# 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 10 # clash_penalty 4 nats/clash # ss_bond_bonus 50 # known_ss_bond_bonus 1 # chain_break_penalty 5 nats/Angstrom # wet_spot_weight 1 # dry_spot_weight 3 # command:# Prefix for input files set to # command:Created new target T0128 from ../T0128.seq # command:# Will now start reporting scores to t128-6.5-12+rot.rdb # command:# naming current conformation t128-rand # command:# Will do 1 iterations of optimization # best score in initial pool at pool[5] -16.6249 bits/residue, 207 clashes # optimizing backbone with 50 conformations in pool # doing 4 generations, with 200 new conformations in each generation. # keep at most 20 conformations from old pool # generation 1: best score -18.2702 bits/residue, 220 clashes # Cumulative usage by method: ## InsertFragment 12 ## ReduceClash 6 ## CrossOver 0 ## CrossAndInsert 9 ## TwoFragment 17 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 0 ## InsertAlignment 0 ## ReduceBreak 0 # generation 2: best score -22.2684 bits/residue, 121 clashes # Cumulative usage by method: ## InsertFragment 22 ## ReduceClash 16 ## CrossOver 0 ## CrossAndInsert 20 ## TwoFragment 30 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 0 ## InsertAlignment 0 ## ReduceBreak 0 # generation 3: best score -24.6463 bits/residue, 121 clashes # Cumulative usage by method: ## InsertFragment 36 ## ReduceClash 22 ## CrossOver 1 ## CrossAndInsert 33 ## TwoFragment 42 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 0 ## InsertAlignment 0 ## ReduceBreak 0 # generation 4: best score -27.1901 bits/residue, 130 clashes # Cumulative usage by method: ## InsertFragment 45 ## ReduceClash 30 ## CrossOver 1 ## CrossAndInsert 48 ## TwoFragment 58 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 0 ## InsertAlignment 0 ## ReduceBreak 0 # command:# naming current conformation t128-rand-opt # command:# command:# created fragments for T0128 from T0128-1avmA-karplus.index # command:# created conformation for T0128 by applying fragments # command:# naming current conformation t128-init # command:# command:# ScoreConform t128-rand -9.19469 bits/residue, 277 clashes t128-rand-opt at pool[1] -27.1901 bits/residue, 130 clashes t128-init at pool[2] 27.9246 bits/residue, 120 clashes 0 breaks # command:# Will do 6 iterations of optimization # best score in initial pool at pool[1] -30.5256 bits/residue, 119 clashes 0 breaks # optimizing backbone with 50 conformations in pool # doing 5 generations, with 200 new conformations in each generation. # keep at most 20 conformations from old pool # generation 1: best score -32.6146 bits/residue, 106 clashes 0 breaks # Cumulative usage by method: ## InsertFragment 7 ## ReduceClash 5 ## CrossOver 0 ## CrossAndInsert 9 ## TwoFragment 7 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 0 ## InsertAlignment 15 ## ReduceBreak 0 # generation 2: best score -34.5485 bits/residue, 139 clashes 0 breaks # Cumulative usage by method: ## InsertFragment 18 ## ReduceClash 17 ## CrossOver 0 ## CrossAndInsert 21 ## TwoFragment 12 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 0 ## InsertAlignment 19 ## ReduceBreak 0 # generation 3: best score -37.3923 bits/residue, 62 clashes # Cumulative usage by method: ## InsertFragment 24 ## ReduceClash 30 ## CrossOver 0 ## CrossAndInsert 33 ## TwoFragment 20 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 0 ## InsertAlignment 19 ## ReduceBreak 0 # generation 4: best score -38.3877 bits/residue, 47 clashes # Cumulative usage by method: ## InsertFragment 41 ## ReduceClash 41 ## CrossOver 0 ## CrossAndInsert 43 ## TwoFragment 27 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 0 ## InsertAlignment 19 ## ReduceBreak 0 # generation 5: best score -39.0447 bits/residue, 65 clashes # Cumulative usage by method: ## InsertFragment 57 ## ReduceClash 50 ## CrossOver 0 ## CrossAndInsert 51 ## TwoFragment 36 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 0 ## InsertAlignment 19 ## ReduceBreak 0 # best score in initial pool -29.2782 bits/residue, 120 clashes 0 breaks # optimizing backbone with 50 conformations in pool # doing 5 generations, with 200 new conformations in each generation. # keep at most 20 conformations from old pool # generation 1: best score -32.1039 bits/residue, 65 clashes # Cumulative usage by method: ## InsertFragment 5 ## ReduceClash 5 ## CrossOver 0 ## CrossAndInsert 9 ## TwoFragment 9 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 0 ## InsertAlignment 18 ## ReduceBreak 0 # generation 2: best score -32.4678 bits/residue, 108 clashes 0 breaks # Cumulative usage by method: ## InsertFragment 10 ## ReduceClash 13 ## CrossOver 1 ## CrossAndInsert 19 ## TwoFragment 14 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 0 ## InsertAlignment 33 ## ReduceBreak 0 # generation 3: best score -34.7272 bits/residue, 47 clashes # Cumulative usage by method: ## InsertFragment 16 ## ReduceClash 20 ## CrossOver 1 ## CrossAndInsert 32 ## TwoFragment 19 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 0 ## InsertAlignment 44 ## ReduceBreak 0 # generation 4: best score -34.938 bits/residue, 22 clashes # Cumulative usage by method: ## InsertFragment 21 ## ReduceClash 32 ## CrossOver 2 ## CrossAndInsert 39 ## TwoFragment 25 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 0 ## InsertAlignment 49 ## ReduceBreak 0 # generation 5: best score -35.771 bits/residue, 51 clashes # Cumulative usage by method: ## InsertFragment 27 ## ReduceClash 40 ## CrossOver 4 ## CrossAndInsert 52 ## TwoFragment 27 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 0 ## InsertAlignment 57 ## ReduceBreak 0 # best score in initial pool at pool[2] -29.9158 bits/residue, 77 clashes 0 breaks # optimizing backbone with 50 conformations in pool # doing 5 generations, with 200 new conformations in each generation. # keep at most 20 conformations from old pool # generation 1: best score -32.4876 bits/residue, 76 clashes # Cumulative usage by method: ## InsertFragment 6 ## ReduceClash 5 ## CrossOver 0 ## CrossAndInsert 8 ## TwoFragment 9 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 0 ## InsertAlignment 18 ## ReduceBreak 0 # generation 2: best score -34.8953 bits/residue, 77 clashes # Cumulative usage by method: ## InsertFragment 9 ## ReduceClash 12 ## CrossOver 2 ## CrossAndInsert 16 ## TwoFragment 16 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 0 ## InsertAlignment 30 ## ReduceBreak 0 # generation 3: best score -36.1235 bits/residue, 39 clashes # Cumulative usage by method: ## InsertFragment 12 ## ReduceClash 24 ## CrossOver 4 ## CrossAndInsert 25 ## TwoFragment 24 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 0 ## InsertAlignment 39 ## ReduceBreak 0 # generation 4: best score -36.4077 bits/residue, 20 clashes 0 breaks # Cumulative usage by method: ## InsertFragment 20 ## ReduceClash 32 ## CrossOver 8 ## CrossAndInsert 32 ## TwoFragment 27 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 0 ## InsertAlignment 51 ## ReduceBreak 0 # generation 5: best score -37.6093 bits/residue, 33 clashes # Cumulative usage by method: ## InsertFragment 25 ## ReduceClash 39 ## CrossOver 9 ## CrossAndInsert 43 ## TwoFragment 31 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 0 ## InsertAlignment 61 ## ReduceBreak 0 # best score in initial pool at pool[9] -30.2443 bits/residue, 89 clashes 0 breaks # optimizing backbone with 50 conformations in pool # doing 5 generations, with 200 new conformations in each generation. # keep at most 20 conformations from old pool # generation 1: best score -32.4362 bits/residue, 13 clashes 0 breaks # Cumulative usage by method: ## InsertFragment 8 ## ReduceClash 8 ## CrossOver 0 ## CrossAndInsert 5 ## TwoFragment 8 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 0 ## InsertAlignment 15 ## ReduceBreak 0 # generation 2: best score -34.3923 bits/residue, 55 clashes # Cumulative usage by method: ## InsertFragment 15 ## ReduceClash 15 ## CrossOver 0 ## CrossAndInsert 12 ## TwoFragment 12 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 0 ## InsertAlignment 37 ## ReduceBreak 0 # generation 3: best score -36.204 bits/residue, 56 clashes # Cumulative usage by method: ## InsertFragment 22 ## ReduceClash 27 ## CrossOver 0 ## CrossAndInsert 19 ## TwoFragment 16 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 0 ## InsertAlignment 51 ## ReduceBreak 0 # generation 4: best score -36.7753 bits/residue, 56 clashes # Cumulative usage by method: ## InsertFragment 32 ## ReduceClash 44 ## CrossOver 0 ## CrossAndInsert 30 ## TwoFragment 19 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 0 ## InsertAlignment 51 ## ReduceBreak 0 # generation 5: best score -36.924 bits/residue, 48 clashes # Cumulative usage by method: ## InsertFragment 42 ## ReduceClash 54 ## CrossOver 0 ## CrossAndInsert 40 ## TwoFragment 27 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 0 ## InsertAlignment 51 ## ReduceBreak 0 # best score in initial pool at pool[35] -29.9113 bits/residue, 164 clashes 0 breaks # optimizing backbone with 50 conformations in pool # doing 5 generations, with 200 new conformations in each generation. # keep at most 20 conformations from old pool # generation 1: best score -33.5502 bits/residue, 92 clashes 0 breaks # Cumulative usage by method: ## InsertFragment 5 ## ReduceClash 9 ## CrossOver 0 ## CrossAndInsert 7 ## TwoFragment 5 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 0 ## InsertAlignment 20 ## ReduceBreak 0 # generation 2: best score -35.1115 bits/residue, 69 clashes # Cumulative usage by method: ## InsertFragment 7 ## ReduceClash 13 ## CrossOver 0 ## CrossAndInsert 16 ## TwoFragment 8 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 0 ## InsertAlignment 47 ## ReduceBreak 0 # generation 3: best score -35.3027 bits/residue, 60 clashes # Cumulative usage by method: ## InsertFragment 13 ## ReduceClash 18 ## CrossOver 0 ## CrossAndInsert 23 ## TwoFragment 12 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 0 ## InsertAlignment 64 ## ReduceBreak 0 # generation 4: best score -36.1046 bits/residue, 61 clashes # Cumulative usage by method: ## InsertFragment 22 ## ReduceClash 27 ## CrossOver 1 ## CrossAndInsert 33 ## TwoFragment 16 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 0 ## InsertAlignment 68 ## ReduceBreak 0 # generation 5: best score -37.029 bits/residue, 136 clashes # Cumulative usage by method: ## InsertFragment 27 ## ReduceClash 40 ## CrossOver 1 ## CrossAndInsert 42 ## TwoFragment 20 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 0 ## InsertAlignment 71 ## ReduceBreak 0 # best score in initial pool -29.2782 bits/residue, 120 clashes 0 breaks # optimizing backbone with 50 conformations in pool # doing 5 generations, with 200 new conformations in each generation. # keep at most 20 conformations from old pool # generation 1: best score -32.7328 bits/residue, 32 clashes 0 breaks # Cumulative usage by method: ## InsertFragment 4 ## ReduceClash 6 ## CrossOver 0 ## CrossAndInsert 10 ## TwoFragment 5 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 0 ## InsertAlignment 22 ## ReduceBreak 0 # generation 2: best score -33.7822 bits/residue, 62 clashes # Cumulative usage by method: ## InsertFragment 7 ## ReduceClash 13 ## CrossOver 0 ## CrossAndInsert 16 ## TwoFragment 10 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 0 ## InsertAlignment 46 ## ReduceBreak 0 # generation 3: best score -34.0216 bits/residue, 27 clashes 0 breaks # Cumulative usage by method: ## InsertFragment 8 ## ReduceClash 17 ## CrossOver 0 ## CrossAndInsert 20 ## TwoFragment 12 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 0 ## InsertAlignment 77 ## ReduceBreak 0 # generation 4: best score -35.5587 bits/residue, 84 clashes # Cumulative usage by method: ## InsertFragment 10 ## ReduceClash 23 ## CrossOver 0 ## CrossAndInsert 27 ## TwoFragment 16 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 0 ## InsertAlignment 100 ## ReduceBreak 0 # generation 5: best score -38.2161 bits/residue, 37 clashes # Cumulative usage by method: ## InsertFragment 16 ## ReduceClash 29 ## CrossOver 0 ## CrossAndInsert 43 ## TwoFragment 18 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 0 ## InsertAlignment 113 ## ReduceBreak 0 # best score in super_pool -39.0447 bits/residue, 65 clashes # optimizing backbone with 50 conformations in pool # doing 5 generations, with 200 new conformations in each generation. # keep at most 20 conformations from old pool # generation 1: best score -39.6717 bits/residue, 141 clashes # Cumulative usage by method: ## InsertFragment 9 ## ReduceClash 7 ## CrossOver 1 ## CrossAndInsert 14 ## TwoFragment 12 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 0 ## InsertAlignment 0 ## ReduceBreak 0 # generation 2: best score -41.1354 bits/residue, 116 clashes # Cumulative usage by method: ## InsertFragment 15 ## ReduceClash 19 ## CrossOver 2 ## CrossAndInsert 30 ## TwoFragment 20 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 0 ## InsertAlignment 0 ## ReduceBreak 0 # generation 3: best score -42.1306 bits/residue, 61 clashes # Cumulative usage by method: ## InsertFragment 21 ## ReduceClash 34 ## CrossOver 3 ## CrossAndInsert 45 ## TwoFragment 28 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 0 ## InsertAlignment 0 ## ReduceBreak 0 # generation 4: best score -43.6212 bits/residue, 25 clashes # Cumulative usage by method: ## InsertFragment 34 ## ReduceClash 48 ## CrossOver 3 ## CrossAndInsert 55 ## TwoFragment 35 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 0 ## InsertAlignment 0 ## ReduceBreak 0 # generation 5: best score -44.8039 bits/residue, 59 clashes # Cumulative usage by method: ## InsertFragment 47 ## ReduceClash 64 ## CrossOver 3 ## CrossAndInsert 63 ## TwoFragment 41 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 0 ## InsertAlignment 0 ## ReduceBreak 0 # command:# naming current conformation t128-opt # command:# command:# Optimizing rotamers with 10 blocks of 50 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 4 nats/clash # ss_bond bonus 50 # sidechain weight 10 # best score from archetype iter: -44.8039 bits/residue, 59 clashes, rmsd= 0 # best score after iter 1 -44.8039 bits/residue, 59 clashes, rmsd= 0 # best score after iter 2 -54.296 bits/residue, 50 clashes, rmsd= 0 # best score after iter 3 -57.4943 bits/residue, 63 clashes, rmsd= 0 # best score after iter 4 -60.4936 bits/residue, 62 clashes, rmsd= 0 # best score after iter 5 -61.2773 bits/residue, 67 clashes, rmsd= 0 # best score after iter 6 -61.544 bits/residue, 66 clashes, rmsd= 0 # best score after iter 7 -61.9169 bits/residue, 57 clashes, rmsd= 0 # best score after iter 8 -62.0405 bits/residue, 59 clashes, rmsd= 0 # best score after iter 9 -62.198 bits/residue, 59 clashes, rmsd= 0 # command:# naming current conformation 128-opt-rot # command:# command:# ScwrlConform produces command scwrl -i /projects/compbio/tmp/to_scwrl_1128568128.pdb -s /projects/compbio/tmp/to_scwrl_1128568128.seq -o /projects/compbio/tmp/from_scwrl_1128568128.pdb > /projects/compbio/tmp/scwrl.log # conformation set from SCWRL output # command:# naming current conformation t128-opt-scwrl # command:# command:# ScoreConform t128-rand -9.19469 bits/residue, 277 clashes t128-rand-opt at pool[1] -27.1901 bits/residue, 130 clashes t128-init at pool[2] 27.9246 bits/residue, 120 clashes 0 breaks t128-opt at pool[3] -44.8039 bits/residue, 59 clashes 128-opt-rot at pool[4] -62.198 bits/residue, 59 clashes t128-opt-scwrl at pool[5] -62.9554 bits/residue, 24 clashes # command: