# 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 1.5 # clash_penalty 30 nats/clash # ss_bond_bonus 3 # known_ss_bond_bonus 0.1 # chain_break_penalty 15 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:# naming current conformation t113-rand # command:# command:# optimizing backbone with 50 conformations in pool # doing 5 generations, with 100 new conformations in each generation. # keep at most 20 conformations from old pool # best score in initial pool at pool[40] 289.675 bits/residue, 137 clashes 0 breaks # best score after generation 1 285.101 bits/residue, 157 clashes 0 breaks # Cumulative usage by method: ## InsertFragment 12 ## Crossover 0 ## CrossoverAroundFragment 4 ## ClashReducingFragment 17 ## TwoFragments 9 ## InsertSSbond 0 ## RotamerReplacement 0 ## AlignmentInsertion 0 ## BreakReducingFragment 0 # best score after generation 2 281.796 bits/residue, 119 clashes 0 breaks # Cumulative usage by method: ## InsertFragment 27 ## Crossover 0 ## CrossoverAroundFragment 7 ## ClashReducingFragment 34 ## TwoFragments 16 ## InsertSSbond 0 ## RotamerReplacement 0 ## AlignmentInsertion 0 ## BreakReducingFragment 0 # best score after generation 3 274.899 bits/residue, 144 clashes 0 breaks # Cumulative usage by method: ## InsertFragment 36 ## Crossover 0 ## CrossoverAroundFragment 10 ## ClashReducingFragment 53 ## TwoFragments 21 ## InsertSSbond 0 ## RotamerReplacement 0 ## AlignmentInsertion 0 ## BreakReducingFragment 0 # best score after generation 4 273.519 bits/residue, 128 clashes 0 breaks # Cumulative usage by method: ## InsertFragment 41 ## Crossover 0 ## CrossoverAroundFragment 15 ## ClashReducingFragment 69 ## TwoFragments 25 ## InsertSSbond 0 ## RotamerReplacement 0 ## AlignmentInsertion 0 ## BreakReducingFragment 0 # best score after generation 5 272.203 bits/residue, 127 clashes 0 breaks # Cumulative usage by method: ## InsertFragment 51 ## Crossover 0 ## CrossoverAroundFragment 21 ## ClashReducingFragment 81 ## TwoFragments 27 ## InsertSSbond 0 ## RotamerReplacement 0 ## AlignmentInsertion 0 ## BreakReducingFragment 0 # command:# naming current conformation t1133-rand-opt # command:# command:# created fragments for T0113 from T0113-2hsdA.index # command:# created conformation for T0113 by applying fragments # command:# naming current conformation t113-2hsdA # command:# command:# optimizing backbone with 50 conformations in pool # doing 10 generations, with 200 new conformations in each generation. # keep at most 20 conformations from old pool # best score in initial pool at pool[0] 250.526 bits/residue, 220 clashes 29.6513 breaks # best score after generation 1 242.826 bits/residue, 168 clashes 27.6283 breaks # Cumulative usage by method: ## InsertFragment 4 ## Crossover 0 ## CrossoverAroundFragment 10 ## ClashReducingFragment 18 ## TwoFragments 7 ## InsertSSbond 0 ## RotamerReplacement 0 ## AlignmentInsertion 3 ## BreakReducingFragment 4 # best score after generation 2 240.788 bits/residue, 150 clashes 33.3937 breaks # Cumulative usage by method: ## InsertFragment 10 ## Crossover 0 ## CrossoverAroundFragment 11 ## ClashReducingFragment 45 ## TwoFragments 8 ## InsertSSbond 0 ## RotamerReplacement 0 ## AlignmentInsertion 8 ## BreakReducingFragment 6 # best score after generation 3 234.964 bits/residue, 121 clashes 29.8444 breaks # Cumulative usage by method: ## InsertFragment 12 ## Crossover 0 ## CrossoverAroundFragment 14 ## ClashReducingFragment 72 ## TwoFragments 11 ## InsertSSbond 0 ## RotamerReplacement 0 ## AlignmentInsertion 8 ## BreakReducingFragment 9 # best score after generation 4 232.927 bits/residue, 103 clashes 35.6098 breaks # Cumulative usage by method: ## InsertFragment 12 ## Crossover 1 ## CrossoverAroundFragment 16 ## ClashReducingFragment 93 ## TwoFragments 15 ## InsertSSbond 0 ## RotamerReplacement 0 ## AlignmentInsertion 8 ## BreakReducingFragment 14 # best score after generation 5 231.912 bits/residue, 84 clashes 38.5469 breaks # Cumulative usage by method: ## InsertFragment 12 ## Crossover 1 ## CrossoverAroundFragment 17 ## ClashReducingFragment 119 ## TwoFragments 16 ## InsertSSbond 0 ## RotamerReplacement 0 ## AlignmentInsertion 8 ## BreakReducingFragment 20 # best score after generation 6 230.741 bits/residue, 71 clashes 42.1476 breaks # Cumulative usage by method: ## InsertFragment 13 ## Crossover 1 ## CrossoverAroundFragment 19 ## ClashReducingFragment 136 ## TwoFragments 17 ## InsertSSbond 0 ## RotamerReplacement 0 ## AlignmentInsertion 8 ## BreakReducingFragment 29 # best score after generation 7 228.551 bits/residue, 62 clashes 40.1307 breaks # Cumulative usage by method: ## InsertFragment 15 ## Crossover 1 ## CrossoverAroundFragment 20 ## ClashReducingFragment 159 ## TwoFragments 18 ## InsertSSbond 0 ## RotamerReplacement 0 ## AlignmentInsertion 8 ## BreakReducingFragment 32 # best score after generation 8 225.215 bits/residue, 44 clashes 38.4587 breaks # Cumulative usage by method: ## InsertFragment 16 ## Crossover 2 ## CrossoverAroundFragment 22 ## ClashReducingFragment 179 ## TwoFragments 18 ## InsertSSbond 0 ## RotamerReplacement 0 ## AlignmentInsertion 8 ## BreakReducingFragment 38 # best score after generation 9 225.215 bits/residue, 44 clashes 38.4587 breaks # Cumulative usage by method: ## InsertFragment 19 ## Crossover 5 ## CrossoverAroundFragment 23 ## ClashReducingFragment 198 ## TwoFragments 20 ## InsertSSbond 0 ## RotamerReplacement 0 ## AlignmentInsertion 8 ## BreakReducingFragment 40 # best score after generation 10 224.981 bits/residue, 59 clashes 44.7325 breaks # Cumulative usage by method: ## InsertFragment 20 ## Crossover 6 ## CrossoverAroundFragment 26 ## ClashReducingFragment 217 ## TwoFragments 21 ## InsertSSbond 0 ## RotamerReplacement 0 ## AlignmentInsertion 8 ## BreakReducingFragment 45 # command:# naming current conformation t113-2hsdA-opt # command:# 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: 224.981 bits/residue, 59 clashes, rmsd= 0 # best score after iter 1 224.981 bits/residue, 59 clashes, rmsd= 0 # best score after iter 2 224.981 bits/residue, 59 clashes, rmsd= 0 # best score after iter 3 221.506 bits/residue, 36 clashes, rmsd= 0 # best score after iter 4 220.416 bits/residue, 31 clashes, rmsd= 0 # best score after iter 5 220.406 bits/residue, 32 clashes, rmsd= 0 # best score after iter 6 220.055 bits/residue, 30 clashes, rmsd= 0 # best score after iter 7 219.917 bits/residue, 29 clashes, rmsd= 0 # best score after iter 8 219.917 bits/residue, 29 clashes, rmsd= 0 # best score after iter 9 219.917 bits/residue, 29 clashes, rmsd= 0 # best score after iter 10 219.917 bits/residue, 29 clashes, rmsd= 0 # best score after iter 11 219.917 bits/residue, 29 clashes, rmsd= 0 # best score after iter 12 219.869 bits/residue, 29 clashes, rmsd= 0 # best score after iter 13 219.863 bits/residue, 29 clashes, rmsd= 0 # best score after iter 14 219.863 bits/residue, 29 clashes, rmsd= 0 # best score after iter 15 219.863 bits/residue, 29 clashes, rmsd= 0 # best score after iter 16 219.863 bits/residue, 29 clashes, rmsd= 0 # best score after iter 17 219.287 bits/residue, 40 clashes, rmsd= 0 # best score after iter 18 219.287 bits/residue, 40 clashes, rmsd= 0 # best score after iter 19 219.287 bits/residue, 40 clashes, rmsd= 0 # command:# naming current conformation t113-2hsdA-opt-rot # command:# command:# optimizing backbone with 50 conformations in pool # doing 10 generations, with 200 new conformations in each generation. # keep at most 20 conformations from old pool # best score in initial pool at pool[0] 219.287 bits/residue, 40 clashes 44.7325 breaks # best score after generation 1 219.287 bits/residue, 40 clashes 44.7325 breaks # Cumulative usage by method: ## InsertFragment 4 ## Crossover 0 ## CrossoverAroundFragment 8 ## ClashReducingFragment 19 ## TwoFragments 7 ## InsertSSbond 0 ## RotamerReplacement 0 ## AlignmentInsertion 5 ## BreakReducingFragment 3 # best score after generation 2 219.287 bits/residue, 40 clashes 44.7325 breaks # Cumulative usage by method: ## InsertFragment 8 ## Crossover 1 ## CrossoverAroundFragment 12 ## ClashReducingFragment 45 ## TwoFragments 9 ## InsertSSbond 0 ## RotamerReplacement 0 ## AlignmentInsertion 5 ## BreakReducingFragment 7 # best score after generation 3 218.522 bits/residue, 40 clashes 42.1135 breaks # Cumulative usage by method: ## InsertFragment 14 ## Crossover 2 ## CrossoverAroundFragment 15 ## ClashReducingFragment 65 ## TwoFragments 10 ## InsertSSbond 0 ## RotamerReplacement 0 ## AlignmentInsertion 5 ## BreakReducingFragment 13 # best score after generation 4 217.973 bits/residue, 47 clashes 35.6482 breaks # Cumulative usage by method: ## InsertFragment 16 ## Crossover 3 ## CrossoverAroundFragment 16 ## ClashReducingFragment 84 ## TwoFragments 11 ## InsertSSbond 0 ## RotamerReplacement 0 ## AlignmentInsertion 5 ## BreakReducingFragment 19 # best score after generation 5 217.6 bits/residue, 29 clashes 44.2659 breaks # Cumulative usage by method: ## InsertFragment 21 ## Crossover 3 ## CrossoverAroundFragment 17 ## ClashReducingFragment 104 ## TwoFragments 11 ## InsertSSbond 0 ## RotamerReplacement 0 ## AlignmentInsertion 5 ## BreakReducingFragment 23 # best score after generation 6 217.6 bits/residue, 29 clashes 44.2659 breaks # Cumulative usage by method: ## InsertFragment 23 ## Crossover 5 ## CrossoverAroundFragment 18 ## ClashReducingFragment 124 ## TwoFragments 11 ## InsertSSbond 0 ## RotamerReplacement 0 ## AlignmentInsertion 5 ## BreakReducingFragment 28 # best score after generation 7 217.6 bits/residue, 29 clashes 44.2659 breaks # Cumulative usage by method: ## InsertFragment 26 ## Crossover 9 ## CrossoverAroundFragment 19 ## ClashReducingFragment 142 ## TwoFragments 13 ## InsertSSbond 0 ## RotamerReplacement 0 ## AlignmentInsertion 5 ## BreakReducingFragment 30 # best score after generation 8 216.853 bits/residue, 31 clashes 44.5473 breaks # Cumulative usage by method: ## InsertFragment 30 ## Crossover 13 ## CrossoverAroundFragment 21 ## ClashReducingFragment 156 ## TwoFragments 13 ## InsertSSbond 0 ## RotamerReplacement 0 ## AlignmentInsertion 5 ## BreakReducingFragment 36 # best score after generation 9 216.286 bits/residue, 36 clashes 35.1816 breaks # Cumulative usage by method: ## InsertFragment 32 ## Crossover 22 ## CrossoverAroundFragment 22 ## ClashReducingFragment 165 ## TwoFragments 15 ## InsertSSbond 0 ## RotamerReplacement 0 ## AlignmentInsertion 5 ## BreakReducingFragment 43 # best score after generation 10 216.286 bits/residue, 36 clashes 35.1816 breaks # Cumulative usage by method: ## InsertFragment 35 ## Crossover 29 ## CrossoverAroundFragment 23 ## ClashReducingFragment 175 ## TwoFragments 16 ## InsertSSbond 0 ## RotamerReplacement 0 ## AlignmentInsertion 5 ## BreakReducingFragment 51 # command:# naming current conformation t113-2hsdA-opt # command:# 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: 216.286 bits/residue, 36 clashes, rmsd= 0 # best score after iter 1 216.286 bits/residue, 36 clashes, rmsd= 0 # best score after iter 2 216.286 bits/residue, 36 clashes, rmsd= 0 # best score after iter 3 214.716 bits/residue, 34 clashes, rmsd= 0 # best score after iter 4 213.985 bits/residue, 34 clashes, rmsd= 0 # best score after iter 5 213.178 bits/residue, 30 clashes, rmsd= 0 # best score after iter 6 213.178 bits/residue, 30 clashes, rmsd= 0 # best score after iter 7 213.178 bits/residue, 30 clashes, rmsd= 0 # best score after iter 8 213.178 bits/residue, 30 clashes, rmsd= 0 # best score after iter 9 213.178 bits/residue, 30 clashes, rmsd= 0 # best score after iter 10 213.178 bits/residue, 30 clashes, rmsd= 0 # best score after iter 11 213.178 bits/residue, 30 clashes, rmsd= 0 # best score after iter 12 213.178 bits/residue, 30 clashes, rmsd= 0 # best score after iter 13 213.178 bits/residue, 30 clashes, rmsd= 0 # best score after iter 14 213.178 bits/residue, 30 clashes, rmsd= 0 # best score after iter 15 213.178 bits/residue, 30 clashes, rmsd= 0 # best score after iter 16 213.178 bits/residue, 30 clashes, rmsd= 0 # best score after iter 17 213.178 bits/residue, 30 clashes, rmsd= 0 # best score after iter 18 213.178 bits/residue, 30 clashes, rmsd= 0 # best score after iter 19 213.178 bits/residue, 30 clashes, rmsd= 0 # command:# naming current conformation t113-2hsdA-opt-rot # command:# command: