compbio/tmp/scwrl.log # conformation set from SCWRL output # command:# naming current conformation t113-opt-scwrl # command:# command:# ScoreConform t113-rand 80.057 bits/residue, 425 clashes t113-2hsdA at pool[1] 62.3127 bits/residue, 145 clashes 30.5253 breaks t113-opt at pool[2] 22.6672 bits/residue, 43 clashes 25.0754 breaks t113-opt-rot at pool[3] 20.8029 bits/residue, 26 clashes 25.0754 breaks t113-opt-rot-rot at pool[4] 15.245 bits/residue, 32 clashes 25.0754 breaks t113-opt-scwrl at pool[5] 15.7828 bits/residue, 35 clashes 25.0754 breaks # command: