# 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: 408,82795,639989 # 81291 residues have no bad marker # 565 residues lack atoms needed to compute omega # 313 residues have cis peptide # number of each bad type: # NON_STANDARD_RESIDUE 1 # HAS_OXT 265 # TOO_MANY_ATOMS 0 # TOO_FEW_ATOMS 378 # HAS_UNKNOWN_ATOMS 0 # HAS_DUPLICATE_ATOMS 0 # CHAIN_BREAK_BEFORE 139 # NON_PLANAR_PEPTIDE 424 # BAD_PEPTIDE 803 # 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 T0369 numbered 1 through 148 Created new target T0369 from T0369.a2m # command:CPU_time= 6.317 sec, elapsed time= 6.369 sec. # command:# reading script from file all-templates.under # Reading fragments from alignment file # Attempting to read fragment alignments from file 2f22A/T0369-2f22A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2f22A expands to /projects/compbio/data/pdb/2f22.pdb.gz 2f22A:Skipped atom 2, because occupancy 0.5 <= existing 0.500 in 2f22A Skipped atom 4, because occupancy 0.500 <= existing 0.500 in 2f22A Skipped atom 6, because occupancy 0.500 <= existing 0.500 in 2f22A Skipped atom 8, because occupancy 0.500 <= existing 0.500 in 2f22A 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 11, because occupancy 0.500 <= existing 0.500 in 2f22A 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 15, because occupancy 0.500 <= existing 0.500 in 2f22A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 17, because occupancy 0.500 <= existing 0.500 in 2f22A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 19, because occupancy 0.350 <= existing 0.400 in 2f22A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 21, because occupancy 0.500 <= existing 0.500 in 2f22A Skipped atom 88, because occupancy 0.500 <= existing 0.500 in 2f22A Skipped atom 92, because occupancy 0.500 <= existing 0.500 in 2f22A Skipped atom 94, because occupancy 0.500 <= existing 0.500 in 2f22A Skipped atom 96, because occupancy 0.500 <= existing 0.500 in 2f22A Skipped atom 98, because occupancy 0.500 <= existing 0.500 in 2f22A 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 102, because occupancy 0.330 <= existing 0.340 in 2f22A 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 107, because occupancy 0.330 <= existing 0.340 in 2f22A 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 110, because occupancy 0.330 <= existing 0.340 in 2f22A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 112, because occupancy 0.250 <= existing 0.250 in 2f22A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 113, because occupancy 0.250 <= existing 0.250 in 2f22A 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 116, because occupancy 0.330 <= existing 0.340 in 2f22A Skipped atom 161, because occupancy 0.500 <= existing 0.500 in 2f22A Skipped atom 165, because occupancy 0.500 <= existing 0.500 in 2f22A Skipped atom 167, because occupancy 0.500 <= existing 0.500 in 2f22A Skipped atom 169, because occupancy 0.500 <= existing 0.500 in 2f22A Skipped atom 171, because occupancy 0.500 <= existing 0.500 in 2f22A Skipped atom 173, because occupancy 0.500 <= existing 0.500 in 2f22A Skipped atom 176, because occupancy 0.500 <= existing 0.500 in 2f22A Skipped atom 180, because occupancy 0.500 <= existing 0.500 in 2f22A Skipped atom 182, because occupancy 0.500 <= existing 0.500 in 2f22A Skipped atom 184, because occupancy 0.500 <= existing 0.500 in 2f22A Skipped atom 186, because occupancy 0.500 <= existing 0.500 in 2f22A Skipped atom 211, because occupancy 0.500 <= existing 0.500 in 2f22A Skipped atom 215, because occupancy 0.500 <= existing 0.500 in 2f22A Skipped atom 217, because occupancy 0.500 <= existing 0.500 in 2f22A Skipped atom 219, because occupancy 0.500 <= existing 0.500 in 2f22A Skipped atom 221, because occupancy 0.500 <= existing 0.500 in 2f22A Skipped atom 223, because occupancy 0.500 <= existing 0.500 in 2f22A Skipped atom 483, because occupancy 0.500 <= existing 0.500 in 2f22A Skipped atom 487, because occupancy 0.500 <= existing 0.500 in 2f22A Skipped atom 489, because occupancy 0.500 <= existing 0.500 in 2f22A Skipped atom 491, because occupancy 0.500 <= existing 0.500 in 2f22A Skipped atom 493, because occupancy 0.500 <= existing 0.500 in 2f22A Skipped atom 495, because occupancy 0.500 <= existing 0.500 in 2f22A Skipped atom 634, because occupancy 0.400 <= existing 0.600 in 2f22A Skipped atom 638, because occupancy 0.400 <= existing 0.600 in 2f22A Skipped atom 640, because occupancy 0.400 <= existing 0.600 in 2f22A Skipped atom 642, because occupancy 0.400 <= existing 0.600 in 2f22A Skipped atom 644, because occupancy 0.400 <= existing 0.600 in 2f22A 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 864, because occupancy 0.500 <= existing 0.500 in 2f22A Skipped atom 866, because occupancy 0.500 <= existing 0.500 in 2f22A Skipped atom 868, because occupancy 0.500 <= existing 0.500 in 2f22A Skipped atom 870, because occupancy 0.500 <= existing 0.500 in 2f22A Skipped atom 881, because occupancy 0.500 <= existing 0.500 in 2f22A Skipped atom 885, because occupancy 0.500 <= existing 0.500 in 2f22A Skipped atom 887, because occupancy 0.500 <= existing 0.500 in 2f22A Skipped atom 889, because occupancy 0.500 <= existing 0.500 in 2f22A Skipped atom 891, because occupancy 0.500 <= existing 0.500 in 2f22A 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 1083, because occupancy 0.500 <= existing 0.500 in 2f22A Skipped atom 1087, because occupancy 0.500 <= existing 0.500 in 2f22A Skipped atom 1089, because occupancy 0.500 <= existing 0.500 in 2f22A Skipped atom 1091, because occupancy 0.500 <= existing 0.500 in 2f22A Skipped atom 1105, because occupancy 0.500 <= existing 0.500 in 2f22A Skipped atom 1109, because occupancy 0.500 <= existing 0.500 in 2f22A Skipped atom 1111, because occupancy 0.500 <= existing 0.500 in 2f22A Skipped atom 1149, because occupancy 0.500 <= existing 0.500 in 2f22A Skipped atom 1153, because occupancy 0.500 <= existing 0.500 in 2f22A Skipped atom 1155, because occupancy 0.500 <= existing 0.500 in 2f22A Skipped atom 1157, because occupancy 0.500 <= existing 0.500 in 2f22A Skipped atom 1159, because occupancy 0.500 <= existing 0.500 in 2f22A Skipped atom 1161, because occupancy 0.500 <= existing 0.500 in 2f22A Skipped atom 1164, because occupancy 0.500 <= existing 0.500 in 2f22A Skipped atom 1168, because occupancy 0.500 <= existing 0.500 in 2f22A Skipped atom 1170, because occupancy 0.500 <= existing 0.500 in 2f22A Skipped atom 1172, because occupancy 0.500 <= existing 0.500 in 2f22A Skipped atom 1174, because occupancy 0.500 <= existing 0.500 in 2f22A Skipped atom 1176, because occupancy 0.500 <= existing 0.500 in 2f22A # T0369 read from 2f22A/T0369-2f22A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2f22A read from 2f22A/T0369-2f22A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2f22A to template set # found chain 2f22A in template set T0369 12 :VGVGVRTTRDLIRLIQPEDWDKRPISGKRSVYEVAVHLAVLLEADLRIATGATADEMA 2f22A 6 :VLYAANMTNALAKEIPESKWDIQLIPELGTLRKLFIHIVRVRDVYRDGLKTGSIKFPG # choosing archetypes in rotamer library T0369 70 :QFYAVPVLPEQLVDRLDQSWQYYQDRL 2f22A 65 :LASDEHRLLDELERSMEELVFEFKQTT T0369 101 :STETTYWGVTDSTTGWLLEAAVHLYHHRSQLLDYLNLLGYDIK 2f22A 92 :FNSIKMGENYLSIMELLGTVIQHEGIHQGQYYVALKQSGINLP Number of specific fragments extracted= 3 number of extra gaps= 0 total=3 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 2f22A/T0369-2f22A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0369 read from 2f22A/T0369-2f22A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2f22A read from 2f22A/T0369-2f22A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2f22A in template set T0369 12 :VGVGVRTTRDLIRLIQPEDWDKRPISGKRSVYEVAVHLAVLLEADLRIATGATADEMAQFYAVPVLP 2f22A 6 :VLYAANMTNALAKEIPESKWDIQLIPELGTLRKLFIHIVRVRDVYRDGLKTGSIKFPGRLASDEHRL T0369 82 :VDRLDQSWQYYQDRLMA 2f22A 73 :LDELERSMEELVFEFKQ T0369 106 :YWG 2f22A 91 :TFN T0369 109 :VTDSTTGWLLEAAVHLYHHRSQLLDYLNLLGYDIK 2f22A 100 :NYLSIMELLGTVIQHEGIHQGQYYVALKQSGINLP Number of specific fragments extracted= 4 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 2f22A/T0369-2f22A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0369 read from 2f22A/T0369-2f22A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2f22A read from 2f22A/T0369-2f22A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2f22A in template set T0369 11 :HVGVGVRTTRDLIRLIQPEDWDKRPISGKRSVYEVAVHLAVLLEADLRIATGATADEMAQFY 2f22A 5 :GVLYAANMTNALAKEIPESKWDIQLIPELGTLRKLFIHIVRVRDVYRDGLKTGSIKFPGRLA T0369 73 :AVPVLPEQLVDRLDQSWQYYQD 2f22A 68 :DEHRLLDELERSMEELVFEFKQ T0369 101 :STE 2f22A 91 :TFN T0369 107 :WGVTDSTTGWLLEAAVHLYHHRSQLLDYLNLLGYDI 2f22A 98 :GENYLSIMELLGTVIQHEGIHQGQYYVALKQSGINL Number of specific fragments extracted= 4 number of extra gaps= 0 total=11 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 1rxqA/T0369-1rxqA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1rxqA expands to /projects/compbio/data/pdb/1rxq.pdb.gz 1rxqA:Skipped atom 145, because occupancy 0.500 <= existing 0.500 in 1rxqA Skipped atom 147, because occupancy 0.500 <= existing 0.500 in 1rxqA Skipped atom 149, because occupancy 0.500 <= existing 0.500 in 1rxqA Skipped atom 151, because occupancy 0.500 <= existing 0.500 in 1rxqA Skipped atom 153, because occupancy 0.500 <= existing 0.500 in 1rxqA Skipped atom 317, because occupancy 0.500 <= existing 0.500 in 1rxqA Skipped atom 319, because occupancy 0.500 <= existing 0.500 in 1rxqA Skipped atom 321, because occupancy 0.500 <= existing 0.500 in 1rxqA 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 366, because occupancy 0.500 <= existing 0.500 in 1rxqA Skipped atom 368, because occupancy 0.500 <= existing 0.500 in 1rxqA 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 571, because occupancy 0.500 <= existing 0.500 in 1rxqA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 573, because occupancy 0.500 <= existing 0.500 in 1rxqA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 575, because occupancy 0.500 <= existing 0.500 in 1rxqA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 577, because occupancy 0.500 <= existing 0.500 in 1rxqA Skipped atom 908, because occupancy 0.500 <= existing 0.500 in 1rxqA Skipped atom 910, because occupancy 0.500 <= existing 0.500 in 1rxqA Skipped atom 912, because occupancy 0.500 <= existing 0.500 in 1rxqA Skipped atom 914, because occupancy 0.500 <= existing 0.500 in 1rxqA 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 # T0369 read from 1rxqA/T0369-1rxqA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1rxqA read from 1rxqA/T0369-1rxqA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1rxqA to template set # found chain 1rxqA in template set Warning: unaligning (T0369)D141 because last residue in template chain is (1rxqA)S178 T0369 4 :WQQALDRHVGVGVRTTRDLIRLIQPEDWDKRPISGKRSVYEVAVHLAVLLEADLRI 1rxqA 23 :QKDKWIQVLEEVPAKLKQAVEVMTDSQLDTPYRDGGWTVRQVVHHLADSHMNSYIR T0369 60 :ATGATADEMA 1rxqA 90 :IRPYDEKAWS T0369 70 :QFYAVPVLPEQLVDRLDQSWQYYQDRLMADFSTETTYWGVTD 1rxqA 105 :KTADPSGSLALLQELHGRWTALLRTLTDQQFKRGFYHPDTKE T0369 112 :STTGWLLEAAVHLYHHRSQLLDYLNLLGY 1rxqA 149 :TLENALGLYVWHSHHHIAHITELSRRMGW Number of specific fragments extracted= 4 number of extra gaps= 0 total=15 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 1rxqA/T0369-1rxqA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0369 read from 1rxqA/T0369-1rxqA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1rxqA read from 1rxqA/T0369-1rxqA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1rxqA in template set Warning: unaligning (T0369)D141 because last residue in template chain is (1rxqA)S178 T0369 3 :DWQQALDRHVGVGVRTTRDLIRLIQPEDWDKRPISGKRSVYEVAVHLAVLLEADLRIAT 1rxqA 22 :EQKDKWIQVLEEVPAKLKQAVEVMTDSQLDTPYRDGGWTVRQVVHHLADSHMNSYIRFK T0369 68 :MAQFYAVPV 1rxqA 84 :TEETPAIRP T0369 77 :LPE 1rxqA 94 :DEK T0369 80 :QLVDRLDQSWQYYQDRLMADFSTETTYWGVTD 1rxqA 115 :LLQELHGRWTALLRTLTDQQFKRGFYHPDTKE T0369 112 :STTGWLLEAAVHLYHHRSQLLDYLNLLGY 1rxqA 149 :TLENALGLYVWHSHHHIAHITELSRRMGW Number of specific fragments extracted= 5 number of extra gaps= 0 total=20 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 1rxqA/T0369-1rxqA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0369 read from 1rxqA/T0369-1rxqA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1rxqA read from 1rxqA/T0369-1rxqA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1rxqA in template set Warning: unaligning (T0369)D141 because last residue in template chain is (1rxqA)S178 T0369 2 :TDWQQALDRHVGVGVRTTRDLIRLIQPEDWDKRPISGKRSVYEVAVHLAVLLEADLRIATGATADEMAQF 1rxqA 21 :KEQKDKWIQVLEEVPAKLKQAVEVMTDSQLDTPYRDGGWTVRQVVHHLADSHMNSYIRFKLSLTEETPAI T0369 73 :AVPVLPEQLVDRLDQSWQYYQDRLMADFSTE 1rxqA 108 :DPSGSLALLQELHGRWTALLRTLTDQQFKRG T0369 104 :TTYWGVTDSTTGWLLEAAVHLYHHRSQLLDYLNLLGY 1rxqA 141 :HPDTKEIITLENALGLYVWHSHHHIAHITELSRRMGW Number of specific fragments extracted= 3 number of extra gaps= 0 total=23 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 1sqgA/T0369-1sqgA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1sqgA expands to /projects/compbio/data/pdb/1sqg.pdb.gz 1sqgA:Skipped atom 364, because occupancy 0.500 <= existing 0.500 in 1sqgA Skipped atom 366, because occupancy 0.500 <= existing 0.500 in 1sqgA Skipped atom 368, because occupancy 0.500 <= existing 0.500 in 1sqgA Skipped atom 370, because occupancy 0.500 <= existing 0.500 in 1sqgA Skipped atom 372, because occupancy 0.500 <= existing 0.500 in 1sqgA Skipped atom 374, because occupancy 0.500 <= existing 0.500 in 1sqgA # T0369 read from 1sqgA/T0369-1sqgA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1sqgA read from 1sqgA/T0369-1sqgA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1sqgA to template set # found chain 1sqgA in template set T0369 4 :WQQALDRHVGVGVRTTRDL 1sqgA 40 :DKALLQELCFGVLRTLSQL T0369 23 :IRLI 1sqgA 62 :INKL T0369 31 :WDKRPISGKRSVYEVAV 1sqgA 66 :MARPMTGKQRTVHYLIM T0369 53 :LEADLRIATGATADEMA 1sqgA 83 :VGLYQLLYTRIPPHAAL T0369 70 :QFYAVPVLPEQLVDRLDQS 1sqgA 107 :IAIKRPQLKGLINGVLRQF T0369 89 :WQYYQDRLMADF 1sqgA 150 :LKRLQKAYPEQW T0369 101 :STETTYW 1sqgA 169 :NQRPPMW T0369 108 :GVTDSTTGWLLE 1sqgA 180 :RTHHSRDSWLAL T0369 135 :LNLLGYD 1sqgA 192 :LDEAGMK Number of specific fragments extracted= 9 number of extra gaps= 0 total=32 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 1sqgA/T0369-1sqgA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0369 read from 1sqgA/T0369-1sqgA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1sqgA read from 1sqgA/T0369-1sqgA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1sqgA in template set T0369 3 :DWQQALDRHVGVGVRTTRDL 1sqgA 39 :KDKALLQELCFGVLRTLSQL T0369 23 :IRLI 1sqgA 62 :INKL T0369 31 :WDKRPISGKRSV 1sqgA 66 :MARPMTGKQRTV T0369 48 :HLAVLLEADLRIATGATADE 1sqgA 78 :HYLIMVGLYQLLYTRIPPHA T0369 68 :MA 1sqgA 99 :LA T0369 70 :QFYAVPVLPEQLVDRLDQSWQYY 1sqgA 107 :IAIKRPQLKGLINGVLRQFQRQQ T0369 94 :DRLMADFSTETTYWG 1sqgA 130 :EELLAEFNASDARYL Number of specific fragments extracted= 7 number of extra gaps= 0 total=39 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 1sqgA/T0369-1sqgA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0369 read from 1sqgA/T0369-1sqgA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1sqgA read from 1sqgA/T0369-1sqgA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1sqgA in template set T0369 2 :TDWQQALDRHVGVGVRTTRDLIRLI 1sqgA 41 :KALLQELCFGVLRTLSQLDWLINKL T0369 33 :KRPISGKRSVYEVAVHLAVLLEADLRIATGATADEMAQFY 1sqgA 67 :ARPMTGKQRTVHYLIMVGLYQLLYTRIPPHAALAETVEGA T0369 73 :AVPVLPEQLVDRLDQSWQY 1sqgA 110 :KRPQLKGLINGVLRQFQRQ T0369 93 :QDRLMADFSTETTYWGVTDSTTGWLLEA 1sqgA 129 :QEELLAEFNASDARYLHPSWLLKRLQKA Number of specific fragments extracted= 4 number of extra gaps= 0 total=43 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 1ovlA/T0369-1ovlA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1ovlA expands to /projects/compbio/data/pdb/1ovl.pdb.gz 1ovlA: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 # T0369 read from 1ovlA/T0369-1ovlA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ovlA read from 1ovlA/T0369-1ovlA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1ovlA to template set # found chain 1ovlA in template set T0369 3 :DWQQALDRHVGVGVRTTRDLIRL 1ovlA 401 :QHIQQFYDLLTGSMEIIRGWAEK T0369 26 :IQPEDWD 1ovlA 430 :LPKADQD T0369 41 :SVYEVAVHLAVLLEADLRI 1ovlA 437 :LLFESAFLELFVLRLAYRS T0369 60 :ATGATADEMA 1ovlA 493 :LQNMNIDISA T0369 70 :QFYAVPVLPEQLVDRLDQSWQYYQDRLM 1ovlA 513 :TERHGLKEPKRVEELQNKIVNCLKDHVT T0369 98 :ADFST 1ovlA 542 :NNGGL T0369 108 :GVTD 1ovlA 547 :NRPN T0369 112 :STTGWLLEAAVHLYH 1ovlA 557 :GKLPELRTLCTQGLQ T0369 130 :QLLDYLNLLGYDIK 1ovlA 572 :RIFYLKLEDLVPPP Number of specific fragments extracted= 9 number of extra gaps= 0 total=52 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 1ovlA/T0369-1ovlA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0369 read from 1ovlA/T0369-1ovlA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ovlA read from 1ovlA/T0369-1ovlA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1ovlA in template set T0369 3 :DWQQALDRHVGVGVRTTRDLIRLI 1ovlA 401 :QHIQQFYDLLTGSMEIIRGWAEKI T0369 27 :QPEDWD 1ovlA 431 :PKADQD T0369 41 :SVYEVAVHLAVLLEA 1ovlA 437 :LLFESAFLELFVLRL T0369 56 :DLRIATGATADEMA 1ovlA 489 :FSSNLQNMNIDISA T0369 71 :FYAVPV 1ovlA 512 :VTERHG T0369 77 :LPEQL 1ovlA 520 :EPKRV T0369 86 :DQSWQYYQDRLMADFSTETTYWGVTDSTTGW 1ovlA 525 :EELQNKIVNCLKDHVTFNNGGLNRPNYLSKL T0369 117 :LLEAAVHLY 1ovlA 562 :LRTLCTQGL T0369 130 :QLLDYLNLLG 1ovlA 571 :QRIFYLKLED T0369 140 :YDIK 1ovlA 582 :VPPP Number of specific fragments extracted= 10 number of extra gaps= 0 total=62 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 1ovlA/T0369-1ovlA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0369 read from 1ovlA/T0369-1ovlA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ovlA read from 1ovlA/T0369-1ovlA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1ovlA in template set T0369 2 :TDWQQALDRHVGVGVRTTRDLIRLIQP 1ovlA 400 :TQHIQQFYDLLTGSMEIIRGWAEKIPG T0369 31 :WDKRPISGKRSVYEVAVHLAVLLEADL 1ovlA 427 :FADLPKADQDLLFESAFLELFVLRLAY T0369 73 :AVPVLPEQLVDRLDQSWQYYQDRLMADF 1ovlA 516 :HGLKEPKRVEELQNKIVNCLKDHVTFNN T0369 105 :TYWGVTDSTTGWLL 1ovlA 544 :GGLNRPNYLSKLLG T0369 119 :EAAVHLYHHRSQLLDYLNLLGYDIK 1ovlA 561 :ELRTLCTQGLQRIFYLKLEDLVPPP Number of specific fragments extracted= 5 number of extra gaps= 0 total=67 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 1xo0A/T0369-1xo0A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1xo0A expands to /projects/compbio/data/pdb/1xo0.pdb.gz 1xo0A:# T0369 read from 1xo0A/T0369-1xo0A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1xo0A read from 1xo0A/T0369-1xo0A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1xo0A to template set # found chain 1xo0A in template set T0369 77 :LPEQLVDRLDQSWQYYQDRL 1xo0A 41 :TWKMLLSVCRSWAAWCKLNN T0369 104 :TTYWGVTD 1xo0A 61 :RKWFPAEP T0369 112 :STTGWLLEAAV 1xo0A 70 :DVRDYLLYLQA T0369 123 :HLYHHRSQLLDYLNLLGYDIKLD 1xo0A 87 :TIQQHLGQLNMLHRRSGLPRPSD Number of specific fragments extracted= 4 number of extra gaps= 0 total=71 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 1xo0A/T0369-1xo0A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0369 read from 1xo0A/T0369-1xo0A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1xo0A read from 1xo0A/T0369-1xo0A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1xo0A in template set T0369 3 :DWQQALDRHVGVG 1xo0A 47 :SVCRSWAAWCKLN T0369 16 :VRTTRDLIRLI 1xo0A 68 :PEDVRDYLLYL T0369 38 :GKRSVYEVAVHLAVLLEADLR 1xo0A 81 :RGLAVKTIQQHLGQLNMLHRR T0369 61 :TGATADEM 1xo0A 102 :SGLPRPSD T0369 72 :Y 1xo0A 110 :S T0369 83 :DRLDQSWQYYQDRLMADFSTETTYWG 1xo0A 111 :NAVSLVMRRIRKENVDAGERAKQALA T0369 109 :VTDSTTGWLLEAA 1xo0A 151 :NSDRCQDIRNLAF Number of specific fragments extracted= 7 number of extra gaps= 0 total=78 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 1xo0A/T0369-1xo0A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0369 read from 1xo0A/T0369-1xo0A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1xo0A read from 1xo0A/T0369-1xo0A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1xo0A in template set T0369 73 :AVPVLPEQLVDRLDQSWQYYQDRLMAD 1xo0A 33 :DRQAFSEHTWKMLLSVCRSWAAWCKLN T0369 102 :TETTYWGVTDSTTGWLLEAAV 1xo0A 60 :NRKWFPAEPEDVRDYLLYLQA T0369 124 :LYHHRSQLLDYLNLLGYD 1xo0A 88 :IQQHLGQLNMLHRRSGLP Number of specific fragments extracted= 3 number of extra gaps= 0 total=81 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 1lrv/T0369-1lrv-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1lrv expands to /projects/compbio/data/pdb/1lrv.pdb.gz 1lrv:Warning: there is no chain 1lrv will retry with 1lrvA # T0369 read from 1lrv/T0369-1lrv-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1lrv read from 1lrv/T0369-1lrv-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1lrv to template set # found chain 1lrv in template set Warning: unaligning (T0369)Q27 because of BadResidue code BAD_PEPTIDE in next template residue (1lrv)L124 Warning: unaligning (T0369)P28 because of BadResidue code BAD_PEPTIDE at template residue (1lrv)L124 T0369 17 :RTTRDLIRLI 1lrv 113 :EVRITVADRL T0369 29 :EDWDKRPISGKR 1lrv 125 :EQLEQMAADRDY T0369 51 :VLLEADLRI 1lrv 137 :LVRAYVVQR T0369 63 :ATADEMAQFYAVPV 1lrv 146 :IPPGRLFRFMRDED T0369 82 :VDRLDQSWQY 1lrv 160 :RQVRKLVAKR T0369 95 :RLMADFST 1lrv 170 :LPEESLGL T0369 106 :YWGVTD 1lrv 178 :MTQDPE T0369 112 :STTGWLL 1lrv 185 :EVRRIVA Number of specific fragments extracted= 8 number of extra gaps= 1 total=89 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 1lrv/T0369-1lrv-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0369 read from 1lrv/T0369-1lrv-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1lrv read from 1lrv/T0369-1lrv-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1lrv in template set Warning: unaligning (T0369)Q27 because of BadResidue code BAD_PEPTIDE in next template residue (1lrv)L124 Warning: unaligning (T0369)P28 because of BadResidue code BAD_PEPTIDE at template residue (1lrv)L124 T0369 16 :VRTTRDLIRLI 1lrv 112 :REVRITVADRL T0369 29 :EDWDKRPISG 1lrv 125 :EQLEQMAADR T0369 50 :AVLLEADLRI 1lrv 136 :YLVRAYVVQR T0369 63 :ATADEMAQFYAVPV 1lrv 146 :IPPGRLFRFMRDED T0369 86 :DQSWQYYQDRLMADFSTETTYWGVTDSTTGWLLE 1lrv 160 :RQVRKLVAKRLPEESLGLMTQDPEPEVRRIVASR Number of specific fragments extracted= 5 number of extra gaps= 1 total=94 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 1lrv/T0369-1lrv-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0369 read from 1lrv/T0369-1lrv-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1lrv read from 1lrv/T0369-1lrv-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1lrv in template set Warning: unaligning (T0369)Q27 because of BadResidue code BAD_PEPTIDE in next template residue (1lrv)L124 Warning: unaligning (T0369)P28 because of BadResidue code BAD_PEPTIDE at template residue (1lrv)L124 T0369 17 :RTTRDLIRLI 1lrv 113 :EVRITVADRL T0369 29 :EDWDK 1lrv 125 :EQLEQ T0369 51 :VLLEADLRIATGATADEMAQFY 1lrv 137 :LVRAYVVQRIPPGRLFRFMRDE T0369 74 :VPV 1lrv 159 :DRQ T0369 88 :SWQ 1lrv 162 :VRK T0369 95 :RLMADFSTETTYWGVTDSTTGWLLEAAV 1lrv 165 :LVAKRLPEESLGLMTQDPEPEVRRIVAS Number of specific fragments extracted= 6 number of extra gaps= 1 total=100 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 1vb5A/T0369-1vb5A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1vb5A expands to /projects/compbio/data/pdb/1vb5.pdb.gz 1vb5A:# T0369 read from 1vb5A/T0369-1vb5A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1vb5A read from 1vb5A/T0369-1vb5A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1vb5A to template set # found chain 1vb5A in template set T0369 3 :DWQQALDRH 1vb5A 5 :RVLEILREM T0369 12 :VGVGVRTTRDLIRLIQPEDWD 1vb5A 25 :AKKGAEAFLTLAEELDESLLE T0369 41 :SVYEVAVHLAVLLEADLRIA 1vb5A 47 :AIMELREEVVKVNPSMASLY T0369 67 :EMAQFYAVPVLPEQLVDRLDQSWQYYQDRLMA 1vb5A 67 :NLARFIPVTNRRDILKSRALEFLRRMEEAKRE T0369 99 :DFSTETTYW 1vb5A 102 :IGAQLIDDG T0369 108 :GVTDSTTGWLLEAAV 1vb5A 117 :SFSSTVLEIIRTAKE T0369 130 :QLLDYLNLLGYDIK 1vb5A 151 :HLARELEFSGIEFE Number of specific fragments extracted= 7 number of extra gaps= 0 total=107 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 1vb5A/T0369-1vb5A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0369 read from 1vb5A/T0369-1vb5A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1vb5A read from 1vb5A/T0369-1vb5A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1vb5A in template set T0369 3 :DWQQALDRH 1vb5A 5 :RVLEILREM T0369 12 :VGVGVRTTRDLIRLIQPEDW 1vb5A 25 :AKKGAEAFLTLAEELDESLL T0369 41 :SVYEVAVHLAVLLE 1vb5A 47 :AIMELREEVVKVNP T0369 55 :ADLRIA 1vb5A 63 :ASLYNL T0369 69 :AQFYAVPVLPEQLVDRLDQSWQYYQD 1vb5A 69 :ARFIPVTNRRDILKSRALEFLRRMEE T0369 95 :RLMADFSTETTYWG 1vb5A 98 :ELASIGAQLIDDGD T0369 109 :VTDSTTGWLLEAAV 1vb5A 118 :FSSTVLEIIRTAKE T0369 131 :LLDYLNLLGYDIK 1vb5A 152 :LARELEFSGIEFE T0369 144 :L 1vb5A 167 :T Number of specific fragments extracted= 9 number of extra gaps= 0 total=116 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 1vb5A/T0369-1vb5A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0369 read from 1vb5A/T0369-1vb5A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1vb5A read from 1vb5A/T0369-1vb5A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1vb5A in template set T0369 2 :TDWQQALDRH 1vb5A 7 :LEILREMKRE T0369 12 :VGVGVRTTRDLIRLIQPEDWD 1vb5A 25 :AKKGAEAFLTLAEELDESLLE T0369 41 :SVYEVAVHLAV 1vb5A 47 :AIMELREEVVK T0369 52 :LLEADLRIAT 1vb5A 64 :SLYNLARFIP T0369 70 :QFYAVPVLPEQLVDR 1vb5A 74 :VTNRRDILKSRALEF T0369 85 :LDQSWQYYQDRLMADFSTE 1vb5A 92 :MEEAKRELASIGAQLIDDG T0369 106 :YWGVTDSTTGWLLEAAV 1vb5A 115 :THSFSSTVLEIIRTAKE T0369 129 :SQLLDYLNLLGYDI 1vb5A 150 :LHLARELEFSGIEF Number of specific fragments extracted= 8 number of extra gaps= 0 total=124 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 1xrsA/T0369-1xrsA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1xrsA expands to /projects/compbio/data/pdb/1xrs.pdb.gz 1xrsA:# T0369 read from 1xrsA/T0369-1xrsA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1xrsA read from 1xrsA/T0369-1xrsA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1xrsA to template set # found chain 1xrsA in template set T0369 3 :DWQQALDRHVGVGVRTTRDLIRL 1xrsA 10 :NLVEKARAKAKAIAIDTQEFIEK T0369 32 :DKRPISGKRSVYEVAVHL 1xrsA 49 :DGVDTDEVPLPNIVVDHI T0369 50 :AVLLEADLRIATGATADEMA 1xrsA 76 :AAMYIANAVLNTGKTPQEIA T0369 70 :QFYAVPV 1xrsA 106 :TKLPMKD T0369 77 :LPEQLVDRLDQSWQYYQ 1xrsA 116 :VKTKALSMAKETVEKIK T0369 94 :DRLMADFSTETTYWG 1xrsA 136 :SIRESRFEEYGDKSG T0369 109 :VTDSTTGWLLEA 1xrsA 158 :ATGNIYEDITQA T0369 132 :LDYLNL 1xrsA 170 :VAAAKQ Number of specific fragments extracted= 8 number of extra gaps= 0 total=132 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 1xrsA/T0369-1xrsA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0369 read from 1xrsA/T0369-1xrsA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1xrsA read from 1xrsA/T0369-1xrsA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1xrsA in template set T0369 3 :DWQQALDRHVGVGVRTTRDLIR 1xrsA 10 :NLVEKARAKAKAIAIDTQEFIE T0369 34 :R 1xrsA 50 :G T0369 35 :PISGKRSVYEVAVHLA 1xrsA 52 :DTDEVPLPNIVVDHIK T0369 52 :LLEADLRIATG 1xrsA 76 :AAMYIANAVLN T0369 63 :ATADEMAQ 1xrsA 89 :KTPQEIAQ T0369 71 :FYAVPV 1xrsA 105 :LTKLPM T0369 77 :LPEQLVDRL 1xrsA 112 :DLFEVKTKA T0369 86 :DQSWQYYQ 1xrsA 125 :KETVEKIK T0369 94 :DRLMADFSTETTYWG 1xrsA 136 :SIRESRFEEYGDKSG T0369 109 :VTDSTTGWLLEAAV 1xrsA 158 :ATGNIYEDITQAVA Number of specific fragments extracted= 10 number of extra gaps= 0 total=142 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 1xrsA/T0369-1xrsA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0369 read from 1xrsA/T0369-1xrsA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1xrsA read from 1xrsA/T0369-1xrsA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1xrsA in template set T0369 2 :TDWQQALDRHVGVGVRTTRDLIRL 1xrsA 9 :FNLVEKARAKAKAIAIDTQEFIEK T0369 33 :KRPISGKRSVYEVAVHLAV 1xrsA 50 :GVDTDEVPLPNIVVDHIKE T0369 52 :LLEADL 1xrsA 79 :YIANAV T0369 58 :RIATGATA 1xrsA 96 :QAISAGEL T0369 67 :EMAQFY 1xrsA 104 :DLTKLP T0369 73 :AVPVLPEQLVDRLDQSWQYYQDRL 1xrsA 112 :DLFEVKTKALSMAKETVEKIKNNR T0369 97 :MADFSTE 1xrsA 139 :ESRFEEY T0369 106 :YWGVTDSTTGWLLEAAVH 1xrsA 155 :VIVATGNIYEDITQAVAA Number of specific fragments extracted= 8 number of extra gaps= 0 total=150 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 1vi0A/T0369-1vi0A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1vi0A expands to /projects/compbio/data/pdb/1vi0.pdb.gz 1vi0A: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 Skipped atom 615, because occupancy 0.500 <= existing 0.500 in 1vi0A Skipped atom 617, because occupancy 0.500 <= existing 0.500 in 1vi0A Skipped atom 619, because occupancy 0.500 <= existing 0.500 in 1vi0A Skipped atom 1077, because occupancy 0.500 <= existing 0.500 in 1vi0A Skipped atom 1079, because occupancy 0.500 <= existing 0.500 in 1vi0A Skipped atom 1081, because occupancy 0.500 <= existing 0.500 in 1vi0A Skipped atom 1083, because occupancy 0.500 <= existing 0.500 in 1vi0A 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 1187, because occupancy 0.500 <= existing 0.500 in 1vi0A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1189, because occupancy 0.500 <= existing 0.500 in 1vi0A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1191, because occupancy 0.500 <= existing 0.500 in 1vi0A 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 # T0369 read from 1vi0A/T0369-1vi0A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1vi0A read from 1vi0A/T0369-1vi0A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1vi0A to template set # found chain 1vi0A in template set Warning: unaligning (T0369)Y92 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1vi0A)D131 Warning: unaligning (T0369)Q93 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1vi0A)D131 T0369 2 :TDWQQALDRHVGVGVRTTRDLIRL 1vi0A 48 :KNKEDILISLFKEKMGQFIERMEE T0369 31 :WD 1vi0A 73 :IK T0369 38 :GKRSVYEVAV 1vi0A 75 :EKATAKEKLA T0369 51 :VLLEADLRIATGATA 1vi0A 85 :LVISKHFSLLAGDHN T0369 67 :EMA 1vi0A 100 :LAI T0369 70 :QFYAVPV 1vi0A 106 :LELRQSN T0369 77 :LPEQLVDRLDQSWQY 1vi0A 115 :LRQKINEILKGYLNI T0369 94 :DRLMADF 1vi0A 132 :GILTEGI T0369 101 :STETT 1vi0A 140 :SGEIK T0369 108 :GVTDST 1vi0A 146 :GLDVRL T0369 114 :TGWLLEAAV 1vi0A 153 :RQMIFGTID T0369 129 :SQLLDY 1vi0A 162 :ETVTTW T0369 136 :NLLGYDIK 1vi0A 168 :VMNDQKYD T0369 144 :LDL 1vi0A 177 :VAL Number of specific fragments extracted= 14 number of extra gaps= 1 total=164 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 1vi0A/T0369-1vi0A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0369 read from 1vi0A/T0369-1vi0A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1vi0A read from 1vi0A/T0369-1vi0A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1vi0A in template set Warning: unaligning (T0369)L96 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1vi0A)D131 Warning: unaligning (T0369)M97 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1vi0A)D131 T0369 3 :DWQQALDRHVGVGVRTTRDLIR 1vi0A 49 :NKEDILISLFKEKMGQFIERME T0369 29 :EDWD 1vi0A 71 :EDIK T0369 38 :GKRSVYEVAV 1vi0A 75 :EKATAKEKLA T0369 51 :VLLEADLRIATGATA 1vi0A 85 :LVISKHFSLLAGDHN T0369 67 :E 1vi0A 102 :I T0369 68 :MAQFYAVPV 1vi0A 104 :TQLELRQSN T0369 79 :EQLVDRLDQSWQYYQDR 1vi0A 113 :LELRQKINEILKGYLNI T0369 98 :ADFSTE 1vi0A 132 :GILTEG T0369 104 :TTYWGVTDSTTGWLLEAAVHLYH 1vi0A 140 :SGEIKEGLDVRLARQMIFGTIDE T0369 130 :QL 1vi0A 163 :TV T0369 133 :DYLNLLGYDIK 1vi0A 165 :TTWVMNDQKYD T0369 144 :LDL 1vi0A 177 :VAL Number of specific fragments extracted= 12 number of extra gaps= 1 total=176 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 1vi0A/T0369-1vi0A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0369 read from 1vi0A/T0369-1vi0A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1vi0A read from 1vi0A/T0369-1vi0A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1vi0A in template set Warning: unaligning (T0369)Y92 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1vi0A)D131 Warning: unaligning (T0369)Q93 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1vi0A)D131 T0369 6 :QALDRHVGVGVRTTRDLIRL 1vi0A 52 :DILISLFKEKMGQFIERMEE T0369 36 :ISGKRSVYEVAVHLAVLLEADL 1vi0A 73 :IKEKATAKEKLALVISKHFSLL T0369 73 :AVPVLPEQLVDRLDQSWQY 1vi0A 111 :SNLELRQKINEILKGYLNI T0369 94 :DRLMADFSTE 1vi0A 132 :GILTEGIQSG T0369 104 :TTYWGVTDSTTGWLLEAAVHLY 1vi0A 144 :KEGLDVRLARQMIFGTIDETVT T0369 134 :YLNLLGYDIKL 1vi0A 166 :TWVMNDQKYDL Number of specific fragments extracted= 6 number of extra gaps= 1 total=182 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 2bh4X/T0369-2bh4X-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2bh4X expands to /projects/compbio/data/pdb/2bh4.pdb.gz 2bh4X:Skipped atom 279, because occupancy 0.500 <= existing 0.500 in 2bh4X Skipped atom 281, because occupancy 0.500 <= existing 0.500 in 2bh4X Skipped atom 283, because occupancy 0.500 <= existing 0.500 in 2bh4X Skipped atom 285, because occupancy 0.500 <= existing 0.500 in 2bh4X Skipped atom 287, because occupancy 0.500 <= existing 0.500 in 2bh4X Skipped atom 289, because occupancy 0.500 <= existing 0.500 in 2bh4X Skipped atom 291, because occupancy 0.500 <= existing 0.500 in 2bh4X Skipped atom 293, because occupancy 0.500 <= existing 0.500 in 2bh4X Skipped atom 505, because occupancy 0.500 <= existing 0.500 in 2bh4X Skipped atom 507, because occupancy 0.500 <= existing 0.500 in 2bh4X Skipped atom 723, because occupancy 0.500 <= existing 0.500 in 2bh4X Skipped atom 725, because occupancy 0.500 <= existing 0.500 in 2bh4X Skipped atom 727, because occupancy 0.500 <= existing 0.500 in 2bh4X Skipped atom 729, because occupancy 0.500 <= existing 0.500 in 2bh4X Skipped atom 731, because occupancy 0.500 <= existing 0.500 in 2bh4X Skipped atom 733, because occupancy 0.500 <= existing 0.500 in 2bh4X Skipped atom 735, because occupancy 0.500 <= existing 0.500 in 2bh4X Skipped atom 737, because occupancy 0.500 <= existing 0.500 in 2bh4X Skipped atom 739, because occupancy 0.500 <= existing 0.500 in 2bh4X Skipped atom 741, because occupancy 0.500 <= existing 0.500 in 2bh4X Skipped atom 743, because occupancy 0.500 <= existing 0.500 in 2bh4X Skipped atom 745, because occupancy 0.500 <= existing 0.500 in 2bh4X Skipped atom 747, because occupancy 0.500 <= existing 0.500 in 2bh4X Skipped atom 749, because occupancy 0.500 <= existing 0.500 in 2bh4X Skipped atom 751, because occupancy 0.500 <= existing 0.500 in 2bh4X Skipped atom 753, because occupancy 0.500 <= existing 0.500 in 2bh4X Skipped atom 755, because occupancy 0.500 <= existing 0.500 in 2bh4X Skipped atom 757, because occupancy 0.500 <= existing 0.500 in 2bh4X Skipped atom 759, because occupancy 0.500 <= existing 0.500 in 2bh4X Skipped atom 761, because occupancy 0.500 <= existing 0.500 in 2bh4X Skipped atom 763, because occupancy 0.500 <= existing 0.500 in 2bh4X Skipped atom 765, because occupancy 0.500 <= existing 0.500 in 2bh4X Skipped atom 767, because occupancy 0.500 <= existing 0.500 in 2bh4X Skipped atom 769, because occupancy 0.500 <= existing 0.500 in 2bh4X Skipped atom 771, because occupancy 0.500 <= existing 0.500 in 2bh4X Skipped atom 773, because occupancy 0.500 <= existing 0.500 in 2bh4X Skipped atom 775, because occupancy 0.500 <= existing 0.500 in 2bh4X Skipped atom 777, because occupancy 0.500 <= existing 0.500 in 2bh4X Skipped atom 779, because occupancy 0.500 <= existing 0.500 in 2bh4X Skipped atom 781, because occupancy 0.500 <= existing 0.500 in 2bh4X Skipped atom 783, because occupancy 0.500 <= existing 0.500 in 2bh4X Skipped atom 785, because occupancy 0.500 <= existing 0.500 in 2bh4X Skipped atom 787, because occupancy 0.500 <= existing 0.500 in 2bh4X Skipped atom 789, because occupancy 0.500 <= existing 0.500 in 2bh4X Skipped atom 791, because occupancy 0.500 <= existing 0.500 in 2bh4X Skipped atom 793, because occupancy 0.500 <= existing 0.500 in 2bh4X Skipped atom 795, because occupancy 0.500 <= existing 0.500 in 2bh4X Skipped atom 797, because occupancy 0.500 <= existing 0.500 in 2bh4X Skipped atom 799, because occupancy 0.500 <= existing 0.500 in 2bh4X Skipped atom 801, because occupancy 0.500 <= existing 0.500 in 2bh4X Skipped atom 878, because occupancy 0.500 <= existing 0.500 in 2bh4X Skipped atom 880, because occupancy 0.500 <= existing 0.500 in 2bh4X Skipped atom 882, because occupancy 0.500 <= existing 0.500 in 2bh4X # T0369 read from 2bh4X/T0369-2bh4X-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2bh4X read from 2bh4X/T0369-2bh4X-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2bh4X to template set # found chain 2bh4X in template set Warning: unaligning (T0369)T102 because of BadResidue code BAD_PEPTIDE in next template residue (2bh4X)K97 Warning: unaligning (T0369)E103 because of BadResidue code BAD_PEPTIDE at template residue (2bh4X)K97 T0369 60 :ATGATADEMA 2bh4X 50 :VEGFKYGDGI T0369 70 :QFYAVPVLPEQLVDRLDQSWQYYQDRLMAD 2bh4X 65 :KNPDMVWSEADLIEYVTDPKPWLVEKTGDS T0369 101 :S 2bh4X 95 :A T0369 104 :TTYW 2bh4X 98 :TKKT T0369 108 :GVTDSTTGWLLEAAVH 2bh4X 103 :KLGKNQADVVAFLAQH Number of specific fragments extracted= 5 number of extra gaps= 1 total=187 Will force an alignment to be made, even if fragment is small Number of alignments=28 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2bh4X/T0369-2bh4X-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0369 read from 2bh4X/T0369-2bh4X-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2bh4X read from 2bh4X/T0369-2bh4X-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2bh4X in template set Warning: unaligning (T0369)S101 because of BadResidue code BAD_PEPTIDE in next template residue (2bh4X)K97 Warning: unaligning (T0369)T102 because of BadResidue code BAD_PEPTIDE at template residue (2bh4X)K97 T0369 62 :GATA 2bh4X 52 :GFKY T0369 66 :DE 2bh4X 57 :DG T0369 68 :MAQFYAVPVLPEQLVDRLDQSWQYYQDRLMADF 2bh4X 63 :AEKNPDMVWSEADLIEYVTDPKPWLVEKTGDSA T0369 103 :ETTYWGVTDSTTGWLLEAAVH 2bh4X 98 :TKKTFKLGKNQADVVAFLAQH Number of specific fragments extracted= 4 number of extra gaps= 1 total=191 Will force an alignment to be made, even if fragment is small Number of alignments=29 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2bh4X/T0369-2bh4X-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0369 read from 2bh4X/T0369-2bh4X-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2bh4X read from 2bh4X/T0369-2bh4X-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2bh4X in template set T0369 17 :RTTRDLIRL 2bh4X 57 :DGILEVAEK T0369 35 :PISGKRSVYEVAVHLA 2bh4X 66 :NPDMVWSEADLIEYVT T0369 76 :VLPEQLVDR 2bh4X 82 :DPKPWLVEK T0369 100 :FSTE 2bh4X 91 :TGDS T0369 104 :TTYWGVTDSTTGWLLEAAVH 2bh4X 99 :KKTFKLGKNQADVVAFLAQH Number of specific fragments extracted= 5 number of extra gaps= 0 total=196 Will force an alignment to be made, even if fragment is small Number of alignments=30 # command:CPU_time= 12.948 sec, elapsed time= 13.741 sec. # command:Using radius: 8.000 NUMB_ALIGNS: 30 Adding 10878 constraints to all_contacts Done adding distance constraints # command:CPU_time= 12.979 sec, elapsed time= 13.776 sec. # command:Reading probabilities from T0369.t06.CB8-sep9.rdb Reading constraints from ConstraintSet all_contacts maxweight: 5.563 Optimizing... Probability sum: -249.518, CN propb: -249.518 weights: 0.390 constraints: 206 # command:CPU_time= 20.508 sec, elapsed time= 21.344 sec. # command:Found ConstraintSet # PrintContacts log_align.constraints Number of constraints in align 206 # command:Found ConstraintSet # PrintContacts log_align_bonus.constraints Number of constraints in align.bonus 206 # command:Found ConstraintSet # PrintContacts log_rejected.constraints Number of constraints in rejected 1171 # command:Found ConstraintSet # PrintContacts log_rejected_bonus.constraints Number of constraints in rejected.bonus 1171 # command:Found ConstraintSet # PrintContacts log_noncontact.constraints Number of constraints in noncontact 8353 # command:Found ConstraintSet # PrintContacts log_noncontact_bonus.constraints Number of constraints in noncontact.bonus 8353 # command:CPU_time= 20.686 sec, elapsed time= 21.671 sec. # command: