# 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 T0518 numbered 1 through 288 Created new target T0518 from T0518.a2m # command:CPU_time= 5.635 sec, elapsed time= 5.684 sec. # command:# reading script from file all-templates.under # Reading fragments from alignment file # Attempting to read fragment alignments from file 3h3lA/T0518-3h3lA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 3h3lA expands to /projects/compbio/data/pdb/3h3l.pdb.gz 3h3lA:Skipped atom 3, because occupancy 0.5 <= existing 0.500 in 3h3lA Skipped atom 7, because occupancy 0.500 <= existing 0.500 in 3h3lA Skipped atom 9, because occupancy 0.500 <= existing 0.500 in 3h3lA Skipped atom 11, because occupancy 0.500 <= existing 0.500 in 3h3lA Skipped atom 13, because occupancy 0.500 <= existing 0.500 in 3h3lA Skipped atom 15, because occupancy 0.500 <= existing 0.500 in 3h3lA Skipped atom 39, because occupancy 0.500 <= existing 0.500 in 3h3lA Skipped atom 43, because occupancy 0.500 <= existing 0.500 in 3h3lA Skipped atom 45, because occupancy 0.500 <= existing 0.500 in 3h3lA 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 327, because occupancy 0.500 <= existing 0.500 in 3h3lA Skipped atom 331, because occupancy 0.500 <= existing 0.500 in 3h3lA Skipped atom 333, because occupancy 0.500 <= existing 0.500 in 3h3lA Skipped atom 335, because occupancy 0.500 <= existing 0.500 in 3h3lA Skipped atom 337, because occupancy 0.500 <= existing 0.500 in 3h3lA Skipped atom 524, because occupancy 0.500 <= existing 0.500 in 3h3lA Skipped atom 528, because occupancy 0.500 <= existing 0.500 in 3h3lA Skipped atom 530, because occupancy 0.500 <= existing 0.500 in 3h3lA Skipped atom 532, because occupancy 0.500 <= existing 0.500 in 3h3lA Skipped atom 534, because occupancy 0.500 <= existing 0.500 in 3h3lA Skipped atom 536, because occupancy 0.500 <= existing 0.500 in 3h3lA 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 1174, because occupancy 0.500 <= existing 0.500 in 3h3lA Skipped atom 1178, because occupancy 0.500 <= existing 0.500 in 3h3lA Skipped atom 1180, because occupancy 0.500 <= existing 0.500 in 3h3lA Skipped atom 1182, because occupancy 0.500 <= existing 0.500 in 3h3lA Skipped atom 1184, because occupancy 0.500 <= existing 0.500 in 3h3lA Skipped atom 1186, because occupancy 0.500 <= existing 0.500 in 3h3lA Skipped atom 1188, because occupancy 0.500 <= existing 0.500 in 3h3lA Skipped atom 1190, because occupancy 0.500 <= existing 0.500 in 3h3lA Skipped atom 1244, because occupancy 0.500 <= existing 0.500 in 3h3lA Skipped atom 1248, because occupancy 0.500 <= existing 0.500 in 3h3lA Skipped atom 1250, because occupancy 0.500 <= existing 0.500 in 3h3lA Skipped atom 1252, because occupancy 0.500 <= existing 0.500 in 3h3lA Skipped atom 1254, because occupancy 0.500 <= existing 0.500 in 3h3lA Skipped atom 1256, because occupancy 0.500 <= existing 0.500 in 3h3lA Skipped atom 1258, because occupancy 0.500 <= existing 0.500 in 3h3lA Skipped atom 1260, because occupancy 0.500 <= existing 0.500 in 3h3lA 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 1300, because occupancy 0.500 <= existing 0.500 in 3h3lA 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 1304, because occupancy 0.500 <= existing 0.500 in 3h3lA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1306, because occupancy 0.500 <= existing 0.500 in 3h3lA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1308, because occupancy 0.370 <= existing 0.380 in 3h3lA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1310, because occupancy 0.500 <= existing 0.500 in 3h3lA Skipped atom 1381, because occupancy 0.500 <= existing 0.500 in 3h3lA Skipped atom 1385, because occupancy 0.500 <= existing 0.500 in 3h3lA Skipped atom 1387, because occupancy 0.500 <= existing 0.500 in 3h3lA Skipped atom 1389, because occupancy 0.500 <= existing 0.500 in 3h3lA Skipped atom 1391, because occupancy 0.500 <= existing 0.500 in 3h3lA Skipped atom 1393, because occupancy 0.500 <= existing 0.500 in 3h3lA Skipped atom 1591, because occupancy 0.500 <= existing 0.500 in 3h3lA Skipped atom 1595, because occupancy 0.500 <= existing 0.500 in 3h3lA Skipped atom 1597, because occupancy 0.500 <= existing 0.500 in 3h3lA 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 1649, because occupancy 0.500 <= existing 0.500 in 3h3lA 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 1653, because occupancy 0.500 <= existing 0.500 in 3h3lA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1655, because occupancy 0.500 <= existing 0.500 in 3h3lA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1657, because occupancy 0.370 <= existing 0.380 in 3h3lA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1659, because occupancy 0.500 <= existing 0.500 in 3h3lA 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 1758, because occupancy 0.500 <= existing 0.500 in 3h3lA Skipped atom 1760, because occupancy 0.500 <= existing 0.500 in 3h3lA Skipped atom 1762, because occupancy 0.500 <= existing 0.500 in 3h3lA Skipped atom 1764, because occupancy 0.500 <= existing 0.500 in 3h3lA Skipped atom 1766, because occupancy 0.500 <= existing 0.500 in 3h3lA Skipped atom 1768, because occupancy 0.500 <= existing 0.500 in 3h3lA Skipped atom 1770, because occupancy 0.500 <= existing 0.500 in 3h3lA Skipped atom 1772, because occupancy 0.500 <= existing 0.500 in 3h3lA # T0518 read from 3h3lA/T0518-3h3lA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3h3lA read from 3h3lA/T0518-3h3lA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3h3lA to template set # found chain 3h3lA in template set Warning: unaligning (T0518)P47 because first residue in template chain is (3h3lA)Q39 Warning: unaligning (T0518)S186 because of BadResidue code BAD_PEPTIDE in next template residue (3h3lA)V167 Warning: unaligning (T0518)L187 because of BadResidue code BAD_PEPTIDE at template residue (3h3lA)V167 Warning: unaligning (T0518)Q271 because of BadResidue code BAD_PEPTIDE in next template residue (3h3lA)D255 Warning: unaligning (T0518)D272 because of BadResidue code BAD_PEPTIDE at template residue (3h3lA)D255 Warning: unaligning (T0518)L287 because last residue in template chain is (3h3lA)L270 T0518 48 :ETDSLNLP 3h3lA 40 :ALDSDGIP # choosing archetypes in rotamer library T0518 57 :DENGYITIFDGETFNGWRGYGKDRVPTKWTIEDGCIKFNGSGGG 3h3lA 48 :TGGEWITMFDGKTLNGWRGYCRQDVPLGWVVEDGSITYKGSDNK T0518 103 :QDGDGGDLIFAHKFKNFELELEWKVAKGSNSGILYLAQEVTSKDK 3h3lA 92 :ADTGFGDLIYDKKFKNFVFEIEWKIDKAGNSGIFYTAQEIEGTPI T0518 157 :YISAPEYQILDNANHPDAKLGKDNNRQSA 3h3lA 137 :YYSSPEYQLLDNENMPDAWEGCDGNRQAG T0518 188 :YDMIPAVPQNSKPFGEWNKAKIMVYKGTVVHGQNDENVLEYHLWTKQWTDMLQASKFS 3h3lA 168 :YDMIMPDPQPVKPYGNWNKTRIVVYNQRVIHYMNDVKILEFQFGTPVWRALVDHSKFS T0518 246 :EDKWPLAFELLNN 3h3lA 231 :PEKCPEAYDLMLQ T0518 261 :GENHEGFIGL 3h3lA 244 :CGKQPGYIGM T0518 273 :HGDDVWFRNIRVKV 3h3lA 256 :HGYGVCFRNIRIKE Number of specific fragments extracted= 8 number of extra gaps= 2 total=8 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 3h3lA/T0518-3h3lA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0518 read from 3h3lA/T0518-3h3lA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3h3lA read from 3h3lA/T0518-3h3lA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3h3lA in template set Warning: unaligning (T0518)E48 because first residue in template chain is (3h3lA)Q39 Warning: unaligning (T0518)S186 because of BadResidue code BAD_PEPTIDE in next template residue (3h3lA)V167 Warning: unaligning (T0518)L187 because of BadResidue code BAD_PEPTIDE at template residue (3h3lA)V167 Warning: unaligning (T0518)Q271 because of BadResidue code BAD_PEPTIDE in next template residue (3h3lA)D255 Warning: unaligning (T0518)D272 because of BadResidue code BAD_PEPTIDE at template residue (3h3lA)D255 Warning: unaligning (T0518)L287 because last residue in template chain is (3h3lA)L270 T0518 49 :TDSLNLPVDENGYITIFDGETFNGWRGYGKDRVPTKWTIEDGCIKFNGSGGGE 3h3lA 40 :ALDSDGIPTGGEWITMFDGKTLNGWRGYCRQDVPLGWVVEDGSITYKGSDNKA T0518 104 :DGDGGDLIFAHKFKNFELELEWKVAKGSNSGILYLAQEVTSKDK 3h3lA 93 :DTGFGDLIYDKKFKNFVFEIEWKIDKAGNSGIFYTAQEIEGTPI T0518 157 :YISAPEYQILDNANHPDAKLGKDNNRQSA 3h3lA 137 :YYSSPEYQLLDNENMPDAWEGCDGNRQAG T0518 188 :YDMIPAVPQNSKPFGEWNKAKIMVYKGTVVHGQNDENVLEYHLWTKQWTDMLQA 3h3lA 168 :YDMIMPDPQPVKPYGNWNKTRIVVYNQRVIHYMNDVKILEFQFGTPVWRALVDH T0518 242 :SKFSEDKWPLAFELLNNCGGENHEGFIGL 3h3lA 225 :SKFSTSPEKCPEAYDLMLQCGKQPGYIGM T0518 273 :HGDDVWFRNIRVKV 3h3lA 256 :HGYGVCFRNIRIKE Number of specific fragments extracted= 6 number of extra gaps= 2 total=14 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 3h3lA/T0518-3h3lA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0518 read from 3h3lA/T0518-3h3lA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3h3lA read from 3h3lA/T0518-3h3lA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3h3lA in template set Warning: unaligning (T0518)E48 because first residue in template chain is (3h3lA)Q39 Warning: unaligning (T0518)S186 because of BadResidue code BAD_PEPTIDE in next template residue (3h3lA)V167 Warning: unaligning (T0518)L187 because of BadResidue code BAD_PEPTIDE at template residue (3h3lA)V167 Warning: unaligning (T0518)Q271 because of BadResidue code BAD_PEPTIDE in next template residue (3h3lA)D255 Warning: unaligning (T0518)D272 because of BadResidue code BAD_PEPTIDE at template residue (3h3lA)D255 Warning: unaligning (T0518)L287 because last residue in template chain is (3h3lA)L270 T0518 49 :TDSLNLPVDENGYITIFDGETFNGWRGYGKDRVPTKWTIEDGCIKFNGSGGGE 3h3lA 40 :ALDSDGIPTGGEWITMFDGKTLNGWRGYCRQDVPLGWVVEDGSITYKGSDNKA T0518 104 :DGDGGDLIFAHKFKNFELELEWKVAKGSNSGILYLAQEVTS 3h3lA 93 :DTGFGDLIYDKKFKNFVFEIEWKIDKAGNSGIFYTAQEIEG T0518 154 :EPIYISAPEYQILDNANHPDAKLGKDNNRQSA 3h3lA 134 :TPIYYSSPEYQLLDNENMPDAWEGCDGNRQAG T0518 188 :YDMIPAVPQNSKPFGEWNKAKIMVYKGTVVHGQNDENVLEYHLWTKQWTDMLQASKFSED 3h3lA 168 :YDMIMPDPQPVKPYGNWNKTRIVVYNQRVIHYMNDVKILEFQFGTPVWRALVDHSKFSKF T0518 248 :KWPLAFELLNNCGGENHEGFIGL 3h3lA 231 :PEKCPEAYDLMLQCGKQPGYIGM T0518 273 :HGDDVWFRNIRVKV 3h3lA 256 :HGYGVCFRNIRIKE Number of specific fragments extracted= 6 number of extra gaps= 2 total=20 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 3hbkA/T0518-3hbkA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 3hbkA expands to /projects/compbio/data/pdb/3hbk.pdb.gz 3hbkA:Skipped atom 298, because occupancy 0.500 <= existing 0.500 in 3hbkA Skipped atom 302, because occupancy 0.500 <= existing 0.500 in 3hbkA Skipped atom 304, because occupancy 0.500 <= existing 0.500 in 3hbkA Skipped atom 306, because occupancy 0.500 <= existing 0.500 in 3hbkA Skipped atom 308, because occupancy 0.500 <= existing 0.500 in 3hbkA Skipped atom 310, because occupancy 0.500 <= existing 0.500 in 3hbkA Skipped atom 312, because occupancy 0.500 <= existing 0.500 in 3hbkA 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 333, because occupancy 0.500 <= existing 0.500 in 3hbkA 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 337, because occupancy 0.500 <= existing 0.500 in 3hbkA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 339, because occupancy 0.500 <= existing 0.500 in 3hbkA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 341, because occupancy 0.370 <= existing 0.380 in 3hbkA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 343, because occupancy 0.500 <= existing 0.500 in 3hbkA Skipped atom 372, because occupancy 0.500 <= existing 0.500 in 3hbkA Skipped atom 376, because occupancy 0.500 <= existing 0.500 in 3hbkA Skipped atom 378, because occupancy 0.500 <= existing 0.500 in 3hbkA Skipped atom 380, because occupancy 0.500 <= existing 0.500 in 3hbkA Skipped atom 382, because occupancy 0.500 <= existing 0.500 in 3hbkA Skipped atom 384, because occupancy 0.500 <= existing 0.500 in 3hbkA Skipped atom 456, because occupancy 0.500 <= existing 0.500 in 3hbkA Skipped atom 460, because occupancy 0.500 <= existing 0.500 in 3hbkA Skipped atom 462, because occupancy 0.500 <= existing 0.500 in 3hbkA Skipped atom 1021, because occupancy 0.500 <= existing 0.500 in 3hbkA Skipped atom 1025, because occupancy 0.500 <= existing 0.500 in 3hbkA Skipped atom 1027, because occupancy 0.500 <= existing 0.500 in 3hbkA Skipped atom 1444, because occupancy 0.500 <= existing 0.500 in 3hbkA Skipped atom 1448, because occupancy 0.500 <= existing 0.500 in 3hbkA Skipped atom 1450, because occupancy 0.500 <= existing 0.500 in 3hbkA Skipped atom 1452, because occupancy 0.500 <= existing 0.500 in 3hbkA Skipped atom 1454, because occupancy 0.500 <= existing 0.500 in 3hbkA Skipped atom 1456, because occupancy 0.500 <= existing 0.500 in 3hbkA Skipped atom 1458, because occupancy 0.500 <= existing 0.500 in 3hbkA Skipped atom 1460, because occupancy 0.500 <= existing 0.500 in 3hbkA # T0518 read from 3hbkA/T0518-3hbkA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3hbkA read from 3hbkA/T0518-3hbkA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3hbkA to template set # found chain 3hbkA in template set T0518 50 :DSLNLPV 3hbkA 41 :AINQLTD T0518 57 :DENGYITIFDGETFNGWRGYGKDRV 3hbkA 50 :KAEGWALLFDGKTTKGWRGAHKDAF T0518 82 :PTKWTIEDGCIKFNGSGGGEAQD 3hbkA 76 :DHGWMVKDGELIVQKSDGSESTN T0518 107 :GGDLIFAHKFKNFELELEWKVAKGSNSGILYLAQEVTSKDK 3hbkA 99 :GGDIVTEGEYSAFEFSVDFKITEGANSGIKYFVTEQEKQKG T0518 157 :YISAPEYQILDNANHPDAKLGKDN 3hbkA 140 :SAYGLEFQLLDDAKHPDAKLYTTF T0518 181 :NRQSASLYDMIPAVPQNSKPFGEWNKAKIMVYKG 3hbkA 166 :SRTLGSLYDLKKSENIHFNGVGEWNTAVVKVFPN T0518 215 :TVVHGQNDENVLEYHLWTKQWTDMLQASKFSEDKWP 3hbkA 201 :HVEHWLNGVKVLEYERGSKEFRDLVKGSKYADPSYN T0518 256 :LNNCGGENHEGFIGLQDHGDDVWFRNIRVKVLD 3hbkA 237 :AGGAFGEAPKGHILLQDHGDEVAFRNIKVKELK Number of specific fragments extracted= 8 number of extra gaps= 0 total=28 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 3hbkA/T0518-3hbkA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0518 read from 3hbkA/T0518-3hbkA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3hbkA read from 3hbkA/T0518-3hbkA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3hbkA in template set Warning: unaligning (T0518)A46 because first residue in template chain is (3hbkA)T39 T0518 47 :PETDSLNLPVDENGYITIFDGETFNGWRGYGKDRV 3hbkA 40 :PAINQLTDQEKAEGWALLFDGKTTKGWRGAHKDAF T0518 82 :PTKWTIEDGCIKFNGSGGGE 3hbkA 76 :DHGWMVKDGELIVQKSDGSE T0518 104 :DGDGGDLIFAHKFKNFELELEWKVAKGSNSGILYLAQEVTSKDK 3hbkA 96 :STNGGDIVTEGEYSAFEFSVDFKITEGANSGIKYFVTEQEKQKG T0518 157 :YISAPEYQILDNANHPDAKLGKDNNRQS 3hbkA 140 :SAYGLEFQLLDDAKHPDAKLYTTFPGSR T0518 185 :ASLYDMIPAVPQNSKPFGEWNKAKIMVYKG 3hbkA 170 :GSLYDLKKSENIHFNGVGEWNTAVVKVFPN T0518 215 :TVVHGQNDENVLEYHLWTKQWTDMLQASKFSEDKWPLA 3hbkA 201 :HVEHWLNGVKVLEYERGSKEFRDLVKGSKYADPSYNAG T0518 258 :NCGGENHEGFIGLQDHGDDVWFRNIRVKVLD 3hbkA 239 :GAFGEAPKGHILLQDHGDEVAFRNIKVKELK Number of specific fragments extracted= 7 number of extra gaps= 0 total=35 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 3hbkA/T0518-3hbkA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0518 read from 3hbkA/T0518-3hbkA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3hbkA read from 3hbkA/T0518-3hbkA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3hbkA in template set Warning: unaligning (T0518)A46 because first residue in template chain is (3hbkA)T39 T0518 47 :PETDSLNLPVDENGYITIFDGETFNGWRGY 3hbkA 40 :PAINQLTDQEKAEGWALLFDGKTTKGWRGA T0518 77 :GKDRVPTKWTIEDGCIKFNGSGGGE 3hbkA 71 :KDAFPDHGWMVKDGELIVQKSDGSE T0518 104 :DGDGGDLIFAHKFKNFELELEWKVAKGSNSGILYLAQEVTS 3hbkA 96 :STNGGDIVTEGEYSAFEFSVDFKITEGANSGIKYFVTEQEK T0518 154 :EPIYISAPEYQILDNANHPDA 3hbkA 137 :QKGSAYGLEFQLLDDAKHPDA T0518 175 :KLGKDNNRQSASLYDMIPAVPQNSKPFGEWNKAKIMVYKG 3hbkA 160 :YTTFPGSRTLGSLYDLKKSENIHFNGVGEWNTAVVKVFPN T0518 215 :TVVHGQNDENVLEYHLWTKQWTDMLQASKFSEDKW 3hbkA 201 :HVEHWLNGVKVLEYERGSKEFRDLVKGSKYADPSY T0518 255 :LLNNCGGENHEGFIGLQDHGDDVWFRNIRVKVLD 3hbkA 236 :NAGGAFGEAPKGHILLQDHGDEVAFRNIKVKELK Number of specific fragments extracted= 7 number of extra gaps= 0 total=42 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 3immA/T0518-3immA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 3immA expands to /projects/compbio/data/pdb/3imm.pdb.gz 3immA:Skipped atom 116, because occupancy 0.500 <= existing 0.500 in 3immA Skipped atom 118, because occupancy 0.500 <= existing 0.500 in 3immA Skipped atom 120, because occupancy 0.500 <= existing 0.500 in 3immA Skipped atom 122, because occupancy 0.500 <= existing 0.500 in 3immA Skipped atom 124, because occupancy 0.500 <= existing 0.500 in 3immA Skipped atom 126, because occupancy 0.500 <= existing 0.500 in 3immA Skipped atom 128, because occupancy 0.500 <= existing 0.500 in 3immA Skipped atom 130, because occupancy 0.500 <= existing 0.500 in 3immA 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 1035, because occupancy 0.500 <= existing 0.500 in 3immA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1037, because occupancy 0.500 <= existing 0.500 in 3immA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1039, because occupancy 0.500 <= existing 0.500 in 3immA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1041, because occupancy 0.500 <= existing 0.500 in 3immA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1043, because occupancy 0.500 <= existing 0.500 in 3immA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1045, because occupancy 0.500 <= existing 0.500 in 3immA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1047, because occupancy 0.370 <= existing 0.380 in 3immA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1049, because occupancy 0.500 <= existing 0.500 in 3immA 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 1336, because occupancy 0.500 <= existing 0.500 in 3immA Skipped atom 1338, because occupancy 0.500 <= existing 0.500 in 3immA Skipped atom 1340, because occupancy 0.500 <= existing 0.500 in 3immA Skipped atom 1342, because occupancy 0.500 <= existing 0.500 in 3immA Skipped atom 1344, because occupancy 0.500 <= existing 0.500 in 3immA Skipped atom 1346, because occupancy 0.500 <= existing 0.500 in 3immA Skipped atom 1348, because occupancy 0.500 <= existing 0.500 in 3immA Skipped atom 1350, because occupancy 0.500 <= existing 0.500 in 3immA Skipped atom 1352, because occupancy 0.500 <= existing 0.500 in 3immA Skipped atom 1420, because occupancy 0.500 <= existing 0.500 in 3immA Skipped atom 1422, because occupancy 0.500 <= existing 0.500 in 3immA Skipped atom 1424, because occupancy 0.500 <= existing 0.500 in 3immA Skipped atom 1426, because occupancy 0.500 <= existing 0.500 in 3immA Skipped atom 1428, because occupancy 0.500 <= existing 0.500 in 3immA Skipped atom 1430, because occupancy 0.500 <= existing 0.500 in 3immA Skipped atom 1432, because occupancy 0.500 <= existing 0.500 in 3immA Skipped atom 1434, because occupancy 0.500 <= existing 0.500 in 3immA Skipped atom 1436, because occupancy 0.500 <= existing 0.500 in 3immA Skipped atom 1438, because occupancy 0.500 <= existing 0.500 in 3immA Skipped atom 1440, because occupancy 0.500 <= existing 0.500 in 3immA Skipped atom 1442, because occupancy 0.500 <= existing 0.500 in 3immA Skipped atom 1444, because occupancy 0.500 <= existing 0.500 in 3immA # T0518 read from 3immA/T0518-3immA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3immA read from 3immA/T0518-3immA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3immA to template set # found chain 3immA in template set Warning: unaligning (T0518)N59 because first residue in template chain is (3immA)N26 Warning: unaligning (T0518)V127 because of BadResidue code BAD_PEPTIDE in next template residue (3immA)D79 Warning: unaligning (T0518)A128 because of BadResidue code BAD_PEPTIDE at template residue (3immA)D79 Warning: unaligning (T0518)Q196 because of BadResidue code BAD_PEPTIDE in next template residue (3immA)V136 Warning: unaligning (T0518)N197 because of BadResidue code BAD_PEPTIDE at template residue (3immA)V136 Warning: unaligning (T0518)L287 because last residue in template chain is (3immA)L222 T0518 60 :GYITIF 3immA 27 :KWKPLF T0518 67 :GETFNGWRGY 3immA 33 :GKNLENANYN T0518 82 :PTKWTIEDGCIKFNG 3immA 43 :PEVWSETDGVLGAVK T0518 107 :GGDLIFAHKFKNFELELEWK 3immA 58 :DESIWTKDEYENFELDLDFK T0518 129 :KGSNSGILYLAQEVTSKDKD 3immA 80 :VGTNSGVVVYCTDTKDWIPN T0518 160 :APEYQILDNANHPDAKLG 3immA 100 :SVEIQIADDHCEKWGNGK T0518 180 :NNRQSASLYDMIPAVP 3immA 118 :PYEKCGAIYGHLGAVQ T0518 198 :SKPFGEWNKAKIMVYKGTVVHGQNDENVLEYHL 3immA 137 :VKKPGEWNHMRIKCAGQHIMVILNGKKVTEMDM T0518 232 :TKQWTDMLQASKFS 3immA 170 :SKWTSGTKNPDGSD T0518 246 :EDKWP 3immA 185 :PSWLP T0518 257 :NNCGGENHEGFIGLQDHGDD 3immA 190 :KPFAELPTKGFIGLQGKHGD T0518 277 :VWFRNIRVKV 3immA 212 :IWFRNIKIRS Number of specific fragments extracted= 12 number of extra gaps= 2 total=54 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 3immA/T0518-3immA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0518 read from 3immA/T0518-3immA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3immA read from 3immA/T0518-3immA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3immA in template set Warning: unaligning (T0518)N59 because first residue in template chain is (3immA)N26 Warning: unaligning (T0518)V127 because of BadResidue code BAD_PEPTIDE in next template residue (3immA)D79 Warning: unaligning (T0518)A128 because of BadResidue code BAD_PEPTIDE at template residue (3immA)D79 Warning: unaligning (T0518)Q196 because of BadResidue code BAD_PEPTIDE in next template residue (3immA)V136 Warning: unaligning (T0518)N197 because of BadResidue code BAD_PEPTIDE at template residue (3immA)V136 Warning: unaligning (T0518)L287 because last residue in template chain is (3immA)L222 T0518 60 :GYITIFD 3immA 27 :KWKPLFG T0518 68 :ETFNGWRGY 3immA 34 :KNLENANYN T0518 82 :PTKWTIEDGCIKF 3immA 43 :PEVWSETDGVLGA T0518 105 :GDGGDLIFAHKFKNFELELEWK 3immA 56 :VKDESIWTKDEYENFELDLDFK T0518 129 :KGSNSGILYLAQEVTSK 3immA 80 :VGTNSGVVVYCTDTKDW T0518 157 :YISAPEYQILDNAN 3immA 97 :IPNSVEIQIADDHC T0518 173 :DAKLGKDNNRQSASLYDMIPA 3immA 111 :EKWGNGKPYEKCGAIYGHLGA T0518 194 :VP 3immA 133 :QD T0518 198 :SKPFGEWNKAKIMVYKGTVVHGQNDENVLEYH 3immA 137 :VKKPGEWNHMRIKCAGQHIMVILNGKKVTEMD T0518 231 :WTKQWTDMLQASKFSEDKWPLAFE 3immA 169 :MSKWTSGTKNPDGSDIPSWLPKPF T0518 260 :GGENHEGFIGLQDHGDD 3immA 193 :AELPTKGFIGLQGKHGD T0518 277 :VWFRNIRVKV 3immA 212 :IWFRNIKIRS Number of specific fragments extracted= 12 number of extra gaps= 2 total=66 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 3immA/T0518-3immA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0518 read from 3immA/T0518-3immA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3immA read from 3immA/T0518-3immA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3immA in template set Warning: unaligning (T0518)G60 because first residue in template chain is (3immA)N26 Warning: unaligning (T0518)V127 because of BadResidue code BAD_PEPTIDE in next template residue (3immA)D79 Warning: unaligning (T0518)A128 because of BadResidue code BAD_PEPTIDE at template residue (3immA)D79 Warning: unaligning (T0518)Q196 because of BadResidue code BAD_PEPTIDE in next template residue (3immA)V136 Warning: unaligning (T0518)N197 because of BadResidue code BAD_PEPTIDE at template residue (3immA)V136 Warning: unaligning (T0518)L287 because last residue in template chain is (3immA)L222 T0518 61 :YITIFDGETFNGWRGYGKD 3immA 27 :KWKPLFGKNLENANYNPEV T0518 85 :WTIEDGCIKFN 3immA 46 :WSETDGVLGAV T0518 106 :DGGDLIFAHKFKNFELELEWK 3immA 57 :KDESIWTKDEYENFELDLDFK T0518 129 :KGSNSGILYLAQEVTS 3immA 80 :VGTNSGVVVYCTDTKD T0518 156 :IYISAPEYQILDNANHPD 3immA 96 :WIPNSVEIQIADDHCEKW T0518 176 :LGKDNNRQSASLYDMIPA 3immA 114 :GNGKPYEKCGAIYGHLGA T0518 194 :VP 3immA 133 :QD T0518 198 :SKPFGEWNKAKIMVYKGTVVHGQNDENVLEYHLWTKQWTDMLQASKFSEDKW 3immA 137 :VKKPGEWNHMRIKCAGQHIMVILNGKKVTEMDMSKWTSGTKNPDGSDIPSWL T0518 256 :LNNCGGENHEGFIGLQDHGDD 3immA 189 :PKPFAELPTKGFIGLQGKHGD T0518 277 :VWFRNIRVKV 3immA 212 :IWFRNIKIRS Number of specific fragments extracted= 10 number of extra gaps= 2 total=76 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 1dypA/T0518-1dypA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1dypA expands to /projects/compbio/data/pdb/1dyp.pdb.gz 1dypA: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 15, because occupancy 0.500 <= existing 0.500 in 1dypA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 16, because occupancy 0.500 <= existing 0.500 in 1dypA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 17, because occupancy 0.500 <= existing 0.500 in 1dypA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 18, because occupancy 0.500 <= existing 0.500 in 1dypA 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 1392, because occupancy 0.500 <= existing 0.500 in 1dypA 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 2051, because occupancy 0.500 <= existing 0.500 in 1dypA Skipped atom 2052, because occupancy 0.500 <= existing 0.500 in 1dypA Skipped atom 2053, because occupancy 0.500 <= existing 0.500 in 1dypA Skipped atom 2054, because occupancy 0.500 <= existing 0.500 in 1dypA Skipped atom 2055, because occupancy 0.500 <= existing 0.500 in 1dypA Skipped atom 2111, because occupancy 0.500 <= existing 0.500 in 1dypA 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 2129, because occupancy 0.500 <= existing 0.500 in 1dypA Skipped atom 2130, because occupancy 0.500 <= existing 0.500 in 1dypA Skipped atom 2131, because occupancy 0.500 <= existing 0.500 in 1dypA Skipped atom 2132, because occupancy 0.500 <= existing 0.500 in 1dypA Skipped atom 2133, because occupancy 0.500 <= existing 0.500 in 1dypA # T0518 read from 1dypA/T0518-1dypA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1dypA read from 1dypA/T0518-1dypA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1dypA to template set # found chain 1dypA in template set T0518 46 :APETDSLN 1dypA 33 :AKPGETWI T0518 57 :DENGYITIFDGETFNGWRGYGKDR 1dypA 41 :LQAKRSDEFNVKDATKWNFQTENY T0518 83 :TKW 1dypA 65 :GVW T0518 86 :TIEDGCIKFNGSGG 1dypA 75 :TVSKGKLKLTTKRE T0518 103 :QDGDGGDLIFAHKFKNFELELEWKVAKGS 1dypA 108 :LYYTSGVAKSRATGNYGYYEARIKGASTF T0518 132 :NSGILYLAQEVTSKDKDG 1dypA 140 :SPAFWMYSTIDRSLTKEG T0518 157 :YISAPEYQILD 1dypA 158 :DVQYSEIDVVE T0518 168 :NAN 1dypA 171 :QKS T0518 171 :HPDAKLGKDNNRQSASLYDMIP 1dypA 181 :DLHNIVVKNGKPTWMRPGSFPQ T0518 196 :QNSKPFGEWNKAKIMVYKGTVVHGQNDENVLEYHLW 1dypA 210 :LPFDPRNDFHTYGVNVTKDKITWYVDGEIVGEKDNL T0518 261 :GENHEGFIGLQDH 1dypA 246 :YWHRQMNLTLSQG T0518 274 :GDD 1dypA 274 :SAN T0518 277 :VWFRNIRVK 1dypA 286 :MEVDYVRTW Number of specific fragments extracted= 13 number of extra gaps= 0 total=89 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 1dypA/T0518-1dypA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0518 read from 1dypA/T0518-1dypA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1dypA read from 1dypA/T0518-1dypA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1dypA in template set T0518 45 :KAPETDSLNLPVDENGYITIFDGETFNGWRGYGKDRV 1dypA 29 :QPPIAKPGETWILQAKRSDEFNVKDATKWNFQTENYG T0518 82 :PTKWTIEDGCIKFNGSG 1dypA 71 :NENATVSKGKLKLTTKR T0518 99 :GGEAQDGDGGDLIFAHKFKNFELELEWKVAKGSN 1dypA 104 :ANYPLYYTSGVAKSRATGNYGYYEARIKGASTFP T0518 134 :GILYLAQEVTSK 1dypA 138 :GVSPAFWMYSTI T0518 146 :DKDGN 1dypA 153 :LTKEG T0518 157 :YISAPEYQILDNANHPDAKLG 1dypA 158 :DVQYSEIDVVELTQKSAVRES T0518 190 :MIPA 1dypA 187 :VKNG T0518 197 :NSKPFGEWNKAKIMVYKGTVVHGQNDENVLEYHL 1dypA 211 :PFDPRNDFHTYGVNVTKDKITWYVDGEIVGEKDN T0518 260 :GGENHEGFIGLQDH 1dypA 245 :LYWHRQMNLTLSQG T0518 274 :GDD 1dypA 274 :SAN T0518 277 :VWFRNIRVKVLD 1dypA 286 :MEVDYVRTWVKV Number of specific fragments extracted= 11 number of extra gaps= 0 total=100 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 1dypA/T0518-1dypA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0518 read from 1dypA/T0518-1dypA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1dypA read from 1dypA/T0518-1dypA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1dypA in template set T0518 52 :LNLPVDENGYIT 1dypA 30 :PPIAKPGETWIL T0518 65 :FDGETFNGWRGYGKDRVP 1dypA 49 :FNVKDATKWNFQTENYGV T0518 83 :TKWTIEDGCIKFNGS 1dypA 72 :ENATVSKGKLKLTTK T0518 98 :GGGEAQDGDGGD 1dypA 98 :CNQQQVANYPLY T0518 110 :LIFAHKFKNFELELEWKVAK 1dypA 115 :AKSRATGNYGYYEARIKGAS T0518 131 :SNSGI 1dypA 135 :TFPGV T0518 136 :LYLAQEVTS 1dypA 142 :AFWMYSTID T0518 150 :NDVLEPIYISAPEYQILDNANHPDA 1dypA 151 :RSLTKEGDVQYSEIDVVELTQKSAV T0518 179 :DNNRQSASLYDMI 1dypA 188 :KNGKPTWMRPGSF T0518 196 :QNSKPFGEWNKAKIMVYKGTVVHGQNDENVLEYHL 1dypA 210 :LPFDPRNDFHTYGVNVTKDKITWYVDGEIVGEKDN Number of specific fragments extracted= 10 number of extra gaps= 0 total=110 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 2hykA/T0518-2hykA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2hykA expands to /projects/compbio/data/pdb/2hyk.pdb.gz 2hykA:Skipped atom 109, because occupancy 0.500 <= existing 0.500 in 2hykA Skipped atom 111, because occupancy 0.500 <= existing 0.500 in 2hykA Skipped atom 332, because occupancy 0.330 <= existing 0.340 in 2hykA Skipped atom 333, because occupancy 0.330 <= existing 0.340 in 2hykA Skipped atom 335, because occupancy 0.330 <= existing 0.340 in 2hykA Skipped atom 336, because occupancy 0.330 <= existing 0.340 in 2hykA Skipped atom 338, because occupancy 0.330 <= existing 0.340 in 2hykA Skipped atom 339, because occupancy 0.330 <= existing 0.340 in 2hykA Skipped atom 341, because occupancy 0.330 <= existing 0.340 in 2hykA Skipped atom 342, because occupancy 0.330 <= existing 0.340 in 2hykA Skipped atom 344, because occupancy 0.330 <= existing 0.340 in 2hykA Skipped atom 345, because occupancy 0.330 <= existing 0.340 in 2hykA Skipped atom 347, because occupancy 0.330 <= existing 0.340 in 2hykA Skipped atom 348, because occupancy 0.330 <= existing 0.340 in 2hykA Skipped atom 350, because occupancy 0.330 <= existing 0.340 in 2hykA Skipped atom 351, because occupancy 0.330 <= existing 0.340 in 2hykA Skipped atom 401, because occupancy 0.500 <= existing 0.500 in 2hykA Skipped atom 403, because occupancy 0.500 <= existing 0.500 in 2hykA Skipped atom 405, because occupancy 0.500 <= existing 0.500 in 2hykA Skipped atom 407, because occupancy 0.500 <= existing 0.500 in 2hykA Skipped atom 898, because occupancy 0.500 <= existing 0.500 in 2hykA Skipped atom 900, because occupancy 0.500 <= existing 0.500 in 2hykA Skipped atom 902, because occupancy 0.500 <= existing 0.500 in 2hykA Skipped atom 904, because occupancy 0.500 <= existing 0.500 in 2hykA Skipped atom 1205, because occupancy 0.350 <= existing 0.650 in 2hykA Skipped atom 1207, because occupancy 0.350 <= existing 0.650 in 2hykA Skipped atom 1209, because occupancy 0.350 <= existing 0.650 in 2hykA Skipped atom 1211, because occupancy 0.350 <= existing 0.650 in 2hykA Skipped atom 1235, because occupancy 0.500 <= existing 0.500 in 2hykA Skipped atom 1237, because occupancy 0.500 <= existing 0.500 in 2hykA Skipped atom 1488, because occupancy 0.500 <= existing 0.500 in 2hykA Skipped atom 1490, because occupancy 0.500 <= existing 0.500 in 2hykA Skipped atom 1633, because occupancy 0.500 <= existing 0.500 in 2hykA Skipped atom 1636, because occupancy 0.500 <= existing 0.500 in 2hykA # T0518 read from 2hykA/T0518-2hykA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2hykA read from 2hykA/T0518-2hykA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2hykA to template set # found chain 2hykA in template set Warning: unaligning (T0518)D57 because first residue in template chain is (2hykA)A7 Warning: unaligning (T0518)C91 because of BadResidue code BAD_PEPTIDE in next template residue (2hykA)L60 Warning: unaligning (T0518)I92 because of BadResidue code BAD_PEPTIDE at template residue (2hykA)L60 Warning: unaligning (T0518)K208 because of BadResidue code BAD_PEPTIDE in next template residue (2hykA)V173 Warning: unaligning (T0518)I209 because of BadResidue code BAD_PEPTIDE at template residue (2hykA)V173 Warning: unaligning (T0518)M210 because of BadResidue code BAD_PEPTIDE in next template residue (2hykA)W175 Warning: unaligning (T0518)V211 because of BadResidue code BAD_PEPTIDE at template residue (2hykA)W175 Warning: unaligning (T0518)V286 because last residue in template chain is (2hykA)E243 T0518 58 :ENGYITIFDGE 2hykA 8 :TLVWSDEFDGP T0518 69 :TFNGWRGYGK 2hykA 24 :DPANWNHETG T0518 82 :PTKW 2hykA 34 :DHGW T0518 86 :TI 2hykA 53 :AL T0518 88 :EDG 2hykA 56 :GNG T0518 93 :KFNGSG 2hykA 61 :VITARQ T0518 100 :GEAQDGDGGDLIFAHK 2hykA 67 :EADGGYTSARLTTQNK T0518 116 :FKNFELELEWKV 2hykA 85 :PQYGRVEASIQI T0518 128 :AKGSNSGILYLAQEVTSKD 2hykA 99 :GQGIWPAFWMLGADFPNTP T0518 157 :YISAPEYQILD 2hykA 118 :WPDSGEIDIME T0518 168 :NANHPDA 2hykA 130 :IGREPHL T0518 175 :KLGKDNNRQSASLYDMIP 2hykA 140 :SLHGPGYFGGEPLTGSYM T0518 194 :VPQNSKPFGEWNKA 2hykA 158 :HPQGWSFADTFHTF T0518 212 :YKGTVVHGQNDENVLEYHLW 2hykA 176 :RPGSITWSVDGVAYQTYTSA T0518 234 :QWTDMLQASK 2hykA 196 :DTRGNPWVFD T0518 245 :SEDKWPLAFELLNNCGGENHEGF 2hykA 206 :QPFFMILNVAVGGDWPGYPDGST T0518 272 :DHGDDVWFRNIRVK 2hykA 229 :QFPQEMRVDYVRVY Number of specific fragments extracted= 17 number of extra gaps= 2 total=127 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 2hykA/T0518-2hykA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0518 read from 2hykA/T0518-2hykA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2hykA read from 2hykA/T0518-2hykA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2hykA in template set Warning: unaligning (T0518)D57 because first residue in template chain is (2hykA)A7 Warning: unaligning (T0518)C91 because of BadResidue code BAD_PEPTIDE in next template residue (2hykA)L60 Warning: unaligning (T0518)I92 because of BadResidue code BAD_PEPTIDE at template residue (2hykA)L60 Warning: unaligning (T0518)K208 because of BadResidue code BAD_PEPTIDE in next template residue (2hykA)V173 Warning: unaligning (T0518)I209 because of BadResidue code BAD_PEPTIDE at template residue (2hykA)V173 Warning: unaligning (T0518)M210 because of BadResidue code BAD_PEPTIDE in next template residue (2hykA)W175 Warning: unaligning (T0518)V211 because of BadResidue code BAD_PEPTIDE at template residue (2hykA)W175 Warning: unaligning (T0518)V286 because last residue in template chain is (2hykA)E243 T0518 58 :ENGYITIFDGE 2hykA 8 :TLVWSDEFDGP T0518 69 :TFNGWRGYGKDRV 2hykA 24 :DPANWNHETGDHG T0518 82 :PTKWTI 2hykA 49 :RANSAL T0518 88 :EDG 2hykA 56 :GNG T0518 93 :KFNGSGGGEA 2hykA 61 :VITARQEADG T0518 104 :DGDGGDLIFAHK 2hykA 71 :GYTSARLTTQNK T0518 116 :FKNFELELEWKVAKGS 2hykA 85 :PQYGRVEASIQIPRGQ T0518 134 :GILYLAQEVTSKDKDGN 2hykA 101 :GIWPAFWMLGADFPNTP T0518 157 :YISAPEYQILD 2hykA 118 :WPDSGEIDIME T0518 168 :NANHPD 2hykA 130 :IGREPH T0518 174 :AKLGKDNNRQSASLYDMI 2hykA 139 :GSLHGPGYFGGEPLTGSY T0518 193 :AVPQNSKPFGEWNKA 2hykA 157 :MHPQGWSFADTFHTF T0518 212 :YKGTVVHGQNDENVLEYHLWTK 2hykA 176 :RPGSITWSVDGVAYQTYTSADT T0518 246 :EDKWP 2hykA 198 :RGNPW T0518 261 :GENHEGFIGLQDH 2hykA 203 :VFDQPFFMILNVA T0518 277 :VWFRNIRVK 2hykA 234 :MRVDYVRVY Number of specific fragments extracted= 16 number of extra gaps= 2 total=143 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 2hykA/T0518-2hykA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0518 read from 2hykA/T0518-2hykA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2hykA read from 2hykA/T0518-2hykA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2hykA in template set Warning: unaligning (T0518)C91 because of BadResidue code BAD_PEPTIDE in next template residue (2hykA)L60 Warning: unaligning (T0518)I92 because of BadResidue code BAD_PEPTIDE at template residue (2hykA)L60 Warning: unaligning (T0518)K208 because of BadResidue code BAD_PEPTIDE in next template residue (2hykA)V173 Warning: unaligning (T0518)I209 because of BadResidue code BAD_PEPTIDE at template residue (2hykA)V173 Warning: unaligning (T0518)M210 because of BadResidue code BAD_PEPTIDE in next template residue (2hykA)W175 Warning: unaligning (T0518)V211 because of BadResidue code BAD_PEPTIDE at template residue (2hykA)W175 T0518 51 :SLNLPVDENGYITI 2hykA 18 :PAGSAPDPANWNHE T0518 68 :ETFNGWRGY 2hykA 32 :TGDHGWGNN T0518 83 :TKWTI 2hykA 50 :ANSAL T0518 88 :EDG 2hykA 56 :GNG T0518 93 :KFNGSGG 2hykA 61 :VITARQE T0518 104 :DGDG 2hykA 68 :ADGG T0518 108 :GDLIFAHKF 2hykA 75 :ARLTTQNKV T0518 117 :KNFELELEWKVAKGSNSGILYLAQEVTS 2hykA 86 :QYGRVEASIQIPRGQGIWPAFWMLGADF T0518 153 :LEPIYISAPEYQILDNANHPDA 2hykA 114 :PNTPWPDSGEIDIMENIGREPH T0518 175 :KLGKD 2hykA 145 :GYFGG T0518 194 :VPQNSKPFGEWNKA 2hykA 158 :HPQGWSFADTFHTF T0518 212 :YKGTVVHGQNDENVLEYHLW 2hykA 176 :RPGSITWSVDGVAYQTYTSA T0518 254 :ELLNNCGGENHEGFIGLQ 2hykA 196 :DTRGNPWVFDQPFFMILN T0518 272 :DHGDD 2hykA 219 :DWPGY T0518 277 :VWFRNIRVK 2hykA 234 :MRVDYVRVY Number of specific fragments extracted= 15 number of extra gaps= 2 total=158 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 2vy0A/T0518-2vy0A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2vy0A expands to /projects/compbio/data/pdb/2vy0.pdb.gz 2vy0A:Skipped atom 922, because occupancy 0.500 <= existing 0.500 in 2vy0A Skipped atom 923, because occupancy 0.500 <= existing 0.500 in 2vy0A Skipped atom 924, because occupancy 0.500 <= existing 0.500 in 2vy0A Skipped atom 925, because occupancy 0.500 <= existing 0.500 in 2vy0A Skipped atom 926, because occupancy 0.500 <= existing 0.500 in 2vy0A Skipped atom 927, because occupancy 0.500 <= existing 0.500 in 2vy0A Skipped atom 1746, because occupancy 0.500 <= existing 0.500 in 2vy0A Skipped atom 1747, because occupancy 0.500 <= existing 0.500 in 2vy0A Skipped atom 1748, because occupancy 0.500 <= existing 0.500 in 2vy0A Skipped atom 1749, because occupancy 0.500 <= existing 0.500 in 2vy0A Skipped atom 1750, because occupancy 0.500 <= existing 0.500 in 2vy0A Skipped atom 1751, because occupancy 0.500 <= existing 0.500 in 2vy0A Skipped atom 1752, because occupancy 0.500 <= existing 0.500 in 2vy0A Skipped atom 1753, because occupancy 0.500 <= existing 0.500 in 2vy0A Skipped atom 1944, because occupancy 0.500 <= existing 0.500 in 2vy0A Skipped atom 1945, because occupancy 0.500 <= existing 0.500 in 2vy0A Skipped atom 1946, because occupancy 0.500 <= existing 0.500 in 2vy0A Skipped atom 1947, because occupancy 0.500 <= existing 0.500 in 2vy0A Skipped atom 1948, because occupancy 0.500 <= existing 0.500 in 2vy0A Skipped atom 1949, because occupancy 0.500 <= existing 0.500 in 2vy0A Skipped atom 1950, because occupancy 0.500 <= existing 0.500 in 2vy0A Skipped atom 1951, because occupancy 0.500 <= existing 0.500 in 2vy0A Skipped atom 1952, because occupancy 0.500 <= existing 0.500 in 2vy0A Skipped atom 1953, because occupancy 0.500 <= existing 0.500 in 2vy0A Skipped atom 1954, because occupancy 0.500 <= existing 0.500 in 2vy0A Skipped atom 1955, because occupancy 0.500 <= existing 0.500 in 2vy0A Skipped atom 1956, because occupancy 0.500 <= existing 0.500 in 2vy0A Skipped atom 1957, because occupancy 0.500 <= existing 0.500 in 2vy0A # T0518 read from 2vy0A/T0518-2vy0A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2vy0A read from 2vy0A/T0518-2vy0A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2vy0A to template set # found chain 2vy0A in template set Warning: unaligning (T0518)N118 because of BadResidue code BAD_PEPTIDE at template residue (2vy0A)P134 Warning: unaligning (T0518)Y157 because of BadResidue code BAD_PEPTIDE in next template residue (2vy0A)P166 Warning: unaligning (T0518)I158 because of BadResidue code BAD_PEPTIDE at template residue (2vy0A)P166 Warning: unaligning (T0518)I209 because of BadResidue code BAD_PEPTIDE in next template residue (2vy0A)V222 Warning: unaligning (T0518)M210 because of BadResidue code BAD_PEPTIDE at template residue (2vy0A)V222 Warning: unaligning (T0518)D275 because of BadResidue code BAD_PEPTIDE in next template residue (2vy0A)P281 Warning: unaligning (T0518)D276 because of BadResidue code BAD_PEPTIDE at template residue (2vy0A)P281 T0518 60 :GYITIFDGE 2vy0A 49 :IWHDEFEGS T0518 69 :TFNGWRGY 2vy0A 60 :NKEYWTFE T0518 77 :G 2vy0A 88 :T T0518 82 :PTKWTIEDGCIKFNGSGG 2vy0A 89 :ENNTYIVNGTLVIEARKE T0518 101 :EAQDGDGGDLIFAHK 2vy0A 114 :GTFLYTSSRLKTEGK T0518 116 :FK 2vy0A 131 :FS T0518 119 :FELELEWKV 2vy0A 135 :VVVEARIKL T0518 128 :AKGSNSGILYLAQEVTSKD 2vy0A 146 :GKGLWPAFWMLGSNIREVG T0518 159 :SAPEYQILDNANHPDA 2vy0A 167 :NCGEIDIMEFLGHEPR T0518 175 :KLGKDNNRQSASLYDMIPAVPQNSKPFGEWNKAK 2vy0A 187 :TVHGPGYSGSKGITRAYTLPEGVPDFTEDFHVFG T0518 211 :VYKGTVVHGQNDENVLEYHL 2vy0A 223 :WYPDKIKWYVDGTFYHEVTK T0518 236 :TDMLQASKFS 2vy0A 243 :EQVEAMGYEW T0518 246 :EDKWPLAFELLNNCGGENHEGF 2vy0A 257 :PFYIILNLAVGGYWPGNPDATT T0518 274 :G 2vy0A 279 :P T0518 277 :VWFRNIRVK 2vy0A 284 :MVVDYVRVY Number of specific fragments extracted= 15 number of extra gaps= 4 total=173 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 2vy0A/T0518-2vy0A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0518 read from 2vy0A/T0518-2vy0A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2vy0A read from 2vy0A/T0518-2vy0A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2vy0A in template set Warning: unaligning (T0518)N118 because of BadResidue code BAD_PEPTIDE at template residue (2vy0A)P134 Warning: unaligning (T0518)Y157 because of BadResidue code BAD_PEPTIDE in next template residue (2vy0A)P166 Warning: unaligning (T0518)I158 because of BadResidue code BAD_PEPTIDE at template residue (2vy0A)P166 Warning: unaligning (T0518)I209 because of BadResidue code BAD_PEPTIDE in next template residue (2vy0A)V222 Warning: unaligning (T0518)M210 because of BadResidue code BAD_PEPTIDE at template residue (2vy0A)V222 T0518 61 :YITIFDGE 2vy0A 50 :WHDEFEGS T0518 69 :TFNGWRGYGKDRV 2vy0A 60 :NKEYWTFEKGNGI T0518 82 :PTKWTIEDGCIKFNGSGGG 2vy0A 89 :ENNTYIVNGTLVIEARKEI T0518 101 :EAQDGDGGDLIFAHK 2vy0A 114 :GTFLYTSSRLKTEGK T0518 116 :FK 2vy0A 131 :FS T0518 119 :FELELEWKVAKGS 2vy0A 135 :VVVEARIKLPKGK T0518 134 :GILYLAQEVTSKDKDGN 2vy0A 148 :GLWPAFWMLGSNIREVG T0518 159 :SAPEYQILD 2vy0A 167 :NCGEIDIME T0518 168 :NANHPDA 2vy0A 177 :LGHEPRT T0518 175 :KLGKDNNRQSASLYDMIPAVPQNSKPFGEWNKAK 2vy0A 187 :TVHGPGYSGSKGITRAYTLPEGVPDFTEDFHVFG T0518 211 :VYKGTVVHGQNDENVLEYH 2vy0A 223 :WYPDKIKWYVDGTFYHEVT T0518 236 :TDMLQASKFSE 2vy0A 242 :KEQVEAMGYEW T0518 261 :GENHEGFIGLQDH 2vy0A 253 :VFDKPFYIILNLA T0518 275 :DD 2vy0A 272 :GN T0518 277 :VWFRNIRVKVL 2vy0A 284 :MVVDYVRVYSF Number of specific fragments extracted= 15 number of extra gaps= 3 total=188 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 2vy0A/T0518-2vy0A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0518 read from 2vy0A/T0518-2vy0A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2vy0A read from 2vy0A/T0518-2vy0A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2vy0A in template set Warning: unaligning (T0518)N118 because of BadResidue code BAD_PEPTIDE at template residue (2vy0A)P134 Warning: unaligning (T0518)Y157 because of BadResidue code BAD_PEPTIDE in next template residue (2vy0A)P166 Warning: unaligning (T0518)I158 because of BadResidue code BAD_PEPTIDE at template residue (2vy0A)P166 Warning: unaligning (T0518)I209 because of BadResidue code BAD_PEPTIDE in next template residue (2vy0A)V222 Warning: unaligning (T0518)M210 because of BadResidue code BAD_PEPTIDE at template residue (2vy0A)V222 T0518 65 :FDGETF 2vy0A 54 :FEGSEV T0518 71 :NGWRGY 2vy0A 62 :EYWTFE T0518 77 :GKDR 2vy0A 88 :TENN T0518 85 :WTIEDGCIKFNGSGGGEAQDGDG 2vy0A 92 :TYIVNGTLVIEARKEIITDPNEG T0518 108 :GDLIFAHKFK 2vy0A 121 :SRLKTEGKVE T0518 119 :FELELEWKVAKGSNSGILYLAQEVTS 2vy0A 135 :VVVEARIKLPKGKGLWPAFWMLGSNI T0518 153 :LEPI 2vy0A 161 :REVG T0518 159 :SAPEYQILDNANHPDA 2vy0A 167 :NCGEIDIMEFLGHEPR T0518 177 :GKDNNRQSASLYDMIPAVPQNSKPFGEWNKAK 2vy0A 189 :HGPGYSGSKGITRAYTLPEGVPDFTEDFHVFG T0518 211 :VYKGTVVHGQNDENVLEYH 2vy0A 223 :WYPDKIKWYVDGTFYHEVT T0518 236 :TDMLQASKFS 2vy0A 242 :KEQVEAMGYE T0518 260 :GGENHEGFIGLQDH 2vy0A 252 :WVFDKPFYIILNLA T0518 277 :VWFRNIRV 2vy0A 284 :MVVDYVRV Number of specific fragments extracted= 13 number of extra gaps= 3 total=201 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 2ayhA/T0518-2ayhA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2ayhA expands to /projects/compbio/data/pdb/2ayh.pdb.gz 2ayhA:Skipped atom 1354, because occupancy 0.500 <= existing 0.500 in 2ayhA Skipped atom 1356, because occupancy 0.500 <= existing 0.500 in 2ayhA Skipped atom 1358, because occupancy 0.500 <= existing 0.500 in 2ayhA Skipped atom 1423, because occupancy 0.250 <= existing 0.750 in 2ayhA # T0518 read from 2ayhA/T0518-2ayhA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2ayhA read from 2ayhA/T0518-2ayhA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2ayhA to template set # found chain 2ayhA in template set Warning: unaligning (T0518)G98 because of BadResidue code BAD_PEPTIDE in next template residue (2ayhA)S54 Warning: unaligning (T0518)G99 because of BadResidue code BAD_PEPTIDE at template residue (2ayhA)S54 Warning: unaligning (T0518)L287 because last residue in template chain is (2ayhA)N214 T0518 57 :DENGYITIFDGETFNGWRGY 2ayhA 2 :TGGSFFEPFNSYNSGTWEKA T0518 77 :GKDRVPTKW 2ayhA 26 :NGGVFNCTW T0518 86 :TI 2ayhA 40 :NF T0518 88 :EDGCIKFNGS 2ayhA 43 :NDGKLKLGLT T0518 100 :GEAQ 2ayhA 55 :AYNK T0518 105 :GDGGDLIFAHKFKNFELELEWKV 2ayhA 59 :FDCAEYRSTNIYGYGLYEVSMKP T0518 128 :AKGSNSGILYLAQEVT 2ayhA 84 :NTGIVSSFFTYTGPAH T0518 157 :YISAPEYQILD 2ayhA 100 :GTQWDEIDIEF T0518 168 :NANHPDAKLGKDNNRQSASLYDMIPAVPQN 2ayhA 114 :DTTKVQFNYYTNGVGGHEKVISLGFDASKG T0518 204 :WNKAKIMVYKGTVVHGQNDENVLEYHL 2ayhA 144 :FHTYAFDWQPGYIKWYVDGVLKHTATA T0518 261 :GENHE 2ayhA 171 :NIPST T0518 266 :GFIGLQDHGDD 2ayhA 179 :IMMNLWNGTGV T0518 277 :VWFRNIRVKV 2ayhA 204 :AEYDWVKYTS Number of specific fragments extracted= 13 number of extra gaps= 1 total=214 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 2ayhA/T0518-2ayhA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0518 read from 2ayhA/T0518-2ayhA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2ayhA read from 2ayhA/T0518-2ayhA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2ayhA in template set Warning: unaligning (T0518)G98 because of BadResidue code BAD_PEPTIDE in next template residue (2ayhA)S54 Warning: unaligning (T0518)G99 because of BadResidue code BAD_PEPTIDE at template residue (2ayhA)S54 T0518 59 :NGYITIFDGETFNGWRGYGKDRV 2ayhA 4 :GSFFEPFNSYNSGTWEKADGYSN T0518 82 :PTKWTI 2ayhA 36 :ANNVNF T0518 88 :EDGCIKFNGS 2ayhA 43 :NDGKLKLGLT T0518 100 :GEA 2ayhA 55 :AYN T0518 104 :DGDGGDLIFAHKFKNFELELEWKVAKGS 2ayhA 58 :KFDCAEYRSTNIYGYGLYEVSMKPAKNT T0518 134 :GILYLAQEVTSKDK 2ayhA 86 :GIVSSFFTYTGPAH T0518 157 :YISAPEYQILDNANHPDA 2ayhA 100 :GTQWDEIDIEFLGKDTTK T0518 175 :KLGKDNNRQSASLYDMIPAVPQ 2ayhA 121 :NYYTNGVGGHEKVISLGFDASK T0518 203 :EWNKAKIMVYKGTVVHGQNDENVLEYHLW 2ayhA 143 :GFHTYAFDWQPGYIKWYVDGVLKHTATAN T0518 261 :GENHEGF 2ayhA 172 :IPSTPGK T0518 268 :IGLQDHGDD 2ayhA 181 :MNLWNGTGV T0518 277 :VWFRNIRVKV 2ayhA 204 :AEYDWVKYTS Number of specific fragments extracted= 12 number of extra gaps= 1 total=226 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 2ayhA/T0518-2ayhA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0518 read from 2ayhA/T0518-2ayhA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2ayhA read from 2ayhA/T0518-2ayhA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2ayhA in template set Warning: unaligning (T0518)F94 because of BadResidue code BAD_PEPTIDE in next template residue (2ayhA)S54 Warning: unaligning (T0518)N95 because of BadResidue code BAD_PEPTIDE at template residue (2ayhA)S54 T0518 83 :TKWTIEDG 2ayhA 37 :NNVNFTND T0518 91 :CIK 2ayhA 50 :GLT T0518 96 :GSG 2ayhA 55 :AYN T0518 104 :DGDGGDLIFAHKFKNFELELEWKVAKGSNSGILYLAQEVTS 2ayhA 58 :KFDCAEYRSTNIYGYGLYEVSMKPAKNTGIVSSFFTYTGPA T0518 156 :IYISAPEYQILDNANHPDA 2ayhA 99 :HGTQWDEIDIEFLGKDTTK T0518 178 :KDNNRQSASLYDM 2ayhA 124 :TNGVGGHEKVISL T0518 197 :NSKPFGEWNKAKIMVYKGTVVHGQNDENVLEYHLWT 2ayhA 137 :GFDASKGFHTYAFDWQPGYIKWYVDGVLKHTATANI T0518 260 :GGENHEGFIGLQDHGDD 2ayhA 173 :PSTPGKIMMNLWNGTGV T0518 277 :VWFRNIRVKV 2ayhA 204 :AEYDWVKYTS Number of specific fragments extracted= 9 number of extra gaps= 1 total=235 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 2ayh/T0518-2ayh-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2ayh expands to /projects/compbio/data/pdb/2ayh.pdb.gz 2ayh:Warning: there is no chain 2ayh will retry with 2ayhA Skipped atom 1354, because occupancy 0.500 <= existing 0.500 in 2ayh Skipped atom 1356, because occupancy 0.500 <= existing 0.500 in 2ayh Skipped atom 1358, because occupancy 0.500 <= existing 0.500 in 2ayh Skipped atom 1423, because occupancy 0.250 <= existing 0.750 in 2ayh # T0518 read from 2ayh/T0518-2ayh-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2ayh read from 2ayh/T0518-2ayh-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2ayh to template set # found chain 2ayh in template set Warning: unaligning (T0518)E31 because first residue in template chain is (2ayh)Q1 Warning: unaligning (T0518)G98 because of BadResidue code BAD_PEPTIDE in next template residue (2ayh)S54 Warning: unaligning (T0518)G99 because of BadResidue code BAD_PEPTIDE at template residue (2ayh)S54 T0518 57 :DENGYITIFDGETFNGWRGY 2ayh 2 :TGGSFFEPFNSYNSGTWEKA T0518 77 :GKDRVPTKW 2ayh 26 :NGGVFNCTW T0518 86 :TI 2ayh 40 :NF T0518 88 :EDGCIKFNGS 2ayh 43 :NDGKLKLGLT T0518 100 :GEAQD 2ayh 55 :AYNKF T0518 106 :DGGDLIFAHKFKNFELELEWKV 2ayh 60 :DCAEYRSTNIYGYGLYEVSMKP T0518 128 :AKGSNSGILYLAQEVT 2ayh 84 :NTGIVSSFFTYTGPAH T0518 157 :YISAPEYQILD 2ayh 100 :GTQWDEIDIEF T0518 168 :NANHPDAKLGKDNNRQSASLYDMIPAVP 2ayh 114 :DTTKVQFNYYTNGVGGHEKVISLGFDAS T0518 202 :GEWNKAKIMVYKGTVVHGQNDENVLEYHL 2ayh 142 :KGFHTYAFDWQPGYIKWYVDGVLKHTATA T0518 261 :GENHE 2ayh 171 :NIPST T0518 266 :GFIGLQDHGDD 2ayh 179 :IMMNLWNGTGV T0518 277 :VWFRNIRVKV 2ayh 204 :AEYDWVKYTS Number of specific fragments extracted= 13 number of extra gaps= 1 total=248 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 2ayh/T0518-2ayh-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0518 read from 2ayh/T0518-2ayh-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2ayh read from 2ayh/T0518-2ayh-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2ayh in template set Warning: unaligning (T0518)G98 because of BadResidue code BAD_PEPTIDE in next template residue (2ayh)S54 Warning: unaligning (T0518)G99 because of BadResidue code BAD_PEPTIDE at template residue (2ayh)S54 T0518 60 :GYITIFDGETFNGWRGYGKDRV 2ayh 5 :SFFEPFNSYNSGTWEKADGYSN T0518 82 :PTKWTI 2ayh 36 :ANNVNF T0518 88 :EDGCIKFNGS 2ayh 43 :NDGKLKLGLT T0518 100 :GEA 2ayh 55 :AYN T0518 104 :DGDGGDLIFAHKFKNFELELEWKVAKGS 2ayh 58 :KFDCAEYRSTNIYGYGLYEVSMKPAKNT T0518 134 :GILYLAQEVTSKDKDGN 2ayh 86 :GIVSSFFTYTGPAHGTQ T0518 157 :YI 2ayh 103 :WD T0518 162 :EYQILDNANHPDA 2ayh 105 :EIDIEFLGKDTTK T0518 175 :KLGKDNNRQSASLYDMIPAVPQ 2ayh 121 :NYYTNGVGGHEKVISLGFDASK T0518 203 :EWNKAKIMVYKGTVVHGQNDENVLEYHLW 2ayh 143 :GFHTYAFDWQPGYIKWYVDGVLKHTATAN T0518 261 :GENHEGF 2ayh 172 :IPSTPGK T0518 268 :IGLQDHGDD 2ayh 181 :MNLWNGTGV T0518 277 :VWFRNIRVKV 2ayh 204 :AEYDWVKYTS Number of specific fragments extracted= 13 number of extra gaps= 1 total=261 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 2ayh/T0518-2ayh-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0518 read from 2ayh/T0518-2ayh-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2ayh read from 2ayh/T0518-2ayh-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2ayh in template set Warning: unaligning (T0518)G98 because of BadResidue code BAD_PEPTIDE in next template residue (2ayh)S54 Warning: unaligning (T0518)G99 because of BadResidue code BAD_PEPTIDE at template residue (2ayh)S54 T0518 65 :FDGETFNGWRGYGKDRVPT 2ayh 10 :FNSYNSGTWEKADGYSNGG T0518 85 :WTI 2ayh 39 :VNF T0518 88 :EDGCIKFNGS 2ayh 43 :NDGKLKLGLT T0518 100 :GEA 2ayh 55 :AYN T0518 104 :DGDGGDLIFAHKFKNFELELEWKVAKGSNSGILYLAQEVTS 2ayh 58 :KFDCAEYRSTNIYGYGLYEVSMKPAKNTGIVSSFFTYTGPA T0518 156 :IYISAPEYQILDNANHPDA 2ayh 99 :HGTQWDEIDIEFLGKDTTK T0518 178 :KDNNRQSASLYDM 2ayh 124 :TNGVGGHEKVISL T0518 197 :NSKPFGEWNKAKIMVYKGTVVHGQNDENVLEYHLWT 2ayh 137 :GFDASKGFHTYAFDWQPGYIKWYVDGVLKHTATANI T0518 260 :GGENHEGFIGLQDHGDD 2ayh 173 :PSTPGKIMMNLWNGTGV T0518 277 :VWFRNIRVKV 2ayh 204 :AEYDWVKYTS Number of specific fragments extracted= 10 number of extra gaps= 1 total=271 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 1gbgA/T0518-1gbgA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1gbgA expands to /projects/compbio/data/pdb/1gbg.pdb.gz 1gbgA:Skipped atom 397, because occupancy 0.500 <= existing 0.500 in 1gbgA # T0518 read from 1gbgA/T0518-1gbgA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1gbgA read from 1gbgA/T0518-1gbgA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1gbgA to template set # found chain 1gbgA in template set T0518 57 :DENGYITIFDGETFNGWRGY 1gbgA 2 :TGGSFYEPFNNYNTGLWQKA T0518 77 :GKDRVPTKW 1gbgA 26 :NGNMFNCTW T0518 86 :TI 1gbgA 40 :SM T0518 88 :EDGCIKFNGSG 1gbgA 43 :SLGEMRLSLTS T0518 100 :GEAQDGDGGDLIFAHKFKNFELELEWKV 1gbgA 54 :PSYNKFDCGENRSVQTYGYGLYEVNMKP T0518 128 :AKGSNSGILYLAQEVT 1gbgA 84 :NVGIVSSFFTYTGPTD T0518 157 :YISAPEYQILD 1gbgA 100 :GTPWDEIDIEF T0518 168 :NANHPDAKLGKDNNRQSASLYDMIPAVP 1gbgA 114 :DTTKVQFNYYTNGVGNHEKIVNLGFDAA T0518 202 :GEWNKAKIMVYKGTVVHGQNDENVLEYHL 1gbgA 142 :NSYHTYAFDWQPNSIKWYVDGQLKHTATT T0518 261 :GENHE 1gbgA 171 :QIPQT T0518 266 :GFIGLQDHGDD 1gbgA 179 :IMMNLWNGAGV T0518 277 :VWFRNIRVKV 1gbgA 204 :AHYNWVRYTK Number of specific fragments extracted= 12 number of extra gaps= 0 total=283 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 1gbgA/T0518-1gbgA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0518 read from 1gbgA/T0518-1gbgA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1gbgA read from 1gbgA/T0518-1gbgA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1gbgA in template set Warning: unaligning (T0518)L287 because last residue in template chain is (1gbgA)R214 T0518 59 :NGYITIFDGETFNGWR 1gbgA 4 :GSFYEPFNNYNTGLWQ T0518 75 :GYGKDRV 1gbgA 24 :YSNGNMF T0518 82 :PTKWTI 1gbgA 36 :ANNVSM T0518 88 :EDGCIKFNGSGGGEA 1gbgA 43 :SLGEMRLSLTSPSYN T0518 104 :DGDGGDLIFAHKFKNFELELEWKVAKGS 1gbgA 58 :KFDCGENRSVQTYGYGLYEVNMKPAKNV T0518 134 :GILYLAQEVTSKDK 1gbgA 86 :GIVSSFFTYTGPTD T0518 157 :YISAPEYQILDNANHPDA 1gbgA 100 :GTPWDEIDIEFLGKDTTK T0518 175 :KLGKDNNRQSASLYDMIPAV 1gbgA 121 :NYYTNGVGNHEKIVNLGFDA T0518 201 :FGEWNKAKIMVYKGTVVHGQNDENVLEYHLWTK 1gbgA 141 :ANSYHTYAFDWQPNSIKWYVDGQLKHTATTQIP T0518 261 :GENHEGFIGLQDHGDD 1gbgA 174 :QTPGKIMMNLWNGAGV T0518 277 :VWFRNIRVKV 1gbgA 204 :AHYNWVRYTK Number of specific fragments extracted= 11 number of extra gaps= 0 total=294 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 1gbgA/T0518-1gbgA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0518 read from 1gbgA/T0518-1gbgA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1gbgA read from 1gbgA/T0518-1gbgA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1gbgA in template set T0518 68 :ETFNGWRGYGKDRVPT 1gbgA 13 :YNTGLWQKADGYSNGN T0518 84 :KWTIEDGCIKFNGSGGGEAQDGDGGDLIFAHKFKNFELELEWKVAKGSNSGILYLAQEVTS 1gbgA 38 :NVSMTSLGEMRLSLTSPSYNKFDCGENRSVQTYGYGLYEVNMKPAKNVGIVSSFFTYTGPT T0518 156 :IYISAPEYQILDNANHPDA 1gbgA 99 :DGTPWDEIDIEFLGKDTTK T0518 175 :KLGKDNNRQSASLYDM 1gbgA 121 :NYYTNGVGNHEKIVNL T0518 197 :NSKPFGEWNKAKIMVYKGTVVHGQNDENVLEYHLWT 1gbgA 137 :GFDAANSYHTYAFDWQPNSIKWYVDGQLKHTATTQI T0518 260 :GGENHEGFIGLQDHGDD 1gbgA 173 :PQTPGKIMMNLWNGAGV T0518 277 :VWFRNIRVKV 1gbgA 204 :AHYNWVRYTK Number of specific fragments extracted= 7 number of extra gaps= 0 total=301 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 3juuA/T0518-3juuA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 3juuA expands to /projects/compbio/data/pdb/3juu.pdb.gz 3juuA:Skipped atom 24, because occupancy 0.500 <= existing 0.500 in 3juuA Skipped atom 28, because occupancy 0.500 <= existing 0.500 in 3juuA Skipped atom 30, because occupancy 0.500 <= existing 0.500 in 3juuA Skipped atom 32, because occupancy 0.500 <= existing 0.500 in 3juuA Skipped atom 34, because occupancy 0.500 <= existing 0.500 in 3juuA Skipped atom 36, because occupancy 0.500 <= existing 0.500 in 3juuA Skipped atom 38, because occupancy 0.500 <= existing 0.500 in 3juuA # T0518 read from 3juuA/T0518-3juuA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3juuA read from 3juuA/T0518-3juuA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3juuA to template set # found chain 3juuA in template set Warning: unaligning (T0518)K45 because first residue in template chain is (3juuA)E23 Warning: unaligning (T0518)Q140 because of BadResidue code BAD_PEPTIDE in next template residue (3juuA)G144 Warning: unaligning (T0518)V142 because of BadResidue code BAD_PEPTIDE at template residue (3juuA)G144 Warning: unaligning (T0518)N168 because of BadResidue code BAD_PEPTIDE in next template residue (3juuA)V163 Warning: unaligning (T0518)A169 because of BadResidue code BAD_PEPTIDE at template residue (3juuA)V163 T0518 46 :APETDSLNLPVDENG 3juuA 24 :APHFKPGEDPRQPHQ T0518 61 :YITI 3juuA 40 :WKLI T0518 65 :FDGE 3juuA 50 :FEGK T0518 69 :TFNGWRGYGKDRV 3juuA 56 :DEKKWQISGQGWI T0518 82 :PTKW 3juuA 70 :RAPG T0518 86 :TIEDGCIKFNGSGG 3juuA 81 :SLNNGSLQITTTML T0518 100 :GEAQDGDGGDLIFAHKFKNFELELEWKV 3juuA 102 :NKTYTHGGGYVGSRNGMTYGYYECEMKA T0518 128 :AKGSNSGILYLA 3juuA 131 :KTFMSSTFWLIN T0518 143 :TSKDKD 3juuA 145 :KDRLGC T0518 157 :YISAPEYQILD 3juuA 151 :DKRTTELDIQE T0518 170 :NHPDAKLGKDNNRQSASLYDMI 3juuA 164 :GQITNDADWMKYFDQTMNSNTH T0518 192 :PAVPQNSKP 3juuA 188 :NIPEGCEYE T0518 201 :FGEWNKAKIMVY 3juuA 211 :YEDFHVYGVWWK T0518 213 :KGTVVHGQNDENVLEYHLW 3juuA 224 :KDEIIFFLDGKMQSKVTPP T0518 242 :SKFS 3juuA 243 :ADFD T0518 246 :EDKWPLAFELLNNCGGENHEG 3juuA 248 :EMYLRMVVETYDWNPVPKDGG T0518 272 :DHGDD 3juuA 269 :MTGSK T0518 277 :VWFRNIRVKVL 3juuA 278 :TTYNWVRSWQL Number of specific fragments extracted= 18 number of extra gaps= 2 total=319 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 3juuA/T0518-3juuA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0518 read from 3juuA/T0518-3juuA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3juuA read from 3juuA/T0518-3juuA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3juuA in template set Warning: unaligning (T0518)S144 because of BadResidue code BAD_PEPTIDE at template residue (3juuA)G144 Warning: unaligning (T0518)N168 because of BadResidue code BAD_PEPTIDE in next template residue (3juuA)V163 Warning: unaligning (T0518)A169 because of BadResidue code BAD_PEPTIDE at template residue (3juuA)V163 T0518 45 :KAPETDSLNLPVDENGYITI 3juuA 24 :APHFKPGEDPRQPHQEWKLI T0518 65 :FDGE 3juuA 50 :FEGK T0518 69 :TFNGWRGYGKDRV 3juuA 56 :DEKKWQISGQGWI T0518 82 :PTKWTIEDGCIKFNGSG 3juuA 77 :AENISLNNGSLQITTTM T0518 100 :GEAQDGDGGDLIFAHKFKNFELELEWKVAKG 3juuA 102 :NKTYTHGGGYVGSRNGMTYGYYECEMKANKT T0518 134 :GILYLAQEVT 3juuA 133 :FMSSTFWLIN T0518 145 :KDKDGN 3juuA 145 :KDRLGC T0518 157 :YISAPEYQILD 3juuA 151 :DKRTTELDIQE T0518 170 :NHPDAKLGKDNNR 3juuA 164 :GQITNDADWMKYF T0518 183 :QSASLYDMIPA 3juuA 181 :NSNTHSRNIPE T0518 194 :VPQNSKPF 3juuA 203 :KAELGGKA T0518 202 :GEWNKAKIMVY 3juuA 212 :EDFHVYGVWWK T0518 213 :KGTVVHGQNDENVLEYHLWT 3juuA 224 :KDEIIFFLDGKMQSKVTPPA T0518 261 :GENHEGFIGLQDHGDD 3juuA 244 :DFDIEMYLRMVVETYD T0518 277 :VWFRNIRV 3juuA 278 :TTYNWVRS T0518 285 :KVLD 3juuA 287 :QLVD Number of specific fragments extracted= 16 number of extra gaps= 2 total=335 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 3juuA/T0518-3juuA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0518 read from 3juuA/T0518-3juuA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3juuA read from 3juuA/T0518-3juuA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3juuA in template set Warning: unaligning (T0518)L44 because first residue in template chain is (3juuA)E23 Warning: unaligning (T0518)Q140 because of BadResidue code BAD_PEPTIDE in next template residue (3juuA)V163 Warning: unaligning (T0518)E141 because of BadResidue code BAD_PEPTIDE at template residue (3juuA)V163 T0518 45 :KAPETDSLNLPVDENGYITI 3juuA 24 :APHFKPGEDPRQPHQEWKLI T0518 65 :FDGE 3juuA 50 :FEGK T0518 69 :TFNGWRGY 3juuA 56 :DEKKWQIS T0518 77 :GK 3juuA 76 :LA T0518 83 :TKWTIEDGCIKFNGS 3juuA 78 :ENISLNNGSLQITTT T0518 98 :GGGEA 3juuA 96 :EPIVK T0518 104 :DGD 3juuA 101 :NNK T0518 108 :GDLIFAHKFKNFELELEWKVAKG 3juuA 110 :GYVGSRNGMTYGYYECEMKANKT T0518 131 :SNSGILYLA 3juuA 153 :RTTELDIQE T0518 142 :VTSKDKDGNDVLEPIYISAPEYQILDNANHPD 3juuA 164 :GQITNDADWMKYFDQTMNSNTHSRNIPEGCEY T0518 180 :NNRQSASLYDMIPA 3juuA 196 :EKGSSKGKAELGGK T0518 200 :PFGEWNKAKIMVYKG 3juuA 210 :AYEDFHVYGVWWKSK T0518 215 :TVVHGQNDENVLEYHLW 3juuA 226 :EIIFFLDGKMQSKVTPP T0518 260 :GGENHEGFIGLQDHGDD 3juuA 243 :ADFDIEMYLRMVVETYD T0518 277 :VWFRNIRV 3juuA 278 :TTYNWVRS Number of specific fragments extracted= 15 number of extra gaps= 1 total=350 Will force an alignment to be made, even if fragment is small Number of alignments=30 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1upsA/T0518-1upsA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1upsA expands to /projects/compbio/data/pdb/1ups.pdb.gz 1upsA:Skipped atom 178, because occupancy 0.350 <= existing 0.650 in 1upsA Skipped atom 179, because occupancy 0.350 <= existing 0.650 in 1upsA Skipped atom 180, because occupancy 0.350 <= existing 0.650 in 1upsA Skipped atom 181, because occupancy 0.350 <= existing 0.650 in 1upsA Skipped atom 236, because occupancy 0.350 <= existing 0.650 in 1upsA Skipped atom 237, because occupancy 0.350 <= existing 0.650 in 1upsA Skipped atom 238, because occupancy 0.350 <= existing 0.650 in 1upsA Skipped atom 239, because occupancy 0.350 <= existing 0.650 in 1upsA Skipped atom 1814, because occupancy 0.350 <= existing 0.650 in 1upsA Skipped atom 1815, because occupancy 0.350 <= existing 0.650 in 1upsA Skipped atom 1823, because occupancy 0.350 <= existing 0.650 in 1upsA Skipped atom 1824, because occupancy 0.350 <= existing 0.650 in 1upsA Skipped atom 1825, because occupancy 0.350 <= existing 0.650 in 1upsA Skipped atom 3060, because occupancy 0.350 <= existing 0.650 in 1upsA Skipped atom 3061, because occupancy 0.350 <= existing 0.650 in 1upsA Skipped atom 3197, because occupancy 0.350 <= existing 0.650 in 1upsA Skipped atom 3198, because occupancy 0.350 <= existing 0.650 in 1upsA Skipped atom 3199, because occupancy 0.350 <= existing 0.650 in 1upsA Skipped atom 3200, because occupancy 0.350 <= existing 0.650 in 1upsA # T0518 read from 1upsA/T0518-1upsA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1upsA read from 1upsA/T0518-1upsA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1upsA to template set # found chain 1upsA in template set Warning: unaligning (T0518)E48 because first residue in template chain is (1upsA)A17 Warning: unaligning (T0518)W73 because of BadResidue code BAD_PEPTIDE in next template residue (1upsA)T49 Warning: unaligning (T0518)R74 because of BadResidue code BAD_PEPTIDE at template residue (1upsA)T49 Warning: unaligning (T0518)H273 because of BadResidue code BAD_PEPTIDE in next template residue (1upsA)T254 T0518 49 :TDSLNLPVDENGYITIF 1upsA 18 :KDFPANPIEKAGYKLDF T0518 66 :DGE 1upsA 39 :NGP T0518 69 :TFNG 1upsA 44 :DREK T0518 75 :GY 1upsA 50 :DY T0518 77 :GKDRV 1upsA 58 :KDPES T0518 82 :PTKWTIEDGCIKFNGSGG 1upsA 64 :KANYRFENGSLVEYITED T0518 102 :AQDGDGGDLIFAHK 1upsA 111 :GTTDNHERNEWRGY T0518 116 :FKNFELELEWKV 1upsA 126 :TKYGYFEIRAKL T0518 128 :AKGSNSGILYLAQEVTSKDKDG 1upsA 141 :GGGGHQAWWMVGMQDDTNDWFN T0518 157 :YISAPEYQILD 1upsA 163 :SKQTGEIDILE T0518 168 :N 1upsA 177 :S T0518 171 :HPDAKLGKDN 1upsA 188 :GWNDPNFQTS T0518 183 :QSASLYDMIPAVP 1upsA 198 :WTISEDKVPSGDP T0518 201 :FGEWNKAKIMVYKGTVVHGQNDENVLEYHL 1upsA 211 :TSEYHIYAMEWTPTALKFYYDNELFKVIYG T0518 261 :GENHEGFIGLQD 1upsA 241 :SPDYEMGTILNI T0518 274 :GDD 1upsA 257 :GSG T0518 277 :VWFRNIRVK 1upsA 269 :WAIDYMRVW Number of specific fragments extracted= 17 number of extra gaps= 2 total=367 Will force an alignment to be made, even if fragment is small Number of alignments=31 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1upsA/T0518-1upsA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0518 read from 1upsA/T0518-1upsA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1upsA read from 1upsA/T0518-1upsA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1upsA in template set Warning: unaligning (T0518)E48 because first residue in template chain is (1upsA)A17 Warning: unaligning (T0518)W73 because of BadResidue code BAD_PEPTIDE in next template residue (1upsA)T49 Warning: unaligning (T0518)R74 because of BadResidue code BAD_PEPTIDE at template residue (1upsA)T49 Warning: unaligning (T0518)P172 because of BadResidue code TOO_FEW_ATOMS+BAD_PEPTIDE in next template residue (1upsA)K179 Warning: unaligning (T0518)D173 because of BadResidue code TOO_FEW_ATOMS+BAD_PEPTIDE at template residue (1upsA)K179 Warning: unaligning (T0518)H273 because of BadResidue code BAD_PEPTIDE in next template residue (1upsA)T254 T0518 49 :TDSLNLPVDENGYITIF 1upsA 18 :KDFPANPIEKAGYKLDF T0518 66 :DGETFNG 1upsA 39 :NGPTLDR T0518 75 :GYGKD 1upsA 56 :WCKDP T0518 82 :PTKWTIEDGCIKFNGSG 1upsA 64 :KANYRFENGSLVEYITE T0518 99 :G 1upsA 110 :S T0518 102 :AQDGDGGDLIFAHK 1upsA 111 :GTTDNHERNEWRGY T0518 116 :FKNFELELEWKVAKGS 1upsA 126 :TKYGYFEIRAKLSNTG T0518 133 :SGILYLAQEVTSKDKDGNDVL 1upsA 142 :GGGHQAWWMVGMQDDTNDWFN T0518 157 :YISAPEYQILDNANH 1upsA 163 :SKQTGEIDILETFFS T0518 174 :AKLGK 1upsA 180 :DTWRI T0518 179 :DNNRQSA 1upsA 192 :PNFQTSW T0518 194 :VPQNSKPFGEWNKAKIMVYKGTVVHGQNDENVLEYHL 1upsA 204 :KVPSGDPTSEYHIYAMEWTPTALKFYYDNELFKVIYG T0518 261 :GENHEGFIGLQD 1upsA 241 :SPDYEMGTILNI T0518 274 :GDD 1upsA 257 :GSG T0518 277 :VWFRNIRVKV 1upsA 269 :WAIDYMRVWK Number of specific fragments extracted= 15 number of extra gaps= 3 total=382 Will force an alignment to be made, even if fragment is small Number of alignments=32 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1upsA/T0518-1upsA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0518 read from 1upsA/T0518-1upsA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1upsA read from 1upsA/T0518-1upsA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1upsA in template set Warning: unaligning (T0518)E48 because first residue in template chain is (1upsA)A17 Warning: unaligning (T0518)W73 because of BadResidue code BAD_PEPTIDE in next template residue (1upsA)T49 Warning: unaligning (T0518)R74 because of BadResidue code BAD_PEPTIDE at template residue (1upsA)T49 Warning: unaligning (T0518)P172 because of BadResidue code TOO_FEW_ATOMS+BAD_PEPTIDE in next template residue (1upsA)K179 Warning: unaligning (T0518)D173 because of BadResidue code TOO_FEW_ATOMS+BAD_PEPTIDE at template residue (1upsA)K179 T0518 49 :TDSLNLPVDENGYITIF 1upsA 18 :KDFPANPIEKAGYKLDF T0518 66 :DGE 1upsA 39 :NGP T0518 69 :TFNG 1upsA 44 :DREK T0518 75 :GY 1upsA 50 :DY T0518 77 :GKDRVPTKWTIEDGCIKFNGSGGGEA 1upsA 59 :DPESAKANYRFENGSLVEYITEDQKP T0518 103 :QDGDGGDLIFAHK 1upsA 91 :GTVRSSAIMSFDK T0518 116 :FKNFELELEWKVAKG 1upsA 126 :TKYGYFEIRAKLSNT T0518 131 :SNSGILYLAQEVTSK 1upsA 144 :GHQAWWMVGMQDDTN T0518 153 :LEPIYISAPEYQILDNANH 1upsA 159 :DWFNSKQTGEIDILETFFS T0518 174 :A 1upsA 180 :D T0518 175 :KLGKDNNRQSASLYDMIPA 1upsA 190 :NDPNFQTSWTISEDKVPSG T0518 199 :KPFGEWNKAKIMVYKGTVVHGQNDENVLEYH 1upsA 209 :DPTSEYHIYAMEWTPTALKFYYDNELFKVIY T0518 260 :GGENHEGFIGLQD 1upsA 240 :GSPDYEMGTILNI Number of specific fragments extracted= 13 number of extra gaps= 2 total=395 Will force an alignment to be made, even if fragment is small Number of alignments=33 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1gbg/T0518-1gbg-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1gbg expands to /projects/compbio/data/pdb/1gbg.pdb.gz 1gbg:Warning: there is no chain 1gbg will retry with 1gbgA Skipped atom 397, because occupancy 0.500 <= existing 0.500 in 1gbg # T0518 read from 1gbg/T0518-1gbg-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1gbg read from 1gbg/T0518-1gbg-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1gbg to template set # found chain 1gbg in template set T0518 57 :DENGYITIFDGETFNGWRGY 1gbg 2 :TGGSFYEPFNNYNTGLWQKA T0518 77 :GKDRVPTKW 1gbg 26 :NGNMFNCTW T0518 86 :TI 1gbg 40 :SM T0518 88 :EDGCIKFNGSGGGEAQ 1gbg 43 :SLGEMRLSLTSPSYNK T0518 105 :GDGGDLIFAHKFKNFELELEWKV 1gbg 59 :FDCGENRSVQTYGYGLYEVNMKP T0518 128 :AKGSNSGILYLAQEVT 1gbg 84 :NVGIVSSFFTYTGPTD T0518 157 :YISAPEYQILD 1gbg 100 :GTPWDEIDIEF T0518 168 :NANHPDAKLGKDNNRQSASLYDMIPAVP 1gbg 114 :DTTKVQFNYYTNGVGNHEKIVNLGFDAA T0518 202 :GEWNKAKIMVYKGTVVHGQNDENVLEYHLWTK 1gbg 142 :NSYHTYAFDWQPNSIKWYVDGQLKHTATTQIP T0518 261 :GENHEGFIGLQDHGDD 1gbg 174 :QTPGKIMMNLWNGAGV T0518 277 :VWFRNIRVKV 1gbg 204 :AHYNWVRYTK Number of specific fragments extracted= 11 number of extra gaps= 0 total=406 Will force an alignment to be made, even if fragment is small Number of alignments=34 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1gbg/T0518-1gbg-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0518 read from 1gbg/T0518-1gbg-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1gbg read from 1gbg/T0518-1gbg-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1gbg in template set T0518 60 :GYITIFDGETFNGWRGYGKDRV 1gbg 5 :SFYEPFNNYNTGLWQKADGYSN T0518 82 :PTKWTI 1gbg 36 :ANNVSM T0518 88 :EDGCIKFNGSGGGEA 1gbg 43 :SLGEMRLSLTSPSYN T0518 104 :DGDGGDLIFAHKFKNFELELEWKVAKGS 1gbg 58 :KFDCGENRSVQTYGYGLYEVNMKPAKNV T0518 134 :GILYLAQEVTSKDK 1gbg 86 :GIVSSFFTYTGPTD T0518 157 :YISAPEYQILDNANHP 1gbg 100 :GTPWDEIDIEFLGKDT T0518 173 :D 1gbg 117 :K T0518 175 :KLGKDNNRQSASLYDMIPA 1gbg 121 :NYYTNGVGNHEKIVNLGFD T0518 200 :PFGEWNKAKIMVYKGTVVHGQNDENVLEYHLWTK 1gbg 140 :AANSYHTYAFDWQPNSIKWYVDGQLKHTATTQIP T0518 261 :GENHEGFIGLQDHGDD 1gbg 174 :QTPGKIMMNLWNGAGV T0518 277 :VWFRNIRVKV 1gbg 204 :AHYNWVRYTK Number of specific fragments extracted= 11 number of extra gaps= 0 total=417 Will force an alignment to be made, even if fragment is small Number of alignments=35 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1gbg/T0518-1gbg-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0518 read from 1gbg/T0518-1gbg-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1gbg read from 1gbg/T0518-1gbg-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1gbg in template set T0518 65 :FDGETFNGWRGYGKDRVPT 1gbg 10 :FNNYNTGLWQKADGYSNGN T0518 84 :KWTI 1gbg 31 :NCTW T0518 88 :EDGCIKFNGSGGGEA 1gbg 43 :SLGEMRLSLTSPSYN T0518 104 :DGDGGDLIFAHKFKNFELELEWKVAKGSNSGILYLAQEVTS 1gbg 58 :KFDCGENRSVQTYGYGLYEVNMKPAKNVGIVSSFFTYTGPT T0518 156 :IYISAPEYQILDNANHPDA 1gbg 99 :DGTPWDEIDIEFLGKDTTK T0518 177 :GKDNNRQSASLYDM 1gbg 123 :YTNGVGNHEKIVNL T0518 197 :NSKPFGEWNKAKIMVYKGTVVHGQNDENVLEYHLWT 1gbg 137 :GFDAANSYHTYAFDWQPNSIKWYVDGQLKHTATTQI T0518 260 :GGENHEGFIGLQDHGDD 1gbg 173 :PQTPGKIMMNLWNGAGV T0518 277 :VWFRNIRVKV 1gbg 204 :AHYNWVRYTK Number of specific fragments extracted= 9 number of extra gaps= 0 total=426 Will force an alignment to be made, even if fragment is small Number of alignments=36 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3dgtA/T0518-3dgtA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 3dgtA expands to /projects/compbio/data/pdb/3dgt.pdb.gz 3dgtA:# T0518 read from 3dgtA/T0518-3dgtA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3dgtA read from 3dgtA/T0518-3dgtA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3dgtA to template set # found chain 3dgtA in template set Warning: unaligning (T0518)N53 because first residue in template chain is (3dgtA)S1 Warning: unaligning (T0518)L187 because of BadResidue code BAD_PEPTIDE in next template residue (3dgtA)T172 Warning: unaligning (T0518)Y188 because of BadResidue code BAD_PEPTIDE at template residue (3dgtA)T172 Warning: unaligning (T0518)V277 because of BadResidue code BAD_PEPTIDE at template residue (3dgtA)M266 T0518 54 :LPVDENGYITIF 3dgtA 2 :APAPPSGWSQVF T0518 66 :DGE 3dgtA 18 :DGA T0518 69 :TFNGWRGY 3dgtA 26 :NTANWQFD T0518 86 :TI 3dgtA 61 :SL T0518 88 :EDGCIKFNGSG 3dgtA 64 :GNGDLLITPRR T0518 100 :GEAQDGDGGDLIFAHK 3dgtA 75 :DASGNWTSGRIETTRT T0518 116 :F 3dgtA 94 :P T0518 117 :KNFELELEWKV 3dgtA 98 :GKLRVEARLQM T0518 128 :AK 3dgtA 113 :GD T0518 132 :NSGILYLAQEVTSKDKD 3dgtA 120 :WPAFWMLGAPFRGNYQN T0518 157 :YISAPEYQILDNANHPDAKLG 3dgtA 137 :WPGVGELDIMENVQGLNKTWA T0518 178 :KDNNRQSAS 3dgtA 162 :GTSPGGPCN T0518 189 :DMIP 3dgtA 173 :SGIG T0518 193 :AVPQNSKPFGEWNKAKIMVY 3dgtA 179 :TACPNTTCQSGFHTYTMEWD T0518 213 :KGTVVHGQNDENVLEYHLWTKQ 3dgtA 203 :PEAIRFSVDGVTYQTVTANQMD T0518 236 :TDMLQASKFSEDKWPLAFELL 3dgtA 225 :AATWTNATNHGFFVILNVAMG T0518 257 :NNCGGENHEG 3dgtA 250 :GAFGGGPTGA T0518 278 :WFRNIRVKVLD 3dgtA 267 :VVDYVQVTSLS Number of specific fragments extracted= 18 number of extra gaps= 2 total=444 Will force an alignment to be made, even if fragment is small Number of alignments=37 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3dgtA/T0518-3dgtA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0518 read from 3dgtA/T0518-3dgtA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3dgtA read from 3dgtA/T0518-3dgtA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3dgtA in template set Warning: unaligning (T0518)N53 because first residue in template chain is (3dgtA)S1 Warning: unaligning (T0518)M190 because of BadResidue code BAD_PEPTIDE in next template residue (3dgtA)T172 Warning: unaligning (T0518)I191 because of BadResidue code BAD_PEPTIDE at template residue (3dgtA)T172 Warning: unaligning (T0518)V277 because of BadResidue code BAD_PEPTIDE at template residue (3dgtA)M266 T0518 54 :LPVDENGYITIF 3dgtA 2 :APAPPSGWSQVF T0518 69 :TFNGWR 3dgtA 26 :NTANWQ T0518 82 :PTKWTI 3dgtA 57 :TSNVSL T0518 88 :EDGCIKFNGSGGGEA 3dgtA 64 :GNGDLLITPRRDASG T0518 104 :DGDGGDLIFAHK 3dgtA 79 :NWTSGRIETTRT T0518 116 :FK 3dgtA 94 :PP T0518 118 :NFELELEWKVAKGS 3dgtA 99 :KLRVEARLQMPNVT T0518 132 :NSGILYLAQEVTSK 3dgtA 116 :AAGYWPAFWMLGAP T0518 146 :DKDGN 3dgtA 132 :GNYQN T0518 157 :YISAPEYQILDNANHPDAKLGK 3dgtA 137 :WPGVGELDIMENVQGLNKTWAT T0518 179 :DNNRQSASL 3dgtA 161 :CGTSPGGPC T0518 189 :D 3dgtA 170 :N T0518 192 :PA 3dgtA 173 :SG T0518 194 :VPQNSKPFGEWNKAKIMVYKG 3dgtA 180 :ACPNTTCQSGFHTYTMEWDRS T0518 215 :TVVHGQNDENVLEYHLW 3dgtA 205 :AIRFSVDGVTYQTVTAN T0518 235 :WTDMLQAS 3dgtA 224 :DAATWTNA T0518 262 :ENHEGFIGLQDH 3dgtA 232 :TNHGFFVILNVA T0518 278 :WFRNIRVKVLD 3dgtA 267 :VVDYVQVTSLS Number of specific fragments extracted= 18 number of extra gaps= 2 total=462 Will force an alignment to be made, even if fragment is small Number of alignments=38 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3dgtA/T0518-3dgtA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0518 read from 3dgtA/T0518-3dgtA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3dgtA read from 3dgtA/T0518-3dgtA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3dgtA in template set Warning: unaligning (T0518)N53 because first residue in template chain is (3dgtA)S1 Warning: unaligning (T0518)K178 because of BadResidue code BAD_PEPTIDE in next template residue (3dgtA)T172 Warning: unaligning (T0518)D179 because of BadResidue code BAD_PEPTIDE at template residue (3dgtA)T172 T0518 54 :LPVDENGYITIF 3dgtA 2 :APAPPSGWSQVF T0518 66 :DGETFNGWRGY 3dgtA 18 :DGAAGSSVNTA T0518 77 :GK 3dgtA 56 :ST T0518 83 :TKWTI 3dgtA 58 :SNVSL T0518 88 :EDGCIKFNGSGG 3dgtA 64 :GNGDLLITPRRD T0518 104 :DGDGGDLIF 3dgtA 76 :ASGNWTSGR T0518 113 :A 3dgtA 86 :E T0518 114 :HKFKNFELELEWKVAKG 3dgtA 95 :PAGGKLRVEARLQMPNV T0518 132 :NSGILYLAQ 3dgtA 116 :AAGYWPAFW T0518 141 :EVTSKDKDGNDVL 3dgtA 126 :LGAPFRGNYQNWP T0518 156 :IYISAPEYQILDNANHPDAKLG 3dgtA 149 :VQGLNKTWATMHCGTSPGGPCN T0518 180 :NNRQSASLYD 3dgtA 173 :SGIGNSTACP T0518 197 :NSKPFGEWNKAKIMVYKG 3dgtA 183 :NTTCQSGFHTYTMEWDRS T0518 215 :TVVHGQNDENVLEYH 3dgtA 205 :AIRFSVDGVTYQTVT T0518 230 :LWTKQWTDMLQ 3dgtA 222 :QMDAATWTNAT T0518 263 :NHEGFIGL 3dgtA 233 :NHGFFVIL Number of specific fragments extracted= 16 number of extra gaps= 1 total=478 Will force an alignment to be made, even if fragment is small Number of alignments=39 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1o4yA/T0518-1o4yA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1o4yA expands to /projects/compbio/data/pdb/1o4y.pdb.gz 1o4yA:Skipped atom 119, because occupancy 0.500 <= existing 0.500 in 1o4yA Skipped atom 121, because occupancy 0.500 <= existing 0.500 in 1o4yA Skipped atom 123, because occupancy 0.500 <= existing 0.500 in 1o4yA Skipped atom 125, because occupancy 0.500 <= existing 0.500 in 1o4yA Skipped atom 169, because occupancy 0.330 <= existing 0.670 in 1o4yA Skipped atom 171, because occupancy 0.330 <= existing 0.670 in 1o4yA Skipped atom 173, because occupancy 0.330 <= existing 0.670 in 1o4yA Skipped atom 175, because occupancy 0.330 <= existing 0.670 in 1o4yA Skipped atom 177, because occupancy 0.330 <= existing 0.670 in 1o4yA Skipped atom 650, because occupancy 0.500 <= existing 0.500 in 1o4yA Skipped atom 652, because occupancy 0.500 <= existing 0.500 in 1o4yA Skipped atom 654, because occupancy 0.500 <= existing 0.500 in 1o4yA Skipped atom 656, because occupancy 0.500 <= existing 0.500 in 1o4yA Skipped atom 658, because occupancy 0.500 <= existing 0.500 in 1o4yA Skipped atom 846, because occupancy 0.500 <= existing 0.500 in 1o4yA Skipped atom 848, because occupancy 0.500 <= existing 0.500 in 1o4yA Skipped atom 1328, because occupancy 0.500 <= existing 0.500 in 1o4yA Skipped atom 1330, because occupancy 0.500 <= existing 0.500 in 1o4yA Skipped atom 1453, because occupancy 0.500 <= existing 0.500 in 1o4yA Skipped atom 1455, because occupancy 0.500 <= existing 0.500 in 1o4yA Skipped atom 1491, because occupancy 0.500 <= existing 0.500 in 1o4yA Skipped atom 1493, because occupancy 0.500 <= existing 0.500 in 1o4yA Skipped atom 1495, because occupancy 0.500 <= existing 0.500 in 1o4yA Skipped atom 1497, because occupancy 0.500 <= existing 0.500 in 1o4yA Skipped atom 1604, because occupancy 0.500 <= existing 0.500 in 1o4yA Skipped atom 1606, because occupancy 0.500 <= existing 0.500 in 1o4yA Skipped atom 1728, because occupancy 0.500 <= existing 0.500 in 1o4yA Skipped atom 1730, because occupancy 0.500 <= existing 0.500 in 1o4yA Skipped atom 1732, because occupancy 0.500 <= existing 0.500 in 1o4yA Skipped atom 1734, because occupancy 0.500 <= existing 0.500 in 1o4yA Skipped atom 1933, because occupancy 0.500 <= existing 0.500 in 1o4yA Skipped atom 1935, because occupancy 0.500 <= existing 0.500 in 1o4yA Skipped atom 1937, because occupancy 0.500 <= existing 0.500 in 1o4yA Skipped atom 2049, because occupancy 0.500 <= existing 0.500 in 1o4yA Skipped atom 2058, because occupancy 0.500 <= existing 0.500 in 1o4yA Skipped atom 2060, because occupancy 0.500 <= existing 0.500 in 1o4yA # T0518 read from 1o4yA/T0518-1o4yA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1o4yA read from 1o4yA/T0518-1o4yA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1o4yA to template set # found chain 1o4yA in template set Warning: unaligning (T0518)G105 because of BadResidue code BAD_PEPTIDE in next template residue (1o4yA)Y106 Warning: unaligning (T0518)D106 because of BadResidue code BAD_PEPTIDE at template residue (1o4yA)Y106 Warning: unaligning (T0518)D109 because of BadResidue code BAD_PEPTIDE in next template residue (1o4yA)I110 Warning: unaligning (T0518)L110 because of BadResidue code BAD_PEPTIDE at template residue (1o4yA)I110 T0518 49 :TDSLNLPV 1o4yA 25 :GIPVPANP T0518 57 :DENGYITIFDGE 1o4yA 40 :LQDNVSDSFNYT T0518 69 :T 1o4yA 56 :N T0518 71 :NGWRGY 1o4yA 63 :SKWKPS T0518 77 :GKDRV 1o4yA 71 :NGWTG T0518 82 :PTKWTIEDGCIKFNGSGGGE 1o4yA 83 :APQAWTNGSQLAIQAQPAGN T0518 103 :QD 1o4yA 103 :GK T0518 107 :GG 1o4yA 107 :NG T0518 111 :IFAHKFK 1o4yA 111 :TSKNKIQ T0518 118 :NFELELEWKV 1o4yA 119 :PVYMEIKAKI T0518 128 :AKGSNSGILYLA 1o4yA 130 :DQVLANAFWTLT T0518 157 :YISAPEYQILD 1o4yA 142 :DDETQEIDIME T0518 168 :NAN 1o4yA 155 :GSD T0518 171 :HPDAKLG 1o4yA 176 :RNPFTDY T0518 179 :DNNRQSASLYDMIPAVP 1o4yA 183 :QPMGDATWYYNGGTPWR T0518 202 :GEWNKAKIMVYKG 1o4yA 200 :SAYHRYGCYWKDP T0518 215 :TVVHGQNDENVLEYHL 1o4yA 214 :TLEYYIDGVKVRTVTR T0518 237 :DMLQASKFSEDKWP 1o4yA 230 :AEIDPNNHLGGTGL T0518 261 :GENHEGFIGLQDHGDD 1o4yA 244 :NQATNIIIDCENQTDW T0518 277 :VWFRNIRVK 1o4yA 276 :FWVDWIRVY Number of specific fragments extracted= 20 number of extra gaps= 2 total=498 Will force an alignment to be made, even if fragment is small Number of alignments=40 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1o4yA/T0518-1o4yA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0518 read from 1o4yA/T0518-1o4yA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1o4yA read from 1o4yA/T0518-1o4yA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1o4yA in template set Warning: unaligning (T0518)G105 because of BadResidue code BAD_PEPTIDE in next template residue (1o4yA)Y106 Warning: unaligning (T0518)D106 because of BadResidue code BAD_PEPTIDE at template residue (1o4yA)Y106 Warning: unaligning (T0518)D109 because of BadResidue code BAD_PEPTIDE in next template residue (1o4yA)I110 Warning: unaligning (T0518)L110 because of BadResidue code BAD_PEPTIDE at template residue (1o4yA)I110 Warning: unaligning (T0518)D179 because of BadResidue code BAD_PEPTIDE in next template residue (1o4yA)I175 Warning: unaligning (T0518)N180 because of BadResidue code BAD_PEPTIDE at template residue (1o4yA)I175 T0518 45 :KAPETDSLNLPVDENG 1o4yA 21 :QDWNGIPVPANPGNGM T0518 61 :YITIFDGE 1o4yA 44 :VSDSFNYT T0518 69 :TFN 1o4yA 56 :NRP T0518 72 :GWR 1o4yA 64 :KWK T0518 75 :GYGKDRV 1o4yA 68 :SYINGWT T0518 82 :PTKWTIEDGCIKFNGSG 1o4yA 83 :APQAWTNGSQLAIQAQP T0518 100 :GEA 1o4yA 101 :GNG T0518 104 :D 1o4yA 104 :K T0518 107 :GG 1o4yA 107 :NG T0518 111 :IFAHKFK 1o4yA 111 :TSKNKIQ T0518 118 :NFELELEWKVAKG 1o4yA 119 :PVYMEIKAKIMDQ T0518 134 :GILYLAQEVTSK 1o4yA 132 :VLANAFWTLTDD T0518 159 :SAPEYQILD 1o4yA 144 :ETQEIDIME T0518 168 :NAN 1o4yA 155 :GSD T0518 174 :AKLGK 1o4yA 169 :LSHHT T0518 181 :NRQSASL 1o4yA 176 :RNPFTDY T0518 189 :DMIPA 1o4yA 183 :QPMGD T0518 194 :VPQNSKPFGEWNKAKIMVYK 1o4yA 192 :YNGGTPWRSAYHRYGCYWKD T0518 214 :GTVVHGQNDENVLEYHLW 1o4yA 213 :FTLEYYIDGVKVRTVTRA T0518 238 :ML 1o4yA 231 :EI T0518 247 :DK 1o4yA 233 :DP T0518 256 :LNNCGGENHE 1o4yA 235 :NNHLGGTGLN T0518 266 :GFIGLQDHGDD 1o4yA 249 :IIIDCENQTDW T0518 277 :VWFRNIRVK 1o4yA 276 :FWVDWIRVY Number of specific fragments extracted= 24 number of extra gaps= 3 total=522 Will force an alignment to be made, even if fragment is small Number of alignments=41 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1o4yA/T0518-1o4yA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0518 read from 1o4yA/T0518-1o4yA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1o4yA read from 1o4yA/T0518-1o4yA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1o4yA in template set Warning: unaligning (T0518)D109 because of BadResidue code BAD_PEPTIDE in next template residue (1o4yA)I110 Warning: unaligning (T0518)L110 because of BadResidue code BAD_PEPTIDE at template residue (1o4yA)I110 T0518 51 :SLNLPVDENGY 1o4yA 26 :IPVPANPGNGM T0518 72 :GWRGY 1o4yA 37 :TWQLQ T0518 81 :VPTKWTIEDGCIKFNGSGG 1o4yA 82 :NAPQAWTNGSQLAIQAQPA T0518 104 :DGDG 1o4yA 101 :GNGK T0518 108 :G 1o4yA 108 :G T0518 111 :IFAHKF 1o4yA 111 :TSKNKI T0518 118 :NFELELEWKVA 1o4yA 119 :PVYMEIKAKIM T0518 132 :NSGILYLAQEVTS 1o4yA 130 :DQVLANAFWTLTD T0518 158 :ISAPEYQILDNANHPDA 1o4yA 143 :DETQEIDIMEGYGSDRG T0518 178 :KDNNRQSASLYDMIPAVPQNSKPFGEWNKAKIMVYKG 1o4yA 176 :RNPFTDYQPMGDATWYYNGGTPWRSAYHRYGCYWKDP T0518 215 :TVVHGQNDENVLEYH 1o4yA 214 :TLEYYIDGVKVRTVT T0518 236 :TDMLQASKFSEDKW 1o4yA 229 :RAEIDPNNHLGGTG T0518 260 :GGENHEGFIGLQDHGDD 1o4yA 243 :LNQATNIIIDCENQTDW T0518 277 :VWFRNIRV 1o4yA 276 :FWVDWIRV Number of specific fragments extracted= 14 number of extra gaps= 1 total=536 Will force an alignment to be made, even if fragment is small Number of alignments=42 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2uwaA/T0518-2uwaA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2uwaA expands to /projects/compbio/data/pdb/2uwa.pdb.gz 2uwaA:# T0518 read from 2uwaA/T0518-2uwaA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2uwaA read from 2uwaA/T0518-2uwaA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2uwaA to template set # found chain 2uwaA in template set Warning: unaligning (T0518)T63 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2uwaA)Q1 Warning: unaligning (T0518)Q164 because of BadResidue code BAD_PEPTIDE in next template residue (2uwaA)I97 Warning: unaligning (T0518)I165 because of BadResidue code BAD_PEPTIDE at template residue (2uwaA)I97 Warning: unaligning (T0518)Y188 because of BadResidue code BAD_PEPTIDE in next template residue (2uwaA)H132 Warning: unaligning (T0518)D189 because of BadResidue code BAD_PEPTIDE at template residue (2uwaA)H132 Warning: unaligning (T0518)K285 because of BadResidue code BAD_PEPTIDE in next template residue (2uwaA)S217 Warning: unaligning (T0518)V286 because of BadResidue code BAD_PEPTIDE at template residue (2uwaA)S217 T0518 64 :IFDGE 2uwaA 2 :GPPSP T0518 69 :TFNGWRGY 2uwaA 9 :YPSSQITS T0518 77 :GKDRVPTKWTIEDGCIKFNGSGGG 2uwaA 24 :TNLWGPQHQRVDQGSLTIWLDSTS T0518 107 :GGDLIFAHKFKNFELELEWKVAKGS 2uwaA 48 :GSGFKSINRYRSGYFGANIKLQSGY T0518 132 :NSGILYLAQEVTSK 2uwaA 77 :ITSFYLSNNQDYPG T0518 159 :SAPEY 2uwaA 91 :KHDEI T0518 166 :L 2uwaA 98 :E T0518 167 :D 2uwaA 101 :G T0518 168 :NANHP 2uwaA 103 :IPGKP T0518 175 :KLGKDN 2uwaA 113 :NVFIEG T0518 181 :NRQSASL 2uwaA 124 :IIGREMR T0518 190 :MIPAVP 2uwaA 133 :LWFDPT T0518 202 :GEWNKAKIMVYKGTVVHGQNDENVLEYHLWTKQ 2uwaA 139 :QDYHNYAIYWTPSEIIFFVDDVPIRRYPRKSDA T0518 258 :NCGGENHEGFIGLQDHGDD 2uwaA 172 :TFPLRPLWVYGSVWDASSW T0518 277 :VWFRNIRV 2uwaA 208 :GKYEDFKL T0518 287 :L 2uwaA 218 :C Number of specific fragments extracted= 16 number of extra gaps= 4 total=552 Will force an alignment to be made, even if fragment is small Number of alignments=43 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2uwaA/T0518-2uwaA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0518 read from 2uwaA/T0518-2uwaA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2uwaA read from 2uwaA/T0518-2uwaA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2uwaA in template set Warning: unaligning (T0518)Q164 because of BadResidue code BAD_PEPTIDE in next template residue (2uwaA)I97 Warning: unaligning (T0518)I165 because of BadResidue code BAD_PEPTIDE at template residue (2uwaA)I97 Warning: unaligning (T0518)Y188 because of BadResidue code BAD_PEPTIDE in next template residue (2uwaA)H132 Warning: unaligning (T0518)D189 because of BadResidue code BAD_PEPTIDE at template residue (2uwaA)H132 Warning: unaligning (T0518)K285 because of BadResidue code BAD_PEPTIDE in next template residue (2uwaA)S217 Warning: unaligning (T0518)V286 because of BadResidue code BAD_PEPTIDE at template residue (2uwaA)S217 T0518 75 :GYGK 2uwaA 25 :NLWG T0518 82 :PTKWTIEDGCIKFNGS 2uwaA 29 :PQHQRVDQGSLTIWLD T0518 104 :DGDGGDLIFAHKFKNFELELEWKVAKGSNSGILYLAQEVTSKDK 2uwaA 45 :STSGSGFKSINRYRSGYFGANIKLQSGYTAGVITSFYLSNNQDY T0518 157 :YISAPEY 2uwaA 89 :PGKHDEI T0518 166 :L 2uwaA 98 :E T0518 167 :DNANHP 2uwaA 102 :TIPGKP T0518 175 :KLGKDNNR 2uwaA 113 :NVFIEGSG T0518 183 :QSASL 2uwaA 126 :GREMR T0518 190 :MIPAV 2uwaA 133 :LWFDP T0518 201 :FGEWNKAKIMVYKGTVVHGQNDENVLEYHLWTKQW 2uwaA 138 :TQDYHNYAIYWTPSEIIFFVDDVPIRRYPRKSDAT T0518 261 :GENHEGFIGLQDH 2uwaA 173 :FPLRPLWVYGSVW T0518 274 :GDD 2uwaA 188 :SSW T0518 277 :VWFRNIRV 2uwaA 208 :GKYEDFKL T0518 287 :L 2uwaA 218 :C Number of specific fragments extracted= 14 number of extra gaps= 3 total=566 Will force an alignment to be made, even if fragment is small Number of alignments=44 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2uwaA/T0518-2uwaA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0518 read from 2uwaA/T0518-2uwaA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2uwaA read from 2uwaA/T0518-2uwaA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2uwaA in template set Warning: unaligning (T0518)Y188 because of BadResidue code BAD_PEPTIDE in next template residue (2uwaA)H132 Warning: unaligning (T0518)D189 because of BadResidue code BAD_PEPTIDE at template residue (2uwaA)H132 T0518 74 :RGYGK 2uwaA 24 :TNLWG T0518 82 :PTKWTIEDGCIKFNGS 2uwaA 29 :PQHQRVDQGSLTIWLD T0518 104 :DGDGGDLIFAHKFKNFELELEWKVAKGSNSGILYLAQEVTSKDKDGNDVL 2uwaA 45 :STSGSGFKSINRYRSGYFGANIKLQSGYTAGVITSFYLSNNQDYPGKHDE T0518 155 :PIYISAPEYQILDNANH 2uwaA 102 :TIPGKPYTLQTNVFIEG T0518 176 :LGKDNNRQSASL 2uwaA 119 :SGDYNIIGREMR T0518 190 :MI 2uwaA 133 :LW T0518 198 :SKPFGEWNKAKIMVYKGTVVHGQNDENVLEYHLWTKQ 2uwaA 135 :FDPTQDYHNYAIYWTPSEIIFFVDDVPIRRYPRKSDA T0518 260 :GGENHEGFIGLQ 2uwaA 172 :TFPLRPLWVYGS Number of specific fragments extracted= 8 number of extra gaps= 1 total=574 Will force an alignment to be made, even if fragment is small Number of alignments=45 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3ilfA/T0518-3ilfA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 3ilfA expands to /projects/compbio/data/pdb/3ilf.pdb.gz 3ilfA:Skipped atom 31, because occupancy 0.500 <= existing 0.500 in 3ilfA Skipped atom 33, because occupancy 0.500 <= existing 0.500 in 3ilfA Skipped atom 35, because occupancy 0.500 <= existing 0.500 in 3ilfA Skipped atom 37, because occupancy 0.500 <= existing 0.500 in 3ilfA Skipped atom 39, because occupancy 0.500 <= existing 0.500 in 3ilfA Skipped atom 41, because occupancy 0.500 <= existing 0.500 in 3ilfA Skipped atom 540, because occupancy 0.500 <= existing 0.500 in 3ilfA Skipped atom 544, because occupancy 0.500 <= existing 0.500 in 3ilfA Skipped atom 546, because occupancy 0.500 <= existing 0.500 in 3ilfA Skipped atom 548, because occupancy 0.500 <= existing 0.500 in 3ilfA Skipped atom 550, because occupancy 0.500 <= existing 0.500 in 3ilfA Skipped atom 552, because occupancy 0.500 <= existing 0.500 in 3ilfA Skipped atom 554, because occupancy 0.500 <= existing 0.500 in 3ilfA Skipped atom 556, because occupancy 0.500 <= existing 0.500 in 3ilfA Skipped atom 590, because occupancy 0.500 <= existing 0.500 in 3ilfA Skipped atom 594, because occupancy 0.500 <= existing 0.500 in 3ilfA Skipped atom 596, because occupancy 0.500 <= existing 0.500 in 3ilfA Skipped atom 828, because occupancy 0.500 <= existing 0.500 in 3ilfA Skipped atom 832, because occupancy 0.500 <= existing 0.500 in 3ilfA Skipped atom 834, because occupancy 0.500 <= existing 0.500 in 3ilfA Skipped atom 836, because occupancy 0.500 <= existing 0.500 in 3ilfA Skipped atom 838, because occupancy 0.500 <= existing 0.500 in 3ilfA Skipped atom 840, because occupancy 0.500 <= existing 0.500 in 3ilfA Skipped atom 842, because occupancy 0.500 <= existing 0.500 in 3ilfA Skipped atom 844, because occupancy 0.500 <= existing 0.500 in 3ilfA Skipped atom 1860, because occupancy 0.200 <= existing 0.200 in 3ilfA Skipped atom 1862, because occupancy 0.200 <= existing 0.200 in 3ilfA Skipped atom 1864, because occupancy 0.200 <= existing 0.200 in 3ilfA Skipped atom 1866, because occupancy 0.200 <= existing 0.200 in 3ilfA Skipped atom 1868, because occupancy 0.200 <= existing 0.200 in 3ilfA Skipped atom 1870, because occupancy 0.200 <= existing 0.200 in 3ilfA Skipped atom 1872, because occupancy 0.200 <= existing 0.200 in 3ilfA Skipped atom 1874, because occupancy 0.200 <= existing 0.200 in 3ilfA Skipped atom 1876, because occupancy 0.200 <= existing 0.200 in 3ilfA Skipped atom 1878, because occupancy 0.200 <= existing 0.200 in 3ilfA Skipped atom 1880, because occupancy 0.200 <= existing 0.200 in 3ilfA Skipped atom 1882, because occupancy 0.200 <= existing 0.200 in 3ilfA Skipped atom 1884, because occupancy 0.200 <= existing 0.200 in 3ilfA Skipped atom 1886, because occupancy 0.200 <= existing 0.200 in 3ilfA Skipped atom 1888, because occupancy 0.200 <= existing 0.200 in 3ilfA Skipped atom 1890, because occupancy 0.200 <= existing 0.200 in 3ilfA Skipped atom 1955, because occupancy 0.500 <= existing 0.500 in 3ilfA Skipped atom 1957, because occupancy 0.500 <= existing 0.500 in 3ilfA Skipped atom 1959, because occupancy 0.500 <= existing 0.500 in 3ilfA Skipped atom 1961, because occupancy 0.500 <= existing 0.500 in 3ilfA Skipped atom 1963, because occupancy 0.500 <= existing 0.500 in 3ilfA Skipped atom 1965, because occupancy 0.500 <= existing 0.500 in 3ilfA Skipped atom 1967, because occupancy 0.500 <= existing 0.500 in 3ilfA Skipped atom 1969, because occupancy 0.500 <= existing 0.500 in 3ilfA Skipped atom 1971, because occupancy 0.500 <= existing 0.500 in 3ilfA # T0518 read from 3ilfA/T0518-3ilfA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3ilfA read from 3ilfA/T0518-3ilfA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3ilfA to template set # found chain 3ilfA in template set Warning: unaligning (T0518)W73 because of BadResidue code BAD_PEPTIDE in next template residue (3ilfA)Y50 Warning: unaligning (T0518)R74 because of BadResidue code BAD_PEPTIDE at template residue (3ilfA)Y50 Warning: unaligning (T0518)C91 because of BadResidue code BAD_PEPTIDE in next template residue (3ilfA)L76 Warning: unaligning (T0518)I92 because of BadResidue code BAD_PEPTIDE at template residue (3ilfA)L76 Warning: unaligning (T0518)N132 because of BadResidue code BAD_PEPTIDE in next template residue (3ilfA)S128 Warning: unaligning (T0518)S133 because of BadResidue code BAD_PEPTIDE at template residue (3ilfA)S128 Warning: unaligning (T0518)A174 because of BadResidue code BAD_PEPTIDE in next template residue (3ilfA)E152 Warning: unaligning (T0518)K175 because of BadResidue code BAD_PEPTIDE at template residue (3ilfA)E152 Warning: unaligning (T0518)E203 because of BadResidue code BAD_PEPTIDE in next template residue (3ilfA)F192 Warning: unaligning (T0518)W204 because of BadResidue code BAD_PEPTIDE at template residue (3ilfA)F192 T0518 25 :KKANAQ 3ilfA 19 :QLPSPT T0518 57 :DENGYITI 3ilfA 25 :NGKKWEKV T0518 65 :FDGE 3ilfA 39 :FDGN T0518 69 :TFNG 3ilfA 45 :DTNK T0518 75 :GYGKDRV 3ilfA 51 :DYHPFWE T0518 82 :PTKWTIEDG 3ilfA 66 :KGDAFVSDG T0518 93 :KFNGSGG 3ilfA 77 :NLRSTLR T0518 100 :GEAQDGDGGDLIFAHKFK 3ilfA 93 :FKDIWVDAAAAVSKTKAQ T0518 118 :NFELELEWKV 3ilfA 112 :GYYYEARFMA T0518 128 :AKGS 3ilfA 123 :SLSM T0518 134 :GILYL 3ilfA 129 :SFWFR T0518 157 :YISAPEYQILDNANHPD 3ilfA 134 :VGQFSSIDVIEHIGDPS T0518 176 :LGKDNNRQSAS 3ilfA 153 :NRQDDLPYQYH T0518 188 :YDMIPAVPQNSKP 3ilfA 164 :VNTHYYGKHAGLQ T0518 201 :FG 3ilfA 189 :RD T0518 205 :NKAKIMVY 3ilfA 193 :YTYGFWWK T0518 213 :KGTVVHGQNDENVLEYHL 3ilfA 202 :PNELLFYFNGKQVMRIVP T0518 261 :GENHEGFIGLQDH 3ilfA 220 :RVPLDEELRMIFD T0518 277 :VWFRNIRVK 3ilfA 262 :MKVDWVRVY Number of specific fragments extracted= 19 number of extra gaps= 5 total=593 Will force an alignment to be made, even if fragment is small Number of alignments=46 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3ilfA/T0518-3ilfA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0518 read from 3ilfA/T0518-3ilfA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3ilfA read from 3ilfA/T0518-3ilfA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3ilfA in template set Warning: unaligning (T0518)D50 because first residue in template chain is (3ilfA)A18 Warning: unaligning (T0518)W73 because of BadResidue code BAD_PEPTIDE in next template residue (3ilfA)Y50 Warning: unaligning (T0518)R74 because of BadResidue code BAD_PEPTIDE at template residue (3ilfA)Y50 Warning: unaligning (T0518)C91 because of BadResidue code BAD_PEPTIDE in next template residue (3ilfA)L76 Warning: unaligning (T0518)I92 because of BadResidue code BAD_PEPTIDE at template residue (3ilfA)L76 Warning: unaligning (T0518)L136 because of BadResidue code BAD_PEPTIDE in next template residue (3ilfA)S128 Warning: unaligning (T0518)Y137 because of BadResidue code BAD_PEPTIDE at template residue (3ilfA)S128 Warning: unaligning (T0518)A174 because of BadResidue code BAD_PEPTIDE in next template residue (3ilfA)E152 Warning: unaligning (T0518)K175 because of BadResidue code BAD_PEPTIDE at template residue (3ilfA)E152 Warning: unaligning (T0518)E203 because of BadResidue code BAD_PEPTIDE in next template residue (3ilfA)F192 Warning: unaligning (T0518)W204 because of BadResidue code BAD_PEPTIDE at template residue (3ilfA)F192 Warning: unaligning (T0518)A252 because of BadResidue code BAD_PEPTIDE in next template residue (3ilfA)N245 T0518 51 :SLNLPVDENGYITI 3ilfA 19 :QLPSPTNGKKWEKV T0518 65 :FDGETFN 3ilfA 39 :FDGNSID T0518 72 :G 3ilfA 48 :K T0518 75 :GYGKDRV 3ilfA 51 :DYHPFWE T0518 82 :PTKWTIEDG 3ilfA 66 :KGDAFVSDG T0518 93 :KFNGSGGGEAQDGD 3ilfA 77 :NLRSTLRKEPSSVQ T0518 107 :GGDLIFAHKFK 3ilfA 100 :AAAAVSKTKAQ T0518 118 :NFELELEWKVAKG 3ilfA 112 :GYYYEARFMASSL T0518 134 :GI 3ilfA 125 :SM T0518 138 :LAQEVTSK 3ilfA 129 :SFWFRVGQ T0518 160 :APEYQILDNANHPD 3ilfA 137 :FSSIDVIEHIGDPS T0518 176 :LGKDNNRQS 3ilfA 153 :NRQDDLPYQ T0518 185 :ASLYDMIPA 3ilfA 169 :YGKHAGLQP T0518 197 :NSKPF 3ilfA 184 :MPGRG T0518 202 :G 3ilfA 190 :D T0518 205 :NKAKIMVY 3ilfA 193 :YTYGFWWK T0518 213 :KGTVVHGQNDENVLEYHLWTKQWTDM 3ilfA 202 :PNELLFYFNGKQVMRIVPRVPLDEEL T0518 239 :LQASKFSEDKWPL 3ilfA 231 :FDTEVFPFATAGV T0518 253 :FELLN 3ilfA 246 :IGLPK T0518 258 :NCGGE 3ilfA 255 :RDNSK T0518 275 :DDVWFRNIRVKV 3ilfA 260 :NTMKVDWVRVYK Number of specific fragments extracted= 21 number of extra gaps= 6 total=614 Will force an alignment to be made, even if fragment is small Number of alignments=47 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3ilfA/T0518-3ilfA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0518 read from 3ilfA/T0518-3ilfA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3ilfA read from 3ilfA/T0518-3ilfA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3ilfA in template set Warning: unaligning (T0518)D50 because first residue in template chain is (3ilfA)A18 Warning: unaligning (T0518)W73 because of BadResidue code BAD_PEPTIDE in next template residue (3ilfA)Y50 Warning: unaligning (T0518)R74 because of BadResidue code BAD_PEPTIDE at template residue (3ilfA)Y50 Warning: unaligning (T0518)C91 because of BadResidue code BAD_PEPTIDE in next template residue (3ilfA)L76 Warning: unaligning (T0518)I92 because of BadResidue code BAD_PEPTIDE at template residue (3ilfA)L76 Warning: unaligning (T0518)N150 because of BadResidue code BAD_PEPTIDE in next template residue (3ilfA)E152 Warning: unaligning (T0518)D151 because of BadResidue code BAD_PEPTIDE at template residue (3ilfA)E152 Warning: unaligning (T0518)E203 because of BadResidue code BAD_PEPTIDE in next template residue (3ilfA)F192 Warning: unaligning (T0518)W204 because of BadResidue code BAD_PEPTIDE at template residue (3ilfA)F192 T0518 51 :SLNLPVDENGYITI 3ilfA 19 :QLPSPTNGKKWEKV T0518 65 :FDGETF 3ilfA 39 :FDGNSI T0518 71 :NG 3ilfA 47 :NK T0518 75 :GY 3ilfA 51 :DY T0518 83 :TKWTIEDG 3ilfA 67 :GDAFVSDG T0518 93 :KFNGSGGGEA 3ilfA 77 :NLRSTLRKEP T0518 103 :QDGDG 3ilfA 91 :DPFKD T0518 108 :GDLIFAHKF 3ilfA 101 :AAAVSKTKA T0518 117 :KNFELELE 3ilfA 113 :YYYEARFM T0518 125 :WKVAKGSNSGILYLAQEVTS 3ilfA 130 :FWFRVGQFSSIDVIEHIGDP T0518 149 :G 3ilfA 150 :S T0518 152 :VLEPIYISAPEYQILDNANH 3ilfA 153 :NRQDDLPYQYHVNTHYYGKH T0518 179 :DNNRQSASLYDMIPAVP 3ilfA 173 :AGLQPLGTEYKMPGRGR T0518 202 :G 3ilfA 190 :D T0518 205 :NKAKIMVYKG 3ilfA 193 :YTYGFWWKSP T0518 215 :TVVHGQNDENVLEYHLW 3ilfA 204 :ELLFYFNGKQVMRIVPR T0518 260 :GGENHEGFIGLQDH 3ilfA 221 :VPLDEELRMIFDTE T0518 274 :GDD 3ilfA 236 :FPF T0518 277 :VWFRNIRV 3ilfA 262 :MKVDWVRV Number of specific fragments extracted= 19 number of extra gaps= 4 total=633 Will force an alignment to be made, even if fragment is small Number of alignments=48 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2w39A/T0518-2w39A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2w39A expands to /projects/compbio/data/pdb/2w39.pdb.gz 2w39A:Skipped atom 129, because occupancy 0.500 <= existing 0.500 in 2w39A Skipped atom 130, because occupancy 0.500 <= existing 0.500 in 2w39A Skipped atom 131, because occupancy 0.500 <= existing 0.500 in 2w39A Skipped atom 132, because occupancy 0.500 <= existing 0.500 in 2w39A Skipped atom 133, because occupancy 0.500 <= existing 0.500 in 2w39A Skipped atom 134, because occupancy 0.500 <= existing 0.500 in 2w39A Skipped atom 380, because occupancy 0.250 <= existing 0.250 in 2w39A Skipped atom 381, because occupancy 0.250 <= existing 0.250 in 2w39A Skipped atom 382, because occupancy 0.250 <= existing 0.250 in 2w39A Skipped atom 383, because occupancy 0.250 <= existing 0.250 in 2w39A Skipped atom 384, because occupancy 0.250 <= existing 0.250 in 2w39A Skipped atom 385, because occupancy 0.250 <= existing 0.250 in 2w39A Skipped atom 446, because occupancy 0.500 <= existing 0.500 in 2w39A Skipped atom 447, because occupancy 0.500 <= existing 0.500 in 2w39A Skipped atom 448, because occupancy 0.500 <= existing 0.500 in 2w39A Skipped atom 449, because occupancy 0.500 <= existing 0.500 in 2w39A Skipped atom 450, because occupancy 0.500 <= existing 0.500 in 2w39A Skipped atom 451, because occupancy 0.500 <= existing 0.500 in 2w39A Skipped atom 452, because occupancy 0.500 <= existing 0.500 in 2w39A Skipped atom 453, because occupancy 0.500 <= existing 0.500 in 2w39A Skipped atom 454, because occupancy 0.500 <= existing 0.500 in 2w39A Skipped atom 455, because occupancy 0.500 <= existing 0.500 in 2w39A Skipped atom 456, because occupancy 0.500 <= existing 0.500 in 2w39A Skipped atom 528, because occupancy 0.500 <= existing 0.500 in 2w39A Skipped atom 529, because occupancy 0.500 <= existing 0.500 in 2w39A Skipped atom 530, because occupancy 0.500 <= existing 0.500 in 2w39A Skipped atom 531, because occupancy 0.500 <= existing 0.500 in 2w39A Skipped atom 532, because occupancy 0.500 <= existing 0.500 in 2w39A Skipped atom 533, because occupancy 0.500 <= existing 0.500 in 2w39A Skipped atom 931, because occupancy 0.500 <= existing 0.500 in 2w39A Skipped atom 932, because occupancy 0.500 <= existing 0.500 in 2w39A Skipped atom 933, because occupancy 0.500 <= existing 0.500 in 2w39A Skipped atom 934, because occupancy 0.500 <= existing 0.500 in 2w39A Skipped atom 935, because occupancy 0.500 <= existing 0.500 in 2w39A Skipped atom 936, because occupancy 0.500 <= existing 0.500 in 2w39A Skipped atom 937, because occupancy 0.500 <= existing 0.500 in 2w39A Skipped atom 1013, because occupancy 0.500 <= existing 0.500 in 2w39A Skipped atom 1014, because occupancy 0.500 <= existing 0.500 in 2w39A Skipped atom 1015, because occupancy 0.500 <= existing 0.500 in 2w39A Skipped atom 1016, because occupancy 0.500 <= existing 0.500 in 2w39A Skipped atom 1017, because occupancy 0.500 <= existing 0.500 in 2w39A Skipped atom 1018, because occupancy 0.500 <= existing 0.500 in 2w39A Skipped atom 1096, because occupancy 0.500 <= existing 0.500 in 2w39A Skipped atom 1097, because occupancy 0.500 <= existing 0.500 in 2w39A Skipped atom 1098, because occupancy 0.500 <= existing 0.500 in 2w39A Skipped atom 1099, because occupancy 0.500 <= existing 0.500 in 2w39A Skipped atom 1100, because occupancy 0.500 <= existing 0.500 in 2w39A Skipped atom 1101, because occupancy 0.500 <= existing 0.500 in 2w39A Skipped atom 1102, because occupancy 0.500 <= existing 0.500 in 2w39A Skipped atom 1103, because occupancy 0.500 <= existing 0.500 in 2w39A Skipped atom 1208, because occupancy 0.500 <= existing 0.500 in 2w39A Skipped atom 1209, because occupancy 0.500 <= existing 0.500 in 2w39A Skipped atom 1210, because occupancy 0.500 <= existing 0.500 in 2w39A Skipped atom 1211, because occupancy 0.500 <= existing 0.500 in 2w39A Skipped atom 1212, because occupancy 0.500 <= existing 0.500 in 2w39A Skipped atom 1213, because occupancy 0.500 <= existing 0.500 in 2w39A Skipped atom 1214, because occupancy 0.500 <= existing 0.500 in 2w39A Skipped atom 1215, because occupancy 0.500 <= existing 0.500 in 2w39A Skipped atom 1276, because occupancy 0.500 <= existing 0.500 in 2w39A Skipped atom 1277, because occupancy 0.500 <= existing 0.500 in 2w39A Skipped atom 1278, because occupancy 0.500 <= existing 0.500 in 2w39A Skipped atom 1279, because occupancy 0.500 <= existing 0.500 in 2w39A Skipped atom 1280, because occupancy 0.500 <= existing 0.500 in 2w39A Skipped atom 1281, because occupancy 0.500 <= existing 0.500 in 2w39A Skipped atom 1282, because occupancy 0.500 <= existing 0.500 in 2w39A Skipped atom 1283, because occupancy 0.500 <= existing 0.500 in 2w39A Skipped atom 1288, because occupancy 0.500 <= existing 0.500 in 2w39A Skipped atom 1289, because occupancy 0.500 <= existing 0.500 in 2w39A Skipped atom 1290, because occupancy 0.500 <= existing 0.500 in 2w39A Skipped atom 1291, because occupancy 0.500 <= existing 0.500 in 2w39A Skipped atom 1300, because occupancy 0.500 <= existing 0.500 in 2w39A Skipped atom 1301, because occupancy 0.500 <= existing 0.500 in 2w39A Skipped atom 1302, because occupancy 0.500 <= existing 0.500 in 2w39A Skipped atom 1303, because occupancy 0.500 <= existing 0.500 in 2w39A Skipped atom 1304, because occupancy 0.500 <= existing 0.500 in 2w39A Skipped atom 1305, because occupancy 0.500 <= existing 0.500 in 2w39A Skipped atom 1306, because occupancy 0.500 <= existing 0.500 in 2w39A Skipped atom 1307, because occupancy 0.500 <= existing 0.500 in 2w39A Skipped atom 1345, because occupancy 0.500 <= existing 0.500 in 2w39A Skipped atom 1346, because occupancy 0.500 <= existing 0.500 in 2w39A Skipped atom 1347, because occupancy 0.500 <= existing 0.500 in 2w39A Skipped atom 1348, because occupancy 0.500 <= existing 0.500 in 2w39A Skipped atom 1349, because occupancy 0.500 <= existing 0.500 in 2w39A Skipped atom 1350, because occupancy 0.500 <= existing 0.500 in 2w39A Skipped atom 1351, because occupancy 0.500 <= existing 0.500 in 2w39A Skipped atom 1352, because occupancy 0.500 <= existing 0.500 in 2w39A Skipped atom 1353, because occupancy 0.500 <= existing 0.500 in 2w39A Skipped atom 1623, because occupancy 0.500 <= existing 0.500 in 2w39A Skipped atom 1624, because occupancy 0.500 <= existing 0.500 in 2w39A Skipped atom 1625, because occupancy 0.500 <= existing 0.500 in 2w39A Skipped atom 1626, because occupancy 0.500 <= existing 0.500 in 2w39A Skipped atom 1627, because occupancy 0.500 <= existing 0.500 in 2w39A Skipped atom 1628, because occupancy 0.500 <= existing 0.500 in 2w39A Skipped atom 1629, because occupancy 0.500 <= existing 0.500 in 2w39A Skipped atom 1934, because occupancy 0.500 <= existing 0.500 in 2w39A Skipped atom 1935, because occupancy 0.500 <= existing 0.500 in 2w39A Skipped atom 1936, because occupancy 0.500 <= existing 0.500 in 2w39A Skipped atom 1937, because occupancy 0.500 <= existing 0.500 in 2w39A Skipped atom 1938, because occupancy 0.500 <= existing 0.500 in 2w39A Skipped atom 1939, because occupancy 0.500 <= existing 0.500 in 2w39A Skipped atom 1940, because occupancy 0.500 <= existing 0.500 in 2w39A Skipped atom 1941, because occupancy 0.500 <= existing 0.500 in 2w39A Skipped atom 2021, because occupancy 0.500 <= existing 0.500 in 2w39A Skipped atom 2022, because occupancy 0.500 <= existing 0.500 in 2w39A Skipped atom 2023, because occupancy 0.500 <= existing 0.500 in 2w39A Skipped atom 2024, because occupancy 0.500 <= existing 0.500 in 2w39A Skipped atom 2025, because occupancy 0.500 <= existing 0.500 in 2w39A Skipped atom 2026, because occupancy 0.500 <= existing 0.500 in 2w39A Skipped atom 2027, because occupancy 0.500 <= existing 0.500 in 2w39A Skipped atom 2028, because occupancy 0.500 <= existing 0.500 in 2w39A Skipped atom 2029, because occupancy 0.500 <= existing 0.500 in 2w39A Skipped atom 2030, because occupancy 0.500 <= existing 0.500 in 2w39A Skipped atom 2031, because occupancy 0.500 <= existing 0.500 in 2w39A Skipped atom 2050, because occupancy 0.500 <= existing 0.500 in 2w39A Skipped atom 2051, because occupancy 0.500 <= existing 0.500 in 2w39A Skipped atom 2052, because occupancy 0.500 <= existing 0.500 in 2w39A Skipped atom 2053, because occupancy 0.500 <= existing 0.500 in 2w39A Skipped atom 2054, because occupancy 0.500 <= existing 0.500 in 2w39A Skipped atom 2055, because occupancy 0.500 <= existing 0.500 in 2w39A Skipped atom 2056, because occupancy 0.500 <= existing 0.500 in 2w39A Skipped atom 2057, because occupancy 0.500 <= existing 0.500 in 2w39A Skipped atom 2185, because occupancy 0.500 <= existing 0.500 in 2w39A Skipped atom 2186, because occupancy 0.500 <= existing 0.500 in 2w39A Skipped atom 2187, because occupancy 0.500 <= existing 0.500 in 2w39A Skipped atom 2188, because occupancy 0.500 <= existing 0.500 in 2w39A Skipped atom 2189, because occupancy 0.500 <= existing 0.500 in 2w39A Skipped atom 2190, because occupancy 0.500 <= existing 0.500 in 2w39A Skipped atom 2191, because occupancy 0.500 <= existing 0.500 in 2w39A Skipped atom 2192, because occupancy 0.500 <= existing 0.500 in 2w39A Skipped atom 2249, because occupancy 0.500 <= existing 0.500 in 2w39A Skipped atom 2250, because occupancy 0.500 <= existing 0.500 in 2w39A Skipped atom 2251, because occupancy 0.500 <= existing 0.500 in 2w39A Skipped atom 2252, because occupancy 0.500 <= existing 0.500 in 2w39A Skipped atom 2253, because occupancy 0.500 <= existing 0.500 in 2w39A Skipped atom 2254, because occupancy 0.500 <= existing 0.500 in 2w39A # T0518 read from 2w39A/T0518-2w39A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2w39A read from 2w39A/T0518-2w39A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2w39A to template set # found chain 2w39A in template set T0518 59 :NGYITIFDGE 2w39A 3 :YHLEDNWVGS T0518 69 :TFNGWRGY 2w39A 16 :STFTHEAI T0518 86 :TIEDGCIKFNGSGGGEAQDG 2w39A 46 :YASGDTLILRADHTTTLSPS T0518 106 :DGGDLIFAHKFKNFELELEWKV 2w39A 70 :NSVRIRSIKTYTTHVAVFDVRH T0518 128 :AKGSNSGILYLA 2w39A 95 :GCGTWPAAWETD T0518 142 :VTS 2w39A 107 :EGD T0518 157 :YISAPEYQILDNAN 2w39A 110 :WPNGGEVDIIEGVN T0518 171 :HPDAKLGKDNNRQSASLYDMIP 2w39A 134 :TGANCAMPASRTMTGHATNNNC T0518 202 :G 2w39A 183 :G T0518 204 :WNKAKIMVYKGTVVHGQ 2w39A 184 :GGWYAMERTNSFIKVWF T0518 226 :LEYH 2w39A 201 :FPRN Number of specific fragments extracted= 11 number of extra gaps= 0 total=644 Will force an alignment to be made, even if fragment is small Number of alignments=49 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2w39A/T0518-2w39A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0518 read from 2w39A/T0518-2w39A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2w39A read from 2w39A/T0518-2w39A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2w39A in template set T0518 61 :YITIFDGE 2w39A 5 :LEDNWVGS T0518 69 :TFNGWRGYGKDRV 2w39A 16 :STFTHEAIADPTH T0518 82 :PTKWTIEDGCIKFNGSGGGEAQDGD 2w39A 42 :KNLTYASGDTLILRADHTTTLSPSG T0518 107 :GGDLIFAHKFKNFELELEWK 2w39A 71 :SVRIRSIKTYTTHVAVFDVR T0518 127 :VAKGS 2w39A 92 :MPQGC T0518 134 :GILYLAQEVTSKD 2w39A 97 :GTWPAAWETDEGD T0518 157 :YISAPEYQILDNAN 2w39A 110 :WPNGGEVDIIEGVN T0518 171 :HPD 2w39A 135 :GAN T0518 175 :KLGKDNNRQSASLY 2w39A 138 :CAMPASRTMTGHAT T0518 191 :IPA 2w39A 152 :NNN T0518 195 :P 2w39A 182 :N T0518 203 :EWNKAKIMVYKGTVVHGQNDENVLEYHLWTKQWTDMLQASKFSEDKWPLAFELLNNC 2w39A 183 :GGGWYAMERTNSFIKVWFFPRNAGNVPNDIASGPATINTDNWGTPTAFFPNTNCDIG T0518 261 :GENHEGFIGLQ 2w39A 240 :SHFDANNIIIN Number of specific fragments extracted= 13 number of extra gaps= 0 total=657 Will force an alignment to be made, even if fragment is small Number of alignments=50 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2w39A/T0518-2w39A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0518 read from 2w39A/T0518-2w39A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2w39A read from 2w39A/T0518-2w39A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2w39A in template set T0518 83 :TKWTIEDGCIKFNGSGGGEAQDGDGGD 2w39A 43 :NLTYASGDTLILRADHTTTLSPSGPGR T0518 110 :LIFAHKFKNFELELEW 2w39A 74 :IRSIKTYTTHVAVFDV T0518 126 :KVAKGSNSGILYLAQEV 2w39A 91 :HMPQGCGTWPAAWETDE T0518 155 :PIYISAPEYQILDNANHPDA 2w39A 108 :GDWPNGGEVDIIEGVNDQSP T0518 175 :KLGKDNNRQSASLYDMIP 2w39A 139 :AMPASRTMTGHATNNNCD T0518 202 :GEWNKAKIMVYKGTVVHGQND 2w39A 182 :NGGGWYAMERTNSFIKVWFFP Number of specific fragments extracted= 6 number of extra gaps= 0 total=663 Will force an alignment to be made, even if fragment is small Number of alignments=51 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2cl2A/T0518-2cl2A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2cl2A expands to /projects/compbio/data/pdb/2cl2.pdb.gz 2cl2A:Skipped atom 280, because occupancy 0.500 <= existing 0.500 in 2cl2A Skipped atom 281, because occupancy 0.500 <= existing 0.500 in 2cl2A Skipped atom 282, because occupancy 0.500 <= existing 0.500 in 2cl2A Skipped atom 283, because occupancy 0.500 <= existing 0.500 in 2cl2A Skipped atom 284, because occupancy 0.500 <= existing 0.500 in 2cl2A Skipped atom 285, because occupancy 0.500 <= existing 0.500 in 2cl2A Skipped atom 286, because occupancy 0.500 <= existing 0.500 in 2cl2A Skipped atom 287, because occupancy 0.500 <= existing 0.500 in 2cl2A Skipped atom 436, because occupancy 0.500 <= existing 0.500 in 2cl2A Skipped atom 437, because occupancy 0.500 <= existing 0.500 in 2cl2A Skipped atom 438, because occupancy 0.500 <= existing 0.500 in 2cl2A Skipped atom 439, because occupancy 0.500 <= existing 0.500 in 2cl2A Skipped atom 440, because occupancy 0.500 <= existing 0.500 in 2cl2A Skipped atom 441, because occupancy 0.500 <= existing 0.500 in 2cl2A Skipped atom 442, because occupancy 0.500 <= existing 0.500 in 2cl2A Skipped atom 443, because occupancy 0.500 <= existing 0.500 in 2cl2A Skipped atom 444, because occupancy 0.500 <= existing 0.500 in 2cl2A Skipped atom 445, because occupancy 0.500 <= existing 0.500 in 2cl2A Skipped atom 446, because occupancy 0.500 <= existing 0.500 in 2cl2A Skipped atom 2133, because occupancy 0.500 <= existing 0.500 in 2cl2A Skipped atom 2134, because occupancy 0.500 <= existing 0.500 in 2cl2A Skipped atom 2135, because occupancy 0.500 <= existing 0.500 in 2cl2A Skipped atom 2136, because occupancy 0.500 <= existing 0.500 in 2cl2A Skipped atom 2137, because occupancy 0.500 <= existing 0.500 in 2cl2A Skipped atom 2138, because occupancy 0.500 <= existing 0.500 in 2cl2A Skipped atom 2273, because occupancy 0.500 <= existing 0.500 in 2cl2A Skipped atom 2274, because occupancy 0.500 <= existing 0.500 in 2cl2A Skipped atom 2275, because occupancy 0.500 <= existing 0.500 in 2cl2A Skipped atom 2276, because occupancy 0.500 <= existing 0.500 in 2cl2A Skipped atom 2277, because occupancy 0.500 <= existing 0.500 in 2cl2A Skipped atom 2278, because occupancy 0.500 <= existing 0.500 in 2cl2A Skipped atom 2279, because occupancy 0.500 <= existing 0.500 in 2cl2A Skipped atom 2280, because occupancy 0.500 <= existing 0.500 in 2cl2A Skipped atom 2281, because occupancy 0.500 <= existing 0.500 in 2cl2A Skipped atom 2282, because occupancy 0.500 <= existing 0.500 in 2cl2A # T0518 read from 2cl2A/T0518-2cl2A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2cl2A read from 2cl2A/T0518-2cl2A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2cl2A to template set # found chain 2cl2A in template set T0518 61 :YITIFDGE 2cl2A 5 :LEDNWVGS T0518 69 :TFNGWRGY 2cl2A 16 :STFTHEAI T0518 82 :PTKWTIEDGCIKFNGSGGGEAQDG 2cl2A 42 :KNLTYASGDTLILRADHTTTLSPS T0518 106 :DGGDLIFAHKFKNFELELEWKV 2cl2A 70 :NSVRIRSIKTYTTHVAVFDVRH T0518 128 :AKGSNSGILYLA 2cl2A 95 :GCGTWPAAWETD T0518 142 :VTS 2cl2A 107 :EGD T0518 157 :YISAPEYQILDNAN 2cl2A 110 :WPNGGEVDIIEGVN T0518 171 :HPDAKLGKDNNRQSASLYDMIP 2cl2A 135 :GANCAMPASRTMTGHATNNNCD T0518 202 :G 2cl2A 183 :G T0518 204 :WNKAKIMVYKGTVVHG 2cl2A 184 :GGWYAMERTNSFIKVW T0518 225 :VLEYHL 2cl2A 200 :FFPRNA T0518 233 :KQWTDMLQAS 2cl2A 206 :GNVPNDIASG T0518 243 :KFSEDKWPLAFELLNNCGGE 2cl2A 218 :TINTDNWGTPTAFFPNTNCD T0518 263 :NHEGFIGLQDH 2cl2A 242 :FDANNIIINLT T0518 274 :GDD 2cl2A 270 :PGS T0518 277 :VWFRNIRV 2cl2A 289 :WDIASVRV Number of specific fragments extracted= 16 number of extra gaps= 0 total=679 Will force an alignment to be made, even if fragment is small Number of alignments=52 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2cl2A/T0518-2cl2A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0518 read from 2cl2A/T0518-2cl2A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2cl2A read from 2cl2A/T0518-2cl2A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2cl2A in template set T0518 61 :YITIFDGETF 2cl2A 5 :LEDNWVGSAF T0518 71 :NGWR 2cl2A 18 :FTHE T0518 75 :GYGKDRV 2cl2A 24 :ADPTHGR T0518 82 :PTKWTIEDGCIKFNGSGGGEAQDGD 2cl2A 42 :KNLTYASGDTLILRADHTTTLSPSG T0518 107 :GGDLIFAHKFKNFELELEWK 2cl2A 71 :SVRIRSIKTYTTHVAVFDVR T0518 127 :VAKGS 2cl2A 92 :MPQGC T0518 134 :GILYLAQEVTSKD 2cl2A 97 :GTWPAAWETDEGD T0518 157 :YISAPEYQILDNAN 2cl2A 110 :WPNGGEVDIIEGVN T0518 171 :HPDAKLGKDNNR 2cl2A 135 :GANCAMPASRTM T0518 202 :GEWNKAKIMVYKGTVVHGQNDENV 2cl2A 182 :NGGGWYAMERTNSFIKVWFFPRNA Number of specific fragments extracted= 10 number of extra gaps= 0 total=689 Will force an alignment to be made, even if fragment is small Number of alignments=53 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2cl2A/T0518-2cl2A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0518 read from 2cl2A/T0518-2cl2A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2cl2A read from 2cl2A/T0518-2cl2A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2cl2A in template set T0518 82 :PTKWTIEDGCIKFNGSGGGEAQDGDGGD 2cl2A 42 :KNLTYASGDTLILRADHTTTLSPSGPGR T0518 110 :LIFAHKFKNFELELEW 2cl2A 74 :IRSIKTYTTHVAVFDV T0518 126 :KVAKGSNSGILYLAQEVTS 2cl2A 91 :HMPQGCGTWPAAWETDEGD T0518 157 :YISAPEYQILDNANHPDA 2cl2A 110 :WPNGGEVDIIEGVNDQSP T0518 175 :KLGKDNNRQSASLYDMIPA 2cl2A 139 :AMPASRTMTGHATNNNCDV T0518 202 :GEWNKAKIMVYKGTVVHGQND 2cl2A 182 :NGGGWYAMERTNSFIKVWFFP Number of specific fragments extracted= 6 number of extra gaps= 0 total=695 Will force an alignment to be made, even if fragment is small Number of alignments=54 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1umzA/T0518-1umzA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1umzA expands to /projects/compbio/data/pdb/1umz.pdb.gz 1umzA:# T0518 read from 1umzA/T0518-1umzA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1umzA read from 1umzA/T0518-1umzA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1umzA to template set # found chain 1umzA in template set Warning: unaligning (T0518)G100 because of BadResidue code BAD_PEPTIDE in next template residue (1umzA)G42 Warning: unaligning (T0518)G107 because of BadResidue code BAD_PEPTIDE at template residue (1umzA)G42 Warning: unaligning (T0518)E162 because of BadResidue code BAD_PEPTIDE in next template residue (1umzA)F88 Warning: unaligning (T0518)Y163 because of BadResidue code BAD_PEPTIDE at template residue (1umzA)F88 Warning: unaligning (T0518)A185 because of BadResidue code BAD_PEPTIDE in next template residue (1umzA)Q115 Warning: unaligning (T0518)S186 because of BadResidue code BAD_PEPTIDE at template residue (1umzA)Q115 Warning: unaligning (T0518)Y188 because of BadResidue code BAD_PEPTIDE in next template residue (1umzA)Y118 Warning: unaligning (T0518)D189 because of BadResidue code BAD_PEPTIDE at template residue (1umzA)Y118 T0518 75 :GY 1umzA 19 :WA T0518 82 :PTKWTIEDG 1umzA 21 :FDHIKYFNG T0518 91 :CIKFNGSGG 1umzA 32 :EIQLHLDKY T0518 108 :GDLIFAHKFKNFELELEWKVAKGS 1umzA 43 :TGFQSKGSYLFGHFSMQMKLVPGD T0518 132 :NSGILYLAQEVTSK 1umzA 71 :VTAFYLSSQNSEHD T0518 160 :AP 1umzA 85 :EI T0518 164 :QILD 1umzA 89 :EFLG T0518 168 :NANHPDA 1umzA 94 :RTGQPYI T0518 175 :KLGKDNNRQS 1umzA 104 :NVFTGGKGDR T0518 187 :L 1umzA 116 :R T0518 190 :MIPAVP 1umzA 119 :LWFDPT T0518 202 :GEWNKAKIMVYKGTVVHGQNDENVLEYHLWTKQ 1umzA 125 :KEFHYYSVLWNMYMIVFLVDDVPIRVFKNCKDL T0518 246 :ED 1umzA 158 :GV T0518 261 :GENHEGF 1umzA 160 :KFPFNQP T0518 268 :IGLQDHGDD 1umzA 171 :SSLWNADDW T0518 277 :VWFRNIRVKVL 1umzA 197 :ASYRSFHIDGC Number of specific fragments extracted= 16 number of extra gaps= 4 total=711 Will force an alignment to be made, even if fragment is small Number of alignments=55 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1umzA/T0518-1umzA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0518 read from 1umzA/T0518-1umzA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1umzA read from 1umzA/T0518-1umzA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1umzA in template set Warning: unaligning (T0518)F70 because first residue in template chain is (1umzA)P6 Warning: unaligning (T0518)D106 because of BadResidue code BAD_PEPTIDE in next template residue (1umzA)G42 Warning: unaligning (T0518)G107 because of BadResidue code BAD_PEPTIDE at template residue (1umzA)G42 Warning: unaligning (T0518)E162 because of BadResidue code BAD_PEPTIDE in next template residue (1umzA)F88 Warning: unaligning (T0518)Y163 because of BadResidue code BAD_PEPTIDE at template residue (1umzA)F88 Warning: unaligning (T0518)A185 because of BadResidue code BAD_PEPTIDE in next template residue (1umzA)Q115 Warning: unaligning (T0518)S186 because of BadResidue code BAD_PEPTIDE at template residue (1umzA)Q115 Warning: unaligning (T0518)Y188 because of BadResidue code BAD_PEPTIDE in next template residue (1umzA)Y118 Warning: unaligning (T0518)D189 because of BadResidue code BAD_PEPTIDE at template residue (1umzA)Y118 T0518 71 :NGWR 1umzA 7 :VDVA T0518 75 :GY 1umzA 19 :WA T0518 82 :PTKWTIEDG 1umzA 21 :FDHIKYFNG T0518 91 :CIKFNGS 1umzA 32 :EIQLHLD T0518 104 :DG 1umzA 39 :KY T0518 108 :GDLIFAHKFKNFELELEWKVAKGSNSGILYLAQEVTSKD 1umzA 43 :TGFQSKGSYLFGHFSMQMKLVPGDSAGTVTAFYLSSQNS T0518 157 :YISAP 1umzA 82 :EHDEI T0518 164 :QILD 1umzA 89 :EFLG T0518 168 :NANHPDA 1umzA 94 :RTGQPYI T0518 175 :KLGKDNNRQS 1umzA 104 :NVFTGGKGDR T0518 187 :L 1umzA 116 :R T0518 190 :MIPAV 1umzA 119 :LWFDP T0518 201 :FGEWNKAKIMVYKGTVVHGQNDENVLEYHLWTKQ 1umzA 124 :TKEFHYYSVLWNMYMIVFLVDDVPIRVFKNCKDL T0518 248 :KWPLAF 1umzA 158 :GVKFPF T0518 261 :GENHEGFIGLQDHGDD 1umzA 164 :NQPMKIYSSLWNADDW T0518 277 :VWFRNIRVKVL 1umzA 197 :ASYRSFHIDGC Number of specific fragments extracted= 16 number of extra gaps= 4 total=727 Will force an alignment to be made, even if fragment is small Number of alignments=56 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1umzA/T0518-1umzA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0518 read from 1umzA/T0518-1umzA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1umzA read from 1umzA/T0518-1umzA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1umzA in template set Warning: unaligning (T0518)D106 because of BadResidue code BAD_PEPTIDE in next template residue (1umzA)G42 Warning: unaligning (T0518)G107 because of BadResidue code BAD_PEPTIDE at template residue (1umzA)G42 Warning: unaligning (T0518)E162 because of BadResidue code BAD_PEPTIDE in next template residue (1umzA)F88 Warning: unaligning (T0518)Y163 because of BadResidue code BAD_PEPTIDE at template residue (1umzA)F88 Warning: unaligning (T0518)A185 because of BadResidue code BAD_PEPTIDE in next template residue (1umzA)Q115 Warning: unaligning (T0518)S186 because of BadResidue code BAD_PEPTIDE at template residue (1umzA)Q115 Warning: unaligning (T0518)Y188 because of BadResidue code BAD_PEPTIDE in next template residue (1umzA)Y118 Warning: unaligning (T0518)D189 because of BadResidue code BAD_PEPTIDE at template residue (1umzA)Y118 T0518 73 :WRGYGKD 1umzA 15 :YVPTWAF T0518 83 :TKWTIEDG 1umzA 22 :DHIKYFNG T0518 91 :CIKFNGS 1umzA 32 :EIQLHLD T0518 104 :DG 1umzA 39 :KY T0518 108 :GDLIFAHKFKNFELELEWKVAKGSNSGILYLAQEVTS 1umzA 43 :TGFQSKGSYLFGHFSMQMKLVPGDSAGTVTAFYLSSQ T0518 155 :PIYISAP 1umzA 80 :NSEHDEI T0518 164 :QILDNANHPDA 1umzA 89 :EFLGNRTGQPY T0518 177 :GKDNNRQS 1umzA 106 :FTGGKGDR T0518 187 :L 1umzA 116 :R T0518 190 :M 1umzA 119 :L T0518 197 :NSKPFGEWNKAKIMVYKGTVVHGQNDENVLEYHLWTK 1umzA 120 :WFDPTKEFHYYSVLWNMYMIVFLVDDVPIRVFKNCKD T0518 254 :ELLNNCGGENHEGFIGLQDHGDD 1umzA 157 :LGVKFPFNQPMKIYSSLWNADDW T0518 277 :VWFRNIRVK 1umzA 197 :ASYRSFHID Number of specific fragments extracted= 13 number of extra gaps= 4 total=740 Will force an alignment to be made, even if fragment is small Number of alignments=57 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1cpnA/T0518-1cpnA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1cpnA expands to /projects/compbio/data/pdb/1cpn.pdb.gz 1cpnA:Skipped atom 970, because occupancy 0.500 <= existing 0.500 in 1cpnA # T0518 read from 1cpnA/T0518-1cpnA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1cpnA read from 1cpnA/T0518-1cpnA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1cpnA to template set # found chain 1cpnA in template set Warning: unaligning (T0518)K129 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1cpnA)G28 Warning: unaligning (T0518)G130 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1cpnA)G28 Warning: unaligning (T0518)M210 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1cpnA)W93 Warning: unaligning (T0518)V211 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1cpnA)W93 T0518 107 :GGDLIFAHKFKNFELELEWKV 1cpnA 3 :CAEYRSTNIYGYGLYEVSMKP T0518 128 :A 1cpnA 26 :N T0518 131 :SNSGILYLAQEVT 1cpnA 29 :IVSSFFTYTGPAH T0518 157 :YISAPEYQILD 1cpnA 42 :GTQWDEIDIEF T0518 168 :NANHPDA 1cpnA 54 :GKDTTKV T0518 175 :KLGKDNNRQSASLYDMIPAVPQN 1cpnA 63 :NYYTNGVGGHEKVISLGFDASKG T0518 204 :WNKAKI 1cpnA 86 :FHTYAF T0518 212 :YKGTVVHGQNDENVLEYHLW 1cpnA 94 :QPGYIKWYVDGVLKHTATAN T0518 261 :GENHEGF 1cpnA 114 :IPSTPGK T0518 268 :IGLQDHGDD 1cpnA 123 :MNLWNGTGV T0518 277 :VWFRNIRVKVL 1cpnA 146 :AEYDWVKYTSN Number of specific fragments extracted= 11 number of extra gaps= 2 total=751 Will force an alignment to be made, even if fragment is small Number of alignments=58 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1cpnA/T0518-1cpnA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0518 read from 1cpnA/T0518-1cpnA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1cpnA read from 1cpnA/T0518-1cpnA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1cpnA in template set Warning: unaligning (T0518)S131 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1cpnA)G28 Warning: unaligning (T0518)G134 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1cpnA)G28 Warning: unaligning (T0518)M210 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1cpnA)W93 Warning: unaligning (T0518)V211 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1cpnA)W93 T0518 107 :GGDLIFAHKFKNFELELEWKVAKG 1cpnA 3 :CAEYRSTNIYGYGLYEVSMKPAKN T0518 135 :ILYLAQEVTSKDK 1cpnA 29 :IVSSFFTYTGPAH T0518 157 :YISAPEYQIL 1cpnA 42 :GTQWDEIDIE T0518 167 :DNANHPDAKLGKDNNRQSASLYDMIPAVPQ 1cpnA 55 :KDTTKVQFNYYTNGVGGHEKVISLGFDASK T0518 203 :EWNKAKI 1cpnA 85 :GFHTYAF T0518 212 :YKGTVVHGQNDENVLEYHLW 1cpnA 94 :QPGYIKWYVDGVLKHTATAN T0518 261 :GENHEGF 1cpnA 114 :IPSTPGK T0518 268 :IGLQDHGDD 1cpnA 123 :MNLWNGTGV T0518 277 :VWFRNIRVKVL 1cpnA 146 :AEYDWVKYTSN Number of specific fragments extracted= 9 number of extra gaps= 2 total=760 Will force an alignment to be made, even if fragment is small Number of alignments=59 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1cpnA/T0518-1cpnA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0518 read from 1cpnA/T0518-1cpnA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1cpnA read from 1cpnA/T0518-1cpnA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1cpnA in template set Warning: unaligning (T0518)S131 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1cpnA)G28 Warning: unaligning (T0518)N132 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1cpnA)G28 Warning: unaligning (T0518)M210 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1cpnA)W93 Warning: unaligning (T0518)V211 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1cpnA)W93 T0518 108 :GDLIFAHKFKNFELELEWKVAKG 1cpnA 4 :AEYRSTNIYGYGLYEVSMKPAKN T0518 133 :SGILYLAQEVTS 1cpnA 29 :IVSSFFTYTGPA T0518 156 :IYISAPEYQILDNANHPDA 1cpnA 41 :HGTQWDEIDIEFLGKDTTK T0518 178 :KDNNRQSASLYDM 1cpnA 66 :TNGVGGHEKVISL T0518 197 :NSKPFGEWNKAKI 1cpnA 79 :GFDASKGFHTYAF T0518 212 :YKGTVVHGQNDENVLEYHLWT 1cpnA 94 :QPGYIKWYVDGVLKHTATANI T0518 260 :GGENHEGFIGLQDHGDD 1cpnA 115 :PSTPGKIMMNLWNGTGV T0518 277 :VWFRNIRV 1cpnA 146 :AEYDWVKY Number of specific fragments extracted= 8 number of extra gaps= 2 total=768 Will force an alignment to be made, even if fragment is small Number of alignments=60 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3hr9A/T0518-3hr9A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 3hr9A expands to /projects/compbio/data/pdb/3hr9.pdb.gz 3hr9A:# T0518 read from 3hr9A/T0518-3hr9A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3hr9A read from 3hr9A/T0518-3hr9A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3hr9A to template set # found chain 3hr9A in template set T0518 107 :GGDLIFAHKFKNFELELEWKV 3hr9A 9 :GAELYTLEEVQYGKFEARMKM T0518 128 :AKGSNSGILYLAQEVTSKD 3hr9A 32 :ASGTVSSMILYQNGSEIAD T0518 157 :YISAPEYQILDNANHPDA 3hr9A 51 :GRPWVEVDIEVLGKNPGS T0518 175 :KLG 3hr9A 72 :NII T0518 178 :KDNNRQSASLYDMIPAV 3hr9A 78 :AGAQKTSEKHHAVSPAA T0518 201 :FGEWNKAKIMVYKGTVVHGQNDENVLEYHLWTKQ 3hr9A 95 :DQAFHTYGLEWTPNYVRWTVDGQEVRKTEGGQVS T0518 261 :GENHEGFIGLQDH 3hr9A 129 :NLTGTQGLRFNLW T0518 277 :VWFRNIRVKVL 3hr9A 161 :QFINWVKVYKY Number of specific fragments extracted= 8 number of extra gaps= 0 total=776 Will force an alignment to be made, even if fragment is small Number of alignments=61 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3hr9A/T0518-3hr9A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0518 read from 3hr9A/T0518-3hr9A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3hr9A read from 3hr9A/T0518-3hr9A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3hr9A in template set T0518 104 :DGDGGDLIFAHKFKNFELELEWKVAKGS 3hr9A 6 :DFSGAELYTLEEVQYGKFEARMKMAAAS T0518 134 :GILYLAQEVTSK 3hr9A 34 :GTVSSMILYQNG T0518 146 :DKDGN 3hr9A 47 :EIADG T0518 157 :YISA 3hr9A 52 :RPWV T0518 162 :EYQILDNANHPDAKLGKDNNRQSASLYDMIPAVPQNSKPFGEWNKAKIMVYKGTVVHGQNDENVLEYHLWTKQ 3hr9A 56 :EVDIEVLGKNPGSFQSNIITGKAGAQKTSEKHHAVSPAADQAFHTYGLEWTPNYVRWTVDGQEVRKTEGGQVS T0518 261 :GENHEGFIGLQDH 3hr9A 129 :NLTGTQGLRFNLW T0518 274 :GDD 3hr9A 143 :SES T0518 277 :VWFRNIRVKVL 3hr9A 161 :QFINWVKVYKY Number of specific fragments extracted= 8 number of extra gaps= 0 total=784 Will force an alignment to be made, even if fragment is small Number of alignments=62 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3hr9A/T0518-3hr9A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0518 read from 3hr9A/T0518-3hr9A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3hr9A read from 3hr9A/T0518-3hr9A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3hr9A in template set T0518 108 :GDLIFAHKFKNFELELEWKVAKGS 3hr9A 10 :AELYTLEEVQYGKFEARMKMAAAS T0518 134 :GILYLAQEVTSK 3hr9A 34 :GTVSSMILYQNG T0518 152 :VLEPIYISAPEYQILDNANHPDA 3hr9A 46 :SEIADGRPWVEVDIEVLGKNPGS T0518 183 :QSASLYDMIPAVPQNSKPFGEWNKAKIMVYKGTVVHGQNDENVLEYHL 3hr9A 77 :KAGAQKTSEKHHAVSPAADQAFHTYGLEWTPNYVRWTVDGQEVRKTEG T0518 237 :DMLQ 3hr9A 125 :GQVS T0518 259 :CGGENHEGFIGLQDHGDD 3hr9A 129 :NLTGTQGLRFNLWSSESA T0518 277 :VWFRNIRV 3hr9A 161 :QFINWVKV Number of specific fragments extracted= 7 number of extra gaps= 0 total=791 Will force an alignment to be made, even if fragment is small Number of alignments=63 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1mveA/T0518-1mveA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1mveA expands to /projects/compbio/data/pdb/1mve.pdb.gz 1mveA: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 # T0518 read from 1mveA/T0518-1mveA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1mveA read from 1mveA/T0518-1mveA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1mveA to template set # found chain 1mveA in template set T0518 107 :GGDLIFAHKFKNFELELEWKV 1mveA 9 :GAELYTLEEVQYGKFEARMKM T0518 128 :AKGSNSGILYLAQEVTSKD 1mveA 32 :ASGTVSSMFLYQNGSEIAD T0518 157 :YISAPEYQILD 1mveA 51 :GRPWVEVDIEV T0518 168 :NANHPDAKLG 1mveA 65 :NPGSFQSNII T0518 178 :KDNNRQSASLYDMIPAVP 1mveA 78 :AGAQKTSEKHHAVSPAAD T0518 202 :GEWNKAKIMVYKGTVVHGQNDENVLEYHLWTKQ 1mveA 96 :QAFHTYGLEWTPNYVRWTVDGQEVRKTEGGQVS T0518 261 :GENHEGFIGLQDH 1mveA 129 :NLTGTQGLRFNLW T0518 274 :G 1mveA 144 :E T0518 277 :VWFRNIRVKVL 1mveA 161 :QFINWVKVYKY Number of specific fragments extracted= 9 number of extra gaps= 0 total=800 Will force an alignment to be made, even if fragment is small Number of alignments=64 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1mveA/T0518-1mveA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0518 read from 1mveA/T0518-1mveA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1mveA read from 1mveA/T0518-1mveA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1mveA in template set T0518 104 :DGDGGDLIFAHKFKNFELELEWKVAKGS 1mveA 6 :DFSGAELYTLEEVQYGKFEARMKMAAAS T0518 134 :GILYLAQEVTSK 1mveA 34 :GTVSSMFLYQNG T0518 146 :DKDGND 1mveA 47 :EIADGR T0518 157 :YISAPEYQILDNANH 1mveA 53 :PWVEVDIEVLGKNPG T0518 172 :PDAKLGKDNNRQSASLYDMIPA 1mveA 69 :FQSNIITGKAGAQKTSEKHHAV T0518 197 :NSKPFGEWNKAKIMVYKGTVVHGQNDENVLEYHLWTKQ 1mveA 91 :SPAADQAFHTYGLEWTPNYVRWTVDGQEVRKTEGGQVS T0518 254 :EL 1mveA 129 :NL T0518 261 :GENHEGFIGLQDHG 1mveA 131 :TGTQGLRFNLWSSE T0518 275 :DD 1mveA 150 :GQ T0518 277 :VWFRNIRV 1mveA 161 :QFINWVKV Number of specific fragments extracted= 10 number of extra gaps= 0 total=810 Will force an alignment to be made, even if fragment is small Number of alignments=65 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1mveA/T0518-1mveA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0518 read from 1mveA/T0518-1mveA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1mveA read from 1mveA/T0518-1mveA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1mveA in template set T0518 108 :GDLIFAHKFKNFELELEWKVAKG 1mveA 10 :AELYTLEEVQYGKFEARMKMAAA T0518 133 :SGILYLAQEVTSK 1mveA 33 :SGTVSSMFLYQNG T0518 152 :VLEPIYISAPEYQILDNANHPDA 1mveA 46 :SEIADGRPWVEVDIEVLGKNPGS T0518 177 :GKDNNRQSASLYDMI 1mveA 77 :KAGAQKTSEKHHAVS T0518 198 :SKPFGEWNKAKIMVYKGTVVHGQNDENVLEYHLWT 1mveA 92 :PAADQAFHTYGLEWTPNYVRWTVDGQEVRKTEGGQ T0518 257 :NNCGGENHEGFIGLQDHGDD 1mveA 127 :VSNLTGTQGLRFNLWSSESA T0518 277 :VWFRNIRV 1mveA 161 :QFINWVKV Number of specific fragments extracted= 7 number of extra gaps= 0 total=817 Will force an alignment to be made, even if fragment is small Number of alignments=66 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ajkA/T0518-1ajkA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1ajkA expands to /projects/compbio/data/pdb/1ajk.pdb.gz 1ajkA:# T0518 read from 1ajkA/T0518-1ajkA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ajkA read from 1ajkA/T0518-1ajkA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1ajkA to template set # found chain 1ajkA in template set Warning: unaligning (T0518)V194 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1ajkA)S58 Warning: unaligning (T0518)P195 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1ajkA)S58 Warning: unaligning (T0518)D247 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1ajkA)K95 Warning: unaligning (T0518)K248 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1ajkA)K95 Warning: unaligning (T0518)N257 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ajkA)D107 Warning: unaligning (T0518)G260 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ajkA)D107 T0518 129 :KGSNSGILYLAQEVTSKD 1ajkA 2 :TGIVSSFFTYTGPAHGTQ T0518 160 :APEYQILD 1ajkA 20 :WDEIDIEF T0518 168 :NANHPDAKLGKDNNRQSASLYDMIPA 1ajkA 31 :DTTKVQFNYYTNGVGGHEKVISLGFD T0518 196 :QN 1ajkA 59 :KG T0518 204 :WNKAKIMVYKGTVVHGQNDENVLEYHLWTKQ 1ajkA 61 :FHTYAFDWQPGYIKWYVDGVLKHTATANIPS T0518 245 :SE 1ajkA 92 :TP T0518 249 :WPLAFELL 1ajkA 96 :IMMNLWNG T0518 261 :GENHE 1ajkA 108 :DWLGS T0518 271 :QDHGDD 1ajkA 113 :YNGANP T0518 277 :VWFRNIRVKV 1ajkA 121 :AEYDWVKYTS Number of specific fragments extracted= 10 number of extra gaps= 2 total=827 Will force an alignment to be made, even if fragment is small Number of alignments=67 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ajkA/T0518-1ajkA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0518 read from 1ajkA/T0518-1ajkA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ajkA read from 1ajkA/T0518-1ajkA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1ajkA in template set Warning: unaligning (T0518)V194 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1ajkA)S58 Warning: unaligning (T0518)P195 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1ajkA)S58 Warning: unaligning (T0518)G266 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1ajkA)K95 Warning: unaligning (T0518)F267 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1ajkA)K95 T0518 133 :SGILYLAQEVTSKDK 1ajkA 2 :TGIVSSFFTYTGPAH T0518 157 :YISAPEYQILDNANHP 1ajkA 17 :GTQWDEIDIEFLGKDT T0518 173 :DAKLGKDNNRQSASLYDMIPA 1ajkA 36 :QFNYYTNGVGGHEKVISLGFD T0518 196 :Q 1ajkA 59 :K T0518 203 :EWNKAKIMVYKGTVVHGQNDENVLEYHL 1ajkA 60 :GFHTYAFDWQPGYIKWYVDGVLKHTATA T0518 243 :K 1ajkA 88 :N T0518 261 :GENHE 1ajkA 89 :IPSTP T0518 268 :IGLQDH 1ajkA 96 :IMMNLW T0518 277 :VWFRNIRVKVLD 1ajkA 121 :AEYDWVKYTSNQ Number of specific fragments extracted= 9 number of extra gaps= 2 total=836 Will force an alignment to be made, even if fragment is small Number of alignments=68 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ajkA/T0518-1ajkA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0518 read from 1ajkA/T0518-1ajkA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ajkA read from 1ajkA/T0518-1ajkA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1ajkA in template set Warning: unaligning (T0518)P200 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1ajkA)S58 Warning: unaligning (T0518)F201 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1ajkA)S58 Warning: unaligning (T0518)H264 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1ajkA)K95 Warning: unaligning (T0518)E265 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1ajkA)K95 Warning: unaligning (T0518)G274 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ajkA)D107 T0518 135 :ILYL 1ajkA 8 :FFTY T0518 141 :EV 1ajkA 12 :TG T0518 154 :EPIYISAPEYQILDNANHPDA 1ajkA 14 :PAHGTQWDEIDIEFLGKDTTK T0518 176 :LGKDNNRQSASLYDM 1ajkA 39 :YYTNGVGGHEKVISL T0518 197 :NSK 1ajkA 54 :GFD T0518 202 :GEWNKAKIMVYKGTVVHGQNDENVLEYHLWT 1ajkA 59 :KGFHTYAFDWQPGYIKWYVDGVLKHTATANI T0518 260 :GGEN 1ajkA 90 :PSTP T0518 266 :GFIGLQDH 1ajkA 96 :IMMNLWNG T0518 277 :VWFRNIRV 1ajkA 121 :AEYDWVKY Number of specific fragments extracted= 9 number of extra gaps= 2 total=845 Will force an alignment to be made, even if fragment is small Number of alignments=69 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ajoA/T0518-1ajoA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1ajoA expands to /projects/compbio/data/pdb/1ajo.pdb.gz 1ajoA:# T0518 read from 1ajoA/T0518-1ajoA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ajoA read from 1ajoA/T0518-1ajoA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1ajoA to template set # found chain 1ajoA in template set T0518 50 :DSLNLPV 1ajoA 45 :NIPSTPG T0518 57 :DENGYITI 1ajoA 89 :QTGGSFFE T0518 65 :FDGETFNGWRGY 1ajoA 98 :FNSYNSGTWEKA T0518 77 :GKDRVPTKW 1ajoA 114 :NGGVFNCTW T0518 86 :TI 1ajoA 128 :NF T0518 88 :EDGCIKFNGSGGGE 1ajoA 131 :NDGKLKLGLTSSAY T0518 103 :QDGDGGDLIFAHKFKNFELELEWKV 1ajoA 145 :NKFDCAEYRSTNIYGYGLYEVSMKP T0518 128 :AKGSNSGILYLAQEVTSKD 1ajoA 172 :NTGIVSSFFTYTGPAHGTQ T0518 160 :APEYQILD 1ajoA 191 :WDEIDIEF T0518 168 :NANHPDA 1ajoA 200 :GKDTTKV Number of specific fragments extracted= 10 number of extra gaps= 0 total=855 Will force an alignment to be made, even if fragment is small Number of alignments=70 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ajoA/T0518-1ajoA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0518 read from 1ajoA/T0518-1ajoA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ajoA read from 1ajoA/T0518-1ajoA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1ajoA in template set T0518 57 :DENGYITI 1ajoA 89 :QTGGSFFE T0518 65 :FDGETFNGWRGYGKDRV 1ajoA 98 :FNSYNSGTWEKADGYSN T0518 82 :PTKWTI 1ajoA 124 :ANNVNF T0518 88 :EDGCIKFNGSGGGEA 1ajoA 131 :NDGKLKLGLTSSAYN T0518 104 :DGDGGDLIFAHKFKNFELELEWKVAKGS 1ajoA 146 :KFDCAEYRSTNIYGYGLYEVSMKPAKNT T0518 134 :GILYLAQEVTSKDKDG 1ajoA 174 :GIVSSFFTYTGPAHGT T0518 157 :YISAPEYQILDN 1ajoA 190 :QWDEIDIEFLGK T0518 171 :HPD 1ajoA 202 :DTT Number of specific fragments extracted= 8 number of extra gaps= 0 total=863 Will force an alignment to be made, even if fragment is small Number of alignments=71 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ajoA/T0518-1ajoA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0518 read from 1ajoA/T0518-1ajoA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ajoA read from 1ajoA/T0518-1ajoA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1ajoA in template set T0518 200 :PFGEWNKAKIMVYKGTVVHGQNDENVLEYHLWT 1ajoA 14 :ASKGFHTYAFDWQPGYIKWYVDGVLKHTATANI T0518 260 :GGENHEGFIGLQDHGDD 1ajoA 47 :PSTPGKIMMNLWNGTGV Number of specific fragments extracted= 2 number of extra gaps= 0 total=865 Will force an alignment to be made, even if fragment is small Number of alignments=72 # command:CPU_time= 23.422 sec, elapsed time= 31.231 sec. # command:DEBUG: alignment library has 72 conformations DEBUG: current conformations has 0 conformations # in ExtractAlignmentsContacts extracting from alignment library using radius 8.000 separation >= 9 style evalue NUMB_ALIGNS: 72 # Adding 3682 constraints to all_contacts Done adding distance constraints # command:CPU_time= 23.560 sec, elapsed time= 31.375 sec. # command:Reading probabilities from T0518.t06.CB8-sep9.rdb Reading constraints from ConstraintSet all_contacts maxweight: 68.696 Optimizing... Probability sum: -579.303, CN propb: -579.303 weights: 0.304 constraints: 694 # command:CPU_time= 541.823 sec, elapsed time= 549.588 sec. # command:Found ConstraintSet # PrintContacts align.constraints Number of constraints in align 694 # command:Found ConstraintSet # PrintContacts align_bonus.constraints Number of constraints in align.bonus 694 # command:Found ConstraintSet # PrintContacts rejected.constraints Number of constraints in rejected 2988 # command:Found ConstraintSet # PrintContacts rejected_bonus.constraints Number of constraints in rejected.bonus 2988 # 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= 541.881 sec, elapsed time= 551.538 sec. # command: