# 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:Error: unrecognized command ApplyFragments skipped # 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[40] 295.284 bits/residue, 137 clashes 0 breaks # best score after generation 1 248.75 bits/residue, 147 clashes 49.9561 breaks # Cumulative usage by method: ## InsertFragment 13 ## ReduceClash 10 ## CrossOver 0 ## CrossAndInsert 8 ## TwoFragment 7 ## InsertSSBond 0 ## OneRotamer 0 ## InsertAlignment 7 ## ReduceBreak 0 # best score after generation 2 243.503 bits/residue, 130 clashes 37.7901 breaks # Cumulative usage by method: ## InsertFragment 26 ## ReduceClash 14 ## CrossOver 0 ## CrossAndInsert 11 ## TwoFragment 12 ## InsertSSBond 0 ## OneRotamer 0 ## InsertAlignment 21 ## ReduceBreak 7 # best score after generation 3 240.084 bits/residue, 91 clashes 42.699 breaks # Cumulative usage by method: ## InsertFragment 36 ## ReduceClash 21 ## CrossOver 0 ## CrossAndInsert 13 ## TwoFragment 14 ## InsertSSBond 0 ## OneRotamer 0 ## InsertAlignment 35 ## ReduceBreak 10 # best score after generation 4 235.747 bits/residue, 87 clashes 28.45 breaks # Cumulative usage by method: ## InsertFragment 43 ## ReduceClash 27 ## CrossOver 1 ## CrossAndInsert 14 ## TwoFragment 15 ## InsertSSBond 0 ## OneRotamer 0 ## InsertAlignment 53 ## ReduceBreak 13 # best score after generation 5 234.577 bits/residue, 82 clashes 27.678 breaks # Cumulative usage by method: ## InsertFragment 45 ## ReduceClash 36 ## CrossOver 1 ## CrossAndInsert 15 ## TwoFragment 17 ## InsertSSBond 0 ## OneRotamer 0 ## InsertAlignment 66 ## ReduceBreak 19 # best score after generation 6 234.007 bits/residue, 77 clashes 27.035 breaks # Cumulative usage by method: ## InsertFragment 49 ## ReduceClash 44 ## CrossOver 2 ## CrossAndInsert 15 ## TwoFragment 17 ## InsertSSBond 0 ## OneRotamer 0 ## InsertAlignment 83 ## ReduceBreak 23 # best score after generation 7 231.222 bits/residue, 54 clashes 28.7573 breaks # Cumulative usage by method: ## InsertFragment 53 ## ReduceClash 51 ## CrossOver 3 ## CrossAndInsert 16 ## TwoFragment 18 ## InsertSSBond 0 ## OneRotamer 0 ## InsertAlignment 98 ## ReduceBreak 24 # best score after generation 8 230.07 bits/residue, 49 clashes 27.9851 breaks # Cumulative usage by method: ## InsertFragment 58 ## ReduceClash 55 ## CrossOver 4 ## CrossAndInsert 19 ## TwoFragment 18 ## InsertSSBond 0 ## OneRotamer 0 ## InsertAlignment 112 ## ReduceBreak 27 # best score after generation 9 230.07 bits/residue, 49 clashes 27.9851 breaks # Cumulative usage by method: ## InsertFragment 65 ## ReduceClash 61 ## CrossOver 5 ## CrossAndInsert 21 ## TwoFragment 19 ## InsertSSBond 0 ## OneRotamer 0 ## InsertAlignment 121 ## ReduceBreak 31 # best score after generation 10 229.477 bits/residue, 42 clashes 31.122 breaks # Cumulative usage by method: ## InsertFragment 71 ## ReduceClash 66 ## CrossOver 8 ## CrossAndInsert 24 ## TwoFragment 21 ## InsertSSBond 0 ## OneRotamer 0 ## InsertAlignment 130 ## ReduceBreak 33 # 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: 229.477 bits/residue, 42 clashes, rmsd= 0 # best score after iter 1 229.477 bits/residue, 42 clashes, rmsd= 0 # best score after iter 2 229.477 bits/residue, 42 clashes, rmsd= 0 # best score after iter 3 227.989 bits/residue, 28 clashes, rmsd= 0 # best score after iter 4 227.611 bits/residue, 27 clashes, rmsd= 0 # best score after iter 5 227.611 bits/residue, 27 clashes, rmsd= 0 # best score after iter 6 227.408 bits/residue, 26 clashes, rmsd= 0 # best score after iter 7 227.408 bits/residue, 26 clashes, rmsd= 0 # best score after iter 8 227.408 bits/residue, 26 clashes, rmsd= 0 # best score after iter 9 226.984 bits/residue, 49 clashes, rmsd= 0 # best score after iter 10 226.984 bits/residue, 49 clashes, rmsd= 0 # best score after iter 11 226.984 bits/residue, 49 clashes, rmsd= 0 # best score after iter 12 226.984 bits/residue, 49 clashes, rmsd= 0 # best score after iter 13 226.984 bits/residue, 49 clashes, rmsd= 0 # best score after iter 14 226.984 bits/residue, 49 clashes, rmsd= 0 # best score after iter 15 226.18 bits/residue, 46 clashes, rmsd= 0 # best score after iter 16 226.18 bits/residue, 46 clashes, rmsd= 0 # best score after iter 17 226.18 bits/residue, 46 clashes, rmsd= 0 # best score after iter 18 226.18 bits/residue, 46 clashes, rmsd= 0 # best score after iter 19 225.932 bits/residue, 46 clashes, rmsd= 0 # best score after iter 20 225.932 bits/residue, 46 clashes, rmsd= 0 # best score after iter 21 225.599 bits/residue, 47 clashes, rmsd= 0 # best score after iter 22 225.565 bits/residue, 47 clashes, rmsd= 0 # best score after iter 23 225.319 bits/residue, 48 clashes, rmsd= 0 # best score after iter 24 225.319 bits/residue, 48 clashes, rmsd= 0 # best score after iter 25 224.847 bits/residue, 38 clashes, rmsd= 0 # best score after iter 26 223.526 bits/residue, 32 clashes, rmsd= 0 # best score after iter 27 223.195 bits/residue, 33 clashes, rmsd= 0 # best score after iter 28 222.884 bits/residue, 33 clashes, rmsd= 0 # best score after iter 29 222.884 bits/residue, 33 clashes, rmsd= 0 # command:# naming current conformation t113-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] 222.884 bits/residue, 33 clashes 31.122 breaks # best score after generation 1 222.884 bits/residue, 33 clashes 31.122 breaks # Cumulative usage by method: ## InsertFragment 4 ## ReduceClash 4 ## CrossOver 1 ## CrossAndInsert 8 ## TwoFragment 13 ## InsertSSBond 1 ## OneRotamer 0 ## InsertAlignment 5 ## ReduceBreak 11 # best score after generation 2 221.481 bits/residue, 33 clashes 22.5092 breaks # Cumulative usage by method: ## InsertFragment 9 ## ReduceClash 10 ## CrossOver 1 ## CrossAndInsert 16 ## TwoFragment 18 ## InsertSSBond 1 ## OneRotamer 0 ## InsertAlignment 11 ## ReduceBreak 22 # best score after generation 3 221.481 bits/residue, 33 clashes 22.5092 breaks # Cumulative usage by method: ## InsertFragment 13 ## ReduceClash 15 ## CrossOver 3 ## CrossAndInsert 20 ## TwoFragment 19 ## InsertSSBond 1 ## OneRotamer 0 ## InsertAlignment 11 ## ReduceBreak 36 # best score after generation 4 221.387 bits/residue, 36 clashes 34.1071 breaks # Cumulative usage by method: ## InsertFragment 22 ## ReduceClash 23 ## CrossOver 6 ## CrossAndInsert 25 ## TwoFragment 19 ## InsertSSBond 1 ## OneRotamer 0 ## InsertAlignment 11 ## ReduceBreak 41 # best score after generation 5 220.178 bits/residue, 38 clashes 22.5092 breaks # Cumulative usage by method: ## InsertFragment 29 ## ReduceClash 33 ## CrossOver 12 ## CrossAndInsert 28 ## TwoFragment 19 ## InsertSSBond 1 ## OneRotamer 0 ## InsertAlignment 11 ## ReduceBreak 45 # best score after generation 6 219.993 bits/residue, 38 clashes 22.5092 breaks # Cumulative usage by method: ## InsertFragment 31 ## ReduceClash 39 ## CrossOver 18 ## CrossAndInsert 34 ## TwoFragment 20 ## InsertSSBond 1 ## OneRotamer 0 ## InsertAlignment 11 ## ReduceBreak 54 # best score after generation 7 219.816 bits/residue, 36 clashes 22.0379 breaks # Cumulative usage by method: ## InsertFragment 34 ## ReduceClash 45 ## CrossOver 27 ## CrossAndInsert 37 ## TwoFragment 20 ## InsertSSBond 1 ## OneRotamer 0 ## InsertAlignment 11 ## ReduceBreak 63 # best score after generation 8 219.107 bits/residue, 32 clashes 22.5086 breaks # Cumulative usage by method: ## InsertFragment 36 ## ReduceClash 51 ## CrossOver 43 ## CrossAndInsert 39 ## TwoFragment 20 ## InsertSSBond 1 ## OneRotamer 0 ## InsertAlignment 11 ## ReduceBreak 67 # best score after generation 9 218.551 bits/residue, 25 clashes 22.9906 breaks # Cumulative usage by method: ## InsertFragment 38 ## ReduceClash 55 ## CrossOver 63 ## CrossAndInsert 40 ## TwoFragment 20 ## InsertSSBond 1 ## OneRotamer 0 ## InsertAlignment 11 ## ReduceBreak 70 # best score after generation 10 217.776 bits/residue, 23 clashes 22.4718 breaks # Cumulative usage by method: ## InsertFragment 38 ## ReduceClash 57 ## CrossOver 87 ## CrossAndInsert 41 ## TwoFragment 20 ## InsertSSBond 1 ## OneRotamer 0 ## InsertAlignment 11 ## ReduceBreak 73 # command:# naming current conformation t113-opt # 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: 20.7806 bits/residue, 23 clashes, rmsd= 0 # best score after iter 1 20.7806 bits/residue, 23 clashes, rmsd= 0 # best score after iter 2 20.2501 bits/residue, 50 clashes, rmsd= 0 # best score after iter 3 19.2404 bits/residue, 48 clashes, rmsd= 0 # best score after iter 4 18.5263 bits/residue, 48 clashes, rmsd= 0 # best score after iter 5 16.131 bits/residue, 35 clashes, rmsd= 0 # best score after iter 6 16.131 bits/residue, 35 clashes, rmsd= 0 # best score after iter 7 16.131 bits/residue, 35 clashes, rmsd= 0 # best score after iter 8 16.131 bits/residue, 35 clashes, rmsd= 0 # best score after iter 9 16.131 bits/residue, 35 clashes, rmsd= 0 # best score after iter 10 16.131 bits/residue, 35 clashes, rmsd= 0 # best score after iter 11 16.131 bits/residue, 35 clashes, rmsd= 0 # best score after iter 12 16.131 bits/residue, 35 clashes, rmsd= 0 # best score after iter 13 16.131 bits/residue, 35 clashes, rmsd= 0 # best score after iter 14 16.131 bits/residue, 35 clashes, rmsd= 0 # best score after iter 15 15.1345 bits/residue, 31 clashes, rmsd= 0 # best score after iter 16 15.12 bits/residue, 31 clashes, rmsd= 0 # best score after iter 17 15.1162 bits/residue, 31 clashes, rmsd= 0 # best score after iter 18 15.1125 bits/residue, 31 clashes, rmsd= 0 # best score after iter 19 14.9178 bits/residue, 30 clashes, rmsd= 0 # command:# naming current conformation t113-opt-rot-opt-rot # command:# command:# ScwrlConform produces command scwrl -i /projects/compbio/tmp/to_scwrl_220018009.pdb -s /projects/compbio/tmp/to_scwrl_220018009.seq -o /projects/compbio/tmp/from_scwrl_220018009.pdb > /projects/compbio/tmp/scwrl.log # conformation set from SCWRL output # command:# naming current conformation t113-opt-rot-opt-scwrl # command:# command:# ScoreConform t113-2hsdA -log2(score)= 13382.3 (51.2731 bits/residue) 262 clashes 0 breaks t113-opt -log2(score)= 5854.97 (22.4328 bits/residue) 42 clashes 31.122 breaks t113-opt-rot -log2(score)= 6493.21 (24.8782 bits/residue) 33 clashes 31.122 breaks t113-opt -log2(score)= 5423.73 (20.7806 bits/residue) 23 clashes 22.4718 breaks t113-opt-rot-opt-rot -log2(score)= 3893.55 (14.9178 bits/residue) 30 clashes 22.4718 breaks t113-opt-rot-opt-scwrl -log2(score)= 3556.69 (13.6272 bits/residue) 26 clashes 0 breaks # command: