# command:# Prefix for input files set to /projects/compbio/experiments/undertaker/atoms-inputs/ # command:# reading cullpdb_pc80_res1.2_R0.2_d070810_chains408.atoms.gz # #computed average backbone with maximum peptide_sq_deviance = 0.002 # computed average trans backbone unit from 1600 examples # computed average trans backbone unit before proline from 52 examples # trans (non-proline) backbone unit: # CA= -2.2097 1.0151 -0.0046 # O= -0.1488 2.2425 0.0020 # C= -0.6903 1.1357 0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4580 -0.0000 -0.0000 # cis backbone unit: # CA= -0.1462 2.4515 0.0018 # O= -2.0272 0.9713 0.0022 # C= -0.8006 1.0755 0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4659 0.0000 0.0000 # trans backbone unit before proline: # CA= -2.2063 1.0654 0.0002 # O= -0.1193 2.2442 0.0054 # C= -0.6842 1.1479 -0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4661 -0.0000 0.0000 # After reading cullpdb_pc80_res1.2_R0.2_d070810_chains408.atoms.gz have 408 chains in training database # Count of chains,residues,atoms: 408,82794,639987 # 79931 residues have no bad marker # 573 residues lack atoms needed to compute omega # 313 residues have cis peptide # number of each bad type: # NON_STANDARD_RESIDUE 0 # HAS_OXT 264 # TOO_MANY_ATOMS 0 # TOO_FEW_ATOMS 378 # HAS_UNKNOWN_ATOMS 0 # HAS_DUPLICATE_ATOMS 0 # CHAIN_BREAK_BEFORE 148 # NON_PLANAR_PEPTIDE 17 # BAD_PEPTIDE 812 # HIGH_B_FACTOR 1566 # Note: may sum to more than number of residues, # because one residue may have multiple problems # command:# Reading rotamer library from dunbrack-40pc-3157.rot # command:# Prefix for input files set to /projects/compbio/experiments/undertaker/spots/ # command:# ReadAtomType exp-pdb.types Read AtomType exp-pdb with 49 types. # command:# ReadClashTable exp-pdb-2191-2symm.clash # Read ClashTable exp-pdb-2191-2symm checking bonds symmetric at MaxSep 2 # command:# command:# Prefix for input files set to # command:# Making conformation for sequence T0581 numbered 1 through 136 Created new target T0581 from T0581.a2m # command:CPU_time= 5.753 sec, elapsed time= 10.594 sec. # command:# reading script from file all-templates.under # Reading fragments from alignment file # Attempting to read fragment alignments from file 3lfkA/T0581-3lfkA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 3lfkA expands to /projects/compbio/data/pdb/3lfk.pdb.gz 3lfkA:# T0581 read from 3lfkA/T0581-3lfkA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3lfkA read from 3lfkA/T0581-3lfkA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3lfkA to template set # found chain 3lfkA in template set T0581 7 :LALCFVLPTAAHAAS 3lfkA 36 :VSLLLFLKTHGGKIP # choosing archetypes in rotamer library T0581 31 :LEKVAKESSVGTPRAINEDILDQGYTVEGNQ 3lfkA 51 :LYRIKNETGLKDPESVLKNLMDYGFALEDKE T0581 64 :NHLSVRAS 3lfkA 85 :EKIVLTSE T0581 73 :AERMRSNPDSVRSQ 3lfkA 97 :AQAIRVRDEELRLK Number of specific fragments extracted= 4 number of extra gaps= 0 total=4 Will force an alignment to be made, even if fragment is small Number of alignments=1 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3lfkA/T0581-3lfkA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0581 read from 3lfkA/T0581-3lfkA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3lfkA read from 3lfkA/T0581-3lfkA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3lfkA in template set T0581 6 :ALALCFVLPTAAHAASL 3lfkA 35 :EVSLLLFLKTHGGKIPL T0581 32 :EKVAKESSVGTPRAINEDILDQGYTVEGNQ 3lfkA 52 :YRIKNETGLKDPESVLKNLMDYGFALEDKE T0581 62 :LINHLSVRASHAERMRSNPDSVRS 3lfkA 86 :KIVLTSEGEFVAQAIRVRDEELRL Number of specific fragments extracted= 3 number of extra gaps= 0 total=7 Will force an alignment to be made, even if fragment is small Number of alignments=2 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3lfkA/T0581-3lfkA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0581 read from 3lfkA/T0581-3lfkA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3lfkA read from 3lfkA/T0581-3lfkA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3lfkA in template set T0581 5 :MALALCFVLPTAAHAAS 3lfkA 34 :DEVSLLLFLKTHGGKIP T0581 31 :LEKVAKESSVGTPRAINEDILDQGYTVEGNQ 3lfkA 51 :LYRIKNETGLKDPESVLKNLMDYGFALEDKE T0581 62 :LINHLSVRASHAERMRSNPDSVRS 3lfkA 86 :KIVLTSEGEFVAQAIRVRDEELRL Number of specific fragments extracted= 3 number of extra gaps= 0 total=10 Will force an alignment to be made, even if fragment is small Number of alignments=3 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1gp8A/T0581-1gp8A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1gp8A expands to /projects/compbio/data/pdb/1gp8.pdb.gz 1gp8A:# T0581 read from 1gp8A/T0581-1gp8A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1gp8A read from 1gp8A/T0581-1gp8A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1gp8A to template set # found chain 1gp8A in template set T0581 22 :LKDFELSKMLE 1gp8A 271 :ANKDAIRKQMD T0581 36 :KESSVGT 1gp8A 282 :AAASKGD T0581 70 :ASHAERMRSNP 1gp8A 289 :VETYRKLKAKL Number of specific fragments extracted= 3 number of extra gaps= 0 total=13 Will force an alignment to be made, even if fragment is small Number of alignments=4 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1gp8A/T0581-1gp8A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0581 read from 1gp8A/T0581-1gp8A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1gp8A read from 1gp8A/T0581-1gp8A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1gp8A in template set T0581 22 :LKDFELSKMLEKVA 1gp8A 271 :ANKDAIRKQMDAAA T0581 39 :SVG 1gp8A 285 :SKG T0581 69 :RASHAERMRSNP 1gp8A 288 :DVETYRKLKAKL Number of specific fragments extracted= 3 number of extra gaps= 0 total=16 Will force an alignment to be made, even if fragment is small Number of alignments=5 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1gp8A/T0581-1gp8A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0581 read from 1gp8A/T0581-1gp8A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1gp8A read from 1gp8A/T0581-1gp8A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1gp8A in template set T0581 22 :LKDFELSKMLEKVA 1gp8A 271 :ANKDAIRKQMDAAA T0581 39 :SVG 1gp8A 285 :SKG T0581 69 :RASHAERMRSNP 1gp8A 288 :DVETYRKLKAKL Number of specific fragments extracted= 3 number of extra gaps= 0 total=19 Will force an alignment to be made, even if fragment is small Number of alignments=6 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2qswA/T0581-2qswA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2qswA expands to /projects/compbio/data/pdb/2qsw.pdb.gz 2qswA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 68, because occupancy 0.5 <= existing 0.500 in 2qswA Skipped atom 72, because occupancy 0.500 <= existing 0.500 in 2qswA Skipped atom 74, because occupancy 0.500 <= existing 0.500 in 2qswA Skipped atom 76, because occupancy 0.500 <= existing 0.500 in 2qswA Skipped atom 78, because occupancy 0.500 <= existing 0.500 in 2qswA Skipped atom 80, because occupancy 0.500 <= existing 0.500 in 2qswA Skipped atom 83, because occupancy 0.400 <= existing 0.600 in 2qswA Skipped atom 87, because occupancy 0.400 <= existing 0.600 in 2qswA Skipped atom 89, because occupancy 0.400 <= existing 0.600 in 2qswA Skipped atom 91, because occupancy 0.400 <= existing 0.600 in 2qswA Skipped atom 93, because occupancy 0.400 <= existing 0.600 in 2qswA Skipped atom 95, because occupancy 0.400 <= existing 0.600 in 2qswA Skipped atom 97, because occupancy 0.400 <= existing 0.600 in 2qswA Skipped atom 99, because occupancy 0.400 <= existing 0.600 in 2qswA Skipped atom 101, because occupancy 0.400 <= existing 0.600 in 2qswA Skipped atom 246, because occupancy 0.500 <= existing 0.500 in 2qswA Skipped atom 250, because occupancy 0.500 <= existing 0.500 in 2qswA Skipped atom 252, because occupancy 0.500 <= existing 0.500 in 2qswA Skipped atom 254, because occupancy 0.500 <= existing 0.500 in 2qswA Skipped atom 256, because occupancy 0.500 <= existing 0.500 in 2qswA Skipped atom 283, because occupancy 0.500 <= existing 0.500 in 2qswA Skipped atom 287, because occupancy 0.500 <= existing 0.500 in 2qswA Skipped atom 289, because occupancy 0.500 <= existing 0.500 in 2qswA Skipped atom 291, because occupancy 0.500 <= existing 0.500 in 2qswA Skipped atom 293, because occupancy 0.500 <= existing 0.500 in 2qswA Skipped atom 303, because occupancy 0.300 <= existing 0.700 in 2qswA Skipped atom 307, because occupancy 0.300 <= existing 0.700 in 2qswA Skipped atom 309, because occupancy 0.300 <= existing 0.700 in 2qswA Skipped atom 311, because occupancy 0.300 <= existing 0.700 in 2qswA Skipped atom 313, because occupancy 0.300 <= existing 0.700 in 2qswA Skipped atom 315, because occupancy 0.300 <= existing 0.700 in 2qswA Skipped atom 355, because occupancy 0.400 <= existing 0.600 in 2qswA Skipped atom 359, because occupancy 0.400 <= existing 0.600 in 2qswA Skipped atom 361, because occupancy 0.400 <= existing 0.600 in 2qswA Skipped atom 363, because occupancy 0.400 <= existing 0.600 in 2qswA Skipped atom 365, because occupancy 0.400 <= existing 0.600 in 2qswA Skipped atom 367, because occupancy 0.400 <= existing 0.600 in 2qswA Skipped atom 399, because occupancy 0.400 <= existing 0.600 in 2qswA Skipped atom 403, because occupancy 0.400 <= existing 0.600 in 2qswA Skipped atom 405, because occupancy 0.400 <= existing 0.600 in 2qswA Skipped atom 407, because occupancy 0.400 <= existing 0.600 in 2qswA Skipped atom 409, because occupancy 0.400 <= existing 0.600 in 2qswA Skipped atom 411, because occupancy 0.400 <= existing 0.600 in 2qswA Skipped atom 426, because occupancy 0.500 <= existing 0.500 in 2qswA Skipped atom 430, because occupancy 0.500 <= existing 0.500 in 2qswA Skipped atom 432, because occupancy 0.500 <= existing 0.500 in 2qswA Skipped atom 434, because occupancy 0.500 <= existing 0.500 in 2qswA Skipped atom 436, because occupancy 0.500 <= existing 0.500 in 2qswA Skipped atom 448, because occupancy 0.400 <= existing 0.600 in 2qswA Skipped atom 452, because occupancy 0.400 <= existing 0.600 in 2qswA Skipped atom 454, because occupancy 0.400 <= existing 0.600 in 2qswA Skipped atom 456, because occupancy 0.400 <= existing 0.600 in 2qswA Skipped atom 458, because occupancy 0.400 <= existing 0.600 in 2qswA Skipped atom 460, because occupancy 0.400 <= existing 0.600 in 2qswA Skipped atom 479, because occupancy 0.400 <= existing 0.600 in 2qswA Skipped atom 483, because occupancy 0.400 <= existing 0.600 in 2qswA Skipped atom 485, because occupancy 0.400 <= existing 0.600 in 2qswA Skipped atom 487, because occupancy 0.400 <= existing 0.600 in 2qswA Skipped atom 489, because occupancy 0.400 <= existing 0.600 in 2qswA Skipped atom 491, because occupancy 0.400 <= existing 0.600 in 2qswA Skipped atom 520, because occupancy 0.500 <= existing 0.500 in 2qswA Skipped atom 524, because occupancy 0.500 <= existing 0.500 in 2qswA Skipped atom 526, because occupancy 0.500 <= existing 0.500 in 2qswA Skipped atom 528, because occupancy 0.500 <= existing 0.500 in 2qswA Skipped atom 530, because occupancy 0.500 <= existing 0.500 in 2qswA Skipped atom 582, because occupancy 0.400 <= existing 0.600 in 2qswA Skipped atom 586, because occupancy 0.400 <= existing 0.600 in 2qswA Skipped atom 588, because occupancy 0.400 <= existing 0.600 in 2qswA Skipped atom 590, because occupancy 0.400 <= existing 0.600 in 2qswA Skipped atom 592, because occupancy 0.400 <= existing 0.600 in 2qswA Skipped atom 594, because occupancy 0.400 <= existing 0.600 in 2qswA Skipped atom 606, because occupancy 0.500 <= existing 0.500 in 2qswA Skipped atom 610, because occupancy 0.500 <= existing 0.500 in 2qswA Skipped atom 612, because occupancy 0.500 <= existing 0.500 in 2qswA Skipped atom 614, because occupancy 0.500 <= existing 0.500 in 2qswA Skipped atom 616, because occupancy 0.500 <= existing 0.500 in 2qswA Skipped atom 618, because occupancy 0.500 <= existing 0.500 in 2qswA Skipped atom 621, because occupancy 0.300 <= existing 0.700 in 2qswA Skipped atom 625, because occupancy 0.300 <= existing 0.700 in 2qswA Skipped atom 627, because occupancy 0.300 <= existing 0.700 in 2qswA Skipped atom 629, because occupancy 0.300 <= existing 0.700 in 2qswA Skipped atom 631, because occupancy 0.300 <= existing 0.700 in 2qswA Skipped atom 689, because occupancy 0.500 <= existing 0.500 in 2qswA Skipped atom 693, because occupancy 0.500 <= existing 0.500 in 2qswA Skipped atom 695, because occupancy 0.500 <= existing 0.500 in 2qswA Skipped atom 697, because occupancy 0.500 <= existing 0.500 in 2qswA Skipped atom 699, because occupancy 0.500 <= existing 0.500 in 2qswA Skipped atom 701, because occupancy 0.500 <= existing 0.500 in 2qswA Skipped atom 703, because occupancy 0.500 <= existing 0.500 in 2qswA Skipped atom 705, because occupancy 0.500 <= existing 0.500 in 2qswA # T0581 read from 2qswA/T0581-2qswA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2qswA read from 2qswA/T0581-2qswA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2qswA to template set # found chain 2qswA in template set T0581 107 :LTYSFTEYKTNQPVATERFDAGSCRI 2qswA 271 :VRLLFHGEQAKLPIISHIVQEYQVEV Number of specific fragments extracted= 1 number of extra gaps= 0 total=20 Will force an alignment to be made, even if fragment is small Number of alignments=7 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2qswA/T0581-2qswA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0581 read from 2qswA/T0581-2qswA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2qswA read from 2qswA/T0581-2qswA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2qswA in template set T0581 81 :DSVRSQLG 2qswA 259 :EEMLEQYP T0581 103 :RGAILTYSFTEYKTNQPVATERFDAGSCRI 2qswA 267 :NGKIVRLLFHGEQAKLPIISHIVQEYQVEV Number of specific fragments extracted= 2 number of extra gaps= 0 total=22 Will force an alignment to be made, even if fragment is small Number of alignments=8 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2qswA/T0581-2qswA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0581 read from 2qswA/T0581-2qswA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2qswA read from 2qswA/T0581-2qswA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2qswA in template set T0581 103 :RGAILTYSFTEYKTNQPVATERFDAGSCRI 2qswA 267 :NGKIVRLLFHGEQAKLPIISHIVQEYQVEV Number of specific fragments extracted= 1 number of extra gaps= 0 total=23 Will force an alignment to be made, even if fragment is small Number of alignments=9 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3cqbA/T0581-3cqbA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 3cqbA expands to /projects/compbio/data/pdb/3cqb.pdb.gz 3cqbA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 119, because occupancy 0.500 <= existing 0.500 in 3cqbA Skipped atom 121, because occupancy 0.500 <= existing 0.500 in 3cqbA Skipped atom 123, because occupancy 0.500 <= existing 0.500 in 3cqbA Skipped atom 125, because occupancy 0.500 <= existing 0.500 in 3cqbA Skipped atom 127, because occupancy 0.500 <= existing 0.500 in 3cqbA Skipped atom 129, because occupancy 0.500 <= existing 0.500 in 3cqbA Skipped atom 222, because occupancy 0.500 <= existing 0.500 in 3cqbA Skipped atom 224, because occupancy 0.500 <= existing 0.500 in 3cqbA Skipped atom 226, because occupancy 0.500 <= existing 0.500 in 3cqbA Skipped atom 228, because occupancy 0.500 <= existing 0.500 in 3cqbA Skipped atom 230, because occupancy 0.500 <= existing 0.500 in 3cqbA Skipped atom 232, because occupancy 0.500 <= existing 0.500 in 3cqbA Skipped atom 234, because occupancy 0.500 <= existing 0.500 in 3cqbA Skipped atom 236, because occupancy 0.500 <= existing 0.500 in 3cqbA Skipped atom 238, because occupancy 0.500 <= existing 0.500 in 3cqbA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0581 read from 3cqbA/T0581-3cqbA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3cqbA read from 3cqbA/T0581-3cqbA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3cqbA to template set # found chain 3cqbA in template set Warning: unaligning (T0581)Q61 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (3cqbA)D62 Warning: unaligning (T0581)N64 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (3cqbA)D62 T0581 22 :LKDFELSKMLEKVAKESSVGTPR 3cqbA 20 :ETEHWLLETVGRQAQQAGIGMPT T0581 52 :DQGYTVEGN 3cqbA 50 :DINAFATGA T0581 65 :HLSVRASHAERM 3cqbA 64 :LVAVSTGLLHNM T0581 79 :NPDSVRSQLGD 3cqbA 76 :TRDEAEAVLAH T0581 97 :YRQLLARGAILTYSFT 3cqbA 87 :EVSHIANGDMVTMTLM Number of specific fragments extracted= 5 number of extra gaps= 0 total=28 Will force an alignment to be made, even if fragment is small Number of alignments=10 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3cqbA/T0581-3cqbA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0581 read from 3cqbA/T0581-3cqbA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3cqbA read from 3cqbA/T0581-3cqbA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3cqbA in template set T0581 21 :SLKDFELSKMLEKVAKESSVGTPR 3cqbA 19 :NETEHWLLETVGRQAQQAGIGMPT T0581 55 :YTVEGNQLIN 3cqbA 43 :VAIYDSADIN T0581 65 :HLSVRASHAERM 3cqbA 64 :LVAVSTGLLHNM T0581 79 :NPDSVRSQLGD 3cqbA 76 :TRDEAEAVLAH T0581 97 :YRQLLARGAILTYSFT 3cqbA 87 :EVSHIANGDMVTMTLM Number of specific fragments extracted= 5 number of extra gaps= 0 total=33 Will force an alignment to be made, even if fragment is small Number of alignments=11 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3cqbA/T0581-3cqbA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0581 read from 3cqbA/T0581-3cqbA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3cqbA read from 3cqbA/T0581-3cqbA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3cqbA in template set Warning: unaligning (T0581)Q61 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (3cqbA)D62 Warning: unaligning (T0581)N64 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (3cqbA)D62 T0581 21 :SLKDFELSKMLEKVAKESSVGTPR 3cqbA 19 :NETEHWLLETVGRQAQQAGIGMPT T0581 52 :DQGYTVEGN 3cqbA 50 :DINAFATGA T0581 65 :HLSVRASHAERM 3cqbA 64 :LVAVSTGLLHNM T0581 79 :NPDSVRSQLGD 3cqbA 76 :TRDEAEAVLAH T0581 97 :YRQLLARGAILTYSFT 3cqbA 87 :EVSHIANGDMVTMTLM Number of specific fragments extracted= 5 number of extra gaps= 0 total=38 Will force an alignment to be made, even if fragment is small Number of alignments=12 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3chxA/T0581-3chxA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 3chxA expands to /projects/compbio/data/pdb/3chx.pdb.gz 3chxA:# T0581 read from 3chxA/T0581-3chxA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3chxA read from 3chxA/T0581-3chxA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3chxA to template set # found chain 3chxA in template set T0581 25 :FELSKMLEKVAKESSV 3chxA 247 :LAVTILATIIGYAVTN Number of specific fragments extracted= 1 number of extra gaps= 0 total=39 Will force an alignment to be made, even if fragment is small Number of alignments=13 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3chxA/T0581-3chxA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0581 read from 3chxA/T0581-3chxA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3chxA read from 3chxA/T0581-3chxA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3chxA in template set T0581 21 :SLKDFELSKMLEKVAKESSV 3chxA 243 :GAIVLAVTILATIIGYAVTN Number of specific fragments extracted= 1 number of extra gaps= 0 total=40 Will force an alignment to be made, even if fragment is small Number of alignments=14 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3chxA/T0581-3chxA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0581 read from 3chxA/T0581-3chxA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3chxA read from 3chxA/T0581-3chxA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3chxA in template set T0581 21 :SLKDFELSKMLEKVAKES 3chxA 243 :GAIVLAVTILATIIGYAV Number of specific fragments extracted= 1 number of extra gaps= 0 total=41 Will force an alignment to be made, even if fragment is small Number of alignments=15 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2k3cA/T0581-2k3cA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2k3cA expands to /projects/compbio/data/pdb/2k3c.pdb.gz 2k3cA:# T0581 read from 2k3cA/T0581-2k3cA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2k3cA read from 2k3cA/T0581-2k3cA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2k3cA to template set # found chain 2k3cA in template set T0581 125 :FDAGSCRIQGK 2k3cA 354 :MALIASGVVMR Number of specific fragments extracted= 1 number of extra gaps= 0 total=42 Will force an alignment to be made, even if fragment is small Number of alignments=16 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2k3cA/T0581-2k3cA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0581 read from 2k3cA/T0581-2k3cA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2k3cA read from 2k3cA/T0581-2k3cA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2k3cA in template set T0581 126 :DAGSCRIQG 2k3cA 355 :ALIASGVVM Number of specific fragments extracted= 1 number of extra gaps= 0 total=43 Will force an alignment to be made, even if fragment is small Number of alignments=17 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2k3cA/T0581-2k3cA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0581 read from 2k3cA/T0581-2k3cA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2k3cA read from 2k3cA/T0581-2k3cA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2k3cA in template set Number of specific fragments extracted= 0 number of extra gaps= 0 total=43 Will force an alignment to be made, even if fragment is small # Reading fragments from alignment file # Attempting to read fragment alignments from file 2ko6A/T0581-2ko6A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2ko6A expands to /projects/compbio/data/pdb/2ko6.pdb.gz 2ko6A:# T0581 read from 2ko6A/T0581-2ko6A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2ko6A read from 2ko6A/T0581-2ko6A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2ko6A to template set # found chain 2ko6A in template set T0581 23 :KDFELSKMLEKVAKESS 2ko6A 21 :PDFNLLQFLQKLAKESG T0581 40 :VGTPRAINEDIL 2ko6A 39 :DGELADLTDDIL Number of specific fragments extracted= 2 number of extra gaps= 0 total=45 Will force an alignment to be made, even if fragment is small Number of alignments=18 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2ko6A/T0581-2ko6A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0581 read from 2ko6A/T0581-2ko6A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2ko6A read from 2ko6A/T0581-2ko6A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2ko6A in template set T0581 22 :LKDFELSKMLEKVAKESS 2ko6A 20 :EPDFNLLQFLQKLAKESG T0581 40 :VGTPRAINEDIL 2ko6A 39 :DGELADLTDDIL Number of specific fragments extracted= 2 number of extra gaps= 0 total=47 Will force an alignment to be made, even if fragment is small Number of alignments=19 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2ko6A/T0581-2ko6A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0581 read from 2ko6A/T0581-2ko6A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2ko6A read from 2ko6A/T0581-2ko6A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2ko6A in template set T0581 21 :SLKDFELSKMLEKVAKESS 2ko6A 19 :KEPDFNLLQFLQKLAKESG T0581 40 :VGTPRAINEDIL 2ko6A 39 :DGELADLTDDIL Number of specific fragments extracted= 2 number of extra gaps= 0 total=49 Will force an alignment to be made, even if fragment is small Number of alignments=20 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3cedA/T0581-3cedA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 3cedA expands to /projects/compbio/data/pdb/3ced.pdb.gz 3cedA:Skipped atom 294, because occupancy 0.500 <= existing 0.500 in 3cedA Skipped atom 296, because occupancy 0.500 <= existing 0.500 in 3cedA Skipped atom 298, because occupancy 0.500 <= existing 0.500 in 3cedA Skipped atom 300, because occupancy 0.500 <= existing 0.500 in 3cedA Skipped atom 302, because occupancy 0.500 <= existing 0.500 in 3cedA Skipped atom 304, because occupancy 0.500 <= existing 0.500 in 3cedA Skipped atom 579, because occupancy 0.500 <= existing 0.500 in 3cedA Skipped atom 581, because occupancy 0.500 <= existing 0.500 in 3cedA Skipped atom 583, because occupancy 0.500 <= existing 0.500 in 3cedA Skipped atom 585, because occupancy 0.500 <= existing 0.500 in 3cedA Skipped atom 587, because occupancy 0.500 <= existing 0.500 in 3cedA Skipped atom 589, because occupancy 0.500 <= existing 0.500 in 3cedA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0581 read from 3cedA/T0581-3cedA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3cedA read from 3cedA/T0581-3cedA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3cedA to template set # found chain 3cedA in template set T0581 29 :KMLEKVAKESSV 3cedA 278 :PIVSSLSTAYDI T0581 47 :NEDILDQGYTVEGNQLINHLSV 3cedA 290 :KINILEANIKNTKNGTVGFLVL T0581 69 :RASHAERMRSN 3cedA 317 :SSVDFGKFEKE T0581 100 :LLARGA 3cedA 328 :LIERQV Number of specific fragments extracted= 4 number of extra gaps= 0 total=53 Will force an alignment to be made, even if fragment is small Number of alignments=21 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3cedA/T0581-3cedA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0581 read from 3cedA/T0581-3cedA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3cedA read from 3cedA/T0581-3cedA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3cedA in template set T0581 28 :SKMLEKVAKESSV 3cedA 277 :EPIVSSLSTAYDI T0581 47 :NEDILDQGYTVEGNQ 3cedA 290 :KINILEANIKNTKNG T0581 62 :LINHLSVRASHAERMRSNPD 3cedA 310 :VLHIPYISSVDFGKFEKELI Number of specific fragments extracted= 3 number of extra gaps= 0 total=56 Will force an alignment to be made, even if fragment is small Number of alignments=22 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3cedA/T0581-3cedA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0581 read from 3cedA/T0581-3cedA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3cedA read from 3cedA/T0581-3cedA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3cedA in template set T0581 28 :SKMLEKVAKESSV 3cedA 277 :EPIVSSLSTAYDI T0581 47 :NEDILDQGYTVEGNQLINHLSV 3cedA 290 :KINILEANIKNTKNGTVGFLVL T0581 69 :RASHAERMRSNP 3cedA 317 :SSVDFGKFEKEL Number of specific fragments extracted= 3 number of extra gaps= 0 total=59 Will force an alignment to be made, even if fragment is small Number of alignments=23 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3fppA/T0581-3fppA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 3fppA expands to /projects/compbio/data/pdb/3fpp.pdb.gz 3fppA:# T0581 read from 3fppA/T0581-3fppA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3fppA read from 3fppA/T0581-3fppA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3fppA to template set # found chain 3fppA in template set T0581 18 :HAASLKDFELS 3fppA 115 :RQQAEAELKLA T0581 29 :KMLEKVAKESSVGT 3fppA 127 :VTYSRQQRLAQTQA T0581 68 :VRASHAERMRSNPDSVRSQLGD 3fppA 141 :VSQQDLDNAATEMAVKQAQIGT Number of specific fragments extracted= 3 number of extra gaps= 0 total=62 Will force an alignment to be made, even if fragment is small Number of alignments=24 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3fppA/T0581-3fppA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0581 read from 3fppA/T0581-3fppA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3fppA read from 3fppA/T0581-3fppA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3fppA in template set T0581 17 :AHAASLKDFELSKMLEKVAKESSV 3fppA 108 :LMELRAQRQQAEAELKLARVTYSR T0581 47 :NEDILDQG 3fppA 132 :QQRLAQTQ T0581 67 :SVRASHAERMRSNPDSVRSQLG 3fppA 140 :AVSQQDLDNAATEMAVKQAQIG Number of specific fragments extracted= 3 number of extra gaps= 0 total=65 Will force an alignment to be made, even if fragment is small Number of alignments=25 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3fppA/T0581-3fppA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0581 read from 3fppA/T0581-3fppA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3fppA read from 3fppA/T0581-3fppA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3fppA in template set T0581 14 :PTAAHAASLKDFELSKMLEKVAKESSV 3fppA 105 :EATLMELRAQRQQAEAELKLARVTYSR T0581 47 :NEDILDQG 3fppA 132 :QQRLAQTQ T0581 67 :SVRASHAERMRSNPDSVRSQLGD 3fppA 140 :AVSQQDLDNAATEMAVKQAQIGT Number of specific fragments extracted= 3 number of extra gaps= 0 total=68 Will force an alignment to be made, even if fragment is small Number of alignments=26 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ede/T0581-1ede-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1ede expands to /projects/compbio/data/pdb/1ede.pdb.gz 1ede:Warning: there is no chain 1ede will retry with 1edeA # T0581 read from 1ede/T0581-1ede-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ede read from 1ede/T0581-1ede-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1ede to template set # found chain 1ede in template set Number of specific fragments extracted= 0 number of extra gaps= 0 total=68 Will force an alignment to be made, even if fragment is small # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ede/T0581-1ede-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0581 read from 1ede/T0581-1ede-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ede read from 1ede/T0581-1ede-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1ede in template set T0581 9 :LCFVLPTAAHAASL 1ede 218 :GVRKFPKMVAQRDQ T0581 26 :ELSKMLEKVAKES 1ede 232 :ACIDISTEAISFW Number of specific fragments extracted= 2 number of extra gaps= 0 total=70 Will force an alignment to be made, even if fragment is small Number of alignments=27 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ede/T0581-1ede-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0581 read from 1ede/T0581-1ede-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ede read from 1ede/T0581-1ede-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1ede in template set T0581 8 :ALCFVLPTAAHAAS 1ede 217 :AGVRKFPKMVAQRD T0581 25 :FELSKMLEKVAKES 1ede 231 :QACIDISTEAISFW Number of specific fragments extracted= 2 number of extra gaps= 0 total=72 Will force an alignment to be made, even if fragment is small Number of alignments=28 # command:CPU_time= 9.580 sec, elapsed time= 22.120 sec. # command:DEBUG: alignment library has 28 conformations DEBUG: current conformations has 0 conformations # in ExtractAlignmentsContacts extracting from alignment library using radius 8.000 separation >= 9 style evalue NUMB_ALIGNS: 28 # Adding 432 constraints to all_contacts Done adding distance constraints # command:CPU_time= 9.598 sec, elapsed time= 22.138 sec. # command:Reading probabilities from T0581.t06.CB8-sep9.rdb Reading constraints from ConstraintSet all_contacts maxweight: 3.902 Optimizing... Probability sum: -285.310, CN propb: -285.310 weights: 0.370 constraints: 168 # command:CPU_time= 10.557 sec, elapsed time= 23.187 sec. # command:Found ConstraintSet # PrintContacts align.constraints Number of constraints in align 168 # command:Found ConstraintSet # PrintContacts align_bonus.constraints Number of constraints in align.bonus 168 # command:Found ConstraintSet # PrintContacts rejected.constraints Number of constraints in rejected 264 # command:Found ConstraintSet # PrintContacts rejected_bonus.constraints Number of constraints in rejected.bonus 264 # command:Found ConstraintSet # PrintContacts noncontact.constraints Number of constraints in noncontact 0 # command:Found ConstraintSet # PrintContacts noncontact_bonus.constraints Number of constraints in noncontact.bonus 0 # command:CPU_time= 10.563 sec, elapsed time= 24.469 sec. # command: