# 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 50 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:# created conformation for T0113 by applying fragments # command:# naming current conformation t113-2hsdA # command:# command:# Will do 12 iterations of optimization kestrel rte: ERROR in InitializeSocket: can't connect to kestrel server Couldn't initialize socket to Kestrel. Sleep and retry kestrel rte: ERROR in InitializeSocket: can't connect to kestrel server Couldn't initialize socket to Kestrel. Sleep and retry kestrel rte: ERROR in InitializeSocket: can't connect to kestrel server Couldn't initialize socket to Kestrel. Sleep and retry kestrel rte: ERROR in InitializeSocket: can't connect to kestrel server Couldn't initialize socket to Kestrel. Sleep and retry kestrel rte: ERROR in InitializeSocket: can't connect to kestrel server Couldn't initialize socket to Kestrel. Sleep and retry kestrel rte: ERROR in InitializeSocket: can't connect to kestrel server Couldn't initialize socket to Kestrel. Sleep and retry kestrel rte: ERROR in InitializeSocket: can't connect to kestrel server Couldn't initialize socket to Kestrel. Sleep and retry kestrel rte: ERROR in InitializeSocket: can't connect to kestrel server Couldn't initialize socket to Kestrel. Sleep and retry kestrel rte: ERROR in InitializeSocket: can't connect to kestrel server Couldn't initialize socket to Kestrel. Sleep and retry kestrel rte: ERROR in InitializeSocket: can't connect to kestrel server Couldn't initialize socket to Kestrel. Sleep and retry kestrel rte: ERROR in InitializeSocket: can't connect to kestrel server Couldn't initialize socket to Kestrel. Sleep and retry kestrel rte: ERROR in InitializeSocket: can't connect to kestrel server Couldn't initialize socket to Kestrel. Sleep and retry kestrel rte: ERROR in InitializeSocket: can't connect to kestrel server Couldn't initialize socket to Kestrel. Sleep and retry kestrel rte: ERROR in InitializeSocket: can't connect to kestrel server Couldn't initialize socket to Kestrel. Sleep and retry kestrel rte: ERROR in InitializeSocket: can't connect to kestrel server Couldn't initialize socket to Kestrel. Sleep and retry kestrel rte: ERROR in InitializeSocket: can't connect to kestrel server Couldn't initialize socket to Kestrel. Sleep and retry kestrel rte: ERROR in InitializeSocket: can't connect to kestrel server Couldn't initialize socket to Kestrel. Sleep and retry kestrel rte: ERROR in InitializeSocket: can't connect to kestrel server Couldn't initialize socket to Kestrel. Sleep and retry kestrel rte: ERROR in InitializeSocket: can't connect to kestrel server Couldn't initialize socket to Kestrel. Sleep and retry kestrel rte: ERROR in InitializeSocket: can't connect to kestrel server Couldn't initialize socket to Kestrel. Sleep and retry kestrel rte: ERROR in InitializeSocket: can't connect to kestrel server Couldn't initialize socket to Kestrel. Sleep and retry kestrel rte: ERROR in InitializeSocket: can't connect to kestrel server Couldn't initialize socket to Kestrel. Sleep and retry kestrel rte: ERROR in InitializeSocket: can't connect to kestrel server Couldn't initialize socket to Kestrel. Sleep and retry kestrel rte: ERROR in InitializeSocket: can't connect to kestrel server Couldn't initialize socket to Kestrel. Sleep and retry kestrel rte: ERROR in InitializeSocket: can't connect to kestrel server Couldn't initialize socket to Kestrel. Sleep and retry kestrel rte: ERROR in InitializeSocket: can't connect to kestrel server Couldn't initialize socket to Kestrel. Sleep and retry kestrel rte: ERROR in InitializeSocket: can't connect to kestrel server Couldn't initialize socket to Kestrel. Sleep and retry kestrel rte: ERROR in InitializeSocket: can't connect to kestrel server Couldn't initialize socket to Kestrel. Sleep and retry kestrel rte: ERROR in InitializeSocket: can't connect to kestrel server Couldn't initialize socket to Kestrel. Sleep and retry kestrel rte: ERROR in InitializeSocket: can't connect to kestrel server Couldn't initialize socket to Kestrel. Sleep and retry kestrel rte: ERROR in InitializeSocket: can't connect to kestrel server Couldn't initialize socket to Kestrel. Sleep and retry kestrel rte: ERROR in InitializeSocket: can't connect to kestrel server Couldn't initialize socket to Kestrel. Sleep and retry kestrel rte: ERROR in InitializeSocket: can't connect to kestrel server Couldn't initialize socket to Kestrel. Sleep and retry # best score in initial pool 244.868 bits/residue, 145 clashes 30.5253 breaks # optimizing backbone with 50 conformations in pool # doing 3 generations, with 250 new conformations in each generation. # keep at most 20 conformations from old pool # generation 1: best score 239.386 bits/residue, 113 clashes 30.4148 breaks # Cumulative usage by method: ## InsertFragment 2 ## ReduceClash 5 ## CrossOver 0 ## CrossAndInsert 6 ## TwoFragment 9 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 2 ## InsertAlignment 23 ## ReduceBreak 1 # generation 2: best score 237.934 bits/residue, 100 clashes 30.8699 breaks # Cumulative usage by method: ## InsertFragment 3 ## ReduceClash 11 ## CrossOver 0 ## CrossAndInsert 6 ## TwoFragment 12 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 2 ## InsertAlignment 56 ## ReduceBreak 1 # generation 3: best score 237.934 bits/residue, 100 clashes 30.8699 breaks # Cumulative usage by method: ## InsertFragment 3 ## ReduceClash 13 ## CrossOver 0 ## CrossAndInsert 6 ## TwoFragment 12 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 3 ## InsertAlignment 92 ## ReduceBreak 1 # best score in initial pool 244.868 bits/residue, 145 clashes 30.5253 breaks # optimizing backbone with 50 conformations in pool # doing 3 generations, with 250 new conformations in each generation. # keep at most 20 conformations from old pool # generation 1: best score 240.276 bits/residue, 111 clashes 34.9761 breaks # Cumulative usage by method: ## InsertFragment 3 ## ReduceClash 5 ## CrossOver 0 ## CrossAndInsert 3 ## TwoFragment 2 ## InsertSSBond 3 ## OneRotamer 0 ## ClashingRotamer 3 ## InsertAlignment 28 ## ReduceBreak 1 # generation 2: best score 240.276 bits/residue, 111 clashes 34.9761 breaks # Cumulative usage by method: ## InsertFragment 10 ## ReduceClash 5 ## CrossOver 1 ## CrossAndInsert 3 ## TwoFragment 2 ## InsertSSBond 3 ## OneRotamer 0 ## ClashingRotamer 3 ## InsertAlignment 62 ## ReduceBreak 2 # generation 3: best score 240.227 bits/residue, 108 clashes 35.9908 breaks # Cumulative usage by method: ## InsertFragment 13 ## ReduceClash 10 ## CrossOver 2 ## CrossAndInsert 3 ## TwoFragment 3 ## InsertSSBond 3 ## OneRotamer 0 ## ClashingRotamer 3 ## InsertAlignment 90 ## ReduceBreak 3 # best score in initial pool 244.868 bits/residue, 145 clashes 30.5253 breaks # optimizing backbone with 50 conformations in pool # doing 3 generations, with 250 new conformations in each generation. # keep at most 20 conformations from old pool # generation 1: best score 243.97 bits/residue, 129 clashes 34.6441 breaks # Cumulative usage by method: ## InsertFragment 2 ## ReduceClash 4 ## CrossOver 0 ## CrossAndInsert 5 ## TwoFragment 5 ## InsertSSBond 1 ## OneRotamer 0 ## ClashingRotamer 0 ## InsertAlignment 27 ## ReduceBreak 4 # generation 2: best score 240.119 bits/residue, 119 clashes 27.3298 breaks # Cumulative usage by method: ## InsertFragment 3 ## ReduceClash 7 ## CrossOver 0 ## CrossAndInsert 8 ## TwoFragment 5 ## InsertSSBond 1 ## OneRotamer 0 ## ClashingRotamer 0 ## InsertAlignment 63 ## ReduceBreak 5 # generation 3: best score 239.919 bits/residue, 118 clashes 27.4315 breaks # Cumulative usage by method: ## InsertFragment 4 ## ReduceClash 7 ## CrossOver 0 ## CrossAndInsert 8 ## TwoFragment 5 ## InsertSSBond 1 ## OneRotamer 0 ## ClashingRotamer 0 ## InsertAlignment 105 ## ReduceBreak 6 # best score in initial pool 244.868 bits/residue, 145 clashes 30.5253 breaks # optimizing backbone with 50 conformations in pool # doing 3 generations, with 250 new conformations in each generation. # keep at most 20 conformations from old pool # generation 1: best score 236.87 bits/residue, 68 clashes 32.1872 breaks # Cumulative usage by method: ## InsertFragment 6 ## ReduceClash 1 ## CrossOver 0 ## CrossAndInsert 4 ## TwoFragment 4 ## InsertSSBond 1 ## OneRotamer 0 ## ClashingRotamer 2 ## InsertAlignment 30 ## ReduceBreak 1 # generation 2: best score 236.123 bits/residue, 65 clashes 29.1628 breaks # Cumulative usage by method: ## InsertFragment 6 ## ReduceClash 2 ## CrossOver 0 ## CrossAndInsert 6 ## TwoFragment 4 ## InsertSSBond 1 ## OneRotamer 0 ## ClashingRotamer 4 ## InsertAlignment 68 ## ReduceBreak 1 # generation 3: best score 236.104 bits/residue, 63 clashes 32.7832 breaks # Cumulative usage by method: ## InsertFragment 9 ## ReduceClash 4 ## CrossOver 0 ## CrossAndInsert 8 ## TwoFragment 4 ## InsertSSBond 1 ## OneRotamer 0 ## ClashingRotamer 6 ## InsertAlignment 100 ## ReduceBreak 1 # best score in initial pool 244.868 bits/residue, 145 clashes 30.5253 breaks # optimizing backbone with 50 conformations in pool # doing 3 generations, with 250 new conformations in each generation. # keep at most 20 conformations from old pool # generation 1: best score 242.895 bits/residue, 121 clashes 30.2059 breaks # Cumulative usage by method: ## InsertFragment 4 ## ReduceClash 5 ## CrossOver 0 ## CrossAndInsert 11 ## TwoFragment 4 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 2 ## InsertAlignment 21 ## ReduceBreak 0 # generation 2: best score 238.819 bits/residue, 105 clashes 32.4742 breaks # Cumulative usage by method: ## InsertFragment 5 ## ReduceClash 7 ## CrossOver 0 ## CrossAndInsert 12 ## TwoFragment 4 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 2 ## InsertAlignment 61 ## ReduceBreak 1 # generation 3: best score 238.654 bits/residue, 104 clashes 32.4762 breaks # Cumulative usage by method: ## InsertFragment 7 ## ReduceClash 8 ## CrossOver 1 ## CrossAndInsert 14 ## TwoFragment 4 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 4 ## InsertAlignment 94 ## ReduceBreak 2 # best score in initial pool 244.868 bits/residue, 145 clashes 30.5253 breaks # optimizing backbone with 50 conformations in pool # doing 3 generations, with 250 new conformations in each generation. # keep at most 20 conformations from old pool # generation 1: best score 240.742 bits/residue, 119 clashes 31.5521 breaks # Cumulative usage by method: ## InsertFragment 4 ## ReduceClash 4 ## CrossOver 0 ## CrossAndInsert 6 ## TwoFragment 3 ## InsertSSBond 3 ## OneRotamer 0 ## ClashingRotamer 4 ## InsertAlignment 23 ## ReduceBreak 1 # generation 2: best score 240.742 bits/residue, 119 clashes 31.5521 breaks # Cumulative usage by method: ## InsertFragment 5 ## ReduceClash 6 ## CrossOver 1 ## CrossAndInsert 9 ## TwoFragment 4 ## InsertSSBond 3 ## OneRotamer 0 ## ClashingRotamer 6 ## InsertAlignment 58 ## ReduceBreak 2 # generation 3: best score 240.244 bits/residue, 110 clashes 31.1714 breaks # Cumulative usage by method: ## InsertFragment 6 ## ReduceClash 7 ## CrossOver 1 ## CrossAndInsert 9 ## TwoFragment 4 ## InsertSSBond 3 ## OneRotamer 0 ## ClashingRotamer 6 ## InsertAlignment 101 ## ReduceBreak 2 # best score in initial pool 244.868 bits/residue, 145 clashes 30.5253 breaks # optimizing backbone with 50 conformations in pool # doing 3 generations, with 250 new conformations in each generation. # keep at most 20 conformations from old pool # generation 1: best score 244.868 bits/residue, 145 clashes 30.5253 breaks # Cumulative usage by method: ## InsertFragment 8 ## ReduceClash 6 ## CrossOver 0 ## CrossAndInsert 8 ## TwoFragment 3 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 3 ## InsertAlignment 20 ## ReduceBreak 0 # generation 2: best score 240.742 bits/residue, 119 clashes 31.5521 breaks # Cumulative usage by method: ## InsertFragment 12 ## ReduceClash 9 ## CrossOver 0 ## CrossAndInsert 10 ## TwoFragment 3 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 5 ## InsertAlignment 55 ## ReduceBreak 0 # generation 3: best score 238.705 bits/residue, 116 clashes 26.5794 breaks # Cumulative usage by method: ## InsertFragment 16 ## ReduceClash 12 ## CrossOver 0 ## CrossAndInsert 12 ## TwoFragment 4 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 6 ## InsertAlignment 88 ## ReduceBreak 1 # best score in initial pool 244.868 bits/residue, 145 clashes 30.5253 breaks # optimizing backbone with 50 conformations in pool # doing 3 generations, with 250 new conformations in each generation. # keep at most 20 conformations from old pool # generation 1: best score 237.924 bits/residue, 103 clashes 30.0556 breaks # Cumulative usage by method: ## InsertFragment 4 ## ReduceClash 3 ## CrossOver 0 ## CrossAndInsert 1 ## TwoFragment 5 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 4 ## InsertAlignment 28 ## ReduceBreak 3 # generation 2: best score 236.832 bits/residue, 91 clashes 31.9201 breaks # Cumulative usage by method: ## InsertFragment 6 ## ReduceClash 5 ## CrossOver 0 ## CrossAndInsert 3 ## TwoFragment 6 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 6 ## InsertAlignment 61 ## ReduceBreak 5 # generation 3: best score 234.677 bits/residue, 79 clashes 30.4081 breaks # Cumulative usage by method: ## InsertFragment 7 ## ReduceClash 6 ## CrossOver 0 ## CrossAndInsert 3 ## TwoFragment 6 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 6 ## InsertAlignment 102 ## ReduceBreak 5 # best score in initial pool 244.868 bits/residue, 145 clashes 30.5253 breaks # optimizing backbone with 50 conformations in pool # doing 3 generations, with 250 new conformations in each generation. # keep at most 20 conformations from old pool # generation 1: best score 241.543 bits/residue, 124 clashes 30.7351 breaks # Cumulative usage by method: ## InsertFragment 3 ## ReduceClash 4 ## CrossOver 0 ## CrossAndInsert 7 ## TwoFragment 10 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 1 ## InsertAlignment 19 ## ReduceBreak 3 # generation 2: best score 241.543 bits/residue, 124 clashes 30.7351 breaks # Cumulative usage by method: ## InsertFragment 5 ## ReduceClash 6 ## CrossOver 0 ## CrossAndInsert 8 ## TwoFragment 11 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 1 ## InsertAlignment 58 ## ReduceBreak 3 # generation 3: best score 238.599 bits/residue, 97 clashes 34.7333 breaks # Cumulative usage by method: ## InsertFragment 5 ## ReduceClash 9 ## CrossOver 1 ## CrossAndInsert 10 ## TwoFragment 13 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 1 ## InsertAlignment 92 ## ReduceBreak 4 # best score in initial pool 244.868 bits/residue, 145 clashes 30.5253 breaks # optimizing backbone with 50 conformations in pool # doing 3 generations, with 250 new conformations in each generation. # keep at most 20 conformations from old pool # generation 1: best score 244.868 bits/residue, 145 clashes 30.5253 breaks # Cumulative usage by method: ## InsertFragment 5 ## ReduceClash 3 ## CrossOver 0 ## CrossAndInsert 10 ## TwoFragment 6 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 3 ## InsertAlignment 18 ## ReduceBreak 3 # generation 2: best score 240.247 bits/residue, 96 clashes 37.5947 breaks # Cumulative usage by method: ## InsertFragment 8 ## ReduceClash 3 ## CrossOver 0 ## CrossAndInsert 10 ## TwoFragment 7 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 4 ## InsertAlignment 58 ## ReduceBreak 4 # generation 3: best score 238.328 bits/residue, 94 clashes 33.7118 breaks # Cumulative usage by method: ## InsertFragment 8 ## ReduceClash 5 ## CrossOver 0 ## CrossAndInsert 11 ## TwoFragment 7 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 4 ## InsertAlignment 97 ## ReduceBreak 5 # best score in initial pool 244.868 bits/residue, 145 clashes 30.5253 breaks # optimizing backbone with 50 conformations in pool # doing 3 generations, with 250 new conformations in each generation. # keep at most 20 conformations from old pool # generation 1: best score 242.405 bits/residue, 103 clashes 36.4748 breaks # Cumulative usage by method: ## InsertFragment 4 ## ReduceClash 2 ## CrossOver 0 ## CrossAndInsert 7 ## TwoFragment 3 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 1 ## InsertAlignment 30 ## ReduceBreak 1 # generation 2: best score 238.931 bits/residue, 88 clashes 43.5215 breaks # Cumulative usage by method: ## InsertFragment 5 ## ReduceClash 4 ## CrossOver 0 ## CrossAndInsert 9 ## TwoFragment 4 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 1 ## InsertAlignment 66 ## ReduceBreak 1 # generation 3: best score 236.89 bits/residue, 77 clashes 43.5874 breaks # Cumulative usage by method: ## InsertFragment 5 ## ReduceClash 5 ## CrossOver 0 ## CrossAndInsert 14 ## TwoFragment 5 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 1 ## InsertAlignment 100 ## ReduceBreak 1 # best score in initial pool 244.868 bits/residue, 145 clashes 30.5253 breaks # optimizing backbone with 50 conformations in pool # doing 3 generations, with 250 new conformations in each generation. # keep at most 20 conformations from old pool # generation 1: best score 239.794 bits/residue, 119 clashes 29.0142 breaks # Cumulative usage by method: ## InsertFragment 2 ## ReduceClash 7 ## CrossOver 0 ## CrossAndInsert 3 ## TwoFragment 5 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 2 ## InsertAlignment 27 ## ReduceBreak 1 # generation 2: best score 239.794 bits/residue, 119 clashes 29.0142 breaks # Cumulative usage by method: ## InsertFragment 3 ## ReduceClash 10 ## CrossOver 0 ## CrossAndInsert 3 ## TwoFragment 5 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 2 ## InsertAlignment 67 ## ReduceBreak 1 # generation 3: best score 238.291 bits/residue, 107 clashes 30.5679 breaks # Cumulative usage by method: ## InsertFragment 3 ## ReduceClash 12 ## CrossOver 0 ## CrossAndInsert 4 ## TwoFragment 5 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 2 ## InsertAlignment 110 ## ReduceBreak 1 # best score in super_pool at pool[7] 234.677 bits/residue, 79 clashes 30.4081 breaks # optimizing backbone with 50 conformations in pool # doing 3 generations, with 250 new conformations in each generation. # keep at most 20 conformations from old pool # generation 1: best score 234.264 bits/residue, 77 clashes 30.4081 breaks # Cumulative usage by method: ## InsertFragment 5 ## ReduceClash 5 ## CrossOver 1 ## CrossAndInsert 3 ## TwoFragment 1 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 5 ## InsertAlignment 18 ## ReduceBreak 0 # generation 2: best score 233.842 bits/residue, 77 clashes 30.1181 breaks # Cumulative usage by method: ## InsertFragment 8 ## ReduceClash 9 ## CrossOver 3 ## CrossAndInsert 5 ## TwoFragment 1 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 9 ## InsertAlignment 36 ## ReduceBreak 0 # generation 3: best score 233.21 bits/residue, 65 clashes 33.175 breaks # Cumulative usage by method: ## InsertFragment 11 ## ReduceClash 10 ## CrossOver 6 ## CrossAndInsert 5 ## TwoFragment 2 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 15 ## InsertAlignment 59 ## ReduceBreak 0 # 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: 233.21 bits/residue, 65 clashes, rmsd= 0 # best score after iter 1 233.21 bits/residue, 65 clashes, rmsd= 0 # best score after iter 2 230.365 bits/residue, 41 clashes, rmsd= 0 # best score after iter 3 227.75 bits/residue, 28 clashes, rmsd= 0 # best score after iter 4 227.166 bits/residue, 25 clashes, rmsd= 0 # best score after iter 5 227.073 bits/residue, 23 clashes, rmsd= 0 # best score after iter 6 226.902 bits/residue, 21 clashes, rmsd= 0 # best score after iter 7 226.902 bits/residue, 21 clashes, rmsd= 0 # best score after iter 8 226.902 bits/residue, 21 clashes, rmsd= 0 # best score after iter 9 226.902 bits/residue, 21 clashes, rmsd= 0 # best score after iter 10 226.902 bits/residue, 21 clashes, rmsd= 0 # best score after iter 11 226.902 bits/residue, 21 clashes, rmsd= 0 # best score after iter 12 226.245 bits/residue, 40 clashes, rmsd= 0 # best score after iter 13 226.245 bits/residue, 40 clashes, rmsd= 0 # best score after iter 14 226.245 bits/residue, 40 clashes, rmsd= 0 # best score after iter 15 226.245 bits/residue, 40 clashes, rmsd= 0 # best score after iter 16 226.245 bits/residue, 40 clashes, rmsd= 0 # best score after iter 17 226.245 bits/residue, 40 clashes, rmsd= 0 # best score after iter 18 226.245 bits/residue, 40 clashes, rmsd= 0 # best score after iter 19 226.245 bits/residue, 40 clashes, rmsd= 0 # best score after iter 20 226.245 bits/residue, 40 clashes, rmsd= 0 # best score after iter 21 226.245 bits/residue, 40 clashes, rmsd= 0 # best score after iter 22 225.498 bits/residue, 40 clashes, rmsd= 0 # best score after iter 23 225.014 bits/residue, 38 clashes, rmsd= 0 # best score after iter 24 224.273 bits/residue, 39 clashes, rmsd= 0 # best score after iter 25 224.273 bits/residue, 39 clashes, rmsd= 0 # best score after iter 26 223.923 bits/residue, 36 clashes, rmsd= 0 # best score after iter 27 223.469 bits/residue, 35 clashes, rmsd= 0 # best score after iter 28 223.469 bits/residue, 35 clashes, rmsd= 0 # best score after iter 29 222.852 bits/residue, 30 clashes, rmsd= 0 # command:# naming current conformation t113-opt-rot # command:# command:# Will do 12 iterations of optimization # best score in initial pool 222.852 bits/residue, 30 clashes 33.175 breaks # optimizing backbone with 50 conformations in pool # doing 3 generations, with 250 new conformations in each generation. # keep at most 20 conformations from old pool # generation 1: best score 222.852 bits/residue, 30 clashes 33.175 breaks # Cumulative usage by method: ## InsertFragment 2 ## ReduceClash 4 ## CrossOver 0 ## CrossAndInsert 2 ## TwoFragment 7 ## InsertSSBond 3 ## OneRotamer 0 ## ClashingRotamer 0 ## InsertAlignment 27 ## ReduceBreak 4 # generation 2: best score 222.852 bits/residue, 30 clashes 33.175 breaks # Cumulative usage by method: ## InsertFragment 2 ## ReduceClash 6 ## CrossOver 0 ## CrossAndInsert 7 ## TwoFragment 9 ## InsertSSBond 3 ## OneRotamer 0 ## ClashingRotamer 2 ## InsertAlignment 61 ## ReduceBreak 4 # generation 3: best score 222.852 bits/residue, 30 clashes 33.175 breaks # Cumulative usage by method: ## InsertFragment 4 ## ReduceClash 9 ## CrossOver 0 ## CrossAndInsert 7 ## TwoFragment 9 ## InsertSSBond 3 ## OneRotamer 0 ## ClashingRotamer 2 ## InsertAlignment 88 ## ReduceBreak 4 # best score in initial pool 222.852 bits/residue, 30 clashes 33.175 breaks # optimizing backbone with 50 conformations in pool # doing 3 generations, with 250 new conformations in each generation. # keep at most 20 conformations from old pool # generation 1: best score 222.852 bits/residue, 30 clashes 33.175 breaks # Cumulative usage by method: ## InsertFragment 5 ## ReduceClash 4 ## CrossOver 0 ## CrossAndInsert 3 ## TwoFragment 3 ## InsertSSBond 1 ## OneRotamer 0 ## ClashingRotamer 0 ## InsertAlignment 30 ## ReduceBreak 2 # generation 2: best score 222.852 bits/residue, 30 clashes 33.175 breaks # Cumulative usage by method: ## InsertFragment 9 ## ReduceClash 7 ## CrossOver 0 ## CrossAndInsert 3 ## TwoFragment 4 ## InsertSSBond 1 ## OneRotamer 0 ## ClashingRotamer 1 ## InsertAlignment 65 ## ReduceBreak 2 # generation 3: best score 222.852 bits/residue, 30 clashes 33.175 breaks # Cumulative usage by method: ## InsertFragment 15 ## ReduceClash 7 ## CrossOver 1 ## CrossAndInsert 4 ## TwoFragment 6 ## InsertSSBond 1 ## OneRotamer 0 ## ClashingRotamer 1 ## InsertAlignment 87 ## ReduceBreak 4 # best score in initial pool 222.852 bits/residue, 30 clashes 33.175 breaks # optimizing backbone with 50 conformations in pool # doing 3 generations, with 250 new conformations in each generation. # keep at most 20 conformations from old pool # generation 1: best score 222.852 bits/residue, 30 clashes 33.175 breaks # Cumulative usage by method: ## InsertFragment 4 ## ReduceClash 2 ## CrossOver 0 ## CrossAndInsert 2 ## TwoFragment 4 ## InsertSSBond 1 ## OneRotamer 0 ## ClashingRotamer 3 ## InsertAlignment 31 ## ReduceBreak 2 # generation 2: best score 222.852 bits/residue, 30 clashes 33.175 breaks # Cumulative usage by method: ## InsertFragment 6 ## ReduceClash 3 ## CrossOver 0 ## CrossAndInsert 5 ## TwoFragment 4 ## InsertSSBond 1 ## OneRotamer 0 ## ClashingRotamer 8 ## InsertAlignment 59 ## ReduceBreak 3 # generation 3: best score 222.852 bits/residue, 30 clashes 33.175 breaks # Cumulative usage by method: ## InsertFragment 8 ## ReduceClash 6 ## CrossOver 0 ## CrossAndInsert 9 ## TwoFragment 5 ## InsertSSBond 1 ## OneRotamer 0 ## ClashingRotamer 12 ## InsertAlignment 74 ## ReduceBreak 4 # best score in initial pool 222.852 bits/residue, 30 clashes 33.175 breaks # optimizing backbone with 50 conformations in pool # doing 3 generations, with 250 new conformations in each generation. # keep at most 20 conformations from old pool # generation 1: best score 222.852 bits/residue, 30 clashes 33.175 breaks # Cumulative usage by method: ## InsertFragment 3 ## ReduceClash 2 ## CrossOver 0 ## CrossAndInsert 4 ## TwoFragment 6 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 1 ## InsertAlignment 30 ## ReduceBreak 2 # generation 2: best score 222.852 bits/residue, 30 clashes 33.175 breaks # Cumulative usage by method: ## InsertFragment 5 ## ReduceClash 4 ## CrossOver 2 ## CrossAndInsert 5 ## TwoFragment 7 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 2 ## InsertAlignment 62 ## ReduceBreak 3 # generation 3: best score 222.852 bits/residue, 30 clashes 33.175 breaks # Cumulative usage by method: ## InsertFragment 9 ## ReduceClash 5 ## CrossOver 7 ## CrossAndInsert 6 ## TwoFragment 7 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 4 ## InsertAlignment 85 ## ReduceBreak 4 # best score in initial pool 222.852 bits/residue, 30 clashes 33.175 breaks # optimizing backbone with 50 conformations in pool # doing 3 generations, with 250 new conformations in each generation. # keep at most 20 conformations from old pool # generation 1: best score 222.852 bits/residue, 30 clashes 33.175 breaks # Cumulative usage by method: ## InsertFragment 2 ## ReduceClash 2 ## CrossOver 0 ## CrossAndInsert 7 ## TwoFragment 3 ## InsertSSBond 1 ## OneRotamer 0 ## ClashingRotamer 5 ## InsertAlignment 27 ## ReduceBreak 2 # generation 2: best score 222.852 bits/residue, 30 clashes 33.175 breaks # Cumulative usage by method: ## InsertFragment 5 ## ReduceClash 6 ## CrossOver 0 ## CrossAndInsert 10 ## TwoFragment 4 ## InsertSSBond 1 ## OneRotamer 0 ## ClashingRotamer 12 ## InsertAlignment 47 ## ReduceBreak 4 # generation 3: best score 222.852 bits/residue, 30 clashes 33.175 breaks # Cumulative usage by method: ## InsertFragment 9 ## ReduceClash 7 ## CrossOver 0 ## CrossAndInsert 12 ## TwoFragment 4 ## InsertSSBond 1 ## OneRotamer 0 ## ClashingRotamer 21 ## InsertAlignment 60 ## ReduceBreak 5 # best score in initial pool 222.852 bits/residue, 30 clashes 33.175 breaks # optimizing backbone with 50 conformations in pool # doing 3 generations, with 250 new conformations in each generation. # keep at most 20 conformations from old pool # generation 1: best score 222.852 bits/residue, 30 clashes 33.175 breaks # Cumulative usage by method: ## InsertFragment 5 ## ReduceClash 5 ## CrossOver 0 ## CrossAndInsert 2 ## TwoFragment 9 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 0 ## InsertAlignment 25 ## ReduceBreak 2 # generation 2: best score 222.852 bits/residue, 30 clashes 33.175 breaks # Cumulative usage by method: ## InsertFragment 6 ## ReduceClash 5 ## CrossOver 0 ## CrossAndInsert 6 ## TwoFragment 11 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 2 ## InsertAlignment 59 ## ReduceBreak 3 # generation 3: best score 222.852 bits/residue, 30 clashes 33.175 breaks # Cumulative usage by method: ## InsertFragment 6 ## ReduceClash 6 ## CrossOver 1 ## CrossAndInsert 8 ## TwoFragment 11 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 4 ## InsertAlignment 86 ## ReduceBreak 3 # best score in initial pool 222.852 bits/residue, 30 clashes 33.175 breaks # optimizing backbone with 50 conformations in pool # doing 3 generations, with 250 new conformations in each generation. # keep at most 20 conformations from old pool # generation 1: best score 222.852 bits/residue, 30 clashes 33.175 breaks # Cumulative usage by method: ## InsertFragment 3 ## ReduceClash 5 ## CrossOver 0 ## CrossAndInsert 6 ## TwoFragment 2 ## InsertSSBond 4 ## OneRotamer 0 ## ClashingRotamer 1 ## InsertAlignment 25 ## ReduceBreak 2 # generation 2: best score 222.852 bits/residue, 30 clashes 33.175 breaks # Cumulative usage by method: ## InsertFragment 5 ## ReduceClash 8 ## CrossOver 0 ## CrossAndInsert 11 ## TwoFragment 3 ## InsertSSBond 4 ## OneRotamer 0 ## ClashingRotamer 3 ## InsertAlignment 50 ## ReduceBreak 5 # generation 3: best score 222.852 bits/residue, 30 clashes 33.175 breaks # Cumulative usage by method: ## InsertFragment 6 ## ReduceClash 11 ## CrossOver 0 ## CrossAndInsert 13 ## TwoFragment 3 ## InsertSSBond 4 ## OneRotamer 0 ## ClashingRotamer 6 ## InsertAlignment 72 ## ReduceBreak 5 # best score in initial pool 222.852 bits/residue, 30 clashes 33.175 breaks # optimizing backbone with 50 conformations in pool # doing 3 generations, with 250 new conformations in each generation. # keep at most 20 conformations from old pool # generation 1: best score 222.852 bits/residue, 30 clashes 33.175 breaks # Cumulative usage by method: ## InsertFragment 1 ## ReduceClash 2 ## CrossOver 0 ## CrossAndInsert 0 ## TwoFragment 5 ## InsertSSBond 2 ## OneRotamer 0 ## ClashingRotamer 1 ## InsertAlignment 36 ## ReduceBreak 1 # generation 2: best score 222.852 bits/residue, 30 clashes 33.175 breaks # Cumulative usage by method: ## InsertFragment 8 ## ReduceClash 5 ## CrossOver 0 ## CrossAndInsert 3 ## TwoFragment 5 ## InsertSSBond 2 ## OneRotamer 0 ## ClashingRotamer 2 ## InsertAlignment 62 ## ReduceBreak 3 # generation 3: best score 222.852 bits/residue, 30 clashes 33.175 breaks # Cumulative usage by method: ## InsertFragment 12 ## ReduceClash 8 ## CrossOver 0 ## CrossAndInsert 5 ## TwoFragment 6 ## InsertSSBond 2 ## OneRotamer 0 ## ClashingRotamer 3 ## InsertAlignment 81 ## ReduceBreak 5 # best score in initial pool 222.852 bits/residue, 30 clashes 33.175 breaks # optimizing backbone with 50 conformations in pool # doing 3 generations, with 250 new conformations in each generation. # keep at most 20 conformations from old pool # generation 1: best score 222.852 bits/residue, 30 clashes 33.175 breaks # Cumulative usage by method: ## InsertFragment 3 ## ReduceClash 2 ## CrossOver 0 ## CrossAndInsert 3 ## TwoFragment 9 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 1 ## InsertAlignment 24 ## ReduceBreak 5 # generation 2: best score 222.852 bits/residue, 30 clashes 33.175 breaks # Cumulative usage by method: ## InsertFragment 7 ## ReduceClash 3 ## CrossOver 0 ## CrossAndInsert 6 ## TwoFragment 11 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 2 ## InsertAlignment 53 ## ReduceBreak 8 # generation 3: best score 222.852 bits/residue, 30 clashes 33.175 breaks # Cumulative usage by method: ## InsertFragment 10 ## ReduceClash 5 ## CrossOver 1 ## CrossAndInsert 8 ## TwoFragment 12 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 5 ## InsertAlignment 72 ## ReduceBreak 9 # best score in initial pool 222.852 bits/residue, 30 clashes 33.175 breaks # optimizing backbone with 50 conformations in pool # doing 3 generations, with 250 new conformations in each generation. # keep at most 20 conformations from old pool # generation 1: best score 222.852 bits/residue, 30 clashes 33.175 breaks # Cumulative usage by method: ## InsertFragment 3 ## ReduceClash 6 ## CrossOver 0 ## CrossAndInsert 6 ## TwoFragment 4 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 1 ## InsertAlignment 27 ## ReduceBreak 2 # generation 2: best score 222.763 bits/residue, 28 clashes 33.175 breaks # Cumulative usage by method: ## InsertFragment 6 ## ReduceClash 11 ## CrossOver 0 ## CrossAndInsert 9 ## TwoFragment 5 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 6 ## InsertAlignment 52 ## ReduceBreak 2 # generation 3: best score 222.597 bits/residue, 27 clashes 32.8175 breaks # Cumulative usage by method: ## InsertFragment 10 ## ReduceClash 15 ## CrossOver 0 ## CrossAndInsert 13 ## TwoFragment 6 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 8 ## InsertAlignment 66 ## ReduceBreak 3 # best score in initial pool 222.852 bits/residue, 30 clashes 33.175 breaks # optimizing backbone with 50 conformations in pool # doing 3 generations, with 250 new conformations in each generation. # keep at most 20 conformations from old pool # generation 1: best score 222.852 bits/residue, 30 clashes 33.175 breaks # Cumulative usage by method: ## InsertFragment 3 ## ReduceClash 6 ## CrossOver 0 ## CrossAndInsert 4 ## TwoFragment 9 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 3 ## InsertAlignment 22 ## ReduceBreak 1 # generation 2: best score 222.852 bits/residue, 30 clashes 33.175 breaks # Cumulative usage by method: ## InsertFragment 8 ## ReduceClash 8 ## CrossOver 1 ## CrossAndInsert 7 ## TwoFragment 10 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 7 ## InsertAlignment 45 ## ReduceBreak 1 # generation 3: best score 222.852 bits/residue, 30 clashes 33.175 breaks # Cumulative usage by method: ## InsertFragment 11 ## ReduceClash 11 ## CrossOver 3 ## CrossAndInsert 10 ## TwoFragment 10 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 10 ## InsertAlignment 62 ## ReduceBreak 1 # best score in initial pool 222.852 bits/residue, 30 clashes 33.175 breaks # optimizing backbone with 50 conformations in pool # doing 3 generations, with 250 new conformations in each generation. # keep at most 20 conformations from old pool # generation 1: best score 222.852 bits/residue, 30 clashes 33.175 breaks # Cumulative usage by method: ## InsertFragment 5 ## ReduceClash 2 ## CrossOver 1 ## CrossAndInsert 2 ## TwoFragment 3 ## InsertSSBond 1 ## OneRotamer 0 ## ClashingRotamer 4 ## InsertAlignment 31 ## ReduceBreak 0 # generation 2: best score 222.852 bits/residue, 30 clashes 33.175 breaks # Cumulative usage by method: ## InsertFragment 8 ## ReduceClash 4 ## CrossOver 1 ## CrossAndInsert 2 ## TwoFragment 3 ## InsertSSBond 1 ## OneRotamer 0 ## ClashingRotamer 14 ## InsertAlignment 56 ## ReduceBreak 1 # generation 3: best score 222.529 bits/residue, 30 clashes 31.4215 breaks # Cumulative usage by method: ## InsertFragment 11 ## ReduceClash 7 ## CrossOver 2 ## CrossAndInsert 7 ## TwoFragment 3 ## InsertSSBond 1 ## OneRotamer 0 ## ClashingRotamer 18 ## InsertAlignment 69 ## ReduceBreak 2 # best score in super_pool at pool[11] 222.529 bits/residue, 30 clashes 31.4215 breaks # optimizing backbone with 50 conformations in pool # doing 3 generations, with 250 new conformations in each generation. # keep at most 20 conformations from old pool # generation 1: best score 222.529 bits/residue, 30 clashes 31.4215 breaks # Cumulative usage by method: ## InsertFragment 3 ## ReduceClash 4 ## CrossOver 0 ## CrossAndInsert 6 ## TwoFragment 3 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 8 ## InsertAlignment 11 ## ReduceBreak 3 # generation 2: best score 222.529 bits/residue, 30 clashes 31.4215 breaks # Cumulative usage by method: ## InsertFragment 9 ## ReduceClash 10 ## CrossOver 0 ## CrossAndInsert 13 ## TwoFragment 4 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 13 ## InsertAlignment 16 ## ReduceBreak 3 # generation 3: best score 222.529 bits/residue, 30 clashes 31.4215 breaks # Cumulative usage by method: ## InsertFragment 20 ## ReduceClash 15 ## CrossOver 1 ## CrossAndInsert 18 ## TwoFragment 5 ## InsertSSBond 0 ## OneRotamer 0 ## ClashingRotamer 16 ## InsertAlignment 19 ## ReduceBreak 4 # command:# naming current conformation t113-opt-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: 222.529 bits/residue, 30 clashes, rmsd= 0 # best score after iter 1 222.529 bits/residue, 30 clashes, rmsd= 0 # best score after iter 2 222.529 bits/residue, 30 clashes, rmsd= 0 # best score after iter 3 222.529 bits/residue, 30 clashes, rmsd= 0 # best score after iter 4 220.846 bits/residue, 23 clashes, rmsd= 0 # best score after iter 5 220.218 bits/residue, 19 clashes, rmsd= 0 # best score after iter 6 219.903 bits/residue, 18 clashes, rmsd= 0 # best score after iter 7 219.747 bits/residue, 17 clashes, rmsd= 0 # best score after iter 8 219.686 bits/residue, 17 clashes, rmsd= 0 # best score after iter 9 219.322 bits/residue, 15 clashes, rmsd= 0 # best score after iter 10 219.322 bits/residue, 15 clashes, rmsd= 0 # best score after iter 11 219.292 bits/residue, 15 clashes, rmsd= 0 # best score after iter 12 219.292 bits/residue, 15 clashes, rmsd= 0 # best score after iter 13 219.292 bits/residue, 15 clashes, rmsd= 0 # best score after iter 14 219.292 bits/residue, 15 clashes, rmsd= 0 # best score after iter 15 219.292 bits/residue, 15 clashes, rmsd= 0 # best score after iter 16 219.292 bits/residue, 15 clashes, rmsd= 0 # best score after iter 17 219.292 bits/residue, 15 clashes, rmsd= 0 # best score after iter 18 219.292 bits/residue, 15 clashes, rmsd= 0 # best score after iter 19 219.292 bits/residue, 15 clashes, rmsd= 0 # best score after iter 20 219.292 bits/residue, 15 clashes, rmsd= 0 # best score after iter 21 219.292 bits/residue, 15 clashes, rmsd= 0 # best score after iter 22 219.292 bits/residue, 15 clashes, rmsd= 0 # best score after iter 23 219.292 bits/residue, 15 clashes, rmsd= 0 # best score after iter 24 219.292 bits/residue, 15 clashes, rmsd= 0 # best score after iter 25 219.292 bits/residue, 15 clashes, rmsd= 0 # best score after iter 26 219.292 bits/residue, 15 clashes, rmsd= 0 # best score after iter 27 219.292 bits/residue, 15 clashes, rmsd= 0 # best score after iter 28 219.292 bits/residue, 15 clashes, rmsd= 0 # best score after iter 29 219.292 bits/residue, 15 clashes, rmsd= 0 # command:# naming current conformation t113-opt-rot-opt-rot # 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: 17.6995 bits/residue, 15 clashes, rmsd= 0 # best score after iter 1 16.27 bits/residue, 14 clashes, rmsd= 0 # best score after iter 2 16.27 bits/residue, 14 clashes, rmsd= 0 # best score after iter 3 15.6874 bits/residue, 24 clashes, rmsd= 0 # best score after iter 4 15.026 bits/residue, 21 clashes, rmsd= 0 # best score after iter 5 14.9803 bits/residue, 21 clashes, rmsd= 0 # best score after iter 6 14.9375 bits/residue, 21 clashes, rmsd= 0 # best score after iter 7 14.9375 bits/residue, 21 clashes, rmsd= 0 # best score after iter 8 14.9375 bits/residue, 21 clashes, rmsd= 0 # best score after iter 9 14.9375 bits/residue, 21 clashes, rmsd= 0 # best score after iter 10 14.9375 bits/residue, 21 clashes, rmsd= 0 # best score after iter 11 14.9375 bits/residue, 21 clashes, rmsd= 0 # best score after iter 12 14.9375 bits/residue, 21 clashes, rmsd= 0 # best score after iter 13 14.9375 bits/residue, 21 clashes, rmsd= 0 # best score after iter 14 14.9375 bits/residue, 21 clashes, rmsd= 0 # best score after iter 15 14.9375 bits/residue, 21 clashes, rmsd= 0 # best score after iter 16 14.9375 bits/residue, 21 clashes, rmsd= 0 # best score after iter 17 14.9375 bits/residue, 21 clashes, rmsd= 0 # best score after iter 18 14.9375 bits/residue, 21 clashes, rmsd= 0 # best score after iter 19 14.9375 bits/residue, 21 clashes, rmsd= 0 # command:# naming current conformation t113-opt-rot-opt-rot-rot # command:# command:# ScwrlConform produces command scwrl -i /projects/compbio/tmp/to_scwrl_1314980191.pdb -s /projects/compbio/tmp/to_scwrl_1314980191.seq -o /projects/compbio/tmp/from_scwrl_1314980191.pdb > /projects/compbio/tmp/scwrl.log # conformation set from SCWRL output # command:# naming current conformation t113-opt-scwrl # command:# command:# ScoreConform t113-rand 80.057 bits/residue, 425 clashes t113-2hsdA at pool[1] 62.3127 bits/residue, 145 clashes 30.5253 breaks t113-opt at pool[2] 25.7239 bits/residue, 65 clashes 33.175 breaks t113-opt-rot at pool[3] 22.7893 bits/residue, 30 clashes 33.175 breaks t113-opt-opt at pool[4] 22.5312 bits/residue, 30 clashes 31.4215 breaks t113-opt-rot-opt-rot at pool[5] 17.6995 bits/residue, 15 clashes 31.4215 breaks t113-opt-rot-opt-rot-rot at pool[6] 14.9375 bits/residue, 21 clashes 31.4215 breaks t113-opt-scwrl at pool[7] 18.845 bits/residue, 44 clashes 31.4215 breaks # command: