# 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 1.5 # clash_penalty 30 nats/clash # ss_bond_bonus 3 # known_ss_bond_bonus 0.1 # chain_break_penalty 15 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:# naming current conformation t113-rand # command:# command:# optimizing backbone with 50 conformations in pool # doing 5 generations, with 100 new conformations in each generation. # keep at most 20 conformations from old pool # best score in initial pool at pool[40] 289.675 bits/residue, 137 clashes 0 breaks # best score after generation 1 283.04 bits/residue, 120 clashes 0 breaks # Cumulative usage by method: ## InsertFragment 4 ## Crossover 0 ## CrossoverAroundFragment 8 ## ClashReducingFragment 20 ## TwoFragments 11 ## InsertSSbond 0 ## RotamerReplacement 0 # best score after generation 2 279.855 bits/residue, 164 clashes 0 breaks # Cumulative usage by method: ## InsertFragment 9 ## Crossover 0 ## CrossoverAroundFragment 15 ## ClashReducingFragment 39 ## TwoFragments 18 ## InsertSSbond 1 ## RotamerReplacement 0 # best score after generation 3 275.15 bits/residue, 147 clashes 0 breaks # Cumulative usage by method: ## InsertFragment 14 ## Crossover 1 ## CrossoverAroundFragment 22 ## ClashReducingFragment 52 ## TwoFragments 25 ## InsertSSbond 1 ## RotamerReplacement 0 # best score after generation 4 273.736 bits/residue, 156 clashes 0 breaks # Cumulative usage by method: ## InsertFragment 20 ## Crossover 1 ## CrossoverAroundFragment 31 ## ClashReducingFragment 64 ## TwoFragments 30 ## InsertSSbond 1 ## RotamerReplacement 0 # best score after generation 5 273.151 bits/residue, 166 clashes 0 breaks # Cumulative usage by method: ## InsertFragment 26 ## Crossover 1 ## CrossoverAroundFragment 42 ## ClashReducingFragment 71 ## TwoFragments 36 ## InsertSSbond 1 ## RotamerReplacement 0 # command:# naming current conformation t1133-rand-opt # command:# command:# created fragments for T0113 from index file. # command:# created conformation for T0113 by applying fragments # command:# naming current conformation t113-2hsdA # command:# command:# optimizing backbone with 50 conformations in pool # doing 20 generations, with 200 new conformations in each generation. # keep at most 20 conformations from old pool # best score in initial pool at pool[0] 245.626 bits/residue, 218 clashes 29.6562 breaks # best score after generation 1 245.626 bits/residue, 218 clashes 29.6562 breaks # Cumulative usage by method: ## InsertFragment 2 ## Crossover 2 ## CrossoverAroundFragment 8 ## ClashReducingFragment 26 ## TwoFragments 8 ## InsertSSbond 0 ## RotamerReplacement 0 # best score after generation 2 240.293 bits/residue, 173 clashes 37.9383 breaks # Cumulative usage by method: ## InsertFragment 11 ## Crossover 2 ## CrossoverAroundFragment 10 ## ClashReducingFragment 51 ## TwoFragments 13 ## InsertSSbond 0 ## RotamerReplacement 0 # best score after generation 3 236.302 bits/residue, 142 clashes 44.8797 breaks # Cumulative usage by method: ## InsertFragment 14 ## Crossover 2 ## CrossoverAroundFragment 13 ## ClashReducingFragment 83 ## TwoFragments 13 ## InsertSSbond 0 ## RotamerReplacement 0 # best score after generation 4 230.964 bits/residue, 117 clashes 40.646 breaks # Cumulative usage by method: ## InsertFragment 16 ## Crossover 3 ## CrossoverAroundFragment 14 ## ClashReducingFragment 115 ## TwoFragments 14 ## InsertSSbond 0 ## RotamerReplacement 0 # best score after generation 5 227.222 bits/residue, 98 clashes 37.4468 breaks # Cumulative usage by method: ## InsertFragment 20 ## Crossover 3 ## CrossoverAroundFragment 15 ## ClashReducingFragment 144 ## TwoFragments 14 ## InsertSSbond 0 ## RotamerReplacement 0 # best score after generation 6 226.599 bits/residue, 109 clashes 37.4468 breaks # Cumulative usage by method: ## InsertFragment 23 ## Crossover 3 ## CrossoverAroundFragment 16 ## ClashReducingFragment 175 ## TwoFragments 16 ## InsertSSbond 0 ## RotamerReplacement 0 # best score after generation 7 223.196 bits/residue, 78 clashes 31.1704 breaks # Cumulative usage by method: ## InsertFragment 26 ## Crossover 4 ## CrossoverAroundFragment 16 ## ClashReducingFragment 202 ## TwoFragments 16 ## InsertSSbond 0 ## RotamerReplacement 0 # best score after generation 8 223.153 bits/residue, 76 clashes 31.9876 breaks # Cumulative usage by method: ## InsertFragment 28 ## Crossover 5 ## CrossoverAroundFragment 17 ## ClashReducingFragment 228 ## TwoFragments 16 ## InsertSSbond 0 ## RotamerReplacement 0 # best score after generation 9 221.024 bits/residue, 77 clashes 31.1704 breaks # Cumulative usage by method: ## InsertFragment 28 ## Crossover 7 ## CrossoverAroundFragment 17 ## ClashReducingFragment 256 ## TwoFragments 17 ## InsertSSbond 0 ## RotamerReplacement 0 # best score after generation 10 220.491 bits/residue, 75 clashes 35.2474 breaks # Cumulative usage by method: ## InsertFragment 30 ## Crossover 7 ## CrossoverAroundFragment 17 ## ClashReducingFragment 284 ## TwoFragments 17 ## InsertSSbond 0 ## RotamerReplacement 0 # best score after generation 11 220.062 bits/residue, 76 clashes 32.0115 breaks # Cumulative usage by method: ## InsertFragment 32 ## Crossover 9 ## CrossoverAroundFragment 17 ## ClashReducingFragment 309 ## TwoFragments 18 ## InsertSSbond 0 ## RotamerReplacement 0 # best score after generation 12 219.77 bits/residue, 67 clashes 32.2397 breaks # Cumulative usage by method: ## InsertFragment 35 ## Crossover 12 ## CrossoverAroundFragment 17 ## ClashReducingFragment 332 ## TwoFragments 19 ## InsertSSbond 0 ## RotamerReplacement 0 # best score after generation 13 218.546 bits/residue, 59 clashes 37.4959 breaks # Cumulative usage by method: ## InsertFragment 36 ## Crossover 16 ## CrossoverAroundFragment 17 ## ClashReducingFragment 357 ## TwoFragments 19 ## InsertSSbond 0 ## RotamerReplacement 0 # best score after generation 14 218.461 bits/residue, 56 clashes 40.8089 breaks # Cumulative usage by method: ## InsertFragment 38 ## Crossover 19 ## CrossoverAroundFragment 17 ## ClashReducingFragment 382 ## TwoFragments 19 ## InsertSSbond 0 ## RotamerReplacement 0 # best score after generation 15 218.461 bits/residue, 56 clashes 40.8089 breaks # Cumulative usage by method: ## InsertFragment 41 ## Crossover 23 ## CrossoverAroundFragment 19 ## ClashReducingFragment 402 ## TwoFragments 20 ## InsertSSbond 0 ## RotamerReplacement 0 # best score after generation 16 217.761 bits/residue, 54 clashes 31.9187 breaks # Cumulative usage by method: ## InsertFragment 42 ## Crossover 28 ## CrossoverAroundFragment 19 ## ClashReducingFragment 425 ## TwoFragments 21 ## InsertSSbond 0 ## RotamerReplacement 0 # best score after generation 17 217.594 bits/residue, 56 clashes 35.9903 breaks # Cumulative usage by method: ## InsertFragment 42 ## Crossover 36 ## CrossoverAroundFragment 20 ## ClashReducingFragment 446 ## TwoFragments 21 ## InsertSSbond 0 ## RotamerReplacement 0 # best score after generation 18 217.594 bits/residue, 56 clashes 35.9903 breaks # Cumulative usage by method: ## InsertFragment 42 ## Crossover 47 ## CrossoverAroundFragment 21 ## ClashReducingFragment 464 ## TwoFragments 21 ## InsertSSbond 0 ## RotamerReplacement 0 # best score after generation 19 217.041 bits/residue, 53 clashes 28.4226 breaks # Cumulative usage by method: ## InsertFragment 42 ## Crossover 57 ## CrossoverAroundFragment 22 ## ClashReducingFragment 483 ## TwoFragments 21 ## InsertSSbond 0 ## RotamerReplacement 0 # best score after generation 20 216.644 bits/residue, 57 clashes 30.2652 breaks # Cumulative usage by method: ## InsertFragment 42 ## Crossover 76 ## CrossoverAroundFragment 22 ## ClashReducingFragment 494 ## TwoFragments 21 ## InsertSSbond 0 ## RotamerReplacement 0 # command:# naming current conformation t113-2hsdA-opt # command:# command:# created fragments for T0113 from index file. # command:# created conformation for T0113 by applying fragments # command:# naming current conformation t113-2hsdA-opt-2hsdA # command:# command:# optimizing backbone with 50 conformations in pool # doing 20 generations, with 200 new conformations in each generation. # keep at most 20 conformations from old pool # best score in initial pool at pool[0] 239.528 bits/residue, 187 clashes 29.4336 breaks # best score after generation 1 239.528 bits/residue, 187 clashes 29.4336 breaks # Cumulative usage by method: ## InsertFragment 12 ## Crossover 0 ## CrossoverAroundFragment 12 ## ClashReducingFragment 16 ## TwoFragments 7 ## InsertSSbond 0 ## RotamerReplacement 0 # best score after generation 2 237.493 bits/residue, 178 clashes 23.2318 breaks # Cumulative usage by method: ## InsertFragment 22 ## Crossover 0 ## CrossoverAroundFragment 20 ## ClashReducingFragment 35 ## TwoFragments 12 ## InsertSSbond 0 ## RotamerReplacement 0 # best score after generation 3 235.733 bits/residue, 168 clashes 35.1118 breaks # Cumulative usage by method: ## InsertFragment 26 ## Crossover 0 ## CrossoverAroundFragment 24 ## ClashReducingFragment 56 ## TwoFragments 13 ## InsertSSbond 0 ## RotamerReplacement 0 # best score after generation 4 233.377 bits/residue, 146 clashes 33.0615 breaks # Cumulative usage by method: ## InsertFragment 33 ## Crossover 1 ## CrossoverAroundFragment 25 ## ClashReducingFragment 77 ## TwoFragments 14 ## InsertSSbond 0 ## RotamerReplacement 0 # best score after generation 5 231.82 bits/residue, 132 clashes 40.1083 breaks # Cumulative usage by method: ## InsertFragment 38 ## Crossover 1 ## CrossoverAroundFragment 26 ## ClashReducingFragment 104 ## TwoFragments 14 ## InsertSSbond 0 ## RotamerReplacement 0 # best score after generation 6 230.27 bits/residue, 79 clashes 26.5718 breaks # Cumulative usage by method: ## InsertFragment 45 ## Crossover 3 ## CrossoverAroundFragment 27 ## ClashReducingFragment 124 ## TwoFragments 14 ## InsertSSbond 0 ## RotamerReplacement 0 # best score after generation 7 228.451 bits/residue, 67 clashes 28.2687 breaks # Cumulative usage by method: ## InsertFragment 50 ## Crossover 3 ## CrossoverAroundFragment 30 ## ClashReducingFragment 146 ## TwoFragments 14 ## InsertSSbond 0 ## RotamerReplacement 0 # best score after generation 8 226.895 bits/residue, 71 clashes 23.5595 breaks # Cumulative usage by method: ## InsertFragment 53 ## Crossover 4 ## CrossoverAroundFragment 31 ## ClashReducingFragment 171 ## TwoFragments 14 ## InsertSSbond 0 ## RotamerReplacement 0 # best score after generation 9 225.605 bits/residue, 77 clashes 23.5595 breaks # Cumulative usage by method: ## InsertFragment 58 ## Crossover 5 ## CrossoverAroundFragment 36 ## ClashReducingFragment 195 ## TwoFragments 14 ## InsertSSbond 0 ## RotamerReplacement 0 # best score after generation 10 224.374 bits/residue, 72 clashes 18.5798 breaks # Cumulative usage by method: ## InsertFragment 61 ## Crossover 6 ## CrossoverAroundFragment 39 ## ClashReducingFragment 219 ## TwoFragments 16 ## InsertSSbond 0 ## RotamerReplacement 0 # best score after generation 11 222.746 bits/residue, 36 clashes 28.0238 breaks # Cumulative usage by method: ## InsertFragment 65 ## Crossover 9 ## CrossoverAroundFragment 41 ## ClashReducingFragment 239 ## TwoFragments 17 ## InsertSSbond 0 ## RotamerReplacement 0 # best score after generation 12 221.862 bits/residue, 41 clashes 23.176 breaks # Cumulative usage by method: ## InsertFragment 68 ## Crossover 12 ## CrossoverAroundFragment 41 ## ClashReducingFragment 263 ## TwoFragments 17 ## InsertSSbond 0 ## RotamerReplacement 0 # best score after generation 13 221.053 bits/residue, 48 clashes 16.9053 breaks # Cumulative usage by method: ## InsertFragment 73 ## Crossover 16 ## CrossoverAroundFragment 43 ## ClashReducingFragment 284 ## TwoFragments 17 ## InsertSSbond 0 ## RotamerReplacement 0 # best score after generation 14 220.602 bits/residue, 47 clashes 23.176 breaks # Cumulative usage by method: ## InsertFragment 77 ## Crossover 21 ## CrossoverAroundFragment 44 ## ClashReducingFragment 304 ## TwoFragments 17 ## InsertSSbond 0 ## RotamerReplacement 0 # best score after generation 15 219.695 bits/residue, 45 clashes 22.7693 breaks # Cumulative usage by method: ## InsertFragment 80 ## Crossover 27 ## CrossoverAroundFragment 44 ## ClashReducingFragment 325 ## TwoFragments 17 ## InsertSSbond 0 ## RotamerReplacement 0 # best score after generation 16 219.526 bits/residue, 45 clashes 21.7055 breaks # Cumulative usage by method: ## InsertFragment 83 ## Crossover 35 ## CrossoverAroundFragment 45 ## ClashReducingFragment 343 ## TwoFragments 17 ## InsertSSbond 0 ## RotamerReplacement 0 # best score after generation 17 219.526 bits/residue, 45 clashes 21.7055 breaks # Cumulative usage by method: ## InsertFragment 88 ## Crossover 45 ## CrossoverAroundFragment 45 ## ClashReducingFragment 358 ## TwoFragments 17 ## InsertSSbond 0 ## RotamerReplacement 0 # best score after generation 18 218.935 bits/residue, 41 clashes 22.6613 breaks # Cumulative usage by method: ## InsertFragment 92 ## Crossover 53 ## CrossoverAroundFragment 46 ## ClashReducingFragment 375 ## TwoFragments 17 ## InsertSSbond 0 ## RotamerReplacement 0 # best score after generation 19 218.548 bits/residue, 42 clashes 22.6613 breaks # Cumulative usage by method: ## InsertFragment 97 ## Crossover 62 ## CrossoverAroundFragment 46 ## ClashReducingFragment 391 ## TwoFragments 17 ## InsertSSbond 0 ## RotamerReplacement 0 # best score after generation 20 218.461 bits/residue, 46 clashes 20.5925 breaks # Cumulative usage by method: ## InsertFragment 101 ## Crossover 74 ## CrossoverAroundFragment 47 ## ClashReducingFragment 403 ## TwoFragments 18 ## InsertSSbond 0 ## RotamerReplacement 0 # command:# naming current conformation t113-2hsdA-opt-2hsdA-opt # command:# command:# Optimizing rotamers with 50 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: 218.461 bits/residue, 46 clashes, rmsd= 0 # best score after iter 1 218.461 bits/residue, 46 clashes, rmsd= 0 # best score after iter 2 218.461 bits/residue, 46 clashes, rmsd= 0 # best score after iter 3 218.461 bits/residue, 46 clashes, rmsd= 0 # best score after iter 4 216.375 bits/residue, 14 clashes, rmsd= 0 # best score after iter 5 216.375 bits/residue, 14 clashes, rmsd= 0 # best score after iter 6 216.279 bits/residue, 16 clashes, rmsd= 0 # best score after iter 7 216.13 bits/residue, 16 clashes, rmsd= 0 # best score after iter 8 216.113 bits/residue, 16 clashes, rmsd= 0 # best score after iter 9 215.986 bits/residue, 15 clashes, rmsd= 0 # best score after iter 10 215.962 bits/residue, 15 clashes, rmsd= 0 # best score after iter 11 215.912 bits/residue, 15 clashes, rmsd= 0 # best score after iter 12 215.912 bits/residue, 15 clashes, rmsd= 0 # best score after iter 13 215.912 bits/residue, 15 clashes, rmsd= 0 # best score after iter 14 215.912 bits/residue, 15 clashes, rmsd= 0 # best score after iter 15 215.912 bits/residue, 15 clashes, rmsd= 0 # best score after iter 16 215.912 bits/residue, 15 clashes, rmsd= 0 # best score after iter 17 215.9 bits/residue, 31 clashes, rmsd= 0 # best score after iter 18 215.9 bits/residue, 31 clashes, rmsd= 0 # best score after iter 19 215.9 bits/residue, 31 clashes, rmsd= 0 # best score after iter 20 215.9 bits/residue, 31 clashes, rmsd= 0 # best score after iter 21 215.9 bits/residue, 31 clashes, rmsd= 0 # best score after iter 22 215.9 bits/residue, 31 clashes, rmsd= 0 # best score after iter 23 215.9 bits/residue, 31 clashes, rmsd= 0 # best score after iter 24 215.9 bits/residue, 31 clashes, rmsd= 0 # best score after iter 25 215.9 bits/residue, 31 clashes, rmsd= 0 # best score after iter 26 215.9 bits/residue, 31 clashes, rmsd= 0 # best score after iter 27 215.798 bits/residue, 29 clashes, rmsd= 0 # best score after iter 28 215.548 bits/residue, 28 clashes, rmsd= 0 # best score after iter 29 215.269 bits/residue, 31 clashes, rmsd= 0 # best score after iter 30 213.571 bits/residue, 22 clashes, rmsd= 0 # best score after iter 31 213.374 bits/residue, 19 clashes, rmsd= 0 # best score after iter 32 213.374 bits/residue, 19 clashes, rmsd= 0 # best score after iter 33 213.374 bits/residue, 19 clashes, rmsd= 0 # best score after iter 34 213.339 bits/residue, 18 clashes, rmsd= 0 # best score after iter 35 212.758 bits/residue, 14 clashes, rmsd= 0 # best score after iter 36 212.415 bits/residue, 16 clashes, rmsd= 0 # best score after iter 37 212.2 bits/residue, 17 clashes, rmsd= 0 # best score after iter 38 211.786 bits/residue, 15 clashes, rmsd= 0 # best score after iter 39 211.786 bits/residue, 15 clashes, rmsd= 0 # best score after iter 40 211.786 bits/residue, 15 clashes, rmsd= 0 # best score after iter 41 211.708 bits/residue, 18 clashes, rmsd= 0 # best score after iter 42 211.435 bits/residue, 15 clashes, rmsd= 0 # best score after iter 43 211.435 bits/residue, 15 clashes, rmsd= 0 # best score after iter 44 211.355 bits/residue, 15 clashes, rmsd= 0 # best score after iter 45 211.227 bits/residue, 15 clashes, rmsd= 0 # best score after iter 46 211.227 bits/residue, 15 clashes, rmsd= 0 # best score after iter 47 210.803 bits/residue, 15 clashes, rmsd= 0 # best score after iter 48 210.803 bits/residue, 15 clashes, rmsd= 0 # best score after iter 49 210.803 bits/residue, 15 clashes, rmsd= 0 # command:# naming current conformation t113-2hsdA-opt-2hsdA-opt-rot # command:# command: