# 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:# Will do 10 iterations of optimization # best score in initial pool at pool[46] 262.219 bits/residue, 2 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 260.469 bits/residue, 1 clashes 0 breaks # Cumulative usage by method: ## InsertFragment 5 ## ReduceClash 2 ## CrossOver 0 ## CrossAndInsert 8 ## TwoFragment 2 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 7 ## InsertAlignment 16 ## ReduceBreak 3 # generation 2: best score 259.389 bits/residue, 0 clashes 0 breaks # Cumulative usage by method: ## InsertFragment 8 ## ReduceClash 3 ## CrossOver 0 ## CrossAndInsert 9 ## TwoFragment 2 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 24 ## InsertAlignment 28 ## ReduceBreak 3 # generation 3: best score 258.165 bits/residue, 1 clashes 0 breaks # Cumulative usage by method: ## InsertFragment 9 ## ReduceClash 4 ## CrossOver 0 ## CrossAndInsert 10 ## TwoFragment 2 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 48 ## InsertAlignment 37 ## ReduceBreak 3 # generation 4: best score 257.855 bits/residue, 1 clashes 0 breaks # Cumulative usage by method: ## InsertFragment 10 ## ReduceClash 5 ## CrossOver 0 ## CrossAndInsert 11 ## TwoFragment 2 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 76 ## InsertAlignment 39 ## ReduceBreak 3 # generation 5: best score 257.33 bits/residue, 0 clashes 0 breaks # Cumulative usage by method: ## InsertFragment 11 ## ReduceClash 7 ## CrossOver 0 ## CrossAndInsert 12 ## TwoFragment 2 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 112 ## InsertAlignment 39 ## ReduceBreak 3 # generation 6: best score 257.33 bits/residue, 0 clashes 0 breaks # Cumulative usage by method: ## InsertFragment 11 ## ReduceClash 8 ## CrossOver 0 ## CrossAndInsert 12 ## TwoFragment 2 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 144 ## InsertAlignment 39 ## ReduceBreak 3 # best score in initial pool at pool[31] 262.032 bits/residue, 2 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 259.713 bits/residue, 0 clashes 0 breaks # Cumulative usage by method: ## InsertFragment 6 ## ReduceClash 2 ## CrossOver 0 ## CrossAndInsert 3 ## TwoFragment 0 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 6 ## InsertAlignment 15 ## ReduceBreak 6 # generation 2: best score 259.009 bits/residue, 0 clashes 0 breaks # Cumulative usage by method: ## InsertFragment 11 ## ReduceClash 2 ## CrossOver 0 ## CrossAndInsert 5 ## TwoFragment 0 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 21 ## InsertAlignment 26 ## ReduceBreak 6 # generation 3: best score 258.717 bits/residue, 0 clashes 0 breaks # Cumulative usage by method: ## InsertFragment 12 ## ReduceClash 2 ## CrossOver 0 ## CrossAndInsert 6 ## TwoFragment 0 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 42 ## InsertAlignment 33 ## ReduceBreak 6 # generation 4: best score 258.717 bits/residue, 0 clashes 0 breaks # Cumulative usage by method: ## InsertFragment 14 ## ReduceClash 2 ## CrossOver 1 ## CrossAndInsert 10 ## TwoFragment 1 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 53 ## InsertAlignment 44 ## ReduceBreak 6 # generation 5: best score 258.717 bits/residue, 0 clashes 0 breaks # Cumulative usage by method: ## InsertFragment 14 ## ReduceClash 2 ## CrossOver 6 ## CrossAndInsert 10 ## TwoFragment 1 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 68 ## InsertAlignment 54 ## ReduceBreak 6 # generation 6: best score 258.717 bits/residue, 0 clashes 0 breaks # Cumulative usage by method: ## InsertFragment 14 ## ReduceClash 2 ## CrossOver 12 ## CrossAndInsert 10 ## TwoFragment 1 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 92 ## InsertAlignment 54 ## ReduceBreak 6 # best score in initial pool at pool[49] 261.788 bits/residue, 4 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 259.383 bits/residue, 0 clashes 0 breaks # Cumulative usage by method: ## InsertFragment 3 ## ReduceClash 4 ## CrossOver 2 ## CrossAndInsert 3 ## TwoFragment 2 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 9 ## InsertAlignment 13 ## ReduceBreak 2 # generation 2: best score 259.383 bits/residue, 0 clashes 0 breaks # Cumulative usage by method: ## InsertFragment 4 ## ReduceClash 5 ## CrossOver 7 ## CrossAndInsert 3 ## TwoFragment 2 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 20 ## InsertAlignment 26 ## ReduceBreak 2 # generation 3: best score 258.229 bits/residue, 1 clashes # Cumulative usage by method: ## InsertFragment 5 ## ReduceClash 7 ## CrossOver 13 ## CrossAndInsert 4 ## TwoFragment 2 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 48 ## InsertAlignment 31 ## ReduceBreak 2 # generation 4: best score 257.506 bits/residue, 0 clashes 0 breaks # Cumulative usage by method: ## InsertFragment 5 ## ReduceClash 12 ## CrossOver 17 ## CrossAndInsert 4 ## TwoFragment 2 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 84 ## InsertAlignment 31 ## ReduceBreak 2 # generation 5: best score 257.423 bits/residue, 0 clashes # Cumulative usage by method: ## InsertFragment 5 ## ReduceClash 14 ## CrossOver 29 ## CrossAndInsert 4 ## TwoFragment 2 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 110 ## InsertAlignment 31 ## ReduceBreak 2 # generation 6: best score 257.198 bits/residue, 0 clashes # Cumulative usage by method: ## InsertFragment 5 ## ReduceClash 15 ## CrossOver 46 ## CrossAndInsert 4 ## TwoFragment 2 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 130 ## InsertAlignment 31 ## ReduceBreak 2 # best score in initial pool at pool[4] 262.058 bits/residue, 2 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 259.654 bits/residue, 0 clashes 0 breaks # Cumulative usage by method: ## InsertFragment 6 ## ReduceClash 2 ## CrossOver 0 ## CrossAndInsert 1 ## TwoFragment 3 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 16 ## InsertAlignment 10 ## ReduceBreak 3 # generation 2: best score 258.479 bits/residue, 0 clashes 0 breaks # Cumulative usage by method: ## InsertFragment 9 ## ReduceClash 2 ## CrossOver 0 ## CrossAndInsert 4 ## TwoFragment 3 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 36 ## InsertAlignment 18 ## ReduceBreak 3 # generation 3: best score 257.239 bits/residue, 0 clashes 0 breaks # Cumulative usage by method: ## InsertFragment 12 ## ReduceClash 2 ## CrossOver 0 ## CrossAndInsert 5 ## TwoFragment 3 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 64 ## InsertAlignment 19 ## ReduceBreak 3 # generation 4: best score 257.239 bits/residue, 0 clashes 0 breaks # Cumulative usage by method: ## InsertFragment 12 ## ReduceClash 2 ## CrossOver 0 ## CrossAndInsert 6 ## TwoFragment 3 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 100 ## InsertAlignment 20 ## ReduceBreak 3 # generation 5: best score 257.239 bits/residue, 0 clashes 0 breaks # Cumulative usage by method: ## InsertFragment 12 ## ReduceClash 3 ## CrossOver 0 ## CrossAndInsert 6 ## TwoFragment 3 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 129 ## InsertAlignment 20 ## ReduceBreak 3 # generation 6: best score 257.239 bits/residue, 0 clashes 0 breaks # Cumulative usage by method: ## InsertFragment 13 ## ReduceClash 3 ## CrossOver 0 ## CrossAndInsert 6 ## TwoFragment 3 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 158 ## InsertAlignment 20 ## ReduceBreak 3 # best score in initial pool 263.128 bits/residue, 1 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 261.797 bits/residue, 2 clashes 0 breaks # Cumulative usage by method: ## InsertFragment 5 ## ReduceClash 6 ## CrossOver 0 ## CrossAndInsert 2 ## TwoFragment 1 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 7 ## InsertAlignment 20 ## ReduceBreak 0 # generation 2: best score 259.683 bits/residue, 0 clashes 0 breaks # Cumulative usage by method: ## InsertFragment 9 ## ReduceClash 6 ## CrossOver 0 ## CrossAndInsert 4 ## TwoFragment 2 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 19 ## InsertAlignment 34 ## ReduceBreak 0 # generation 3: best score 259.402 bits/residue, 0 clashes 0 breaks # Cumulative usage by method: ## InsertFragment 10 ## ReduceClash 7 ## CrossOver 0 ## CrossAndInsert 4 ## TwoFragment 2 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 32 ## InsertAlignment 56 ## ReduceBreak 0 # generation 4: best score 259.106 bits/residue, 2 clashes 0 breaks # Cumulative usage by method: ## InsertFragment 15 ## ReduceClash 7 ## CrossOver 0 ## CrossAndInsert 5 ## TwoFragment 2 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 44 ## InsertAlignment 68 ## ReduceBreak 0 # generation 5: best score 258.52 bits/residue, 1 clashes 0 breaks # Cumulative usage by method: ## InsertFragment 17 ## ReduceClash 8 ## CrossOver 0 ## CrossAndInsert 5 ## TwoFragment 2 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 61 ## InsertAlignment 78 ## ReduceBreak 0 # generation 6: best score 258.291 bits/residue, 1 clashes 0 breaks # Cumulative usage by method: ## InsertFragment 17 ## ReduceClash 8 ## CrossOver 0 ## CrossAndInsert 5 ## TwoFragment 2 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 100 ## InsertAlignment 78 ## ReduceBreak 0 # best score in initial pool at pool[14] 262.045 bits/residue, 2 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 262.045 bits/residue, 2 clashes 0 breaks # Cumulative usage by method: ## InsertFragment 4 ## ReduceClash 3 ## CrossOver 0 ## CrossAndInsert 6 ## TwoFragment 3 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 7 ## InsertAlignment 13 ## ReduceBreak 2 # generation 2: best score 259.384 bits/residue, 0 clashes 0 breaks # Cumulative usage by method: ## InsertFragment 9 ## ReduceClash 4 ## CrossOver 0 ## CrossAndInsert 8 ## TwoFragment 3 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 23 ## InsertAlignment 21 ## ReduceBreak 2 # generation 3: best score 258.844 bits/residue, 0 clashes 0 breaks # Cumulative usage by method: ## InsertFragment 11 ## ReduceClash 4 ## CrossOver 0 ## CrossAndInsert 9 ## TwoFragment 3 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 52 ## InsertAlignment 27 ## ReduceBreak 2 # generation 4: best score 258.626 bits/residue, 1 clashes 0 breaks # Cumulative usage by method: ## InsertFragment 12 ## ReduceClash 5 ## CrossOver 0 ## CrossAndInsert 10 ## TwoFragment 3 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 74 ## InsertAlignment 32 ## ReduceBreak 2 # generation 5: best score 258.387 bits/residue, 1 clashes 0 breaks # Cumulative usage by method: ## InsertFragment 13 ## ReduceClash 5 ## CrossOver 1 ## CrossAndInsert 10 ## TwoFragment 3 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 106 ## InsertAlignment 32 ## ReduceBreak 2 # generation 6: best score 258.374 bits/residue, 1 clashes 0 breaks # Cumulative usage by method: ## InsertFragment 13 ## ReduceClash 5 ## CrossOver 2 ## CrossAndInsert 10 ## TwoFragment 3 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 146 ## InsertAlignment 32 ## ReduceBreak 2 # best score in initial pool at pool[19] 262.219 bits/residue, 2 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 259.22 bits/residue, 0 clashes 0 breaks # Cumulative usage by method: ## InsertFragment 2 ## ReduceClash 2 ## CrossOver 0 ## CrossAndInsert 7 ## TwoFragment 1 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 11 ## InsertAlignment 14 ## ReduceBreak 2 # generation 2: best score 259.22 bits/residue, 0 clashes 0 breaks # Cumulative usage by method: ## InsertFragment 2 ## ReduceClash 2 ## CrossOver 0 ## CrossAndInsert 10 ## TwoFragment 1 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 31 ## InsertAlignment 29 ## ReduceBreak 2 # generation 3: best score 258.567 bits/residue, 1 clashes # Cumulative usage by method: ## InsertFragment 3 ## ReduceClash 2 ## CrossOver 0 ## CrossAndInsert 14 ## TwoFragment 1 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 60 ## InsertAlignment 31 ## ReduceBreak 2 # generation 4: best score 258.171 bits/residue, 1 clashes # Cumulative usage by method: ## InsertFragment 7 ## ReduceClash 3 ## CrossOver 0 ## CrossAndInsert 16 ## TwoFragment 1 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 91 ## InsertAlignment 31 ## ReduceBreak 2 # generation 5: best score 257.769 bits/residue, 0 clashes # Cumulative usage by method: ## InsertFragment 8 ## ReduceClash 3 ## CrossOver 0 ## CrossAndInsert 17 ## TwoFragment 1 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 132 ## InsertAlignment 31 ## ReduceBreak 2 # generation 6: best score 257.769 bits/residue, 0 clashes # Cumulative usage by method: ## InsertFragment 8 ## ReduceClash 3 ## CrossOver 0 ## CrossAndInsert 17 ## TwoFragment 1 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 162 ## InsertAlignment 31 ## ReduceBreak 2 # best score in initial pool at pool[1] 262.783 bits/residue, 3 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 262.045 bits/residue, 2 clashes 0 breaks # Cumulative usage by method: ## InsertFragment 4 ## ReduceClash 3 ## CrossOver 0 ## CrossAndInsert 3 ## TwoFragment 2 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 6 ## InsertAlignment 20 ## ReduceBreak 3 # generation 2: best score 260.127 bits/residue, 0 clashes 0 breaks # Cumulative usage by method: ## InsertFragment 6 ## ReduceClash 4 ## CrossOver 0 ## CrossAndInsert 6 ## TwoFragment 2 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 16 ## InsertAlignment 38 ## ReduceBreak 3 # generation 3: best score 258.326 bits/residue, 0 clashes # Cumulative usage by method: ## InsertFragment 6 ## ReduceClash 4 ## CrossOver 0 ## CrossAndInsert 7 ## TwoFragment 2 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 37 ## InsertAlignment 51 ## ReduceBreak 3 # generation 4: best score 258.326 bits/residue, 0 clashes # Cumulative usage by method: ## InsertFragment 7 ## ReduceClash 4 ## CrossOver 2 ## CrossAndInsert 9 ## TwoFragment 2 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 47 ## InsertAlignment 66 ## ReduceBreak 3 # generation 5: best score 258.312 bits/residue, 0 clashes # Cumulative usage by method: ## InsertFragment 7 ## ReduceClash 4 ## CrossOver 8 ## CrossAndInsert 10 ## TwoFragment 2 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 58 ## InsertAlignment 78 ## ReduceBreak 3 # generation 6: best score 257.561 bits/residue, 0 clashes # Cumulative usage by method: ## InsertFragment 8 ## ReduceClash 4 ## CrossOver 20 ## CrossAndInsert 11 ## TwoFragment 2 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 73 ## InsertAlignment 79 ## ReduceBreak 3 # best score in initial pool 263.128 bits/residue, 1 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 261.255 bits/residue, 1 clashes 0 breaks # Cumulative usage by method: ## InsertFragment 3 ## ReduceClash 2 ## CrossOver 0 ## CrossAndInsert 6 ## TwoFragment 1 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 8 ## InsertAlignment 19 ## ReduceBreak 2 # generation 2: best score 259.343 bits/residue, 0 clashes 0 breaks # Cumulative usage by method: ## InsertFragment 4 ## ReduceClash 2 ## CrossOver 0 ## CrossAndInsert 7 ## TwoFragment 1 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 27 ## InsertAlignment 34 ## ReduceBreak 3 # generation 3: best score 259.343 bits/residue, 0 clashes 0 breaks # Cumulative usage by method: ## InsertFragment 5 ## ReduceClash 2 ## CrossOver 0 ## CrossAndInsert 7 ## TwoFragment 1 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 47 ## InsertAlignment 46 ## ReduceBreak 3 # generation 4: best score 258.802 bits/residue, 0 clashes 0 breaks # Cumulative usage by method: ## InsertFragment 5 ## ReduceClash 2 ## CrossOver 2 ## CrossAndInsert 8 ## TwoFragment 1 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 76 ## InsertAlignment 51 ## ReduceBreak 3 # generation 5: best score 258.802 bits/residue, 0 clashes 0 breaks # Cumulative usage by method: ## InsertFragment 5 ## ReduceClash 2 ## CrossOver 10 ## CrossAndInsert 9 ## TwoFragment 1 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 91 ## InsertAlignment 57 ## ReduceBreak 3 # generation 6: best score 258.404 bits/residue, 0 clashes 0 breaks # Cumulative usage by method: ## InsertFragment 9 ## ReduceClash 2 ## CrossOver 31 ## CrossAndInsert 10 ## TwoFragment 1 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 95 ## InsertAlignment 57 ## ReduceBreak 3 # best score in initial pool at pool[31] 262.045 bits/residue, 2 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 259.317 bits/residue, 0 clashes 0 breaks # Cumulative usage by method: ## InsertFragment 3 ## ReduceClash 2 ## CrossOver 2 ## CrossAndInsert 10 ## TwoFragment 0 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 9 ## InsertAlignment 13 ## ReduceBreak 1 # generation 2: best score 259.308 bits/residue, 0 clashes 0 breaks # Cumulative usage by method: ## InsertFragment 3 ## ReduceClash 2 ## CrossOver 6 ## CrossAndInsert 15 ## TwoFragment 0 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 25 ## InsertAlignment 25 ## ReduceBreak 1 # generation 3: best score 259.308 bits/residue, 0 clashes 0 breaks # Cumulative usage by method: ## InsertFragment 3 ## ReduceClash 2 ## CrossOver 12 ## CrossAndInsert 16 ## TwoFragment 0 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 39 ## InsertAlignment 39 ## ReduceBreak 1 # generation 4: best score 257.497 bits/residue, 0 clashes # Cumulative usage by method: ## InsertFragment 3 ## ReduceClash 2 ## CrossOver 22 ## CrossAndInsert 19 ## TwoFragment 0 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 51 ## InsertAlignment 44 ## ReduceBreak 1 # generation 5: best score 256.192 bits/residue, 0 clashes # Cumulative usage by method: ## InsertFragment 3 ## ReduceClash 3 ## CrossOver 32 ## CrossAndInsert 19 ## TwoFragment 0 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 78 ## InsertAlignment 44 ## ReduceBreak 1 # generation 6: best score 256.192 bits/residue, 0 clashes # Cumulative usage by method: ## InsertFragment 3 ## ReduceClash 3 ## CrossOver 49 ## CrossAndInsert 19 ## TwoFragment 0 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 101 ## InsertAlignment 44 ## ReduceBreak 1 # best score in super_pool at pool[9] 256.192 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 256.192 bits/residue, 0 clashes # Cumulative usage by method: ## InsertFragment 5 ## ReduceClash 5 ## CrossOver 0 ## CrossAndInsert 6 ## TwoFragment 3 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 8 ## InsertAlignment 6 ## ReduceBreak 0 # generation 2: best score 256.192 bits/residue, 0 clashes # Cumulative usage by method: ## InsertFragment 5 ## ReduceClash 8 ## CrossOver 1 ## CrossAndInsert 9 ## TwoFragment 3 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 23 ## InsertAlignment 14 ## ReduceBreak 0 # generation 3: best score 256.192 bits/residue, 0 clashes # Cumulative usage by method: ## InsertFragment 8 ## ReduceClash 9 ## CrossOver 3 ## CrossAndInsert 9 ## TwoFragment 3 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 47 ## InsertAlignment 14 ## ReduceBreak 0 # generation 4: best score 256.192 bits/residue, 0 clashes # Cumulative usage by method: ## InsertFragment 9 ## ReduceClash 9 ## CrossOver 8 ## CrossAndInsert 10 ## TwoFragment 3 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 70 ## InsertAlignment 14 ## ReduceBreak 0 # generation 5: best score 256.192 bits/residue, 0 clashes # Cumulative usage by method: ## InsertFragment 10 ## ReduceClash 9 ## CrossOver 19 ## CrossAndInsert 10 ## TwoFragment 3 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 87 ## InsertAlignment 15 ## ReduceBreak 0 # generation 6: best score 255.956 bits/residue, 0 clashes # Cumulative usage by method: ## InsertFragment 10 ## ReduceClash 9 ## CrossOver 39 ## CrossAndInsert 11 ## TwoFragment 3 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 97 ## InsertAlignment 15 ## ReduceBreak 0 # command:# naming current conformation t99-opt # command:# command:# Saving current conformation as real # command:# ScwrlConform produces command scwrl -i /projects/compbio/tmp/to_scwrl_704615822.pdb -s /projects/compbio/tmp/to_scwrl_704615822.seq -o /projects/compbio/tmp/from_scwrl_704615822.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= 15.1482 t99-5hck at pool[1] 459.236 bits/residue, 2 clashes 0 breaks, rmsd= 2.4834 t99-5hck-scwrl at pool[2] 455.607 bits/residue, 1 clashes 0 breaks, rmsd= 2.81377 t99-opt at pool[3] 255.956 bits/residue, 0 clashes , rmsd= 0 t99-opt-scwrl at pool[4] 258.874 bits/residue, 1 clashes , rmsd= 1.39849 # command: