# 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:# created conformation for T0113 by applying fragments # command:# naming current conformation t113-2hsdA # command:# command:# optimizing backbone with 50 conformations in pool # doing 15 generations, with 200 new conformations in each generation. # keep at most 20 conformations from old pool # best score in initial pool at pool[0] 268.104 bits/residue, 202 clashes 134.367 breaks # best score after generation 1 259.868 bits/residue, 145 clashes 136.34 breaks # Cumulative usage by method: ## InsertFragment 12 ## ReduceClash 7 ## CrossOver 0 ## CrossAndInsert 5 ## TwoFragment 6 ## InsertSSBond 1 ## OneRotamer 0 ## InsertAlignment 5 ## ReduceBreak 9 # best score after generation 2 257.236 bits/residue, 141 clashes 123.515 breaks # Cumulative usage by method: ## InsertFragment 22 ## ReduceClash 10 ## CrossOver 0 ## CrossAndInsert 10 ## TwoFragment 7 ## InsertSSBond 1 ## OneRotamer 0 ## InsertAlignment 16 ## ReduceBreak 23 # best score after generation 3 251.112 bits/residue, 112 clashes 117.343 breaks # Cumulative usage by method: ## InsertFragment 28 ## ReduceClash 13 ## CrossOver 1 ## CrossAndInsert 11 ## TwoFragment 7 ## InsertSSBond 1 ## OneRotamer 0 ## InsertAlignment 27 ## ReduceBreak 43 # best score after generation 4 249.399 bits/residue, 89 clashes 126.957 breaks # Cumulative usage by method: ## InsertFragment 30 ## ReduceClash 19 ## CrossOver 2 ## CrossAndInsert 12 ## TwoFragment 10 ## InsertSSBond 1 ## OneRotamer 0 ## InsertAlignment 36 ## ReduceBreak 58 # best score after generation 5 245.635 bits/residue, 89 clashes 97.9231 breaks # Cumulative usage by method: ## InsertFragment 35 ## ReduceClash 24 ## CrossOver 2 ## CrossAndInsert 13 ## TwoFragment 11 ## InsertSSBond 1 ## OneRotamer 0 ## InsertAlignment 51 ## ReduceBreak 68 # best score after generation 6 241.523 bits/residue, 78 clashes 89.7588 breaks # Cumulative usage by method: ## InsertFragment 44 ## ReduceClash 29 ## CrossOver 2 ## CrossAndInsert 13 ## TwoFragment 12 ## InsertSSBond 1 ## OneRotamer 0 ## InsertAlignment 64 ## ReduceBreak 77 # best score after generation 7 241.501 bits/residue, 78 clashes 89.636 breaks # Cumulative usage by method: ## InsertFragment 54 ## ReduceClash 36 ## CrossOver 4 ## CrossAndInsert 14 ## TwoFragment 13 ## InsertSSBond 1 ## OneRotamer 0 ## InsertAlignment 80 ## ReduceBreak 78 # best score after generation 8 239.431 bits/residue, 78 clashes 76.2643 breaks # Cumulative usage by method: ## InsertFragment 58 ## ReduceClash 41 ## CrossOver 8 ## CrossAndInsert 14 ## TwoFragment 13 ## InsertSSBond 1 ## OneRotamer 0 ## InsertAlignment 91 ## ReduceBreak 84 # best score after generation 9 239.07 bits/residue, 71 clashes 81.4593 breaks # Cumulative usage by method: ## InsertFragment 63 ## ReduceClash 48 ## CrossOver 11 ## CrossAndInsert 15 ## TwoFragment 14 ## InsertSSBond 1 ## OneRotamer 0 ## InsertAlignment 100 ## ReduceBreak 88 # best score after generation 10 237.52 bits/residue, 82 clashes 64.8095 breaks # Cumulative usage by method: ## InsertFragment 68 ## ReduceClash 52 ## CrossOver 16 ## CrossAndInsert 15 ## TwoFragment 15 ## InsertSSBond 1 ## OneRotamer 0 ## InsertAlignment 111 ## ReduceBreak 92 # best score after generation 11 236.89 bits/residue, 78 clashes 63.8884 breaks # Cumulative usage by method: ## InsertFragment 71 ## ReduceClash 56 ## CrossOver 23 ## CrossAndInsert 16 ## TwoFragment 15 ## InsertSSBond 1 ## OneRotamer 0 ## InsertAlignment 123 ## ReduceBreak 95 # best score after generation 12 235.163 bits/residue, 69 clashes 55.3066 breaks # Cumulative usage by method: ## InsertFragment 75 ## ReduceClash 60 ## CrossOver 34 ## CrossAndInsert 17 ## TwoFragment 15 ## InsertSSBond 1 ## OneRotamer 0 ## InsertAlignment 130 ## ReduceBreak 98 # best score after generation 13 233.472 bits/residue, 51 clashes 54.8551 breaks # Cumulative usage by method: ## InsertFragment 79 ## ReduceClash 65 ## CrossOver 45 ## CrossAndInsert 18 ## TwoFragment 15 ## InsertSSBond 1 ## OneRotamer 0 ## InsertAlignment 133 ## ReduceBreak 104 # best score after generation 14 233.472 bits/residue, 51 clashes 54.8551 breaks # Cumulative usage by method: ## InsertFragment 82 ## ReduceClash 70 ## CrossOver 63 ## CrossAndInsert 19 ## TwoFragment 15 ## InsertSSBond 1 ## OneRotamer 0 ## InsertAlignment 135 ## ReduceBreak 105 # best score after generation 15 231.781 bits/residue, 41 clashes 55.0162 breaks # Cumulative usage by method: ## InsertFragment 87 ## ReduceClash 80 ## CrossOver 77 ## CrossAndInsert 19 ## TwoFragment 16 ## InsertSSBond 1 ## OneRotamer 0 ## InsertAlignment 135 ## ReduceBreak 105 # 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: 231.781 bits/residue, 41 clashes, rmsd= 0 # best score after iter 1 231.781 bits/residue, 41 clashes, rmsd= 0 # best score after iter 2 231.781 bits/residue, 41 clashes, rmsd= 0 # best score after iter 3 231.781 bits/residue, 41 clashes, rmsd= 0 # best score after iter 4 231.781 bits/residue, 41 clashes, rmsd= 0 # best score after iter 5 231.781 bits/residue, 41 clashes, rmsd= 0 # best score after iter 6 231.781 bits/residue, 41 clashes, rmsd= 0 # best score after iter 7 231.781 bits/residue, 41 clashes, rmsd= 0 # best score after iter 8 231.781 bits/residue, 41 clashes, rmsd= 0 # best score after iter 9 231.781 bits/residue, 41 clashes, rmsd= 0 # best score after iter 10 231.781 bits/residue, 41 clashes, rmsd= 0 # best score after iter 11 231.781 bits/residue, 41 clashes, rmsd= 0 # best score after iter 12 231.781 bits/residue, 41 clashes, rmsd= 0 # best score after iter 13 231.781 bits/residue, 41 clashes, rmsd= 0 # best score after iter 14 231.781 bits/residue, 41 clashes, rmsd= 0 # best score after iter 15 231.781 bits/residue, 41 clashes, rmsd= 0 # best score after iter 16 231.781 bits/residue, 41 clashes, rmsd= 0 # best score after iter 17 231.781 bits/residue, 41 clashes, rmsd= 0 # best score after iter 18 231.781 bits/residue, 41 clashes, rmsd= 0 # best score after iter 19 231.781 bits/residue, 41 clashes, rmsd= 0 # best score after iter 20 231.781 bits/residue, 41 clashes, rmsd= 0 # best score after iter 21 229.702 bits/residue, 54 clashes, rmsd= 0 # best score after iter 22 227.876 bits/residue, 44 clashes, rmsd= 0 # best score after iter 23 227.803 bits/residue, 44 clashes, rmsd= 0 # best score after iter 24 227.8 bits/residue, 44 clashes, rmsd= 0 # best score after iter 25 227.8 bits/residue, 44 clashes, rmsd= 0 # best score after iter 26 227.8 bits/residue, 44 clashes, rmsd= 0 # best score after iter 27 227.378 bits/residue, 41 clashes, rmsd= 0 # best score after iter 28 226.793 bits/residue, 44 clashes, rmsd= 0 # best score after iter 29 226.634 bits/residue, 46 clashes, rmsd= 0 # command:# naming current conformation t113-opt-rot # command:# command:# optimizing backbone with 50 conformations in pool # doing 115 generations, with 200 new conformations in each generation. # keep at most 20 conformations from old pool # best score in initial pool at pool[0] 226.634 bits/residue, 46 clashes 55.0162 breaks # best score after generation 1 226.27 bits/residue, 51 clashes 44.0185 breaks # Cumulative usage by method: ## InsertFragment 10 ## ReduceClash 2 ## CrossOver 0 ## CrossAndInsert 10 ## TwoFragment 10 ## InsertSSBond 0 ## OneRotamer 0 ## InsertAlignment 6 ## ReduceBreak 8 # best score after generation 2 226.27 bits/residue, 51 clashes 44.0185 breaks # Cumulative usage by method: ## InsertFragment 23 ## ReduceClash 8 ## CrossOver 0 ## CrossAndInsert 15 ## TwoFragment 16 ## InsertSSBond 0 ## OneRotamer 0 ## InsertAlignment 8 ## ReduceBreak 16 # best score after generation 3 226.27 bits/residue, 51 clashes 44.0185 breaks # Cumulative usage by method: ## InsertFragment 31 ## ReduceClash 13 ## CrossOver 0 ## CrossAndInsert 21 ## TwoFragment 21 ## InsertSSBond 0 ## OneRotamer 0 ## InsertAlignment 8 ## ReduceBreak 22 # best score after generation 4 226.27 bits/residue, 51 clashes 44.0185 breaks # Cumulative usage by method: ## InsertFragment 37 ## ReduceClash 17 ## CrossOver 0 ## CrossAndInsert 33 ## TwoFragment 22 ## InsertSSBond 0 ## OneRotamer 0 ## InsertAlignment 8 ## ReduceBreak 29 # best score after generation 5 226.159 bits/residue, 49 clashes 48.027 breaks # Cumulative usage by method: ## InsertFragment 45 ## ReduceClash 20 ## CrossOver 0 ## CrossAndInsert 45 ## TwoFragment 23 ## InsertSSBond 0 ## OneRotamer 0 ## InsertAlignment 8 ## ReduceBreak 35 # best score after generation 6 225.686 bits/residue, 46 clashes 44.0154 breaks # Cumulative usage by method: ## InsertFragment 61 ## ReduceClash 22 ## CrossOver 0 ## CrossAndInsert 51 ## TwoFragment 25 ## InsertSSBond 0 ## OneRotamer 0 ## InsertAlignment 8 ## ReduceBreak 39 # best score after generation 7 225.686 bits/residue, 46 clashes 44.0154 breaks # Cumulative usage by method: ## InsertFragment 74 ## ReduceClash 24 ## CrossOver 0 ## CrossAndInsert 61 ## TwoFragment 26 ## InsertSSBond 0 ## OneRotamer 0 ## InsertAlignment 8 ## ReduceBreak 43 # best score after generation 8 225.405 bits/residue, 45 clashes 44.0185 breaks # Cumulative usage by method: ## InsertFragment 85 ## ReduceClash 27 ## CrossOver 0 ## CrossAndInsert 70 ## TwoFragment 29 ## InsertSSBond 0 ## OneRotamer 0 ## InsertAlignment 8 ## ReduceBreak 47 # best score after generation 9 224.545 bits/residue, 43 clashes 45.2108 breaks # Cumulative usage by method: ## InsertFragment 97 ## ReduceClash 34 ## CrossOver 0 ## CrossAndInsert 79 ## TwoFragment 30 ## InsertSSBond 0 ## OneRotamer 0 ## InsertAlignment 8 ## ReduceBreak 48 # best score after generation 10 224.545 bits/residue, 43 clashes 45.2108 breaks # Cumulative usage by method: ## InsertFragment 107 ## ReduceClash 38 ## CrossOver 1 ## CrossAndInsert 90 ## TwoFragment 30 ## InsertSSBond 0 ## OneRotamer 0 ## InsertAlignment 8 ## ReduceBreak 52 # best score after generation 11 224.529 bits/residue, 46 clashes 37.5965 breaks # Cumulative usage by method: ## InsertFragment 122 ## ReduceClash 43 ## CrossOver 1 ## CrossAndInsert 98 ## TwoFragment 30 ## InsertSSBond 0 ## OneRotamer 0 ## InsertAlignment 8 ## ReduceBreak 54 # best score after generation 12 224.432 bits/residue, 43 clashes 37.5965 breaks # Cumulative usage by method: ## InsertFragment 135 ## ReduceClash 50 ## CrossOver 2 ## CrossAndInsert 107 ## TwoFragment 30 ## InsertSSBond 0 ## OneRotamer 0 ## InsertAlignment 8 ## ReduceBreak 54 # best score after generation 13 224.432 bits/residue, 43 clashes 37.5965 breaks # Cumulative usage by method: ## InsertFragment 148 ## ReduceClash 56 ## CrossOver 3 ## CrossAndInsert 116 ## TwoFragment 30 ## InsertSSBond 0 ## OneRotamer 0 ## InsertAlignment 8 ## ReduceBreak 55 # best score after generation 14 223.626 bits/residue, 39 clashes 44.0185 breaks # Cumulative usage by method: ## InsertFragment 167 ## ReduceClash 60 ## CrossOver 5 ## CrossAndInsert 120 ## TwoFragment 30 ## InsertSSBond 0 ## OneRotamer 0 ## InsertAlignment 8 ## ReduceBreak 56 # best score after generation 15 223.626 bits/residue, 39 clashes 44.0185 breaks # Cumulative usage by method: ## InsertFragment 186 ## ReduceClash 62 ## CrossOver 7 ## CrossAndInsert 127 ## TwoFragment 30 ## InsertSSBond 0 ## OneRotamer 0 ## InsertAlignment 8 ## ReduceBreak 56 # best score after generation 16 223.089 bits/residue, 40 clashes 38.7888 breaks # Cumulative usage by method: ## InsertFragment 202 ## ReduceClash 64 ## CrossOver 10 ## CrossAndInsert 134 ## TwoFragment 30 ## InsertSSBond 0 ## OneRotamer 0 ## InsertAlignment 8 ## ReduceBreak 58 # best score after generation 17 222.013 bits/residue, 43 clashes 28.5502 breaks # Cumulative usage by method: ## InsertFragment 219 ## ReduceClash 67 ## CrossOver 12 ## CrossAndInsert 141 ## TwoFragment 31 ## InsertSSBond 0 ## OneRotamer 0 ## InsertAlignment 8 ## ReduceBreak 58 # best score after generation 18 222.013 bits/residue, 43 clashes 28.5502 breaks # Cumulative usage by method: ## InsertFragment 237 ## ReduceClash 69 ## CrossOver 16 ## CrossAndInsert 147 ## TwoFragment 31 ## InsertSSBond 0 ## OneRotamer 0 ## InsertAlignment 8 ## ReduceBreak 58 # best score after generation 19 221.65 bits/residue, 41 clashes 28.5502 breaks # Cumulative usage by method: ## InsertFragment 250 ## ReduceClash 72 ## CrossOver 23 ## CrossAndInsert 154 ## TwoFragment 31 ## InsertSSBond 0 ## OneRotamer 0 ## InsertAlignment 8 ## ReduceBreak 58 # best score after generation 20 221.65 bits/residue, 41 clashes 28.5502 breaks # Cumulative usage by method: ## InsertFragment 263 ## ReduceClash 74 ## CrossOver 28 ## CrossAndInsert 163 ## TwoFragment 31 ## InsertSSBond 0 ## OneRotamer 0 ## InsertAlignment 8 ## ReduceBreak 59 # best score after generation 21 221.634 bits/residue, 41 clashes 28.5502 breaks # Cumulative usage by method: ## InsertFragment 275 ## ReduceClash 76 ## CrossOver 37 ## CrossAndInsert 169 ## TwoFragment 32 ## InsertSSBond 0 ## OneRotamer 0 ## InsertAlignment 8 ## ReduceBreak 59 # best score after generation 22 221.634 bits/residue, 41 clashes 28.5502 breaks # Cumulative usage by method: ## InsertFragment 287 ## ReduceClash 77 ## CrossOver 49 ## CrossAndInsert 174 ## TwoFragment 32 ## InsertSSBond 0 ## OneRotamer 0 ## InsertAlignment 8 ## ReduceBreak 59 # best score after generation 23 221.322 bits/residue, 38 clashes 28.5502 breaks # Cumulative usage by method: ## InsertFragment 296 ## ReduceClash 80 ## CrossOver 61 ## CrossAndInsert 180 ## TwoFragment 32 ## InsertSSBond 0 ## OneRotamer 0 ## InsertAlignment 8 ## ReduceBreak 59 # best score after generation 24 221.322 bits/residue, 38 clashes 28.5502 breaks # Cumulative usage by method: ## InsertFragment 304 ## ReduceClash 83 ## CrossOver 74 ## CrossAndInsert 186 ## TwoFragment 32 ## InsertSSBond 0 ## OneRotamer 0 ## InsertAlignment 8 ## ReduceBreak 59 # best score after generation 25 221.322 bits/residue, 38 clashes 28.5502 breaks # Cumulative usage by method: ## InsertFragment 315 ## ReduceClash 83 ## CrossOver 90 ## CrossAndInsert 189 ## TwoFragment 32 ## InsertSSBond 0 ## OneRotamer 0 ## InsertAlignment 8 ## ReduceBreak 59 # best score after generation 26 221.159 bits/residue, 38 clashes 28.5502 breaks # Cumulative usage by method: ## InsertFragment 324 ## ReduceClash 83 ## CrossOver 109 ## CrossAndInsert 191 ## TwoFragment 32 ## InsertSSBond 0 ## OneRotamer 0 ## InsertAlignment 8 ## ReduceBreak 59 # best score after generation 27 221.159 bits/residue, 38 clashes 28.5502 breaks # Cumulative usage by method: ## InsertFragment 330 ## ReduceClash 83 ## CrossOver 131 ## CrossAndInsert 193 ## TwoFragment 32 ## InsertSSBond 0 ## OneRotamer 0 ## InsertAlignment 8 ## ReduceBreak 59 # best score after generation 28 220.921 bits/residue, 38 clashes 28.5502 breaks # Cumulative usage by method: ## InsertFragment 333 ## ReduceClash 83 ## CrossOver 155 ## CrossAndInsert 196 ## TwoFragment 32 ## InsertSSBond 0 ## OneRotamer 0 ## InsertAlignment 8 ## ReduceBreak 59 # best score after generation 29 220.921 bits/residue, 38 clashes 28.5502 breaks # Cumulative usage by method: ## InsertFragment 335 ## ReduceClash 83 ## CrossOver 182 ## CrossAndInsert 197 ## TwoFragment 32 ## InsertSSBond 0 ## OneRotamer 0 ## InsertAlignment 8 ## ReduceBreak 59 # best score after generation 30 220.809 bits/residue, 38 clashes 28.5502 breaks # Cumulative usage by method: ## InsertFragment 336 ## ReduceClash 83 ## CrossOver 209 ## CrossAndInsert 199 ## TwoFragment 32 ## InsertSSBond 0 ## OneRotamer 0 ## InsertAlignment 8 ## ReduceBreak 59 # best score after generation 31 220.766 bits/residue, 36 clashes 28.5113 breaks # Cumulative usage by method: ## InsertFragment 337 ## ReduceClash 83 ## CrossOver 237 ## CrossAndInsert 200 ## TwoFragment 32 ## InsertSSBond 0 ## OneRotamer 0 ## InsertAlignment 8 ## ReduceBreak 59 # best score after generation 32 220.724 bits/residue, 36 clashes 28.5502 breaks # Cumulative usage by method: ## InsertFragment 337 ## ReduceClash 83 ## CrossOver 265 ## CrossAndInsert 202 ## TwoFragment 32 ## InsertSSBond 0 ## OneRotamer 0 ## InsertAlignment 8 ## ReduceBreak 59 # best score after generation 33 220.502 bits/residue, 36 clashes 28.5113 breaks # Cumulative usage by method: ## InsertFragment 337 ## ReduceClash 84 ## CrossOver 293 ## CrossAndInsert 203 ## TwoFragment 32 ## InsertSSBond 0 ## OneRotamer 0 ## InsertAlignment 8 ## ReduceBreak 59 # best score after generation 34 220.502 bits/residue, 36 clashes 28.5113 breaks # Cumulative usage by method: ## InsertFragment 338 ## ReduceClash 84 ## CrossOver 322 ## CrossAndInsert 203 ## TwoFragment 32 ## InsertSSBond 0 ## OneRotamer 0 ## InsertAlignment 8 ## ReduceBreak 59 # best score after generation 35 220.426 bits/residue, 34 clashes 28.5113 breaks # Cumulative usage by method: ## InsertFragment 339 ## ReduceClash 84 ## CrossOver 348 ## CrossAndInsert 206 ## TwoFragment 32 ## InsertSSBond 0 ## OneRotamer 0 ## InsertAlignment 8 ## ReduceBreak 59 # best score after generation 36 220.202 bits/residue, 33 clashes 28.5113 breaks # Cumulative usage by method: ## InsertFragment 339 ## ReduceClash 84 ## CrossOver 379 ## CrossAndInsert 207 ## TwoFragment 32 ## InsertSSBond 0 ## OneRotamer 0 ## InsertAlignment 8 ## ReduceBreak 59 # best score after generation 37 220.083 bits/residue, 34 clashes 28.5113 breaks # Cumulative usage by method: ## InsertFragment 341 ## ReduceClash 84 ## CrossOver 410 ## CrossAndInsert 207 ## TwoFragment 32 ## InsertSSBond 0 ## OneRotamer 0 ## InsertAlignment 8 ## ReduceBreak 59 # best score after generation 38 219.728 bits/residue, 34 clashes 28.5113 breaks # Cumulative usage by method: ## InsertFragment 341 ## ReduceClash 84 ## CrossOver 443 ## CrossAndInsert 209 ## TwoFragment 32 ## InsertSSBond 0 ## OneRotamer 0 ## InsertAlignment 8 ## ReduceBreak 59 # best score after generation 39 219.504 bits/residue, 33 clashes 28.5113 breaks # Cumulative usage by method: ## InsertFragment 342 ## ReduceClash 84 ## CrossOver 480 ## CrossAndInsert 209 ## TwoFragment 32 ## InsertSSBond 0 ## OneRotamer 0 ## InsertAlignment 8 ## ReduceBreak 59 # best score after generation 40 219.504 bits/residue, 33 clashes 28.5113 breaks # Cumulative usage by method: ## InsertFragment 344 ## ReduceClash 84 ## CrossOver 509 ## CrossAndInsert 210 ## TwoFragment 32 ## InsertSSBond 0 ## OneRotamer 0 ## InsertAlignment 8 ## ReduceBreak 59 # best score after generation 41 219.307 bits/residue, 32 clashes 28.5113 breaks # Cumulative usage by method: ## InsertFragment 344 ## ReduceClash 84 ## CrossOver 542 ## CrossAndInsert 210 ## TwoFragment 32 ## InsertSSBond 0 ## OneRotamer 0 ## InsertAlignment 8 ## ReduceBreak 59 # best score after generation 42 219.163 bits/residue, 30 clashes 28.5113 breaks # Cumulative usage by method: ## InsertFragment 344 ## ReduceClash 84 ## CrossOver 572 ## CrossAndInsert 210 ## TwoFragment 32 ## InsertSSBond 0 ## OneRotamer 0 ## InsertAlignment 8 ## ReduceBreak 59 # best score after generation 43 218.779 bits/residue, 31 clashes 28.5113 breaks # Cumulative usage by method: ## InsertFragment 347 ## ReduceClash 84 ## CrossOver 606 ## CrossAndInsert 211 ## TwoFragment 32 ## InsertSSBond 0 ## OneRotamer 0 ## InsertAlignment 8 ## ReduceBreak 59 # best score after generation 44 218.779 bits/residue, 31 clashes 28.5113 breaks # Cumulative usage by method: ## InsertFragment 348 ## ReduceClash 84 ## CrossOver 643 ## CrossAndInsert 212 ## TwoFragment 32 ## InsertSSBond 0 ## OneRotamer 0 ## InsertAlignment 8 ## ReduceBreak 59 # best score after generation 45 218.679 bits/residue, 31 clashes 28.5113 breaks # Cumulative usage by method: ## InsertFragment 349 ## ReduceClash 84 ## CrossOver 678 ## CrossAndInsert 212 ## TwoFragment 32 ## InsertSSBond 0 ## OneRotamer 0 ## InsertAlignment 8 ## ReduceBreak 59 # best score after generation 46 218.679 bits/residue, 31 clashes 28.5113 breaks # Cumulative usage by method: ## InsertFragment 350 ## ReduceClash 84 ## CrossOver 713 ## CrossAndInsert 212 ## TwoFragment 32 ## InsertSSBond 0 ## OneRotamer 0 ## InsertAlignment 8 ## ReduceBreak 59 # best score after generation 47 218.677 bits/residue, 31 clashes 28.5113 breaks # Cumulative usage by method: ## InsertFragment 350 ## ReduceClash 84 ## CrossOver 748 ## CrossAndInsert 212 ## TwoFragment 32 ## InsertSSBond 0 ## OneRotamer 0 ## InsertAlignment 8 ## ReduceBreak 59 # best score after generation 48 218.677 bits/residue, 31 clashes 28.5113 breaks # Cumulative usage by method: ## InsertFragment 350 ## ReduceClash 84 ## CrossOver 781 ## CrossAndInsert 212 ## TwoFragment 32 ## InsertSSBond 0 ## OneRotamer 0 ## InsertAlignment 8 ## ReduceBreak 59 # best score after generation 49 218.663 bits/residue, 31 clashes 28.4153 breaks # Cumulative usage by method: ## InsertFragment 350 ## ReduceClash 84 ## CrossOver 812 ## CrossAndInsert 212 ## TwoFragment 32 ## InsertSSBond 0 ## OneRotamer 0 ## InsertAlignment 8 ## ReduceBreak 59 # best score after generation 50 218.663 bits/residue, 31 clashes 28.4153 breaks # Cumulative usage by method: ## InsertFragment 350 ## ReduceClash 84 ## CrossOver 843 ## CrossAndInsert 212 ## TwoFragment 32 ## InsertSSBond 0 ## OneRotamer 0 ## InsertAlignment 8 ## ReduceBreak 59 # best score after generation 51 218.497 bits/residue, 31 clashes 27.1724 breaks # Cumulative usage by method: ## InsertFragment 351 ## ReduceClash 84 ## CrossOver 877 ## CrossAndInsert 212 ## TwoFragment 32 ## InsertSSBond 0 ## OneRotamer 0 ## InsertAlignment 8 ## ReduceBreak 59 # best score after generation 52 218.497 bits/residue, 31 clashes 27.1724 breaks # Cumulative usage by method: ## InsertFragment 351 ## ReduceClash 84 ## CrossOver 907 ## CrossAndInsert 212 ## TwoFragment 32 ## InsertSSBond 0 ## OneRotamer 0 ## InsertAlignment 8 ## ReduceBreak 59 # best score after generation 53 218.497 bits/residue, 31 clashes 27.1724 breaks # Cumulative usage by method: ## InsertFragment 351 ## ReduceClash 84 ## CrossOver 941 ## CrossAndInsert 212 ## TwoFragment 32 ## InsertSSBond 0 ## OneRotamer 0 ## InsertAlignment 8 ## ReduceBreak 59 # best score after generation 54 218.317 bits/residue, 32 clashes 27.1724 breaks # Cumulative usage by method: ## InsertFragment 352 ## ReduceClash 84 ## CrossOver 971 ## CrossAndInsert 212 ## TwoFragment 32 ## InsertSSBond 0 ## OneRotamer 0 ## InsertAlignment 8 ## ReduceBreak 59 # best score after generation 55 218.317 bits/residue, 32 clashes 27.1724 breaks # Cumulative usage by method: ## InsertFragment 353 ## ReduceClash 84 ## CrossOver 1010 ## CrossAndInsert 212 ## TwoFragment 32 ## InsertSSBond 0 ## OneRotamer 0 ## InsertAlignment 8 ## ReduceBreak 59 # best score after generation 56 218.317 bits/residue, 32 clashes 27.1724 breaks # Cumulative usage by method: ## InsertFragment 353 ## ReduceClash 84 ## CrossOver 1047 ## CrossAndInsert 212 ## TwoFragment 32 ## InsertSSBond 0 ## OneRotamer 0 ## InsertAlignment 8 ## ReduceBreak 59 # best score after generation 57 218.159 bits/residue, 32 clashes 27.1724 breaks # Cumulative usage by method: ## InsertFragment 353 ## ReduceClash 84 ## CrossOver 1083 ## CrossAndInsert 213 ## TwoFragment 32 ## InsertSSBond 0 ## OneRotamer 0 ## InsertAlignment 8 ## ReduceBreak 59 # best score after generation 58 218.159 bits/residue, 32 clashes 27.1724 breaks # Cumulative usage by method: ## InsertFragment 353 ## ReduceClash 84 ## CrossOver 1119 ## CrossAndInsert 214 ## TwoFragment 32 ## InsertSSBond 0 ## OneRotamer 0 ## InsertAlignment 8 ## ReduceBreak 59 # best score after generation 59 218.146 bits/residue, 32 clashes 27.0963 breaks # Cumulative usage by method: ## InsertFragment 353 ## ReduceClash 84 ## CrossOver 1163 ## CrossAndInsert 214 ## TwoFragment 32 ## InsertSSBond 0 ## OneRotamer 0 ## InsertAlignment 8 ## ReduceBreak 59 # best score after generation 60 218.145 bits/residue, 32 clashes 27.0963 breaks # Cumulative usage by method: ## InsertFragment 353 ## ReduceClash 84 ## CrossOver 1199 ## CrossAndInsert 214 ## TwoFragment 32 ## InsertSSBond 0 ## OneRotamer 0 ## InsertAlignment 8 ## ReduceBreak 59 # best score after generation 61 218.145 bits/residue, 32 clashes 27.0963 breaks # Cumulative usage by method: ## InsertFragment 353 ## ReduceClash 84 ## CrossOver 1233 ## CrossAndInsert 214 ## TwoFragment 32 ## InsertSSBond 0 ## OneRotamer 0 ## InsertAlignment 8 ## ReduceBreak 59 # best score after generation 62 218.141 bits/residue, 32 clashes 27.0963 breaks # Cumulative usage by method: ## InsertFragment 354 ## ReduceClash 84 ## CrossOver 1263 ## CrossAndInsert 214 ## TwoFragment 32 ## InsertSSBond 0 ## OneRotamer 0 ## InsertAlignment 8 ## ReduceBreak 59 # best score after generation 63 218.141 bits/residue, 32 clashes 27.0963 breaks # Cumulative usage by method: ## InsertFragment 354 ## ReduceClash 84 ## CrossOver 1300 ## CrossAndInsert 214 ## TwoFragment 32 ## InsertSSBond 0 ## OneRotamer 0 ## InsertAlignment 8 ## ReduceBreak 59 # best score after generation 64 218.141 bits/residue, 32 clashes 27.0963 breaks # Cumulative usage by method: ## InsertFragment 354 ## ReduceClash 84 ## CrossOver 1342 ## CrossAndInsert 214 ## TwoFragment 32 ## InsertSSBond 0 ## OneRotamer 0 ## InsertAlignment 8 ## ReduceBreak 59 # best score after generation 65 217.752 bits/residue, 30 clashes 27.0963 breaks # Cumulative usage by method: ## InsertFragment 355 ## ReduceClash 84 ## CrossOver 1372 ## CrossAndInsert 214 ## TwoFragment 32 ## InsertSSBond 0 ## OneRotamer 0 ## InsertAlignment 8 ## ReduceBreak 59 # best score after generation 66 217.752 bits/residue, 30 clashes 27.0963 breaks # Cumulative usage by method: ## InsertFragment 355 ## ReduceClash 84 ## CrossOver 1413 ## CrossAndInsert 214 ## TwoFragment 32 ## InsertSSBond 0 ## OneRotamer 0 ## InsertAlignment 8 ## ReduceBreak 59 # best score after generation 67 217.75 bits/residue, 30 clashes 27.0963 breaks # Cumulative usage by method: ## InsertFragment 355 ## ReduceClash 84 ## CrossOver 1451 ## CrossAndInsert 214 ## TwoFragment 32 ## InsertSSBond 0 ## OneRotamer 0 ## InsertAlignment 8 ## ReduceBreak 59 # best score after generation 68 217.75 bits/residue, 30 clashes 27.0963 breaks # Cumulative usage by method: ## InsertFragment 355 ## ReduceClash 84 ## CrossOver 1490 ## CrossAndInsert 214 ## TwoFragment 32 ## InsertSSBond 0 ## OneRotamer 0 ## InsertAlignment 8 ## ReduceBreak 59 # best score after generation 69 217.75 bits/residue, 30 clashes 27.0963 breaks # Cumulative usage by method: ## InsertFragment 355 ## ReduceClash 84 ## CrossOver 1530 ## CrossAndInsert 214 ## TwoFragment 32 ## InsertSSBond 0 ## OneRotamer 0 ## InsertAlignment 8 ## ReduceBreak 59 # best score after generation 70 217.75 bits/residue, 30 clashes 27.0963 breaks # Cumulative usage by method: ## InsertFragment 355 ## ReduceClash 84 ## CrossOver 1567 ## CrossAndInsert 214 ## TwoFragment 32 ## InsertSSBond 0 ## OneRotamer 0 ## InsertAlignment 8 ## ReduceBreak 59 # best score after generation 71 217.75 bits/residue, 30 clashes 27.0963 breaks # Cumulative usage by method: ## InsertFragment 355 ## ReduceClash 84 ## CrossOver 1598 ## CrossAndInsert 214 ## TwoFragment 32 ## InsertSSBond 0 ## OneRotamer 0 ## InsertAlignment 8 ## ReduceBreak 59 # best score after generation 72 217.75 bits/residue, 30 clashes 27.0963 breaks # Cumulative usage by method: ## InsertFragment 355 ## ReduceClash 84 ## CrossOver 1629 ## CrossAndInsert 214 ## TwoFragment 32 ## InsertSSBond 0 ## OneRotamer 0 ## InsertAlignment 8 ## ReduceBreak 59 # best score after generation 73 217.75 bits/residue, 30 clashes 27.0963 breaks # Cumulative usage by method: ## InsertFragment 355 ## ReduceClash 84 ## CrossOver 1660 ## CrossAndInsert 214 ## TwoFragment 32 ## InsertSSBond 0 ## OneRotamer 0 ## InsertAlignment 8 ## ReduceBreak 59 # best score after generation 74 217.75 bits/residue, 30 clashes 27.0963 breaks # Cumulative usage by method: ## InsertFragment 355 ## ReduceClash 84 ## CrossOver 1691 ## CrossAndInsert 214 ## TwoFragment 32 ## InsertSSBond 0 ## OneRotamer 0 ## InsertAlignment 8 ## ReduceBreak 59 # best score after generation 75 217.74 bits/residue, 30 clashes 27.0963 breaks # Cumulative usage by method: ## InsertFragment 355 ## ReduceClash 84 ## CrossOver 1723 ## CrossAndInsert 215 ## TwoFragment 32 ## InsertSSBond 0 ## OneRotamer 0 ## InsertAlignment 8 ## ReduceBreak 59 # best score after generation 76 217.74 bits/residue, 30 clashes 27.0963 breaks # Cumulative usage by method: ## InsertFragment 355 ## ReduceClash 84 ## CrossOver 1768 ## CrossAndInsert 215 ## TwoFragment 32 ## InsertSSBond 0 ## OneRotamer 0 ## InsertAlignment 8 ## ReduceBreak 59 # best score after generation 77 217.74 bits/residue, 30 clashes 27.0963 breaks # Cumulative usage by method: ## InsertFragment 355 ## ReduceClash 84 ## CrossOver 1806 ## CrossAndInsert 215 ## TwoFragment 32 ## InsertSSBond 0 ## OneRotamer 0 ## InsertAlignment 8 ## ReduceBreak 59 # best score after generation 78 217.739 bits/residue, 30 clashes 27.0963 breaks # Cumulative usage by method: ## InsertFragment 355 ## ReduceClash 84 ## CrossOver 1843 ## CrossAndInsert 215 ## TwoFragment 32 ## InsertSSBond 0 ## OneRotamer 0 ## InsertAlignment 8 ## ReduceBreak 59 # best score after generation 79 217.739 bits/residue, 30 clashes 27.0963 breaks # Cumulative usage by method: ## InsertFragment 355 ## ReduceClash 84 ## CrossOver 1883 ## CrossAndInsert 215 ## TwoFragment 32 ## InsertSSBond 0 ## OneRotamer 0 ## InsertAlignment 8 ## ReduceBreak 59 # best score after generation 80 217.739 bits/residue, 30 clashes 27.0963 breaks # Cumulative usage by method: ## InsertFragment 355 ## ReduceClash 84 ## CrossOver 1914 ## CrossAndInsert 215 ## TwoFragment 32 ## InsertSSBond 0 ## OneRotamer 0 ## InsertAlignment 8 ## ReduceBreak 59 # best score after generation 81 217.739 bits/residue, 30 clashes 27.0963 breaks # Cumulative usage by method: ## InsertFragment 355 ## ReduceClash 84 ## CrossOver 1945 ## CrossAndInsert 215 ## TwoFragment 32 ## InsertSSBond 0 ## OneRotamer 0 ## InsertAlignment 8 ## ReduceBreak 59 # best score after generation 82 217.611 bits/residue, 30 clashes 27.0963 breaks # Cumulative usage by method: ## InsertFragment 356 ## ReduceClash 84 ## CrossOver 1975 ## CrossAndInsert 215 ## TwoFragment 32 ## InsertSSBond 0 ## OneRotamer 0 ## InsertAlignment 8 ## ReduceBreak 59 # best score after generation 83 217.611 bits/residue, 30 clashes 27.0963 breaks # Cumulative usage by method: ## InsertFragment 356 ## ReduceClash 84 ## CrossOver 2013 ## CrossAndInsert 215 ## TwoFragment 32 ## InsertSSBond 0 ## OneRotamer 0 ## InsertAlignment 8 ## ReduceBreak 59 # best score after generation 84 217.604 bits/residue, 30 clashes 27.0963 breaks # Cumulative usage by method: ## InsertFragment 356 ## ReduceClash 84 ## CrossOver 2055 ## CrossAndInsert 215 ## TwoFragment 32 ## InsertSSBond 0 ## OneRotamer 0 ## InsertAlignment 8 ## ReduceBreak 59 # best score after generation 85 217.604 bits/residue, 30 clashes 27.0963 breaks # Cumulative usage by method: ## InsertFragment 356 ## ReduceClash 84 ## CrossOver 2093 ## CrossAndInsert 215 ## TwoFragment 32 ## InsertSSBond 0 ## OneRotamer 0 ## InsertAlignment 8 ## ReduceBreak 59 # best score after generation 86 217.604 bits/residue, 30 clashes 27.0963 breaks # Cumulative usage by method: ## InsertFragment 356 ## ReduceClash 84 ## CrossOver 2133 ## CrossAndInsert 215 ## TwoFragment 32 ## InsertSSBond 0 ## OneRotamer 0 ## InsertAlignment 8 ## ReduceBreak 59 # best score after generation 87 217.604 bits/residue, 30 clashes 27.0963 breaks # Cumulative usage by method: ## InsertFragment 356 ## ReduceClash 84 ## CrossOver 2164 ## CrossAndInsert 215 ## TwoFragment 32 ## InsertSSBond 0 ## OneRotamer 0 ## InsertAlignment 8 ## ReduceBreak 59 # best score after generation 88 217.604 bits/residue, 30 clashes 27.0963 breaks # Cumulative usage by method: ## InsertFragment 356 ## ReduceClash 84 ## CrossOver 2195 ## CrossAndInsert 215 ## TwoFragment 32 ## InsertSSBond 0 ## OneRotamer 0 ## InsertAlignment 8 ## ReduceBreak 59 # best score after generation 89 217.604 bits/residue, 30 clashes 27.0963 breaks # Cumulative usage by method: ## InsertFragment 356 ## ReduceClash 84 ## CrossOver 2226 ## CrossAndInsert 215 ## TwoFragment 32 ## InsertSSBond 0 ## OneRotamer 0 ## InsertAlignment 8 ## ReduceBreak 59 # best score after generation 90 217.604 bits/residue, 30 clashes 27.0963 breaks # Cumulative usage by method: ## InsertFragment 356 ## ReduceClash 84 ## CrossOver 2257 ## CrossAndInsert 215 ## TwoFragment 32 ## InsertSSBond 0 ## OneRotamer 0 ## InsertAlignment 8 ## ReduceBreak 59 # best score after generation 91 217.604 bits/residue, 30 clashes 27.0963 breaks # Cumulative usage by method: ## InsertFragment 356 ## ReduceClash 84 ## CrossOver 2288 ## CrossAndInsert 215 ## TwoFragment 32 ## InsertSSBond 0 ## OneRotamer 0 ## InsertAlignment 8 ## ReduceBreak 59 # best score after generation 92 217.348 bits/residue, 29 clashes 27.0963 breaks # Cumulative usage by method: ## InsertFragment 357 ## ReduceClash 84 ## CrossOver 2318 ## CrossAndInsert 215 ## TwoFragment 32 ## InsertSSBond 0 ## OneRotamer 0 ## InsertAlignment 8 ## ReduceBreak 59 # best score after generation 93 217.348 bits/residue, 29 clashes 27.0963 breaks # Cumulative usage by method: ## InsertFragment 357 ## ReduceClash 84 ## CrossOver 2357 ## CrossAndInsert 215 ## TwoFragment 32 ## InsertSSBond 0 ## OneRotamer 0 ## InsertAlignment 8 ## ReduceBreak 59 # best score after generation 94 217.348 bits/residue, 29 clashes 27.0963 breaks # Cumulative usage by method: ## InsertFragment 357 ## ReduceClash 84 ## CrossOver 2398 ## CrossAndInsert 215 ## TwoFragment 32 ## InsertSSBond 0 ## OneRotamer 0 ## InsertAlignment 8 ## ReduceBreak 59 # best score after generation 95 217.348 bits/residue, 29 clashes 27.0963 breaks # Cumulative usage by method: ## InsertFragment 357 ## ReduceClash 84 ## CrossOver 2429 ## CrossAndInsert 215 ## TwoFragment 32 ## InsertSSBond 0 ## OneRotamer 0 ## InsertAlignment 8 ## ReduceBreak 59 # best score after generation 96 217.348 bits/residue, 29 clashes 27.0963 breaks # Cumulative usage by method: ## InsertFragment 357 ## ReduceClash 84 ## CrossOver 2460 ## CrossAndInsert 215 ## TwoFragment 32 ## InsertSSBond 0 ## OneRotamer 0 ## InsertAlignment 8 ## ReduceBreak 59 # best score after generation 97 217.346 bits/residue, 29 clashes 27.0963 breaks # Cumulative usage by method: ## InsertFragment 357 ## ReduceClash 84 ## CrossOver 2492 ## CrossAndInsert 215 ## TwoFragment 32 ## InsertSSBond 0 ## OneRotamer 0 ## InsertAlignment 8 ## ReduceBreak 59 # best score after generation 98 217.136 bits/residue, 27 clashes 27.2133 breaks # Cumulative usage by method: ## InsertFragment 358 ## ReduceClash 84 ## CrossOver 2527 ## CrossAndInsert 215 ## TwoFragment 33 ## InsertSSBond 0 ## OneRotamer 0 ## InsertAlignment 8 ## ReduceBreak 59 # best score after generation 99 217.136 bits/residue, 27 clashes 27.2133 breaks # Cumulative usage by method: ## InsertFragment 359 ## ReduceClash 84 ## CrossOver 2569 ## CrossAndInsert 215 ## TwoFragment 33 ## InsertSSBond 0 ## OneRotamer 0 ## InsertAlignment 8 ## ReduceBreak 59 # best score after generation 100 217.136 bits/residue, 27 clashes 27.2133 breaks # Cumulative usage by method: ## InsertFragment 359 ## ReduceClash 84 ## CrossOver 2605 ## CrossAndInsert 215 ## TwoFragment 33 ## InsertSSBond 0 ## OneRotamer 0 ## InsertAlignment 8 ## ReduceBreak 59 # best score after generation 101 217.107 bits/residue, 27 clashes 27.2133 breaks # Cumulative usage by method: ## InsertFragment 359 ## ReduceClash 84 ## CrossOver 2643 ## CrossAndInsert 215 ## TwoFragment 33 ## InsertSSBond 0 ## OneRotamer 0 ## InsertAlignment 8 ## ReduceBreak 59 # best score after generation 102 217.107 bits/residue, 27 clashes 27.2133 breaks # Cumulative usage by method: ## InsertFragment 359 ## ReduceClash 84 ## CrossOver 2681 ## CrossAndInsert 215 ## TwoFragment 33 ## InsertSSBond 0 ## OneRotamer 0 ## InsertAlignment 8 ## ReduceBreak 59 # best score after generation 103 217.107 bits/residue, 27 clashes 27.2133 breaks # Cumulative usage by method: ## InsertFragment 359 ## ReduceClash 84 ## CrossOver 2722 ## CrossAndInsert 215 ## TwoFragment 33 ## InsertSSBond 0 ## OneRotamer 0 ## InsertAlignment 8 ## ReduceBreak 59 # best score after generation 104 217.103 bits/residue, 27 clashes 27.1918 breaks # Cumulative usage by method: ## InsertFragment 360 ## ReduceClash 85 ## CrossOver 2753 ## CrossAndInsert 215 ## TwoFragment 33 ## InsertSSBond 0 ## OneRotamer 0 ## InsertAlignment 8 ## ReduceBreak 59 # best score after generation 105 217.103 bits/residue, 27 clashes 27.1918 breaks # Cumulative usage by method: ## InsertFragment 360 ## ReduceClash 85 ## CrossOver 2799 ## CrossAndInsert 215 ## TwoFragment 33 ## InsertSSBond 0 ## OneRotamer 0 ## InsertAlignment 8 ## ReduceBreak 59 # best score after generation 106 217.103 bits/residue, 27 clashes 27.1918 breaks # Cumulative usage by method: ## InsertFragment 360 ## ReduceClash 85 ## CrossOver 2835 ## CrossAndInsert 215 ## TwoFragment 33 ## InsertSSBond 0 ## OneRotamer 0 ## InsertAlignment 8 ## ReduceBreak 59 # best score after generation 107 217.103 bits/residue, 27 clashes 27.1918 breaks # Cumulative usage by method: ## InsertFragment 360 ## ReduceClash 85 ## CrossOver 2868 ## CrossAndInsert 215 ## TwoFragment 33 ## InsertSSBond 0 ## OneRotamer 0 ## InsertAlignment 8 ## ReduceBreak 59 # best score after generation 108 217.103 bits/residue, 27 clashes 27.1918 breaks # Cumulative usage by method: ## InsertFragment 360 ## ReduceClash 85 ## CrossOver 2899 ## CrossAndInsert 215 ## TwoFragment 33 ## InsertSSBond 0 ## OneRotamer 0 ## InsertAlignment 8 ## ReduceBreak 59 # best score after generation 109 217.103 bits/residue, 27 clashes 27.1918 breaks # Cumulative usage by method: ## InsertFragment 360 ## ReduceClash 85 ## CrossOver 2930 ## CrossAndInsert 215 ## TwoFragment 33 ## InsertSSBond 0 ## OneRotamer 0 ## InsertAlignment 8 ## ReduceBreak 59 # best score after generation 110 217.099 bits/residue, 27 clashes 27.1654 breaks # Cumulative usage by method: ## InsertFragment 361 ## ReduceClash 85 ## CrossOver 2961 ## CrossAndInsert 215 ## TwoFragment 33 ## InsertSSBond 0 ## OneRotamer 0 ## InsertAlignment 8 ## ReduceBreak 59 # best score after generation 111 217.099 bits/residue, 27 clashes 27.1654 breaks # Cumulative usage by method: ## InsertFragment 361 ## ReduceClash 85 ## CrossOver 3000 ## CrossAndInsert 215 ## TwoFragment 33 ## InsertSSBond 0 ## OneRotamer 0 ## InsertAlignment 8 ## ReduceBreak 59 # best score after generation 112 217.099 bits/residue, 27 clashes 27.1654 breaks # Cumulative usage by method: ## InsertFragment 361 ## ReduceClash 85 ## CrossOver 3037 ## CrossAndInsert 215 ## TwoFragment 33 ## InsertSSBond 0 ## OneRotamer 0 ## InsertAlignment 8 ## ReduceBreak 59 # best score after generation 113 217.099 bits/residue, 27 clashes 27.1655 breaks # Cumulative usage by method: ## InsertFragment 361 ## ReduceClash 85 ## CrossOver 3068 ## CrossAndInsert 215 ## TwoFragment 33 ## InsertSSBond 0 ## OneRotamer 0 ## InsertAlignment 8 ## ReduceBreak 59 # best score after generation 114 217.099 bits/residue, 27 clashes 27.1654 breaks # Cumulative usage by method: ## InsertFragment 361 ## ReduceClash 85 ## CrossOver 3099 ## CrossAndInsert 215 ## TwoFragment 33 ## InsertSSBond 0 ## OneRotamer 0 ## InsertAlignment 8 ## ReduceBreak 59 # best score after generation 115 217.099 bits/residue, 27 clashes 27.1654 breaks # Cumulative usage by method: ## InsertFragment 361 ## ReduceClash 85 ## CrossOver 3130 ## CrossAndInsert 215 ## TwoFragment 33 ## InsertSSBond 0 ## OneRotamer 0 ## InsertAlignment 8 ## ReduceBreak 59 # 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: 19.3001 bits/residue, 27 clashes, rmsd= 0 # best score after iter 1 19.3001 bits/residue, 27 clashes, rmsd= 0 # best score after iter 2 18.0166 bits/residue, 41 clashes, rmsd= 0 # best score after iter 3 16.4836 bits/residue, 34 clashes, rmsd= 0 # best score after iter 4 15.4048 bits/residue, 30 clashes, rmsd= 0 # best score after iter 5 15.1275 bits/residue, 29 clashes, rmsd= 0 # best score after iter 6 15.1275 bits/residue, 29 clashes, rmsd= 0 # best score after iter 7 15.1275 bits/residue, 29 clashes, rmsd= 0 # best score after iter 8 14.0484 bits/residue, 24 clashes, rmsd= 0 # best score after iter 9 13.7678 bits/residue, 23 clashes, rmsd= 0 # best score after iter 10 13.7617 bits/residue, 23 clashes, rmsd= 0 # best score after iter 11 13.7617 bits/residue, 23 clashes, rmsd= 0 # best score after iter 12 13.7617 bits/residue, 23 clashes, rmsd= 0 # best score after iter 13 13.7617 bits/residue, 23 clashes, rmsd= 0 # best score after iter 14 13.7617 bits/residue, 23 clashes, rmsd= 0 # best score after iter 15 13.7617 bits/residue, 23 clashes, rmsd= 0 # best score after iter 16 13.7617 bits/residue, 23 clashes, rmsd= 0 # best score after iter 17 13.7617 bits/residue, 23 clashes, rmsd= 0 # best score after iter 18 13.7617 bits/residue, 23 clashes, rmsd= 0 # best score after iter 19 13.7617 bits/residue, 23 clashes, rmsd= 0 # command:# naming current conformation t113-opt-rot-opt-rot # command:# command:# ScwrlConform produces command scwrl -i /projects/compbio/tmp/to_scwrl_1905062737.pdb -s /projects/compbio/tmp/to_scwrl_1905062737.seq -o /projects/compbio/tmp/from_scwrl_1905062737.pdb > /projects/compbio/tmp/scwrl.log # conformation set from SCWRL output # command:# naming current conformation t113-opt-rot-opt-scwrl # command:# command:# ScoreConform t113-rand -log2(score)= 13382.3 (51.2731 bits/residue) 262 clashes 0 breaks t113-2hsdA -log2(score)= 21997.1 (84.2803 bits/residue) 202 clashes 134.367 breaks t113-opt -log2(score)= 6638.6 (25.4353 bits/residue) 41 clashes 55.0162 breaks t113-opt-rot -log2(score)= 7389.83 (28.3135 bits/residue) 46 clashes 55.0162 breaks t113-opt -log2(score)= 5037.34 (19.3001 bits/residue) 27 clashes 27.1654 breaks t113-opt-rot-opt-rot -log2(score)= 3591.79 (13.7617 bits/residue) 23 clashes 27.1654 breaks t113-opt-rot-opt-scwrl -log2(score)= 3612.64 (13.8415 bits/residue) 36 clashes 0 breaks # command: