# 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 40 nats/clash # ss_bond_bonus 0 # 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 T0099 from ../T0099.seq # command:# Will now start reporting scores to t99-6.5w-12d.rdb # command:# created fragments for T0099 from 1ckaA-1.index # command:# created fragments for T0099 from 1ckaA-2.index # command:# created fragments for T0099 from 1pht-N.index # command:# created fragments for T0099 from 1pht-T0099-local.index # command:# created fragments for T0099 from 1ckaA-T0099-local.index # command:# created fragments for T0099 from 5hck-all.index # command:# created conformation for T0099 by applying fragments # command:# naming current conformation t99-5hck # command:# command:# ScwrlConform produces command scwrl -i /projects/compbio/tmp/to_scwrl_63107222.pdb -s /projects/compbio/tmp/to_scwrl_63107222.seq -o /projects/compbio/tmp/from_scwrl_63107222.pdb > /projects/compbio/tmp/scwrl.log # conformation set from SCWRL output # command:# naming current conformation t99-5hck-scwrl # command:# command:# Optimizing rotamers with 40 blocks of 250 conformations # P(change) = 1 * 0.95^ iter # P(new) = 0.1 * 0.95^ iter # P(neighbor) = 0.5 * 0.95^ iter # P(archetype) = 0.9 * 0.9^ iter # P(best_residue) = 1 * 0.95^ iter # clash penalty 40 nats/clash # ss_bond bonus 0 # sidechain weight 1 # best score from archetype iter: 273.971 bits/residue, 11 clashes, rmsd= 0 # best score after iter 1 268.627 bits/residue, 5 clashes, rmsd= 0 # best score after iter 2 257.89 bits/residue, 1 clashes, rmsd= 0 # best score after iter 3 255.017 bits/residue, 1 clashes, rmsd= 0 # best score after iter 4 254.298 bits/residue, 1 clashes, rmsd= 0 # best score after iter 5 254.209 bits/residue, 1 clashes, rmsd= 0 # best score after iter 6 253.718 bits/residue, 1 clashes, rmsd= 0 # best score after iter 7 253.539 bits/residue, 1 clashes, rmsd= 0 # best score after iter 8 253.161 bits/residue, 0 clashes, rmsd= 0 # best score after iter 9 252.652 bits/residue, 0 clashes, rmsd= 0 # best score after iter 10 252.1 bits/residue, 0 clashes, rmsd= 0 # best score after iter 11 252.093 bits/residue, 0 clashes, rmsd= 0 # best score after iter 12 252.03 bits/residue, 0 clashes, rmsd= 0 # best score after iter 13 251.893 bits/residue, 0 clashes, rmsd= 0 # best score after iter 14 251.893 bits/residue, 0 clashes, rmsd= 0 # best score after iter 15 251.893 bits/residue, 0 clashes, rmsd= 0 # best score after iter 16 251.893 bits/residue, 0 clashes, rmsd= 0 # best score after iter 17 251.859 bits/residue, 0 clashes, rmsd= 0 # best score after iter 18 251.66 bits/residue, 0 clashes, rmsd= 0 # best score after iter 19 251.408 bits/residue, 0 clashes, rmsd= 0 # best score after iter 20 251.408 bits/residue, 0 clashes, rmsd= 0 # best score after iter 21 251.223 bits/residue, 0 clashes, rmsd= 0 # best score after iter 22 251.223 bits/residue, 0 clashes, rmsd= 0 # best score after iter 23 251.216 bits/residue, 0 clashes, rmsd= 0 # best score after iter 24 251.128 bits/residue, 0 clashes, rmsd= 0 # best score after iter 25 251.12 bits/residue, 0 clashes, rmsd= 0 # best score after iter 26 251.039 bits/residue, 0 clashes, rmsd= 0 # best score after iter 27 251.033 bits/residue, 0 clashes, rmsd= 0 # best score after iter 28 251.033 bits/residue, 0 clashes, rmsd= 0 # best score after iter 29 251.033 bits/residue, 0 clashes, rmsd= 0 # best score after iter 30 250.979 bits/residue, 0 clashes, rmsd= 0 # best score after iter 31 250.979 bits/residue, 0 clashes, rmsd= 0 # best score after iter 32 250.979 bits/residue, 0 clashes, rmsd= 0 # best score after iter 33 250.979 bits/residue, 0 clashes, rmsd= 0 # best score after iter 34 250.979 bits/residue, 0 clashes, rmsd= 0 # best score after iter 35 250.894 bits/residue, 0 clashes, rmsd= 0 # best score after iter 36 250.894 bits/residue, 0 clashes, rmsd= 0 # best score after iter 37 250.894 bits/residue, 0 clashes, rmsd= 0 # best score after iter 38 250.877 bits/residue, 0 clashes, rmsd= 0 # best score after iter 39 250.877 bits/residue, 0 clashes, rmsd= 0 # command:# naming current conformation t99-5hck-rot # command:# command:# Will do 5 iterations of optimization # best score in initial pool 250.877 bits/residue, 0 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 250.877 bits/residue, 0 clashes 0 breaks # Cumulative usage by method: ## InsertFragment 3 ## ReduceClash 3 ## CrossOver 0 ## CrossAndInsert 3 ## TwoFragment 1 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 7 ## InsertAlignment 23 ## ReduceBreak 2 # generation 2: best score 250.877 bits/residue, 0 clashes 0 breaks # Cumulative usage by method: ## InsertFragment 4 ## ReduceClash 5 ## CrossOver 0 ## CrossAndInsert 8 ## TwoFragment 1 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 25 ## InsertAlignment 37 ## ReduceBreak 2 # generation 3: best score 250.877 bits/residue, 0 clashes 0 breaks # Cumulative usage by method: ## InsertFragment 4 ## ReduceClash 6 ## CrossOver 1 ## CrossAndInsert 9 ## TwoFragment 1 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 38 ## InsertAlignment 51 ## ReduceBreak 2 # generation 4: best score 250.877 bits/residue, 0 clashes 0 breaks # Cumulative usage by method: ## InsertFragment 6 ## ReduceClash 6 ## CrossOver 1 ## CrossAndInsert 10 ## TwoFragment 1 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 55 ## InsertAlignment 61 ## ReduceBreak 2 # generation 5: best score 250.016 bits/residue, 2 clashes 0 breaks # Cumulative usage by method: ## InsertFragment 7 ## ReduceClash 7 ## CrossOver 3 ## CrossAndInsert 12 ## TwoFragment 1 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 76 ## InsertAlignment 64 ## ReduceBreak 2 # generation 6: best score 249.253 bits/residue, 1 clashes 0 breaks # Cumulative usage by method: ## InsertFragment 7 ## ReduceClash 7 ## CrossOver 6 ## CrossAndInsert 13 ## TwoFragment 1 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 103 ## InsertAlignment 64 ## ReduceBreak 2 # best score in initial pool 250.877 bits/residue, 0 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 250.877 bits/residue, 0 clashes 0 breaks # Cumulative usage by method: ## InsertFragment 5 ## ReduceClash 5 ## CrossOver 0 ## CrossAndInsert 3 ## TwoFragment 1 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 9 ## InsertAlignment 20 ## ReduceBreak 0 # generation 2: best score 250.877 bits/residue, 0 clashes 0 breaks # Cumulative usage by method: ## InsertFragment 5 ## ReduceClash 5 ## CrossOver 1 ## CrossAndInsert 3 ## TwoFragment 1 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 24 ## InsertAlignment 36 ## ReduceBreak 0 # generation 3: best score 250.877 bits/residue, 0 clashes 0 breaks # Cumulative usage by method: ## InsertFragment 6 ## ReduceClash 5 ## CrossOver 8 ## CrossAndInsert 3 ## TwoFragment 1 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 42 ## InsertAlignment 40 ## ReduceBreak 0 # generation 4: best score 250.877 bits/residue, 0 clashes # Cumulative usage by method: ## InsertFragment 8 ## ReduceClash 5 ## CrossOver 17 ## CrossAndInsert 5 ## TwoFragment 1 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 62 ## InsertAlignment 40 ## ReduceBreak 0 # generation 5: best score 250.482 bits/residue, 0 clashes # Cumulative usage by method: ## InsertFragment 8 ## ReduceClash 5 ## CrossOver 23 ## CrossAndInsert 7 ## TwoFragment 1 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 91 ## InsertAlignment 40 ## ReduceBreak 0 # generation 6: best score 250.482 bits/residue, 0 clashes # Cumulative usage by method: ## InsertFragment 9 ## ReduceClash 5 ## CrossOver 41 ## CrossAndInsert 7 ## TwoFragment 1 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 107 ## InsertAlignment 40 ## ReduceBreak 0 # best score in initial pool 250.877 bits/residue, 0 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 249.962 bits/residue, 2 clashes 0 breaks # Cumulative usage by method: ## InsertFragment 2 ## ReduceClash 7 ## CrossOver 0 ## CrossAndInsert 6 ## TwoFragment 2 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 8 ## InsertAlignment 13 ## ReduceBreak 2 # generation 2: best score 249.945 bits/residue, 2 clashes 0 breaks # Cumulative usage by method: ## InsertFragment 3 ## ReduceClash 9 ## CrossOver 0 ## CrossAndInsert 8 ## TwoFragment 2 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 25 ## InsertAlignment 28 ## ReduceBreak 2 # generation 3: best score 248.783 bits/residue, 0 clashes 0 breaks # Cumulative usage by method: ## InsertFragment 4 ## ReduceClash 12 ## CrossOver 0 ## CrossAndInsert 13 ## TwoFragment 3 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 54 ## InsertAlignment 28 ## ReduceBreak 2 # generation 4: best score 248.783 bits/residue, 0 clashes 0 breaks # Cumulative usage by method: ## InsertFragment 5 ## ReduceClash 15 ## CrossOver 0 ## CrossAndInsert 13 ## TwoFragment 4 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 84 ## InsertAlignment 28 ## ReduceBreak 2 # generation 5: best score 248.783 bits/residue, 0 clashes 0 breaks # Cumulative usage by method: ## InsertFragment 5 ## ReduceClash 18 ## CrossOver 0 ## CrossAndInsert 15 ## TwoFragment 4 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 113 ## InsertAlignment 28 ## ReduceBreak 2 # generation 6: best score 247.928 bits/residue, 0 clashes 0 breaks # Cumulative usage by method: ## InsertFragment 6 ## ReduceClash 20 ## CrossOver 1 ## CrossAndInsert 16 ## TwoFragment 4 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 138 ## InsertAlignment 28 ## ReduceBreak 2 # best score in initial pool 250.877 bits/residue, 0 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 250.877 bits/residue, 0 clashes 0 breaks # Cumulative usage by method: ## InsertFragment 6 ## ReduceClash 4 ## CrossOver 0 ## CrossAndInsert 4 ## TwoFragment 1 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 4 ## InsertAlignment 19 ## ReduceBreak 4 # generation 2: best score 250.877 bits/residue, 0 clashes 0 breaks # Cumulative usage by method: ## InsertFragment 13 ## ReduceClash 4 ## CrossOver 0 ## CrossAndInsert 6 ## TwoFragment 3 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 14 ## InsertAlignment 31 ## ReduceBreak 4 # generation 3: best score 250.85 bits/residue, 0 clashes # Cumulative usage by method: ## InsertFragment 17 ## ReduceClash 5 ## CrossOver 2 ## CrossAndInsert 9 ## TwoFragment 3 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 24 ## InsertAlignment 41 ## ReduceBreak 4 # generation 4: best score 249.208 bits/residue, 0 clashes # Cumulative usage by method: ## InsertFragment 20 ## ReduceClash 6 ## CrossOver 2 ## CrossAndInsert 14 ## TwoFragment 3 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 41 ## InsertAlignment 47 ## ReduceBreak 4 # generation 5: best score 249.208 bits/residue, 0 clashes # Cumulative usage by method: ## InsertFragment 24 ## ReduceClash 6 ## CrossOver 5 ## CrossAndInsert 18 ## TwoFragment 3 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 59 ## InsertAlignment 48 ## ReduceBreak 4 # generation 6: best score 249.208 bits/residue, 0 clashes # Cumulative usage by method: ## InsertFragment 24 ## ReduceClash 9 ## CrossOver 6 ## CrossAndInsert 18 ## TwoFragment 3 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 94 ## InsertAlignment 48 ## ReduceBreak 4 # best score in initial pool 250.877 bits/residue, 0 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 250.877 bits/residue, 0 clashes 0 breaks # Cumulative usage by method: ## InsertFragment 7 ## ReduceClash 3 ## CrossOver 1 ## CrossAndInsert 11 ## TwoFragment 2 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 4 ## InsertAlignment 17 ## ReduceBreak 0 # generation 2: best score 250.877 bits/residue, 0 clashes 0 breaks # Cumulative usage by method: ## InsertFragment 7 ## ReduceClash 6 ## CrossOver 2 ## CrossAndInsert 17 ## TwoFragment 2 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 14 ## InsertAlignment 33 ## ReduceBreak 0 # generation 3: best score 250.096 bits/residue, 2 clashes # Cumulative usage by method: ## InsertFragment 12 ## ReduceClash 7 ## CrossOver 5 ## CrossAndInsert 21 ## TwoFragment 2 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 24 ## InsertAlignment 41 ## ReduceBreak 0 # generation 4: best score 249.791 bits/residue, 1 clashes # Cumulative usage by method: ## InsertFragment 13 ## ReduceClash 8 ## CrossOver 15 ## CrossAndInsert 21 ## TwoFragment 2 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 40 ## InsertAlignment 43 ## ReduceBreak 0 # generation 5: best score 249.118 bits/residue, 0 clashes # Cumulative usage by method: ## InsertFragment 14 ## ReduceClash 9 ## CrossOver 16 ## CrossAndInsert 22 ## TwoFragment 2 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 78 ## InsertAlignment 43 ## ReduceBreak 0 # generation 6: best score 248.7 bits/residue, 0 clashes # Cumulative usage by method: ## InsertFragment 15 ## ReduceClash 11 ## CrossOver 22 ## CrossAndInsert 22 ## TwoFragment 2 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 108 ## InsertAlignment 43 ## ReduceBreak 0 # best score in super_pool at pool[2] 247.928 bits/residue, 0 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 247.928 bits/residue, 0 clashes 0 breaks # Cumulative usage by method: ## InsertFragment 5 ## ReduceClash 4 ## CrossOver 0 ## CrossAndInsert 8 ## TwoFragment 5 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 4 ## InsertAlignment 13 ## ReduceBreak 0 # generation 2: best score 247.928 bits/residue, 0 clashes 0 breaks # Cumulative usage by method: ## InsertFragment 9 ## ReduceClash 6 ## CrossOver 1 ## CrossAndInsert 15 ## TwoFragment 5 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 9 ## InsertAlignment 25 ## ReduceBreak 0 # generation 3: best score 247.928 bits/residue, 0 clashes 0 breaks # Cumulative usage by method: ## InsertFragment 12 ## ReduceClash 7 ## CrossOver 6 ## CrossAndInsert 17 ## TwoFragment 5 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 22 ## InsertAlignment 32 ## ReduceBreak 0 # generation 4: best score 247.928 bits/residue, 0 clashes 0 breaks # Cumulative usage by method: ## InsertFragment 13 ## ReduceClash 11 ## CrossOver 13 ## CrossAndInsert 18 ## TwoFragment 5 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 41 ## InsertAlignment 32 ## ReduceBreak 0 # generation 5: best score 247.872 bits/residue, 0 clashes # Cumulative usage by method: ## InsertFragment 13 ## ReduceClash 14 ## CrossOver 27 ## CrossAndInsert 19 ## TwoFragment 5 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 56 ## InsertAlignment 32 ## ReduceBreak 0 # generation 6: best score 247.796 bits/residue, 0 clashes # Cumulative usage by method: ## InsertFragment 13 ## ReduceClash 14 ## CrossOver 54 ## CrossAndInsert 21 ## TwoFragment 5 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 59 ## InsertAlignment 32 ## ReduceBreak 0 # command:# naming current conformation t99-opt # command:# command:# Optimizing rotamers with 40 blocks of 250 conformations # P(change) = 1 * 0.95^ iter # P(new) = 0.1 * 0.95^ iter # P(neighbor) = 0.5 * 0.95^ iter # P(archetype) = 0.9 * 0.9^ iter # P(best_residue) = 1 * 0.95^ iter # clash penalty 40 nats/clash # ss_bond bonus 0 # sidechain weight 1 # best score from archetype iter: 247.796 bits/residue, 0 clashes, rmsd= 0 # best score after iter 1 247.796 bits/residue, 0 clashes, rmsd= 0 # best score after iter 2 247.796 bits/residue, 0 clashes, rmsd= 0 # best score after iter 3 247.796 bits/residue, 0 clashes, rmsd= 0 # best score after iter 4 247.796 bits/residue, 0 clashes, rmsd= 0 # best score after iter 5 247.796 bits/residue, 0 clashes, rmsd= 0 # best score after iter 6 247.796 bits/residue, 0 clashes, rmsd= 0 # best score after iter 7 247.796 bits/residue, 0 clashes, rmsd= 0 # best score after iter 8 247.796 bits/residue, 0 clashes, rmsd= 0 # best score after iter 9 247.796 bits/residue, 0 clashes, rmsd= 0 # best score after iter 10 247.796 bits/residue, 0 clashes, rmsd= 0 # best score after iter 11 247.796 bits/residue, 0 clashes, rmsd= 0 # best score after iter 12 247.796 bits/residue, 0 clashes, rmsd= 0 # best score after iter 13 247.796 bits/residue, 0 clashes, rmsd= 0 # best score after iter 14 247.796 bits/residue, 0 clashes, rmsd= 0 # best score after iter 15 247.796 bits/residue, 0 clashes, rmsd= 0 # best score after iter 16 247.796 bits/residue, 0 clashes, rmsd= 0 # best score after iter 17 247.796 bits/residue, 0 clashes, rmsd= 0 # best score after iter 18 247.796 bits/residue, 0 clashes, rmsd= 0 # best score after iter 19 247.796 bits/residue, 0 clashes, rmsd= 0 # best score after iter 20 247.796 bits/residue, 0 clashes, rmsd= 0 # best score after iter 21 247.796 bits/residue, 0 clashes, rmsd= 0 # best score after iter 22 247.796 bits/residue, 0 clashes, rmsd= 0 # best score after iter 23 247.796 bits/residue, 0 clashes, rmsd= 0 # best score after iter 24 247.796 bits/residue, 0 clashes, rmsd= 0 # best score after iter 25 247.796 bits/residue, 0 clashes, rmsd= 0 # best score after iter 26 247.796 bits/residue, 0 clashes, rmsd= 0 # best score after iter 27 247.796 bits/residue, 0 clashes, rmsd= 0 # best score after iter 28 247.796 bits/residue, 0 clashes, rmsd= 0 # best score after iter 29 247.796 bits/residue, 0 clashes, rmsd= 0 # best score after iter 30 247.796 bits/residue, 0 clashes, rmsd= 0 # best score after iter 31 247.796 bits/residue, 0 clashes, rmsd= 0 # best score after iter 32 247.796 bits/residue, 0 clashes, rmsd= 0 # best score after iter 33 247.796 bits/residue, 0 clashes, rmsd= 0 # best score after iter 34 247.796 bits/residue, 0 clashes, rmsd= 0 # best score after iter 35 247.796 bits/residue, 0 clashes, rmsd= 0 # best score after iter 36 247.796 bits/residue, 0 clashes, rmsd= 0 # best score after iter 37 247.796 bits/residue, 0 clashes, rmsd= 0 # best score after iter 38 247.796 bits/residue, 0 clashes, rmsd= 0 # best score after iter 39 247.796 bits/residue, 0 clashes, rmsd= 0 # command:# naming current conformation t99-5hck-opt-rot # command:# command:# Will do 5 iterations of optimization # best score in initial pool 247.796 bits/residue, 0 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 247.796 bits/residue, 0 clashes # Cumulative usage by method: ## InsertFragment 6 ## ReduceClash 2 ## CrossOver 0 ## CrossAndInsert 6 ## TwoFragment 1 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 6 ## InsertAlignment 17 ## ReduceBreak 3 # generation 2: best score 247.796 bits/residue, 0 clashes # Cumulative usage by method: ## InsertFragment 13 ## ReduceClash 3 ## CrossOver 0 ## CrossAndInsert 8 ## TwoFragment 1 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 21 ## InsertAlignment 28 ## ReduceBreak 3 # generation 3: best score 247.796 bits/residue, 0 clashes # Cumulative usage by method: ## InsertFragment 14 ## ReduceClash 4 ## CrossOver 0 ## CrossAndInsert 10 ## TwoFragment 1 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 47 ## InsertAlignment 32 ## ReduceBreak 3 # generation 4: best score 247.796 bits/residue, 0 clashes # Cumulative usage by method: ## InsertFragment 14 ## ReduceClash 5 ## CrossOver 0 ## CrossAndInsert 10 ## TwoFragment 1 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 87 ## InsertAlignment 32 ## ReduceBreak 3 # generation 5: best score 247.796 bits/residue, 0 clashes # Cumulative usage by method: ## InsertFragment 16 ## ReduceClash 5 ## CrossOver 0 ## CrossAndInsert 11 ## TwoFragment 1 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 121 ## InsertAlignment 32 ## ReduceBreak 3 # generation 6: best score 247.796 bits/residue, 0 clashes # Cumulative usage by method: ## InsertFragment 16 ## ReduceClash 6 ## CrossOver 0 ## CrossAndInsert 12 ## TwoFragment 1 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 158 ## InsertAlignment 32 ## ReduceBreak 3 # best score in initial pool 247.796 bits/residue, 0 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 247.796 bits/residue, 0 clashes # Cumulative usage by method: ## InsertFragment 5 ## ReduceClash 4 ## CrossOver 0 ## CrossAndInsert 3 ## TwoFragment 1 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 5 ## InsertAlignment 12 ## ReduceBreak 9 # generation 2: best score 247.796 bits/residue, 0 clashes # Cumulative usage by method: ## InsertFragment 10 ## ReduceClash 7 ## CrossOver 1 ## CrossAndInsert 7 ## TwoFragment 1 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 19 ## InsertAlignment 21 ## ReduceBreak 9 # generation 3: best score 247.796 bits/residue, 0 clashes # Cumulative usage by method: ## InsertFragment 10 ## ReduceClash 8 ## CrossOver 2 ## CrossAndInsert 9 ## TwoFragment 1 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 38 ## InsertAlignment 33 ## ReduceBreak 9 # generation 4: best score 247.796 bits/residue, 0 clashes # Cumulative usage by method: ## InsertFragment 13 ## ReduceClash 8 ## CrossOver 4 ## CrossAndInsert 11 ## TwoFragment 1 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 61 ## InsertAlignment 34 ## ReduceBreak 9 # generation 5: best score 247.796 bits/residue, 0 clashes # Cumulative usage by method: ## InsertFragment 13 ## ReduceClash 8 ## CrossOver 10 ## CrossAndInsert 14 ## TwoFragment 1 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 79 ## InsertAlignment 38 ## ReduceBreak 9 # generation 6: best score 247.796 bits/residue, 0 clashes # Cumulative usage by method: ## InsertFragment 13 ## ReduceClash 8 ## CrossOver 21 ## CrossAndInsert 14 ## TwoFragment 1 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 102 ## InsertAlignment 38 ## ReduceBreak 9 # best score in initial pool 247.796 bits/residue, 0 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 247.796 bits/residue, 0 clashes # Cumulative usage by method: ## InsertFragment 2 ## ReduceClash 8 ## CrossOver 0 ## CrossAndInsert 6 ## TwoFragment 0 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 7 ## InsertAlignment 13 ## ReduceBreak 2 # generation 2: best score 247.796 bits/residue, 0 clashes # Cumulative usage by method: ## InsertFragment 6 ## ReduceClash 10 ## CrossOver 0 ## CrossAndInsert 12 ## TwoFragment 0 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 21 ## InsertAlignment 19 ## ReduceBreak 2 # generation 3: best score 247.796 bits/residue, 0 clashes # Cumulative usage by method: ## InsertFragment 8 ## ReduceClash 10 ## CrossOver 0 ## CrossAndInsert 14 ## TwoFragment 0 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 46 ## InsertAlignment 27 ## ReduceBreak 2 # generation 4: best score 247.796 bits/residue, 0 clashes # Cumulative usage by method: ## InsertFragment 9 ## ReduceClash 15 ## CrossOver 0 ## CrossAndInsert 14 ## TwoFragment 0 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 82 ## InsertAlignment 27 ## ReduceBreak 2 # generation 5: best score 247.796 bits/residue, 0 clashes # Cumulative usage by method: ## InsertFragment 10 ## ReduceClash 21 ## CrossOver 0 ## CrossAndInsert 16 ## TwoFragment 0 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 116 ## InsertAlignment 27 ## ReduceBreak 2 # generation 6: best score 247.796 bits/residue, 0 clashes # Cumulative usage by method: ## InsertFragment 11 ## ReduceClash 25 ## CrossOver 0 ## CrossAndInsert 16 ## TwoFragment 0 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 155 ## InsertAlignment 27 ## ReduceBreak 2 # best score in initial pool 247.796 bits/residue, 0 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 247.796 bits/residue, 0 clashes # Cumulative usage by method: ## InsertFragment 6 ## ReduceClash 0 ## CrossOver 1 ## CrossAndInsert 9 ## TwoFragment 0 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 2 ## InsertAlignment 19 ## ReduceBreak 2 # generation 2: best score 247.796 bits/residue, 0 clashes # Cumulative usage by method: ## InsertFragment 9 ## ReduceClash 0 ## CrossOver 3 ## CrossAndInsert 12 ## TwoFragment 0 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 10 ## InsertAlignment 36 ## ReduceBreak 2 # generation 3: best score 247.796 bits/residue, 0 clashes # Cumulative usage by method: ## InsertFragment 11 ## ReduceClash 1 ## CrossOver 4 ## CrossAndInsert 14 ## TwoFragment 0 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 22 ## InsertAlignment 50 ## ReduceBreak 2 # generation 4: best score 247.796 bits/residue, 0 clashes # Cumulative usage by method: ## InsertFragment 12 ## ReduceClash 2 ## CrossOver 10 ## CrossAndInsert 17 ## TwoFragment 0 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 41 ## InsertAlignment 53 ## ReduceBreak 2 # generation 5: best score 247.796 bits/residue, 0 clashes # Cumulative usage by method: ## InsertFragment 14 ## ReduceClash 2 ## CrossOver 26 ## CrossAndInsert 19 ## TwoFragment 0 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 51 ## InsertAlignment 53 ## ReduceBreak 2 # generation 6: best score 247.789 bits/residue, 0 clashes # Cumulative usage by method: ## InsertFragment 16 ## ReduceClash 2 ## CrossOver 49 ## CrossAndInsert 20 ## TwoFragment 0 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 55 ## InsertAlignment 53 ## ReduceBreak 2 # best score in initial pool 247.796 bits/residue, 0 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 247.796 bits/residue, 0 clashes # Cumulative usage by method: ## InsertFragment 4 ## ReduceClash 3 ## CrossOver 0 ## CrossAndInsert 4 ## TwoFragment 3 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 6 ## InsertAlignment 16 ## ReduceBreak 3 # generation 2: best score 247.796 bits/residue, 0 clashes # Cumulative usage by method: ## InsertFragment 6 ## ReduceClash 3 ## CrossOver 1 ## CrossAndInsert 7 ## TwoFragment 4 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 23 ## InsertAlignment 27 ## ReduceBreak 3 # generation 3: best score 247.796 bits/residue, 0 clashes # Cumulative usage by method: ## InsertFragment 10 ## ReduceClash 3 ## CrossOver 1 ## CrossAndInsert 9 ## TwoFragment 4 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 49 ## InsertAlignment 34 ## ReduceBreak 3 # generation 4: best score 247.796 bits/residue, 0 clashes # Cumulative usage by method: ## InsertFragment 13 ## ReduceClash 4 ## CrossOver 2 ## CrossAndInsert 11 ## TwoFragment 4 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 81 ## InsertAlignment 34 ## ReduceBreak 3 # generation 5: best score 247.796 bits/residue, 0 clashes # Cumulative usage by method: ## InsertFragment 14 ## ReduceClash 4 ## CrossOver 2 ## CrossAndInsert 11 ## TwoFragment 4 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 121 ## InsertAlignment 34 ## ReduceBreak 3 # generation 6: best score 247.796 bits/residue, 0 clashes # Cumulative usage by method: ## InsertFragment 15 ## ReduceClash 4 ## CrossOver 4 ## CrossAndInsert 11 ## TwoFragment 4 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 155 ## InsertAlignment 34 ## ReduceBreak 3 # best score in super_pool at pool[3] 247.789 bits/residue, 0 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 247.789 bits/residue, 0 clashes # Cumulative usage by method: ## InsertFragment 10 ## ReduceClash 1 ## CrossOver 1 ## CrossAndInsert 7 ## TwoFragment 1 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 4 ## InsertAlignment 13 ## ReduceBreak 1 # generation 2: best score 247.743 bits/residue, 0 clashes # Cumulative usage by method: ## InsertFragment 16 ## ReduceClash 1 ## CrossOver 1 ## CrossAndInsert 13 ## TwoFragment 1 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 8 ## InsertAlignment 29 ## ReduceBreak 1 # generation 3: best score 247.743 bits/residue, 0 clashes # Cumulative usage by method: ## InsertFragment 20 ## ReduceClash 1 ## CrossOver 7 ## CrossAndInsert 16 ## TwoFragment 2 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 16 ## InsertAlignment 37 ## ReduceBreak 1 # generation 4: best score 247.743 bits/residue, 0 clashes # Cumulative usage by method: ## InsertFragment 22 ## ReduceClash 1 ## CrossOver 22 ## CrossAndInsert 22 ## TwoFragment 2 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 18 ## InsertAlignment 42 ## ReduceBreak 1 # generation 5: best score 247.743 bits/residue, 0 clashes # Cumulative usage by method: ## InsertFragment 26 ## ReduceClash 1 ## CrossOver 44 ## CrossAndInsert 24 ## TwoFragment 2 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 20 ## InsertAlignment 42 ## ReduceBreak 1 # generation 6: best score 247.739 bits/residue, 0 clashes # Cumulative usage by method: ## InsertFragment 26 ## ReduceClash 1 ## CrossOver 74 ## CrossAndInsert 24 ## TwoFragment 2 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 20 ## InsertAlignment 42 ## ReduceBreak 1 # command:# naming current conformation t99-opt2 # command:# command:# Optimizing rotamers with 40 blocks of 250 conformations # P(change) = 1 * 0.95^ iter # P(new) = 0.1 * 0.95^ iter # P(neighbor) = 0.5 * 0.95^ iter # P(archetype) = 0.9 * 0.9^ iter # P(best_residue) = 1 * 0.95^ iter # clash penalty 40 nats/clash # ss_bond bonus 0 # sidechain weight 1 # best score from archetype iter: 247.739 bits/residue, 0 clashes, rmsd= 0 # best score after iter 1 247.739 bits/residue, 0 clashes, rmsd= 0 # best score after iter 2 247.739 bits/residue, 0 clashes, rmsd= 0 # best score after iter 3 247.739 bits/residue, 0 clashes, rmsd= 0 # best score after iter 4 247.739 bits/residue, 0 clashes, rmsd= 0 # best score after iter 5 247.739 bits/residue, 0 clashes, rmsd= 0 # best score after iter 6 247.739 bits/residue, 0 clashes, rmsd= 0 # best score after iter 7 247.739 bits/residue, 0 clashes, rmsd= 0 # best score after iter 8 247.739 bits/residue, 0 clashes, rmsd= 0 # best score after iter 9 247.739 bits/residue, 0 clashes, rmsd= 0 # best score after iter 10 247.739 bits/residue, 0 clashes, rmsd= 0 # best score after iter 11 247.739 bits/residue, 0 clashes, rmsd= 0 # best score after iter 12 247.739 bits/residue, 0 clashes, rmsd= 0 # best score after iter 13 247.739 bits/residue, 0 clashes, rmsd= 0 # best score after iter 14 247.739 bits/residue, 0 clashes, rmsd= 0 # best score after iter 15 247.739 bits/residue, 0 clashes, rmsd= 0 # best score after iter 16 247.739 bits/residue, 0 clashes, rmsd= 0 # best score after iter 17 247.739 bits/residue, 0 clashes, rmsd= 0 # best score after iter 18 247.739 bits/residue, 0 clashes, rmsd= 0 # best score after iter 19 247.739 bits/residue, 0 clashes, rmsd= 0 # best score after iter 20 247.739 bits/residue, 0 clashes, rmsd= 0 # best score after iter 21 247.739 bits/residue, 0 clashes, rmsd= 0 # best score after iter 22 247.739 bits/residue, 0 clashes, rmsd= 0 # best score after iter 23 247.739 bits/residue, 0 clashes, rmsd= 0 # best score after iter 24 247.739 bits/residue, 0 clashes, rmsd= 0 # best score after iter 25 247.739 bits/residue, 0 clashes, rmsd= 0 # best score after iter 26 247.739 bits/residue, 0 clashes, rmsd= 0 # best score after iter 27 247.739 bits/residue, 0 clashes, rmsd= 0 # best score after iter 28 247.739 bits/residue, 0 clashes, rmsd= 0 # best score after iter 29 247.739 bits/residue, 0 clashes, rmsd= 0 # best score after iter 30 247.739 bits/residue, 0 clashes, rmsd= 0 # best score after iter 31 247.739 bits/residue, 0 clashes, rmsd= 0 # best score after iter 32 247.739 bits/residue, 0 clashes, rmsd= 0 # best score after iter 33 247.739 bits/residue, 0 clashes, rmsd= 0 # best score after iter 34 247.739 bits/residue, 0 clashes, rmsd= 0 # best score after iter 35 247.739 bits/residue, 0 clashes, rmsd= 0 # best score after iter 36 247.739 bits/residue, 0 clashes, rmsd= 0 # best score after iter 37 247.739 bits/residue, 0 clashes, rmsd= 0 # best score after iter 38 247.739 bits/residue, 0 clashes, rmsd= 0 # best score after iter 39 247.739 bits/residue, 0 clashes, rmsd= 0 # command:# naming current conformation t99-5hck-opt2-rot # command:# command:# Saving current conformation as real # command:# ScwrlConform produces command scwrl -i /projects/compbio/tmp/to_scwrl_1142393007.pdb -s /projects/compbio/tmp/to_scwrl_1142393007.seq -o /projects/compbio/tmp/from_scwrl_1142393007.pdb > /projects/compbio/tmp/scwrl.log # conformation set from SCWRL output # command:# naming current conformation t99-opt-scwrl # command:# command:# ScoreConformVsReal T0099 446.938 bits/residue, 121 clashes , rmsd= 15.2565 t99-5hck at pool[1] 459.236 bits/residue, 2 clashes 0 breaks, rmsd= 2.74904 t99-5hck-scwrl at pool[2] 455.607 bits/residue, 1 clashes 0 breaks, rmsd= 2.78148 t99-5hck-rot at pool[3] 250.877 bits/residue, 0 clashes 0 breaks, rmsd= 2.34379 t99-opt at pool[4] 247.796 bits/residue, 0 clashes , rmsd= 0.252637 t99-5hck-opt-rot at pool[5] 247.796 bits/residue, 0 clashes , rmsd= 0.252637 t99-opt2 at pool[6] 247.739 bits/residue, 0 clashes , rmsd= 0 t99-5hck-opt2-rot at pool[7] 247.739 bits/residue, 0 clashes , rmsd= 0 t99-opt-scwrl at pool[8] 252.48 bits/residue, 4 clashes , rmsd= 1.61003 # command: