# command:# Prefix for input files set to /projects/compbio/experiments/undertaker/atoms-inputs/ # command:# reading cullpdb_pc80_res1.2_R0.2_d070810_chains408.atoms.gz # #computed average backbone with maximum peptide_sq_deviance = 0.002 # computed average trans backbone unit from 1600 examples # computed average trans backbone unit before proline from 52 examples # trans (non-proline) backbone unit: # CA= -2.2097 1.0151 -0.0046 # O= -0.1488 2.2425 0.0020 # C= -0.6903 1.1357 0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4580 -0.0000 -0.0000 # cis backbone unit: # CA= -0.1462 2.4515 0.0018 # O= -2.0272 0.9713 0.0022 # C= -0.8006 1.0755 0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4659 0.0000 0.0000 # trans backbone unit before proline: # CA= -2.2063 1.0654 0.0002 # O= -0.1193 2.2442 0.0054 # C= -0.6842 1.1479 -0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4661 -0.0000 0.0000 # After reading cullpdb_pc80_res1.2_R0.2_d070810_chains408.atoms.gz have 408 chains in training database # Count of chains,residues,atoms: 408,82795,639989 # 81291 residues have no bad marker # 565 residues lack atoms needed to compute omega # 313 residues have cis peptide # number of each bad type: # NON_STANDARD_RESIDUE 1 # HAS_OXT 265 # TOO_MANY_ATOMS 0 # TOO_FEW_ATOMS 378 # HAS_UNKNOWN_ATOMS 0 # HAS_DUPLICATE_ATOMS 0 # CHAIN_BREAK_BEFORE 139 # NON_PLANAR_PEPTIDE 424 # BAD_PEPTIDE 803 # Note: may sum to more than number of residues, # because one residue may have multiple problems # command:# Reading rotamer library from dunbrack-40pc-3157.rot # command:# Prefix for input files set to /projects/compbio/experiments/undertaker/spots/ # command:# ReadAtomType exp-pdb.types Read AtomType exp-pdb with 49 types. # command:# ReadClashTable exp-pdb-2191-2symm.clash # Read ClashTable exp-pdb-2191-2symm checking bonds symmetric at MaxSep 2 # command:# command:# Prefix for input files set to # command:# Making conformation for sequence T0381 numbered 1 through 265 Created new target T0381 from T0381.a2m # command:CPU_time= 6.317 sec, elapsed time= 6.355 sec. # command:# reading script from file all-templates.under # Reading fragments from alignment file # Attempting to read fragment alignments from file 1mkmA/T0381-1mkmA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1mkmA expands to /projects/compbio/data/pdb/1mkm.pdb.gz 1mkmA:# T0381 read from 1mkmA/T0381-1mkmA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1mkmA read from 1mkmA/T0381-1mkmA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1mkmA to template set # found chain 1mkmA in template set Warning: unaligning (T0381)T262 because last residue in template chain is (1mkmA)Y246 T0381 20 :LARGLAVIRCFDHRNQRRTLSDVARATDLTRATARRFLLTLVELGYVATDG 1mkmA 4 :LKKAFEILDFIVKNPGDVSVSEIAEKFNMSVSNAYKYMVVLEEKGFVLRKK # choosing archetypes in rotamer library T0381 71 :SAFWLTPRVLELGYSYLSSLSLPEVAQPHLEKLSHKVHESSSVSILDGADIVYVARVPVSRIMTVGITIGTRLPAYATSMGRVLLAGLPDDELDAYLEKLDIQRLTERTITARDELKAAILAVRADGICVLDQELEAGLRSMAAPIRGASGLTVAAVNISTPAARYSLEDL 1mkmA 56 :KRYVPGYKLIEYGSFVLRRFNIRDIAHDHLVDIMKRTGETVHLILKDGFEGVYIDKVEGEQSIPMVSRLGMKVDLYSTASGKSILAFVPEKELKEYLKIVELKPKTPNTITNPRVLKRELEKIRKRGYAVDNEENEIGIMCVGVPIFDHNGYPVAGVSISGVARKFTEEKI T0381 243 :SDLIPSLRVTATDIEQDLA 1mkmA 227 :EEYSDVLKEKAEEISRKLG Number of specific fragments extracted= 3 number of extra gaps= 0 total=3 Will force an alignment to be made, even if fragment is small Number of alignments=1 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1mkmA/T0381-1mkmA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0381 read from 1mkmA/T0381-1mkmA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1mkmA read from 1mkmA/T0381-1mkmA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1mkmA in template set Warning: unaligning (T0381)T262 because last residue in template chain is (1mkmA)Y246 T0381 21 :ARGLAVIRCFDHRNQRRTLSDVARATDLTRATARRFLLTLVELGYVATDG 1mkmA 5 :KKAFEILDFIVKNPGDVSVSEIAEKFNMSVSNAYKYMVVLEEKGFVLRKK T0381 71 :SAFWLTPRVLELGYSYLSSLSLPEVAQPHLEKLSHKVHESSSVSILDGADIVYVARVPVSRIMTVGITIGTRLPAYATSMGRVLLAGLPDDELDAYLEKLDIQRLTERTITARDELKAAILAVRADGICVLDQELEAGLRSMAAPIRGASGLTVAAVNISTPAARYSLEDL 1mkmA 56 :KRYVPGYKLIEYGSFVLRRFNIRDIAHDHLVDIMKRTGETVHLILKDGFEGVYIDKVEGEQSIPMVSRLGMKVDLYSTASGKSILAFVPEKELKEYLKIVELKPKTPNTITNPRVLKRELEKIRKRGYAVDNEENEIGIMCVGVPIFDHNGYPVAGVSISGVARKFTEEKI T0381 243 :SDLIPSLRVTATDIEQDLA 1mkmA 227 :EEYSDVLKEKAEEISRKLG Number of specific fragments extracted= 3 number of extra gaps= 0 total=6 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 1mkmA/T0381-1mkmA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0381 read from 1mkmA/T0381-1mkmA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1mkmA read from 1mkmA/T0381-1mkmA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1mkmA in template set Warning: unaligning (T0381)T262 because last residue in template chain is (1mkmA)Y246 T0381 21 :ARGLAVIRCFDHRNQRRTLSDVARATDLTRATARRFLLTLVELGYVATDG 1mkmA 5 :KKAFEILDFIVKNPGDVSVSEIAEKFNMSVSNAYKYMVVLEEKGFVLRKK T0381 71 :SAFWLTPRVLELGYSYLSSLSLPEVAQPHLEKLSHKVHESSSVSILDGADIVYVARVPVSRIMTVGITIGTRLPAYATSMGRVLLAGLPDDELDAYLEKLDIQRLTERTITARDELKAAILAVRADGICVLDQELEAGLRSMAAPIRGASGLTVAAVNISTPAARYSLEDLHS 1mkmA 56 :KRYVPGYKLIEYGSFVLRRFNIRDIAHDHLVDIMKRTGETVHLILKDGFEGVYIDKVEGEQSIPMVSRLGMKVDLYSTASGKSILAFVPEKELKEYLKIVELKPKTPNTITNPRVLKRELEKIRKRGYAVDNEENEIGIMCVGVPIFDHNGYPVAGVSISGVARKFTEEKIEE T0381 245 :LIPSLRVTATDIEQDLA 1mkmA 229 :YSDVLKEKAEEISRKLG Number of specific fragments extracted= 3 number of extra gaps= 0 total=9 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 2g7uA/T0381-2g7uA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2g7uA expands to /projects/compbio/data/pdb/2g7u.pdb.gz 2g7uA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0381 read from 2g7uA/T0381-2g7uA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2g7uA read from 2g7uA/T0381-2g7uA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2g7uA to template set # found chain 2g7uA in template set Warning: unaligning (T0381)S13 because first residue in template chain is (2g7uA)D5 Warning: unaligning (T0381)Y236 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (2g7uA)T229 Warning: unaligning (T0381)S237 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (2g7uA)T229 Warning: unaligning (T0381)V263 because last residue in template chain is (2g7uA)A255 T0381 14 :PDYVQSLARGLAVIRCFDHRNQRRTLSDVARATDLTRATARRFLLTLVELGYVATDGSAFWLTPRVLELGYSYLSSLSLPEVAQPHLEKLSHKVHESSSVSILDGADIVYVARVPVSRIMTVGITIGTRLPAYATSMGRVLLAGLPDDELDAYLEKLDIQRLTERTITARDELKAAILAVRADGICVLDQELEAGLRSMAAPIRGASGLTVAAVNISTPAAR 2g7uA 6 :RDYIQSIERGFAVLLAFDAQRPNPTLAELATEAGLSRPAVRRILLTLQKLGYVAGSGGRWSLTPRVLSIGQHYSESHALIEAAMPRLLEVAEKTQESASLGVLDGADVVYAARVPVRRIMSINVSVGTRVPAYATSMGRALLAWAPADVVERVVAESTFQKLGPETIGTAAELERELAKVREQGFALTSEELEKGLISLAAPVHDAGGTVVGVVACSTSSAR T0381 238 :LEDLHSDLIPSLRVTATDIEQDLAT 2g7uA 230 :PAQFREQAVPCVLAAAAALSADMGF Number of specific fragments extracted= 2 number of extra gaps= 1 total=11 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 2g7uA/T0381-2g7uA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0381 read from 2g7uA/T0381-2g7uA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2g7uA read from 2g7uA/T0381-2g7uA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2g7uA in template set Warning: unaligning (T0381)S13 because first residue in template chain is (2g7uA)D5 Warning: unaligning (T0381)Y236 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (2g7uA)T229 Warning: unaligning (T0381)S237 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (2g7uA)T229 Warning: unaligning (T0381)V263 because last residue in template chain is (2g7uA)A255 T0381 14 :PDYVQSLARGLAVIRCFDHRNQRRTLSDVARATDLTRATARRFLLTLVELGYVATDGSAFWLTPRVLELGYSYLSSLSLPEVAQPHLEKLSHKVHESSSVSILDGADIVYVARVPVSRIMTVGITIGTRLPAYATSMGRVLLAGLPDDELDAYLEKLDIQRLTERTITARDELKAAILAVRADGICVLDQELEAGLRSMAAPIRGASGLTVAAVNISTPAAR 2g7uA 6 :RDYIQSIERGFAVLLAFDAQRPNPTLAELATEAGLSRPAVRRILLTLQKLGYVAGSGGRWSLTPRVLSIGQHYSESHALIEAAMPRLLEVAEKTQESASLGVLDGADVVYAARVPVRRIMSINVSVGTRVPAYATSMGRALLAWAPADVVERVVAESTFQKLGPETIGTAAELERELAKVREQGFALTSEELEKGLISLAAPVHDAGGTVVGVVACSTSSAR T0381 238 :LEDLHSDLIPSLRVTATDIEQDLAT 2g7uA 230 :PAQFREQAVPCVLAAAAALSADMGF Number of specific fragments extracted= 2 number of extra gaps= 1 total=13 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 2g7uA/T0381-2g7uA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0381 read from 2g7uA/T0381-2g7uA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2g7uA read from 2g7uA/T0381-2g7uA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2g7uA in template set Warning: unaligning (T0381)S13 because first residue in template chain is (2g7uA)D5 Warning: unaligning (T0381)Y236 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (2g7uA)T229 Warning: unaligning (T0381)S237 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (2g7uA)T229 Warning: unaligning (T0381)V263 because last residue in template chain is (2g7uA)A255 T0381 14 :PDYVQSLARGLAVIRCFDHRNQRRTLSDVARATDLTRATARRFLLTLVELGYVATDGSAFWLTPRVLELGYSYLSSLSLPEVAQPHLEKLSHKVHESSSVSILDGADIVYVARVPVSRIMTVGITIGTRLPAYATSMGRVLLAGLPDDELDAYLEKLDIQRLTERTITARDELKAAILAVRADGICVLDQELEAGLRSMAAPIRGASGLTVAAVNISTPAAR 2g7uA 6 :RDYIQSIERGFAVLLAFDAQRPNPTLAELATEAGLSRPAVRRILLTLQKLGYVAGSGGRWSLTPRVLSIGQHYSESHALIEAAMPRLLEVAEKTQESASLGVLDGADVVYAARVPVRRIMSINVSVGTRVPAYATSMGRALLAWAPADVVERVVAESTFQKLGPETIGTAAELERELAKVREQGFALTSEELEKGLISLAAPVHDAGGTVVGVVACSTSSAR T0381 238 :LEDLHSDLIPSLRVTATDIEQDLAT 2g7uA 230 :PAQFREQAVPCVLAAAAALSADMGF Number of specific fragments extracted= 2 number of extra gaps= 1 total=15 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 1yspA/T0381-1yspA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1yspA expands to /projects/compbio/data/pdb/1ysp.pdb.gz 1yspA:Skipped atom 621, because occupancy 0.5 <= existing 0.500 in 1yspA Skipped atom 625, because occupancy 0.500 <= existing 0.500 in 1yspA Skipped atom 627, because occupancy 0.500 <= existing 0.500 in 1yspA Skipped atom 629, because occupancy 0.500 <= existing 0.500 in 1yspA Skipped atom 631, because occupancy 0.500 <= existing 0.500 in 1yspA Skipped atom 633, because occupancy 0.500 <= existing 0.500 in 1yspA Skipped atom 635, because occupancy 0.500 <= existing 0.500 in 1yspA Skipped atom 637, because occupancy 0.500 <= existing 0.500 in 1yspA Skipped atom 653, because occupancy 0.500 <= existing 0.500 in 1yspA Skipped atom 657, because occupancy 0.500 <= existing 0.500 in 1yspA Skipped atom 659, because occupancy 0.500 <= existing 0.500 in 1yspA Skipped atom 661, because occupancy 0.500 <= existing 0.500 in 1yspA Skipped atom 663, because occupancy 0.500 <= existing 0.500 in 1yspA Skipped atom 665, because occupancy 0.500 <= existing 0.500 in 1yspA Skipped atom 1061, because occupancy 0.500 <= existing 0.500 in 1yspA Skipped atom 1063, because occupancy 0.500 <= existing 0.500 in 1yspA Skipped atom 1065, because occupancy 0.500 <= existing 0.500 in 1yspA Skipped atom 1067, because occupancy 0.500 <= existing 0.500 in 1yspA Skipped atom 1069, because occupancy 0.500 <= existing 0.500 in 1yspA Skipped atom 1071, because occupancy 0.500 <= existing 0.500 in 1yspA Skipped atom 1073, because occupancy 0.500 <= existing 0.500 in 1yspA Skipped atom 1075, because occupancy 0.500 <= existing 0.500 in 1yspA Skipped atom 1077, because occupancy 0.500 <= existing 0.500 in 1yspA Skipped atom 1079, because occupancy 0.500 <= existing 0.500 in 1yspA Skipped atom 1081, because occupancy 0.500 <= existing 0.500 in 1yspA Skipped atom 1083, because occupancy 0.500 <= existing 0.500 in 1yspA Skipped atom 1085, because occupancy 0.500 <= existing 0.500 in 1yspA Skipped atom 1087, because occupancy 0.500 <= existing 0.500 in 1yspA Skipped atom 1089, because occupancy 0.500 <= existing 0.500 in 1yspA Skipped atom 1091, because occupancy 0.500 <= existing 0.500 in 1yspA Skipped atom 1093, because occupancy 0.500 <= existing 0.500 in 1yspA Skipped atom 1095, because occupancy 0.500 <= existing 0.500 in 1yspA Skipped atom 1097, because occupancy 0.500 <= existing 0.500 in 1yspA Skipped atom 1099, because occupancy 0.500 <= existing 0.500 in 1yspA Skipped atom 1101, because occupancy 0.500 <= existing 0.500 in 1yspA Skipped atom 1103, because occupancy 0.500 <= existing 0.500 in 1yspA Skipped atom 1105, because occupancy 0.500 <= existing 0.500 in 1yspA Skipped atom 1107, because occupancy 0.500 <= existing 0.500 in 1yspA Skipped atom 1109, because occupancy 0.500 <= existing 0.500 in 1yspA Skipped atom 1111, because occupancy 0.500 <= existing 0.500 in 1yspA Skipped atom 1113, because occupancy 0.500 <= existing 0.500 in 1yspA Skipped atom 1115, because occupancy 0.500 <= existing 0.500 in 1yspA Skipped atom 1117, because occupancy 0.500 <= existing 0.500 in 1yspA Skipped atom 1119, because occupancy 0.500 <= existing 0.500 in 1yspA Skipped atom 1121, because occupancy 0.500 <= existing 0.500 in 1yspA Skipped atom 1123, because occupancy 0.500 <= existing 0.500 in 1yspA Skipped atom 1125, because occupancy 0.500 <= existing 0.500 in 1yspA Skipped atom 1127, because occupancy 0.500 <= existing 0.500 in 1yspA Skipped atom 1129, because occupancy 0.500 <= existing 0.500 in 1yspA Skipped atom 1131, because occupancy 0.500 <= existing 0.500 in 1yspA Skipped atom 1133, because occupancy 0.500 <= existing 0.500 in 1yspA Skipped atom 1135, because occupancy 0.500 <= existing 0.500 in 1yspA Skipped atom 1137, because occupancy 0.500 <= existing 0.500 in 1yspA Skipped atom 1139, because occupancy 0.500 <= existing 0.500 in 1yspA Skipped atom 1141, because occupancy 0.500 <= existing 0.500 in 1yspA Skipped atom 1143, because occupancy 0.500 <= existing 0.500 in 1yspA Skipped atom 1145, because occupancy 0.500 <= existing 0.500 in 1yspA Skipped atom 1147, because occupancy 0.500 <= existing 0.500 in 1yspA Skipped atom 1149, because occupancy 0.500 <= existing 0.500 in 1yspA Skipped atom 1151, because occupancy 0.500 <= existing 0.500 in 1yspA Skipped atom 1153, because occupancy 0.500 <= existing 0.500 in 1yspA Skipped atom 1155, because occupancy 0.500 <= existing 0.500 in 1yspA Skipped atom 1157, because occupancy 0.500 <= existing 0.500 in 1yspA Skipped atom 1159, because occupancy 0.500 <= existing 0.500 in 1yspA Skipped atom 1161, because occupancy 0.500 <= existing 0.500 in 1yspA Skipped atom 1163, because occupancy 0.500 <= existing 0.500 in 1yspA Skipped atom 1165, because occupancy 0.500 <= existing 0.500 in 1yspA Skipped atom 1167, because occupancy 0.500 <= existing 0.500 in 1yspA Skipped atom 1169, because occupancy 0.500 <= existing 0.500 in 1yspA Skipped atom 1171, because occupancy 0.500 <= existing 0.500 in 1yspA Skipped atom 1173, because occupancy 0.500 <= existing 0.500 in 1yspA Skipped atom 1175, because occupancy 0.500 <= existing 0.500 in 1yspA Skipped atom 1177, because occupancy 0.500 <= existing 0.500 in 1yspA Skipped atom 1179, because occupancy 0.500 <= existing 0.500 in 1yspA Skipped atom 1181, because occupancy 0.500 <= existing 0.500 in 1yspA Skipped atom 1183, because occupancy 0.500 <= existing 0.500 in 1yspA Skipped atom 1185, because occupancy 0.500 <= existing 0.500 in 1yspA Skipped atom 1187, because occupancy 0.500 <= existing 0.500 in 1yspA Skipped atom 1189, because occupancy 0.500 <= existing 0.500 in 1yspA Skipped atom 1191, because occupancy 0.500 <= existing 0.500 in 1yspA Skipped atom 1193, because occupancy 0.500 <= existing 0.500 in 1yspA Skipped atom 1195, because occupancy 0.500 <= existing 0.500 in 1yspA Skipped atom 1197, because occupancy 0.500 <= existing 0.500 in 1yspA Skipped atom 1328, because occupancy 0.500 <= existing 0.500 in 1yspA Skipped atom 1332, because occupancy 0.500 <= existing 0.500 in 1yspA Skipped atom 1334, because occupancy 0.500 <= existing 0.500 in 1yspA Skipped atom 1336, because occupancy 0.500 <= existing 0.500 in 1yspA Skipped atom 1338, because occupancy 0.500 <= existing 0.500 in 1yspA Skipped atom 1340, because occupancy 0.500 <= existing 0.500 in 1yspA Skipped atom 1342, because occupancy 0.500 <= existing 0.500 in 1yspA Skipped atom 1344, because occupancy 0.500 <= existing 0.500 in 1yspA # T0381 read from 1yspA/T0381-1yspA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1yspA read from 1yspA/T0381-1yspA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1yspA to template set # found chain 1yspA in template set Warning: unaligning (T0381)L90 because first residue in template chain is (1yspA)M1 Warning: unaligning (T0381)S130 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1yspA)I50 Warning: unaligning (T0381)I139 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1yspA)I50 Warning: unaligning (T0381)G140 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1yspA)G51 Warning: unaligning (T0381)T231 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1yspA)P143 Warning: unaligning (T0381)P232 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1yspA)P143 Warning: unaligning (T0381)A233 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1yspA)L145 Warning: unaligning (T0381)A234 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1yspA)L145 Warning: unaligning (T0381)T262 because last residue in template chain is (1yspA)Y172 T0381 91 :SLPEVAQPHLEKLSHKVHESSSVSILDGADIVYVARVPV 1yspA 2 :DLIRSADIQMRELSRLTKETIHLGALDEDSIVYIHKIDS T0381 141 :TRLPAYATSMGRVLLAGLPDDELDAYLEKLDIQRLTERTITARDELKAAILAVRADGICVLDQELEAGLRSMAAPIRGASGLTVAAVNIS 1yspA 52 :RRNPLYSTAIGKVLLAWRDRDEVKQILEGVEYKRSTERTITSTEALLPVLDQVREQGYGEDNEEQEEGLRCIAVPVFDRFGVVIAGLSIS T0381 235 :RYSLEDL 1yspA 146 :RFSEERL T0381 243 :SDLIPSLRVTATDIEQDLA 1yspA 153 :QEYVAMLHTAARKISAQMG Number of specific fragments extracted= 4 number of extra gaps= 1 total=19 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 1yspA/T0381-1yspA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0381 read from 1yspA/T0381-1yspA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1yspA read from 1yspA/T0381-1yspA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1yspA in template set Warning: unaligning (T0381)L90 because first residue in template chain is (1yspA)M1 Warning: unaligning (T0381)S130 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1yspA)I50 Warning: unaligning (T0381)I139 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1yspA)I50 Warning: unaligning (T0381)G140 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1yspA)G51 Warning: unaligning (T0381)T231 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1yspA)P143 Warning: unaligning (T0381)P232 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1yspA)P143 Warning: unaligning (T0381)A233 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1yspA)L145 Warning: unaligning (T0381)A234 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1yspA)L145 Warning: unaligning (T0381)T262 because last residue in template chain is (1yspA)Y172 T0381 91 :SLPEVAQPHLEKLSHKVHESSSVSILDGADIVYVARVPV 1yspA 2 :DLIRSADIQMRELSRLTKETIHLGALDEDSIVYIHKIDS T0381 141 :TRLPAYATSMGRVLLAGLPDDELDAYLEKLDIQRLTERTITARDELKAAILAVRADGICVLDQELEAGLRSMAAPIRGASGLTVAAVNIS 1yspA 52 :RRNPLYSTAIGKVLLAWRDRDEVKQILEGVEYKRSTERTITSTEALLPVLDQVREQGYGEDNEEQEEGLRCIAVPVFDRFGVVIAGLSIS T0381 235 :RYSLEDL 1yspA 146 :RFSEERL T0381 243 :SDLIPSLRVTATDIEQDLA 1yspA 153 :QEYVAMLHTAARKISAQMG Number of specific fragments extracted= 4 number of extra gaps= 1 total=23 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 1yspA/T0381-1yspA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0381 read from 1yspA/T0381-1yspA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1yspA read from 1yspA/T0381-1yspA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1yspA in template set Warning: unaligning (T0381)L90 because first residue in template chain is (1yspA)M1 Warning: unaligning (T0381)S130 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1yspA)I50 Warning: unaligning (T0381)I139 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1yspA)I50 Warning: unaligning (T0381)G140 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1yspA)G51 Warning: unaligning (T0381)T231 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1yspA)P143 Warning: unaligning (T0381)P232 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1yspA)P143 Warning: unaligning (T0381)A233 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1yspA)L145 Warning: unaligning (T0381)A234 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1yspA)L145 Warning: unaligning (T0381)T262 because last residue in template chain is (1yspA)Y172 T0381 91 :SLPEVAQPHLEKLSHKVHESSSVSILDGADIVYVARVPV 1yspA 2 :DLIRSADIQMRELSRLTKETIHLGALDEDSIVYIHKIDS T0381 141 :TRLPAYATSMGRVLLAGLPDDELDAYLEKLDIQRLTERTITARDELKAAILAVRADGICVLDQELEAGLRSMAAPIRGASGLTVAAVNIS 1yspA 52 :RRNPLYSTAIGKVLLAWRDRDEVKQILEGVEYKRSTERTITSTEALLPVLDQVREQGYGEDNEEQEEGLRCIAVPVFDRFGVVIAGLSIS T0381 235 :RYSLEDLHS 1yspA 146 :RFSEERLQE T0381 245 :LIPSLRVTATDIEQDLA 1yspA 155 :YVAMLHTAARKISAQMG Number of specific fragments extracted= 4 number of extra gaps= 1 total=27 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 1tf1A/T0381-1tf1A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1tf1A expands to /projects/compbio/data/pdb/1tf1.pdb.gz 1tf1A:# T0381 read from 1tf1A/T0381-1tf1A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1tf1A read from 1tf1A/T0381-1tf1A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1tf1A to template set # found chain 1tf1A in template set Warning: unaligning (T0381)N264 because last residue in template chain is (1tf1A)A184 T0381 91 :SLPEVAQPHLEKLSHKVHESSSVSILDGADIVYVARVPVSRIMTVGITIGTRLPAYATSMGRVLLAGLPDDELDAYLEKLDIQRLTERTITARDELKAAILAVRADGICVLDQELEAGLRSMAAPIRGASGLTVAAVNISTPAARYSLEDL 1tf1A 12 :DVLSVAGPFMRRLMLLSGETVNVAIRNGNEAVLIGQLECKSMVRMCAPLGSRLPLHASGAGKALLYPLAEEELMSIILQTGLQQFTPTTLVDMPTLLKDLEQARELGYTVDKEEHVVGLNCIASAIYDDVGSVVAAISISGPSSRLTEDRF T0381 243 :SDLIPSLRVTATDIEQDLATV 1tf1A 163 :VSQGELVRDTARDISTALGLK Number of specific fragments extracted= 2 number of extra gaps= 0 total=29 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 1tf1A/T0381-1tf1A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0381 read from 1tf1A/T0381-1tf1A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1tf1A read from 1tf1A/T0381-1tf1A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1tf1A in template set Warning: unaligning (T0381)N264 because last residue in template chain is (1tf1A)A184 T0381 90 :LSLPEVAQPHLEKLSHKVHESSSVSILDGADIVYVARVPVSRIMTVGITIGTRLPAYATSMGRVLLAGLPDDELDAYLEKLDIQRLTERTITARDELKAAILAVRADGICVLDQELEAGLRSMAAPIRGASGLTVAAVNISTPAARYSLEDL 1tf1A 11 :MDVLSVAGPFMRRLMLLSGETVNVAIRNGNEAVLIGQLECKSMVRMCAPLGSRLPLHASGAGKALLYPLAEEELMSIILQTGLQQFTPTTLVDMPTLLKDLEQARELGYTVDKEEHVVGLNCIASAIYDDVGSVVAAISISGPSSRLTEDRF T0381 243 :SDLIPSLRVTATDIEQDLATV 1tf1A 163 :VSQGELVRDTARDISTALGLK Number of specific fragments extracted= 2 number of extra gaps= 0 total=31 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 1tf1A/T0381-1tf1A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0381 read from 1tf1A/T0381-1tf1A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1tf1A read from 1tf1A/T0381-1tf1A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1tf1A in template set Warning: unaligning (T0381)N264 because last residue in template chain is (1tf1A)A184 T0381 90 :LSLPEVAQPHLEKLSHKVHESSSVSILDGADIVYVARVPVSRIMTVGITIGTRLPAYATSMGRVLLAGLPDDELDAYLEKLDIQRLTERTITARDELKAAILAVRADGICVLDQELEAGLRSMAAPIRGASGLTVAAVNISTPAARYSLEDL 1tf1A 11 :MDVLSVAGPFMRRLMLLSGETVNVAIRNGNEAVLIGQLECKSMVRMCAPLGSRLPLHASGAGKALLYPLAEEELMSIILQTGLQQFTPTTLVDMPTLLKDLEQARELGYTVDKEEHVVGLNCIASAIYDDVGSVVAAISISGPSSRLTEDRF T0381 243 :SDLIPSLRVTATDIEQDLATV 1tf1A 163 :VSQGELVRDTARDISTALGLK Number of specific fragments extracted= 2 number of extra gaps= 0 total=33 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 1td5A/T0381-1td5A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1td5A expands to /projects/compbio/data/pdb/1td5.pdb.gz 1td5A:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0381 read from 1td5A/T0381-1td5A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1td5A read from 1td5A/T0381-1td5A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1td5A to template set # found chain 1td5A in template set Warning: unaligning (T0381)V263 because last residue in template chain is (1td5A)M179 T0381 91 :SLPEVAQPHLEKLSHKVHESSSVSILD 1td5A 6 :NLLAIVHPILRNLMEESGETVNMAVLD T0381 118 :GADIVYVARVPVSRIMTVGITIGTRLPAYATSMGRVLLAGLPDDELDAYLEKLDIQRLTERTITARDELKAAILAVRADGICVLDQELEAGLRSMAAPIRGASGLTVAAVNISTPAARYSLEDL 1td5A 35 :DHEAIIIDQVQCTHLMRMSAPIGGKLPMHASGAGKAFLAQLSEEQVTKLLHRKGLHAYTHATLVSPVHLKEDLAQTRKRGYSFDDEEHALGLRCLAACIFDEHREPFAAISISGPISRITDDRV T0381 243 :SDLIPSLRVTATDIEQDLAT 1td5A 159 :TEFGAMVIKAAKEVTLAYGG Number of specific fragments extracted= 3 number of extra gaps= 0 total=36 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 1td5A/T0381-1td5A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0381 read from 1td5A/T0381-1td5A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1td5A read from 1td5A/T0381-1td5A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1td5A in template set Warning: unaligning (T0381)V263 because last residue in template chain is (1td5A)M179 T0381 90 :LSLPEVAQPHLEKLSHKVHESSSVSILD 1td5A 5 :RNLLAIVHPILRNLMEESGETVNMAVLD T0381 118 :GADIVYVARVPVSRIMTVGITIGTRLPAYATSMGRVLLAGLPDDELDAYLEKLDIQRLTERTITARDELKAAILAVRADGICVLDQELEAGLRSMAAPIRGASGLTVAAVNISTPAARYSLEDL 1td5A 35 :DHEAIIIDQVQCTHLMRMSAPIGGKLPMHASGAGKAFLAQLSEEQVTKLLHRKGLHAYTHATLVSPVHLKEDLAQTRKRGYSFDDEEHALGLRCLAACIFDEHREPFAAISISGPISRITDDRV T0381 243 :SDLIPSLRVTATDIEQDLAT 1td5A 159 :TEFGAMVIKAAKEVTLAYGG Number of specific fragments extracted= 3 number of extra gaps= 0 total=39 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 1td5A/T0381-1td5A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0381 read from 1td5A/T0381-1td5A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1td5A read from 1td5A/T0381-1td5A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1td5A in template set Warning: unaligning (T0381)V263 because last residue in template chain is (1td5A)M179 T0381 90 :LSLPEVAQPHLEKLSHKVHESSSVSILD 1td5A 5 :RNLLAIVHPILRNLMEESGETVNMAVLD T0381 118 :GADIVYVARVPVSRIMTVGITIGTRLPAYATSMGRVLLAGLPDDELDAYLEKLDIQRLTERTITARDELKAAILAVRADGICVLDQELEAGLRSMAAPIRGASGLTVAAVNISTPAARYSLEDLHS 1td5A 35 :DHEAIIIDQVQCTHLMRMSAPIGGKLPMHASGAGKAFLAQLSEEQVTKLLHRKGLHAYTHATLVSPVHLKEDLAQTRKRGYSFDDEEHALGLRCLAACIFDEHREPFAAISISGPISRITDDRVTE T0381 245 :LIPSLRVTATDIEQDLAT 1td5A 161 :FGAMVIKAAKEVTLAYGG Number of specific fragments extracted= 3 number of extra gaps= 0 total=42 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 1ysqA/T0381-1ysqA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1ysqA expands to /projects/compbio/data/pdb/1ysq.pdb.gz 1ysqA:# T0381 read from 1ysqA/T0381-1ysqA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ysqA read from 1ysqA/T0381-1ysqA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1ysqA to template set # found chain 1ysqA in template set Warning: unaligning (T0381)S89 because first residue in template chain is (1ysqA)S5 Warning: unaligning (T0381)V200 because of BadResidue code BAD_PEPTIDE in next template residue (1ysqA)D120 Warning: unaligning (T0381)L201 because of BadResidue code BAD_PEPTIDE at template residue (1ysqA)D120 T0381 90 :LSLPEVAQPHLEKLSHKVHESSSVSILDGADIVYVARVPVSRI 1ysqA 6 :LNIIHIAAPHLEALNIATGETINFSSREDDHAILIYKLEPTTG T0381 133 :MTVGITIGTRLPAYATSMGRVLLAGLPDDELDAYLEKL 1ysqA 50 :LRTRAYIGQHMPLYCSAMGKIYMAFGHPDYVKSYWESH T0381 171 :DIQRLTERTITARDELKAAILAVRADGIC 1ysqA 90 :EIQPLTRNTITELPAMFDELAHIRESGAA T0381 202 :DQELEAGLRSMAAPIRGASGLTVAAVNISTPAARY 1ysqA 121 :REENELGVSCIAVPVFDIHGRVPYAVSISLSTSRL T0381 237 :SL 1ysqA 159 :GE T0381 243 :SDLIPSLRVTATDIEQDLAT 1ysqA 161 :KNLLKPLRETAQAISNELGF Number of specific fragments extracted= 6 number of extra gaps= 1 total=48 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 1ysqA/T0381-1ysqA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0381 read from 1ysqA/T0381-1ysqA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ysqA read from 1ysqA/T0381-1ysqA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1ysqA in template set Warning: unaligning (T0381)S89 because first residue in template chain is (1ysqA)S5 Warning: unaligning (T0381)V200 because of BadResidue code BAD_PEPTIDE in next template residue (1ysqA)D120 Warning: unaligning (T0381)L201 because of BadResidue code BAD_PEPTIDE at template residue (1ysqA)D120 T0381 90 :LSLPEVAQPHLEKLSHKVHESSSVSILDGADIVYVARVPVSR 1ysqA 6 :LNIIHIAAPHLEALNIATGETINFSSREDDHAILIYKLEPTT T0381 132 :IMTVGITIGTRLPAYATSMGRVLLAGLPDDELDAYLEKL 1ysqA 49 :MLRTRAYIGQHMPLYCSAMGKIYMAFGHPDYVKSYWESH T0381 171 :DIQRLTERTITARDELKAAILAVRADGIC 1ysqA 90 :EIQPLTRNTITELPAMFDELAHIRESGAA T0381 202 :DQELEAGLRSMAAPIRGASGLTVAAVNISTP 1ysqA 121 :REENELGVSCIAVPVFDIHGRVPYAVSISLS T0381 238 :LEDL 1ysqA 152 :TSRL T0381 242 :HSDLIPSLRVTATDIEQDLAT 1ysqA 160 :EKNLLKPLRETAQAISNELGF Number of specific fragments extracted= 6 number of extra gaps= 1 total=54 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 1ysqA/T0381-1ysqA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0381 read from 1ysqA/T0381-1ysqA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ysqA read from 1ysqA/T0381-1ysqA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1ysqA in template set Warning: unaligning (T0381)S89 because first residue in template chain is (1ysqA)S5 Warning: unaligning (T0381)V200 because of BadResidue code BAD_PEPTIDE in next template residue (1ysqA)D120 Warning: unaligning (T0381)L201 because of BadResidue code BAD_PEPTIDE at template residue (1ysqA)D120 T0381 90 :LSLPEVAQPHLEKLSHKVHESSSVSILDGADIVYVARVPVS 1ysqA 6 :LNIIHIAAPHLEALNIATGETINFSSREDDHAILIYKLEPT T0381 131 :RIMTVGITIGTRLPAYATSMGRVLLAGLPDDELDAYLEKL 1ysqA 48 :GMLRTRAYIGQHMPLYCSAMGKIYMAFGHPDYVKSYWESH T0381 171 :DIQRLTERTITARDELKAAILAVRADGIC 1ysqA 90 :EIQPLTRNTITELPAMFDELAHIRESGAA T0381 202 :DQELEAGLRSMAAPIRGASGLTVAAVNISTPAARY 1ysqA 121 :REENELGVSCIAVPVFDIHGRVPYAVSISLSTSRL T0381 237 :SLEDLHSDLIPSLRVTATDIEQ 1ysqA 159 :GEKNLLKPLRETAQAISNELGF Number of specific fragments extracted= 5 number of extra gaps= 1 total=59 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 1on2A/T0381-1on2A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1on2A expands to /projects/compbio/data/pdb/1on2.pdb.gz 1on2A:# T0381 read from 1on2A/T0381-1on2A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1on2A read from 1on2A/T0381-1on2A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1on2A to template set # found chain 1on2A in template set T0381 15 :D 1on2A 5 :S T0381 19 :SLARGLAVIRCFDHR 1on2A 6 :MEMYIEQIYMLIEEK T0381 35 :QRRTLSDVARATDLTRATARRFLLTLVELGYVATDG 1on2A 21 :GYARVSDIAEALAVHPSSVTKMVQKLDKDEYLIYEK T0381 71 :SAFWLTPRVLELGYSYLSS 1on2A 58 :RGLVLTSKGKKIGKRLVYR T0381 97 :QPHLEKLSHKVH 1on2A 77 :HELLEQFLRIIG T0381 158 :LPDDELDAYLEK 1on2A 89 :VDEEKIYNDVEG T0381 232 :PAARYSLEDL 1on2A 101 :IEHHLSWNSI T0381 243 :SDLIPSLRVT 1on2A 111 :DRIGDLVQYF T0381 253 :ATDI 1on2A 127 :KKDL Number of specific fragments extracted= 9 number of extra gaps= 0 total=68 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 1on2A/T0381-1on2A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0381 read from 1on2A/T0381-1on2A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1on2A read from 1on2A/T0381-1on2A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1on2A in template set T0381 14 :PDYV 1on2A 4 :PSME T0381 21 :ARGLAVIRCFDHR 1on2A 8 :MYIEQIYMLIEEK T0381 35 :QRRTLSDVARATDLTRATARRFLLTLVELGYVATDG 1on2A 21 :GYARVSDIAEALAVHPSSVTKMVQKLDKDEYLIYEK T0381 71 :SAFWLTPRVLELGYSYLSS 1on2A 58 :RGLVLTSKGKKIGKRLVYR T0381 97 :QPHLEKLSHKVH 1on2A 77 :HELLEQFLRIIG T0381 158 :LPDDELDAYLEKL 1on2A 89 :VDEEKIYNDVEGI T0381 233 :AARYSLEDL 1on2A 102 :EHHLSWNSI T0381 243 :SDLIPSLRVT 1on2A 111 :DRIGDLVQYF Number of specific fragments extracted= 8 number of extra gaps= 0 total=76 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 1on2A/T0381-1on2A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0381 read from 1on2A/T0381-1on2A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1on2A read from 1on2A/T0381-1on2A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1on2A in template set T0381 15 :DYV 1on2A 5 :SME T0381 21 :ARGLAVIRCFDHRN 1on2A 8 :MYIEQIYMLIEEKG T0381 36 :RRTLSDVARATDLTRATARRFLLTLVELGYVATDG 1on2A 22 :YARVSDIAEALAVHPSSVTKMVQKLDKDEYLIYEK T0381 71 :SAFWLTPRVLELGYSYLSS 1on2A 58 :RGLVLTSKGKKIGKRLVYR T0381 97 :QPHLEKLSHKVHE 1on2A 77 :HELLEQFLRIIGV T0381 159 :PDDELDAYLEKL 1on2A 90 :DEEKIYNDVEGI T0381 233 :AARYSLEDLHSDLIPSLR 1on2A 102 :EHHLSWNSIDRIGDLVQY T0381 251 :VTATDIEQD 1on2A 125 :ARKKDLKSI Number of specific fragments extracted= 8 number of extra gaps= 0 total=84 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 1ulyA/T0381-1ulyA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1ulyA expands to /projects/compbio/data/pdb/1uly.pdb.gz 1ulyA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0381 read from 1ulyA/T0381-1ulyA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ulyA read from 1ulyA/T0381-1ulyA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1ulyA to template set # found chain 1ulyA in template set T0381 12 :PSPDYVQSL 1ulyA 9 :TDPEVIKVM T0381 21 :ARGLAVIRCF 1ulyA 20 :DTRRKILKLL T0381 33 :RNQRRTLSDVARATDLTRATARRFLLTLVELGYVATDG 1ulyA 30 :RNKEMTISQLSEILGKTPQTIYHHIEKLKEAGLVEVKR T0381 71 :SAFWLT 1ulyA 77 :KYYGRT T0381 85 :SYLSSLSLPEVAQPHLEKLSHKVH 1ulyA 90 :LYLGDEELRYIARSRLKTKIDIFK T0381 139 :IGTR 1ulyA 115 :LGYQ T0381 158 :LPDDELDAYLEKL 1ulyA 119 :FEENELLNIMDRM T0381 182 :ARDELKAAILAVRAD 1ulyA 135 :EFDATVRISKYIEEK T0381 232 :PAARYSLEDLHSDLIPSLRVTAT 1ulyA 152 :ALKDFSNEDIIHAIEWLSTAELA Number of specific fragments extracted= 9 number of extra gaps= 0 total=93 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 1ulyA/T0381-1ulyA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0381 read from 1ulyA/T0381-1ulyA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ulyA read from 1ulyA/T0381-1ulyA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1ulyA in template set T0381 12 :PSPDYVQSL 1ulyA 9 :TDPEVIKVM T0381 21 :ARGLAVIRCFD 1ulyA 20 :DTRRKILKLLR T0381 34 :NQRRTLSDVARATDLTRATARRFLLTLVELGYVAT 1ulyA 31 :NKEMTISQLSEILGKTPQTIYHHIEKLKEAGLVEV T0381 71 :SAFWLT 1ulyA 77 :KYYGRT T0381 86 :YLSSLSLPEVAQPHLEKLSHKV 1ulyA 91 :YLGDEELRYIARSRLKTKIDIF T0381 138 :TIGTR 1ulyA 114 :RLGYQ T0381 158 :LPDDELDAYLEKLDI 1ulyA 119 :FEENELLNIMDRMSQ T0381 181 :TARDELKAAILAVRAD 1ulyA 134 :KEFDATVRISKYIEEK T0381 233 :AARYSLEDLHSDLIPSLRVTAT 1ulyA 153 :LKDFSNEDIIHAIEWLSTAELA Number of specific fragments extracted= 9 number of extra gaps= 0 total=102 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 1ulyA/T0381-1ulyA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0381 read from 1ulyA/T0381-1ulyA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ulyA read from 1ulyA/T0381-1ulyA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1ulyA in template set T0381 13 :SPDYVQSL 1ulyA 10 :DPEVIKVM T0381 21 :ARGLAVIRCFD 1ulyA 20 :DTRRKILKLLR T0381 34 :NQRRTLSDVARATDLTRATARRFLLTLVELGYVATDG 1ulyA 31 :NKEMTISQLSEILGKTPQTIYHHIEKLKEAGLVEVKR T0381 71 :SAFWLT 1ulyA 77 :KYYGRT T0381 87 :LSSLSLPEVAQPHLEKLSHKVH 1ulyA 92 :LGDEELRYIARSRLKTKIDIFK T0381 139 :IGT 1ulyA 115 :LGY T0381 157 :GLPDDELDAYLEKL 1ulyA 118 :QFEENELLNIMDRM T0381 179 :TITARDELKAAILAVRADG 1ulyA 132 :SQKEFDATVRISKYIEEKE T0381 203 :QE 1ulyA 151 :DA T0381 233 :AARYSLEDLHSDLIPSLRVTA 1ulyA 153 :LKDFSNEDIIHAIEWLSTAEL Number of specific fragments extracted= 10 number of extra gaps= 0 total=112 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 1r7jA/T0381-1r7jA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1r7jA expands to /projects/compbio/data/pdb/1r7j.pdb.gz 1r7jA:# T0381 read from 1r7jA/T0381-1r7jA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1r7jA read from 1r7jA/T0381-1r7jA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1r7jA to template set # found chain 1r7jA in template set T0381 20 :LARGLAVIRCFD 1r7jA 7 :LEIIQAILEACK T0381 35 :QRRTLSDVARATDLTRATARRFLLTLVELGYVATDGSAFWLTPRVLELGYSYLSSLSLPEVAQPHLEKLSHK 1r7jA 19 :SGSPKTRIMYGANLSYALTGRYIKMLMDLEIIRQEGKQYMLTKKGEELLEDIRKFNEMRKNMDQLKEKINSV Number of specific fragments extracted= 2 number of extra gaps= 0 total=114 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 1r7jA/T0381-1r7jA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0381 read from 1r7jA/T0381-1r7jA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1r7jA read from 1r7jA/T0381-1r7jA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1r7jA in template set T0381 13 :SPD 1r7jA 4 :KSK T0381 20 :LARGLAVIRCFD 1r7jA 7 :LEIIQAILEACK T0381 35 :QRRTLSDVARATDLTRATARRFLLTLVELGYVATDGSAFWLTPRVLELGYSYLSSLSLPEVAQPHLEKLSHK 1r7jA 19 :SGSPKTRIMYGANLSYALTGRYIKMLMDLEIIRQEGKQYMLTKKGEELLEDIRKFNEMRKNMDQLKEKINSV Number of specific fragments extracted= 3 number of extra gaps= 0 total=117 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 1r7jA/T0381-1r7jA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0381 read from 1r7jA/T0381-1r7jA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1r7jA read from 1r7jA/T0381-1r7jA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1r7jA in template set T0381 20 :LARGLAVIRCFD 1r7jA 7 :LEIIQAILEACK T0381 35 :QRRTLSDVARATDLTRATARRFLLTLVELGYVATDGSAFWLTPRVLELGYSYLSSLSLPEVAQPHLEKLSH 1r7jA 19 :SGSPKTRIMYGANLSYALTGRYIKMLMDLEIIRQEGKQYMLTKKGEELLEDIRKFNEMRKNMDQLKEKINS Number of specific fragments extracted= 2 number of extra gaps= 0 total=119 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 2fbhA/T0381-2fbhA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2fbhA expands to /projects/compbio/data/pdb/2fbh.pdb.gz 2fbhA:Skipped atom 109, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 111, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 113, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 115, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 117, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 119, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 121, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 123, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 125, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 127, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 129, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 272, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 274, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 276, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 278, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 280, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 282, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 284, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 286, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 403, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 405, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 407, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 409, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 411, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 413, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 415, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 417, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 419, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 421, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 423, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 480, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 482, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 484, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 486, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 488, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 490, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 492, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 494, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 496, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 666, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 668, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 670, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 672, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 674, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 676, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 678, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 680, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 682, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 835, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 837, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 839, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 841, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 843, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 845, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 847, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 849, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 851, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 876, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 878, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 880, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 882, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 884, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 886, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 1002, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 1004, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 1006, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 1008, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 1010, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 1012, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 1014, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 1016, because occupancy 0.500 <= existing 0.500 in 2fbhA # T0381 read from 2fbhA/T0381-2fbhA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2fbhA read from 2fbhA/T0381-2fbhA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2fbhA to template set # found chain 2fbhA in template set Warning: unaligning (T0381)T46 because of BadResidue code BAD_PEPTIDE in next template residue (2fbhA)G61 Warning: unaligning (T0381)D47 because of BadResidue code BAD_PEPTIDE at template residue (2fbhA)G61 T0381 24 :LAVIRCFDHRNQRRTLSDVARA 2fbhA 38 :WLVLLHLARHRDSPTQRELAQS T0381 48 :LTRATARRFLLTLVELGYVAT 2fbhA 62 :VEGPTLARLLDGLESQGLVRR T0381 69 :DG 2fbhA 86 :AE T0381 71 :SAFWLTPRVLELGYSY 2fbhA 92 :KHIVLTPKADVLIADI T0381 93 :PEVAQPHLEKLSH 2fbhA 108 :EAIAASVRNDVLT T0381 157 :GLPDDELDAYLEK 2fbhA 121 :GIDESEQALCQQV T0381 186 :LKAAIL 2fbhA 134 :LLRILA Number of specific fragments extracted= 7 number of extra gaps= 1 total=126 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 2fbhA/T0381-2fbhA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0381 read from 2fbhA/T0381-2fbhA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2fbhA read from 2fbhA/T0381-2fbhA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2fbhA in template set Warning: unaligning (T0381)T46 because of BadResidue code BAD_PEPTIDE in next template residue (2fbhA)G61 Warning: unaligning (T0381)D47 because of BadResidue code BAD_PEPTIDE at template residue (2fbhA)G61 T0381 24 :LAVIRCFDHRNQRRTLSDVARA 2fbhA 38 :WLVLLHLARHRDSPTQRELAQS T0381 48 :LTRATARRFLLTLVELGYVAT 2fbhA 62 :VEGPTLARLLDGLESQGLVRR T0381 69 :DG 2fbhA 86 :AE T0381 71 :SAFWLTPRVLELGYS 2fbhA 92 :KHIVLTPKADVLIAD T0381 92 :LPEVAQPHLEKLSH 2fbhA 107 :IEAIAASVRNDVLT T0381 157 :GLPDDELDAYLEKL 2fbhA 121 :GIDESEQALCQQVL Number of specific fragments extracted= 6 number of extra gaps= 1 total=132 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 2fbhA/T0381-2fbhA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0381 read from 2fbhA/T0381-2fbhA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2fbhA read from 2fbhA/T0381-2fbhA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2fbhA in template set Warning: unaligning (T0381)T46 because of BadResidue code BAD_PEPTIDE in next template residue (2fbhA)G61 Warning: unaligning (T0381)D47 because of BadResidue code BAD_PEPTIDE at template residue (2fbhA)G61 T0381 24 :LAVIRCFDHRNQRRTLSDVARA 2fbhA 38 :WLVLLHLARHRDSPTQRELAQS T0381 48 :LTRATARRFLLTLVELGYVATDG 2fbhA 62 :VEGPTLARLLDGLESQGLVRRLA T0381 71 :SA 2fbhA 88 :DR T0381 131 :RIMTVGI 2fbhA 90 :RAKHIVL T0381 176 :TERTITARDELKAAILAVRADG 2fbhA 97 :TPKADVLIADIEAIAASVRNDV T0381 219 :ASG 2fbhA 119 :LTG T0381 236 :YSLEDLHSDLIPSLRVTATD 2fbhA 122 :IDESEQALCQQVLLRILANL Number of specific fragments extracted= 7 number of extra gaps= 1 total=139 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 1q1hA/T0381-1q1hA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1q1hA expands to /projects/compbio/data/pdb/1q1h.pdb.gz 1q1hA:# T0381 read from 1q1hA/T0381-1q1hA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1q1hA read from 1q1hA/T0381-1q1hA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1q1hA to template set # found chain 1q1hA in template set T0381 24 :LAVIRCFDHRNQRRTLSDVARATDLTRATARRFLLTLVELGYVAT 1q1hA 21 :IDVLRILLDKGTEMTDEEIANQLNIKVNDVRKKLNLLEEQGFVSY T0381 71 :SAFWLTP 1q1hA 76 :FIYYWKP Number of specific fragments extracted= 2 number of extra gaps= 0 total=141 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 1q1hA/T0381-1q1hA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0381 read from 1q1hA/T0381-1q1hA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1q1hA read from 1q1hA/T0381-1q1hA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1q1hA in template set T0381 24 :LAVIRCFDHRNQRRTLSDVARATDLTRATARRFLLTLVELGYVAT 1q1hA 21 :IDVLRILLDKGTEMTDEEIANQLNIKVNDVRKKLNLLEEQGFVSY Number of specific fragments extracted= 1 number of extra gaps= 0 total=142 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 1q1hA/T0381-1q1hA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0381 read from 1q1hA/T0381-1q1hA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1q1hA read from 1q1hA/T0381-1q1hA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1q1hA in template set T0381 24 :LAVIRCFDHRNQRRTLSDVARATDLTRATARRFLLTLVELGYVATD 1q1hA 21 :IDVLRILLDKGTEMTDEEIANQLNIKVNDVRKKLNLLEEQGFVSYR Number of specific fragments extracted= 1 number of extra gaps= 0 total=143 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 2dtr/T0381-2dtr-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2dtr expands to /projects/compbio/data/pdb/2dtr.pdb.gz 2dtr:Warning: there is no chain 2dtr will retry with 2dtrA # T0381 read from 2dtr/T0381-2dtr-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2dtr read from 2dtr/T0381-2dtr-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2dtr to template set # found chain 2dtr in template set T0381 18 :QSLARGLAVIRCFDHRNQRRTLSDVARATDLTRATARRFLLTLVELGYVATDG 2dtr 6 :DTTEMYLRTIYELEEEGVTPLRARIAERLEQSGPTVSQTVARMERDGLVVVAS T0381 71 :SAFWLTPRVLELGYSYLS 2dtr 60 :RSLQMTPTGRTLATAVMR T0381 89 :SLSLPEVAQPH 2dtr 94 :INKVHDEACRW T0381 155 :LAGLPDDELDAYLEKL 2dtr 105 :EHVMSDEVERRLVKVL T0381 171 :DIQRLT 2dtr 122 :DVSRSP T0381 177 :ERTITARDEL 2dtr 129 :GNPIPGLDEL Number of specific fragments extracted= 6 number of extra gaps= 0 total=149 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 2dtr/T0381-2dtr-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0381 read from 2dtr/T0381-2dtr-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2dtr read from 2dtr/T0381-2dtr-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2dtr in template set T0381 19 :SLARGLAVIRCFDHRNQRRTLSDVARATDLTRATARRFLLTLVELGYVATDG 2dtr 7 :TTEMYLRTIYELEEEGVTPLRARIAERLEQSGPTVSQTVARMERDGLVVVAS T0381 71 :SAFWLTPRVLELGYSYLSSLSLPEV 2dtr 60 :RSLQMTPTGRTLATAVMRKHRLAER T0381 96 :AQPHLEK 2dtr 97 :VHDEACR T0381 154 :LLAGLPDDELDAYLEKL 2dtr 104 :WEHVMSDEVERRLVKVL T0381 171 :DIQRLT 2dtr 122 :DVSRSP T0381 177 :ERTITARDEL 2dtr 129 :GNPIPGLDEL Number of specific fragments extracted= 6 number of extra gaps= 0 total=155 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 2dtr/T0381-2dtr-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0381 read from 2dtr/T0381-2dtr-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2dtr read from 2dtr/T0381-2dtr-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2dtr in template set T0381 18 :QS 2dtr 7 :TT T0381 21 :ARGLAVIRCFDHRNQRRTLSDVARATDLTRATARRFLLTLVELGYVATDG 2dtr 9 :EMYLRTIYELEEEGVTPLRARIAERLEQSGPTVSQTVARMERDGLVVVAS T0381 71 :SAFWLTPRVLELGYSYLSSLSLPEVAQ 2dtr 60 :RSLQMTPTGRTLATAVMRKHRLAERLL T0381 104 :SHKVHE 2dtr 87 :TDIIGL T0381 138 :TIGT 2dtr 93 :DINK T0381 154 :LLAGLPDDELDAYLEKL 2dtr 104 :WEHVMSDEVERRLVKVL T0381 171 :DIQRLT 2dtr 122 :DVSRSP T0381 177 :ERTITARDEL 2dtr 129 :GNPIPGLDEL Number of specific fragments extracted= 8 number of extra gaps= 0 total=163 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 1j5yA/T0381-1j5yA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1j5yA expands to /projects/compbio/data/pdb/1j5y.pdb.gz 1j5yA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0381 read from 1j5yA/T0381-1j5yA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1j5yA read from 1j5yA/T0381-1j5yA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1j5yA to template set # found chain 1j5yA in template set Warning: unaligning (T0381)S13 because first residue in template chain is (1j5yA)M3 T0381 14 :PDYV 1j5yA 4 :KTVR T0381 20 :LARGLAVIRCFDHRNQRRTLSDVARATDLTRATARRFLLTLVELGY 1j5yA 8 :QERLKSIVRILERSKEPVSGAQLAEELSVSRQVIVQDIAYLRSLGY T0381 66 :VATDGSAFWL 1j5yA 55 :IVATPRGYVL T0381 92 :LPEVAQPHLEKLSHKVHESSSVSILDG 1j5yA 80 :APEEIKEELLCVVRNGGRIVDVIVEHP T0381 129 :VSRIMTVGITI 1j5yA 107 :VYGEIRGIIDV T0381 158 :LPDDELDAYLEKLDIQRLTERTIT 1j5yA 118 :SSEEEVLKFVNLMEMAKTEPLLTL T0381 219 :ASGLTVAAVNIS 1j5yA 142 :SGGVHLHTIEAP T0381 238 :LEDLHSDLIPSLRV 1j5yA 154 :DEETMERIMRELKK Number of specific fragments extracted= 8 number of extra gaps= 0 total=171 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 1j5yA/T0381-1j5yA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0381 read from 1j5yA/T0381-1j5yA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1j5yA read from 1j5yA/T0381-1j5yA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1j5yA in template set Warning: unaligning (T0381)S13 because first residue in template chain is (1j5yA)M3 Warning: unaligning (T0381)D202 because last residue in template chain is (1j5yA)E174 T0381 14 :PDYV 1j5yA 4 :KTVR T0381 20 :LARGLAVIRCFDHRNQRRTLSDVARATDLTRATARRFLLTLVELGY 1j5yA 8 :QERLKSIVRILERSKEPVSGAQLAEELSVSRQVIVQDIAYLRSLGY T0381 66 :VATDGSAFWL 1j5yA 55 :IVATPRGYVL T0381 93 :PEVAQPHLEKLSHK 1j5yA 81 :PEEIKEELLCVVRN T0381 118 :GADIVYVARVPVSR 1j5yA 95 :GGRIVDVIVEHPVY T0381 132 :IMTVGITI 1j5yA 110 :EIRGIIDV T0381 158 :LPDDELDAYLEKLDIQRLTERTI 1j5yA 118 :SSEEEVLKFVNLMEMAKTEPLLT T0381 181 :TARDELKAAILAVRADGICVL 1j5yA 153 :PDEETMERIMRELKKKGFLIE Number of specific fragments extracted= 8 number of extra gaps= 0 total=179 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 1j5yA/T0381-1j5yA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0381 read from 1j5yA/T0381-1j5yA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1j5yA read from 1j5yA/T0381-1j5yA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1j5yA in template set Warning: unaligning (T0381)D202 because last residue in template chain is (1j5yA)E174 T0381 21 :ARGLAVIRCFDHRNQRRTLSDVARATDLTRATARRFLLTLVELGY 1j5yA 9 :ERLKSIVRILERSKEPVSGAQLAEELSVSRQVIVQDIAYLRSLGY T0381 66 :VATDGSAFWL 1j5yA 55 :IVATPRGYVL T0381 93 :PEVAQPHLEKLSHK 1j5yA 81 :PEEIKEELLCVVRN T0381 118 :GADIVYVARVPVS 1j5yA 95 :GGRIVDVIVEHPV T0381 131 :RIMTVGITI 1j5yA 109 :GEIRGIIDV T0381 158 :LPDDELDAYLEKLDIQRLTERTI 1j5yA 118 :SSEEEVLKFVNLMEMAKTEPLLT T0381 182 :ARDELKAAILAVRADGICVL 1j5yA 154 :DEETMERIMRELKKKGFLIE Number of specific fragments extracted= 7 number of extra gaps= 0 total=186 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 2a61A/T0381-2a61A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2a61A expands to /projects/compbio/data/pdb/2a61.pdb.gz 2a61A:Skipped atom 654, because occupancy 0.500 <= existing 0.500 in 2a61A Skipped atom 656, because occupancy 0.500 <= existing 0.500 in 2a61A Skipped atom 658, because occupancy 0.500 <= existing 0.500 in 2a61A Skipped atom 660, because occupancy 0.500 <= existing 0.500 in 2a61A Skipped atom 662, because occupancy 0.500 <= existing 0.500 in 2a61A Skipped atom 664, because occupancy 0.500 <= existing 0.500 in 2a61A Skipped atom 666, because occupancy 0.500 <= existing 0.500 in 2a61A Skipped atom 668, because occupancy 0.500 <= existing 0.500 in 2a61A Skipped atom 670, because occupancy 0.500 <= existing 0.500 in 2a61A Skipped atom 672, because occupancy 0.500 <= existing 0.500 in 2a61A Skipped atom 674, because occupancy 0.500 <= existing 0.500 in 2a61A Skipped atom 920, because occupancy 0.500 <= existing 0.500 in 2a61A Skipped atom 922, because occupancy 0.500 <= existing 0.500 in 2a61A Skipped atom 924, because occupancy 0.500 <= existing 0.500 in 2a61A Skipped atom 926, because occupancy 0.500 <= existing 0.500 in 2a61A Skipped atom 928, because occupancy 0.500 <= existing 0.500 in 2a61A Skipped atom 930, because occupancy 0.500 <= existing 0.500 in 2a61A Skipped atom 932, because occupancy 0.500 <= existing 0.500 in 2a61A Skipped atom 934, because occupancy 0.500 <= existing 0.500 in 2a61A Skipped atom 1079, because occupancy 0.500 <= existing 0.500 in 2a61A Skipped atom 1081, because occupancy 0.500 <= existing 0.500 in 2a61A Skipped atom 1083, because occupancy 0.500 <= existing 0.500 in 2a61A Skipped atom 1085, because occupancy 0.500 <= existing 0.500 in 2a61A Skipped atom 1087, because occupancy 0.500 <= existing 0.500 in 2a61A Skipped atom 1089, because occupancy 0.500 <= existing 0.500 in 2a61A Skipped atom 1091, because occupancy 0.500 <= existing 0.500 in 2a61A Skipped atom 1093, because occupancy 0.500 <= existing 0.500 in 2a61A # T0381 read from 2a61A/T0381-2a61A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2a61A read from 2a61A/T0381-2a61A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2a61A to template set # found chain 2a61A in template set T0381 23 :GLAVIRCFDHR 2a61A 36 :QFDILQKIYFE T0381 35 :QRRTLSDVARATDLTRATARRFLLTLVELGYVAT 2a61A 47 :GPKRPGELSVLLGVAKSTVTGLVKRLEADGYLTR T0381 69 :DG 2a61A 83 :DP T0381 72 :AFWLTPRVLELGYSY 2a61A 91 :FLVITRKGEEVIEKV T0381 93 :PEVAQPHLEKLSHKV 2a61A 106 :IERRENFIEKITSDL T0381 159 :PDDELDAYLEK 2a61A 121 :GKEKSSKILDY T0381 187 :KAAILAVRAD 2a61A 132 :LKELKGVMER Number of specific fragments extracted= 7 number of extra gaps= 0 total=193 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 2a61A/T0381-2a61A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0381 read from 2a61A/T0381-2a61A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2a61A read from 2a61A/T0381-2a61A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2a61A in template set T0381 23 :GLAVIRCFDHR 2a61A 36 :QFDILQKIYFE T0381 35 :QRRTLSDVARATDLTRATARRFLLTLVELGYVAT 2a61A 47 :GPKRPGELSVLLGVAKSTVTGLVKRLEADGYLTR T0381 69 :DG 2a61A 83 :DP T0381 71 :SAFWLTPRVLELGYSY 2a61A 90 :YFLVITRKGEEVIEKV T0381 93 :PEVAQPHLEKLSHKV 2a61A 106 :IERRENFIEKITSDL T0381 159 :PDDELDAYLEK 2a61A 121 :GKEKSSKILDY T0381 187 :KAAILAVRAD 2a61A 132 :LKELKGVMER Number of specific fragments extracted= 7 number of extra gaps= 0 total=200 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 2a61A/T0381-2a61A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0381 read from 2a61A/T0381-2a61A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2a61A read from 2a61A/T0381-2a61A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2a61A in template set T0381 23 :GLAVIRCFDHR 2a61A 36 :QFDILQKIYFE T0381 35 :QRRTLSDVARATDLTRATARRFLLTLVELGYVATDG 2a61A 47 :GPKRPGELSVLLGVAKSTVTGLVKRLEADGYLTRTP T0381 72 :AFWLTPRVLELGYSY 2a61A 91 :FLVITRKGEEVIEKV T0381 93 :PEVAQPHLEKLSHK 2a61A 106 :IERRENFIEKITSD T0381 158 :LPDDELDAYLEK 2a61A 120 :LGKEKSSKILDY T0381 187 :KAAILAVRAD 2a61A 132 :LKELKGVMER Number of specific fragments extracted= 6 number of extra gaps= 0 total=206 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 1r1tA/T0381-1r1tA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1r1tA expands to /projects/compbio/data/pdb/1r1t.pdb.gz 1r1tA:# T0381 read from 1r1tA/T0381-1r1tA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1r1tA read from 1r1tA/T0381-1r1tA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1r1tA to template set # found chain 1r1tA in template set T0381 4 :TE 1r1tA 25 :LQ T0381 11 :LPSPDYVQSLA 1r1tA 27 :AIAPEVAQSLA T0381 22 :RGLAVIRCFDH 1r1tA 47 :NRLRLLSLLAR T0381 35 :QRRTLSDVARATDLTRATARRFLLTLVELGYVAT 1r1tA 58 :SELCVGDLAQAIGVSESAVSHQLRSLRNLRLVSY T0381 69 :DGSA 1r1tA 94 :QGRH T0381 73 :FWLT 1r1tA 100 :YQLQ T0381 94 :EVAQPHLEKLSHKV 1r1tA 105 :HHIVALYQNALDHL Number of specific fragments extracted= 7 number of extra gaps= 0 total=213 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 1r1tA/T0381-1r1tA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0381 read from 1r1tA/T0381-1r1tA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1r1tA read from 1r1tA/T0381-1r1tA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1r1tA in template set T0381 4 :TEP 1r1tA 25 :LQA T0381 12 :PSPDYVQSLA 1r1tA 28 :IAPEVAQSLA T0381 22 :RGLAVIRCFDH 1r1tA 47 :NRLRLLSLLAR T0381 35 :QRRTLSDVARATDLTRATARRFLLTLVELGYVAT 1r1tA 58 :SELCVGDLAQAIGVSESAVSHQLRSLRNLRLVSY T0381 69 :DGSA 1r1tA 94 :QGRH T0381 73 :FWLT 1r1tA 100 :YQLQ T0381 77 :P 1r1tA 105 :H T0381 91 :SLPEVAQPHLEK 1r1tA 106 :HIVALYQNALDH Number of specific fragments extracted= 8 number of extra gaps= 0 total=221 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 1r1tA/T0381-1r1tA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0381 read from 1r1tA/T0381-1r1tA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1r1tA read from 1r1tA/T0381-1r1tA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1r1tA in template set T0381 22 :RGLAVIRCFDH 1r1tA 47 :NRLRLLSLLAR T0381 35 :QRRTLSDVARATDLTRATARRFLLTLVELGYVATDG 1r1tA 58 :SELCVGDLAQAIGVSESAVSHQLRSLRNLRLVSYRK T0381 71 :S 1r1tA 96 :R T0381 72 :AFWLT 1r1tA 99 :YYQLQ T0381 89 :SLSLPEVAQPHLEK 1r1tA 104 :DHHIVALYQNALDH Number of specific fragments extracted= 5 number of extra gaps= 0 total=226 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 2ethA/T0381-2ethA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2ethA expands to /projects/compbio/data/pdb/2eth.pdb.gz 2ethA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 1046, because occupancy 0.500 <= existing 0.500 in 2ethA Skipped atom 1050, because occupancy 0.500 <= existing 0.500 in 2ethA Skipped atom 1052, because occupancy 0.500 <= existing 0.500 in 2ethA # T0381 read from 2ethA/T0381-2ethA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2ethA read from 2ethA/T0381-2ethA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2ethA to template set # found chain 2ethA in template set T0381 9 :KILPSPDYVQSL 2ethA 19 :SYLPSNEEISDM T0381 21 :ARGLAVIRCFDHR 2ethA 32 :TTELYAFLYVALF T0381 35 :QRRTLSDVARATDLTRATARRFLLTLVELGYVAT 2ethA 45 :GPKKMKEIAEFLSTTKSNVTNVVDSLEKRGLVVR T0381 69 :DG 2ethA 81 :DP T0381 71 :S 2ethA 86 :R T0381 72 :AFWLTPRVLELGYSYLSS 2ethA 89 :RVVLTEKGKEIFGEILSN T0381 97 :QPHLEKLSHK 2ethA 107 :FESLLKSVLE T0381 157 :GLPDDELDAYLEK 2ethA 117 :KFSEEDFKVVSEG Number of specific fragments extracted= 8 number of extra gaps= 0 total=234 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 2ethA/T0381-2ethA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0381 read from 2ethA/T0381-2ethA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2ethA read from 2ethA/T0381-2ethA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2ethA in template set T0381 9 :KILPSPDYVQSL 2ethA 19 :SYLPSNEEISDM T0381 21 :ARGLAVIRCFDHR 2ethA 32 :TTELYAFLYVALF T0381 35 :QRRTLSDVARATDLTRATARRFLLTLVELGYVAT 2ethA 45 :GPKKMKEIAEFLSTTKSNVTNVVDSLEKRGLVVR T0381 69 :DG 2ethA 81 :DP T0381 71 :SAFWLTPRVLELGYSYLSS 2ethA 88 :YRVVLTEKGKEIFGEILSN T0381 97 :QPHLEKLSHK 2ethA 107 :FESLLKSVLE T0381 157 :GLPDDELDAYLEKL 2ethA 117 :KFSEEDFKVVSEGF Number of specific fragments extracted= 7 number of extra gaps= 0 total=241 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 2ethA/T0381-2ethA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0381 read from 2ethA/T0381-2ethA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2ethA read from 2ethA/T0381-2ethA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2ethA in template set T0381 12 :PSPDYVQ 2ethA 22 :PSNEEIS T0381 21 :ARGLAVIRCFDHRN 2ethA 32 :TTELYAFLYVALFG T0381 36 :RRTLSDVARATDLTRATARRFLLTLVELGYVATDG 2ethA 46 :PKKMKEIAEFLSTTKSNVTNVVDSLEKRGLVVREM T0381 130 :SRIMTVGIT 2ethA 85 :RRTYRVVLT T0381 161 :DELDAYLEKL 2ethA 94 :EKGKEIFGEI T0381 180 :ITARDELKAAIL 2ethA 104 :LSNFESLLKSVL T0381 234 :ARYSLEDLHSDLIPSLRVTATDI 2ethA 116 :EKFSEEDFKVVSEGFNRMVEALS Number of specific fragments extracted= 7 number of extra gaps= 0 total=248 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 1lnwA/T0381-1lnwA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1lnwA expands to /projects/compbio/data/pdb/1lnw.pdb.gz 1lnwA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0381 read from 1lnwA/T0381-1lnwA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1lnwA read from 1lnwA/T0381-1lnwA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1lnwA to template set # found chain 1lnwA in template set T0381 24 :LAVIRCFDHRNQ 1lnwA 40 :VHVLKLIDEQRG T0381 37 :RTLSDVARATDLTRATARRFLLTLVELGYVAT 1lnwA 52 :LNLQDLGRQMCRDKALITRKIRELEGRNLVRR T0381 69 :DG 1lnwA 86 :NP T0381 71 :S 1lnwA 91 :R T0381 72 :AFWLTPRVLELGYS 1lnwA 94 :QLFLTDEGLAIHQH T0381 96 :AQPHLEKLSHKV 1lnwA 108 :AEAIMSRVHDEL T0381 155 :LAGLPDDELDAYLEK 1lnwA 120 :FAPLTPVEQATLVHL T0381 183 :RDELKA 1lnwA 135 :LDQCLA Number of specific fragments extracted= 8 number of extra gaps= 0 total=256 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 1lnwA/T0381-1lnwA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0381 read from 1lnwA/T0381-1lnwA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1lnwA read from 1lnwA/T0381-1lnwA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1lnwA in template set T0381 23 :GLAVIRCFDHR 1lnwA 39 :DVHVLKLIDEQ T0381 35 :QRRTLSDVARATDLTRATARRFLLTLVELGYVAT 1lnwA 50 :RGLNLQDLGRQMCRDKALITRKIRELEGRNLVRR T0381 69 :DG 1lnwA 86 :NP T0381 71 :S 1lnwA 91 :R T0381 73 :FWLTPRVLELG 1lnwA 95 :LFLTDEGLAIH T0381 94 :EVAQPHLEKLSHK 1lnwA 106 :QHAEAIMSRVHDE T0381 154 :LLAGLPDDELDAYLEKLD 1lnwA 119 :LFAPLTPVEQATLVHLLD Number of specific fragments extracted= 7 number of extra gaps= 0 total=263 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 1lnwA/T0381-1lnwA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0381 read from 1lnwA/T0381-1lnwA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1lnwA read from 1lnwA/T0381-1lnwA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1lnwA in template set T0381 24 :LAVIRCFDHRNQ 1lnwA 40 :VHVLKLIDEQRG T0381 37 :RTLSDVARATDLTRATARRFLLTLVELGYVATDG 1lnwA 52 :LNLQDLGRQMCRDKALITRKIRELEGRNLVRRER T0381 71 :SA 1lnwA 91 :RS T0381 73 :FWLTPRVLELGYS 1lnwA 95 :LFLTDEGLAIHQH T0381 96 :AQPHLEKLSHKV 1lnwA 108 :AEAIMSRVHDEL T0381 155 :LAGLPDDELDAYLEKL 1lnwA 120 :FAPLTPVEQATLVHLL T0381 191 :L 1lnwA 136 :D Number of specific fragments extracted= 7 number of extra gaps= 0 total=270 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 1b1bA/T0381-1b1bA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1b1bA expands to /projects/compbio/data/pdb/1b1b.pdb.gz 1b1bA:# T0381 read from 1b1bA/T0381-1b1bA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1b1bA read from 1b1bA/T0381-1b1bA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1b1bA to template set # found chain 1b1bA in template set Warning: unaligning (T0381)S13 because first residue in template chain is (1b1bA)M1 T0381 14 :PDYVQSLARGLAVIRCFDHRNQRRTLSDVARATDLTRATARRFLLTLVELGYVATDG 1b1bA 2 :NELVDTTEMYLRTIYDLEEEGVTPLRARIAERLDQSGPTVSQTVSRMERDGLLRVAG T0381 71 :SAFWLTPRVLELGYSYLS 1b1bA 60 :RHLELTEKGRALAIAVMR T0381 89 :SLS 1b1bA 89 :VIG T0381 92 :LPEVAQPHLEK 1b1bA 93 :PWEEVHAEACR T0381 154 :LLAGLPDDELDAYLEKL 1b1bA 104 :WEHVMSEDVERRLVKVL T0381 171 :DIQRLT 1b1bA 122 :NPTTSP T0381 177 :ERTITARDEL 1b1bA 129 :GNPIPGLVEL Number of specific fragments extracted= 7 number of extra gaps= 0 total=277 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 1b1bA/T0381-1b1bA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0381 read from 1b1bA/T0381-1b1bA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1b1bA read from 1b1bA/T0381-1b1bA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1b1bA in template set T0381 14 :PDYVQSLARGLAVIRCFDHRNQRRTLSDVARATDLTRATARRFLLTLVELGYVATDG 1b1bA 2 :NELVDTTEMYLRTIYDLEEEGVTPLRARIAERLDQSGPTVSQTVSRMERDGLLRVAG T0381 71 :SAFWLTPRVLELGYSYLSSLSLP 1b1bA 60 :RHLELTEKGRALAIAVMRKHRLA T0381 94 :EVAQPHLEK 1b1bA 95 :EEVHAEACR T0381 154 :LLAGLPDDELDAYLEKL 1b1bA 104 :WEHVMSEDVERRLVKVL T0381 171 :DIQRLT 1b1bA 122 :NPTTSP T0381 177 :ERTITARDEL 1b1bA 129 :GNPIPGLVEL Number of specific fragments extracted= 6 number of extra gaps= 0 total=283 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 1b1bA/T0381-1b1bA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0381 read from 1b1bA/T0381-1b1bA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1b1bA read from 1b1bA/T0381-1b1bA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1b1bA in template set T0381 14 :PDYVQSLARGLAVIRCFDHRNQRRTLSDVARATDLTRATARRFLLTLVELGYVATDG 1b1bA 2 :NELVDTTEMYLRTIYDLEEEGVTPLRARIAERLDQSGPTVSQTVSRMERDGLLRVAG T0381 71 :SAFWLTPRVLELGYSYLSSLSLPEV 1b1bA 60 :RHLELTEKGRALAIAVMRKHRLAER T0381 96 :AQPHLEK 1b1bA 97 :VHAEACR T0381 154 :LLAGLPDDELDAYLEKL 1b1bA 104 :WEHVMSEDVERRLVKVL T0381 171 :DIQRLT 1b1bA 122 :NPTTSP T0381 177 :ERTITARDEL 1b1bA 129 :GNPIPGLVEL Number of specific fragments extracted= 6 number of extra gaps= 0 total=289 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 1smtA/T0381-1smtA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1smtA expands to /projects/compbio/data/pdb/1smt.pdb.gz 1smtA:# T0381 read from 1smtA/T0381-1smtA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1smtA read from 1smtA/T0381-1smtA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1smtA to template set # found chain 1smtA in template set T0381 4 :TE 1smtA 25 :LQ T0381 11 :LPSPDYVQSLA 1smtA 27 :AIAPEVAQSLA T0381 22 :RGLAVIRCF 1smtA 47 :NRLRLLSLL T0381 33 :RNQRRTLSDVARATDLTRATARRFLLTLVELGYVAT 1smtA 56 :ARSELCVGDLAQAIGVSESAVSHQLRSLRNLRLVSY T0381 69 :DGS 1smtA 94 :QGR T0381 72 :AFWLT 1smtA 99 :YYQLQ T0381 89 :SLSLPEVAQPHLEKL 1smtA 104 :DHHIVALYQNALDHL Number of specific fragments extracted= 7 number of extra gaps= 0 total=296 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 1smtA/T0381-1smtA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0381 read from 1smtA/T0381-1smtA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1smtA read from 1smtA/T0381-1smtA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1smtA in template set T0381 4 :TEP 1smtA 25 :LQA T0381 12 :PSPDYVQSLA 1smtA 28 :IAPEVAQSLA T0381 22 :RGLAVIRCFDH 1smtA 47 :NRLRLLSLLAR T0381 35 :QRRTLSDVARATDLTRATARRFLLTLVELGYVAT 1smtA 58 :SELCVGDLAQAIGVSESAVSHQLRSLRNLRLVSY T0381 69 :DGSA 1smtA 94 :QGRH T0381 73 :FWLT 1smtA 100 :YQLQ T0381 89 :SLSLPEVAQPHLEK 1smtA 104 :DHHIVALYQNALDH Number of specific fragments extracted= 7 number of extra gaps= 0 total=303 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 1smtA/T0381-1smtA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0381 read from 1smtA/T0381-1smtA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1smtA read from 1smtA/T0381-1smtA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1smtA in template set T0381 22 :RGLAVIRCFD 1smtA 47 :NRLRLLSLLA T0381 34 :NQRRTLSDVARATDLTRATARRFLLTLVELGYVATDG 1smtA 57 :RSELCVGDLAQAIGVSESAVSHQLRSLRNLRLVSYRK T0381 71 :S 1smtA 95 :G T0381 72 :AFWLT 1smtA 99 :YYQLQ T0381 89 :SLSLPEVAQPHLEKL 1smtA 104 :DHHIVALYQNALDHL Number of specific fragments extracted= 5 number of extra gaps= 0 total=308 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 1sfxA/T0381-1sfxA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1sfxA expands to /projects/compbio/data/pdb/1sfx.pdb.gz 1sfxA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 76, because occupancy 0.480 <= existing 0.520 in 1sfxA Skipped atom 78, because occupancy 0.480 <= existing 0.520 in 1sfxA Skipped atom 80, because occupancy 0.480 <= existing 0.520 in 1sfxA Skipped atom 82, because occupancy 0.480 <= existing 0.520 in 1sfxA Skipped atom 84, because occupancy 0.480 <= existing 0.520 in 1sfxA Skipped atom 103, because occupancy 0.370 <= existing 0.630 in 1sfxA Skipped atom 105, because occupancy 0.370 <= existing 0.630 in 1sfxA Skipped atom 107, because occupancy 0.370 <= existing 0.630 in 1sfxA Skipped atom 109, because occupancy 0.370 <= existing 0.630 in 1sfxA Skipped atom 111, because occupancy 0.370 <= existing 0.630 in 1sfxA Skipped atom 117, because occupancy 0.410 <= existing 0.590 in 1sfxA Skipped atom 119, because occupancy 0.410 <= existing 0.590 in 1sfxA Skipped atom 121, because occupancy 0.410 <= existing 0.590 in 1sfxA Skipped atom 123, because occupancy 0.410 <= existing 0.590 in 1sfxA Skipped atom 125, because occupancy 0.410 <= existing 0.590 in 1sfxA Skipped atom 156, because occupancy 0.350 <= existing 0.650 in 1sfxA Skipped atom 158, because occupancy 0.350 <= existing 0.650 in 1sfxA Skipped atom 160, because occupancy 0.350 <= existing 0.650 in 1sfxA Skipped atom 162, because occupancy 0.350 <= existing 0.650 in 1sfxA Skipped atom 164, because occupancy 0.350 <= existing 0.650 in 1sfxA Skipped atom 177, because occupancy 0.350 <= existing 0.650 in 1sfxA Skipped atom 179, because occupancy 0.350 <= existing 0.650 in 1sfxA Skipped atom 231, because occupancy 0.490 <= existing 0.510 in 1sfxA Skipped atom 233, because occupancy 0.490 <= existing 0.510 in 1sfxA Skipped atom 263, because occupancy 0.370 <= existing 0.630 in 1sfxA Skipped atom 265, because occupancy 0.370 <= existing 0.630 in 1sfxA Skipped atom 267, because occupancy 0.370 <= existing 0.630 in 1sfxA Skipped atom 269, because occupancy 0.370 <= existing 0.630 in 1sfxA Skipped atom 271, because occupancy 0.370 <= existing 0.630 in 1sfxA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 405, because occupancy 0.430 <= existing 0.570 in 1sfxA Skipped atom 407, because occupancy 0.430 <= existing 0.570 in 1sfxA Skipped atom 409, because occupancy 0.430 <= existing 0.570 in 1sfxA Skipped atom 411, because occupancy 0.430 <= existing 0.570 in 1sfxA Skipped atom 413, because occupancy 0.430 <= existing 0.570 in 1sfxA Skipped atom 415, because occupancy 0.430 <= existing 0.570 in 1sfxA Skipped atom 417, because occupancy 0.430 <= existing 0.570 in 1sfxA Skipped atom 441, because occupancy 0.330 <= existing 0.670 in 1sfxA Skipped atom 443, because occupancy 0.330 <= existing 0.670 in 1sfxA Skipped atom 445, because occupancy 0.330 <= existing 0.670 in 1sfxA Skipped atom 447, because occupancy 0.330 <= existing 0.670 in 1sfxA Skipped atom 449, because occupancy 0.330 <= existing 0.670 in 1sfxA Skipped atom 451, because occupancy 0.330 <= existing 0.670 in 1sfxA Skipped atom 453, because occupancy 0.330 <= existing 0.670 in 1sfxA Skipped atom 486, because occupancy 0.440 <= existing 0.560 in 1sfxA Skipped atom 488, because occupancy 0.440 <= existing 0.560 in 1sfxA Skipped atom 490, because occupancy 0.440 <= existing 0.560 in 1sfxA Skipped atom 492, because occupancy 0.440 <= existing 0.560 in 1sfxA Skipped atom 494, because occupancy 0.440 <= existing 0.560 in 1sfxA Skipped atom 523, because occupancy 0.370 <= existing 0.630 in 1sfxA Skipped atom 525, because occupancy 0.370 <= existing 0.630 in 1sfxA Skipped atom 527, because occupancy 0.370 <= existing 0.630 in 1sfxA Skipped atom 529, because occupancy 0.370 <= existing 0.630 in 1sfxA Skipped atom 531, because occupancy 0.370 <= existing 0.630 in 1sfxA Skipped atom 625, because occupancy 0.470 <= existing 0.530 in 1sfxA Skipped atom 627, because occupancy 0.470 <= existing 0.530 in 1sfxA Skipped atom 629, because occupancy 0.470 <= existing 0.530 in 1sfxA Skipped atom 631, because occupancy 0.470 <= existing 0.530 in 1sfxA Skipped atom 633, because occupancy 0.470 <= existing 0.530 in 1sfxA Skipped atom 657, because occupancy 0.390 <= existing 0.610 in 1sfxA Skipped atom 659, because occupancy 0.390 <= existing 0.610 in 1sfxA Skipped atom 661, because occupancy 0.390 <= existing 0.610 in 1sfxA Skipped atom 703, because occupancy 0.420 <= existing 0.580 in 1sfxA Skipped atom 705, because occupancy 0.420 <= existing 0.580 in 1sfxA Skipped atom 750, because occupancy 0.320 <= existing 0.680 in 1sfxA Skipped atom 752, because occupancy 0.320 <= existing 0.680 in 1sfxA Skipped atom 754, because occupancy 0.320 <= existing 0.680 in 1sfxA Skipped atom 756, because occupancy 0.320 <= existing 0.680 in 1sfxA Skipped atom 758, because occupancy 0.320 <= existing 0.680 in 1sfxA Skipped atom 779, because occupancy 0.370 <= existing 0.630 in 1sfxA Skipped atom 781, because occupancy 0.370 <= existing 0.630 in 1sfxA Skipped atom 783, because occupancy 0.370 <= existing 0.630 in 1sfxA Skipped atom 785, because occupancy 0.370 <= existing 0.630 in 1sfxA Skipped atom 787, because occupancy 0.370 <= existing 0.630 in 1sfxA Skipped atom 793, because occupancy 0.350 <= existing 0.650 in 1sfxA Skipped atom 795, because occupancy 0.350 <= existing 0.650 in 1sfxA Skipped atom 797, because occupancy 0.350 <= existing 0.650 in 1sfxA Skipped atom 799, because occupancy 0.350 <= existing 0.650 in 1sfxA Skipped atom 801, because occupancy 0.350 <= existing 0.650 in 1sfxA Skipped atom 833, because occupancy 0.420 <= existing 0.580 in 1sfxA Skipped atom 835, because occupancy 0.420 <= existing 0.580 in 1sfxA Skipped atom 878, because occupancy 0.420 <= existing 0.580 in 1sfxA Skipped atom 880, because occupancy 0.420 <= existing 0.580 in 1sfxA Skipped atom 882, because occupancy 0.420 <= existing 0.580 in 1sfxA Skipped atom 884, because occupancy 0.420 <= existing 0.580 in 1sfxA Skipped atom 886, because occupancy 0.420 <= existing 0.580 in 1sfxA Skipped atom 892, because occupancy 0.340 <= existing 0.660 in 1sfxA Skipped atom 894, because occupancy 0.340 <= existing 0.660 in 1sfxA Skipped atom 896, because occupancy 0.340 <= existing 0.660 in 1sfxA Skipped atom 898, because occupancy 0.340 <= existing 0.660 in 1sfxA Skipped atom 900, because occupancy 0.340 <= existing 0.660 in 1sfxA Skipped atom 902, because occupancy 0.340 <= existing 0.660 in 1sfxA Skipped atom 904, because occupancy 0.340 <= existing 0.660 in 1sfxA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 962, because occupancy 0.310 <= existing 0.690 in 1sfxA Skipped atom 964, because occupancy 0.310 <= existing 0.690 in 1sfxA Skipped atom 966, because occupancy 0.310 <= existing 0.690 in 1sfxA Skipped atom 968, because occupancy 0.310 <= existing 0.690 in 1sfxA # T0381 read from 1sfxA/T0381-1sfxA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1sfxA read from 1sfxA/T0381-1sfxA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1sfxA to template set # found chain 1sfxA in template set T0381 16 :YVQSLAR 1sfxA 8 :LVKALEK T0381 24 :LAVIRCFDHRNQ 1sfxA 22 :VRIYSLLLERGG T0381 37 :RTLSDVARATDLTRATARRFLLTLVELGYVAT 1sfxA 34 :MRVSEIARELDLSARFVRDRLKVLLKRGFVRR T0381 126 :RVPVSRIMTVGITI 1sfxA 67 :IVEKGWVGYIYSAE T0381 159 :PDDELDAYLEKL 1sfxA 81 :KPEKVLKEFKSS T0381 186 :LKAAILAVRAD 1sfxA 93 :ILGEIERIEKM Number of specific fragments extracted= 6 number of extra gaps= 0 total=314 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 1sfxA/T0381-1sfxA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0381 read from 1sfxA/T0381-1sfxA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1sfxA read from 1sfxA/T0381-1sfxA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1sfxA in template set T0381 13 :SPDYVQSLARG 1sfxA 1 :MSNPLGELVKA T0381 24 :LAVIRCFDHR 1sfxA 22 :VRIYSLLLER T0381 35 :QRRTLSDVARATDLTRATARRFLLTLVELGYVAT 1sfxA 32 :GGMRVSEIARELDLSARFVRDRLKVLLKRGFVRR T0381 125 :ARVPVSRIMTVGITI 1sfxA 66 :EIVEKGWVGYIYSAE T0381 159 :PDDELDAYLEKL 1sfxA 81 :KPEKVLKEFKSS T0381 186 :LKAAILAVRAD 1sfxA 93 :ILGEIERIEKM Number of specific fragments extracted= 6 number of extra gaps= 0 total=320 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 1sfxA/T0381-1sfxA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0381 read from 1sfxA/T0381-1sfxA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1sfxA read from 1sfxA/T0381-1sfxA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1sfxA in template set T0381 11 :LPSPDYVQSLAR 1sfxA 3 :NPLGELVKALEK T0381 23 :GLAVIRCFDHRNQ 1sfxA 21 :DVRIYSLLLERGG T0381 37 :RTLSDVARATDLTRATARRFLLTLVELGYVATD 1sfxA 34 :MRVSEIARELDLSARFVRDRLKVLLKRGFVRRE T0381 126 :RVPVSRIMTVGI 1sfxA 67 :IVEKGWVGYIYS T0381 157 :GLPDDELDAYLEKL 1sfxA 79 :AEKPEKVLKEFKSS T0381 186 :LKAAILAVRAD 1sfxA 93 :ILGEIERIEKM Number of specific fragments extracted= 6 number of extra gaps= 0 total=326 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 1u2wA/T0381-1u2wA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1u2wA expands to /projects/compbio/data/pdb/1u2w.pdb.gz 1u2wA:# T0381 read from 1u2wA/T0381-1u2wA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1u2wA read from 1u2wA/T0381-1u2wA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1u2wA to template set # found chain 1u2wA in template set Warning: unaligning (T0381)D69 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1u2wA)L94 T0381 17 :VQSL 1u2wA 36 :LKAI T0381 21 :ARGLAVIRCFDHR 1u2wA 42 :ENRAKITYALCQD T0381 35 :QRRTLSDVARATDLTRATARRFLLTLVELGYVAT 1u2wA 55 :EELCVCDIANILGVTIANASHHLRTLYKQGVVNF T0381 71 :SAFWLT 1u2wA 95 :ALYSLG T0381 93 :PEVAQPHLEKLSHKVHE 1u2wA 101 :DEHIRQIMMIALAHKKE Number of specific fragments extracted= 5 number of extra gaps= 0 total=331 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 1u2wA/T0381-1u2wA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0381 read from 1u2wA/T0381-1u2wA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1u2wA read from 1u2wA/T0381-1u2wA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1u2wA in template set Warning: unaligning (T0381)D69 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1u2wA)L94 T0381 16 :YVQSL 1u2wA 35 :ILKAI T0381 21 :ARGLAVIRCFDHR 1u2wA 42 :ENRAKITYALCQD T0381 35 :QRRTLSDVARATDLTRATARRFLLTLVELGYVAT 1u2wA 55 :EELCVCDIANILGVTIANASHHLRTLYKQGVVNF T0381 71 :SAFWLT 1u2wA 95 :ALYSLG T0381 77 :PRVLELGYSYLSS 1u2wA 102 :EHIRQIMMIALAH Number of specific fragments extracted= 5 number of extra gaps= 0 total=336 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 1u2wA/T0381-1u2wA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0381 read from 1u2wA/T0381-1u2wA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1u2wA read from 1u2wA/T0381-1u2wA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1u2wA in template set Warning: unaligning (T0381)D69 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1u2wA)L94 T0381 15 :DYVQSLA 1u2wA 34 :QILKAIA T0381 22 :RGLAVIRCFDH 1u2wA 43 :NRAKITYALCQ T0381 34 :NQRRTLSDVARATDLTRATARRFLLTLVELGYVAT 1u2wA 54 :DEELCVCDIANILGVTIANASHHLRTLYKQGVVNF T0381 71 :SAFWLT 1u2wA 95 :ALYSLG T0381 89 :SLSLPEVAQPHLEK 1u2wA 101 :DEHIRQIMMIALAH Number of specific fragments extracted= 5 number of extra gaps= 0 total=341 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 1qbjA/T0381-1qbjA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1qbjA expands to /projects/compbio/data/pdb/1qbj.pdb.gz 1qbjA:# T0381 read from 1qbjA/T0381-1qbjA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1qbjA read from 1qbjA/T0381-1qbjA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1qbjA to template set # found chain 1qbjA in template set Warning: unaligning (T0381)T76 because last residue in template chain is (1qbjA)A198 T0381 15 :DYVQSLARGLAVIRCF 1qbjA 135 :IYQDQEQRILKFLEEL T0381 32 :HRNQRRTLSDVARATDLTRATARRFLLTLVELGYVATDG 1qbjA 151 :GEGKATTAHDLSGKLGTPKKEINRVLYSLAKKGKLQKEA T0381 71 :SAFWL 1qbjA 193 :PLWKI Number of specific fragments extracted= 3 number of extra gaps= 0 total=344 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 1qbjA/T0381-1qbjA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0381 read from 1qbjA/T0381-1qbjA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1qbjA read from 1qbjA/T0381-1qbjA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1qbjA in template set Warning: unaligning (T0381)P14 because first residue in template chain is (1qbjA)S134 Warning: unaligning (T0381)T76 because last residue in template chain is (1qbjA)A198 T0381 15 :DYVQSLARGLAVIRCF 1qbjA 135 :IYQDQEQRILKFLEEL T0381 32 :HRNQRRTLSDVARATDLTRATARRFLLTLVELGYVATDG 1qbjA 151 :GEGKATTAHDLSGKLGTPKKEINRVLYSLAKKGKLQKEA T0381 71 :SAFWL 1qbjA 193 :PLWKI Number of specific fragments extracted= 3 number of extra gaps= 0 total=347 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 1qbjA/T0381-1qbjA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0381 read from 1qbjA/T0381-1qbjA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1qbjA read from 1qbjA/T0381-1qbjA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1qbjA in template set Warning: unaligning (T0381)T76 because last residue in template chain is (1qbjA)A198 T0381 16 :YVQSLARGLAVIRCFDH 1qbjA 136 :YQDQEQRILKFLEELGE T0381 34 :NQRRTLSDVARATDLTRATARRFLLTLVELGYVATDG 1qbjA 153 :GKATTAHDLSGKLGTPKKEINRVLYSLAKKGKLQKEA T0381 71 :SAFWL 1qbjA 193 :PLWKI Number of specific fragments extracted= 3 number of extra gaps= 0 total=350 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 1fx7A/T0381-1fx7A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1fx7A expands to /projects/compbio/data/pdb/1fx7.pdb.gz 1fx7A:Skipped atom 596, because occupancy 0.500 <= existing 0.500 in 1fx7A Skipped atom 598, because occupancy 0.500 <= existing 0.500 in 1fx7A Skipped atom 600, because occupancy 0.500 <= existing 0.500 in 1fx7A Skipped atom 602, because occupancy 0.500 <= existing 0.500 in 1fx7A Skipped atom 872, because occupancy 0.500 <= existing 0.500 in 1fx7A Skipped atom 874, because occupancy 0.500 <= existing 0.500 in 1fx7A Skipped atom 876, because occupancy 0.500 <= existing 0.500 in 1fx7A Skipped atom 878, because occupancy 0.500 <= existing 0.500 in 1fx7A Skipped atom 1703, because occupancy 0.500 <= existing 0.500 in 1fx7A Skipped atom 1705, because occupancy 0.500 <= existing 0.500 in 1fx7A Skipped atom 1707, because occupancy 0.500 <= existing 0.500 in 1fx7A Skipped atom 1709, because occupancy 0.500 <= existing 0.500 in 1fx7A # T0381 read from 1fx7A/T0381-1fx7A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1fx7A read from 1fx7A/T0381-1fx7A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1fx7A to template set # found chain 1fx7A in template set Warning: unaligning (T0381)S13 because first residue in template chain is (1fx7A)M1 T0381 14 :PDYVQSLARGLAVIRCFDHRNQRRTLSDVARATDLTRATARRFLLTLVELGYVATDG 1fx7A 2 :NELVDTTEMYLRTIYDLEEEGVTPLRARIAERLDQSGPTVSQTVSRMERDGLLRVAG T0381 71 :SAFWLTPRVLELGYSYLS 1fx7A 60 :RHLELTEKGRALAIAVMR T0381 89 :SLSLPEV 1fx7A 91 :GLPWEEV T0381 100 :LEKLSHKVH 1fx7A 98 :HAEACRWEH T0381 157 :GLPDDELDAYLEKLDIQRLTERTIT 1fx7A 107 :VMSEDVERRLVKVLNNPTTSPFGNP T0381 187 :KAAILAVRADGI 1fx7A 178 :IDLITRLKDAGV T0381 206 :EAGLRSM 1fx7A 190 :VPNARVT T0381 216 :I 1fx7A 197 :V T0381 217 :RGASGLTVA 1fx7A 199 :TTPGGGVTI Number of specific fragments extracted= 9 number of extra gaps= 0 total=359 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 1fx7A/T0381-1fx7A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0381 read from 1fx7A/T0381-1fx7A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1fx7A read from 1fx7A/T0381-1fx7A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1fx7A in template set Warning: unaligning (T0381)S13 because first residue in template chain is (1fx7A)M1 T0381 14 :PDYVQSLARGLAVIRCFDHRNQRRTLSDVARATDLTRATARRFLLTLVELGYVATDG 1fx7A 2 :NELVDTTEMYLRTIYDLEEEGVTPLRARIAERLDQSGPTVSQTVSRMERDGLLRVAG T0381 71 :SAFWLTPRVLELGYSYLSSLSLPEVAQ 1fx7A 60 :RHLELTEKGRALAIAVMRKHRLAERLL T0381 98 :PHLEKLSHKV 1fx7A 96 :EVHAEACRWE T0381 156 :AGLPDDELDAYLEKLDIQRLTERTIT 1fx7A 106 :HVMSEDVERRLVKVLNNPTTSPFGNP Number of specific fragments extracted= 4 number of extra gaps= 0 total=363 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 1fx7A/T0381-1fx7A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0381 read from 1fx7A/T0381-1fx7A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1fx7A read from 1fx7A/T0381-1fx7A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1fx7A in template set T0381 14 :PDYVQSLARGLAVIRCFDHRNQRRTLSDVARATDLTRATARRFLLTLVELGYVATDG 1fx7A 2 :NELVDTTEMYLRTIYDLEEEGVTPLRARIAERLDQSGPTVSQTVSRMERDGLLRVAG T0381 71 :SAFWLTPRVLELGYSYLSSLSLPEVAQ 1fx7A 60 :RHLELTEKGRALAIAVMRKHRLAERLL T0381 98 :PHLEKLSHKVH 1fx7A 96 :EVHAEACRWEH T0381 157 :GLPDDELDAYLEKLDIQRLTERTIT 1fx7A 107 :VMSEDVERRLVKVLNNPTTSPFGNP Number of specific fragments extracted= 4 number of extra gaps= 0 total=367 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 1f5tA/T0381-1f5tA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1f5tA expands to /projects/compbio/data/pdb/1f5t.pdb.gz 1f5tA:# T0381 read from 1f5tA/T0381-1f5tA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1f5tA read from 1f5tA/T0381-1f5tA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1f5tA to template set # found chain 1f5tA in template set Warning: unaligning (T0381)P14 because first residue in template chain is (1f5tA)K1002 T0381 15 :DYVQSLARGLAVIRCFDHRNQRRTLSDVARATDLTRATARRFLLTLVELGYVATDG 1f5tA 1003 :DLVDTTEMYLRTIYELEEEGVTPLRARIAERLEQSGPTVSQTVARMERDGLVVVAS T0381 71 :SAFWLTPRVLELGYSYLSS 1f5tA 1060 :RSLQMTPTGRTLATAVMRK T0381 97 :QPHLEKLSHKV 1f5tA 1079 :HRLAERLLTDI T0381 108 :HE 1f5tA 1091 :GL T0381 138 :TIGT 1f5tA 1093 :DINK T0381 147 :ATSMGRVLLAGLPDDELDAYLEKL 1f5tA 1097 :VHDEADRWEHVMSDEVERRLVKVL Number of specific fragments extracted= 6 number of extra gaps= 0 total=373 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 1f5tA/T0381-1f5tA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0381 read from 1f5tA/T0381-1f5tA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1f5tA read from 1f5tA/T0381-1f5tA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1f5tA in template set T0381 16 :YVQSLARGLAVIRCFDHRNQRRTLSDVARATDLTRATARRFLLTLVELGYVATDG 1f5tA 1004 :LVDTTEMYLRTIYELEEEGVTPLRARIAERLEQSGPTVSQTVARMERDGLVVVAS T0381 71 :SAFWLTPRVLELGYSYLSSL 1f5tA 1060 :RSLQMTPTGRTLATAVMRKH T0381 98 :PHLEKLSHKV 1f5tA 1080 :RLAERLLTDI T0381 108 :H 1f5tA 1091 :G T0381 127 :VPVSR 1f5tA 1092 :LDINK T0381 150 :MGRVLLAGLPDDELDAYLEKL 1f5tA 1100 :EADRWEHVMSDEVERRLVKVL Number of specific fragments extracted= 6 number of extra gaps= 0 total=379 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 1f5tA/T0381-1f5tA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0381 read from 1f5tA/T0381-1f5tA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1f5tA read from 1f5tA/T0381-1f5tA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1f5tA in template set T0381 15 :DYVQSLARGLAVIRCFDHRNQRRTLSDVARATDLTRATARRFLLTLVELGYVATDG 1f5tA 1003 :DLVDTTEMYLRTIYELEEEGVTPLRARIAERLEQSGPTVSQTVARMERDGLVVVAS T0381 71 :SAFWLTPRVLELGYSYLSSL 1f5tA 1060 :RSLQMTPTGRTLATAVMRKH T0381 94 :EVAQPHLE 1f5tA 1080 :RLAERLLT T0381 106 :KV 1f5tA 1088 :DI T0381 139 :IGTR 1f5tA 1090 :IGLD T0381 154 :LLAGLPDDELDAYLEKL 1f5tA 1104 :WEHVMSDEVERRLVKVL Number of specific fragments extracted= 6 number of extra gaps= 0 total=385 Will force an alignment to be made, even if fragment is small Number of alignments=72 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1j75A/T0381-1j75A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1j75A expands to /projects/compbio/data/pdb/1j75.pdb.gz 1j75A:# T0381 read from 1j75A/T0381-1j75A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1j75A read from 1j75A/T0381-1j75A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1j75A to template set # found chain 1j75A in template set Warning: unaligning (T0381)T76 because last residue in template chain is (1j75A)G169 T0381 25 :AVIRCFDHRNQRRTLSDVARATDLTRATARRFLLTLVELGYVAT 1j75A 117 :KILQVLSDDGGPVKIGQLVKKCQVPKKTLNQVLYRLKKEDRVSS T0381 69 :DGSAFWL 1j75A 162 :EPATWSI Number of specific fragments extracted= 2 number of extra gaps= 0 total=387 Will force an alignment to be made, even if fragment is small Number of alignments=73 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1j75A/T0381-1j75A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0381 read from 1j75A/T0381-1j75A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1j75A read from 1j75A/T0381-1j75A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1j75A in template set Warning: unaligning (T0381)T76 because last residue in template chain is (1j75A)G169 T0381 25 :AVIRCFDHRNQRRTLSDVARATDLTRATARRFLLTLVELGYVAT 1j75A 117 :KILQVLSDDGGPVKIGQLVKKCQVPKKTLNQVLYRLKKEDRVSS T0381 69 :DGSAFWL 1j75A 162 :EPATWSI Number of specific fragments extracted= 2 number of extra gaps= 0 total=389 Will force an alignment to be made, even if fragment is small Number of alignments=74 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1j75A/T0381-1j75A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0381 read from 1j75A/T0381-1j75A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1j75A read from 1j75A/T0381-1j75A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1j75A in template set T0381 25 :AVIRCFDHRNQRRTLSDVARATDLTRATARRFLLTLVELGYVATDG 1j75A 117 :KILQVLSDDGGPVKIGQLVKKCQVPKKTLNQVLYRLKKEDRVSSPE T0381 71 :SAFWL 1j75A 164 :ATWSI Number of specific fragments extracted= 2 number of extra gaps= 0 total=391 Will force an alignment to be made, even if fragment is small Number of alignments=75 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1c0wA/T0381-1c0wA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1c0wA expands to /projects/compbio/data/pdb/1c0w.pdb.gz 1c0wA:# T0381 read from 1c0wA/T0381-1c0wA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1c0wA read from 1c0wA/T0381-1c0wA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1c0wA to template set # found chain 1c0wA in template set T0381 17 :VQSLARGLAVIRCFDHRNQRRTLSDVARATDLTRATARRFLLTLVELGYVATDG 1c0wA 5 :VDTTEMYLRTIYELEEEGVTPLRARIAERLEQSGPTVSQTVARMERDGLVVVAS T0381 71 :SAFWLTPRVLELGYSYLS 1c0wA 60 :RSLQMTPTGRTLATAVMR T0381 89 :SLSLP 1c0wA 89 :IIGLD T0381 96 :AQPHLEKLSHKVH 1c0wA 94 :INKVHDEACRWEH T0381 157 :GLPDDELDAYLEKL 1c0wA 107 :VMSDEVERRLVKVL T0381 171 :DIQRLT 1c0wA 122 :DVSRSP T0381 177 :ERTITARDEL 1c0wA 129 :GNPIPGLDEL Number of specific fragments extracted= 7 number of extra gaps= 0 total=398 Will force an alignment to be made, even if fragment is small Number of alignments=76 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1c0wA/T0381-1c0wA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0381 read from 1c0wA/T0381-1c0wA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1c0wA read from 1c0wA/T0381-1c0wA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1c0wA in template set T0381 18 :QSLARGLAVIRCFDHRNQRRTLSDVARATDLTRATARRFLLTLVELGYVATDG 1c0wA 6 :DTTEMYLRTIYELEEEGVTPLRARIAERLEQSGPTVSQTVARMERDGLVVVAS T0381 71 :SAFWLTPRVLELGYSYLSSLSLPEVAQ 1c0wA 60 :RSLQMTPTGRTLATAVMRKHRLAERLL T0381 98 :PHLEKLSHKV 1c0wA 96 :KVHDEACRWE T0381 156 :AGLPDDELDAYLEKLDIQRLT 1c0wA 106 :HVMSDEVERRLVKVLKDVSRS T0381 177 :ERTITARDEL 1c0wA 129 :GNPIPGLDEL Number of specific fragments extracted= 5 number of extra gaps= 0 total=403 Will force an alignment to be made, even if fragment is small Number of alignments=77 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1c0wA/T0381-1c0wA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0381 read from 1c0wA/T0381-1c0wA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1c0wA read from 1c0wA/T0381-1c0wA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1c0wA in template set T0381 17 :VQSLARGLAVIRCFDHRNQRRTLSDVARATDLTRATARRFLLTLVELGYVATDG 1c0wA 5 :VDTTEMYLRTIYELEEEGVTPLRARIAERLEQSGPTVSQTVARMERDGLVVVAS T0381 71 :SAFWLTPRVLELGYSYLSSLSLPEVAQ 1c0wA 60 :RSLQMTPTGRTLATAVMRKHRLAERLL T0381 98 :PHLEKLSHKV 1c0wA 96 :KVHDEACRWE T0381 156 :AGLPDDELDAYLEKLDIQRLT 1c0wA 106 :HVMSDEVERRLVKVLKDVSRS T0381 177 :ERTITARDEL 1c0wA 129 :GNPIPGLDEL Number of specific fragments extracted= 5 number of extra gaps= 0 total=408 Will force an alignment to be made, even if fragment is small Number of alignments=78 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2cfxA/T0381-2cfxA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2cfxA expands to /projects/compbio/data/pdb/2cfx.pdb.gz 2cfxA:# T0381 read from 2cfxA/T0381-2cfxA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2cfxA read from 2cfxA/T0381-2cfxA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2cfxA to template set # found chain 2cfxA in template set Warning: unaligning (T0381)R50 because of BadResidue code BAD_PEPTIDE in next template residue (2cfxA)P34 Warning: unaligning (T0381)A51 because of BadResidue code BAD_PEPTIDE at template residue (2cfxA)P34 Warning: unaligning (T0381)A125 because of BadResidue code BAD_PEPTIDE in next template residue (2cfxA)N108 Warning: unaligning (T0381)R126 because of BadResidue code BAD_PEPTIDE at template residue (2cfxA)N108 T0381 21 :ARGLAVIRCFDH 2cfxA 5 :QIDLNIIEELKK T0381 34 :NQRRTLSDVARATDLT 2cfxA 17 :DSRLSMRELGRKIKLS T0381 52 :TARRFLLTLVELGYVAT 2cfxA 35 :SVTERVRQLESFGIIKQ T0381 69 :D 2cfxA 57 :D T0381 71 :SA 2cfxA 62 :GL T0381 93 :PEVAQPHLEKLSHKVHESSSVSILDG 2cfxA 74 :KNADYERFKSYIQTLPNIEFCYRIAG T0381 119 :ADIVYV 2cfxA 101 :ACYMLK T0381 127 :VP 2cfxA 109 :AE T0381 159 :PDDELDAYLEKLD 2cfxA 111 :SLEAVEDFINKTS Number of specific fragments extracted= 9 number of extra gaps= 2 total=417 Will force an alignment to be made, even if fragment is small Number of alignments=79 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2cfxA/T0381-2cfxA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0381 read from 2cfxA/T0381-2cfxA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2cfxA read from 2cfxA/T0381-2cfxA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2cfxA in template set Warning: unaligning (T0381)R50 because of BadResidue code BAD_PEPTIDE in next template residue (2cfxA)P34 Warning: unaligning (T0381)A51 because of BadResidue code BAD_PEPTIDE at template residue (2cfxA)P34 Warning: unaligning (T0381)A125 because of BadResidue code BAD_PEPTIDE in next template residue (2cfxA)N108 Warning: unaligning (T0381)R126 because of BadResidue code BAD_PEPTIDE at template residue (2cfxA)N108 T0381 22 :RGLAVIRCFDH 2cfxA 6 :IDLNIIEELKK T0381 34 :NQRRTLSDVARATDLT 2cfxA 17 :DSRLSMRELGRKIKLS T0381 52 :TARRFLLTLVELGYVAT 2cfxA 35 :SVTERVRQLESFGIIKQ T0381 69 :D 2cfxA 57 :D T0381 71 :SAFW 2cfxA 62 :GLPV T0381 88 :S 2cfxA 74 :K T0381 94 :EVAQPHLEKLSHKVHESSSVSILDG 2cfxA 75 :NADYERFKSYIQTLPNIEFCYRIAG T0381 119 :ADIVYV 2cfxA 101 :ACYMLK T0381 127 :VP 2cfxA 109 :AE T0381 159 :PDDELDAYLEKLD 2cfxA 111 :SLEAVEDFINKTS Number of specific fragments extracted= 10 number of extra gaps= 2 total=427 Will force an alignment to be made, even if fragment is small Number of alignments=80 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2cfxA/T0381-2cfxA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0381 read from 2cfxA/T0381-2cfxA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2cfxA read from 2cfxA/T0381-2cfxA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2cfxA in template set Warning: unaligning (T0381)R50 because of BadResidue code BAD_PEPTIDE in next template residue (2cfxA)P34 Warning: unaligning (T0381)A51 because of BadResidue code BAD_PEPTIDE at template residue (2cfxA)P34 Warning: unaligning (T0381)G70 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2cfxA)L54 Warning: unaligning (T0381)A125 because of BadResidue code BAD_PEPTIDE in next template residue (2cfxA)N108 Warning: unaligning (T0381)R126 because of BadResidue code BAD_PEPTIDE at template residue (2cfxA)N108 T0381 23 :GLAVIRCFDH 2cfxA 7 :DLNIIEELKK T0381 34 :NQRRTLSDVARATDLT 2cfxA 17 :DSRLSMRELGRKIKLS T0381 52 :TARRFLLTLVELGYVATD 2cfxA 35 :SVTERVRQLESFGIIKQY T0381 71 :SA 2cfxA 62 :GL T0381 97 :QPHLEKLSHKVHESSSVSILDG 2cfxA 78 :YERFKSYIQTLPNIEFCYRIAG T0381 119 :ADIVYV 2cfxA 101 :ACYMLK T0381 127 :VP 2cfxA 109 :AE T0381 159 :PDDELDAYLEKLD 2cfxA 111 :SLEAVEDFINKTS Number of specific fragments extracted= 8 number of extra gaps= 3 total=435 Will force an alignment to be made, even if fragment is small Number of alignments=81 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1qgpA/T0381-1qgpA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1qgpA expands to /projects/compbio/data/pdb/1qgp.pdb.gz 1qgpA:# T0381 read from 1qgpA/T0381-1qgpA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1qgpA read from 1qgpA/T0381-1qgpA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1qgpA to template set # found chain 1qgpA in template set T0381 13 :SPDYVQ 1qgpA 132 :ELSIYQ T0381 19 :SLARGLAVIRCF 1qgpA 139 :QEQRILKFLEEL T0381 32 :HRNQRRTLSDVARATDLTRATARRFLLTLVELGYVATDG 1qgpA 151 :GEGKATTAHDLSGKLGTPKKEINRVLYSLAKKGKLQKEA T0381 71 :SAFWL 1qgpA 193 :PLWKI Number of specific fragments extracted= 4 number of extra gaps= 0 total=439 Will force an alignment to be made, even if fragment is small Number of alignments=82 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1qgpA/T0381-1qgpA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0381 read from 1qgpA/T0381-1qgpA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1qgpA read from 1qgpA/T0381-1qgpA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1qgpA in template set T0381 12 :PSPDYVQSLAR 1qgpA 131 :QELSIYQDQEQ T0381 25 :AVIRCFDHRNQRR 1qgpA 142 :RILKFLEELGEGK T0381 38 :TLSDVARATDLTRATARRFLLTLVELGYVATDGSAF 1qgpA 157 :TAHDLSGKLGTPKKEINRVLYSLAKKGKLQKEAGTP Number of specific fragments extracted= 3 number of extra gaps= 0 total=442 Will force an alignment to be made, even if fragment is small Number of alignments=83 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1qgpA/T0381-1qgpA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0381 read from 1qgpA/T0381-1qgpA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1qgpA read from 1qgpA/T0381-1qgpA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1qgpA in template set T0381 8 :EKILPSPDYVQ 1qgpA 127 :SSHFQELSIYQ T0381 19 :SLARGLAVIRCFDH 1qgpA 139 :QEQRILKFLEELGE T0381 34 :NQRRTLSDVARATDLTRATARRFLLTLVELGYVATDGSA 1qgpA 153 :GKATTAHDLSGKLGTPKKEINRVLYSLAKKGKLQKEAGT Number of specific fragments extracted= 3 number of extra gaps= 0 total=445 Will force an alignment to be made, even if fragment is small Number of alignments=84 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1lvaA/T0381-1lvaA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1lvaA expands to /projects/compbio/data/pdb/1lva.pdb.gz 1lvaA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0381 read from 1lvaA/T0381-1lvaA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1lvaA read from 1lvaA/T0381-1lvaA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1lvaA to template set # found chain 1lvaA in template set T0381 21 :ARGLA 1lvaA 381 :KILAQ T0381 29 :CFDHRNQRRTLSDVARATDLTRATARRFLLTLVELGYVAT 1lvaA 386 :IIQEHREGLDWQEAATRASLSLEETRKLLQSMAAAGQVTL T0381 69 :DGSAFWLTPRVLELGYSY 1lvaA 429 :ENDLYAISTERYQAWWQA T0381 96 :AQPHLEKLSHKVHESSSV 1lvaA 447 :VTRALEEFHSRYPLRPGL T0381 114 :SILDGADI 1lvaA 495 :LQLAANTV T0381 137 :ITIGTRLP 1lvaA 503 :ALAGFTPS T0381 158 :LPDDE 1lvaA 511 :FSETQ T0381 163 :LDAYLEKL 1lvaA 519 :LKDLEDKY T0381 171 :DIQRLTERTITARDELKAAILAVRADGICVL 1lvaA 535 :SFKEVAGSFNLDPSELEELLHYLVREGVLVK T0381 219 :ASGL 1lvaA 566 :INDE T0381 234 :ARYSLEDL 1lvaA 570 :FYWHRQAL T0381 243 :SDLIPSLRVTAT 1lvaA 578 :GEAREVIKNLAS T0381 255 :DIEQDLA 1lvaA 597 :EARDALG Number of specific fragments extracted= 13 number of extra gaps= 0 total=458 Will force an alignment to be made, even if fragment is small Number of alignments=85 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1lvaA/T0381-1lvaA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0381 read from 1lvaA/T0381-1lvaA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1lvaA read from 1lvaA/T0381-1lvaA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1lvaA in template set T0381 21 :ARGL 1lvaA 381 :KILA T0381 28 :RCFDHRNQRRTLSDVARATDLTRATARRFLLTLVELGYVAT 1lvaA 385 :QIIQEHREGLDWQEAATRASLSLEETRKLLQSMAAAGQVTL T0381 69 :DGSAFWLTPRVLELGYSYLSS 1lvaA 429 :ENDLYAISTERYQAWWQAVTR T0381 90 :LSLPEVAQPHL 1lvaA 475 :SRLPARVYQAL T0381 101 :EKLSHK 1lvaA 487 :EEWSRE T0381 108 :HE 1lvaA 493 :GR T0381 114 :SILDGADI 1lvaA 495 :LQLAANTV T0381 137 :ITIGTRLP 1lvaA 503 :ALAGFTPS T0381 158 :LPDDE 1lvaA 511 :FSETQ T0381 163 :LDAYLEKLDI 1lvaA 522 :LEDKYRVSRW T0381 173 :QRLTERTITARDELKAAILAVRADGICVL 1lvaA 537 :KEVAGSFNLDPSELEELLHYLVREGVLVK T0381 202 :DQE 1lvaA 567 :NDE T0381 234 :ARYSLEDL 1lvaA 570 :FYWHRQAL T0381 243 :SDLIPSLRVTAT 1lvaA 578 :GEAREVIKNLAS T0381 255 :DIEQDLA 1lvaA 597 :EARDALG Number of specific fragments extracted= 15 number of extra gaps= 0 total=473 Will force an alignment to be made, even if fragment is small Number of alignments=86 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1lvaA/T0381-1lvaA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0381 read from 1lvaA/T0381-1lvaA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1lvaA read from 1lvaA/T0381-1lvaA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1lvaA in template set T0381 25 :AVIRCFDHRNQRRTLSDVARATDLTRATARRFLLTLVELGYVATDG 1lvaA 382 :ILAQIIQEHREGLDWQEAATRASLSLEETRKLLQSMAAAGQVTLLR T0381 71 :SAFWLTPRVLE 1lvaA 431 :DLYAISTERYQ T0381 91 :SLPEVAQPHLEKLSHKVHE 1lvaA 442 :AWWQAVTRALEEFHSRYPL T0381 130 :SRIMT 1lvaA 461 :RPGLA T0381 160 :DDELDAYLEKLD 1lvaA 467 :EELRSRYFSRLP T0381 184 :DELKAA 1lvaA 479 :ARVYQA T0381 190 :ILAVRADGICVLDQE 1lvaA 486 :LEEWSREGRLQLAAN T0381 226 :AVNISTPAARYSLED 1lvaA 501 :TVALAGFTPSFSETQ T0381 246 :IPSLRVTATDIEQDLATV 1lvaA 516 :KKLLKDLEDKYRVSRWQP Number of specific fragments extracted= 9 number of extra gaps= 0 total=482 Will force an alignment to be made, even if fragment is small Number of alignments=87 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1smtB/T0381-1smtB-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1smtB expands to /projects/compbio/data/pdb/1smt.pdb.gz 1smtB:# T0381 read from 1smtB/T0381-1smtB-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1smtB read from 1smtB/T0381-1smtB-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1smtB to template set # found chain 1smtB in template set Warning: unaligning (T0381)E5 because first residue in template chain is (1smtB)A20 T0381 6 :PTEKILP 1smtB 21 :IASELQA T0381 13 :SPDYVQSLA 1smtB 29 :APEVAQSLA T0381 22 :RGLAVIRCF 1smtB 47 :NRLRLLSLL T0381 33 :RNQRRTLSDVARATDLTRATARRFLLTLVELGYVAT 1smtB 56 :ARSELCVGDLAQAIGVSESAVSHQLRSLRNLRLVSY T0381 69 :DGSA 1smtB 94 :QGRH T0381 73 :FWLT 1smtB 100 :YQLQ T0381 89 :SLSLPEVAQPHLEK 1smtB 104 :DHHIVALYQNALDH Number of specific fragments extracted= 7 number of extra gaps= 0 total=489 Will force an alignment to be made, even if fragment is small Number of alignments=88 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1smtB/T0381-1smtB-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0381 read from 1smtB/T0381-1smtB-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1smtB read from 1smtB/T0381-1smtB-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1smtB in template set Warning: unaligning (T0381)E5 because first residue in template chain is (1smtB)A20 T0381 6 :PTEKILP 1smtB 21 :IASELQA T0381 13 :SPDYVQSLA 1smtB 29 :APEVAQSLA T0381 22 :RGLAVIRCFDH 1smtB 47 :NRLRLLSLLAR T0381 35 :QRRTLSDVARATDLTRATARRFLLTLVELGYVAT 1smtB 58 :SELCVGDLAQAIGVSESAVSHQLRSLRNLRLVSY T0381 69 :DGSA 1smtB 94 :QGRH T0381 73 :FWLT 1smtB 100 :YQLQ T0381 77 :P 1smtB 105 :H T0381 91 :SLPEVAQPHLEK 1smtB 106 :HIVALYQNALDH Number of specific fragments extracted= 8 number of extra gaps= 0 total=497 Will force an alignment to be made, even if fragment is small Number of alignments=89 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1smtB/T0381-1smtB-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0381 read from 1smtB/T0381-1smtB-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1smtB read from 1smtB/T0381-1smtB-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1smtB in template set T0381 22 :RGLAVIRCFD 1smtB 47 :NRLRLLSLLA T0381 34 :NQRRTLSDVARATDLTRATARRFLLTLVELGYVATDG 1smtB 57 :RSELCVGDLAQAIGVSESAVSHQLRSLRNLRLVSYRK T0381 71 :S 1smtB 95 :G T0381 72 :AFWLT 1smtB 99 :YYQLQ T0381 89 :SLSLPEVAQPHLEK 1smtB 104 :DHHIVALYQNALDH Number of specific fragments extracted= 5 number of extra gaps= 0 total=502 Will force an alignment to be made, even if fragment is small Number of alignments=90 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1r1uA/T0381-1r1uA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1r1uA expands to /projects/compbio/data/pdb/1r1u.pdb.gz 1r1uA:# T0381 read from 1r1uA/T0381-1r1uA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1r1uA read from 1r1uA/T0381-1r1uA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1r1uA to template set # found chain 1r1uA in template set Warning: unaligning (T0381)H108 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1r1uA)H100 T0381 21 :ARGLAVIRCFDH 1r1uA 26 :YNRIRIMELLSV T0381 35 :QRRTLSDVARATDLTRATARRFLLTLVELGYVAT 1r1uA 38 :SEASVGHISHQLNLSQSNVSHQLKLLKSVHLVKA T0381 69 :DGS 1r1uA 74 :QGQ T0381 72 :AFWLT 1r1uA 79 :IYSLD T0381 94 :EVAQPHLEKLSHKV 1r1uA 85 :IHVATMLKQAIHHA Number of specific fragments extracted= 5 number of extra gaps= 1 total=507 Will force an alignment to be made, even if fragment is small Number of alignments=91 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1r1uA/T0381-1r1uA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0381 read from 1r1uA/T0381-1r1uA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1r1uA read from 1r1uA/T0381-1r1uA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1r1uA in template set T0381 21 :ARGLAVIRCFDH 1r1uA 26 :YNRIRIMELLSV T0381 35 :QRRTLSDVARATDLTRATARRFLLTLVELGYVAT 1r1uA 38 :SEASVGHISHQLNLSQSNVSHQLKLLKSVHLVKA T0381 69 :DG 1r1uA 74 :QG T0381 71 :SAFWLT 1r1uA 78 :MIYSLD T0381 77 :PRV 1r1uA 85 :IHV T0381 97 :QPHLEKLSHK 1r1uA 88 :ATMLKQAIHH Number of specific fragments extracted= 6 number of extra gaps= 0 total=513 Will force an alignment to be made, even if fragment is small Number of alignments=92 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1r1uA/T0381-1r1uA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0381 read from 1r1uA/T0381-1r1uA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1r1uA read from 1r1uA/T0381-1r1uA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1r1uA in template set T0381 22 :RGLAVIRCFDH 1r1uA 27 :NRIRIMELLSV T0381 35 :QRRTLSDVARATDLTRATARRFLLTLVELGYVATDG 1r1uA 38 :SEASVGHISHQLNLSQSNVSHQLKLLKSVHLVKAKR T0381 71 :S 1r1uA 75 :G T0381 72 :AFWLT 1r1uA 79 :IYSLD T0381 89 :SLSLPEVAQPHLEK 1r1uA 84 :DIHVATMLKQAIHH Number of specific fragments extracted= 5 number of extra gaps= 0 total=518 Will force an alignment to be made, even if fragment is small Number of alignments=93 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1s3jA/T0381-1s3jA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1s3jA expands to /projects/compbio/data/pdb/1s3j.pdb.gz 1s3jA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 993, because occupancy 0.400 <= existing 0.600 in 1s3jA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 995, because occupancy 0.400 <= existing 0.600 in 1s3jA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 997, because occupancy 0.350 <= existing 0.530 in 1s3jA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 999, because occupancy 0.400 <= existing 0.600 in 1s3jA # T0381 read from 1s3jA/T0381-1s3jA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1s3jA read from 1s3jA/T0381-1s3jA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1s3jA to template set # found chain 1s3jA in template set T0381 21 :ARGLAVIRCFDHR 1s3jA 37 :PAQLFVLASLKKH T0381 35 :QRRTLSDVARATDLTRATARRFLLTLVELGYVAT 1s3jA 50 :GSLKVSEIAERMEVKPSAVTLMADRLEQKNLIAR T0381 70 :G 1s3jA 87 :T T0381 71 :S 1s3jA 91 :R T0381 73 :FWLTPRVLELGYSY 1s3jA 95 :LSLTDEGDIKFEEV T0381 93 :PEVAQPHLEKLSH 1s3jA 109 :LAGRKAIMARYLS T0381 157 :GLPDDELDAYLEK 1s3jA 122 :FLTEEEMLQAAHI Number of specific fragments extracted= 7 number of extra gaps= 0 total=525 Will force an alignment to be made, even if fragment is small Number of alignments=94 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1s3jA/T0381-1s3jA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0381 read from 1s3jA/T0381-1s3jA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1s3jA read from 1s3jA/T0381-1s3jA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1s3jA in template set T0381 16 :YVQSLAR 1s3jA 26 :MLESMEK T0381 23 :GLAVIRCFDHR 1s3jA 39 :QLFVLASLKKH T0381 35 :QRRTLSDVARATDLTRATARRFLLTLVELGYVAT 1s3jA 50 :GSLKVSEIAERMEVKPSAVTLMADRLEQKNLIAR T0381 70 :G 1s3jA 87 :T T0381 71 :SA 1s3jA 90 :RR T0381 73 :FWLTPRVLELGYSYL 1s3jA 95 :LSLTDEGDIKFEEVL T0381 94 :EVAQPHLEKLSH 1s3jA 110 :AGRKAIMARYLS T0381 157 :GLPDDELDAYLEK 1s3jA 122 :FLTEEEMLQAAHI Number of specific fragments extracted= 8 number of extra gaps= 0 total=533 Will force an alignment to be made, even if fragment is small Number of alignments=95 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1s3jA/T0381-1s3jA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0381 read from 1s3jA/T0381-1s3jA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1s3jA read from 1s3jA/T0381-1s3jA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1s3jA in template set T0381 22 :RGLAVIRCFDHRNQ 1s3jA 38 :AQLFVLASLKKHGS T0381 37 :RTLSDVARATDLTRATARRFLLTLVELGYVATDG 1s3jA 52 :LKVSEIAERMEVKPSAVTLMADRLEQKNLIARTH T0381 128 :PVSRIMTVGIT 1s3jA 88 :KDRRVIDLSLT T0381 161 :DELDAYLEKL 1s3jA 99 :DEGDIKFEEV T0381 187 :KAAILAVRADG 1s3jA 109 :LAGRKAIMARY T0381 233 :AARYSLEDLHSDLIPSLRVTATDI 1s3jA 120 :LSFLTEEEMLQAAHITAKLAQAAE Number of specific fragments extracted= 6 number of extra gaps= 0 total=539 Will force an alignment to be made, even if fragment is small Number of alignments=96 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2fxaA/T0381-2fxaA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2fxaA expands to /projects/compbio/data/pdb/2fxa.pdb.gz 2fxaA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 461, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 463, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 465, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 467, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 469, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 471, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 473, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 475, because occupancy 0.500 <= existing 0.500 in 2fxaA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 567, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 569, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 571, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 573, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 575, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 577, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 579, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 581, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 583, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 585, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 683, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 685, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 687, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 689, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 691, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 693, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 695, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 697, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 699, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 701, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 703, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 705, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 707, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 709, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 711, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 713, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 715, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 717, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 719, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 721, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 747, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 749, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 751, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 753, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 755, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 757, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 759, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 761, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 763, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 765, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 767, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 833, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 837, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 839, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 841, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 843, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 845, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 918, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 920, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 922, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 924, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 926, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 928, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 930, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 932, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 934, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 936, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 938, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 940, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 942, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 944, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 1117, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 1121, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 1123, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 1125, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 1127, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 1129, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 1131, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 1183, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 1185, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 1187, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 1189, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 1191, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 1193, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 1195, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 1197, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 1199, because occupancy 0.500 <= existing 0.500 in 2fxaA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 1272, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 1276, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 1278, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 1280, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 1282, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 1284, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 1286, because occupancy 0.500 <= existing 0.500 in 2fxaA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0381 read from 2fxaA/T0381-2fxaA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2fxaA read from 2fxaA/T0381-2fxaA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2fxaA to template set # found chain 2fxaA in template set Warning: unaligning (T0381)S71 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2fxaA)T102 T0381 21 :ARGLAVIRCFDHRNQ 2fxaA 46 :INEHHILWIAYQLNG T0381 37 :RTLSDVARATDLTRATARRFLLTLVELGYVATDG 2fxaA 61 :ASISEIAKFGVMHVSTAFNFSKKLEERGYLRFSK T0381 72 :AFWLTPRVLELGYSYLSSLSLPE 2fxaA 103 :YVQLTEEGTEVFWSLLEEFDPTR T0381 95 :VAQPHLEK 2fxaA 131 :GSQPLYHL Number of specific fragments extracted= 4 number of extra gaps= 0 total=543 Will force an alignment to be made, even if fragment is small Number of alignments=97 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2fxaA/T0381-2fxaA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0381 read from 2fxaA/T0381-2fxaA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2fxaA read from 2fxaA/T0381-2fxaA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2fxaA in template set Warning: unaligning (T0381)S71 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2fxaA)T102 T0381 21 :ARGLAVIRCFDHRNQ 2fxaA 46 :INEHHILWIAYQLNG T0381 37 :RTLSDVARATDLTRATARRFLLTLVELGYVATDG 2fxaA 61 :ASISEIAKFGVMHVSTAFNFSKKLEERGYLRFSK T0381 72 :AFWLTPRVLELGYSYLSSLS 2fxaA 103 :YVQLTEEGTEVFWSLLEEFD T0381 92 :LPEVAQPHLEK 2fxaA 128 :VFKGSQPLYHL Number of specific fragments extracted= 4 number of extra gaps= 0 total=547 Will force an alignment to be made, even if fragment is small Number of alignments=98 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2fxaA/T0381-2fxaA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0381 read from 2fxaA/T0381-2fxaA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2fxaA read from 2fxaA/T0381-2fxaA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2fxaA in template set Warning: unaligning (T0381)S71 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2fxaA)T102 T0381 21 :ARGLAVIRCFDHRNQ 2fxaA 46 :INEHHILWIAYQLNG T0381 37 :RTLSDVARATDLTRATARRFLLTLVELGYVATDG 2fxaA 61 :ASISEIAKFGVMHVSTAFNFSKKLEERGYLRFSK T0381 72 :AFWLTPRVLELGYSYLSSLSLPE 2fxaA 103 :YVQLTEEGTEVFWSLLEEFDPTR Number of specific fragments extracted= 3 number of extra gaps= 0 total=550 Will force an alignment to be made, even if fragment is small Number of alignments=99 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1jgsA/T0381-1jgsA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1jgsA expands to /projects/compbio/data/pdb/1jgs.pdb.gz 1jgsA:# T0381 read from 1jgsA/T0381-1jgsA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1jgsA read from 1jgsA/T0381-1jgsA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1jgsA to template set # found chain 1jgsA in template set T0381 22 :RGLAVIRCFDHR 1jgsA 41 :AQFKVLCSIRCA T0381 35 :QRRTLSDVARATDLTRATARRFLLTLVELGYVAT 1jgsA 53 :ACITPVELKKVLSVDLGALTRMLDRLVCKGWVER T0381 69 :DG 1jgsA 89 :NP T0381 71 :S 1jgsA 94 :R T0381 72 :AFWLTPRVLELGYSY 1jgsA 97 :LVKLTTGGAAICEQC T0381 93 :PEVAQPHLEKLS 1jgsA 112 :HQLVGQDLHQEL T0381 175 :LTERTITARDELKA 1jgsA 124 :TKNLTADEVATLEY Number of specific fragments extracted= 7 number of extra gaps= 0 total=557 Will force an alignment to be made, even if fragment is small Number of alignments=100 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1jgsA/T0381-1jgsA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0381 read from 1jgsA/T0381-1jgsA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1jgsA read from 1jgsA/T0381-1jgsA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1jgsA in template set T0381 21 :ARGLAVIRCFDHR 1jgsA 40 :AAQFKVLCSIRCA T0381 35 :QRRTLSDVARATDLTRATARRFLLTLVELGYVAT 1jgsA 53 :ACITPVELKKVLSVDLGALTRMLDRLVCKGWVER T0381 69 :DG 1jgsA 89 :NP T0381 72 :A 1jgsA 94 :R T0381 73 :FWLTPRVLELGYSYL 1jgsA 98 :VKLTTGGAAICEQCH T0381 94 :EVAQPHLEKLS 1jgsA 113 :QLVGQDLHQEL Number of specific fragments extracted= 6 number of extra gaps= 0 total=563 Will force an alignment to be made, even if fragment is small Number of alignments=101 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1jgsA/T0381-1jgsA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0381 read from 1jgsA/T0381-1jgsA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1jgsA read from 1jgsA/T0381-1jgsA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1jgsA in template set T0381 22 :RGLAVIRCFDHRNQ 1jgsA 41 :AQFKVLCSIRCAAC T0381 37 :RTLSDVARATDLTRATARRFLLTLVELGYVATDG 1jgsA 55 :ITPVELKKVLSVDLGALTRMLDRLVCKGWVERLP T0381 72 :AFWLTPRVLELGYSY 1jgsA 97 :LVKLTTGGAAICEQC T0381 93 :PEVAQPHLEK 1jgsA 112 :HQLVGQDLHQ Number of specific fragments extracted= 4 number of extra gaps= 0 total=567 Will force an alignment to be made, even if fragment is small Number of alignments=102 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ft9A/T0381-1ft9A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1ft9A expands to /projects/compbio/data/pdb/1ft9.pdb.gz 1ft9A:# T0381 read from 1ft9A/T0381-1ft9A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ft9A read from 1ft9A/T0381-1ft9A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1ft9A to template set # found chain 1ft9A in template set T0381 20 :LARGLAVIRCFDHR 1ft9A 133 :HDIKQRIAGFFIDH T0381 35 :Q 1ft9A 152 :R T0381 37 :RTLSDVARATDLTRATARRFLLTLVELGYVATDG 1ft9A 164 :FTVEEIANLIGSSRQTTSTALNSLIKEGYISRQG T0381 71 :SAFWLT 1ft9A 199 :GHYTIP Number of specific fragments extracted= 4 number of extra gaps= 0 total=571 Will force an alignment to be made, even if fragment is small Number of alignments=103 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ft9A/T0381-1ft9A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0381 read from 1ft9A/T0381-1ft9A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ft9A read from 1ft9A/T0381-1ft9A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1ft9A in template set T0381 20 :LARGLAVIRCFDHR 1ft9A 133 :HDIKQRIAGFFIDH T0381 35 :QR 1ft9A 152 :RQ T0381 37 :RTLSDVARATDLTRATARRFLLTLVELGYVATDG 1ft9A 164 :FTVEEIANLIGSSRQTTSTALNSLIKEGYISRQG T0381 71 :SAFWLT 1ft9A 199 :GHYTIP T0381 77 :PR 1ft9A 207 :VR Number of specific fragments extracted= 5 number of extra gaps= 0 total=576 Will force an alignment to be made, even if fragment is small Number of alignments=104 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ft9A/T0381-1ft9A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0381 read from 1ft9A/T0381-1ft9A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ft9A read from 1ft9A/T0381-1ft9A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1ft9A in template set T0381 21 :ARGLAVIRCFDH 1ft9A 134 :DIKQRIAGFFID T0381 34 :NQ 1ft9A 151 :GR T0381 37 :RTLSDVARATDLTRATARRFLLTLVELGYVATDG 1ft9A 164 :FTVEEIANLIGSSRQTTSTALNSLIKEGYISRQG T0381 71 :SAFWLT 1ft9A 199 :GHYTIP Number of specific fragments extracted= 4 number of extra gaps= 0 total=580 Will force an alignment to be made, even if fragment is small Number of alignments=105 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1lj9A/T0381-1lj9A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1lj9A expands to /projects/compbio/data/pdb/1lj9.pdb.gz 1lj9A:# T0381 read from 1lj9A/T0381-1lj9A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1lj9A read from 1lj9A/T0381-1lj9A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1lj9A to template set # found chain 1lj9A in template set T0381 8 :EKILPSPDYVQSLARGLA 1lj9A 24 :KELSLTRGQYLYLVRVCE T0381 34 :NQRRTLSDVARATDLTRATARRFLLTLVELGYVAT 1lj9A 42 :NPGIIQEKIAELIKVDRTTAARAIKRLEEQGFIYR T0381 69 :DG 1lj9A 79 :DA T0381 71 :SAFWLTPRVLELG 1lj9A 86 :KRIYATEKGKNVY T0381 94 :EVAQPHLEKLSHKVH 1lj9A 99 :PIIVRENQHSNQVAL T0381 156 :AGLPDDELDAYLEK 1lj9A 114 :QGLSEVEISQLADY T0381 183 :R 1lj9A 128 :L T0381 187 :KAAILAVR 1lj9A 129 :VRMRKNVS Number of specific fragments extracted= 8 number of extra gaps= 0 total=588 Will force an alignment to be made, even if fragment is small Number of alignments=106 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1lj9A/T0381-1lj9A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0381 read from 1lj9A/T0381-1lj9A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1lj9A read from 1lj9A/T0381-1lj9A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1lj9A in template set T0381 8 :EKILPSPDYVQSLARGL 1lj9A 24 :KELSLTRGQYLYLVRVC T0381 32 :HR 1lj9A 41 :EN T0381 35 :QRRTLSDVARATDLTRATARRFLLTLVELGYVAT 1lj9A 43 :PGIIQEKIAELIKVDRTTAARAIKRLEEQGFIYR T0381 69 :DG 1lj9A 79 :DA T0381 71 :SAFWLTPRVLEL 1lj9A 86 :KRIYATEKGKNV T0381 93 :PEVAQPHLEKLSHK 1lj9A 98 :YPIIVRENQHSNQV T0381 154 :LLAGLPDDELDAYLEKL 1lj9A 112 :ALQGLSEVEISQLADYL T0381 187 :KAAIL 1lj9A 129 :VRMRK Number of specific fragments extracted= 8 number of extra gaps= 0 total=596 Will force an alignment to be made, even if fragment is small Number of alignments=107 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1lj9A/T0381-1lj9A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0381 read from 1lj9A/T0381-1lj9A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1lj9A read from 1lj9A/T0381-1lj9A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1lj9A in template set T0381 9 :KILPSPDYVQSLARGLA 1lj9A 25 :ELSLTRGQYLYLVRVCE T0381 34 :NQRRTLSDVARATDLTRATARRFLLTLVELGYVATDG 1lj9A 42 :NPGIIQEKIAELIKVDRTTAARAIKRLEEQGFIYRQE T0381 128 :PVSRIMTVGIT 1lj9A 81 :SNKKIKRIYAT T0381 161 :DELDAYLE 1lj9A 92 :EKGKNVYP T0381 185 :ELKAAILAVRADG 1lj9A 100 :IIVRENQHSNQVA T0381 219 :ASG 1lj9A 113 :LQG T0381 236 :YSLEDLHSDLIPSLRVTATDIEQDLATV 1lj9A 116 :LSEVEISQLADYLVRMRKNVSEDWEFVK Number of specific fragments extracted= 7 number of extra gaps= 0 total=603 Will force an alignment to be made, even if fragment is small Number of alignments=108 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1qzzA/T0381-1qzzA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1qzzA expands to /projects/compbio/data/pdb/1qzz.pdb.gz 1qzzA:# T0381 read from 1qzzA/T0381-1qzzA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1qzzA read from 1qzzA/T0381-1qzzA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1qzzA to template set # found chain 1qzzA in template set Warning: unaligning (T0381)G70 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1qzzA)G86 T0381 10 :ILPSPDYVQSLARGLA 1qzzA 23 :NLGNLVTPMALRVAAT T0381 26 :VIRCFDH 1qzzA 41 :LVDHLLA T0381 35 :QRRTLSDVARATDLTRATARRFLLTLVELGYVAT 1qzzA 48 :GADTLAGLADRTDTHPQALSRLVRHLTVVGVLEG T0381 69 :D 1qzzA 83 :E T0381 71 :SAFWLTP 1qzzA 87 :RPLRPTR T0381 79 :VLELGYSYLSS 1qzzA 115 :AVSHADLAFTG T0381 90 :LSLPEV 1qzzA 127 :LDVVRT T0381 96 :AQPHL 1qzzA 145 :FWEDL T0381 101 :EKLSHKV 1qzzA 153 :VALADSF T0381 117 :DGA 1qzzA 167 :EDL T0381 164 :DAYLEKLDIQRL 1qzzA 172 :EAPADAYDWSAV T0381 176 :TERT 1qzzA 204 :APHL T0381 183 :RDELKAAILAVRA 1qzzA 214 :LAGPAERARRRFA T0381 196 :DGICVLDQELEAGL 1qzzA 232 :DRVTVAEGDFFKPL T0381 226 :AVNISTPAARYSLEDL 1qzzA 251 :VVLLSFVLLNWSDEDA T0381 246 :IPSLRVTAT 1qzzA 267 :LTILRGCVR Number of specific fragments extracted= 16 number of extra gaps= 0 total=619 Will force an alignment to be made, even if fragment is small Number of alignments=109 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1qzzA/T0381-1qzzA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0381 read from 1qzzA/T0381-1qzzA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1qzzA read from 1qzzA/T0381-1qzzA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1qzzA in template set Warning: unaligning (T0381)G70 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1qzzA)G86 T0381 10 :ILPSPDYVQSLARGLA 1qzzA 23 :NLGNLVTPMALRVAAT T0381 26 :VIRCFDH 1qzzA 41 :LVDHLLA T0381 35 :QRRTLSDVARATDLTRATARRFLLTLVELGYVAT 1qzzA 48 :GADTLAGLADRTDTHPQALSRLVRHLTVVGVLEG T0381 69 :D 1qzzA 83 :E T0381 71 :SAFWLTP 1qzzA 87 :RPLRPTR T0381 79 :VLELGYSYLSS 1qzzA 115 :AVSHADLAFTG T0381 90 :LSLPE 1qzzA 127 :LDVVR T0381 96 :AQPHL 1qzzA 145 :FWEDL T0381 101 :EKLSHKV 1qzzA 153 :VALADSF T0381 118 :GA 1qzzA 168 :DL T0381 127 :VPVSRIMTVGITIG 1qzzA 178 :YDWSAVRHVLDVGG T0381 146 :YATSMGRVLLAGLPD 1qzzA 192 :GNGGMLAAIALRAPH T0381 161 :DELDAYLEKLDIQ 1qzzA 219 :ERARRRFADAGLA T0381 196 :DGICVLDQELEAGL 1qzzA 232 :DRVTVAEGDFFKPL T0381 227 :VNISTPAARYSLEDL 1qzzA 252 :VLLSFVLLNWSDEDA T0381 246 :IPSLRVTAT 1qzzA 267 :LTILRGCVR Number of specific fragments extracted= 16 number of extra gaps= 0 total=635 Will force an alignment to be made, even if fragment is small Number of alignments=110 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1qzzA/T0381-1qzzA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0381 read from 1qzzA/T0381-1qzzA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1qzzA read from 1qzzA/T0381-1qzzA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1qzzA in template set T0381 10 :ILPSPDYVQSLARGLA 1qzzA 23 :NLGNLVTPMALRVAAT T0381 26 :VIRCFDH 1qzzA 41 :LVDHLLA T0381 35 :QRRTLSDVARATDLTRATARRFLLTLVELGYVATDG 1qzzA 48 :GADTLAGLADRTDTHPQALSRLVRHLTVVGVLEGGE Number of specific fragments extracted= 3 number of extra gaps= 0 total=638 Will force an alignment to be made, even if fragment is small Number of alignments=111 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1bi0/T0381-1bi0-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1bi0 expands to /projects/compbio/data/pdb/1bi0.pdb.gz 1bi0:Warning: there is no chain 1bi0 will retry with 1bi0A # T0381 read from 1bi0/T0381-1bi0-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1bi0 read from 1bi0/T0381-1bi0-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1bi0 to template set # found chain 1bi0 in template set Warning: unaligning (T0381)L100 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1bi0)R103 Warning: unaligning (T0381)K102 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1bi0)R103 T0381 17 :VQSLARGLAVIRCFDHRNQRRTLSDVARATDLTRATARRFLLTLVELGYVATDG 1bi0 5 :VDTTEMYLRTIYELEEEGVTPLRARIAERLEQSGPTVSQTVARMERDGLVVVAS T0381 71 :SAFWLTPRVLELGYSYLS 1bi0 60 :RSLQMTPTGRTLATAVMR T0381 90 :LSL 1bi0 90 :IGL T0381 93 :PEVAQPH 1bi0 94 :INKVHDE T0381 103 :L 1bi0 104 :W T0381 107 :V 1bi0 105 :E T0381 156 :AGLPDDELDAYLEKL 1bi0 106 :HVMSDEVERRLVKVL T0381 171 :DIQRLT 1bi0 122 :DVSRSP T0381 177 :ERTITARDEL 1bi0 129 :GNPIPGLDEL Number of specific fragments extracted= 9 number of extra gaps= 0 total=647 Will force an alignment to be made, even if fragment is small Number of alignments=112 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1bi0/T0381-1bi0-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0381 read from 1bi0/T0381-1bi0-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1bi0 read from 1bi0/T0381-1bi0-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1bi0 in template set Warning: unaligning (T0381)L103 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1bi0)R103 Warning: unaligning (T0381)H105 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1bi0)R103 T0381 19 :SLARGLAVIRCFDHRNQRRTLSDVARATDLTRATARRFLLTLVELGYVATDG 1bi0 7 :TTEMYLRTIYELEEEGVTPLRARIAERLEQSGPTVSQTVARMERDGLVVVAS T0381 71 :SAFWLTPRVLELGYSYLSSLSLPEVAQ 1bi0 60 :RSLQMTPTGRTLATAVMRKHRLAERLL T0381 98 :PHLEK 1bi0 96 :KVHDE T0381 106 :K 1bi0 104 :W T0381 155 :LAGLPDDELDAYLEKL 1bi0 105 :EHVMSDEVERRLVKVL T0381 171 :DIQRLT 1bi0 122 :DVSRSP T0381 177 :ERTITARDEL 1bi0 129 :GNPIPGLDEL Number of specific fragments extracted= 7 number of extra gaps= 0 total=654 Will force an alignment to be made, even if fragment is small Number of alignments=113 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1bi0/T0381-1bi0-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0381 read from 1bi0/T0381-1bi0-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1bi0 read from 1bi0/T0381-1bi0-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1bi0 in template set Warning: unaligning (T0381)L103 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1bi0)R103 Warning: unaligning (T0381)H105 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1bi0)R103 T0381 19 :SLARGLAVIRCFDHRNQRRTLSDVARATDLTRATARRFLLTLVELGYVATDG 1bi0 7 :TTEMYLRTIYELEEEGVTPLRARIAERLEQSGPTVSQTVARMERDGLVVVAS T0381 71 :SAFWLTPRVLELGYSYLSSLSLPEVAQ 1bi0 60 :RSLQMTPTGRTLATAVMRKHRLAERLL T0381 98 :PHLEK 1bi0 96 :KVHDE T0381 154 :LLAGLPDDELDAYLEKL 1bi0 104 :WEHVMSDEVERRLVKVL T0381 171 :DIQRLT 1bi0 122 :DVSRSP T0381 177 :ERTITARDEL 1bi0 129 :GNPIPGLDEL Number of specific fragments extracted= 6 number of extra gaps= 0 total=660 Will force an alignment to be made, even if fragment is small Number of alignments=114 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ddnA/T0381-1ddnA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1ddnA expands to /projects/compbio/data/pdb/1ddn.pdb.gz 1ddnA:# T0381 read from 1ddnA/T0381-1ddnA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ddnA read from 1ddnA/T0381-1ddnA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1ddnA to template set # found chain 1ddnA in template set Warning: unaligning (T0381)L170 because last residue in template chain is (1ddnA)L120 T0381 16 :YVQSLARGLAVIRCFDHRNQRRTLSDVARATDLTRATARRFLLTLVELGYVATDG 1ddnA 4 :LVDTTEMYLRTIYELEEEGVTPLRARIAERLEQSGPTVSQTVARMERDGLVVVAS T0381 71 :SAFWLTPRVLELGYSYLSS 1ddnA 60 :RSLQMTPTGRTLATAVMRK T0381 93 :PEVAQPHLE 1ddnA 79 :HRLAERLLT T0381 105 :HKVHE 1ddnA 88 :DIIGL T0381 149 :SMGRVLLAGLPDDELDAYLEK 1ddnA 99 :DEADRWEHVMSDEVERRLVKV Number of specific fragments extracted= 5 number of extra gaps= 0 total=665 Will force an alignment to be made, even if fragment is small Number of alignments=115 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ddnA/T0381-1ddnA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0381 read from 1ddnA/T0381-1ddnA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ddnA read from 1ddnA/T0381-1ddnA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1ddnA in template set Warning: unaligning (T0381)L170 because last residue in template chain is (1ddnA)L120 T0381 18 :QSLARGLAVIRCFDHRNQRRTLSDVARATDLTRATARRFLLTLVELGYVATDG 1ddnA 6 :DTTEMYLRTIYELEEEGVTPLRARIAERLEQSGPTVSQTVARMERDGLVVVAS T0381 71 :SAFWLTPRVLELGYSYLSSL 1ddnA 60 :RSLQMTPTGRTLATAVMRKH T0381 94 :EVAQPHLE 1ddnA 80 :RLAERLLT T0381 105 :HKVHE 1ddnA 88 :DIIGL T0381 149 :SMGRVLLAGLPDDELDAYLEK 1ddnA 99 :DEADRWEHVMSDEVERRLVKV Number of specific fragments extracted= 5 number of extra gaps= 0 total=670 Will force an alignment to be made, even if fragment is small Number of alignments=116 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ddnA/T0381-1ddnA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0381 read from 1ddnA/T0381-1ddnA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ddnA read from 1ddnA/T0381-1ddnA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1ddnA in template set Warning: unaligning (T0381)L170 because last residue in template chain is (1ddnA)L120 T0381 17 :VQSLARGLAVIRCFDHRNQRRTLSDVARATDLTRATARRFLLTLVELGYVATDG 1ddnA 5 :VDTTEMYLRTIYELEEEGVTPLRARIAERLEQSGPTVSQTVARMERDGLVVVAS T0381 71 :SAFWLTPRVLELGYSYLSS 1ddnA 60 :RSLQMTPTGRTLATAVMRK T0381 93 :PEVAQPHLEK 1ddnA 79 :HRLAERLLTD T0381 139 :IGTR 1ddnA 90 :IGLD T0381 154 :LLAGLPDDELDAYLEK 1ddnA 104 :WEHVMSDEVERRLVKV Number of specific fragments extracted= 5 number of extra gaps= 0 total=675 Will force an alignment to be made, even if fragment is small Number of alignments=117 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2b0lA/T0381-2b0lA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2b0lA expands to /projects/compbio/data/pdb/2b0l.pdb.gz 2b0lA:Skipped atom 32, because occupancy 0.200 <= existing 0.800 in 2b0lA Skipped atom 34, because occupancy 0.200 <= existing 0.800 in 2b0lA Skipped atom 36, because occupancy 0.200 <= existing 0.800 in 2b0lA Skipped atom 38, because occupancy 0.200 <= existing 0.800 in 2b0lA Skipped atom 40, because occupancy 0.200 <= existing 0.800 in 2b0lA Skipped atom 42, because occupancy 0.200 <= existing 0.800 in 2b0lA Skipped atom 44, because occupancy 0.200 <= existing 0.800 in 2b0lA Skipped atom 46, because occupancy 0.200 <= existing 0.800 in 2b0lA Skipped atom 48, because occupancy 0.200 <= existing 0.800 in 2b0lA Skipped atom 50, because occupancy 0.200 <= existing 0.800 in 2b0lA Skipped atom 123, because occupancy 0.200 <= existing 0.800 in 2b0lA Skipped atom 125, because occupancy 0.200 <= existing 0.800 in 2b0lA Skipped atom 127, because occupancy 0.200 <= existing 0.800 in 2b0lA Skipped atom 129, because occupancy 0.200 <= existing 0.800 in 2b0lA Skipped atom 131, because occupancy 0.200 <= existing 0.800 in 2b0lA Skipped atom 133, because occupancy 0.200 <= existing 0.800 in 2b0lA Skipped atom 135, because occupancy 0.200 <= existing 0.800 in 2b0lA Skipped atom 137, because occupancy 0.200 <= existing 0.800 in 2b0lA # T0381 read from 2b0lA/T0381-2b0lA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2b0lA read from 2b0lA/T0381-2b0lA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2b0lA to template set # found chain 2b0lA in template set Warning: unaligning (T0381)H32 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2b0lA)E193 Warning: unaligning (T0381)R33 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2b0lA)E193 Warning: unaligning (T0381)R55 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2b0lA)A220 Warning: unaligning (T0381)F56 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2b0lA)A220 Warning: unaligning (T0381)V66 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2b0lA)E231 Warning: unaligning (T0381)A67 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2b0lA)E231 Warning: unaligning (T0381)D69 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2b0lA)L235 Warning: unaligning (T0381)G70 because of BadResidue code BAD_PEPTIDE in next template residue (2b0lA)M237 T0381 21 :ARGLAVIRCFD 2b0lA 181 :YSELEAIEHIF T0381 34 :NQR 2b0lA 194 :LDG T0381 37 :RTLSDVARATDLTRATAR 2b0lA 201 :LVASKIADRVGITRSVIV T0381 57 :LLTLVELGY 2b0lA 221 :LRKLESAGV T0381 68 :T 2b0lA 232 :S T0381 71 :SA 2b0lA 238 :KG T0381 73 :F 2b0lA 241 :Y T0381 74 :WLTPRVLELGY 2b0lA 244 :VLNNKFLIELE Number of specific fragments extracted= 8 number of extra gaps= 4 total=683 Will force an alignment to be made, even if fragment is small Number of alignments=118 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2b0lA/T0381-2b0lA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0381 read from 2b0lA/T0381-2b0lA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2b0lA read from 2b0lA/T0381-2b0lA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2b0lA in template set Warning: unaligning (T0381)L11 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2b0lA)H162 Warning: unaligning (T0381)H32 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2b0lA)E193 Warning: unaligning (T0381)R33 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2b0lA)E193 Warning: unaligning (T0381)R55 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2b0lA)A220 Warning: unaligning (T0381)F56 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2b0lA)A220 Warning: unaligning (T0381)V66 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2b0lA)E231 Warning: unaligning (T0381)A67 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2b0lA)E231 Warning: unaligning (T0381)D69 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2b0lA)L235 Warning: unaligning (T0381)G70 because of BadResidue code BAD_PEPTIDE in next template residue (2b0lA)M237 T0381 12 :PSPDYVQSL 2b0lA 163 :HHHHMSKAV T0381 21 :ARG 2b0lA 173 :QMA T0381 24 :LAVIRCFD 2b0lA 184 :LEAIEHIF T0381 34 :NQR 2b0lA 194 :LDG T0381 37 :RTLSDVARATDLTRATAR 2b0lA 201 :LVASKIADRVGITRSVIV T0381 57 :LLTLVELGY 2b0lA 221 :LRKLESAGV T0381 68 :T 2b0lA 232 :S T0381 71 :SAFW 2b0lA 238 :KGTY T0381 75 :LTPRVLELGY 2b0lA 245 :LNNKFLIELE Number of specific fragments extracted= 9 number of extra gaps= 5 total=692 Will force an alignment to be made, even if fragment is small Number of alignments=119 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2b0lA/T0381-2b0lA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0381 read from 2b0lA/T0381-2b0lA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2b0lA read from 2b0lA/T0381-2b0lA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2b0lA in template set Warning: unaligning (T0381)P6 because first residue in template chain is (2b0lA)H161 Warning: unaligning (T0381)T7 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2b0lA)H162 Warning: unaligning (T0381)H32 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2b0lA)E193 Warning: unaligning (T0381)R33 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2b0lA)E193 Warning: unaligning (T0381)R55 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2b0lA)A220 Warning: unaligning (T0381)F56 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2b0lA)A220 Warning: unaligning (T0381)V66 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2b0lA)E231 Warning: unaligning (T0381)A67 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2b0lA)E231 Warning: unaligning (T0381)D69 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2b0lA)S234 Warning: unaligning (T0381)G70 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2b0lA)S234 T0381 8 :EKILPSPDYVQSLA 2b0lA 163 :HHHHMSKAVVQMAI T0381 22 :RGLAVIRCFD 2b0lA 182 :SELEAIEHIF T0381 34 :NQR 2b0lA 194 :LDG T0381 37 :RTLSDVARATDLTRATAR 2b0lA 201 :LVASKIADRVGITRSVIV T0381 57 :LLTLVELGY 2b0lA 221 :LRKLESAGV T0381 68 :T 2b0lA 232 :S T0381 71 :SAFW 2b0lA 238 :KGTY T0381 75 :LTPRVLE 2b0lA 245 :LNNKFLI Number of specific fragments extracted= 8 number of extra gaps= 4 total=700 Will force an alignment to be made, even if fragment is small Number of alignments=120 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1i1gA/T0381-1i1gA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1i1gA expands to /projects/compbio/data/pdb/1i1g.pdb.gz 1i1gA:# T0381 read from 1i1gA/T0381-1i1gA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1i1gA read from 1i1gA/T0381-1i1gA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1i1gA to template set # found chain 1i1gA in template set Warning: unaligning (T0381)R28 because of BadResidue code BAD_PEPTIDE in next template residue (1i1gA)I12 Warning: unaligning (T0381)C29 because of BadResidue code BAD_PEPTIDE at template residue (1i1gA)I12 Warning: unaligning (T0381)V107 because of BadResidue code BAD_PEPTIDE in next template residue (1i1gA)D88 Warning: unaligning (T0381)H108 because of BadResidue code BAD_PEPTIDE at template residue (1i1gA)D88 Warning: unaligning (T0381)I132 because of BadResidue code BAD_PEPTIDE in next template residue (1i1gA)I102 Warning: unaligning (T0381)M133 because of BadResidue code BAD_PEPTIDE at template residue (1i1gA)I102 T0381 22 :RGLAVI 1i1gA 5 :RDKIIL T0381 30 :FDH 1i1gA 13 :LEK T0381 34 :NQRRTLSDVARATDLTRATARRFLLTLVELGYVATDG 1i1gA 16 :DARTPFTEIAKKLGISETAVRKRVKALEEKGIIEGYT T0381 71 :S 1i1gA 61 :G T0381 73 :FWL 1i1gA 62 :YSL T0381 89 :SLSLPEVAQPHLEK 1i1gA 73 :KPEKLFEVAEKLKE T0381 109 :ESSS 1i1gA 89 :FVKE T0381 124 :VARVPVSR 1i1gA 93 :LYLSSGDH T0381 134 :TVGITIG 1i1gA 103 :MAVIWAK T0381 159 :PDDELDAYLEK 1i1gA 110 :DGEDLAEIISN Number of specific fragments extracted= 10 number of extra gaps= 3 total=710 Will force an alignment to be made, even if fragment is small Number of alignments=121 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1i1gA/T0381-1i1gA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0381 read from 1i1gA/T0381-1i1gA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1i1gA read from 1i1gA/T0381-1i1gA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1i1gA in template set Warning: unaligning (T0381)R28 because of BadResidue code BAD_PEPTIDE in next template residue (1i1gA)I12 Warning: unaligning (T0381)C29 because of BadResidue code BAD_PEPTIDE at template residue (1i1gA)I12 Warning: unaligning (T0381)H108 because of BadResidue code BAD_PEPTIDE at template residue (1i1gA)D88 Warning: unaligning (T0381)I132 because of BadResidue code BAD_PEPTIDE in next template residue (1i1gA)I102 Warning: unaligning (T0381)M133 because of BadResidue code BAD_PEPTIDE at template residue (1i1gA)I102 T0381 22 :RGLAVI 1i1gA 5 :RDKIIL T0381 30 :F 1i1gA 13 :L T0381 32 :HRNQRRTLSDVARATDLTRATARRFLLTLVELGYVATDG 1i1gA 14 :EKDARTPFTEIAKKLGISETAVRKRVKALEEKGIIEGYT T0381 71 :SAFWL 1i1gA 61 :GYSLV T0381 89 :SLSLPEVAQPHLEK 1i1gA 73 :KPEKLFEVAEKLKE T0381 109 :ESSS 1i1gA 89 :FVKE T0381 124 :VARVPVSR 1i1gA 93 :LYLSSGDH T0381 134 :TVGITIG 1i1gA 103 :MAVIWAK T0381 159 :PDDELDAYLEK 1i1gA 110 :DGEDLAEIISN Number of specific fragments extracted= 9 number of extra gaps= 3 total=719 Will force an alignment to be made, even if fragment is small Number of alignments=122 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1i1gA/T0381-1i1gA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0381 read from 1i1gA/T0381-1i1gA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1i1gA read from 1i1gA/T0381-1i1gA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1i1gA in template set Warning: unaligning (T0381)R28 because of BadResidue code BAD_PEPTIDE in next template residue (1i1gA)I12 Warning: unaligning (T0381)C29 because of BadResidue code BAD_PEPTIDE at template residue (1i1gA)I12 Warning: unaligning (T0381)H108 because of BadResidue code BAD_PEPTIDE at template residue (1i1gA)D88 Warning: unaligning (T0381)I132 because of BadResidue code BAD_PEPTIDE in next template residue (1i1gA)I102 Warning: unaligning (T0381)M133 because of BadResidue code BAD_PEPTIDE at template residue (1i1gA)I102 T0381 22 :RGLAVI 1i1gA 5 :RDKIIL T0381 30 :FDH 1i1gA 13 :LEK T0381 34 :NQRRTLSDVARATDLTRATARRFLLTLVELGYVATDG 1i1gA 16 :DARTPFTEIAKKLGISETAVRKRVKALEEKGIIEGYT T0381 71 :SAFWL 1i1gA 60 :LGYSL T0381 89 :SLSLPEVAQPHLEK 1i1gA 73 :KPEKLFEVAEKLKE T0381 109 :ESSSV 1i1gA 89 :FVKEL T0381 125 :ARVPVSR 1i1gA 94 :YLSSGDH T0381 134 :TVG 1i1gA 103 :MAV T0381 155 :LAGLPDDELDAYLEK 1i1gA 106 :IWAKDGEDLAEIISN Number of specific fragments extracted= 9 number of extra gaps= 3 total=728 Will force an alignment to be made, even if fragment is small Number of alignments=123 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1stzA/T0381-1stzA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1stzA expands to /projects/compbio/data/pdb/1stz.pdb.gz 1stzA:# T0381 read from 1stzA/T0381-1stzA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1stzA read from 1stzA/T0381-1stzA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1stzA to template set # found chain 1stzA in template set Warning: unaligning (T0381)L209 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1stzA)A288 Warning: unaligning (T0381)R210 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1stzA)A288 Warning: unaligning (T0381)T231 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1stzA)S309 Warning: unaligning (T0381)P232 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1stzA)S309 T0381 14 :PDY 1stzA 16 :NDR T0381 19 :SLARGLAVIRCFDHRNQRRTLSDVARATDL 1stzA 19 :QRKVLYCIVREYIENKKPVSSQRVLEVSNI T0381 49 :TRATARRFLLTLVELGYVATDG 1stzA 51 :SSATIRNDMKKLEYLGYIYQPH T0381 71 :SAFWLTPRVLELGYSYL 1stzA 75 :AGRIPTDKGLRFYYEEM T0381 88 :SSLS 1stzA 96 :KETS T0381 92 :LPEVAQPHLEKLSHKVHESSSV 1stzA 116 :PEKVLFLAGNLLARLTEGYVLI T0381 114 :SIL 1stzA 150 :VML T0381 117 :DGADIVYVARVPVSRIMTVGITIGTRLP 1stzA 156 :SEDYLIFSILTEFGVSKVTPIKTQERLN T0381 145 :AYATSMGRVL 1stzA 195 :LRGRTVGEVL T0381 157 :GLPDDELDAYLEKLD 1stzA 244 :TLTLEDIRNLLEEVK T0381 182 :ARDELKAA 1stzA 259 :DQKFLESL T0381 198 :ICVLDQELE 1stzA 272 :TVRIGREIG T0381 207 :AG 1stzA 285 :EK T0381 211 :SMAAPIR 1stzA 289 :VFSGKYF T0381 219 :ASGLTVAAVNIS 1stzA 296 :KGESPIGSVYLF T0381 233 :A 1stzA 310 :K T0381 235 :RYSLEDL 1stzA 311 :VTKYDRN T0381 246 :IPSLRVTATDIEQDL 1stzA 318 :HRVFEYILNRLSEYF Number of specific fragments extracted= 18 number of extra gaps= 2 total=746 Will force an alignment to be made, even if fragment is small Number of alignments=124 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1stzA/T0381-1stzA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0381 read from 1stzA/T0381-1stzA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1stzA read from 1stzA/T0381-1stzA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1stzA in template set Warning: unaligning (T0381)P12 because first residue in template chain is (1stzA)K14 Warning: unaligning (T0381)L209 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1stzA)A288 Warning: unaligning (T0381)R210 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1stzA)A288 Warning: unaligning (T0381)T231 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1stzA)S309 Warning: unaligning (T0381)P232 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1stzA)S309 T0381 13 :SPDYVQ 1stzA 15 :LNDRQR T0381 21 :ARGLAVIRCFDHRNQRRTLSDVARATDL 1stzA 21 :KVLYCIVREYIENKKPVSSQRVLEVSNI T0381 49 :TRATARRFLLTLVELGYVATDG 1stzA 51 :SSATIRNDMKKLEYLGYIYQPH T0381 71 :SAFWLTPRVLELGYSYLSS 1stzA 75 :AGRIPTDKGLRFYYEEMLK T0381 90 :LS 1stzA 98 :TS T0381 92 :LPEVAQPHLEKLSHKVHESSSV 1stzA 116 :PEKVLFLAGNLLARLTEGYVLI T0381 114 :SIL 1stzA 150 :VML T0381 117 :DGADIVYVARVPVSRIMTVGITIGTRLPA 1stzA 156 :SEDYLIFSILTEFGVSKVTPIKTQERLNW T0381 146 :YATSMGRVL 1stzA 196 :RGRTVGEVL T0381 157 :GLPDDELDAYLEKLD 1stzA 244 :TLTLEDIRNLLEEVK T0381 182 :ARDELKAA 1stzA 259 :DQKFLESL T0381 198 :ICVLDQEL 1stzA 272 :TVRIGREI T0381 206 :EAG 1stzA 284 :LEK T0381 211 :SMAAPIR 1stzA 289 :VFSGKYF T0381 219 :ASGLTVAAVNIS 1stzA 296 :KGESPIGSVYLF T0381 233 :A 1stzA 310 :K T0381 235 :RYSLEDL 1stzA 311 :VTKYDRN T0381 242 :HSDLIPSLRVTATD 1stzA 321 :FEYILNRLSEYFTS Number of specific fragments extracted= 18 number of extra gaps= 2 total=764 Will force an alignment to be made, even if fragment is small Number of alignments=125 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1stzA/T0381-1stzA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0381 read from 1stzA/T0381-1stzA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1stzA read from 1stzA/T0381-1stzA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1stzA in template set Warning: unaligning (T0381)L209 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1stzA)A288 Warning: unaligning (T0381)R210 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1stzA)A288 Warning: unaligning (T0381)T231 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1stzA)S309 Warning: unaligning (T0381)P232 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1stzA)S309 T0381 18 :QSLARGLAVIRCFDHRNQRRTLSDVARATDL 1stzA 18 :RQRKVLYCIVREYIENKKPVSSQRVLEVSNI T0381 49 :TRATARRFLLTLVELGYVATDG 1stzA 51 :SSATIRNDMKKLEYLGYIYQPH T0381 71 :SAFWLTPRVLELGYSYLSS 1stzA 75 :AGRIPTDKGLRFYYEEMLK T0381 90 :LSLPEVAQPHLEKLSHKVHESSSV 1stzA 114 :ADPEKVLFLAGNLLARLTEGYVLI T0381 114 :SIL 1stzA 150 :VML T0381 117 :DGADIVYVARVPVSRIMTVGITIGTRLP 1stzA 156 :SEDYLIFSILTEFGVSKVTPIKTQERLN T0381 146 :YATSMGRVL 1stzA 196 :RGRTVGEVL T0381 157 :GLPDDELDAYLEKL 1stzA 244 :TLTLEDIRNLLEEV T0381 181 :TARDELKAA 1stzA 258 :KDQKFLESL T0381 198 :ICVLDQEL 1stzA 272 :TVRIGREI T0381 206 :EAG 1stzA 284 :LEK T0381 211 :SMAAPIR 1stzA 289 :VFSGKYF T0381 219 :ASGLTVAAVNIS 1stzA 296 :KGESPIGSVYLF T0381 233 :A 1stzA 310 :K T0381 235 :RYSLEDLHSDLIPSLRVTATDIE 1stzA 311 :VTKYDRNHRVFEYILNRLSEYFT Number of specific fragments extracted= 15 number of extra gaps= 2 total=779 Will force an alignment to be made, even if fragment is small Number of alignments=126 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2fnaA/T0381-2fnaA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2fnaA expands to /projects/compbio/data/pdb/2fna.pdb.gz 2fnaA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 996, because occupancy 0.500 <= existing 0.500 in 2fnaA Skipped atom 1000, because occupancy 0.500 <= existing 0.500 in 2fnaA Skipped atom 1002, because occupancy 0.500 <= existing 0.500 in 2fnaA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 1457, because occupancy 0.500 <= existing 0.500 in 2fnaA Skipped atom 1461, because occupancy 0.500 <= existing 0.500 in 2fnaA Skipped atom 1463, because occupancy 0.500 <= existing 0.500 in 2fnaA Skipped atom 1465, because occupancy 0.500 <= existing 0.500 in 2fnaA Skipped atom 1467, because occupancy 0.500 <= existing 0.500 in 2fnaA Skipped atom 1469, because occupancy 0.500 <= existing 0.500 in 2fnaA Skipped atom 1471, because occupancy 0.500 <= existing 0.500 in 2fnaA Skipped atom 1473, because occupancy 0.500 <= existing 0.500 in 2fnaA Skipped atom 1507, because occupancy 0.500 <= existing 0.500 in 2fnaA Skipped atom 1511, because occupancy 0.500 <= existing 0.500 in 2fnaA Skipped atom 1513, because occupancy 0.500 <= existing 0.500 in 2fnaA Skipped atom 1515, because occupancy 0.500 <= existing 0.500 in 2fnaA Skipped atom 1517, because occupancy 0.500 <= existing 0.500 in 2fnaA Skipped atom 1519, because occupancy 0.500 <= existing 0.500 in 2fnaA Skipped atom 1725, because occupancy 0.500 <= existing 0.500 in 2fnaA Skipped atom 1729, because occupancy 0.500 <= existing 0.500 in 2fnaA Skipped atom 1731, because occupancy 0.500 <= existing 0.500 in 2fnaA Skipped atom 1733, because occupancy 0.500 <= existing 0.500 in 2fnaA Skipped atom 1735, because occupancy 0.500 <= existing 0.500 in 2fnaA Skipped atom 1737, because occupancy 0.500 <= existing 0.500 in 2fnaA Skipped atom 1739, because occupancy 0.500 <= existing 0.500 in 2fnaA Skipped atom 1741, because occupancy 0.500 <= existing 0.500 in 2fnaA Skipped atom 2110, because occupancy 0.500 <= existing 0.500 in 2fnaA Skipped atom 2114, because occupancy 0.500 <= existing 0.500 in 2fnaA Skipped atom 2116, because occupancy 0.500 <= existing 0.500 in 2fnaA Skipped atom 2118, because occupancy 0.500 <= existing 0.500 in 2fnaA Skipped atom 2120, because occupancy 0.500 <= existing 0.500 in 2fnaA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0381 read from 2fnaA/T0381-2fnaA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2fnaA read from 2fnaA/T0381-2fnaA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2fnaA to template set # found chain 2fnaA in template set T0381 21 :ARGLAVIRCFD 2fnaA 289 :KRYLNIMRTLS T0381 35 :QRRTLSDVARAT 2fnaA 300 :KCGKWSDVKRAL T0381 47 :DLTRATARRFLLTLVELGYVATDGSAFWLTPRVLELG 2fnaA 318 :EISDSEIYNYLTQLTKHSWIIKEGEKYCPSEPLISLA Number of specific fragments extracted= 3 number of extra gaps= 0 total=782 Will force an alignment to be made, even if fragment is small Number of alignments=127 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2fnaA/T0381-2fnaA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0381 read from 2fnaA/T0381-2fnaA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2fnaA read from 2fnaA/T0381-2fnaA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2fnaA in template set T0381 21 :ARGLAVIRCFD 2fnaA 289 :KRYLNIMRTLS T0381 35 :QRRTLSDVARAT 2fnaA 300 :KCGKWSDVKRAL T0381 47 :DLTRATARRFLLTLVELGYVATDGSAFWLTPRVLELG 2fnaA 318 :EISDSEIYNYLTQLTKHSWIIKEGEKYCPSEPLISLA Number of specific fragments extracted= 3 number of extra gaps= 0 total=785 Will force an alignment to be made, even if fragment is small Number of alignments=128 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2fnaA/T0381-2fnaA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0381 read from 2fnaA/T0381-2fnaA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2fnaA read from 2fnaA/T0381-2fnaA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2fnaA in template set T0381 21 :ARGLAVIRCFDH 2fnaA 289 :KRYLNIMRTLSK T0381 36 :RRTLSDVARAT 2fnaA 301 :CGKWSDVKRAL T0381 47 :DLTRATARRFLLTLVELGYVATDGSAFWLTPRVLELG 2fnaA 318 :EISDSEIYNYLTQLTKHSWIIKEGEKYCPSEPLISLA Number of specific fragments extracted= 3 number of extra gaps= 0 total=788 Will force an alignment to be made, even if fragment is small Number of alignments=129 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ri7A/T0381-1ri7A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1ri7A expands to /projects/compbio/data/pdb/1ri7.pdb.gz 1ri7A:# T0381 read from 1ri7A/T0381-1ri7A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ri7A read from 1ri7A/T0381-1ri7A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1ri7A to template set # found chain 1ri7A in template set T0381 21 :ARGLAVIRCFDHR 1ri7A 27 :EIDKKIIKILQND T0381 35 :QRRTLSDVARATDLTRATARRFLLTLVELGYVATDG 1ri7A 40 :GKAPLREISKITGLAESTIHERIRKLRESGVIKKFT T0381 71 :SAFWL 1ri7A 84 :GYSML T0381 89 :SLSLPEVAQPHLE 1ri7A 96 :KAGKYSEVASNLA T0381 106 :KVHESSSVSIL 1ri7A 109 :KYPEIVEVYET T0381 117 :DGADIVYVARVP 1ri7A 121 :GDYDMVVKIRTK T0381 159 :PDDELDAYLEKL 1ri7A 133 :NSEELNNFLDLI T0381 194 :RA 1ri7A 145 :GS Number of specific fragments extracted= 8 number of extra gaps= 0 total=796 Will force an alignment to be made, even if fragment is small Number of alignments=130 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ri7A/T0381-1ri7A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0381 read from 1ri7A/T0381-1ri7A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ri7A read from 1ri7A/T0381-1ri7A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1ri7A in template set T0381 22 :RGLAVIRCFDH 1ri7A 28 :IDKKIIKILQN T0381 34 :NQRRTLSDVARATDLTRATARRFLLTLVELGYVAT 1ri7A 39 :DGKAPLREISKITGLAESTIHERIRKLRESGVIKK T0381 69 :DG 1ri7A 75 :TA T0381 71 :SAFWL 1ri7A 84 :GYSML T0381 89 :SLSLPEVAQPHLEK 1ri7A 96 :KAGKYSEVASNLAK T0381 107 :V 1ri7A 110 :Y T0381 119 :ADIVYVARVPVSRIMTVGITI 1ri7A 111 :PEIVEVYETTGDYDMVVKIRT T0381 158 :LPDDELDAYLEKLD 1ri7A 132 :KNSEELNNFLDLIG Number of specific fragments extracted= 8 number of extra gaps= 0 total=804 Will force an alignment to be made, even if fragment is small Number of alignments=131 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ri7A/T0381-1ri7A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0381 read from 1ri7A/T0381-1ri7A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ri7A read from 1ri7A/T0381-1ri7A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1ri7A in template set T0381 24 :LAVIRCFDH 1ri7A 30 :KKIIKILQN T0381 34 :NQRRTLSDVARATDLTRATARRFLLTLVELGYVATDG 1ri7A 39 :DGKAPLREISKITGLAESTIHERIRKLRESGVIKKFT T0381 71 :SAFWL 1ri7A 83 :LGYSM T0381 89 :SLSLPEVAQPHLE 1ri7A 96 :KAGKYSEVASNLA T0381 106 :KVHESSSVSIL 1ri7A 109 :KYPEIVEVYET T0381 117 :DGADIVYVARV 1ri7A 121 :GDYDMVVKIRT T0381 158 :LPDDELDAYLEKL 1ri7A 132 :KNSEELNNFLDLI Number of specific fragments extracted= 7 number of extra gaps= 0 total=811 Will force an alignment to be made, even if fragment is small Number of alignments=132 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2gauA/T0381-2gauA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2gauA expands to /projects/compbio/data/pdb/2gau.pdb.gz 2gauA:# T0381 read from 2gauA/T0381-2gauA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2gauA read from 2gauA/T0381-2gauA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2gauA to template set # found chain 2gauA in template set T0381 18 :QSLARGLAVIRCFDHRNQR 2gauA 156 :RLAETLLILKENFGFENDG T0381 37 :RTLSDVARATDLTRATARRFLLTLVELGYVATDGSAFWL 2gauA 181 :LSREELATLSNMTVSNAIRTLSTFVSERMLALDGKRIKI T0381 97 :QPHLEKLSH 2gauA 222 :CDRLQKTAR Number of specific fragments extracted= 3 number of extra gaps= 0 total=814 Will force an alignment to be made, even if fragment is small Number of alignments=133 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2gauA/T0381-2gauA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0381 read from 2gauA/T0381-2gauA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2gauA read from 2gauA/T0381-2gauA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2gauA in template set T0381 20 :LARGLAVIRCFDHR 2gauA 154 :RGRLAETLLILKEN T0381 34 :NQR 2gauA 172 :NDG T0381 37 :RTLSDVARATDLTRATARRFLLTLVELGYVATDGSAFWL 2gauA 181 :LSREELATLSNMTVSNAIRTLSTFVSERMLALDGKRIKI T0381 97 :QPHLEKLSH 2gauA 222 :CDRLQKTAR Number of specific fragments extracted= 4 number of extra gaps= 0 total=818 Will force an alignment to be made, even if fragment is small Number of alignments=134 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2gauA/T0381-2gauA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0381 read from 2gauA/T0381-2gauA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2gauA read from 2gauA/T0381-2gauA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2gauA in template set T0381 17 :VQSLARGLAVIRCFDHRNQR 2gauA 155 :GRLAETLLILKENFGFENDG T0381 37 :RTLSDVARATDLTRATARRFLLTLVELGYVATDGSAFWL 2gauA 181 :LSREELATLSNMTVSNAIRTLSTFVSERMLALDGKRIKI T0381 97 :QPHLEKLSH 2gauA 222 :CDRLQKTAR Number of specific fragments extracted= 3 number of extra gaps= 0 total=821 Will force an alignment to be made, even if fragment is small Number of alignments=135 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1i6xA/T0381-1i6xA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1i6xA expands to /projects/compbio/data/pdb/1i6x.pdb.gz 1i6xA:# T0381 read from 1i6xA/T0381-1i6xA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1i6xA read from 1i6xA/T0381-1i6xA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1i6xA to template set # found chain 1i6xA in template set T0381 19 :SLARGLAVIRCFDHRNQR 1i6xA 139 :VTGRIAQTLLNLAKQPDA T0381 37 :RTLSDVARATDLTRATARRFLLTLVELGYVATDGSAFW 1i6xA 167 :ITRQEIGQIVGCSRETVGRILKMLEDQNLISAHGKTIV Number of specific fragments extracted= 2 number of extra gaps= 0 total=823 Will force an alignment to be made, even if fragment is small Number of alignments=136 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1i6xA/T0381-1i6xA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0381 read from 1i6xA/T0381-1i6xA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1i6xA read from 1i6xA/T0381-1i6xA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1i6xA in template set T0381 19 :SLARGLAVIRCFDHRNQ 1i6xA 139 :VTGRIAQTLLNLAKQPD T0381 37 :RTLSDVARATDLTRATARRFLLTLVELGYVATDGSAFW 1i6xA 167 :ITRQEIGQIVGCSRETVGRILKMLEDQNLISAHGKTIV Number of specific fragments extracted= 2 number of extra gaps= 0 total=825 Will force an alignment to be made, even if fragment is small Number of alignments=137 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1i6xA/T0381-1i6xA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0381 read from 1i6xA/T0381-1i6xA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1i6xA read from 1i6xA/T0381-1i6xA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1i6xA in template set T0381 20 :LARGLAVIRCFDHRNQR 1i6xA 140 :TGRIAQTLLNLAKQPDA T0381 37 :RTLSDVARATDLTRATARRFLLTLVELGYVATDGSAFW 1i6xA 167 :ITRQEIGQIVGCSRETVGRILKMLEDQNLISAHGKTIV Number of specific fragments extracted= 2 number of extra gaps= 0 total=827 Will force an alignment to be made, even if fragment is small Number of alignments=138 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1hw5A/T0381-1hw5A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1hw5A expands to /projects/compbio/data/pdb/1hw5.pdb.gz 1hw5A:Skipped atom 179, because occupancy 0.500 <= existing 0.500 in 1hw5A Skipped atom 181, because occupancy 0.500 <= existing 0.500 in 1hw5A Skipped atom 183, because occupancy 0.500 <= existing 0.500 in 1hw5A Skipped atom 185, because occupancy 0.500 <= existing 0.500 in 1hw5A Skipped atom 187, because occupancy 0.500 <= existing 0.500 in 1hw5A Skipped atom 302, because occupancy 0.500 <= existing 0.500 in 1hw5A Skipped atom 304, because occupancy 0.500 <= existing 0.500 in 1hw5A Skipped atom 306, because occupancy 0.500 <= existing 0.500 in 1hw5A Skipped atom 308, because occupancy 0.500 <= existing 0.500 in 1hw5A Skipped atom 310, because occupancy 0.500 <= existing 0.500 in 1hw5A Skipped atom 408, because occupancy 0.500 <= existing 0.500 in 1hw5A Skipped atom 410, because occupancy 0.500 <= existing 0.500 in 1hw5A Skipped atom 412, because occupancy 0.500 <= existing 0.500 in 1hw5A Skipped atom 414, because occupancy 0.500 <= existing 0.500 in 1hw5A Skipped atom 649, because occupancy 0.500 <= existing 0.500 in 1hw5A Skipped atom 651, because occupancy 0.500 <= existing 0.500 in 1hw5A Skipped atom 653, because occupancy 0.500 <= existing 0.500 in 1hw5A Skipped atom 655, because occupancy 0.500 <= existing 0.500 in 1hw5A Skipped atom 657, because occupancy 0.500 <= existing 0.500 in 1hw5A Skipped atom 715, because occupancy 0.500 <= existing 0.500 in 1hw5A Skipped atom 717, because occupancy 0.500 <= existing 0.500 in 1hw5A Skipped atom 719, because occupancy 0.500 <= existing 0.500 in 1hw5A Skipped atom 721, because occupancy 0.500 <= existing 0.500 in 1hw5A Skipped atom 723, because occupancy 0.500 <= existing 0.500 in 1hw5A Skipped atom 725, because occupancy 0.500 <= existing 0.500 in 1hw5A Skipped atom 727, because occupancy 0.500 <= existing 0.500 in 1hw5A Skipped atom 1001, because occupancy 0.500 <= existing 0.500 in 1hw5A Skipped atom 1003, because occupancy 0.500 <= existing 0.500 in 1hw5A Skipped atom 1005, because occupancy 0.500 <= existing 0.500 in 1hw5A Skipped atom 1007, because occupancy 0.500 <= existing 0.500 in 1hw5A Skipped atom 1009, because occupancy 0.500 <= existing 0.500 in 1hw5A Skipped atom 1011, because occupancy 0.500 <= existing 0.500 in 1hw5A Skipped atom 1013, because occupancy 0.500 <= existing 0.500 in 1hw5A Skipped atom 1076, because occupancy 0.500 <= existing 0.500 in 1hw5A Skipped atom 1078, because occupancy 0.500 <= existing 0.500 in 1hw5A Skipped atom 1080, because occupancy 0.500 <= existing 0.500 in 1hw5A Skipped atom 1082, because occupancy 0.500 <= existing 0.500 in 1hw5A Skipped atom 1084, because occupancy 0.500 <= existing 0.500 in 1hw5A Skipped atom 1375, because occupancy 0.500 <= existing 0.500 in 1hw5A Skipped atom 1377, because occupancy 0.500 <= existing 0.500 in 1hw5A Skipped atom 1379, because occupancy 0.500 <= existing 0.500 in 1hw5A Skipped atom 1381, because occupancy 0.500 <= existing 0.500 in 1hw5A Skipped atom 1383, because occupancy 0.500 <= existing 0.500 in 1hw5A Skipped atom 1385, because occupancy 0.500 <= existing 0.500 in 1hw5A Skipped atom 1387, because occupancy 0.500 <= existing 0.500 in 1hw5A Skipped atom 1474, because occupancy 0.500 <= existing 0.500 in 1hw5A Skipped atom 1476, because occupancy 0.500 <= existing 0.500 in 1hw5A Skipped atom 1478, because occupancy 0.500 <= existing 0.500 in 1hw5A Skipped atom 1480, because occupancy 0.500 <= existing 0.500 in 1hw5A Skipped atom 1482, because occupancy 0.500 <= existing 0.500 in 1hw5A # T0381 read from 1hw5A/T0381-1hw5A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1hw5A read from 1hw5A/T0381-1hw5A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1hw5A to template set # found chain 1hw5A in template set Warning: unaligning (T0381)T49 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1hw5A)R180 Warning: unaligning (T0381)R50 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1hw5A)R180 T0381 19 :SLARGLAVIRCFDHRNQR 1hw5A 139 :VTGRIAQTLLNLAKQPDA T0381 37 :RTLSDVARATDL 1hw5A 167 :ITRQEIGQIVGC T0381 51 :ATARRFLLTLVELGYVATDGSAF 1hw5A 181 :ETVGRILKMLEDQNLISAHGKTI Number of specific fragments extracted= 3 number of extra gaps= 1 total=830 Will force an alignment to be made, even if fragment is small Number of alignments=139 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1hw5A/T0381-1hw5A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0381 read from 1hw5A/T0381-1hw5A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1hw5A read from 1hw5A/T0381-1hw5A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1hw5A in template set Warning: unaligning (T0381)T49 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1hw5A)R180 Warning: unaligning (T0381)R50 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1hw5A)R180 T0381 19 :SLARGLAVIRCFDHRNQR 1hw5A 139 :VTGRIAQTLLNLAKQPDA T0381 37 :RTLSDVARATDL 1hw5A 167 :ITRQEIGQIVGC T0381 51 :ATARRFLLTLVELGYVATDG 1hw5A 181 :ETVGRILKMLEDQNLISAHG T0381 71 :SA 1hw5A 202 :TI Number of specific fragments extracted= 4 number of extra gaps= 1 total=834 Will force an alignment to be made, even if fragment is small Number of alignments=140 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1hw5A/T0381-1hw5A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0381 read from 1hw5A/T0381-1hw5A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1hw5A read from 1hw5A/T0381-1hw5A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1hw5A in template set Warning: unaligning (T0381)T49 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1hw5A)R180 Warning: unaligning (T0381)R50 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1hw5A)R180 T0381 20 :LARGLAVIRCFDHRNQ 1hw5A 140 :TGRIAQTLLNLAKQPD T0381 37 :RTLSDVARATDL 1hw5A 167 :ITRQEIGQIVGC T0381 51 :ATARRFLLTLVELGYVATDG 1hw5A 181 :ETVGRILKMLEDQNLISAHG Number of specific fragments extracted= 3 number of extra gaps= 1 total=837 Will force an alignment to be made, even if fragment is small Number of alignments=141 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1bia/T0381-1bia-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1bia expands to /projects/compbio/data/pdb/1bia.pdb.gz 1bia:Warning: there is no chain 1bia will retry with 1biaA # T0381 read from 1bia/T0381-1bia-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1bia read from 1bia/T0381-1bia-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1bia to template set # found chain 1bia in template set Warning: unaligning (T0381)I139 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1bia)P143 Warning: unaligning (T0381)T141 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1bia)P143 Warning: unaligning (T0381)A145 because of BadResidue code BAD_PEPTIDE in next template residue (1bia)G148 Warning: unaligning (T0381)Y146 because of BadResidue code BAD_PEPTIDE at template residue (1bia)G148 Warning: unaligning (T0381)G218 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1bia)A198 Warning: unaligning (T0381)A233 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1bia)W223 T0381 21 :ARGLAVIRCFDHR 1bia 5 :TVPLKLIALLANG T0381 35 :QRRTLSDVARATDLTRATARRFLLTLVELGY 1bia 18 :EFHSGEQLGETLGMSRAAINKHIQTLRDWGV T0381 66 :VATDG 1bia 50 :VFTVP T0381 71 :SAFWL 1bia 56 :KGYSL T0381 83 :GYSYLSSLS 1bia 69 :AKQILGQLD T0381 92 :LPEVAQPHL 1bia 86 :VIDSTNQYL T0381 104 :SHKVHES 1bia 95 :LDRIGEL T0381 111 :SSVSILDG 1bia 106 :ACIAEYQQ T0381 119 :ADIVYVARVPV 1bia 129 :ANLYLSMFWRL T0381 138 :T 1bia 140 :E T0381 142 :RLP 1bia 144 :AAA T0381 147 :AT 1bia 149 :LS T0381 149 :SMGRVLL 1bia 152 :VIGIVMA T0381 165 :AYLEKLDIQRLT 1bia 159 :EVLRKLGADKVR T0381 200 :VLDQELEAGLRSMA 1bia 173 :WPNDLYLQDRKLAG T0381 214 :APIR 1bia 189 :VELT T0381 222 :LTVAAVNISTP 1bia 200 :QIVIGAGINMA T0381 236 :YSLEDLHSDLIPSLRVTATDIEQD 1bia 233 :LDRNTLAAMLIRELRAALELFEQE Number of specific fragments extracted= 18 number of extra gaps= 1 total=855 Will force an alignment to be made, even if fragment is small Number of alignments=142 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1bia/T0381-1bia-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0381 read from 1bia/T0381-1bia-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1bia read from 1bia/T0381-1bia-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1bia in template set Warning: unaligning (T0381)I139 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1bia)P143 Warning: unaligning (T0381)T141 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1bia)P143 Warning: unaligning (T0381)A145 because of BadResidue code BAD_PEPTIDE in next template residue (1bia)G148 Warning: unaligning (T0381)Y146 because of BadResidue code BAD_PEPTIDE at template residue (1bia)G148 Warning: unaligning (T0381)G218 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1bia)A198 Warning: unaligning (T0381)A233 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1bia)W223 T0381 21 :ARGLAVIRCFDHR 1bia 5 :TVPLKLIALLANG T0381 35 :QRRTLSDVARATDLTRATARRFLLTLVELGY 1bia 18 :EFHSGEQLGETLGMSRAAINKHIQTLRDWGV T0381 66 :VATDG 1bia 50 :VFTVP T0381 71 :SAFWL 1bia 56 :KGYSL T0381 77 :P 1bia 70 :K T0381 85 :SYLSSLS 1bia 71 :QILGQLD T0381 92 :LPEVAQPHLE 1bia 86 :VIDSTNQYLL T0381 107 :VHESSSVSIL 1bia 127 :FGANLYLSMF T0381 125 :A 1bia 137 :W T0381 136 :GIT 1bia 138 :RLE T0381 142 :RLP 1bia 144 :AAA T0381 147 :AT 1bia 149 :LS T0381 149 :SMGRVLL 1bia 152 :VIGIVMA T0381 165 :AYLEKLDIQRLT 1bia 159 :EVLRKLGADKVR T0381 211 :S 1bia 171 :V T0381 212 :MAAPIR 1bia 184 :LAGILV T0381 222 :LTVAAVNISTP 1bia 200 :QIVIGAGINMA T0381 236 :YSLEDLHSDLIPSLRVTATDIEQ 1bia 233 :LDRNTLAAMLIRELRAALELFEQ Number of specific fragments extracted= 18 number of extra gaps= 1 total=873 Will force an alignment to be made, even if fragment is small Number of alignments=143 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1bia/T0381-1bia-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0381 read from 1bia/T0381-1bia-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1bia read from 1bia/T0381-1bia-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1bia in template set Warning: unaligning (T0381)S130 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1bia)S125 Warning: unaligning (T0381)I137 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1bia)S125 Warning: unaligning (T0381)M150 because of BadResidue code BAD_PEPTIDE in next template residue (1bia)G148 Warning: unaligning (T0381)G151 because of BadResidue code BAD_PEPTIDE at template residue (1bia)G148 Warning: unaligning (T0381)D202 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1bia)A198 Warning: unaligning (T0381)A207 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1bia)A198 Warning: unaligning (T0381)S220 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1bia)W223 Warning: unaligning (T0381)P232 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1bia)W223 T0381 22 :RGLAVIRCFDH 1bia 6 :VPLKLIALLAN T0381 34 :NQRRTLSDVARATDLTRATARRFLLTLVELGY 1bia 17 :GEFHSGEQLGETLGMSRAAINKHIQTLRDWGV T0381 66 :VATDG 1bia 50 :VFTVP T0381 71 :SAFWL 1bia 56 :KGYSL T0381 84 :YSYLSSLS 1bia 70 :KQILGQLD T0381 94 :EVAQPHLE 1bia 88 :DSTNQYLL T0381 105 :HKVHE 1bia 96 :DRIGE T0381 116 :LDGADIVYVARVPV 1bia 101 :LKSGDACIAEYQQA T0381 138 :TIGTRLPAYA 1bia 126 :PFGANLYLSM T0381 148 :TS 1bia 145 :AA T0381 152 :RVLLAGL 1bia 149 :LSLVIGI T0381 162 :ELDAYLEKLDIQRL 1bia 156 :VMAEVLRKLGADKV T0381 198 :ICVL 1bia 189 :VELT T0381 208 :GLRSMAAPIRGA 1bia 199 :AQIVIGAGINMA T0381 233 :AAR 1bia 224 :ITL T0381 236 :YSLEDLHSDLIPSLRVTATDIEQD 1bia 233 :LDRNTLAAMLIRELRAALELFEQE Number of specific fragments extracted= 16 number of extra gaps= 1 total=889 Will force an alignment to be made, even if fragment is small Number of alignments=144 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2dbbA/T0381-2dbbA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2dbbA expands to /projects/compbio/data/pdb/2dbb.pdb.gz 2dbbA:# T0381 read from 2dbbA/T0381-2dbbA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2dbbA read from 2dbbA/T0381-2dbbA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2dbbA to template set # found chain 2dbbA in template set T0381 21 :ARGLAVIRCFDHRNQ 2dbbA 9 :RVDMQLVKILSENSR T0381 37 :RTLSDVARATDLTRATARRFLLTLVELGYVAT 2dbbA 24 :LTYRELADILNTTRQRIARRIDKLKKLGIIRK T0381 71 :SAFWL 2dbbA 66 :GYMYA T0381 91 :SLPEVAQPHLEKLSH 2dbbA 77 :KVPSDADKVISEISD T0381 107 :VHESSSVSILDGA 2dbbA 92 :IEYVKSVEKGVGR T0381 120 :DIVYVARVPV 2dbbA 106 :NIIVRLLLPK T0381 182 :ARDELKAAILAVRAD 2dbbA 116 :DIKDAENLISEFLQR Number of specific fragments extracted= 7 number of extra gaps= 0 total=896 Will force an alignment to be made, even if fragment is small Number of alignments=145 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2dbbA/T0381-2dbbA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0381 read from 2dbbA/T0381-2dbbA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2dbbA read from 2dbbA/T0381-2dbbA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2dbbA in template set Warning: unaligning (T0381)P12 because first residue in template chain is (2dbbA)K6 T0381 13 :SPDYV 2dbbA 7 :LDRVD T0381 24 :LAVIRCFDHR 2dbbA 12 :MQLVKILSEN T0381 35 :QRRTLSDVARATDLTRATARRFLLTLVELGYVAT 2dbbA 22 :SRLTYRELADILNTTRQRIARRIDKLKKLGIIRK T0381 69 :DG 2dbbA 60 :PD T0381 71 :SAFW 2dbbA 66 :GYMY T0381 91 :SLPEVAQPHLEKLSH 2dbbA 77 :KVPSDADKVISEISD T0381 107 :VHESSSVSILDG 2dbbA 92 :IEYVKSVEKGVG T0381 119 :ADIVYVARVPV 2dbbA 105 :YNIIVRLLLPK T0381 159 :PDDELDAYLEK 2dbbA 116 :DIKDAENLISE T0381 193 :VRAD 2dbbA 127 :FLQR Number of specific fragments extracted= 10 number of extra gaps= 0 total=906 Will force an alignment to be made, even if fragment is small Number of alignments=146 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2dbbA/T0381-2dbbA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0381 read from 2dbbA/T0381-2dbbA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2dbbA read from 2dbbA/T0381-2dbbA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2dbbA in template set T0381 24 :LAVIRCFDH 2dbbA 12 :MQLVKILSE T0381 34 :NQRRTLSDVARATDLTRATARRFLLTLVELGYVATDG 2dbbA 21 :NSRLTYRELADILNTTRQRIARRIDKLKKLGIIRKFT T0381 72 :AFWL 2dbbA 66 :GYMY T0381 91 :SLPEV 2dbbA 77 :KVPSD T0381 100 :LEKLSHKVH 2dbbA 82 :ADKVISEIS T0381 109 :ESSSVSILDG 2dbbA 94 :YVKSVEKGVG T0381 119 :ADIVYVARVPV 2dbbA 105 :YNIIVRLLLPK T0381 159 :PDDELDAYLEKL 2dbbA 116 :DIKDAENLISEF T0381 172 :IQR 2dbbA 128 :LQR Number of specific fragments extracted= 9 number of extra gaps= 0 total=915 Will force an alignment to be made, even if fragment is small Number of alignments=147 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1hw1A/T0381-1hw1A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1hw1A expands to /projects/compbio/data/pdb/1hw1.pdb.gz 1hw1A:# T0381 read from 1hw1A/T0381-1hw1A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1hw1A read from 1hw1A/T0381-1hw1A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1hw1A to template set # found chain 1hw1A in template set Warning: unaligning (T0381)S13 because first residue in template chain is (1hw1A)A5 T0381 14 :PDYVQSLAR 1hw1A 6 :QSPAGFAEE T0381 25 :AVIRCFDHRN 1hw1A 15 :YIIESIWNNR T0381 35 :Q 1hw1A 28 :G T0381 37 :RTLSDVARATDLTRATARRFLLTLVELGYVATDGSA 1hw1A 32 :PAERELSELIGVTRTTLREVLQRLARDGWLTIQHGK T0381 75 :LTPRVLEL 1hw1A 78 :SGLNILET T0381 84 :YSYLSSLSLPEVAQPHLEKLSHKV 1hw1A 86 :LARLDHESVPQLIDNLLSVRTNIS T0381 145 :AYATSM 1hw1A 112 :FIRTAF T0381 159 :PDDELDAYLEKLD 1hw1A 120 :HPDKAQEVLATAN T0381 178 :RTITARDELKAAILAVRAD 1hw1A 133 :EVADHADAFAELDYNIFRG T0381 237 :SLEDLH 1hw1A 158 :NPIYGL T0381 243 :SDLIPSLRVTATDIEQDL 1hw1A 183 :PEARSLALGFYHKLSALC T0381 261 :A 1hw1A 203 :G Number of specific fragments extracted= 12 number of extra gaps= 0 total=927 Will force an alignment to be made, even if fragment is small Number of alignments=148 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1hw1A/T0381-1hw1A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0381 read from 1hw1A/T0381-1hw1A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1hw1A read from 1hw1A/T0381-1hw1A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1hw1A in template set Warning: unaligning (T0381)S13 because first residue in template chain is (1hw1A)A5 T0381 14 :PDYVQSLAR 1hw1A 6 :QSPAGFAEE T0381 25 :AVIRCFDHRN 1hw1A 15 :YIIESIWNNR T0381 35 :QR 1hw1A 28 :GT T0381 37 :RTLSDVARATDLTRATARRFLLTLVELGYVATDGSA 1hw1A 32 :PAERELSELIGVTRTTLREVLQRLARDGWLTIQHGK T0381 73 :FW 1hw1A 69 :TK T0381 75 :LTPRVLEL 1hw1A 78 :SGLNILET T0381 84 :YSYLSSLSLPEVAQPHLEKLSHKV 1hw1A 86 :LARLDHESVPQLIDNLLSVRTNIS T0381 145 :AYATSM 1hw1A 112 :FIRTAF T0381 159 :PDDELDAYLEKLD 1hw1A 120 :HPDKAQEVLATAN T0381 178 :RTITARDELKAAILAVRAD 1hw1A 133 :EVADHADAFAELDYNIFRG T0381 237 :SLEDL 1hw1A 158 :NPIYG T0381 243 :SDLIPSLRVTATDIEQDL 1hw1A 183 :PEARSLALGFYHKLSALC T0381 261 :A 1hw1A 203 :G Number of specific fragments extracted= 13 number of extra gaps= 0 total=940 Will force an alignment to be made, even if fragment is small Number of alignments=149 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1hw1A/T0381-1hw1A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0381 read from 1hw1A/T0381-1hw1A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1hw1A read from 1hw1A/T0381-1hw1A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1hw1A in template set Warning: unaligning (T0381)S13 because first residue in template chain is (1hw1A)A5 T0381 14 :PDYVQSLAR 1hw1A 6 :QSPAGFAEE T0381 25 :AVIRCFDHRNQR 1hw1A 15 :YIIESIWNNRFP T0381 37 :RTLSDVARATDLTRATARRFLLTLVELGYVATDGSA 1hw1A 32 :PAERELSELIGVTRTTLREVLQRLARDGWLTIQHGK T0381 75 :LTPRVLELG 1hw1A 78 :SGLNILETL T0381 85 :SYLSSLSLPEVAQPHLEKLSHKV 1hw1A 87 :ARLDHESVPQLIDNLLSVRTNIS T0381 147 :AT 1hw1A 114 :RT T0381 155 :LAGLPDDELDAYLEKL 1hw1A 116 :AFRQHPDKAQEVLATA T0381 177 :ERTITARDELKAAILAVRAD 1hw1A 132 :NEVADHADAFAELDYNIFRG T0381 239 :EDLHSDLIPSLRVTATDIEQ 1hw1A 183 :PEARSLALGFYHKLSALCSE Number of specific fragments extracted= 9 number of extra gaps= 0 total=949 Will force an alignment to be made, even if fragment is small Number of alignments=150 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2cg4A/T0381-2cg4A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2cg4A expands to /projects/compbio/data/pdb/2cg4.pdb.gz 2cg4A:# T0381 read from 2cg4A/T0381-2cg4A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2cg4A read from 2cg4A/T0381-2cg4A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2cg4A to template set # found chain 2cg4A in template set Warning: unaligning (T0381)L116 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2cg4A)T102 Warning: unaligning (T0381)D117 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2cg4A)T102 Warning: unaligning (T0381)G118 because of BadResidue code BAD_PEPTIDE at template residue (2cg4A)G103 T0381 16 :YV 2cg4A 9 :LD T0381 24 :LAVIRCFDHRNQ 2cg4A 11 :RGILEALMGNAR T0381 37 :RTLSDVARATDLTRATARRFLLTLVELGYVAT 2cg4A 23 :TAYAELAKQFGVSPETIHVRVEKMKQAGIITG T0381 69 :DG 2cg4A 60 :SP T0381 72 :AFWLT 2cg4A 65 :GYDVG T0381 87 :LSSLSLPEVAQPHLE 2cg4A 76 :LKSAKDYPSALAKLE T0381 106 :KVHESSSVSI 2cg4A 91 :SLDEVTEAYY T0381 119 :A 2cg4A 104 :H T0381 120 :DIVYVARVP 2cg4A 106 :SIFIKVMCR T0381 159 :PDDELDAYLEK 2cg4A 115 :SIDALQHVLIN Number of specific fragments extracted= 10 number of extra gaps= 1 total=959 Will force an alignment to be made, even if fragment is small Number of alignments=151 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2cg4A/T0381-2cg4A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0381 read from 2cg4A/T0381-2cg4A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2cg4A read from 2cg4A/T0381-2cg4A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2cg4A in template set Warning: unaligning (T0381)V127 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2cg4A)T102 Warning: unaligning (T0381)P128 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2cg4A)T102 Warning: unaligning (T0381)V129 because of BadResidue code BAD_PEPTIDE at template residue (2cg4A)G103 T0381 15 :D 2cg4A 8 :N T0381 20 :LAR 2cg4A 9 :LDR T0381 25 :AVIRCFDHR 2cg4A 12 :GILEALMGN T0381 35 :QRRTLSDVARATDLTRATARRFLLTLVELGYVAT 2cg4A 21 :ARTAYAELAKQFGVSPETIHVRVEKMKQAGIITG T0381 69 :DG 2cg4A 60 :SP T0381 71 :SA 2cg4A 65 :GY T0381 73 :FWL 2cg4A 74 :IIL T0381 88 :SSLSLPEVAQPHLEK 2cg4A 77 :KSAKDYPSALAKLES T0381 107 :VH 2cg4A 92 :LD T0381 120 :DIVYVAR 2cg4A 94 :EVTEAYY T0381 130 :SRIMTVGITI 2cg4A 104 :HYSIFIKVMC T0381 158 :LPDDELDAYLEK 2cg4A 114 :RSIDALQHVLIN Number of specific fragments extracted= 12 number of extra gaps= 1 total=971 Will force an alignment to be made, even if fragment is small Number of alignments=152 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2cg4A/T0381-2cg4A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0381 read from 2cg4A/T0381-2cg4A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2cg4A read from 2cg4A/T0381-2cg4A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2cg4A in template set Warning: unaligning (T0381)V127 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2cg4A)T102 Warning: unaligning (T0381)P128 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2cg4A)T102 Warning: unaligning (T0381)V129 because of BadResidue code BAD_PEPTIDE at template residue (2cg4A)G103 T0381 25 :AVIRCFDH 2cg4A 12 :GILEALMG T0381 34 :NQRRTLSDVARATDLTRATARRFLLTLVELGYVATDG 2cg4A 20 :NARTAYAELAKQFGVSPETIHVRVEKMKQAGIITGAR T0381 71 :SAFWLT 2cg4A 64 :LGYDVG T0381 87 :LSSLSLPEVAQPHLEKL 2cg4A 76 :LKSAKDYPSALAKLESL T0381 119 :ADIVYVAR 2cg4A 93 :DEVTEAYY T0381 130 :SRIMTVGITI 2cg4A 104 :HYSIFIKVMC T0381 158 :LPDDELDAYLEK 2cg4A 114 :RSIDALQHVLIN Number of specific fragments extracted= 7 number of extra gaps= 1 total=978 Will force an alignment to be made, even if fragment is small Number of alignments=153 # command:CPU_time= 28.057 sec, elapsed time= 31.132 sec. # command:Using radius: 8.000 NUMB_ALIGNS: 153 Adding 34980 constraints to all_contacts Done adding distance constraints # command:CPU_time= 28.226 sec, elapsed time= 31.312 sec. # command:Reading probabilities from T0381.t06.CB8-sep9.rdb Reading constraints from ConstraintSet all_contacts maxweight: 23.615 Optimizing... Probability sum: -434.613, CN propb: -434.613 weights: 0.352 constraints: 615 # command:CPU_time= 224.559 sec, elapsed time= 227.758 sec. # command:Found ConstraintSet # PrintContacts log_align.constraints Number of constraints in align 615 # command:Found ConstraintSet # PrintContacts log_align_bonus.constraints Number of constraints in align.bonus 615 # command:Found ConstraintSet # PrintContacts log_rejected.constraints Number of constraints in rejected 2517 # command:Found ConstraintSet # PrintContacts log_rejected_bonus.constraints Number of constraints in rejected.bonus 2517 # command:Found ConstraintSet # PrintContacts log_noncontact.constraints Number of constraints in noncontact 29764 # command:Found ConstraintSet # PrintContacts log_noncontact_bonus.constraints Number of constraints in noncontact.bonus 29764 # command:CPU_time= 225.165 sec, elapsed time= 228.772 sec. # command: