# command:# Prefix for input files set to /projects/compbio/experiments/undertaker/atoms-inputs/ # command:# reading cullpdb_pc80_res1.2_R0.2_d070810_chains408.atoms.gz # #computed average backbone with maximum peptide_sq_deviance = 0.002 # computed average trans backbone unit from 1600 examples # computed average trans backbone unit before proline from 52 examples # trans (non-proline) backbone unit: # CA= -2.2097 1.0151 -0.0046 # O= -0.1488 2.2425 0.0020 # C= -0.6903 1.1357 0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4580 -0.0000 -0.0000 # cis backbone unit: # CA= -0.1462 2.4515 0.0018 # O= -2.0272 0.9713 0.0022 # C= -0.8006 1.0755 0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4659 0.0000 0.0000 # trans backbone unit before proline: # CA= -2.2063 1.0654 0.0002 # O= -0.1193 2.2442 0.0054 # C= -0.6842 1.1479 -0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4661 -0.0000 0.0000 # After reading cullpdb_pc80_res1.2_R0.2_d070810_chains408.atoms.gz have 408 chains in training database # Count of chains,residues,atoms: 408,82794,639987 # 79931 residues have no bad marker # 573 residues lack atoms needed to compute omega # 313 residues have cis peptide # number of each bad type: # NON_STANDARD_RESIDUE 0 # HAS_OXT 264 # TOO_MANY_ATOMS 0 # TOO_FEW_ATOMS 378 # HAS_UNKNOWN_ATOMS 0 # HAS_DUPLICATE_ATOMS 0 # CHAIN_BREAK_BEFORE 148 # NON_PLANAR_PEPTIDE 17 # BAD_PEPTIDE 812 # HIGH_B_FACTOR 1566 # Note: may sum to more than number of residues, # because one residue may have multiple problems # command:# Reading rotamer library from dunbrack-40pc-3157.rot # command:# Prefix for input files set to /projects/compbio/experiments/undertaker/spots/ # command:# ReadAtomType exp-pdb.types Read AtomType exp-pdb with 49 types. # command:# ReadClashTable exp-pdb-2191-2symm.clash # Read ClashTable exp-pdb-2191-2symm checking bonds symmetric at MaxSep 2 # command:# command:# Prefix for input files set to # command:# Making conformation for sequence T0528 numbered 1 through 388 Created new target T0528 from T0528.a2m # command:CPU_time= 5.680 sec, elapsed time= 5.737 sec. # command:# reading script from file all-templates.under # Reading fragments from alignment file # Attempting to read fragment alignments from file 3i45A/T0528-3i45A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 3i45A expands to /projects/compbio/data/pdb/3i45.pdb.gz 3i45A:Skipped atom 353, because occupancy 0.5 <= existing 0.500 in 3i45A Skipped atom 357, because occupancy 0.500 <= existing 0.500 in 3i45A Skipped atom 359, because occupancy 0.500 <= existing 0.500 in 3i45A Skipped atom 361, because occupancy 0.500 <= existing 0.500 in 3i45A Skipped atom 363, because occupancy 0.500 <= existing 0.500 in 3i45A Skipped atom 365, because occupancy 0.500 <= existing 0.500 in 3i45A Skipped atom 755, because occupancy 0.500 <= existing 0.500 in 3i45A Skipped atom 759, because occupancy 0.500 <= existing 0.500 in 3i45A Skipped atom 761, because occupancy 0.500 <= existing 0.500 in 3i45A Skipped atom 763, because occupancy 0.500 <= existing 0.500 in 3i45A Skipped atom 765, because occupancy 0.500 <= existing 0.500 in 3i45A Skipped atom 1253, because occupancy 0.500 <= existing 0.500 in 3i45A Skipped atom 1257, because occupancy 0.500 <= existing 0.500 in 3i45A Skipped atom 1259, because occupancy 0.500 <= existing 0.500 in 3i45A Skipped atom 1261, because occupancy 0.500 <= existing 0.500 in 3i45A Skipped atom 1263, because occupancy 0.500 <= existing 0.500 in 3i45A Skipped atom 1265, because occupancy 0.500 <= existing 0.500 in 3i45A Skipped atom 1268, because occupancy 0.500 <= existing 0.500 in 3i45A Skipped atom 1272, because occupancy 0.500 <= existing 0.500 in 3i45A Skipped atom 1274, because occupancy 0.500 <= existing 0.500 in 3i45A Skipped atom 1276, because occupancy 0.500 <= existing 0.500 in 3i45A Skipped atom 1278, because occupancy 0.500 <= existing 0.500 in 3i45A Skipped atom 1280, because occupancy 0.500 <= existing 0.500 in 3i45A Skipped atom 1433, because occupancy 0.500 <= existing 0.500 in 3i45A Skipped atom 1437, because occupancy 0.500 <= existing 0.500 in 3i45A Skipped atom 1439, because occupancy 0.500 <= existing 0.500 in 3i45A Skipped atom 1441, because occupancy 0.500 <= existing 0.500 in 3i45A Skipped atom 1443, because occupancy 0.500 <= existing 0.500 in 3i45A Skipped atom 1445, because occupancy 0.500 <= existing 0.500 in 3i45A Skipped atom 1447, because occupancy 0.500 <= existing 0.500 in 3i45A Skipped atom 1449, because occupancy 0.500 <= existing 0.500 in 3i45A Skipped atom 1451, because occupancy 0.500 <= existing 0.500 in 3i45A Skipped atom 2332, because occupancy 0.500 <= existing 0.500 in 3i45A Skipped atom 2336, because occupancy 0.500 <= existing 0.500 in 3i45A Skipped atom 2338, because occupancy 0.500 <= existing 0.500 in 3i45A Skipped atom 2340, because occupancy 0.500 <= existing 0.500 in 3i45A Skipped atom 2342, because occupancy 0.500 <= existing 0.500 in 3i45A Skipped atom 2779, because occupancy 0.500 <= existing 0.500 in 3i45A Skipped atom 2783, because occupancy 0.500 <= existing 0.500 in 3i45A Skipped atom 2785, because occupancy 0.500 <= existing 0.500 in 3i45A Skipped atom 2787, because occupancy 0.500 <= existing 0.500 in 3i45A Skipped atom 2789, because occupancy 0.500 <= existing 0.500 in 3i45A # T0528 read from 3i45A/T0528-3i45A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3i45A read from 3i45A/T0528-3i45A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3i45A to template set # found chain 3i45A in template set Warning: unaligning (T0528)G93 because of BadResidue code BAD_PEPTIDE in next template residue (3i45A)T80 Warning: unaligning (T0528)T94 because of BadResidue code BAD_PEPTIDE at template residue (3i45A)T80 Warning: unaligning (T0528)G266 because of BadResidue code BAD_PEPTIDE in next template residue (3i45A)T255 Warning: unaligning (T0528)A267 because of BadResidue code BAD_PEPTIDE at template residue (3i45A)T255 T0528 16 :ADDLKIALIYGKTG 3i45A 3 :LEAIRIGEINSYSQ # choosing archetypes in rotamer library T0528 31 :LEAYAKQTETGLMMGLE 3i45A 17 :IPAFTLPYRNGWQLAVE T0528 49 :ATKGTMTLD 3i45A 34 :QINAAGGLL T0528 58 :GRKIVVITKDDQSKPDLSKAALAEAYQDDGADIAI 3i45A 44 :GRPLEVISRDDGGDPGKAVTAAQELLTRHGVHALA T0528 95 :SSSAAALADLPVAEENKKILIVEPAVADQITGEKWNRYIFRTGRNSSQDAISNAVAIGKQG 3i45A 81 :FLSHVGLAVSDFARQRKVLFMASEPLTDALTWEKGNRYTYRLRPSTYMQAAMLAAEAAKLP T0528 156 :VTIATLAQDYAFGRDGVAAFKEALAKT 3i45A 143 :TRWATIAPNYEYGQSAVARFKELLLAA T0528 183 :GATLATEEYVPTTTTDFTAVGQRLFDA 3i45A 172 :EVTFVAEQWPALYKLDAGPTVQALQQA T0528 215 :GKKIIWVIWAGGG 3i45A 199 :EPEGLFNVLFGAD T0528 228 :DPLTKLQDMDPK 3i45A 214 :KFVREGRVRGLF T0528 240 :RYGIELSTGG 3i45A 227 :GRQVVSMLTG T0528 251 :ILPALAAYKR 3i45A 237 :EPEYLNPLKD T0528 261 :LPGME 3i45A 249 :PEGWI T0528 268 :TYYYYDI 3i45A 256 :GYPWYDI T0528 276 :KNPINEWLVTEHQKRFNAPPDFFTAGGFSAAMAVVTAVQKAKSTDTEKLIAAMEGMEFDTPKGKMVFRKEDHQALQSMYHFKVK 3i45A 263 :DTAPHRAFVEAYRARWKEDPFVGSLVGYNTLTAMAVAFEKAGGTESETLVETLKDMAFSTPMGPLSFRASDHQSTMGAWVGRTA T0528 360 :VDPAVA 3i45A 349 :DGKGVM T0528 366 :WAVLEPVRELK 3i45A 357 :WRYVDGGSVLP Number of specific fragments extracted= 16 number of extra gaps= 2 total=16 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 3i45A/T0528-3i45A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0528 read from 3i45A/T0528-3i45A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3i45A read from 3i45A/T0528-3i45A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3i45A in template set Warning: unaligning (T0528)G93 because of BadResidue code BAD_PEPTIDE in next template residue (3i45A)T80 Warning: unaligning (T0528)T94 because of BadResidue code BAD_PEPTIDE at template residue (3i45A)T80 Warning: unaligning (T0528)G266 because of BadResidue code BAD_PEPTIDE in next template residue (3i45A)T255 Warning: unaligning (T0528)A267 because of BadResidue code BAD_PEPTIDE at template residue (3i45A)T255 T0528 16 :ADDLKIALIYGKTGPLE 3i45A 3 :LEAIRIGEINSYSQIPA T0528 34 :YAKQTETGLMMGLEYATKGTMTLDGRKIVVITKDDQSKPDLSKAALAEAYQDDGADIAI 3i45A 20 :FTLPYRNGWQLAVEQINAAGGLLGGRPLEVISRDDGGDPGKAVTAAQELLTRHGVHALA T0528 95 :SSSAAALADLPVAEENKKILIVEPAVADQITGEKWNRYIFRTGRNSSQDAISNAVAIGKQGV 3i45A 81 :FLSHVGLAVSDFARQRKVLFMASEPLTDALTWEKGNRYTYRLRPSTYMQAAMLAAEAAKLPI T0528 157 :TIATLAQDYAFGRDGVAAFKEALAKT 3i45A 144 :RWATIAPNYEYGQSAVARFKELLLAA T0528 183 :GATLATEEYVPTTTTDFTAVGQRLFDA 3i45A 172 :EVTFVAEQWPALYKLDAGPTVQALQQA T0528 213 :KP 3i45A 199 :EP T0528 216 :KKIIWVIWAGGGDPLTK 3i45A 201 :EGLFNVLFGADLPKFVR T0528 233 :LQDMDP 3i45A 219 :GRVRGL T0528 239 :KRYGIE 3i45A 229 :QVVSML T0528 246 :STGGNILPALAA 3i45A 235 :TGEPEYLNPLKD T0528 259 :KRLPGME 3i45A 247 :EAPEGWI T0528 268 :TYYYYDI 3i45A 256 :GYPWYDI T0528 276 :KNPINEWLVTEHQKRFNAPPDFFTAGGFSAAMAVVTAVQKAKSTDTEKLIAAMEGMEFDTPKGKMVFRKEDHQALQSMYHFKVK 3i45A 263 :DTAPHRAFVEAYRARWKEDPFVGSLVGYNTLTAMAVAFEKAGGTESETLVETLKDMAFSTPMGPLSFRASDHQSTMGAWVGRTA T0528 360 :VDPAVAWA 3i45A 349 :DGKGVMVD T0528 372 :VRELKIEEMNIP 3i45A 357 :WRYVDGGSVLPP Number of specific fragments extracted= 15 number of extra gaps= 2 total=31 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 3i45A/T0528-3i45A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0528 read from 3i45A/T0528-3i45A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3i45A read from 3i45A/T0528-3i45A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3i45A in template set Warning: unaligning (T0528)A15 because first residue in template chain is (3i45A)S2 Warning: unaligning (T0528)G93 because of BadResidue code BAD_PEPTIDE in next template residue (3i45A)T80 Warning: unaligning (T0528)T94 because of BadResidue code BAD_PEPTIDE at template residue (3i45A)T80 Warning: unaligning (T0528)G266 because of BadResidue code BAD_PEPTIDE in next template residue (3i45A)T255 Warning: unaligning (T0528)A267 because of BadResidue code BAD_PEPTIDE at template residue (3i45A)T255 T0528 16 :ADDLKIALIYGKTGP 3i45A 3 :LEAIRIGEINSYSQI T0528 32 :EAYAKQTETGLMMGLEYATKGTMTLDGRKIVVITKDDQSKPDLSKAALAEAYQDDGADIAI 3i45A 18 :PAFTLPYRNGWQLAVEQINAAGGLLGGRPLEVISRDDGGDPGKAVTAAQELLTRHGVHALA T0528 95 :SSSAAALADLPVAEENKKILIVEPAVADQITGEKWNRYIFRTGRNSSQDAISNAVAIGK 3i45A 81 :FLSHVGLAVSDFARQRKVLFMASEPLTDALTWEKGNRYTYRLRPSTYMQAAMLAAEAAK T0528 154 :QGVTIATLAQDYAFGRDGVAAFKEALAKT 3i45A 141 :PITRWATIAPNYEYGQSAVARFKELLLAA T0528 183 :GATLATEEYVPTTTTDFTAVGQRL 3i45A 172 :EVTFVAEQWPALYKLDAGPTVQAL T0528 210 :LKDKPGKKIIWVIWAGGGDPLTKLQDMDP 3i45A 196 :QQAEPEGLFNVLFGADLPKFVREGRVRGL T0528 239 :KRYGIELSTGGNILPALAAYKR 3i45A 226 :AGRQVVSMLTGEPEYLNPLKDE T0528 261 :LPGME 3i45A 249 :PEGWI T0528 268 :TYYYYDI 3i45A 256 :GYPWYDI T0528 276 :KNPINEWLVTEHQKRFNAPPDFFTAGGFSAAMAVVTAVQKAKSTDTEKLIAAMEGMEFDTPKGKMVFRKEDHQALQSMYHFKVKVDPAVAWAVLEPVRE 3i45A 263 :DTAPHRAFVEAYRARWKEDPFVGSLVGYNTLTAMAVAFEKAGGTESETLVETLKDMAFSTPMGPLSFRASDHQSTMGAWVGRTALRDGKGVMVDWRYVD Number of specific fragments extracted= 10 number of extra gaps= 2 total=41 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 3i09A/T0528-3i09A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 3i09A expands to /projects/compbio/data/pdb/3i09.pdb.gz 3i09A:Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 88, because occupancy 0.500 <= existing 0.500 in 3i09A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 92, because occupancy 0.500 <= existing 0.500 in 3i09A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 94, because occupancy 0.500 <= existing 0.500 in 3i09A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 96, because occupancy 0.370 <= existing 0.380 in 3i09A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 98, because occupancy 0.500 <= existing 0.500 in 3i09A Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 217, because occupancy 0.250 <= existing 0.500 in 3i09A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 218, because occupancy 0.250 <= existing 0.500 in 3i09A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 222, because occupancy 0.250 <= existing 0.500 in 3i09A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 223, because occupancy 0.250 <= existing 0.500 in 3i09A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 225, because occupancy 0.250 <= existing 0.500 in 3i09A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 226, because occupancy 0.250 <= existing 0.500 in 3i09A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 228, because occupancy 0.190 <= existing 0.380 in 3i09A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 229, because occupancy 0.180 <= existing 0.380 in 3i09A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 231, because occupancy 0.250 <= existing 0.500 in 3i09A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 232, because occupancy 0.250 <= existing 0.500 in 3i09A Skipped atom 389, because occupancy 0.500 <= existing 0.500 in 3i09A Skipped atom 393, because occupancy 0.500 <= existing 0.500 in 3i09A Skipped atom 395, because occupancy 0.500 <= existing 0.500 in 3i09A Skipped atom 397, because occupancy 0.500 <= existing 0.500 in 3i09A Skipped atom 399, because occupancy 0.500 <= existing 0.500 in 3i09A Skipped atom 401, because occupancy 0.500 <= existing 0.500 in 3i09A Skipped atom 452, because occupancy 0.330 <= existing 0.340 in 3i09A Skipped atom 453, because occupancy 0.330 <= existing 0.340 in 3i09A Skipped atom 457, because occupancy 0.330 <= existing 0.340 in 3i09A Skipped atom 458, because occupancy 0.330 <= existing 0.340 in 3i09A Skipped atom 460, because occupancy 0.330 <= existing 0.340 in 3i09A Skipped atom 461, because occupancy 0.330 <= existing 0.340 in 3i09A Skipped atom 464, because occupancy 0.500 <= existing 0.500 in 3i09A Skipped atom 468, because occupancy 0.500 <= existing 0.500 in 3i09A Skipped atom 470, because occupancy 0.500 <= existing 0.500 in 3i09A Skipped atom 472, because occupancy 0.500 <= existing 0.500 in 3i09A Skipped atom 474, because occupancy 0.500 <= existing 0.500 in 3i09A Skipped atom 476, because occupancy 0.500 <= existing 0.500 in 3i09A Skipped atom 484, because occupancy 0.500 <= existing 0.500 in 3i09A Skipped atom 488, because occupancy 0.500 <= existing 0.500 in 3i09A Skipped atom 490, because occupancy 0.500 <= existing 0.500 in 3i09A Skipped atom 492, because occupancy 0.500 <= existing 0.500 in 3i09A Skipped atom 494, because occupancy 0.500 <= existing 0.500 in 3i09A Skipped atom 496, because occupancy 0.500 <= existing 0.500 in 3i09A Skipped atom 498, because occupancy 0.500 <= existing 0.500 in 3i09A Skipped atom 500, because occupancy 0.500 <= existing 0.500 in 3i09A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 1039, because occupancy 0.300 <= existing 0.700 in 3i09A Skipped atom 1043, because occupancy 0.300 <= existing 0.700 in 3i09A Skipped atom 1045, because occupancy 0.300 <= existing 0.700 in 3i09A Skipped atom 1047, because occupancy 0.300 <= existing 0.700 in 3i09A Skipped atom 1049, because occupancy 0.300 <= existing 0.700 in 3i09A Skipped atom 1051, because occupancy 0.300 <= existing 0.700 in 3i09A Skipped atom 1062, because occupancy 0.500 <= existing 0.500 in 3i09A Skipped atom 1066, because occupancy 0.500 <= existing 0.500 in 3i09A Skipped atom 1068, because occupancy 0.500 <= existing 0.500 in 3i09A Skipped atom 1070, because occupancy 0.500 <= existing 0.500 in 3i09A Skipped atom 1072, because occupancy 0.500 <= existing 0.500 in 3i09A Skipped atom 1074, because occupancy 0.500 <= existing 0.500 in 3i09A Skipped atom 1180, because occupancy 0.500 <= existing 0.500 in 3i09A Skipped atom 1184, because occupancy 0.500 <= existing 0.500 in 3i09A Skipped atom 1186, because occupancy 0.500 <= existing 0.500 in 3i09A Skipped atom 1188, because occupancy 0.500 <= existing 0.500 in 3i09A Skipped atom 1190, because occupancy 0.500 <= existing 0.500 in 3i09A Skipped atom 1192, because occupancy 0.500 <= existing 0.500 in 3i09A Skipped atom 1208, because occupancy 0.500 <= existing 0.500 in 3i09A Skipped atom 1212, because occupancy 0.500 <= existing 0.500 in 3i09A Skipped atom 1214, because occupancy 0.500 <= existing 0.500 in 3i09A Skipped atom 1216, because occupancy 0.500 <= existing 0.500 in 3i09A Skipped atom 1218, because occupancy 0.500 <= existing 0.500 in 3i09A Skipped atom 1220, because occupancy 0.500 <= existing 0.500 in 3i09A Skipped atom 1329, because occupancy 0.500 <= existing 0.500 in 3i09A Skipped atom 1333, because occupancy 0.500 <= existing 0.500 in 3i09A Skipped atom 1335, because occupancy 0.500 <= existing 0.500 in 3i09A Skipped atom 1337, because occupancy 0.500 <= existing 0.500 in 3i09A Skipped atom 1339, because occupancy 0.500 <= existing 0.500 in 3i09A Skipped atom 1341, because occupancy 0.500 <= existing 0.500 in 3i09A Skipped atom 1485, because occupancy 0.500 <= existing 0.500 in 3i09A Skipped atom 1489, because occupancy 0.500 <= existing 0.500 in 3i09A Skipped atom 1491, because occupancy 0.500 <= existing 0.500 in 3i09A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 1751, because occupancy 0.500 <= existing 0.500 in 3i09A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 1755, because occupancy 0.500 <= existing 0.500 in 3i09A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1757, because occupancy 0.500 <= existing 0.500 in 3i09A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1759, because occupancy 0.370 <= existing 0.380 in 3i09A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1761, because occupancy 0.500 <= existing 0.500 in 3i09A Skipped atom 1935, because occupancy 0.500 <= existing 0.500 in 3i09A Skipped atom 1939, because occupancy 0.500 <= existing 0.500 in 3i09A Skipped atom 1941, because occupancy 0.500 <= existing 0.500 in 3i09A Skipped atom 1943, because occupancy 0.500 <= existing 0.500 in 3i09A Skipped atom 1945, because occupancy 0.500 <= existing 0.500 in 3i09A Skipped atom 1947, because occupancy 0.500 <= existing 0.500 in 3i09A Skipped atom 1949, because occupancy 0.500 <= existing 0.500 in 3i09A Skipped atom 1951, because occupancy 0.500 <= existing 0.500 in 3i09A Skipped atom 1953, because occupancy 0.500 <= existing 0.500 in 3i09A Skipped atom 2011, because occupancy 0.500 <= existing 0.500 in 3i09A Skipped atom 2015, because occupancy 0.500 <= existing 0.500 in 3i09A Skipped atom 2017, because occupancy 0.500 <= existing 0.500 in 3i09A Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 2114, because occupancy 0.200 <= existing 0.800 in 3i09A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 2118, because occupancy 0.200 <= existing 0.800 in 3i09A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 2120, because occupancy 0.200 <= existing 0.800 in 3i09A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 2122, because occupancy 0.150 <= existing 0.600 in 3i09A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 2124, because occupancy 0.200 <= existing 0.800 in 3i09A Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 2145, because occupancy 0.500 <= existing 0.500 in 3i09A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 2149, because occupancy 0.500 <= existing 0.500 in 3i09A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 2151, because occupancy 0.500 <= existing 0.500 in 3i09A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 2153, because occupancy 0.370 <= existing 0.380 in 3i09A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 2155, because occupancy 0.500 <= existing 0.500 in 3i09A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 2420, because occupancy 0.300 <= existing 0.700 in 3i09A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 2424, because occupancy 0.300 <= existing 0.700 in 3i09A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 2426, because occupancy 0.300 <= existing 0.700 in 3i09A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 2428, because occupancy 0.230 <= existing 0.520 in 3i09A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 2430, because occupancy 0.300 <= existing 0.700 in 3i09A Skipped atom 2433, because occupancy 0.500 <= existing 0.500 in 3i09A Skipped atom 2437, because occupancy 0.500 <= existing 0.500 in 3i09A Skipped atom 2439, because occupancy 0.500 <= existing 0.500 in 3i09A Skipped atom 2441, because occupancy 0.500 <= existing 0.500 in 3i09A Skipped atom 2443, because occupancy 0.500 <= existing 0.500 in 3i09A Skipped atom 2445, because occupancy 0.500 <= existing 0.500 in 3i09A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 2757, because occupancy 0.500 <= existing 0.500 in 3i09A Skipped atom 2761, because occupancy 0.500 <= existing 0.500 in 3i09A Skipped atom 2763, because occupancy 0.500 <= existing 0.500 in 3i09A Skipped atom 2765, because occupancy 0.500 <= existing 0.500 in 3i09A Skipped atom 2767, because occupancy 0.500 <= existing 0.500 in 3i09A Skipped atom 2769, because occupancy 0.500 <= existing 0.500 in 3i09A Skipped atom 2771, because occupancy 0.500 <= existing 0.500 in 3i09A Skipped atom 2773, because occupancy 0.500 <= existing 0.500 in 3i09A Skipped atom 2775, because occupancy 0.500 <= existing 0.500 in 3i09A Skipped atom 2898, because occupancy 0.300 <= existing 0.700 in 3i09A Skipped atom 2902, because occupancy 0.300 <= existing 0.700 in 3i09A Skipped atom 2904, because occupancy 0.300 <= existing 0.700 in 3i09A Skipped atom 2906, because occupancy 0.300 <= existing 0.700 in 3i09A Skipped atom 2908, because occupancy 0.300 <= existing 0.700 in 3i09A Skipped atom 2910, because occupancy 0.300 <= existing 0.700 in 3i09A # T0528 read from 3i09A/T0528-3i09A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3i09A read from 3i09A/T0528-3i09A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3i09A to template set # found chain 3i09A in template set Warning: unaligning (T0528)A15 because first residue in template chain is (3i09A)G0 Warning: unaligning (T0528)R135 because of BadResidue code BAD_PEPTIDE in next template residue (3i09A)Y143 Warning: unaligning (T0528)T136 because of BadResidue code BAD_PEPTIDE at template residue (3i09A)Y143 Warning: unaligning (T0528)G338 because of BadResidue code TOO_FEW_ATOMS+BAD_PEPTIDE in next template residue (3i09A)K343 Warning: unaligning (T0528)K339 because of BadResidue code TOO_FEW_ATOMS+BAD_PEPTIDE at template residue (3i09A)K343 T0528 16 :ADDLKIALIYGKTGPLEAY 3i09A 25 :ADSVKIGFITDMSGLYADI T0528 35 :AKQTETGLMMGLE 3i09A 45 :GQGGLEAIKMAVA T0528 49 :AT 3i09A 58 :DF T0528 53 :TMTLDGRKIVVITKDDQSKPDLSKAALAEAYQDDGADIAIGTSSSAAALADLPVAEENKKILIVEPAVADQITGEKWNRYIF 3i09A 60 :GGKVNGKPIEVVYADHQNKADIAASKAREWMDRGGLDLLVGGTNSATALSMNQVAAEKKKVYINIGAGADTLTNEQCTPYTV T0528 137 :GRNSSQDAISNAVAIGKQG 3i09A 144 :AYDTMALAKGTGSAVVKQG T0528 156 :VTIATLAQDYAFGRDGVAAFKEALAKTGATLATEEYVPTTTTDFTAVGQRLFDA 3i09A 164 :KTWFFLTADYAFGKALEKNTADVVKANGGKVLGEVRHPLSASDFSSFLLQAQSS T0528 215 :GKKIIWVIWAGGG 3i09A 218 :KAQILGLANAGGD T0528 228 :DPLTKLQDMDPK 3i09A 233 :NAIKAAKEFGIT T0528 240 :RYGIELSTGG 3i09A 246 :TMKLAALLMF T0528 251 :ILPALAAYKR 3i09A 256 :INDVHALGLE T0528 261 :LPGMEGATYYYYDI 3i09A 267 :TQGLVLTDSWYWNR T0528 277 :NPINEWLVTEHQKRFNAPPDFFTAGGFSAAMAVVTAVQKAKSTDTEKLIAAMEGMEFDTPK 3i09A 281 :DQASRQWAQRYFAKMKKMPSSLQAADYSSVTTYLKAVQAAGSTDSDKVMAQLKKMKIDDFY T0528 340 :MVFRK 3i09A 344 :GYIRT T0528 346 :DHQALQSMYHFKVKVDP 3i09A 349 :DGSMIHDMYLMEVKKPS T0528 363 :AVAWAVLEPVRELKIEEMNIPIKNKK 3i09A 368 :KEPWDYYKVVATIPGEQAFTTKQETR Number of specific fragments extracted= 15 number of extra gaps= 2 total=56 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 3i09A/T0528-3i09A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0528 read from 3i09A/T0528-3i09A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3i09A read from 3i09A/T0528-3i09A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3i09A in template set Warning: unaligning (T0528)A15 because first residue in template chain is (3i09A)G0 Warning: unaligning (T0528)R135 because of BadResidue code BAD_PEPTIDE in next template residue (3i09A)Y143 Warning: unaligning (T0528)T136 because of BadResidue code BAD_PEPTIDE at template residue (3i09A)Y143 Warning: unaligning (T0528)G338 because of BadResidue code TOO_FEW_ATOMS+BAD_PEPTIDE in next template residue (3i09A)K343 Warning: unaligning (T0528)K339 because of BadResidue code TOO_FEW_ATOMS+BAD_PEPTIDE at template residue (3i09A)K343 T0528 16 :ADDLKIALIYGKTGPLEAY 3i09A 25 :ADSVKIGFITDMSGLYADI T0528 35 :AKQTETGLMMGLEYA 3i09A 45 :GQGGLEAIKMAVADF T0528 53 :TMTLDGRKIVVITKDDQSKPDLSKAALAEAYQDDGADIAIGTSSSAAALADLPVAEENKKILIVEPAVADQITGEKWNRYIF 3i09A 60 :GGKVNGKPIEVVYADHQNKADIAASKAREWMDRGGLDLLVGGTNSATALSMNQVAAEKKKVYINIGAGADTLTNEQCTPYTV T0528 137 :GRNSSQDAISNAVAIGKQGV 3i09A 144 :AYDTMALAKGTGSAVVKQGG T0528 157 :TIATLAQDYAFGRDGVAAFKEALAKTGATLATEEYVPTTTTDFTAVGQRLFDA 3i09A 165 :TWFFLTADYAFGKALEKNTADVVKANGGKVLGEVRHPLSASDFSSFLLQAQSS T0528 213 :KP 3i09A 218 :KA T0528 216 :KKIIWVIWAGGGDPLTK 3i09A 220 :QILGLANAGGDTVNAIK T0528 233 :LQDMDP 3i09A 238 :AKEFGI T0528 239 :KRYGIELSTGGNILPALAA 3i09A 246 :TMKLAALLMFINDVHALGL T0528 259 :KRLPGMEGATYYYYDI 3i09A 265 :ETTQGLVLTDSWYWNR T0528 277 :NPINEWLVTEHQKRFNAPPDFFTAGGFSAAMAVVTAVQKAKSTDTEKLIAAMEGMEFDTPK 3i09A 281 :DQASRQWAQRYFAKMKKMPSSLQAADYSSVTTYLKAVQAAGSTDSDKVMAQLKKMKIDDFY T0528 340 :MVFRK 3i09A 344 :GYIRT T0528 346 :DHQALQSMYHFKVKVDPA 3i09A 349 :DGSMIHDMYLMEVKKPSE T0528 364 :VAWAVLEPVRELKIEEMNIPIKNKK 3i09A 369 :EPWDYYKVVATIPGEQAFTTKQETR Number of specific fragments extracted= 14 number of extra gaps= 2 total=70 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 3i09A/T0528-3i09A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0528 read from 3i09A/T0528-3i09A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3i09A read from 3i09A/T0528-3i09A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3i09A in template set Warning: unaligning (T0528)A15 because first residue in template chain is (3i09A)G0 Warning: unaligning (T0528)R135 because of BadResidue code BAD_PEPTIDE in next template residue (3i09A)Y143 Warning: unaligning (T0528)T136 because of BadResidue code BAD_PEPTIDE at template residue (3i09A)Y143 Warning: unaligning (T0528)G338 because of BadResidue code TOO_FEW_ATOMS+BAD_PEPTIDE in next template residue (3i09A)K343 Warning: unaligning (T0528)K339 because of BadResidue code TOO_FEW_ATOMS+BAD_PEPTIDE at template residue (3i09A)K343 T0528 16 :ADDLKIALIYGKTGPLEAY 3i09A 25 :ADSVKIGFITDMSGLYADI T0528 35 :AKQTETGLMMGLEYA 3i09A 45 :GQGGLEAIKMAVADF T0528 52 :GTM 3i09A 60 :GGK T0528 56 :LDGRKIVVITKDDQSKPDLSKAALAEAYQDDGADIAIGTSSSAAALADLPVAEENKKILIVEPAVADQITGEKWNRYIF 3i09A 63 :VNGKPIEVVYADHQNKADIAASKAREWMDRGGLDLLVGGTNSATALSMNQVAAEKKKVYINIGAGADTLTNEQCTPYTV T0528 137 :GRNSSQDAISNAVAIGK 3i09A 144 :AYDTMALAKGTGSAVVK T0528 154 :QGVTIATLAQDYAFGRDGVAAFKEALAKTGATLATEEYVPTTTTDFTAVGQRL 3i09A 162 :GGKTWFFLTADYAFGKALEKNTADVVKANGGKVLGEVRHPLSASDFSSFLLQA T0528 210 :LKDKPGKKIIWVIWAGGGDPLTKLQDMDPKRYGIELSTGGNILPALAAY 3i09A 215 :QSSKAQILGLANAGGDTVNAIKAAKEFGITKTMKLAALLMFINDVHALG T0528 259 :KRLPGMEGATYYYYDI 3i09A 265 :ETTQGLVLTDSWYWNR T0528 277 :NPINEWLVTEHQKRFNAPPDFFTAGGFSAAMAVVTAVQKAKSTDTEKLIAAMEGMEFDTPK 3i09A 281 :DQASRQWAQRYFAKMKKMPSSLQAADYSSVTTYLKAVQAAGSTDSDKVMAQLKKMKIDDFY T0528 340 :MVFRK 3i09A 344 :GYIRT T0528 346 :DHQALQSMYHFKVKVDPAVAWAVLEPVRELKIEE 3i09A 349 :DGSMIHDMYLMEVKKPSESKEPWDYYKVVATIPG Number of specific fragments extracted= 11 number of extra gaps= 2 total=81 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 3hutA/T0528-3hutA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 3hutA expands to /projects/compbio/data/pdb/3hut.pdb.gz 3hutA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0528 read from 3hutA/T0528-3hutA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3hutA read from 3hutA/T0528-3hutA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3hutA to template set # found chain 3hutA in template set Warning: unaligning (T0528)D17 because first residue in template chain is (3hutA)L-1 Warning: unaligning (T0528)W366 because last residue in template chain is (3hutA)I384 T0528 18 :DLKIALIYGKTGPLEAYAKQTETGLMMGLE 3hutA 40 :ALLLGYELPLTGANAAYGRVFQEAARLQLD T0528 49 :ATKGTMTLDGRKIVVITKDDQSKPDLSKAALAEAYQDDGADIAIGTSSSAAALADLPVAEENKKILIVEPAVADQITGE 3hutA 70 :RFNAAGGVGGRPVDILYADSRDDADQARTIARAFVDDPRVVGVLGDFSSTVSMAAGSIYGKEGMPQLSPTAAHPDYIKI T0528 130 :NRYIFRTGRNSSQDAISNAVAIGKQG 3hutA 149 :SPWQFRAITTPAFEGPNNAAWMIGDG T0528 156 :VTIATLAQDYAFGRDGVAAFKEALAKTGATLATEEYVPTTTTDFTAVGQRLFDA 3hutA 176 :TSVAVIGVTTDWGLSSAQAFRKAFELRGGAVVVNEEVPPGNRRFDDVIDEIEDE T0528 215 :GKKIIWVIWAGGG 3hutA 230 :APQAIYLAMAYED T0528 228 :DPLTKLQDMDP 3hutA 245 :PFLRALRARGS T0528 240 :RYGIELSTGGNILPALAAYKR 3hutA 256 :ALPVYGSSALYSPKFIDLGGP T0528 261 :LPGMEGATYYYYDI 3hutA 278 :VEGVRLATAFVLGA T0528 276 :KNPINEWLVTEHQKRFNAPPDFFTAGGFSAAMAVVTAVQKAKS 3hutA 292 :SDPVVVEFVSAYETLYGAIPTLFAAHGYDAVGIMLAAVGRAGP T0528 319 :TDTEKLIAAMEGM 3hutA 336 :VTRESLRDALAAT T0528 332 :EFDTPKGKMVFRKEDHQALQSMYHFKVKVDPAVA 3hutA 350 :RYAGVTGITRFDPETRETTKILTRLVVREGDFRV Number of specific fragments extracted= 11 number of extra gaps= 0 total=92 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 3hutA/T0528-3hutA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0528 read from 3hutA/T0528-3hutA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3hutA read from 3hutA/T0528-3hutA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3hutA in template set Warning: unaligning (T0528)W366 because last residue in template chain is (3hutA)I384 T0528 18 :DLKIALIYGKTGPLEAYAKQTETGLMMGLEYATKGT 3hutA 40 :ALLLGYELPLTGANAAYGRVFQEAARLQLDRFNAAG T0528 55 :TLDGRKIVVITKDDQSKPDLSKAALAEAYQDDGADIAIGTSSSAAALADLPVAEENKKILIVEPAVADQITG 3hutA 76 :GVGGRPVDILYADSRDDADQARTIARAFVDDPRVVGVLGDFSSTVSMAAGSIYGKEGMPQLSPTAAHPDYIK T0528 129 :WNRYIFRTGRNSSQDAISNAVAIGKQGV 3hutA 148 :ISPWQFRAITTPAFEGPNNAAWMIGDGF T0528 157 :TIATLAQDYAFGRDGVAAFKEALAKTGATLATEEYVPTTTTDFTAVGQRLFDA 3hutA 177 :SVAVIGVTTDWGLSSAQAFRKAFELRGGAVVVNEEVPPGNRRFDDVIDEIEDE T0528 213 :KP 3hutA 230 :AP T0528 216 :KKIIWVIWAGGGDPLTK 3hutA 232 :QAIYLAMAYEDAAPFLR T0528 233 :LQDMDP 3hutA 250 :LRARGS T0528 239 :KRYGIELSTGGNILPALA 3hutA 258 :PVYGSSALYSPKFIDLGG T0528 259 :KRLPGMEGATYYYYDI 3hutA 276 :PAVEGVRLATAFVLGA T0528 276 :KNPINEWLVTEHQKRFNAPPDFFTAGGFSAAMAVVTAVQKA 3hutA 292 :SDPVVVEFVSAYETLYGAIPTLFAAHGYDAVGIMLAAVGRA T0528 317 :KSTDTEKLIAAMEGM 3hutA 334 :PEVTRESLRDALAAT T0528 332 :EFDTPKGKMVFRKEDHQALQSMYHFKVKVDPAVA 3hutA 350 :RYAGVTGITRFDPETRETTKILTRLVVREGDFRV Number of specific fragments extracted= 12 number of extra gaps= 0 total=104 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 3hutA/T0528-3hutA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0528 read from 3hutA/T0528-3hutA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3hutA read from 3hutA/T0528-3hutA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3hutA in template set Warning: unaligning (T0528)D17 because first residue in template chain is (3hutA)L-1 Warning: unaligning (T0528)W366 because last residue in template chain is (3hutA)I384 T0528 18 :DLKIALIYGKTGPLEAYAKQTETGLMMGLEYATKGTM 3hutA 40 :ALLLGYELPLTGANAAYGRVFQEAARLQLDRFNAAGG T0528 56 :LDGRKIVVITKDDQSKPDLSKAALAEAYQDDGADIAIGTSSSAAALADLPVAEENKKILIVEPAVADQITGEK 3hutA 77 :VGGRPVDILYADSRDDADQARTIARAFVDDPRVVGVLGDFSSTVSMAAGSIYGKEGMPQLSPTAAHPDYIKIS T0528 131 :RYIFRTGRNSSQDAISNAVAIGK 3hutA 150 :PWQFRAITTPAFEGPNNAAWMIG T0528 154 :QGVTIATLAQDYAFGRDGVAAFKEALAKTGATLATEEYVPTTTTDFTAVGQRL 3hutA 174 :GFTSVAVIGVTTDWGLSSAQAFRKAFELRGGAVVVNEEVPPGNRRFDDVIDEI T0528 210 :LKDKPGKKIIWVIWAGGGDPLTKLQDMDPKRYGIELSTGGNILPALAAYKRLPGMEGATYYYYDI 3hutA 227 :EDEAPQAIYLAMAYEDAAPFLRALRARGSALPVYGSSALYSPKFIDLGGPAVEGVRLATAFVLGA T0528 276 :KNPINEWLVTEHQKRFNAPPDFFTAGGFSAAMAVVTAVQKAKS 3hutA 292 :SDPVVVEFVSAYETLYGAIPTLFAAHGYDAVGIMLAAVGRAGP T0528 319 :TDTEKLIAAMEGM 3hutA 336 :VTRESLRDALAAT T0528 332 :EFDTPKGKMVFRKEDHQALQSMYHFKVKVDPAVA 3hutA 350 :RYAGVTGITRFDPETRETTKILTRLVVREGDFRV Number of specific fragments extracted= 8 number of extra gaps= 0 total=112 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 1usgA/T0528-1usgA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1usgA expands to /projects/compbio/data/pdb/1usg.pdb.gz 1usgA:# T0528 read from 1usgA/T0528-1usgA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1usgA read from 1usgA/T0528-1usgA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1usgA to template set # found chain 1usgA in template set Warning: unaligning (T0528)D17 because first residue in template chain is (1usgA)D1 Warning: unaligning (T0528)G93 because of BadResidue code BAD_PEPTIDE in next template residue (1usgA)H76 Warning: unaligning (T0528)T94 because of BadResidue code BAD_PEPTIDE at template residue (1usgA)H76 Warning: unaligning (T0528)S352 because of BadResidue code BAD_PEPTIDE in next template residue (1usgA)F331 Warning: unaligning (T0528)M353 because of BadResidue code BAD_PEPTIDE at template residue (1usgA)F331 Warning: unaligning (T0528)A365 because of BadResidue code BAD_PEPTIDE in next template residue (1usgA)A345 T0528 18 :DLKIALIYGKTGPLEAYAKQTETGLMMGLE 1usgA 2 :DIKVAVVGAMSGPIAQWGDMEFNGARQAIK T0528 49 :ATKGTMTLDGRKIVVITKDDQSKPDLSKAALAEAYQD 1usgA 32 :DINAKGGIKGDKLVGVEYDDACDPKQAVAVANKIVND T0528 87 :GADIAI 1usgA 69 :GIKYVI T0528 95 :SSSAAALADLPVAEENKKILIVEPAVADQITGEK 1usgA 77 :LCSSSTQPASDIYEDEGILMISPGATNPELTQRG T0528 130 :NRYIFRTGRNSSQDAISNAVAIGK 1usgA 111 :YQHIMRTAGLDSSQGPTAAKYILE T0528 154 :QG 1usgA 136 :VK T0528 156 :VTIATLAQDYAFGRDGVAAFKEALAKTGATLATEEYVPTTTTDFTAVGQRLFDA 1usgA 139 :QRIAIIHDKQQYGEGLARSVQDGLKAANANVVFFDGITAGEKDFSALIARLKKE T0528 215 :GKKIIWVIWAGGG 1usgA 193 :NIDFVYYGGYYPE T0528 228 :DPLTKLQDMDP 1usgA 208 :QMLRQARSVGL T0528 240 :RYGIELSTGGNILPALAAYKR 1usgA 219 :KTQFMGPEGVGNASLSNIAGD T0528 261 :LPGMEGATYYYYDI 1usgA 241 :AEGMLVTMPKRYDQ T0528 277 :NPINEWLVTEHQKRFNAPPDFFTAGGFSAAMAVVTAVQKAKSTDTEKLIAAMEGMEFDTPKGKMVFRKEDHQALQ 1usgA 255 :DPANQGIVDALKADKKDPSGPYVWITYAAVQSLATALERTGSDEPLALVKDLKANGANTVIGPLNWDEKGDLKGF T0528 354 :YHFKVKVDP 1usgA 332 :GVFQWHADG T0528 363 :AV 1usgA 342 :ST Number of specific fragments extracted= 14 number of extra gaps= 3 total=126 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 1usgA/T0528-1usgA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0528 read from 1usgA/T0528-1usgA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1usgA read from 1usgA/T0528-1usgA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1usgA in template set Warning: unaligning (T0528)D17 because first residue in template chain is (1usgA)D1 Warning: unaligning (T0528)G93 because of BadResidue code BAD_PEPTIDE in next template residue (1usgA)H76 Warning: unaligning (T0528)T94 because of BadResidue code BAD_PEPTIDE at template residue (1usgA)H76 Warning: unaligning (T0528)S352 because of BadResidue code BAD_PEPTIDE in next template residue (1usgA)F331 Warning: unaligning (T0528)M353 because of BadResidue code BAD_PEPTIDE at template residue (1usgA)F331 Warning: unaligning (T0528)A365 because of BadResidue code BAD_PEPTIDE in next template residue (1usgA)A345 T0528 18 :DLKIALIYGKTGPLEAYAKQTETGLMMGLEYATKGT 1usgA 2 :DIKVAVVGAMSGPIAQWGDMEFNGARQAIKDINAKG T0528 55 :TLDGRKIVVITKDDQSKPDLSKAALAEAY 1usgA 38 :GIKGDKLVGVEYDDACDPKQAVAVANKIV T0528 85 :DDGADIAI 1usgA 67 :NDGIKYVI T0528 95 :SSSAAALADLPVAEENKKILIVEPAVADQITGEKW 1usgA 77 :LCSSSTQPASDIYEDEGILMISPGATNPELTQRGY T0528 131 :RYIFRTGRNSSQDAISNAVAIGKQ 1usgA 112 :QHIMRTAGLDSSQGPTAAKYILET T0528 155 :GV 1usgA 137 :KP T0528 157 :TIATLAQDYAFGRDGVAAFKEALAKTGATLATEEYVPTTTTDFTAVGQRLFDA 1usgA 140 :RIAIIHDKQQYGEGLARSVQDGLKAANANVVFFDGITAGEKDFSALIARLKKE T0528 213 :KP 1usgA 193 :NI T0528 216 :KKIIWVIWAGGGDPLTK 1usgA 195 :DFVYYGGYYPEMGQMLR T0528 233 :LQDMDP 1usgA 213 :ARSVGL T0528 239 :KRYGIELSTGGNILPALA 1usgA 221 :QFMGPEGVGNASLSNIAG T0528 259 :KRLPGMEGATYYYYDI 1usgA 239 :DAAEGMLVTMPKRYDQ T0528 277 :NPINEWLVTEHQKRFNAPPDFFTAGGFSAAMAVVTAVQKAKSTDTEKLIAAMEGMEFDTPKGKMVFRKEDHQALQ 1usgA 255 :DPANQGIVDALKADKKDPSGPYVWITYAAVQSLATALERTGSDEPLALVKDLKANGANTVIGPLNWDEKGDLKGF T0528 354 :YHFKVK 1usgA 332 :GVFQWH T0528 360 :VDPAV 1usgA 339 :DGSST Number of specific fragments extracted= 15 number of extra gaps= 3 total=141 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 1usgA/T0528-1usgA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0528 read from 1usgA/T0528-1usgA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1usgA read from 1usgA/T0528-1usgA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1usgA in template set Warning: unaligning (T0528)D17 because first residue in template chain is (1usgA)D1 Warning: unaligning (T0528)G93 because of BadResidue code BAD_PEPTIDE in next template residue (1usgA)H76 Warning: unaligning (T0528)T94 because of BadResidue code BAD_PEPTIDE at template residue (1usgA)H76 Warning: unaligning (T0528)S352 because of BadResidue code BAD_PEPTIDE in next template residue (1usgA)F331 Warning: unaligning (T0528)M353 because of BadResidue code BAD_PEPTIDE at template residue (1usgA)F331 Warning: unaligning (T0528)W366 because of BadResidue code BAD_PEPTIDE in next template residue (1usgA)A345 T0528 18 :DLKIALIYGKTGPLEAYAKQTETGLMMGLEYATKGTM 1usgA 2 :DIKVAVVGAMSGPIAQWGDMEFNGARQAIKDINAKGG T0528 56 :LDGRKIVVITKDDQSKPDLSKAALAEAYQD 1usgA 39 :IKGDKLVGVEYDDACDPKQAVAVANKIVND T0528 87 :GADIAI 1usgA 69 :GIKYVI T0528 95 :SSSAAALADLPVAEENKKILIVEPAVADQITGEK 1usgA 77 :LCSSSTQPASDIYEDEGILMISPGATNPELTQRG T0528 130 :NRYIFRTGRNSSQDAISNAVAIGK 1usgA 111 :YQHIMRTAGLDSSQGPTAAKYILE T0528 154 :QGVTIATLAQDYAFGRDGVAAFKEALAKTGATLATEEYVPTTTTDFTAVGQRL 1usgA 137 :KPQRIAIIHDKQQYGEGLARSVQDGLKAANANVVFFDGITAGEKDFSALIARL T0528 210 :LKDKPGKKIIWVIWAGGGDPLTKLQDMDPKRYGIELSTGGNILPALAAYKRLPGMEGATYYYYD 1usgA 190 :KKENIDFVYYGGYYPEMGQMLRQARSVGLKTQFMGPEGVGNASLSNIAGDAAEGMLVTMPKRYD T0528 276 :KNPINEWLVTEHQKRFNAPPDFFTAGGFSAAMAVVTAVQKAKSTDTEKLIAAMEGMEFDTPKGKMVFRKEDHQALQ 1usgA 254 :QDPANQGIVDALKADKKDPSGPYVWITYAAVQSLATALERTGSDEPLALVKDLKANGANTVIGPLNWDEKGDLKGF T0528 354 :YHFKVKVDPAVA 1usgA 332 :GVFQWHADGSST Number of specific fragments extracted= 9 number of extra gaps= 3 total=150 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 3eafA/T0528-3eafA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 3eafA expands to /projects/compbio/data/pdb/3eaf.pdb.gz 3eafA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0528 read from 3eafA/T0528-3eafA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3eafA read from 3eafA/T0528-3eafA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3eafA to template set # found chain 3eafA in template set Warning: unaligning (T0528)S95 because of BadResidue code BAD_PEPTIDE in next template residue (3eafA)G125 Warning: unaligning (T0528)S96 because of BadResidue code BAD_PEPTIDE at template residue (3eafA)G125 Warning: unaligning (T0528)R169 because of BadResidue code BAD_PEPTIDE in next template residue (3eafA)S198 Warning: unaligning (T0528)D170 because of BadResidue code BAD_PEPTIDE at template residue (3eafA)S198 T0528 17 :DDLKIALIYGKTGPLEAYAKQTETGLMMGLE 3eafA 44 :LTINVGLLVDETGPTSDVGKGYSLGAELAFK T0528 49 :ATKGTM 3eafA 75 :YFNEKG T0528 55 :TLDGRKIVV 3eafA 83 :TKDGVRVNI T0528 64 :ITKDDQSKPDLSKAALAEAYQDDGADIAIG 3eafA 94 :IKRDYAYNPTTAEEYYREFRDRYGVIAIIG T0528 97 :SAAALADLPVAEENKKILIVEPAVADQIT 3eafA 126 :TADTEKLSDQVDTDKITYISASYSAKLLV T0528 130 :NRYIFRTGRNSSQDAISNAVAIGK 3eafA 155 :KPFNFYPAPDYSTQACSGLAFLAS T0528 154 :QG 3eafA 180 :FG T0528 156 :VTIATLAQ 3eafA 183 :GKLALAYD T0528 164 :DYAFG 3eafA 192 :KVAYS T0528 171 :GVAAFKEALAKTGATLATEEYVP 3eafA 199 :PIGAIKKAAPSLGLQVVGDYDLP T0528 194 :TTTTDFTAVGQRLFDA 3eafA 224 :ATEADAERIAREMLAA T0528 215 :GKKIIWVIWAGGG 3eafA 240 :DPDYVWCGNTISS T0528 228 :DPLTKLQDMDP 3eafA 255 :LLGRAMAKVGL T0528 240 :RYGIELSTGGNILPALAAYKR 3eafA 266 :DAFLLTNVWGFDERSPQLIGE T0528 261 :LPGMEGA 3eafA 288 :GYGKVFG T0528 268 :TYYYYDIPKNPINEWLVT 3eafA 298 :FIYPMFGQDVEGIQTIFE T0528 287 :HQKRFN 3eafA 316 :AARMNG T0528 293 :APPDFFTAGGFSAAMAVVTAVQKA 3eafA 325 :DQINLRVVQGFVNVWLLIKAIESV T0528 317 :KSTDTEKLIAAMEGMEFD 3eafA 354 :QERGGEALKEALEANTFD T0528 335 :TPKG 3eafA 374 :GITA T0528 339 :KMVFRKEDHQALQSMYHFKVK 3eafA 379 :TIDYEPGFHLAYRKVFIIKLG T0528 360 :VDPAVAWAVLEPVRELK 3eafA 401 :NGELQLMGKFEAPSQVD Number of specific fragments extracted= 22 number of extra gaps= 2 total=172 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 3eafA/T0528-3eafA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0528 read from 3eafA/T0528-3eafA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3eafA read from 3eafA/T0528-3eafA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3eafA in template set Warning: unaligning (T0528)A16 because first residue in template chain is (3eafA)S43 Warning: unaligning (T0528)T94 because of BadResidue code BAD_PEPTIDE in next template residue (3eafA)G125 Warning: unaligning (T0528)S96 because of BadResidue code BAD_PEPTIDE at template residue (3eafA)G125 Warning: unaligning (T0528)R169 because of BadResidue code BAD_PEPTIDE in next template residue (3eafA)S198 Warning: unaligning (T0528)D170 because of BadResidue code BAD_PEPTIDE at template residue (3eafA)S198 T0528 17 :DDLKIALIYGKTGPLEAYAKQTETGLMMGLEYATKGTMTL 3eafA 44 :LTINVGLLVDETGPTSDVGKGYSLGAELAFKYFNEKGIYT T0528 57 :DGR 3eafA 85 :DGV T0528 60 :KIVVITKDDQSKPDLSKAALAEAYQDDGADIAIG 3eafA 90 :NINYIKRDYAYNPTTAEEYYREFRDRYGVIAIIG T0528 97 :SAAALADLPVAEENKKILIV 3eafA 126 :TADTEKLSDQVDTDKITYIS T0528 118 :PAVADQITGE 3eafA 146 :ASYSAKLLVK T0528 131 :RYIFRTGRNSSQDAISNAVAIGKQ 3eafA 156 :PFNFYPAPDYSTQACSGLAFLASE T0528 155 :GV 3eafA 181 :GQ T0528 157 :TIATLAQ 3eafA 184 :KLALAYD T0528 164 :DYAFG 3eafA 192 :KVAYS T0528 171 :GVAAFKEALAKTGATLATEEYVPTTTTD 3eafA 199 :PIGAIKKAAPSLGLQVVGDYDLPLRATE T0528 199 :FTAVGQRLFDA 3eafA 229 :AERIAREMLAA T0528 213 :KP 3eafA 240 :DP T0528 216 :KKIIWVIWAGGGDPLTK 3eafA 242 :DYVWCGNTISSCSLLGR T0528 233 :LQDMDP 3eafA 260 :MAKVGL T0528 239 :KRYGIELSTGGNILPALA 3eafA 268 :FLLTNVWGFDERSPQLIG T0528 259 :KRLPG 3eafA 286 :EGGYG T0528 264 :MEGATYYYY 3eafA 292 :VFGISPFIY T0528 274 :IPKNPINEWLVT 3eafA 304 :GQDVEGIQTIFE T0528 287 :HQKRFN 3eafA 316 :AARMNG T0528 293 :APPDFFTAGGFSAAMAVVTAVQKAKSTD 3eafA 325 :DQINLRVVQGFVNVWLLIKAIESVTSQD T0528 321 :TEKLIAAMEGMEFDTPK 3eafA 358 :GEALKEALEANTFDLGG T0528 339 :KMVFRKEDHQALQSMYHFKVK 3eafA 379 :TIDYEPGFHLAYRKVFIIKLG T0528 360 :VDPAVAWAVLEPV 3eafA 401 :NGELQLMGKFEAP Number of specific fragments extracted= 23 number of extra gaps= 2 total=195 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 3eafA/T0528-3eafA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0528 read from 3eafA/T0528-3eafA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3eafA read from 3eafA/T0528-3eafA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3eafA in template set Warning: unaligning (T0528)A16 because first residue in template chain is (3eafA)S43 Warning: unaligning (T0528)T94 because of BadResidue code BAD_PEPTIDE in next template residue (3eafA)G125 Warning: unaligning (T0528)S96 because of BadResidue code BAD_PEPTIDE at template residue (3eafA)G125 Warning: unaligning (T0528)R169 because of BadResidue code BAD_PEPTIDE in next template residue (3eafA)S198 Warning: unaligning (T0528)D170 because of BadResidue code BAD_PEPTIDE at template residue (3eafA)S198 T0528 17 :DDLKIALIYGKTGPLEAYAKQTETGLMMGLEYATKGTMT 3eafA 44 :LTINVGLLVDETGPTSDVGKGYSLGAELAFKYFNEKGIY T0528 56 :LDGRKI 3eafA 84 :KDGVRV T0528 62 :VVITKDDQSKPDLSKAALAEAYQDDGADIAIG 3eafA 92 :NYIKRDYAYNPTTAEEYYREFRDRYGVIAIIG T0528 97 :SAAALADLPVAEENKKILIVEPAVADQITG 3eafA 126 :TADTEKLSDQVDTDKITYISASYSAKLLVK T0528 131 :RYIFRTGRNSSQDAISNAVAIGK 3eafA 156 :PFNFYPAPDYSTQACSGLAFLAS T0528 154 :QGVTIATLAQDYAFG 3eafA 182 :QGKLALAYDSKVAYS T0528 171 :GVAAFKEALAKTGATLATEEYVPTTT 3eafA 199 :PIGAIKKAAPSLGLQVVGDYDLPLRA T0528 197 :TDFTAVGQRL 3eafA 227 :ADAERIAREM T0528 210 :LKDKPGKKIIWVIWAGGGDPLTKLQDMDPKRYGIELSTGGNILPALAAYKRLPGMEGATYYYYD 3eafA 237 :LAADPDYVWCGNTISSCSLLGRAMAKVGLDAFLLTNVWGFDERSPQLIGEGGYGKVFGISPFIY T0528 274 :IPKNPINEWLVTEHQKRFN 3eafA 304 :GQDVEGIQTIFEAARMNGV T0528 293 :APPDFFTAGGFSAAMAVVTAVQKAKSTD 3eafA 325 :DQINLRVVQGFVNVWLLIKAIESVTSQD T0528 321 :TEKLIAAMEGMEFDTPK 3eafA 358 :GEALKEALEANTFDLGG T0528 338 :GKMVFRKEDHQALQSMYHFKVKVDPAVAWAVLEP 3eafA 378 :DTIDYEPGFHLAYRKVFIIKLGENGELQLMGKFE Number of specific fragments extracted= 13 number of extra gaps= 2 total=208 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 3lopA/T0528-3lopA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 3lopA expands to /projects/compbio/data/pdb/3lop.pdb.gz 3lopA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0528 read from 3lopA/T0528-3lopA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3lopA read from 3lopA/T0528-3lopA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3lopA to template set # found chain 3lopA in template set Warning: unaligning (T0528)D18 because first residue in template chain is (3lopA)D35 Warning: unaligning (T0528)A367 because last residue in template chain is (3lopA)E387 T0528 19 :LKIALIYGKTGPLEAYAKQTETGLMMGLE 3lopA 36 :ISVIQSLPLSGSQAVTGRALNAGARLYFD T0528 49 :ATKGTMTLDGRKIVVITKDDQSKPDLSKAALAEAYQDDGADIAIGTSSSAAALADLP 3lopA 65 :WLNLNGGINGETIRLVARDDEQKIEQTVRNVRDMARVDNPVALLTVVGTANVEALMR T0528 106 :VAEENKKILIVEPAVADQITG 3lopA 124 :VLAEARLPLVGPATGASSMTT T0528 130 :NRYIFRTGRNSSQDAISNAVAIGKQG 3lopA 145 :DPLVFPIKASYQQEIDKMITALVTIG T0528 156 :VTIATLAQDYAFGRDGVAAFKEALAKTGATLATEEYVPTTTTDFTAVGQRLFDA 3lopA 172 :TRIGVLYQEDALGKEAITGVERTLKAHALAITAMASYPRNTANVGPAVDKLLAA T0528 215 :GKKIIWVIWAGGG 3lopA 226 :DVQAIFLGATAEP T0528 228 :DPLTKLQDMDP 3lopA 241 :QFVRQYRARGG T0528 240 :RYGIELSTGGNILPALAAYKR 3lopA 252 :EAQLLGLSSIDPGILQKVAGL T0528 261 :LPGMEGATYYYYDI 3lopA 275 :VRGYSLALVMPNPG T0528 275 :PKNPINEWLVTEHQKRF 3lopA 290 :SVNPVIREFNRARAAVG T0528 292 :NAPPDFFTAGGFSAAMAVVTAVQKAKS 3lopA 309 :DVDLSFRAVEGFVAAKVLAEAIRRAGP T0528 319 :TDTEKLIAAMEGM 3lopA 337 :PTREQVRHALTEL T0528 332 :EFDTPKG 3lopA 351 :DYDVGGG T0528 339 :KMVFRKEDHQALQSMYHFKVKVDPAVAW 3lopA 359 :TVDFTDRSRPGSHYIELGVVGPNGLVIQ Number of specific fragments extracted= 14 number of extra gaps= 0 total=222 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 3lopA/T0528-3lopA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0528 read from 3lopA/T0528-3lopA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3lopA read from 3lopA/T0528-3lopA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3lopA in template set Warning: unaligning (T0528)D18 because first residue in template chain is (3lopA)D35 Warning: unaligning (T0528)W366 because last residue in template chain is (3lopA)E387 T0528 19 :LKIALIYGKTGPLEAYAKQTETGLMMGLEYATKGTMTL 3lopA 36 :ISVIQSLPLSGSQAVTGRALNAGARLYFDWLNLNGGIN T0528 58 :GRKIVVITKDDQSKPDLSKAALAEAYQDDGADIAIGTSSSAAALADLP 3lopA 74 :GETIRLVARDDEQKIEQTVRNVRDMARVDNPVALLTVVGTANVEALMR T0528 106 :VAEENKKILIVEPAVADQITGE 3lopA 124 :VLAEARLPLVGPATGASSMTTD T0528 131 :RYIFRTGRNSSQDAISNAVAIGKQGV 3lopA 146 :PLVFPIKASYQQEIDKMITALVTIGV T0528 157 :TIATLAQDYAFGRDGVAAFKEALAKTGATLATEEYVPTTTTDFTAVGQRLFDA 3lopA 173 :RIGVLYQEDALGKEAITGVERTLKAHALAITAMASYPRNTANVGPAVDKLLAA T0528 213 :KP 3lopA 226 :DV T0528 216 :KKIIWVIWAGGGDPLTK 3lopA 228 :QAIFLGATAEPAAQFVR T0528 233 :LQDMDP 3lopA 246 :YRARGG T0528 239 :KRYGIELSTGGNILPALAA 3lopA 254 :QLLGLSSIDPGILQKVAGL T0528 259 :KRLPGMEGAT 3lopA 273 :DAVRGYSLAL T0528 269 :YYYYDI 3lopA 285 :PNPGKS T0528 276 :KNPINEWLVTEHQKRF 3lopA 291 :VNPVIREFNRARAAVG T0528 292 :NAPPDFFTAGGFSAAMAVVTAVQKAKST 3lopA 309 :DVDLSFRAVEGFVAAKVLAEAIRRAGPK T0528 320 :DTEKLIAAMEGM 3lopA 338 :TREQVRHALTEL T0528 332 :EFDTPKG 3lopA 351 :DYDVGGG T0528 339 :KMVFRKEDHQALQSMYHFKVK 3lopA 359 :TVDFTDRSRPGSHYIELGVVG T0528 360 :VDPAVA 3lopA 381 :NGLVIQ Number of specific fragments extracted= 17 number of extra gaps= 0 total=239 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 3lopA/T0528-3lopA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0528 read from 3lopA/T0528-3lopA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3lopA read from 3lopA/T0528-3lopA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3lopA in template set Warning: unaligning (T0528)D18 because first residue in template chain is (3lopA)D35 T0528 19 :LKIALIYGKTGPLEAYAKQTETGLMMGLEYATKGTM 3lopA 36 :ISVIQSLPLSGSQAVTGRALNAGARLYFDWLNLNGG T0528 56 :LDGRKIVVITKDDQSKPDLSKAALAEAYQDDGADIAIGTSSSAAALADL 3lopA 72 :INGETIRLVARDDEQKIEQTVRNVRDMARVDNPVALLTVVGTANVEALM T0528 105 :PVAEENKKILIVEPAVADQITG 3lopA 123 :GVLAEARLPLVGPATGASSMTT T0528 130 :NRYIFRTGRNSSQDAISNAVAIGK 3lopA 145 :DPLVFPIKASYQQEIDKMITALVT T0528 154 :QGVTIATLAQDYAFGRDGVAAFKEALAKTGATLATEEYVPTTTTDFTAVGQRL 3lopA 170 :GVTRIGVLYQEDALGKEAITGVERTLKAHALAITAMASYPRNTANVGPAVDKL T0528 210 :LKDKPGKKIIWVIWAGGGDPLTKLQDMDPKRYGIELSTGGNILPALAAYKRLPGMEGATYYYYD 3lopA 223 :LAADVQAIFLGATAEPAAQFVRQYRARGGEAQLLGLSSIDPGILQKVAGLDAVRGYSLALVMPN T0528 274 :IPKNPINEWLVTEHQKRFN 3lopA 289 :KSVNPVIREFNRARAAVGA T0528 293 :APPDFFTAGGFSAAMAVVTAVQKAKS 3lopA 310 :VDLSFRAVEGFVAAKVLAEAIRRAGP T0528 319 :TDTEKLIAAMEGMEFDTPKGKMVFRKEDHQAL 3lopA 337 :PTREQVRHALTELRDYDVGGGFTVDFTDRSRP T0528 351 :QSMYHFKVKVDPAVAW 3lopA 371 :HYIELGVVGPNGLVIQ Number of specific fragments extracted= 10 number of extra gaps= 0 total=249 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 1peaA/T0528-1peaA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1peaA expands to /projects/compbio/data/pdb/1pea.pdb.gz 1peaA:# T0528 read from 1peaA/T0528-1peaA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1peaA read from 1peaA/T0528-1peaA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1peaA to template set # found chain 1peaA in template set Warning: unaligning (T0528)L19 because first residue in template chain is (1peaA)P8 Warning: unaligning (T0528)P383 because last residue in template chain is (1peaA)W375 T0528 20 :KIALIYGKTGPLEAYAKQTETGLMMGLE 1peaA 9 :LIGLLFSETGVTADIERSQRYGALLAVE T0528 49 :ATKGTMTLDGRKIVVITKDDQSKPDLSKAALAEAYQDDGADIAIGTSSSAAALADLPVAEENKKILIVEPAVADQIT 1peaA 37 :QLNREGGVGGRPIETLSQDPGGDPDRYRLCAEDFIRNRGVRFLVGCYMSHTRKAVMPVVERADALLCYPTPYEGFEY T0528 130 :NRYIFRTGRNSSQDAISNAVAIGKQG 1peaA 114 :SPNIVYGGPAPNQNSAPLAAYLIRHY T0528 156 :VTIATLAQDYAFGRDGVAAFKEALAKTGATLATEEYVP 1peaA 141 :ERVVFIGSDYIYPRESNHVMRHLYRQHGGTVLEEIYIP T0528 194 :TTTTDFTAVGQRLFDA 1peaA 181 :PSDDDLQRAVERIYQA T0528 215 :GKKIIWVIWAGGG 1peaA 197 :RADVVFSTVVGTG T0528 228 :DPLTKLQDMDPK 1peaA 212 :ELYRAIARRYGD T0528 240 :RYGIELSTGG 1peaA 225 :RRPPIASLTT T0528 251 :ILPALAAYKR 1peaA 235 :SEAEVAKMES T0528 261 :LPGMEGATYYYYDI 1peaA 247 :AEGQVVVAPYFSSI T0528 276 :KNPINEWLVTEHQKRFN 1peaA 261 :DTPASRAFVQACHGFFP T0528 293 :APPDFFTAGGFSAAMAVVTAVQKAKSTDTEKLIAAMEGMEFDTPKGKMVFRKEDHQALQSMYHFKVKVDP 1peaA 280 :ATITAWAEAAYWQTLLLGRAAQAAGNWRVEDVQRHLYDIDIDAPQGPVRVERQNNHSRLSSRIAEIDARG T0528 363 :AVAWAVLE 1peaA 351 :FQVRWQSP T0528 371 :PVRELKIEEMNI 1peaA 363 :PDPYVVVHNLDD Number of specific fragments extracted= 14 number of extra gaps= 0 total=263 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 1peaA/T0528-1peaA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0528 read from 1peaA/T0528-1peaA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1peaA read from 1peaA/T0528-1peaA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1peaA in template set Warning: unaligning (T0528)L19 because first residue in template chain is (1peaA)P8 T0528 20 :KIALIYGKTGPLEAYAKQTETGLMMGLEYATKGT 1peaA 9 :LIGLLFSETGVTADIERSQRYGALLAVEQLNREG T0528 55 :TLDGRKIVVITKDDQSKPDLSKAALAEAYQDDGADIAIGTSSSAAALADLPVAEENKKILIVEPAVADQIT 1peaA 43 :GVGGRPIETLSQDPGGDPDRYRLCAEDFIRNRGVRFLVGCYMSHTRKAVMPVVERADALLCYPTPYEGFEY T0528 130 :NRYIFRTGRNSSQDAISNAVAIGKQGV 1peaA 114 :SPNIVYGGPAPNQNSAPLAAYLIRHYG T0528 157 :TIATLAQDYAFGRDGVAAFKEALAKTGATLATEEYVPT 1peaA 142 :RVVFIGSDYIYPRESNHVMRHLYRQHGGTVLEEIYIPL T0528 195 :TTTDFTAVGQRLFDA 1peaA 182 :SDDDLQRAVERIYQA T0528 213 :KP 1peaA 197 :RA T0528 216 :KKIIWVIWAGGGDPLTK 1peaA 199 :DVVFSTVVGTGTAELYR T0528 233 :LQDMDP 1peaA 217 :IARRYG T0528 239 :KRYGIELSTGGNIL 1peaA 227 :PPIASLTTSEAEVA T0528 254 :ALAA 1peaA 241 :KMES T0528 259 :KRLPGMEGATYYYYDI 1peaA 245 :DVAEGQVVVAPYFSSI T0528 276 :KNPINEWLVTEHQKRFN 1peaA 261 :DTPASRAFVQACHGFFP T0528 293 :APPDFFTAGGFSAAMAVVTAVQKAKSTDTEKLIAAMEGMEFDTPKGKMVFRKEDHQALQSMYHFKVKVDPA 1peaA 280 :ATITAWAEAAYWQTLLLGRAAQAAGNWRVEDVQRHLYDIDIDAPQGPVRVERQNNHSRLSSRIAEIDARGV T0528 364 :VAW 1peaA 352 :QVR T0528 367 :AVLEPVR 1peaA 356 :QSPEPIR T0528 374 :ELKIEEM 1peaA 366 :YVVVHNL Number of specific fragments extracted= 16 number of extra gaps= 0 total=279 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 1peaA/T0528-1peaA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0528 read from 1peaA/T0528-1peaA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1peaA read from 1peaA/T0528-1peaA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1peaA in template set Warning: unaligning (T0528)L19 because first residue in template chain is (1peaA)P8 T0528 20 :KIALIYGKTGPLEAYAKQTETGLMMGLEYATKGTM 1peaA 9 :LIGLLFSETGVTADIERSQRYGALLAVEQLNREGG T0528 56 :LDGRKIVVITKDDQSKPDLSKAALAEAYQDDGADIAIGTSSSAAALADLPVAEENKKILIVEPAVADQITG 1peaA 44 :VGGRPIETLSQDPGGDPDRYRLCAEDFIRNRGVRFLVGCYMSHTRKAVMPVVERADALLCYPTPYEGFEYS T0528 131 :RYIFRTGRNSSQDAISNAVAIGK 1peaA 115 :PNIVYGGPAPNQNSAPLAAYLIR T0528 154 :QGVTIATLAQDYAFGRDGVAAFKEALAKTGATLATEEYVPT 1peaA 139 :YGERVVFIGSDYIYPRESNHVMRHLYRQHGGTVLEEIYIPL T0528 195 :TTTDFTAVGQRL 1peaA 182 :SDDDLQRAVERI T0528 210 :LKDKPGKKIIWVIWAGGGDPLTKLQDMDP 1peaA 194 :YQARADVVFSTVVGTGTAELYRAIARRYG T0528 239 :KRYGIELSTGGNILPALAAYKR 1peaA 224 :GRRPPIASLTTSEAEVAKMESD T0528 261 :LPGMEGATYYYYDI 1peaA 247 :AEGQVVVAPYFSSI T0528 276 :KNPINEWLVTEHQKRFN 1peaA 261 :DTPASRAFVQACHGFFP T0528 293 :APPDFFTAGGFSAAMAVVTAVQKAKSTDTEKLIAAMEGMEFDTPKGKMVFRKEDHQALQSMYHFKVKVDPAVAWAVLEPVREL 1peaA 280 :ATITAWAEAAYWQTLLLGRAAQAAGNWRVEDVQRHLYDIDIDAPQGPVRVERQNNHSRLSSRIAEIDARGVFQVRWQSPEPIR Number of specific fragments extracted= 10 number of extra gaps= 0 total=289 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 3h5lA/T0528-3h5lA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 3h5lA expands to /projects/compbio/data/pdb/3h5l.pdb.gz 3h5lA:Skipped atom 209, because occupancy 0.500 <= existing 0.500 in 3h5lA Skipped atom 213, because occupancy 0.500 <= existing 0.500 in 3h5lA Skipped atom 215, because occupancy 0.500 <= existing 0.500 in 3h5lA Skipped atom 217, because occupancy 0.500 <= existing 0.500 in 3h5lA Skipped atom 219, because occupancy 0.500 <= existing 0.500 in 3h5lA Skipped atom 433, because occupancy 0.500 <= existing 0.500 in 3h5lA Skipped atom 437, because occupancy 0.500 <= existing 0.500 in 3h5lA Skipped atom 439, because occupancy 0.500 <= existing 0.500 in 3h5lA Skipped atom 441, because occupancy 0.500 <= existing 0.500 in 3h5lA Skipped atom 443, because occupancy 0.500 <= existing 0.500 in 3h5lA Skipped atom 445, because occupancy 0.500 <= existing 0.500 in 3h5lA Skipped atom 459, because occupancy 0.500 <= existing 0.500 in 3h5lA Skipped atom 463, because occupancy 0.500 <= existing 0.500 in 3h5lA Skipped atom 465, because occupancy 0.500 <= existing 0.500 in 3h5lA Skipped atom 467, because occupancy 0.500 <= existing 0.500 in 3h5lA Skipped atom 469, because occupancy 0.500 <= existing 0.500 in 3h5lA Skipped atom 471, because occupancy 0.500 <= existing 0.500 in 3h5lA Skipped atom 474, because occupancy 0.500 <= existing 0.500 in 3h5lA Skipped atom 478, because occupancy 0.500 <= existing 0.500 in 3h5lA Skipped atom 480, because occupancy 0.500 <= existing 0.500 in 3h5lA Skipped atom 482, because occupancy 0.500 <= existing 0.500 in 3h5lA Skipped atom 484, because occupancy 0.500 <= existing 0.500 in 3h5lA Skipped atom 486, because occupancy 0.500 <= existing 0.500 in 3h5lA Skipped atom 488, because occupancy 0.500 <= existing 0.500 in 3h5lA Skipped atom 490, because occupancy 0.500 <= existing 0.500 in 3h5lA Skipped atom 622, because occupancy 0.500 <= existing 0.500 in 3h5lA Skipped atom 626, because occupancy 0.500 <= existing 0.500 in 3h5lA Skipped atom 628, because occupancy 0.500 <= existing 0.500 in 3h5lA Skipped atom 630, because occupancy 0.500 <= existing 0.500 in 3h5lA Skipped atom 632, because occupancy 0.500 <= existing 0.500 in 3h5lA Skipped atom 2072, because occupancy 0.500 <= existing 0.500 in 3h5lA Skipped atom 2076, because occupancy 0.500 <= existing 0.500 in 3h5lA Skipped atom 2078, because occupancy 0.500 <= existing 0.500 in 3h5lA Skipped atom 2080, because occupancy 0.500 <= existing 0.500 in 3h5lA Skipped atom 2082, because occupancy 0.500 <= existing 0.500 in 3h5lA Skipped atom 2153, because occupancy 0.500 <= existing 0.500 in 3h5lA Skipped atom 2157, because occupancy 0.500 <= existing 0.500 in 3h5lA Skipped atom 2159, because occupancy 0.500 <= existing 0.500 in 3h5lA Skipped atom 2161, because occupancy 0.500 <= existing 0.500 in 3h5lA Skipped atom 2163, because occupancy 0.500 <= existing 0.500 in 3h5lA Skipped atom 2165, because occupancy 0.500 <= existing 0.500 in 3h5lA Skipped atom 2168, because occupancy 0.500 <= existing 0.500 in 3h5lA Skipped atom 2172, because occupancy 0.500 <= existing 0.500 in 3h5lA Skipped atom 2174, because occupancy 0.500 <= existing 0.500 in 3h5lA Skipped atom 2176, because occupancy 0.500 <= existing 0.500 in 3h5lA Skipped atom 2178, because occupancy 0.500 <= existing 0.500 in 3h5lA Skipped atom 2180, because occupancy 0.500 <= existing 0.500 in 3h5lA Skipped atom 2182, because occupancy 0.500 <= existing 0.500 in 3h5lA Skipped atom 2184, because occupancy 0.500 <= existing 0.500 in 3h5lA Skipped atom 3007, because occupancy 0.500 <= existing 0.500 in 3h5lA Skipped atom 3011, because occupancy 0.500 <= existing 0.500 in 3h5lA Skipped atom 3013, because occupancy 0.500 <= existing 0.500 in 3h5lA Skipped atom 3015, because occupancy 0.500 <= existing 0.500 in 3h5lA Skipped atom 3017, because occupancy 0.500 <= existing 0.500 in 3h5lA # T0528 read from 3h5lA/T0528-3h5lA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3h5lA read from 3h5lA/T0528-3h5lA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3h5lA to template set # found chain 3h5lA in template set Warning: unaligning (T0528)D17 because first residue in template chain is (3h5lA)D41 Warning: unaligning (T0528)T136 because of BadResidue code BAD_PEPTIDE in next template residue (3h5lA)D165 Warning: unaligning (T0528)G137 because of BadResidue code BAD_PEPTIDE at template residue (3h5lA)D165 Warning: unaligning (T0528)W223 because of BadResidue code BAD_PEPTIDE in next template residue (3h5lA)F256 Warning: unaligning (T0528)A224 because of BadResidue code BAD_PEPTIDE at template residue (3h5lA)F256 T0528 18 :DLKIALIYGKTGPLEAYAKQTETGLMMGLE 3h5lA 42 :PVVIGCPAPLTGIVAADGIEFQRGIQMAAD T0528 49 :ATKGTMTLDGRKIVVITKDDQSK 3h5lA 72 :EINAVGGILGRPIELVFADTQSK T0528 72 :PDLSKAALAEAYQDDGADIAIGTSSSAAALADLPVAEENKKILIVEPAVAD 3h5lA 96 :VDVVIQSAQRLIDRDNASALIAGYNLENGTALHDVAADAGVIAMHANTVAV T0528 123 :QITGEKWNRYIFR 3h5lA 151 :VKSDPDRYWGTFQ T0528 138 :RNSSQDAISNAVAIGKQ 3h5lA 166 :PPETLYGGGFLKFLKDI T0528 155 :GVTIATLAQDYAFGRDGVAAFKEALAKTGATLATEEYVPTTTTDFTAVGQRLFDA 3h5lA 192 :NNKIAIITGPGIYSVNIANAIRDGAGEYGYDVSLFETVAIPVSDWGPTLAKLRAD T0528 215 :GKKIIWVI 3h5lA 247 :PPAVIVVT T0528 225 :GGG 3h5lA 257 :YPQ T0528 228 :DPLTKLQDMDP 3h5lA 263 :LFMNQFMTDPT T0528 240 :RYGIELSTGGNILPALAAYKR 3h5lA 274 :NSLVYLQYGASLAAFRDIAGD T0528 261 :LPGMEGATYYYYD 3h5lA 296 :SVGVTYATVLGTL T0528 276 :KNPINEWLVTEHQKRFN 3h5lA 309 :QDEMGDAFAKAYKERYG T0528 293 :APPDFFTAGGFSAAMAVVTAVQKA 3h5lA 327 :LSSTASGCQTYSALYAYSIAAALA T0528 317 :KS 3h5lA 357 :YD T0528 319 :TDTEKLIAAMEGMEFDTPKGKMVFRKEDHQA 3h5lA 360 :VQNKAVADRLRSLIFRGPVGTMRFHADTQSA T0528 350 :LQSMYHFKVKV 3h5lA 403 :GMPHIFSQIFD Number of specific fragments extracted= 16 number of extra gaps= 2 total=305 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 3h5lA/T0528-3h5lA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0528 read from 3h5lA/T0528-3h5lA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3h5lA read from 3h5lA/T0528-3h5lA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3h5lA in template set Warning: unaligning (T0528)D17 because first residue in template chain is (3h5lA)D41 Warning: unaligning (T0528)T136 because of BadResidue code BAD_PEPTIDE in next template residue (3h5lA)D165 Warning: unaligning (T0528)G137 because of BadResidue code BAD_PEPTIDE at template residue (3h5lA)D165 Warning: unaligning (T0528)I222 because of BadResidue code BAD_PEPTIDE in next template residue (3h5lA)F256 Warning: unaligning (T0528)W223 because of BadResidue code BAD_PEPTIDE at template residue (3h5lA)F256 T0528 18 :DLKIALIYGKTGPLEAYAKQTETGLMMGLEYATKGT 3h5lA 42 :PVVIGCPAPLTGIVAADGIEFQRGIQMAADEINAVG T0528 55 :TLDGRKIVVITKDDQSK 3h5lA 78 :GILGRPIELVFADTQSK T0528 72 :PDLSKAALAEAYQDDGADIAIGTSSSAAALADLPVAEENKKILIVEPAVADQIT 3h5lA 96 :VDVVIQSAQRLIDRDNASALIAGYNLENGTALHDVAADAGVIAMHANTVAVHDE T0528 126 :GEKWNRYIFR 3h5lA 154 :DPDRYWGTFQ T0528 138 :RNSSQDAISNAVAI 3h5lA 166 :PPETLYGGGFLKFL T0528 152 :GKQG 3h5lA 183 :EDNG T0528 157 :TIATLAQDYAFGRDGVAAFKEALAKTGATLATEEYVPTTTTDFTAVGQRLFDA 3h5lA 194 :KIAIITGPGIYSVNIANAIRDGAGEYGYDVSLFETVAIPVSDWGPTLAKLRAD T0528 213 :KP 3h5lA 247 :PP T0528 216 :KKIIWV 3h5lA 249 :AVIVVT T0528 224 :AG 3h5lA 257 :YP T0528 226 :GGDPLTK 3h5lA 260 :DQALFMN T0528 233 :LQDMDP 3h5lA 268 :FMTDPT T0528 239 :KRYGIELSTGGNILPALA 3h5lA 276 :LVYLQYGASLAAFRDIAG T0528 259 :KRLPGMEGATYY 3h5lA 294 :DNSVGVTYATVL T0528 272 :YDI 3h5lA 306 :GTL T0528 276 :KNPINEWLVTEHQKRFN 3h5lA 309 :QDEMGDAFAKAYKERYG T0528 293 :APPDFFTAGGFSAAMAVVTAVQKAKST 3h5lA 327 :LSSTASGCQTYSALYAYSIAAALAGGP T0528 320 :DTEKLIAAMEGMEFDTPKGKMVFRKEDHQAL 3h5lA 361 :QNKAVADRLRSLIFRGPVGTMRFHADTQSAW T0528 354 :YHFKVK 3h5lA 407 :IFSQIF T0528 360 :VDPAVA 3h5lA 415 :AEDGVL Number of specific fragments extracted= 20 number of extra gaps= 2 total=325 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 3h5lA/T0528-3h5lA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0528 read from 3h5lA/T0528-3h5lA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3h5lA read from 3h5lA/T0528-3h5lA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3h5lA in template set Warning: unaligning (T0528)D17 because first residue in template chain is (3h5lA)D41 Warning: unaligning (T0528)T136 because of BadResidue code BAD_PEPTIDE in next template residue (3h5lA)D165 Warning: unaligning (T0528)G137 because of BadResidue code BAD_PEPTIDE at template residue (3h5lA)D165 Warning: unaligning (T0528)V221 because of BadResidue code BAD_PEPTIDE in next template residue (3h5lA)F256 Warning: unaligning (T0528)I222 because of BadResidue code BAD_PEPTIDE at template residue (3h5lA)F256 T0528 18 :DLKIALIYGKTGPLEAYAKQTETGLMMGLEYATKGTM 3h5lA 42 :PVVIGCPAPLTGIVAADGIEFQRGIQMAADEINAVGG T0528 56 :LDGRKIVVITKDDQS 3h5lA 79 :ILGRPIELVFADTQS T0528 71 :KPDLSKAALAEAYQDDGADIAIGTSSSAAALADLPVAEENKKILIVEPAVADQIT 3h5lA 95 :GVDVVIQSAQRLIDRDNASALIAGYNLENGTALHDVAADAGVIAMHANTVAVHDE T0528 126 :GEK 3h5lA 155 :PDR T0528 130 :NRYIFR 3h5lA 158 :YWGTFQ T0528 138 :RNSSQDAISNAVAIGK 3h5lA 166 :PPETLYGGGFLKFLKD T0528 154 :QGVTIATLAQDYAFGRDGVAAFKEALAKTGATLATEEYVPTTTTDFTAVGQRL 3h5lA 191 :PNNKIAIITGPGIYSVNIANAIRDGAGEYGYDVSLFETVAIPVSDWGPTLAKL T0528 210 :LKDKPGKKIIW 3h5lA 244 :RADPPAVIVVT T0528 223 :WA 3h5lA 257 :YP T0528 225 :GGGDPLTKLQDMDPKRYGIELSTGGNILPALAAYKRLPGMEGATYYYYDI 3h5lA 260 :DQALFMNQFMTDPTNSLVYLQYGASLAAFRDIAGDNSVGVTYATVLGTLQ T0528 277 :NPINEWLVTEHQKRFN 3h5lA 310 :DEMGDAFAKAYKERYG T0528 293 :APPDFFTAGGFSAAMAVVTAVQKAKS 3h5lA 327 :LSSTASGCQTYSALYAYSIAAALAGG T0528 319 :TDTEKLI 3h5lA 357 :YDDVQNK T0528 326 :AAMEGMEFDTPKGKMVFRKEDHQA 3h5lA 367 :DRLRSLIFRGPVGTMRFHADTQSA Number of specific fragments extracted= 14 number of extra gaps= 2 total=339 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 1pea/T0528-1pea-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1pea expands to /projects/compbio/data/pdb/1pea.pdb.gz 1pea:Warning: there is no chain 1pea will retry with 1peaA # T0528 read from 1pea/T0528-1pea-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1pea read from 1pea/T0528-1pea-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1pea to template set # found chain 1pea in template set Warning: unaligning (T0528)L19 because first residue in template chain is (1pea)P8 Warning: unaligning (T0528)P383 because last residue in template chain is (1pea)W375 T0528 20 :KIALIYGKTGPLEAYAKQTETGLMMGLE 1pea 9 :LIGLLFSETGVTADIERSQRYGALLAVE T0528 49 :ATKGTMTLDGRKIVVITKDDQSKPDLSKAALAEAYQDDGADIAIGTSSSAAALADLPVAEENKKILIVEPAVAD 1pea 37 :QLNREGGVGGRPIETLSQDPGGDPDRYRLCAEDFIRNRGVRFLVGCYMSHTRKAVMPVVERADALLCYPTPYEG T0528 127 :EKWNRYIFRTGRNSSQDAISNAVAIGKQG 1pea 111 :FEYSPNIVYGGPAPNQNSAPLAAYLIRHY T0528 156 :VTIATLAQDYAFGRDGVAAFKEALAKTGATLATEEYVP 1pea 141 :ERVVFIGSDYIYPRESNHVMRHLYRQHGGTVLEEIYIP T0528 194 :TTTTDFTAVGQRLFDA 1pea 181 :PSDDDLQRAVERIYQA T0528 215 :GKKIIWVIWAGGG 1pea 197 :RADVVFSTVVGTG T0528 228 :DPLTKLQD 1pea 212 :ELYRAIAR T0528 236 :MDPKRYGIELSTGGNILPALAAYKR 1pea 221 :YGDGRRPPIASLTTSEAEVAKMESD T0528 261 :LPGMEGATYYYYDI 1pea 247 :AEGQVVVAPYFSSI T0528 276 :KNPINEWLVTEHQKRFN 1pea 261 :DTPASRAFVQACHGFFP T0528 293 :APPDFFTAGGFSAAMAVVTAVQKAKSTDTEKLIAAMEGMEFDTPKGKMVFRKEDHQALQSMYHFKVKVDP 1pea 280 :ATITAWAEAAYWQTLLLGRAAQAAGNWRVEDVQRHLYDIDIDAPQGPVRVERQNNHSRLSSRIAEIDARG T0528 363 :AVAWAVLEPV 1pea 351 :FQVRWQSPEP T0528 373 :RELKIEEMNI 1pea 365 :PYVVVHNLDD Number of specific fragments extracted= 13 number of extra gaps= 0 total=352 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 1pea/T0528-1pea-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0528 read from 1pea/T0528-1pea-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1pea read from 1pea/T0528-1pea-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1pea in template set Warning: unaligning (T0528)L19 because first residue in template chain is (1pea)P8 Warning: unaligning (T0528)P383 because last residue in template chain is (1pea)W375 T0528 20 :KIALIYGKTGPLEAYAKQTETGLMMGLEYATKGT 1pea 9 :LIGLLFSETGVTADIERSQRYGALLAVEQLNREG T0528 55 :TLDGRKIVVITKDDQSKPDLSKAALAEAYQDDGADIAIGTSSSAAALADLPVAEENKKILIVEPAVADQ 1pea 43 :GVGGRPIETLSQDPGGDPDRYRLCAEDFIRNRGVRFLVGCYMSHTRKAVMPVVERADALLCYPTPYEGF T0528 128 :KWNRYIFRTGRNSSQDAISNAVAIGKQ 1pea 112 :EYSPNIVYGGPAPNQNSAPLAAYLIRH T0528 155 :GVTIATLAQDYAFGRDGVAAFKEALAKTGATLATEEYVPT 1pea 140 :GERVVFIGSDYIYPRESNHVMRHLYRQHGGTVLEEIYIPL T0528 195 :TTTDFTAVGQRLFDA 1pea 182 :SDDDLQRAVERIYQA T0528 213 :KP 1pea 197 :RA T0528 216 :KKIIWVIWAGGGDPLTK 1pea 199 :DVVFSTVVGTGTAELYR T0528 233 :LQDMDP 1pea 217 :IARRYG T0528 239 :KRYGIELSTGGNILPALA 1pea 227 :PPIASLTTSEAEVAKMES T0528 259 :KRLPGMEGATYYYYDI 1pea 245 :DVAEGQVVVAPYFSSI T0528 276 :KNPINEWLVTEHQKRFN 1pea 261 :DTPASRAFVQACHGFFP T0528 293 :APPDFFTAGGFSAAMAVVTAVQKAKSTDTEKLIAAMEGMEFDTPKGKMVFRKEDHQALQSMYHFKVKVDPA 1pea 280 :ATITAWAEAAYWQTLLLGRAAQAAGNWRVEDVQRHLYDIDIDAPQGPVRVERQNNHSRLSSRIAEIDARGV T0528 364 :VAWAVLEPVR 1pea 353 :VRWQSPEPIR T0528 374 :ELKIEEMNI 1pea 366 :YVVVHNLDD Number of specific fragments extracted= 14 number of extra gaps= 0 total=366 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 1pea/T0528-1pea-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0528 read from 1pea/T0528-1pea-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1pea read from 1pea/T0528-1pea-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1pea in template set Warning: unaligning (T0528)L19 because first residue in template chain is (1pea)P8 T0528 20 :KIALIYGKTGPLEAYAKQTETGLMMGLEYATKGTM 1pea 9 :LIGLLFSETGVTADIERSQRYGALLAVEQLNREGG T0528 56 :LDGRKIVVITKDDQSKPDLSKAALAEAYQDDGADIAIGTSSSAAALADLPVAEENKKILIVEPAVA 1pea 44 :VGGRPIETLSQDPGGDPDRYRLCAEDFIRNRGVRFLVGCYMSHTRKAVMPVVERADALLCYPTPYE T0528 126 :GEKWNRYIFRTGRNSSQDAISNAVAIGK 1pea 110 :GFEYSPNIVYGGPAPNQNSAPLAAYLIR T0528 154 :QGVTIATLAQDYAFGRDGVAAFKEALAKTGATLATEEYVPT 1pea 139 :YGERVVFIGSDYIYPRESNHVMRHLYRQHGGTVLEEIYIPL T0528 195 :TTTDFTAVGQRL 1pea 182 :SDDDLQRAVERI T0528 210 :LKDKPGKKIIWVIWAGGGDPLTKLQDMDP 1pea 194 :YQARADVVFSTVVGTGTAELYRAIARRYG T0528 239 :KRYGIELSTGGNILPALAAYKRLPGMEGATYYYYDI 1pea 225 :RRPPIASLTTSEAEVAKMESDVAEGQVVVAPYFSSI T0528 276 :KNPINEWLVTEHQKRFN 1pea 261 :DTPASRAFVQACHGFFP T0528 293 :APPDFFTAGGFSAAMAVVTAVQKAKSTDTEKLIAAMEGMEFDTPKGKMVFRKEDHQALQSMYHFKVKVDPAVAWAVLEPVRE 1pea 280 :ATITAWAEAAYWQTLLLGRAAQAAGNWRVEDVQRHLYDIDIDAPQGPVRVERQNNHSRLSSRIAEIDARGVFQVRWQSPEPI Number of specific fragments extracted= 9 number of extra gaps= 0 total=375 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 3lkbA/T0528-3lkbA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 3lkbA expands to /projects/compbio/data/pdb/3lkb.pdb.gz 3lkbA:# T0528 read from 3lkbA/T0528-3lkbA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3lkbA read from 3lkbA/T0528-3lkbA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3lkbA to template set # found chain 3lkbA in template set Warning: unaligning (T0528)L161 because of BadResidue code BAD_PEPTIDE in next template residue (3lkbA)V150 Warning: unaligning (T0528)A162 because of BadResidue code BAD_PEPTIDE at template residue (3lkbA)V150 Warning: unaligning (T0528)T188 because of BadResidue code BAD_PEPTIDE in next template residue (3lkbA)V177 Warning: unaligning (T0528)E189 because of BadResidue code BAD_PEPTIDE at template residue (3lkbA)V177 Warning: unaligning (T0528)K276 because of BadResidue code BAD_PEPTIDE in next template residue (3lkbA)T262 Warning: unaligning (T0528)N277 because of BadResidue code BAD_PEPTIDE at template residue (3lkbA)T262 Warning: unaligning (T0528)K337 because of BadResidue code BAD_PEPTIDE in next template residue (3lkbA)G340 Warning: unaligning (T0528)G338 because of BadResidue code BAD_PEPTIDE at template residue (3lkbA)G340 T0528 15 :AADDLKIALIYGKTGPLEAYAKQTETGLMMGLE 3lkbA 4 :GQQQVTLFWSGAITGPTSDAGAPYGAAVEDYCK T0528 49 :ATKGTMTLDGRKIVVITKDDQSKPDLSKAALAEAYQDDGADIAIG 3lkbA 37 :WANERKLVPGVVFNCVVRDDQYNNANTQRFFEEAVDRFKIPVFLS T0528 95 :SSSAAALADLPVAEENKKILI 3lkbA 82 :YATGANLQLKPLIQELRIPTI T0528 117 :EPAVADQITGEKWNRYIFRTGRNSSQDAISNAVAIGK 3lkbA 103 :PASMHIELIDPPNNDYIFLPTTSYSEQVVALLEYIAR T0528 154 :QG 3lkbA 141 :KK T0528 156 :VTIAT 3lkbA 144 :AKVAL T0528 163 :QDYAFGRDGVAAFKEALAKTGATLA 3lkbA 151 :HPSPFGRAPVEDARKAARELGLQIV T0528 190 :EYVPTTTTDFTAVGQRLFDA 3lkbA 178 :QEVGSGNLDNTALLKRFEQA T0528 215 :GKKIIWVIWAGGG 3lkbA 198 :GVEYVVHQNVAGP T0528 228 :DPLTKLQDMDP 3lkbA 213 :NILKDAKRLGL T0528 240 :RYGIELSTGGNILPALAAYKR 3lkbA 224 :KMRHLGAHYTGGPDLIALAGD T0528 261 :LPGMEGATYYYYDIP 3lkbA 246 :AEGFLWATSFYMAHE T0528 278 :PINEWLVT 3lkbA 263 :PGIRLQKE T0528 287 :HQKRFN 3lkbA 271 :IGRKYG T0528 293 :APPDFFTAGGFSAAMAVVTAVQKA 3lkbA 281 :FIESVNYTNGMLAAAIAVEAIRRA T0528 317 :KSTDTEKLIAAMEGM 3lkbA 309 :KRITNETVYQAIVGM T0528 332 :EFD 3lkbA 325 :GPN T0528 335 :TP 3lkbA 337 :TK T0528 339 :KMVFRKEDHQALQSMYHFKVKVDPAVAWAVLEPV 3lkbA 342 :EIDFTKSEHTGAEGLRILEAKGGRFVPVTEPFTS Number of specific fragments extracted= 19 number of extra gaps= 4 total=394 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 3lkbA/T0528-3lkbA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0528 read from 3lkbA/T0528-3lkbA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3lkbA read from 3lkbA/T0528-3lkbA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3lkbA in template set Warning: unaligning (T0528)L161 because of BadResidue code BAD_PEPTIDE in next template residue (3lkbA)V150 Warning: unaligning (T0528)A162 because of BadResidue code BAD_PEPTIDE at template residue (3lkbA)V150 Warning: unaligning (T0528)T188 because of BadResidue code BAD_PEPTIDE in next template residue (3lkbA)V177 Warning: unaligning (T0528)E189 because of BadResidue code BAD_PEPTIDE at template residue (3lkbA)V177 Warning: unaligning (T0528)N277 because of BadResidue code BAD_PEPTIDE in next template residue (3lkbA)T262 Warning: unaligning (T0528)P278 because of BadResidue code BAD_PEPTIDE at template residue (3lkbA)T262 Warning: unaligning (T0528)K337 because of BadResidue code BAD_PEPTIDE in next template residue (3lkbA)G340 Warning: unaligning (T0528)G338 because of BadResidue code BAD_PEPTIDE at template residue (3lkbA)G340 T0528 16 :ADDLKIALIYGKTGPLEAYAKQTETGLMMGLEYATKGT 3lkbA 5 :QQQVTLFWSGAITGPTSDAGAPYGAAVEDYCKWANERK T0528 55 :TLDGRKIVVITKDDQSKPDLSKAALAEAYQDDGADIAIGTS 3lkbA 43 :LVPGVVFNCVVRDDQYNNANTQRFFEEAVDRFKIPVFLSYA T0528 97 :SAAALADLPVAEENKKILIV 3lkbA 84 :TGANLQLKPLIQELRIPTIP T0528 118 :PAVADQITGEKWNRYIFRTGRNSSQDAISNAVAIGKQ 3lkbA 104 :ASMHIELIDPPNNDYIFLPTTSYSEQVVALLEYIARE T0528 155 :GVTIAT 3lkbA 143 :GAKVAL T0528 163 :QDYAFGRDGVAAFKEALAKTGATLA 3lkbA 151 :HPSPFGRAPVEDARKAARELGLQIV T0528 190 :EYVPTTTTDFTAVGQRLFDA 3lkbA 178 :QEVGSGNLDNTALLKRFEQA T0528 213 :KP 3lkbA 198 :GV T0528 216 :KKIIWVIWAGGGDPLTK 3lkbA 200 :EYVVHQNVAGPVANILK T0528 233 :LQDMDP 3lkbA 218 :AKRLGL T0528 239 :KRYGIELSTGGNILPALA 3lkbA 226 :RHLGAHYTGGPDLIALAG T0528 259 :KRLPGMEGATYYYYDI 3lkbA 244 :DAAEGFLWATSFYMAH T0528 276 :K 3lkbA 260 :E T0528 279 :INEWLVTEHQKRFNAP 3lkbA 263 :PGIRLQKEIGRKYGRP T0528 295 :PDFFTAGGFSAAMAVVTAVQKA 3lkbA 283 :ESVNYTNGMLAAAIAVEAIRRA T0528 317 :KSTDTEKLIAAMEGME 3lkbA 309 :KRITNETVYQAIVGMN T0528 333 :FDTP 3lkbA 335 :VSTK T0528 339 :K 3lkbA 341 :V T0528 340 :MVFRKEDHQALQSMYHFKVKVDPAVAW 3lkbA 343 :IDFTKSEHTGAEGLRILEAKGGRFVPV Number of specific fragments extracted= 19 number of extra gaps= 4 total=413 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 3lkbA/T0528-3lkbA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0528 read from 3lkbA/T0528-3lkbA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3lkbA read from 3lkbA/T0528-3lkbA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3lkbA in template set Warning: unaligning (T0528)L161 because of BadResidue code BAD_PEPTIDE in next template residue (3lkbA)V150 Warning: unaligning (T0528)A162 because of BadResidue code BAD_PEPTIDE at template residue (3lkbA)V150 Warning: unaligning (T0528)T188 because of BadResidue code BAD_PEPTIDE in next template residue (3lkbA)V177 Warning: unaligning (T0528)E189 because of BadResidue code BAD_PEPTIDE at template residue (3lkbA)V177 Warning: unaligning (T0528)K276 because of BadResidue code BAD_PEPTIDE in next template residue (3lkbA)T262 Warning: unaligning (T0528)N277 because of BadResidue code BAD_PEPTIDE at template residue (3lkbA)T262 Warning: unaligning (T0528)P336 because of BadResidue code BAD_PEPTIDE in next template residue (3lkbA)G340 Warning: unaligning (T0528)K337 because of BadResidue code BAD_PEPTIDE at template residue (3lkbA)G340 T0528 16 :ADDLKIALIYGKTGPLEAYAKQTETGLMMGLEYATKGTM 3lkbA 5 :QQQVTLFWSGAITGPTSDAGAPYGAAVEDYCKWANERKL T0528 56 :LDGRKIVVITKDDQSKPDLSKAALAEAYQDDGAD 3lkbA 44 :VPGVVFNCVVRDDQYNNANTQRFFEEAVDRFKIP T0528 91 :AIGTSSSAAALADLPVAEENKKILIVEPAVADQITGEK 3lkbA 78 :VFLSYATGANLQLKPLIQELRIPTIPASMHIELIDPPN T0528 130 :NRYIFRTGRNSSQDAISNAVAIGK 3lkbA 116 :NDYIFLPTTSYSEQVVALLEYIAR T0528 154 :QGVTIAT 3lkbA 142 :KGAKVAL T0528 163 :QDYAFGRDGVAAFKEALAKTGATLA 3lkbA 151 :HPSPFGRAPVEDARKAARELGLQIV T0528 190 :EYVPTTTTDFTAVGQRL 3lkbA 178 :QEVGSGNLDNTALLKRF T0528 210 :LKDKPGKKIIWVIWAGGGDPLTKLQDMDPKRYGIELSTGGNILPALAAYKRLPGMEGATYYYYDIP 3lkbA 195 :EQAGVEYVVHQNVAGPVANILKDAKRLGLKMRHLGAHYTGGPDLIALAGDAAEGFLWATSFYMAHE T0528 278 :PINEWLV 3lkbA 263 :PGIRLQK T0528 286 :EHQKRFN 3lkbA 270 :EIGRKYG T0528 293 :APPDFFTAGGFSAAMAVVTAVQKA 3lkbA 281 :FIESVNYTNGMLAAAIAVEAIRRA T0528 317 :KSTDTEKLIAAMEGM 3lkbA 309 :KRITNETVYQAIVGM T0528 332 :EFDT 3lkbA 335 :VSTK T0528 338 :GKMVFRKEDHQALQSMYHFKVKVDP 3lkbA 341 :VEIDFTKSEHTGAEGLRILEAKGGR T0528 366 :WAVLE 3lkbA 366 :FVPVT Number of specific fragments extracted= 15 number of extra gaps= 4 total=428 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 1z15A/T0528-1z15A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1z15A expands to /projects/compbio/data/pdb/1z15.pdb.gz 1z15A:# T0528 read from 1z15A/T0528-1z15A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1z15A read from 1z15A/T0528-1z15A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1z15A to template set # found chain 1z15A in template set Warning: unaligning (T0528)D17 because first residue in template chain is (1z15A)E1 Warning: unaligning (T0528)G93 because of BadResidue code BAD_PEPTIDE in next template residue (1z15A)H76 Warning: unaligning (T0528)T94 because of BadResidue code BAD_PEPTIDE at template residue (1z15A)H76 T0528 18 :DLKIALIYGKTGPLEAYAKQTETGLMMGLE 1z15A 2 :DIKVAVVGAMSGPVAQYGDQEFTGAEQAVA T0528 49 :ATKGTMTLDGRKIVVITKDDQSKPDLSKAALAEAYQD 1z15A 32 :DINAKGGIKGNKLQIVKYDDACDPKQAVAVANKVVND T0528 87 :GADIAI 1z15A 69 :GIKYVI T0528 95 :SSSAAALADLPVAEENKKILIVEPAVADQITGEK 1z15A 77 :LCSSSTQPASDIYEDEGILMITPAATAPELTARG T0528 130 :NRYIFRTGRNSSQDAISNAVAIGK 1z15A 111 :YQLILRTTGLDSDQGPTAAKYILE T0528 154 :QG 1z15A 136 :VK T0528 156 :VTIATLAQDYAFGRDGVAAFKEALAKTGATLATEEYVPTTTTDFTAVGQRLFDA 1z15A 139 :QRIAIVHDKQQYGEGLARAVQDGLKKGNANVVFFDGITAGEKDFSTLVARLKKE T0528 215 :GKKIIWVIWAGGG 1z15A 193 :NIDFVYYGGYHPE T0528 228 :DPLTKLQDMDP 1z15A 208 :QILRQARAAGL T0528 240 :RYGIELSTGGNILPALAAYKR 1z15A 219 :KTQFMGPEGVANVSLSNIAGE T0528 261 :LPGMEGATYYYYDI 1z15A 241 :AEGLLVTKPKNYDQ T0528 277 :NPINEWLVTEHQKRFNAPPDFFTAGGFSAAMAVVTAVQK 1z15A 255 :VPANKPIVDAIKAKKQDPSGAFVWTTYAALQSLQAGLNQ T0528 318 :STDTEKLIAAMEGMEFDTPKGKMVFRKEDHQALQSMYHFKVKVDP 1z15A 294 :SDDPAEIAKYLKANSVDTVMGPLTWDEKGDLKGFEFGVFDWHANG T0528 363 :AVAW 1z15A 340 :ATDA Number of specific fragments extracted= 14 number of extra gaps= 1 total=442 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 1z15A/T0528-1z15A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0528 read from 1z15A/T0528-1z15A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1z15A read from 1z15A/T0528-1z15A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1z15A in template set Warning: unaligning (T0528)D17 because first residue in template chain is (1z15A)E1 Warning: unaligning (T0528)G93 because of BadResidue code BAD_PEPTIDE in next template residue (1z15A)H76 Warning: unaligning (T0528)T94 because of BadResidue code BAD_PEPTIDE at template residue (1z15A)H76 T0528 18 :DLKIALIYGKTGPLEAYAKQTETGLMMGLEYATKGTM 1z15A 2 :DIKVAVVGAMSGPVAQYGDQEFTGAEQAVADINAKGG T0528 56 :LDGRKIVVITKDDQSKPDLSKAALAEAY 1z15A 39 :IKGNKLQIVKYDDACDPKQAVAVANKVV T0528 85 :DDGADIAI 1z15A 67 :NDGIKYVI T0528 95 :SSSAAALADLPVAEENKKILIVEPAVADQITGEKW 1z15A 77 :LCSSSTQPASDIYEDEGILMITPAATAPELTARGY T0528 131 :RYIFRTGRNSSQDAISNAVAIGKQ 1z15A 112 :QLILRTTGLDSDQGPTAAKYILEK T0528 155 :GV 1z15A 137 :KP T0528 157 :TIATLAQDYAFGRDGVAAFKEALAKTGATLATEEYVPTTTTDFTAVGQRLFDA 1z15A 140 :RIAIVHDKQQYGEGLARAVQDGLKKGNANVVFFDGITAGEKDFSTLVARLKKE T0528 213 :KP 1z15A 193 :NI T0528 216 :KKIIWVIWAGGGDPLTK 1z15A 195 :DFVYYGGYHPEMGQILR T0528 233 :LQDMDP 1z15A 213 :ARAAGL T0528 239 :KRYGIELSTGGNILPALA 1z15A 221 :QFMGPEGVANVSLSNIAG T0528 259 :KRLPGMEGATYYYYD 1z15A 239 :ESAEGLLVTKPKNYD T0528 276 :KNPINEWLVTEHQKRFNAPPDFFTAGGFSAAMAVVTAVQK 1z15A 254 :QVPANKPIVDAIKAKKQDPSGAFVWTTYAALQSLQAGLNQ T0528 318 :STDTEKLIAAMEGMEFDTPKGKMVFRKEDHQALQSMYHFKVK 1z15A 294 :SDDPAEIAKYLKANSVDTVMGPLTWDEKGDLKGFEFGVFDWH T0528 360 :VDPAVAW 1z15A 337 :NGTATDA Number of specific fragments extracted= 15 number of extra gaps= 1 total=457 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 1z15A/T0528-1z15A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0528 read from 1z15A/T0528-1z15A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1z15A read from 1z15A/T0528-1z15A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1z15A in template set Warning: unaligning (T0528)D17 because first residue in template chain is (1z15A)E1 Warning: unaligning (T0528)G93 because of BadResidue code BAD_PEPTIDE in next template residue (1z15A)H76 Warning: unaligning (T0528)T94 because of BadResidue code BAD_PEPTIDE at template residue (1z15A)H76 T0528 18 :DLKIALIYGKTGPLEAYAKQTETGLMMGLEYATKGTM 1z15A 2 :DIKVAVVGAMSGPVAQYGDQEFTGAEQAVADINAKGG T0528 56 :LDGRKIVVITKDDQSKPDLSKAALAEAYQD 1z15A 39 :IKGNKLQIVKYDDACDPKQAVAVANKVVND T0528 87 :GADIAI 1z15A 69 :GIKYVI T0528 95 :SSSAAALADLPVAEENKKILIVEPAVADQITGEK 1z15A 77 :LCSSSTQPASDIYEDEGILMITPAATAPELTARG T0528 130 :NRYIFRTGRNSSQDAISNAVAIGK 1z15A 111 :YQLILRTTGLDSDQGPTAAKYILE T0528 154 :QGVTIATLAQDYAFGRDGVAAFKEALAKTGATLATEEYVPTTTTDFTAVGQRL 1z15A 137 :KPQRIAIVHDKQQYGEGLARAVQDGLKKGNANVVFFDGITAGEKDFSTLVARL T0528 210 :LKDKPGKKIIWVIWAGGGDPLTKLQDMDPKRYGIELSTGGNILPALAAYKRLPGMEGATYYYYD 1z15A 190 :KKENIDFVYYGGYHPEMGQILRQARAAGLKTQFMGPEGVANVSLSNIAGESAEGLLVTKPKNYD T0528 276 :KNPINEWLVTEHQKRFNAPPDFFTAGGFSAAMAVVTAVQ 1z15A 254 :QVPANKPIVDAIKAKKQDPSGAFVWTTYAALQSLQAGLN T0528 317 :KSTDTEKLIAAMEGMEFDTPKGKMVFRKEDHQALQSMYHFKVKVDPAVAW 1z15A 293 :QSDDPAEIAKYLKANSVDTVMGPLTWDEKGDLKGFEFGVFDWHANGTATD Number of specific fragments extracted= 9 number of extra gaps= 1 total=466 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 3lmkA/T0528-3lmkA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 3lmkA expands to /projects/compbio/data/pdb/3lmk.pdb.gz 3lmkA:# T0528 read from 3lmkA/T0528-3lmkA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3lmkA read from 3lmkA/T0528-3lmkA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3lmkA to template set # found chain 3lmkA in template set Warning: unaligning (T0528)Q84 because of BadResidue code BAD_PEPTIDE in next template residue (3lmkA)D115 Warning: unaligning (T0528)D85 because of BadResidue code BAD_PEPTIDE at template residue (3lmkA)D115 Warning: unaligning (T0528)D86 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (3lmkA)K141 Warning: unaligning (T0528)I222 because of BadResidue code BAD_PEPTIDE in next template residue (3lmkA)C278 Warning: unaligning (T0528)W223 because of BadResidue code BAD_PEPTIDE at template residue (3lmkA)C278 T0528 16 :ADDLKIALIYGK 3lmkA 32 :PGDIIIGALFSV T0528 28 :TGPLEAYAKQTETGLMMGLE 3lmkA 58 :GAVREQYGIQRVEAMLHTLE T0528 49 :ATKGTMTLD 3lmkA 78 :RINSDPTLL T0528 58 :GRKIVVITKDDQSKPDLSKAALAEAY 3lmkA 88 :NITLGCEIRDSCWHSAVALEQSIEFI T0528 87 :GADIAIGTSSSAAALADLPVAEENKKILIVEPAVADQITGEKWNRYIFRTGRNSSQDAISNAVAIGKQG 3lmkA 142 :PIVGVIGPGSSSVAIQVQNLLQLFNIPQIAYSATSMDLSDKTLFKYFMRVVPSDAQQARAMVDIVKRYN T0528 156 :VTIATLAQDYAFGRDGVAAFKEALAKTGATLATEEYVP 3lmkA 212 :TYVSAVHTEGNYGESGMEAFKDMSAKEGISIAHSYKIY T0528 194 :TTTTDFTAVGQRLFDA 3lmkA 252 :AGEQSFDKLLKKLTSH T0528 213 :KPGKKIIWV 3lmkA 268 :LPKARVVAC T0528 224 :AGGG 3lmkA 279 :EGMT T0528 228 :DPLTKLQDMDPK 3lmkA 285 :GLLMAMRRLGLA T0528 240 :RYGIELSTGG 3lmkA 298 :EFLLLGSDGW T0528 250 :NILPALAAYKR 3lmkA 309 :DRYDVTDGYQR T0528 261 :LPGMEGATYYYYDI 3lmkA 321 :AVGGITIKLQSPDV T0528 281 :EWLVTEHQK 3lmkA 335 :KWFDDYYLK T0528 291 :FN 3lmkA 346 :PE T0528 293 :APPDFFTAGGFSAAMAVVTAVQKA 3lmkA 391 :HVQDSKMGFVINAIYSMAYGLHNM T0528 317 :KSTDTEKLIAAMEGMEFDTPKG 3lmkA 430 :KPIDGRKLLESLMKTNFTGVSG T0528 339 :KMVFRKEDHQ 3lmkA 453 :TILFDENGDS T0528 350 :LQSMYHFKVKV 3lmkA 463 :PGRYEIMNFKE T0528 361 :DP 3lmkA 476 :KD T0528 363 :AVAWAVLEPVRE 3lmkA 481 :YINVGSWDNGEL Number of specific fragments extracted= 21 number of extra gaps= 2 total=487 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 3lmkA/T0528-3lmkA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0528 read from 3lmkA/T0528-3lmkA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3lmkA read from 3lmkA/T0528-3lmkA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3lmkA in template set Warning: unaligning (T0528)Q84 because of BadResidue code BAD_PEPTIDE in next template residue (3lmkA)D115 Warning: unaligning (T0528)D86 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (3lmkA)K141 Warning: unaligning (T0528)V221 because of BadResidue code BAD_PEPTIDE in next template residue (3lmkA)C278 Warning: unaligning (T0528)I222 because of BadResidue code BAD_PEPTIDE at template residue (3lmkA)C278 T0528 17 :DDLKIALIYG 3lmkA 33 :GDIIIGALFS T0528 27 :KTGPLEAYAKQTETGLMMGLEYATKGTMTLDGRKIVVITKDDQSKPDLSKAALAEAY 3lmkA 57 :CGAVREQYGIQRVEAMLHTLERINSDPTLLPNITLGCEIRDSCWHSAVALEQSIEFI T0528 87 :GADIAIGTSSSAAALADLPVAEENKKILIVEPAVADQITGEKWNRYIFRTGRNSSQDAISNAVAIGKQGV 3lmkA 142 :PIVGVIGPGSSSVAIQVQNLLQLFNIPQIAYSATSMDLSDKTLFKYFMRVVPSDAQQARAMVDIVKRYNW T0528 157 :TIATLAQDYAFGRDGVAAFKEALAKTGATLATEEYVPTTT 3lmkA 213 :YVSAVHTEGNYGESGMEAFKDMSAKEGISIAHSYKIYSNA T0528 197 :TDFTAVGQRLFDALK 3lmkA 255 :QSFDKLLKKLTSHLP T0528 213 :KP 3lmkA 270 :KA T0528 216 :KKIIW 3lmkA 272 :RVVAC T0528 223 :WAGGGDPLTK 3lmkA 279 :EGMTVRGLLM T0528 233 :LQDMDP 3lmkA 290 :MRRLGL T0528 239 :KRYGIELS 3lmkA 298 :EFLLLGSD T0528 247 :TGGNILPALA 3lmkA 309 :DRYDVTDGYQ T0528 259 :KRLPGMEGATYYYY 3lmkA 319 :REAVGGITIKLQSP T0528 273 :DIPKNPINEWLVTEHQ 3lmkA 348 :TNHRNPWFQEFWQHRF T0528 293 :APPDFFTAGGFSAAMAVVTAVQKA 3lmkA 391 :HVQDSKMGFVINAIYSMAYGLHNM T0528 317 :KSTDTEKLIAAMEGMEFDTPKG 3lmkA 430 :KPIDGRKLLESLMKTNFTGVSG T0528 339 :KMVFRK 3lmkA 453 :TILFDE T0528 346 :DHQALQSMYHFKVKVDPA 3lmkA 459 :NGDSPGRYEIMNFKEMGK T0528 364 :VAWAVLEPVRE 3lmkA 482 :INVGSWDNGEL Number of specific fragments extracted= 18 number of extra gaps= 2 total=505 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 3lmkA/T0528-3lmkA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0528 read from 3lmkA/T0528-3lmkA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3lmkA read from 3lmkA/T0528-3lmkA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3lmkA in template set Warning: unaligning (T0528)Q84 because of BadResidue code BAD_PEPTIDE in next template residue (3lmkA)D115 Warning: unaligning (T0528)D85 because of BadResidue code BAD_PEPTIDE at template residue (3lmkA)D115 Warning: unaligning (T0528)W220 because of BadResidue code BAD_PEPTIDE in next template residue (3lmkA)C278 Warning: unaligning (T0528)V221 because of BadResidue code BAD_PEPTIDE at template residue (3lmkA)C278 Warning: unaligning (T0528)K376 because last residue in template chain is (3lmkA)D495 T0528 18 :DLKIALIYG 3lmkA 34 :DIIIGALFS T0528 27 :KTGPLEAYAKQTETGLMMGLEYATKGTMTLDGRKIVVITKDDQSKPDLSKAALAEAY 3lmkA 57 :CGAVREQYGIQRVEAMLHTLERINSDPTLLPNITLGCEIRDSCWHSAVALEQSIEFI T0528 88 :ADIAIGTSSSAAALADLPVAEENKKILIVEPAVADQITGEKWNRYIFRTGRNSSQDAISNAVAIGK 3lmkA 143 :IVGVIGPGSSSVAIQVQNLLQLFNIPQIAYSATSMDLSDKTLFKYFMRVVPSDAQQARAMVDIVKR T0528 154 :QGVTIATLAQDYAFGRDGVAAFKEALAKTGATLATEEYVPTTT 3lmkA 210 :NWTYVSAVHTEGNYGESGMEAFKDMSAKEGISIAHSYKIYSNA T0528 197 :TDFTAVGQRL 3lmkA 257 :FDKLLKKLTS T0528 210 :LKDKPGKKII 3lmkA 267 :HLPKARVVAC T0528 222 :IWAGGGDPLTKLQDMDP 3lmkA 279 :EGMTVRGLLMAMRRLGL T0528 239 :KRYGIELSTG 3lmkA 297 :GEFLLLGSDG T0528 249 :GNILPALAAYKRLPGMEGATYYYYD 3lmkA 309 :DRYDVTDGYQREAVGGITIKLQSPD T0528 277 :NPINEWLVTEHQ 3lmkA 352 :NPWFQEFWQHRF T0528 293 :APPDFFTAGGFSAAMAVVTAVQKA 3lmkA 391 :HVQDSKMGFVINAIYSMAYGLHNM T0528 317 :KSTDTEKLIAAMEGMEFDTPKGKMVFRKEDHQALQSMYHFKVKVDPA 3lmkA 430 :KPIDGRKLLESLMKTNFTGVSGDTILFDENGDSPGRYEIMNFKEMGK T0528 364 :VAWAVLEPVREL 3lmkA 483 :NVGSWDNGELKM Number of specific fragments extracted= 13 number of extra gaps= 2 total=518 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 1ewkA/T0528-1ewkA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1ewkA expands to /projects/compbio/data/pdb/1ewk.pdb.gz 1ewkA:Skipped atom 1764, because occupancy 0.400 <= existing 0.600 in 1ewkA Skipped atom 1766, because occupancy 0.400 <= existing 0.600 in 1ewkA Skipped atom 1768, because occupancy 0.400 <= existing 0.600 in 1ewkA Skipped atom 1770, because occupancy 0.400 <= existing 0.600 in 1ewkA Skipped atom 1772, because occupancy 0.400 <= existing 0.600 in 1ewkA Skipped atom 1774, because occupancy 0.400 <= existing 0.600 in 1ewkA # T0528 read from 1ewkA/T0528-1ewkA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ewkA read from 1ewkA/T0528-1ewkA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1ewkA to template set # found chain 1ewkA in template set Warning: unaligning (T0528)Q84 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ewkA)K154 Warning: unaligning (T0528)D86 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ewkA)K154 T0528 16 :ADDLKIALIYGK 1ewkA 42 :DGDVIIGALFSV T0528 28 :TGPLEAYAKQTETGLMMGLE 1ewkA 68 :GEIREQYGIQRVEAMFHTLD T0528 49 :ATKGTMTLD 1ewkA 88 :KINADPVLL T0528 58 :GRKIVVITKDDQSKPDLSKAALAEAY 1ewkA 98 :NITLGSEIRDSCWHSSVALEQSIEFI T0528 87 :GADIAIGTSSSAAALADLPVAEENKKILIVEPAVADQITGEKWNRYIFRTGRNSSQDAISNAVAIGKQG 1ewkA 155 :PIAGVIGPGSSSVAIQVQNLLQLFDIPQIAYSATSIDLSDKTLYKYFLRVVPSDTLQARAMLDIVKRYN T0528 156 :VTIATLAQDYAFGRDGVAAFKEALAKTGATLATEEYVP 1ewkA 225 :TYVSAVHTEGNYGESGMDAFKELAAQEGLCIAHSDKIY T0528 194 :TTTTDFTAVGQRLFDA 1ewkA 265 :AGEKSFDRLLRKLRER T0528 213 :KPGKKIIWVIWAGGG 1ewkA 281 :LPKARVVVCFCEGMT T0528 228 :DPLTKLQDMDPK 1ewkA 298 :GLLSAMRRLGVV T0528 240 :RYGIELSTGGNI 1ewkA 311 :EFSLIGSDGWAD T0528 252 :LPALAAYKR 1ewkA 324 :DEVIEGYEV T0528 261 :LPGMEGATYYYY 1ewkA 334 :ANGGITIKLQSP T0528 276 :KNPINEW 1ewkA 346 :EVRSFDD T0528 283 :LVTEHQKRFN 1ewkA 368 :FPEFWQHRFQ T0528 293 :APPDFFTAGGFSAAMAVVTAVQKA 1ewkA 404 :YVQDSKMGFVINAIYAMAHGLQNM T0528 317 :KSTDTEKLIAAMEGMEFDTPKG 1ewkA 443 :KPIDGRKLLDFLIKSSFVGVSG T0528 339 :KMVFRKEDHQ 1ewkA 466 :EVWFDEKGDA T0528 350 :LQSMYHFKVKVDP 1ewkA 476 :PGRYDIMNLQYTE T0528 363 :AVAWAVLEPVRE 1ewkA 494 :YVHVGTWHEGVL Number of specific fragments extracted= 19 number of extra gaps= 0 total=537 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 1ewkA/T0528-1ewkA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0528 read from 1ewkA/T0528-1ewkA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ewkA read from 1ewkA/T0528-1ewkA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1ewkA in template set Warning: unaligning (T0528)Q84 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ewkA)K154 Warning: unaligning (T0528)D86 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ewkA)K154 T0528 18 :DLKIALIYG 1ewkA 44 :DVIIGALFS T0528 27 :KTGPLEAYAKQTETGLMMGLEYATKGTMTLDGRKIVVITKDDQSKPDLSKAALAEAY 1ewkA 67 :CGEIREQYGIQRVEAMFHTLDKINADPVLLPNITLGSEIRDSCWHSSVALEQSIEFI T0528 87 :GADIAIGTSSSAAALADLPVAEENKKILIVEPAVADQIT 1ewkA 155 :PIAGVIGPGSSSVAIQVQNLLQLFDIPQIAYSATSIDLS T0528 126 :GEKW 1ewkA 195 :KTLY T0528 131 :RYIFRTGRNSSQDAISNAVAIGKQGV 1ewkA 199 :KYFLRVVPSDTLQARAMLDIVKRYNW T0528 157 :TIATLAQDYAFGRDGVAAFKEALAKTGATLATEEYVPT 1ewkA 226 :YVSAVHTEGNYGESGMDAFKELAAQEGLCIAHSDKIYS T0528 195 :TTTDFTAVGQRLFDA 1ewkA 266 :GEKSFDRLLRKLRER T0528 211 :KDKP 1ewkA 281 :LPKA T0528 216 :KKIIWVIWAGGGDPLTK 1ewkA 285 :RVVVCFCEGMTVRGLLS T0528 233 :LQDMDP 1ewkA 303 :MRRLGV T0528 239 :KRYGIELST 1ewkA 313 :SLIGSDGWA T0528 248 :GGNILPALA 1ewkA 323 :RDEVIEGYE T0528 259 :KRLPGMEGATYYYYDI 1ewkA 332 :VEANGGITIKLQSPEV T0528 278 :PINEWLV 1ewkA 348 :RSFDDYF T0528 285 :TEHQKRF 1ewkA 369 :PEFWQHR T0528 292 :N 1ewkA 377 :Q T0528 293 :APPD 1ewkA 403 :NYVQ T0528 297 :FFTAGGFSAAMAVVTAVQKA 1ewkA 408 :SKMGFVINAIYAMAHGLQNM T0528 317 :KST 1ewkA 434 :GHV T0528 320 :DTEKLIAAMEGMEFDTPKG 1ewkA 446 :DGRKLLDFLIKSSFVGVSG T0528 339 :KMVFRK 1ewkA 466 :EVWFDE T0528 346 :DHQALQSMYHFKVK 1ewkA 472 :KGDAPGRYDIMNLQ T0528 361 :DPA 1ewkA 488 :EAN T0528 364 :VAWAVLEPVR 1ewkA 495 :VHVGTWHEGV Number of specific fragments extracted= 24 number of extra gaps= 0 total=561 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 1ewkA/T0528-1ewkA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0528 read from 1ewkA/T0528-1ewkA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ewkA read from 1ewkA/T0528-1ewkA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1ewkA in template set Warning: unaligning (T0528)Q84 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ewkA)K154 Warning: unaligning (T0528)M380 because last residue in template chain is (1ewkA)I512 T0528 17 :DDLKIALIYGKTGP 1ewkA 43 :GDVIIGALFSVHHQ T0528 31 :LEAYAKQTETGLMMGLEYATKGTMTLDGRKIVVITKDDQSKPDLSKAALAEAY 1ewkA 71 :REQYGIQRVEAMFHTLDKINADPVLLPNITLGSEIRDSCWHSSVALEQSIEFI T0528 88 :ADIAIGTSSSAAALADLPVAEENKKILIVEPAVADQITGEKWNRYIFRTGRNSSQDAISNAVAIGK 1ewkA 156 :IAGVIGPGSSSVAIQVQNLLQLFDIPQIAYSATSIDLSDKTLYKYFLRVVPSDTLQARAMLDIVKR T0528 154 :QGVTIATLAQDYAFGRDGVAAFKEALAKTGATLATEEYVPTTT 1ewkA 223 :NWTYVSAVHTEGNYGESGMDAFKELAAQEGLCIAHSDKIYSNA T0528 197 :TDFTAVGQRLFD 1ewkA 268 :KSFDRLLRKLRE T0528 210 :LKDKPGKKIIWVIWAGGGDPLTKLQDMDP 1ewkA 280 :RLPKARVVVCFCEGMTVRGLLSAMRRLGV T0528 239 :KRYGIELSTG 1ewkA 310 :GEFSLIGSDG T0528 249 :GNILPALAAYKRLPGMEGATYYYYD 1ewkA 322 :DRDEVIEGYEVEANGGITIKLQSPE T0528 277 :NPINEWLV 1ewkA 347 :VRSFDDYF T0528 285 :TEHQKRFN 1ewkA 369 :PEFWQHRF T0528 293 :APPDFFTAGGFSAAMAVVTAVQKA 1ewkA 404 :YVQDSKMGFVINAIYAMAHGLQNM T0528 317 :KSTDTEKLIAAMEGMEFDTPKGKMVFRKEDHQALQSMYHFKVKVDPA 1ewkA 443 :KPIDGRKLLDFLIKSSFVGVSGEEVWFDEKGDAPGRYDIMNLQYTEA T0528 364 :VAWAVLEPVRELKIEE 1ewkA 496 :HVGTWHEGVLNIDDYK Number of specific fragments extracted= 13 number of extra gaps= 0 total=574 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 1dp4A/T0528-1dp4A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1dp4A expands to /projects/compbio/data/pdb/1dp4.pdb.gz 1dp4A:Skipped atom 541, because occupancy 0.500 <= existing 0.500 in 1dp4A Skipped atom 543, because occupancy 0.500 <= existing 0.500 in 1dp4A Skipped atom 545, because occupancy 0.500 <= existing 0.500 in 1dp4A Skipped atom 547, because occupancy 0.500 <= existing 0.500 in 1dp4A Skipped atom 549, because occupancy 0.500 <= existing 0.500 in 1dp4A Skipped atom 551, because occupancy 0.500 <= existing 0.500 in 1dp4A Skipped atom 553, because occupancy 0.500 <= existing 0.500 in 1dp4A Skipped atom 555, because occupancy 0.500 <= existing 0.500 in 1dp4A Skipped atom 557, because occupancy 0.500 <= existing 0.500 in 1dp4A Skipped atom 559, because occupancy 0.500 <= existing 0.500 in 1dp4A Skipped atom 1636, because occupancy 0.500 <= existing 0.500 in 1dp4A Skipped atom 1638, because occupancy 0.500 <= existing 0.500 in 1dp4A Skipped atom 1640, because occupancy 0.500 <= existing 0.500 in 1dp4A Skipped atom 1642, because occupancy 0.500 <= existing 0.500 in 1dp4A Skipped atom 2126, because occupancy 0.500 <= existing 0.500 in 1dp4A Skipped atom 2128, because occupancy 0.500 <= existing 0.500 in 1dp4A Skipped atom 2130, because occupancy 0.500 <= existing 0.500 in 1dp4A Skipped atom 2132, because occupancy 0.500 <= existing 0.500 in 1dp4A Skipped atom 2134, because occupancy 0.500 <= existing 0.500 in 1dp4A # T0528 read from 1dp4A/T0528-1dp4A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1dp4A read from 1dp4A/T0528-1dp4A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1dp4A to template set # found chain 1dp4A in template set Warning: unaligning (T0528)D17 because first residue in template chain is (1dp4A)S1 T0528 18 :DLKIALIYGKTGPLEAY 1dp4A 2 :DLTVAVVLPLTNTSYPW T0528 35 :AKQTETGLMMGLE 1dp4A 20 :WARVGPAVELALA T0528 49 :ATKGTMTLD 1dp4A 33 :RVKARPDLL T0528 58 :GRKIVVITKDDQ 1dp4A 43 :GWTVRMVLGSSE T0528 70 :SKPDLSKAALAEAYQDDGADIAIGTSSSAAALADLPVAEENKKILIVEPAVADQITGEKWNRYIFRTGRNSSQDAISNAVAIGKQG 1dp4A 60 :CSDTAAPLAAVDLKWEHSPAVFLGPGCVYSAAPVGRFTAHWRVPLLTAGAPALGIGVKDEYALTTRTGPSHVKLGDFVTALHRRLG T0528 156 :VTIATLAQDYAFG 1dp4A 147 :EHQALVLYADRLG T0528 169 :RDGVAAFKEALAKT 1dp4A 165 :FFIVEGLYMRVRER T0528 183 :GATLATEEYVP 1dp4A 180 :NITVNHQEFVE T0528 195 :TTTDFTAVGQRLFDA 1dp4A 191 :GDPDHYPKLLRAVRR T0528 215 :GKKIIWVIWAGGG 1dp4A 206 :KGRVIYICSSPDA T0528 228 :DPLTKLQDMDPK 1dp4A 221 :NLMLLALNAGLT T0528 240 :RYGIELSTGG 1dp4A 235 :DYVFFHLDVF T0528 250 :NILPALAAYKR 1dp4A 262 :RGDGQDRSARQ T0528 261 :LPGMEGATYYYY 1dp4A 274 :FQAAKIITYKEP T0528 276 :KNPINEWLVTEHQKRFN 1dp4A 286 :DNPEYLEFLKQLKLLAD T0528 293 :APPDFFTAGGFSAAMAVVTAVQKA 1dp4A 312 :GLKNIIPASFHDGLLLYVQAVTET T0528 317 :KSTDTEKLIAAMEGMEFDTPKGKMVFRKEDHQ 1dp4A 341 :TVTDGENITQRMWNRSFQGVTGYLKIDRNGDR T0528 350 :LQSMYHFKVK 1dp4A 373 :DTDFSLWDMD T0528 360 :VDPAVAWAVLE 1dp4A 385 :TGAFRVVLNYN T0528 371 :PVRELKIEEMNIPIKNKK 1dp4A 398 :SQELMAVSEHKLYWPLGY Number of specific fragments extracted= 20 number of extra gaps= 0 total=594 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 1dp4A/T0528-1dp4A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0528 read from 1dp4A/T0528-1dp4A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1dp4A read from 1dp4A/T0528-1dp4A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1dp4A in template set Warning: unaligning (T0528)D17 because first residue in template chain is (1dp4A)S1 T0528 18 :DLKIALIYGKTGPLEAYAKQTET 1dp4A 2 :DLTVAVVLPLTNTSYPWSWARVG T0528 41 :GLMMGLEYATKGTMTLDGRKIVVITKD 1dp4A 26 :AVELALARVKARPDLLPGWTVRMVLGS T0528 68 :DQSKPDLSKAALAEAYQDDGADIAIGTSSSAAALADLPVAEENKKILIVEPAVADQIT 1dp4A 58 :GVCSDTAAPLAAVDLKWEHSPAVFLGPGCVYSAAPVGRFTAHWRVPLLTAGAPALGIG T0528 126 :GEKW 1dp4A 117 :KDEY T0528 131 :RYIFRTGRNSSQDAISNAVAIGKQGV 1dp4A 121 :ALTTRTGPSHVKLGDFVTALHRRLGW T0528 157 :TIATLAQ 1dp4A 149 :QALVLYA T0528 165 :YAFG 1dp4A 156 :DRLG T0528 169 :RDGVAAFKEALAKT 1dp4A 165 :FFIVEGLYMRVRER T0528 183 :GATLATEEYVPTTTTDFTAVGQRLFDA 1dp4A 180 :NITVNHQEFVEGDPDHYPKLLRAVRRK T0528 214 :P 1dp4A 207 :G T0528 216 :KKIIWVIWAGGGDPLTK 1dp4A 208 :RVIYICSSPDAFRNLML T0528 233 :LQDMDP 1dp4A 226 :ALNAGL T0528 239 :KRYGIELS 1dp4A 235 :DYVFFHLD T0528 247 :TGGNILPALAA 1dp4A 261 :ERGDGQDRSAR T0528 259 :KRLPGMEGATYYYYD 1dp4A 272 :QAFQAAKIITYKEPD T0528 277 :NPINEWLVTEHQKRFN 1dp4A 287 :NPEYLEFLKQLKLLAD T0528 293 :APPDFFTAGGFSAAMAVVTAVQKA 1dp4A 312 :GLKNIIPASFHDGLLLYVQAVTET T0528 318 :S 1dp4A 339 :G T0528 320 :DTEKLIAAMEGMEFDTPKGKMVFRK 1dp4A 344 :DGENITQRMWNRSFQGVTGYLKIDR T0528 346 :DHQALQSMYHFKVK 1dp4A 369 :NGDRDTDFSLWDMD T0528 360 :VDPAVAWAVLEPV 1dp4A 385 :TGAFRVVLNYNGT T0528 373 :RELKIEEMN 1dp4A 400 :ELMAVSEHK Number of specific fragments extracted= 22 number of extra gaps= 0 total=616 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 1dp4A/T0528-1dp4A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0528 read from 1dp4A/T0528-1dp4A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1dp4A read from 1dp4A/T0528-1dp4A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1dp4A in template set Warning: unaligning (T0528)D17 because first residue in template chain is (1dp4A)S1 T0528 18 :DLKIALIYGKTGP 1dp4A 2 :DLTVAVVLPLTNT T0528 31 :LEAYAKQTETGLMMGLEYATKGTMTLDGRKIVVITKDDQS 1dp4A 16 :YPWSWARVGPAVELALARVKARPDLLPGWTVRMVLGSSEN T0528 71 :KPDLSKAALAEAYQDDGADIAIGTSSSAAALADLPVAEENKKILIVEPAVADQITGEKWNRYIFRTGRNSSQDAISNAVAIGK 1dp4A 61 :SDTAAPLAAVDLKWEHSPAVFLGPGCVYSAAPVGRFTAHWRVPLLTAGAPALGIGVKDEYALTTRTGPSHVKLGDFVTALHRR T0528 154 :QGVTIATLAQDYAFG 1dp4A 145 :GWEHQALVLYADRLG T0528 169 :RDGVAAFKEALAKT 1dp4A 165 :FFIVEGLYMRVRER T0528 183 :GATLATEEYVPTTTTDFTAVGQRLFDA 1dp4A 180 :NITVNHQEFVEGDPDHYPKLLRAVRRK T0528 214 :PGKKIIWVIWAGGGDPLTKLQDMDP 1dp4A 207 :GRVIYICSSPDAFRNLMLLALNAGL T0528 239 :KRYGIELSTG 1dp4A 235 :DYVFFHLDVF T0528 249 :GNILPALAAYKRLPGMEGATYYYYD 1dp4A 262 :RGDGQDRSARQAFQAAKIITYKEPD T0528 277 :NPINEWLVTEHQKRFN 1dp4A 287 :NPEYLEFLKQLKLLAD T0528 293 :APPDFFTAGGFSAAMAVVTAVQKA 1dp4A 312 :GLKNIIPASFHDGLLLYVQAVTET T0528 317 :KS 1dp4A 339 :GG T0528 319 :TDTEKLIAAMEGMEFDTPKGKMVFR 1dp4A 343 :TDGENITQRMWNRSFQGVTGYLKID T0528 345 :EDHQALQSMYHFKVKVDPAVAWAVL 1dp4A 368 :RNGDRDTDFSLWDMDPETGAFRVVL T0528 370 :EPVRELKIEEMNIPIKNKK 1dp4A 397 :TSQELMAVSEHKLYWPLGY Number of specific fragments extracted= 15 number of extra gaps= 0 total=631 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 3ks9A/T0528-3ks9A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 3ks9A expands to /projects/compbio/data/pdb/3ks9.pdb.gz 3ks9A:Skipped atom 1290, because occupancy 0.500 <= existing 0.500 in 3ks9A Skipped atom 1292, because occupancy 0.500 <= existing 0.500 in 3ks9A Skipped atom 1294, because occupancy 0.500 <= existing 0.500 in 3ks9A Skipped atom 1296, because occupancy 0.500 <= existing 0.500 in 3ks9A Skipped atom 1298, because occupancy 0.500 <= existing 0.500 in 3ks9A Skipped atom 1300, because occupancy 0.500 <= existing 0.500 in 3ks9A Skipped atom 1302, because occupancy 0.500 <= existing 0.500 in 3ks9A Skipped atom 1304, because occupancy 0.500 <= existing 0.500 in 3ks9A Skipped atom 1306, because occupancy 0.500 <= existing 0.500 in 3ks9A Skipped atom 1308, because occupancy 0.500 <= existing 0.500 in 3ks9A Skipped atom 1310, because occupancy 0.500 <= existing 0.500 in 3ks9A Skipped atom 1312, because occupancy 0.500 <= existing 0.500 in 3ks9A Skipped atom 1369, because occupancy 0.500 <= existing 0.500 in 3ks9A Skipped atom 1371, because occupancy 0.500 <= existing 0.500 in 3ks9A Skipped atom 1373, because occupancy 0.500 <= existing 0.500 in 3ks9A Skipped atom 1375, because occupancy 0.500 <= existing 0.500 in 3ks9A Skipped atom 1377, because occupancy 0.500 <= existing 0.500 in 3ks9A Skipped atom 1379, because occupancy 0.500 <= existing 0.500 in 3ks9A Skipped atom 1381, because occupancy 0.500 <= existing 0.500 in 3ks9A Skipped atom 1383, because occupancy 0.500 <= existing 0.500 in 3ks9A Skipped atom 1834, because occupancy 0.500 <= existing 0.500 in 3ks9A Skipped atom 1836, because occupancy 0.500 <= existing 0.500 in 3ks9A Skipped atom 1838, because occupancy 0.500 <= existing 0.500 in 3ks9A Skipped atom 1840, because occupancy 0.500 <= existing 0.500 in 3ks9A Skipped atom 1842, because occupancy 0.500 <= existing 0.500 in 3ks9A Skipped atom 1844, because occupancy 0.500 <= existing 0.500 in 3ks9A Skipped atom 1846, because occupancy 0.500 <= existing 0.500 in 3ks9A Skipped atom 1848, because occupancy 0.500 <= existing 0.500 in 3ks9A Skipped atom 1966, because occupancy 0.500 <= existing 0.500 in 3ks9A Skipped atom 1968, because occupancy 0.500 <= existing 0.500 in 3ks9A Skipped atom 1970, because occupancy 0.500 <= existing 0.500 in 3ks9A Skipped atom 1972, because occupancy 0.500 <= existing 0.500 in 3ks9A Skipped atom 1974, because occupancy 0.500 <= existing 0.500 in 3ks9A Skipped atom 1976, because occupancy 0.500 <= existing 0.500 in 3ks9A Skipped atom 1978, because occupancy 0.500 <= existing 0.500 in 3ks9A Skipped atom 1980, because occupancy 0.500 <= existing 0.500 in 3ks9A Skipped atom 1982, because occupancy 0.500 <= existing 0.500 in 3ks9A Skipped atom 2937, because occupancy 0.500 <= existing 0.500 in 3ks9A Skipped atom 2939, because occupancy 0.500 <= existing 0.500 in 3ks9A Skipped atom 2941, because occupancy 0.500 <= existing 0.500 in 3ks9A Skipped atom 2943, because occupancy 0.500 <= existing 0.500 in 3ks9A Skipped atom 2945, because occupancy 0.500 <= existing 0.500 in 3ks9A Skipped atom 2947, because occupancy 0.500 <= existing 0.500 in 3ks9A Skipped atom 2949, because occupancy 0.500 <= existing 0.500 in 3ks9A Skipped atom 2951, because occupancy 0.500 <= existing 0.500 in 3ks9A Skipped atom 2953, because occupancy 0.500 <= existing 0.500 in 3ks9A Skipped atom 2955, because occupancy 0.500 <= existing 0.500 in 3ks9A Skipped atom 3175, because occupancy 0.500 <= existing 0.500 in 3ks9A Skipped atom 3177, because occupancy 0.500 <= existing 0.500 in 3ks9A Skipped atom 3179, because occupancy 0.500 <= existing 0.500 in 3ks9A Skipped atom 3181, because occupancy 0.500 <= existing 0.500 in 3ks9A Skipped atom 3183, because occupancy 0.500 <= existing 0.500 in 3ks9A Skipped atom 3185, because occupancy 0.500 <= existing 0.500 in 3ks9A Skipped atom 3187, because occupancy 0.500 <= existing 0.500 in 3ks9A Skipped atom 3189, because occupancy 0.500 <= existing 0.500 in 3ks9A Skipped atom 3191, because occupancy 0.500 <= existing 0.500 in 3ks9A Skipped atom 3200, because occupancy 0.500 <= existing 0.500 in 3ks9A Skipped atom 3202, because occupancy 0.500 <= existing 0.500 in 3ks9A Skipped atom 3204, because occupancy 0.500 <= existing 0.500 in 3ks9A Skipped atom 3206, because occupancy 0.500 <= existing 0.500 in 3ks9A Skipped atom 3208, because occupancy 0.500 <= existing 0.500 in 3ks9A Skipped atom 3210, because occupancy 0.500 <= existing 0.500 in 3ks9A Skipped atom 3212, because occupancy 0.500 <= existing 0.500 in 3ks9A Skipped atom 3214, because occupancy 0.500 <= existing 0.500 in 3ks9A Skipped atom 3216, because occupancy 0.500 <= existing 0.500 in 3ks9A Skipped atom 3218, because occupancy 0.500 <= existing 0.500 in 3ks9A Skipped atom 3220, because occupancy 0.500 <= existing 0.500 in 3ks9A Skipped atom 3222, because occupancy 0.500 <= existing 0.500 in 3ks9A Skipped atom 3224, because occupancy 0.500 <= existing 0.500 in 3ks9A Skipped atom 3226, because occupancy 0.500 <= existing 0.500 in 3ks9A # T0528 read from 3ks9A/T0528-3ks9A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3ks9A read from 3ks9A/T0528-3ks9A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3ks9A to template set # found chain 3ks9A in template set Warning: unaligning (T0528)D86 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (3ks9A)K154 Warning: unaligning (T0528)I222 because of BadResidue code BAD_PEPTIDE in next template residue (3ks9A)C291 Warning: unaligning (T0528)W223 because of BadResidue code BAD_PEPTIDE at template residue (3ks9A)C291 Warning: unaligning (T0528)P362 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (3ks9A)R491 T0528 16 :ADDLKIALIYGK 3ks9A 42 :DGDVIIGALFSV T0528 28 :TGPLEAY 3ks9A 67 :CGEIREQ T0528 35 :AKQTETGLMMGLE 3ks9A 75 :GIQRVEAMFHTLD T0528 49 :ATKGTMTLD 3ks9A 88 :KINADPVLL T0528 58 :GRKIVVITKDDQSKPDLSKAALAEAYQD 3ks9A 98 :NITLGSEIRDSCWHSSVALEQSIEFIRD T0528 87 :GADIAIGTSSSAAALADLPVAEENKKILIVEPAVADQITGEKWNRYIFRTGRNSSQDAISNAVAIGKQG 3ks9A 155 :PIAGVIGPGSSSVAIQVQNLLQLFDIPQIAYSATSIDLSDKTLYKYFLRVVPSDTLQARAMLDIVKRYN T0528 156 :VTIATLAQDYAFGRDGVAAFKEALAKTGATLATEEYVP 3ks9A 225 :TYVSAVHTEGNYGESGMDAFKELAAQEGLSIAHSDKIY T0528 194 :TTTTDFTAVGQRLFDA 3ks9A 265 :AGEKSFDRLLRKLRER T0528 213 :KPGKKIIWV 3ks9A 281 :LPKARVVVC T0528 224 :AGGG 3ks9A 292 :EGMT T0528 228 :DPLTKLQDMDPK 3ks9A 298 :GLLSAMRRLGVV T0528 240 :RYGIELSTGGNI 3ks9A 311 :EFSLIGSDGWAD T0528 252 :LPALAAYKR 3ks9A 324 :DEVIEGYEV T0528 261 :LPGMEGATYYYYDIPK 3ks9A 334 :ANGGITIKLQSPEVRS T0528 277 :NPINEWLVTEH 3ks9A 365 :NPWFPEFWQHR T0528 291 :FN 3ks9A 376 :FQ T0528 293 :APPDFFTAGGFSAAMAVVTAVQKA 3ks9A 404 :YVQDSKMGFVINAIYAMAHGLQNM T0528 317 :KSTDTEKLIAAMEGMEFDTPKG 3ks9A 443 :KPIDGSKLLDFLIKSSFIGVSG T0528 339 :KMVFRKEDHQ 3ks9A 466 :EVWFDEKGDA T0528 350 :LQSMYHFKVKVD 3ks9A 476 :PGRYDIMNLQYT T0528 363 :AVAWAVLEPVRE 3ks9A 494 :YVHVGTWHEGVL T0528 376 :KIEE 3ks9A 506 :NIDD Number of specific fragments extracted= 22 number of extra gaps= 1 total=653 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 3ks9A/T0528-3ks9A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0528 read from 3ks9A/T0528-3ks9A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3ks9A read from 3ks9A/T0528-3ks9A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3ks9A in template set Warning: unaligning (T0528)D86 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (3ks9A)K154 Warning: unaligning (T0528)V221 because of BadResidue code BAD_PEPTIDE in next template residue (3ks9A)C291 Warning: unaligning (T0528)I222 because of BadResidue code BAD_PEPTIDE at template residue (3ks9A)C291 Warning: unaligning (T0528)D361 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (3ks9A)R491 T0528 16 :ADDLKIALIYGK 3ks9A 42 :DGDVIIGALFSV T0528 28 :TGPLEAYAKQTETGLMMGLEYATKGTMTLDGRKIVVITKDDQSKPDLSKAALAEAY 3ks9A 68 :GEIREQYGIQRVEAMFHTLDKINADPVLLPNITLGSEIRDSCWHSSVALEQSIEFI T0528 87 :GADIAIGTSSSAAALADLPVAEENKKILIVEPAVADQITGEKWNRYIFRTGRNSSQDAISNAVAIGKQGV 3ks9A 155 :PIAGVIGPGSSSVAIQVQNLLQLFDIPQIAYSATSIDLSDKTLYKYFLRVVPSDTLQARAMLDIVKRYNW T0528 157 :TIATLAQDYAFGRDGVAAFKEALAKTGATLATEEYVPTTT 3ks9A 226 :YVSAVHTEGNYGESGMDAFKELAAQEGLSIAHSDKIYSNA T0528 197 :TDFTAVGQRLFDALK 3ks9A 268 :KSFDRLLRKLRERLP T0528 213 :KP 3ks9A 283 :KA T0528 216 :KKIIW 3ks9A 285 :RVVVC T0528 223 :WAGGGDPLTK 3ks9A 292 :EGMTVRGLLS T0528 233 :LQDMDP 3ks9A 303 :MRRLGV T0528 239 :KRYGIELST 3ks9A 310 :GEFSLIGSD T0528 248 :GGNILPALA 3ks9A 323 :RDEVIEGYE T0528 259 :KRLPGMEGATYYYYDI 3ks9A 332 :VEANGGITIKLQSPEV T0528 278 :PINEWL 3ks9A 348 :RSFDDY T0528 284 :VTEHQKRF 3ks9A 368 :FPEFWQHR T0528 292 :N 3ks9A 377 :Q T0528 293 :APPDFFTAGGFSAAMAVVTAVQKA 3ks9A 404 :YVQDSKMGFVINAIYAMAHGLQNM T0528 317 :KSTDTEKLIAAMEGMEFDTPKG 3ks9A 443 :KPIDGSKLLDFLIKSSFIGVSG T0528 339 :KMVFRK 3ks9A 466 :EVWFDE T0528 346 :DHQALQSMYHFKVK 3ks9A 472 :KGDAPGRYDIMNLQ T0528 360 :V 3ks9A 487 :T T0528 364 :VAWAVLEPVR 3ks9A 495 :VHVGTWHEGV Number of specific fragments extracted= 21 number of extra gaps= 1 total=674 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 3ks9A/T0528-3ks9A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0528 read from 3ks9A/T0528-3ks9A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3ks9A read from 3ks9A/T0528-3ks9A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3ks9A in template set Warning: unaligning (T0528)G87 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (3ks9A)K154 Warning: unaligning (T0528)W220 because of BadResidue code BAD_PEPTIDE in next template residue (3ks9A)C291 Warning: unaligning (T0528)V221 because of BadResidue code BAD_PEPTIDE at template residue (3ks9A)C291 Warning: unaligning (T0528)P362 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (3ks9A)R491 Warning: unaligning (T0528)A365 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (3ks9A)R491 T0528 16 :ADDLKIALIYGK 3ks9A 42 :DGDVIIGALFSV T0528 28 :TGPLEAYAKQTETGLMMGLEYATKGTMTLDGRKIVVITKDDQSKPDLSKAALAEAYQDD 3ks9A 68 :GEIREQYGIQRVEAMFHTLDKINADPVLLPNITLGSEIRDSCWHSSVALEQSIEFIRDS T0528 88 :ADIAIGTSSSAAALADLPVAEENKKILIVEPAVADQITGEKWNRYIFRTGRNSSQDAISNAVAIGK 3ks9A 156 :IAGVIGPGSSSVAIQVQNLLQLFDIPQIAYSATSIDLSDKTLYKYFLRVVPSDTLQARAMLDIVKR T0528 154 :QGVTIATLAQDYAFGRDGVAAFKEALAKTGATLATEEYVPTTT 3ks9A 223 :NWTYVSAVHTEGNYGESGMDAFKELAAQEGLSIAHSDKIYSNA T0528 197 :TDFTAVGQRL 3ks9A 268 :KSFDRLLRKL T0528 210 :LKD 3ks9A 278 :RER T0528 213 :KPGKKII 3ks9A 283 :KARVVVC T0528 222 :IWAGGGDPLTKLQDMDP 3ks9A 292 :EGMTVRGLLSAMRRLGV T0528 239 :KRYGIELSTG 3ks9A 310 :GEFSLIGSDG T0528 249 :GNILPALAAYKRLPGMEGATYYYYDIPK 3ks9A 322 :DRDEVIEGYEVEANGGITIKLQSPEVRS T0528 277 :NPINEWLVTEH 3ks9A 365 :NPWFPEFWQHR T0528 291 :FN 3ks9A 376 :FQ T0528 293 :APPDFFTAGGFSAAMAVVTAVQKA 3ks9A 404 :YVQDSKMGFVINAIYAMAHGLQNM T0528 317 :KSTDTEKLIAAMEGMEFDTPKGKMVFRKEDHQALQSMYHFKVKVD 3ks9A 443 :KPIDGSKLLDFLIKSSFIGVSGEEVWFDEKGDAPGRYDIMNLQYT T0528 366 :WAVLEP 3ks9A 492 :YDYVHV Number of specific fragments extracted= 15 number of extra gaps= 1 total=689 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 1jdpA/T0528-1jdpA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1jdpA expands to /projects/compbio/data/pdb/1jdp.pdb.gz 1jdpA:# T0528 read from 1jdpA/T0528-1jdpA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1jdpA read from 1jdpA/T0528-1jdpA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1jdpA to template set # found chain 1jdpA in template set Warning: unaligning (T0528)G52 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (1jdpA)R46 Warning: unaligning (T0528)D164 because of BadResidue code BAD_PEPTIDE in next template residue (1jdpA)D162 Warning: unaligning (T0528)Y165 because of BadResidue code BAD_PEPTIDE at template residue (1jdpA)D162 Warning: unaligning (T0528)E379 because last residue in template chain is (1jdpA)P401 T0528 18 :DLKIALIYGKTGPLEAYAKQTETGLMMGLE 1jdpA 7 :KIEVLVLLPQDDSYLFSLTRVRPAIEYALR T0528 49 :ATK 1jdpA 37 :SVE T0528 57 :DGRKIVVITKDDQS 1jdpA 50 :PGTRFQVAYEDSDC T0528 72 :PDLSKAALAEAYQD 1jdpA 64 :GNRALFSLVDRVAA T0528 86 :DGADIAIGTSSSAAALADLPVAEENKKILIVEPAVADQITG 1jdpA 81 :AKPDLILGPVCEYAAAPVARLASHWDLPMLSAGALAAGFQH T0528 127 :EKWNRYIFRTGRNSSQDAISNAVAIGKQG 1jdpA 123 :DSEYSHLTRVAPAYAKMGEMMLALFRHHH T0528 156 :VTIATLAQ 1jdpA 153 :SRAALVYS T0528 166 :AFGRD 1jdpA 163 :KLERN T0528 171 :GVAAFKEALAKTGATLATEEYVPTTTTDFTAVGQRLFDA 1jdpA 171 :TLEGVHEVFQEEGLHTSIYSFDETKDLDLEDIVRNIQAS T0528 215 :G 1jdpA 210 :E T0528 217 :KIIWVIWAGGG 1jdpA 211 :RVVIMCASSDT T0528 228 :DPLTKLQDMDPK 1jdpA 224 :SIMLVAHRHGMT T0528 240 :RYGIELSTGG 1jdpA 238 :DYAFFNIELF T0528 251 :ILPALAAYKR 1jdpA 260 :GDKHDFEAKQ T0528 261 :LPGMEGATYYYY 1jdpA 271 :YSSLQTVTLLRT T0528 276 :KNPINEWLVTEHQKRFN 1jdpA 283 :VKPEFEKFSMEVKSSVE T0528 293 :APPDFFTAGGFSAAMAVVTAVQKA 1jdpA 307 :DYVNMFVEGFHDAILLYVLALHEV T0528 317 :KSTDTEKLIAAMEGMEFDTPKGKMVFRKEDHQ 1jdpA 336 :SKKDGGKIIQQTWNRTFEGIAGQVSIDANGDR T0528 350 :LQSMYHFKVKV 1jdpA 368 :YGDFSVIAMTD T0528 362 :P 1jdpA 380 :E T0528 363 :AVAWAVLEPV 1jdpA 384 :QEVIGDYFGK T0528 373 :RELKIE 1jdpA 395 :GRFEMR Number of specific fragments extracted= 22 number of extra gaps= 1 total=711 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 1jdpA/T0528-1jdpA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0528 read from 1jdpA/T0528-1jdpA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1jdpA read from 1jdpA/T0528-1jdpA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1jdpA in template set Warning: unaligning (T0528)K51 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (1jdpA)R46 Warning: unaligning (T0528)D164 because of BadResidue code BAD_PEPTIDE in next template residue (1jdpA)D162 Warning: unaligning (T0528)Y165 because of BadResidue code BAD_PEPTIDE at template residue (1jdpA)D162 Warning: unaligning (T0528)K376 because last residue in template chain is (1jdpA)P401 T0528 17 :DDLKIALIYGKTGPLEAYAKQTETGLMMGLEYAT 1jdpA 6 :QKIEVLVLLPQDDSYLFSLTRVRPAIEYALRSVE T0528 57 :DGRKIVVITKDDQSKP 1jdpA 50 :PGTRFQVAYEDSDCGN T0528 74 :LSKAALAEAYQ 1jdpA 66 :RALFSLVDRVA T0528 85 :DDGADIAIGTSSSAAALADLPVAEENKKILIVEPAVADQIT 1jdpA 80 :GAKPDLILGPVCEYAAAPVARLASHWDLPMLSAGALAAGFQ T0528 126 :GEKW 1jdpA 123 :DSEY T0528 131 :RYIFRTGRNSSQDAISNAVAIGKQGV 1jdpA 127 :SHLTRVAPAYAKMGEMMLALFRHHHW T0528 157 :TIATLAQ 1jdpA 154 :RAALVYS T0528 166 :AFGRDGV 1jdpA 163 :KLERNCY T0528 173 :AAFKEALAKTGATLATEEYVPTTTTDFTAVGQRLFDA 1jdpA 173 :EGVHEVFQEEGLHTSIYSFDETKDLDLEDIVRNIQAS T0528 214 :P 1jdpA 210 :E T0528 216 :KKIIWVIWAGGGDPLTK 1jdpA 211 :RVVIMCASSDTIRSIML T0528 233 :LQDMDP 1jdpA 229 :AHRHGM T0528 239 :KRYGIELST 1jdpA 238 :DYAFFNIEL T0528 248 :G 1jdpA 249 :S T0528 249 :GNILPALAAYKRLPGMEGATYYYY 1jdpA 259 :RGDKHDFEAKQAYSSLQTVTLLRT T0528 274 :I 1jdpA 283 :V T0528 277 :NPINEWLVTEHQKRFN 1jdpA 284 :KPEFEKFSMEVKSSVE T0528 293 :APPDFFTAGGFSAAMAVVTAVQKA 1jdpA 307 :DYVNMFVEGFHDAILLYVLALHEV T0528 317 :KSTDTEKLIAAMEGMEFDTPKGKMVFRK 1jdpA 336 :SKKDGGKIIQQTWNRTFEGIAGQVSIDA T0528 346 :DHQALQSMYHFKVK 1jdpA 364 :NGDRYGDFSVIAMT T0528 360 :VDPAVAWAVL 1jdpA 381 :AGTQEVIGDY T0528 370 :EPVREL 1jdpA 395 :GRFEMR Number of specific fragments extracted= 22 number of extra gaps= 1 total=733 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 1jdpA/T0528-1jdpA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0528 read from 1jdpA/T0528-1jdpA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1jdpA read from 1jdpA/T0528-1jdpA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1jdpA in template set Warning: unaligning (T0528)K51 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (1jdpA)R46 Warning: unaligning (T0528)D164 because of BadResidue code BAD_PEPTIDE in next template residue (1jdpA)D162 Warning: unaligning (T0528)Y165 because of BadResidue code BAD_PEPTIDE at template residue (1jdpA)D162 Warning: unaligning (T0528)E378 because last residue in template chain is (1jdpA)P401 T0528 18 :DLKIALIYGKTGPLEAYAKQTETGLMMGLEYAT 1jdpA 7 :KIEVLVLLPQDDSYLFSLTRVRPAIEYALRSVE T0528 56 :LDGRKIVVITKDDQSK 1jdpA 49 :PPGTRFQVAYEDSDCG T0528 73 :DLSKAALAEAYQ 1jdpA 65 :NRALFSLVDRVA T0528 87 :GADIAIGTSSSAAALADLPVAEENKKILIVEPAVADQIT 1jdpA 82 :KPDLILGPVCEYAAAPVARLASHWDLPMLSAGALAAGFQ T0528 126 :GEK 1jdpA 123 :DSE T0528 130 :NRYIFRTGRNSSQDAISNAVAIGK 1jdpA 126 :YSHLTRVAPAYAKMGEMMLALFRH T0528 154 :QGVTIATLAQ 1jdpA 151 :HWSRAALVYS T0528 166 :AFGRDGV 1jdpA 163 :KLERNCY T0528 173 :AAFKEALAKTGATLATEEYVPTTTTDFTAVGQRLFDA 1jdpA 173 :EGVHEVFQEEGLHTSIYSFDETKDLDLEDIVRNIQAS T0528 213 :K 1jdpA 210 :E T0528 215 :GKKIIWVIWAGGGDPLTKLQDMDP 1jdpA 211 :RVVIMCASSDTIRSIMLVAHRHGM T0528 239 :KRYGIELSTG 1jdpA 238 :DYAFFNIELF T0528 249 :GNILPALAAYKRLPGMEGATYYYYD 1jdpA 259 :RGDKHDFEAKQAYSSLQTVTLLRTV T0528 277 :NPINEWLVTEHQKRFN 1jdpA 284 :KPEFEKFSMEVKSSVE T0528 293 :APPDFFTAGGFSAAMAVVTAVQKA 1jdpA 307 :DYVNMFVEGFHDAILLYVLALHEV T0528 317 :KS 1jdpA 334 :GY T0528 319 :TDTEKLIAAMEGMEFDTPKGKMVFR 1jdpA 338 :KDGGKIIQQTWNRTFEGIAGQVSID T0528 345 :EDHQALQSMYHFKVKVDPAVAWAVLEPV 1jdpA 363 :ANGDRYGDFSVIAMTDVEAGTQEVIGDY T0528 373 :RELKI 1jdpA 396 :RFEMR Number of specific fragments extracted= 19 number of extra gaps= 1 total=752 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 3h5vA/T0528-3h5vA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 3h5vA expands to /projects/compbio/data/pdb/3h5v.pdb.gz 3h5vA:# T0528 read from 3h5vA/T0528-3h5vA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3h5vA read from 3h5vA/T0528-3h5vA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3h5vA to template set # found chain 3h5vA in template set Warning: unaligning (T0528)A16 because first residue in template chain is (3h5vA)S3 Warning: unaligning (T0528)A162 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (3h5vA)D132 Warning: unaligning (T0528)D164 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3h5vA)D132 Warning: unaligning (T0528)E379 because last residue in template chain is (3h5vA)L378 T0528 17 :DDLKIALIYGKTG 3h5vA 4 :NSIQIGGLFPRGA T0528 36 :KQTETGLMMGLE 3h5vA 17 :DQEYSAFRVGMV T0528 49 :ATKGT 3h5vA 29 :QFSTS T0528 58 :GRKIVVITKD 3h5vA 34 :EFRLTPHIDN T0528 68 :DQSKPDLSKAALAEAYQD 3h5vA 45 :EVANSFAVTNAFCSQFSR T0528 87 :GADIAIGTSSSAAALADLPVAEENKKILIVEPAVADQI 3h5vA 63 :GVYAIFGFYDKKSVNTITSFCGTLHVSFITPSFPTDGT T0528 130 :NRYIFRTGRN 3h5vA 101 :HPFVIQMRPD T0528 143 :DAISNAVAIGKQG 3h5vA 111 :LKGALLSLIEYYQ T0528 156 :VTIATL 3h5vA 125 :DKFAYL T0528 165 :YAFGRDGVAAFKEALAKTGATLATEEYVP 3h5vA 133 :SDRGLSTLQAVLDSAAEKKWQVTAINVGN T0528 194 :TTTTDFTAVGQRLFDA 3h5vA 166 :KKDETYRSLFQDLELK T0528 215 :GKKIIWVIWAGGG 3h5vA 182 :KERRVILDCERDK T0528 228 :DPLTKLQDMDPK 3h5vA 197 :DIVDQVITIGKH T0528 240 :RYGIELSTGGNILPALAAYKR 3h5vA 211 :GYHYIIANLGFTDGDLLKIQF T0528 261 :LPGMEGATYYYY 3h5vA 233 :GANVSGFQIVDY T0528 276 :KNPINEWLVTEHQKRFN 3h5vA 245 :DDSLVSKFIERWSTLEE T0528 293 :APPDFFTAGGFSAAMAVVTAVQKA 3h5vA 270 :ATIKYTSALTYDAVQVMTEAFRNL T0528 320 :D 3h5vA 315 :V T0528 321 :TEKLIAAMEGMEFDTPKGKMVFRKEDHQALQSMYHFKVKVDPAVAWAVLEPVRELKIE 3h5vA 320 :GVEIERALKQVQVEGLSGNIKFDQNGKRINYTINIMELKTNGPRKIGYWSEVDKMVVT Number of specific fragments extracted= 19 number of extra gaps= 1 total=771 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 3h5vA/T0528-3h5vA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0528 read from 3h5vA/T0528-3h5vA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3h5vA read from 3h5vA/T0528-3h5vA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3h5vA in template set Warning: unaligning (T0528)A16 because first residue in template chain is (3h5vA)S3 Warning: unaligning (T0528)A162 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (3h5vA)D132 Warning: unaligning (T0528)Q163 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3h5vA)D132 Warning: unaligning (T0528)K376 because last residue in template chain is (3h5vA)L378 T0528 17 :DDLKIALIYGKTG 3h5vA 4 :NSIQIGGLFPRGA T0528 36 :KQTETGLMMGLEYATKG 3h5vA 17 :DQEYSAFRVGMVQFSTS T0528 58 :GRKIVVITKD 3h5vA 34 :EFRLTPHIDN T0528 68 :DQSKPDLSKAALAEAY 3h5vA 45 :EVANSFAVTNAFCSQF T0528 85 :DDGADIAIGTSSSAAALADLPVAEENKKILIVEPAVADQI 3h5vA 61 :SRGVYAIFGFYDKKSVNTITSFCGTLHVSFITPSFPTDGT T0528 130 :NRYIFRTGRNSSQDAISNAVA 3h5vA 101 :HPFVIQMRPDLKGALLSLIEY T0528 154 :QGV 3h5vA 122 :YQW T0528 157 :TIATL 3h5vA 126 :KFAYL T0528 164 :D 3h5vA 133 :S T0528 166 :AFGRDGVAAFKEALAKTGATLATEEYVPT 3h5vA 134 :DRGLSTLQAVLDSAAEKKWQVTAINVGNI T0528 195 :TTTD 3h5vA 165 :DKKD T0528 199 :FTAVGQRLFDA 3h5vA 171 :YRSLFQDLELK T0528 213 :KP 3h5vA 182 :KE T0528 216 :KKIIWVIWAGGGDPLTK 3h5vA 184 :RRVILDCERDKVNDIVD T0528 233 :LQDMDP 3h5vA 202 :VITIGK T0528 240 :RYGIELSTGGNILPALA 3h5vA 214 :YIIANLGFTDGDLLKIQ T0528 259 :KRLPGMEGATYYYY 3h5vA 231 :FGGANVSGFQIVDY T0528 276 :KNPINEWLVTEH 3h5vA 245 :DDSLVSKFIERW T0528 293 :APPDFFTAGGFSAAMAVVTAVQKA 3h5vA 270 :ATIKYTSALTYDAVQVMTEAFRNL T0528 317 :KSTD 3h5vA 312 :NPAV T0528 321 :TEKLIAAMEGMEFDTPKGKMVFRKEDHQALQSMYHFKVKVDPAVAWAVLEP 3h5vA 320 :GVEIERALKQVQVEGLSGNIKFDQNGKRINYTINIMELKTNGPRKIGYWSE T0528 372 :VREL 3h5vA 374 :MVVT Number of specific fragments extracted= 22 number of extra gaps= 1 total=793 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 3h5vA/T0528-3h5vA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0528 read from 3h5vA/T0528-3h5vA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3h5vA read from 3h5vA/T0528-3h5vA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3h5vA in template set Warning: unaligning (T0528)A16 because first residue in template chain is (3h5vA)S3 Warning: unaligning (T0528)A162 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (3h5vA)D132 Warning: unaligning (T0528)Q163 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3h5vA)D132 Warning: unaligning (T0528)E378 because last residue in template chain is (3h5vA)L378 T0528 17 :DDLKIALIYG 3h5vA 4 :NSIQIGGLFP T0528 33 :AYAKQTETGLMMGLEYATKGTMTL 3h5vA 14 :RGADQEYSAFRVGMVQFSTSEFRL T0528 60 :KIVVITKD 3h5vA 38 :TPHIDNLE T0528 70 :SKPDLSKAALAEAYQD 3h5vA 47 :ANSFAVTNAFCSQFSR T0528 87 :GADIAIGTSSSAAALADLPVAEENKKILIVEPAVA 3h5vA 63 :GVYAIFGFYDKKSVNTITSFCGTLHVSFITPSFPT T0528 127 :EKWNRYIFRTGRNSSQDAISNAVA 3h5vA 98 :DGTHPFVIQMRPDLKGALLSLIEY T0528 154 :QGVTIATL 3h5vA 123 :QWDKFAYL T0528 164 :D 3h5vA 133 :S T0528 166 :AFGRDGVAAFKEALAKTGATLATEEYVP 3h5vA 134 :DRGLSTLQAVLDSAAEKKWQVTAINVGN T0528 194 :TTT 3h5vA 164 :NDK T0528 197 :TDFTAVGQRL 3h5vA 169 :ETYRSLFQDL T0528 210 :LKDKPGKKIIWVIWAGGGDPLTKLQDMDP 3h5vA 179 :ELKKERRVILDCERDKVNDIVDQVITIGK T0528 239 :KRYGIELSTGGNILP 3h5vA 210 :KGYHYIIANLGFTDG T0528 257 :AYKRLPGMEGATYYYYDIPKNPINEWLVTEHQK 3h5vA 226 :LLKIQFGGANVSGFQIVDYDDSLVSKFIERWST T0528 293 :APPDFFTAGGFSAAMAVVTAVQKA 3h5vA 270 :ATIKYTSALTYDAVQVMTEAFRNL T0528 317 :KS 3h5vA 312 :NP T0528 319 :TDTEKLIAAMEGMEFDTPKGKMVFRKEDHQALQSMYHFKVKVDPAVAWAVL 3h5vA 318 :GQGVEIERALKQVQVEGLSGNIKFDQNGKRINYTINIMELKTNGPRKIGYW T0528 370 :EPVRELKI 3h5vA 370 :EVDKMVVT Number of specific fragments extracted= 18 number of extra gaps= 1 total=811 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 2e4uA/T0528-2e4uA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2e4uA expands to /projects/compbio/data/pdb/2e4u.pdb.gz 2e4uA:# T0528 read from 2e4uA/T0528-2e4uA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2e4uA read from 2e4uA/T0528-2e4uA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2e4uA to template set # found chain 2e4uA in template set T0528 16 :ADDLKIALIYGK 2e4uA 36 :EGDLVLGGLFPI T0528 28 :TGPLEAYAKQTETGLMMGLE 2e4uA 58 :GRINEDRGIQRLEAMLFAID T0528 49 :ATKGTMTLD 2e4uA 78 :EINKDNYLL T0528 58 :GRKIVVITKDDQSKPDLSKAALAEAYQD 2e4uA 88 :GVKLGVHILDTCSRDTYALEQSLEFVRA T0528 86 :DGADIAIGTSSSAAALADLPVAEENKKILIVEPAVADQITGEKWNRYIFRTGRNSSQDAISNAVAIGKQG 2e4uA 140 :LLIAGVIGGSYSSVSIQVANLLRLFQIPQISYASTSAKLSDKSRYDYFARTVPPDFYQAKAMAEILRFFN T0528 156 :VTIATLAQDYAFGRDGVAAFKEALAKTGATLATEEYVP 2e4uA 211 :TYVSTVASEGDYGETGIEAFEQEARLRNICIATAEKVG T0528 194 :TTTTDFTAVGQRLFD 2e4uA 251 :NIRKSYDSVIRELLQ T0528 213 :KPGKKIIWVIWAGGG 2e4uA 266 :KPNARVVVLFMRSDD T0528 228 :DPLTKLQDMDP 2e4uA 283 :ELIAAANRVNA T0528 240 :RYGIELSTGGNI 2e4uA 294 :SFTWVASDGWGA T0528 252 :LPALAAYKR 2e4uA 307 :ESIVKGSEH T0528 261 :LPGMEGATYYYYDIPK 2e4uA 317 :AYGAITLELASHPVRQ T0528 277 :NPINEWLVTEH 2e4uA 348 :NPWFRDFWEQK T0528 291 :FN 2e4uA 359 :FQ T0528 293 :APPDFFTAGGFSAAMAVVTAVQKA 2e4uA 384 :YEQESKIMFVVNAVYAMAHALHKM T0528 317 :KSTDTEKLIAAMEG 2e4uA 423 :KILDGKKLYKEYLL T0528 331 :MEFDTPKGKMVFRKEDHQ 2e4uA 445 :NPNKGADSIVKFDTFGDG T0528 350 :LQSMYHFKVK 2e4uA 463 :MGRYNVFNLQ T0528 360 :VDP 2e4uA 475 :GGK T0528 363 :AVAWAVLEPVRELKIEEMNIPIKNKK 2e4uA 480 :YLKVGHWAETLSLDVDSIHWSRNSVP Number of specific fragments extracted= 20 number of extra gaps= 0 total=831 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 2e4uA/T0528-2e4uA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0528 read from 2e4uA/T0528-2e4uA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2e4uA read from 2e4uA/T0528-2e4uA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2e4uA in template set T0528 16 :ADDLKIALIYGK 2e4uA 36 :EGDLVLGGLFPI T0528 28 :TGP 2e4uA 57 :CGR T0528 31 :LEAYAKQTETGLMMGLEYATKGTMTLDGRKIVVITKDDQSKPDLSKAALAEAYQ 2e4uA 61 :NEDRGIQRLEAMLFAIDEINKDNYLLPGVKLGVHILDTCSRDTYALEQSLEFVR T0528 85 :DDGADIAIGTSSSAAALADLPVAEENKKILIVEPAVADQIT 2e4uA 139 :PLLIAGVIGGSYSSVSIQVANLLRLFQIPQISYASTSAKLS T0528 126 :GEKW 2e4uA 181 :KSRY T0528 131 :RYIFRTGRNSSQDAISNAVAIGKQGV 2e4uA 185 :DYFARTVPPDFYQAKAMAEILRFFNW T0528 157 :TIATLAQDYAFGRDGVAAFKEALAKTGATLATEEYVPT 2e4uA 212 :YVSTVASEGDYGETGIEAFEQEARLRNICIATAEKVGR T0528 195 :TTTDFTAVGQRLFDA 2e4uA 252 :IRKSYDSVIRELLQK T0528 212 :DKP 2e4uA 267 :PNA T0528 216 :KKIIWVIWAGGGDPLTK 2e4uA 270 :RVVVLFMRSDDSRELIA T0528 233 :LQDMDPKRYGIE 2e4uA 288 :ANRVNASFTWVA T0528 245 :LSTGGNILPALA 2e4uA 303 :WGAQESIVKGSE T0528 259 :KRLPGMEGATYYYYDI 2e4uA 315 :HVAYGAITLELASHPV T0528 278 :PINEWLV 2e4uA 331 :RQFDRYF T0528 285 :TEHQKRFN 2e4uA 352 :RDFWEQKF T0528 293 :APPDFFTAGGFSAAMAVVTAVQKA 2e4uA 384 :YEQESKIMFVVNAVYAMAHALHKM T0528 317 :KSTDTEKLIAAMEG 2e4uA 423 :KILDGKKLYKEYLL T0528 331 :MEFDTPKGKMVFRK 2e4uA 445 :NPNKGADSIVKFDT T0528 346 :DHQALQSMYHFKVK 2e4uA 459 :FGDGMGRYNVFNLQ T0528 360 :VDPA 2e4uA 474 :TGGK T0528 364 :VAWAVLEPVRELKIEEMNIPIKNK 2e4uA 481 :LKVGHWAETLSLDVDSIHWSRNSV Number of specific fragments extracted= 21 number of extra gaps= 0 total=852 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 2e4uA/T0528-2e4uA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0528 read from 2e4uA/T0528-2e4uA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2e4uA read from 2e4uA/T0528-2e4uA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2e4uA in template set Warning: unaligning (T0528)G87 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (2e4uA)I138 T0528 17 :DDLKIALIYGK 2e4uA 37 :GDLVLGGLFPI T0528 28 :TGPLEAYAKQTETGLMMGLEYATKGTMTLDGRKIVVITKDDQSKPDLSKAALAEAYQDD 2e4uA 58 :GRINEDRGIQRLEAMLFAIDEINKDNYLLPGVKLGVHILDTCSRDTYALEQSLEFVRAS T0528 88 :ADIAIGTSSSAAALADLPVAEENKKILIVEPAVADQITGEKWNRYIFRTGRNSSQDAISNAVAIGK 2e4uA 142 :IAGVIGGSYSSVSIQVANLLRLFQIPQISYASTSAKLSDKSRYDYFARTVPPDFYQAKAMAEILRF T0528 154 :QGVTIATLAQDYAFGRDGVAAFKEALAKTGATLATEEYVPTTT 2e4uA 209 :NWTYVSTVASEGDYGETGIEAFEQEARLRNICIATAEKVGRSN T0528 197 :TDFTAVGQRL 2e4uA 254 :KSYDSVIREL T0528 210 :LKDKPGKKIIWVIWAGGGD 2e4uA 264 :LQKPNARVVVLFMRSDDSR T0528 229 :PLTKLQDMDPKRYGIELSTGGNI 2e4uA 284 :LIAAANRVNASFTWVASDGWGAQ T0528 255 :LAAYKR 2e4uA 307 :ESIVKG T0528 261 :LPGMEGATYYYYD 2e4uA 317 :AYGAITLELASHP T0528 277 :NPINEWL 2e4uA 330 :VRQFDRY T0528 284 :VTEHQKRFN 2e4uA 351 :FRDFWEQKF T0528 293 :APPDFFTAGGFSAAMAVVTAVQKA 2e4uA 384 :YEQESKIMFVVNAVYAMAHALHKM T0528 317 :KSTDTEKLIAAMEGM 2e4uA 423 :KILDGKKLYKEYLLK T0528 332 :EFDTPKGKMVFR 2e4uA 446 :PNKGADSIVKFD T0528 345 :EDHQALQSMYHFKVKVDPA 2e4uA 458 :TFGDGMGRYNVFNLQQTGG T0528 364 :VAWAVLEPVRELKIEEMNI 2e4uA 481 :LKVGHWAETLSLDVDSIHW Number of specific fragments extracted= 16 number of extra gaps= 0 total=868 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 3h6gA/T0528-3h6gA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 3h6gA expands to /projects/compbio/data/pdb/3h6g.pdb.gz 3h6gA:# T0528 read from 3h6gA/T0528-3h6gA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3h6gA read from 3h6gA/T0528-3h6gA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3h6gA to template set # found chain 3h6gA in template set Warning: unaligning (T0528)A16 because first residue in template chain is (3h6gA)T2 Warning: unaligning (T0528)R290 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (3h6gA)K275 Warning: unaligning (T0528)E379 because last residue in template chain is (3h6gA)E384 T0528 17 :DDLKIALIYGK 3h6gA 3 :HVLRFGGIFEY T0528 28 :TGPL 3h6gA 16 :SGPM T0528 36 :KQTETGLMMGLE 3h6gA 20 :GAEELAFRFAVN T0528 49 :ATKGTMTLD 3h6gA 32 :TINRNRTLL T0528 58 :GRKIVVITKD 3h6gA 42 :NTTLTYDTQK T0528 68 :DQSKPDLSKAALAEAYQD 3h6gA 53 :NLYDSFEASKKACDQLSL T0528 87 :GADIAIGTSSSAAALADLPVAEENKKILIVEPAVADQITGE 3h6gA 71 :GVAAIFGPSHSSSANAVQSICNALGVPHIQTRWKHQVSDNK T0528 130 :NRYIFRTGRNSSQDAISNAVAIGKQG 3h6gA 112 :DSFYVSLYPDFSSLSRAILDLVQFFK T0528 156 :VTIATLA 3h6gA 139 :KTVTVVY T0528 164 :DYAFGRDGVAAFKEALAKTGATLAT 3h6gA 146 :DDSTGLIRLQELIKAPSRYNLRLKI T0528 190 :EYVPTTTTDFTAVGQRLFDA 3h6gA 171 :RQLPADTKDAKPLLKEMKRG T0528 215 :GKKIIWVIWAGGG 3h6gA 191 :KEFHVIFDCSHEM T0528 228 :DPLTKLQDMDPK 3h6gA 206 :GILKQALAMGMM T0528 240 :RYGIELSTGGNILPALAAYKR 3h6gA 220 :YYHYIFTTLDLFALDVEPYRY T0528 261 :LPGMEGATYYYY 3h6gA 242 :GVNMTGFRILNT T0528 276 :KNPINEWLVTEHQK 3h6gA 254 :ENTQVSSIIEKWSM T0528 293 :APPDFFTAGGFSAAMAVVTAVQKA 3h6gA 283 :GFMTTDAALMYDAVHVVSVAVQQF T0528 321 :TEKLIAAMEGMEFDTPKGKMVFRKEDH 3h6gA 325 :GTRFMSLIKEAHWEGLTGRITFNKTNG T0528 348 :QALQSMYHFKVKVDPAVAWAVLEPVRELKIE 3h6gA 353 :RTDFDLDVISLKEEGLEKIGTWDPASGLNMT Number of specific fragments extracted= 19 number of extra gaps= 0 total=887 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 3h6gA/T0528-3h6gA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0528 read from 3h6gA/T0528-3h6gA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3h6gA read from 3h6gA/T0528-3h6gA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3h6gA in template set Warning: unaligning (T0528)A16 because first residue in template chain is (3h6gA)T2 Warning: unaligning (T0528)E379 because last residue in template chain is (3h6gA)E384 T0528 17 :DDLKIALIYGKTGP 3h6gA 3 :HVLRFGGIFEYVES T0528 34 :YAKQTETGLMMGLEYATKGTMTLDGRKIVVITKD 3h6gA 18 :PMGAEELAFRFAVNTINRNRTLLPNTTLTYDTQK T0528 68 :DQSKPDLSKAALAEAY 3h6gA 53 :NLYDSFEASKKACDQL T0528 85 :DDGADIAIGTSSSAAALADLPVAEENKKILIVEP 3h6gA 69 :SLGVAAIFGPSHSSSANAVQSICNALGVPHIQTR T0528 120 :VADQITGEKW 3h6gA 103 :WKHQVSDNKD T0528 131 :RYIFRTGRNSSQDAISNAVAIGKQGV 3h6gA 113 :SFYVSLYPDFSSLSRAILDLVQFFKW T0528 157 :TIATLAQD 3h6gA 140 :TVTVVYDD T0528 166 :AFGRDGVAAFKE 3h6gA 148 :STGLIRLQELIK T0528 181 :KTGATLATEEY 3h6gA 163 :RYNLRLKIRQL T0528 193 :PTTTTDFTAVGQRLFDA 3h6gA 174 :PADTKDAKPLLKEMKRG T0528 213 :KP 3h6gA 191 :KE T0528 216 :KKIIWVIWAGGGDPLTK 3h6gA 193 :FHVIFDCSHEMAAGILK T0528 233 :LQDMDP 3h6gA 211 :ALAMGM T0528 239 :KRYGIELSTGGNI 3h6gA 219 :EYYHYIFTTLDLF T0528 252 :LPALA 3h6gA 235 :VEPYR T0528 259 :KRLPGMEGATYYYYD 3h6gA 240 :YSGVNMTGFRILNTE T0528 277 :NPINEWLVTEHQK 3h6gA 255 :NTQVSSIIEKWSM T0528 293 :APPDFFTAGGFSAAMAVVTAVQKAKSTD 3h6gA 283 :GFMTTDAALMYDAVHVVSVAVQQFPQMT T0528 321 :TEKLIAAMEGMEFDTPKGKMVFRKEDH 3h6gA 325 :GTRFMSLIKEAHWEGLTGRITFNKTNG T0528 349 :ALQSMYHFKVKVDPAVAWAVLEPVRELKIE 3h6gA 354 :TDFDLDVISLKEEGLEKIGTWDPASGLNMT Number of specific fragments extracted= 20 number of extra gaps= 0 total=907 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 3h6gA/T0528-3h6gA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0528 read from 3h6gA/T0528-3h6gA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3h6gA read from 3h6gA/T0528-3h6gA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3h6gA in template set Warning: unaligning (T0528)R290 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (3h6gA)K275 T0528 20 :KIALIYGKTGPLEAYAKQTETGLMMGLEYATKGTMTLDGRKIVVITKD 3h6gA 4 :VLRFGGIFEYVESGPMGAEELAFRFAVNTINRNRTLLPNTTLTYDTQK T0528 68 :DQSKPDLSKAALAEAYQD 3h6gA 53 :NLYDSFEASKKACDQLSL T0528 87 :GADIAIGTSSSAAALADLPVAEENKKILIVEPAV 3h6gA 71 :GVAAIFGPSHSSSANAVQSICNALGVPHIQTRWK T0528 123 :QITGEKWNRYIFRTGRNSSQDAISNAVAIGK 3h6gA 105 :HQVSDNKDSFYVSLYPDFSSLSRAILDLVQF T0528 154 :QGVTIATLAQ 3h6gA 137 :KWKTVTVVYD T0528 165 :YAFGRDGVAAFKEA 3h6gA 147 :DSTGLIRLQELIKA T0528 183 :GATLATEEYVPTT 3h6gA 165 :NLRLKIRQLPADT T0528 197 :TDFTAVGQRL 3h6gA 178 :KDAKPLLKEM T0528 210 :LKDKPGKKIIWVIWAGGGDPLTKLQDMDP 3h6gA 188 :KRGKEFHVIFDCSHEMAAGILKQALAMGM T0528 239 :KRYGIELSTGGNILP 3h6gA 219 :EYYHYIFTTLDLFAL T0528 256 :AAYKRLPGMEGATYYYYDIPKNPINEWLVTEHQK 3h6gA 234 :DVEPYRYSGVNMTGFRILNTENTQVSSIIEKWSM T0528 293 :APPDFFTAGGFSAAMAVVTAVQKA 3h6gA 283 :GFMTTDAALMYDAVHVVSVAVQQF T0528 317 :KS 3h6gA 317 :NR T0528 319 :TDTEKLIAAMEGMEFDTPKGKMVFRKEDHQ 3h6gA 323 :RFGTRFMSLIKEAHWEGLTGRITFNKTNGL T0528 349 :ALQSMYHFKVKVDPAVAWAVLEP 3h6gA 354 :TDFDLDVISLKEEGLEKIGTWDP Number of specific fragments extracted= 15 number of extra gaps= 0 total=922 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 2wjwA/T0528-2wjwA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2wjwA expands to /projects/compbio/data/pdb/2wjw.pdb.gz 2wjwA:Skipped atom 1033, because occupancy 0.500 <= existing 0.500 in 2wjwA Skipped atom 1034, because occupancy 0.500 <= existing 0.500 in 2wjwA Skipped atom 1035, because occupancy 0.500 <= existing 0.500 in 2wjwA Skipped atom 1036, because occupancy 0.500 <= existing 0.500 in 2wjwA Skipped atom 1037, because occupancy 0.500 <= existing 0.500 in 2wjwA Skipped atom 1038, because occupancy 0.500 <= existing 0.500 in 2wjwA Skipped atom 1039, because occupancy 0.500 <= existing 0.500 in 2wjwA Skipped atom 1040, because occupancy 0.500 <= existing 0.500 in 2wjwA Skipped atom 1047, because occupancy 0.500 <= existing 0.500 in 2wjwA Skipped atom 1048, because occupancy 0.500 <= existing 0.500 in 2wjwA Skipped atom 1049, because occupancy 0.500 <= existing 0.500 in 2wjwA Skipped atom 1050, because occupancy 0.500 <= existing 0.500 in 2wjwA Skipped atom 1051, because occupancy 0.500 <= existing 0.500 in 2wjwA Skipped atom 1052, because occupancy 0.500 <= existing 0.500 in 2wjwA Skipped atom 1061, because occupancy 0.500 <= existing 0.500 in 2wjwA Skipped atom 1062, because occupancy 0.500 <= existing 0.500 in 2wjwA Skipped atom 1063, because occupancy 0.500 <= existing 0.500 in 2wjwA Skipped atom 1064, because occupancy 0.500 <= existing 0.500 in 2wjwA Skipped atom 1065, because occupancy 0.500 <= existing 0.500 in 2wjwA Skipped atom 1066, because occupancy 0.500 <= existing 0.500 in 2wjwA Skipped atom 1067, because occupancy 0.500 <= existing 0.500 in 2wjwA Skipped atom 1068, because occupancy 0.500 <= existing 0.500 in 2wjwA Skipped atom 1080, because occupancy 0.500 <= existing 0.500 in 2wjwA Skipped atom 1081, because occupancy 0.500 <= existing 0.500 in 2wjwA Skipped atom 1082, because occupancy 0.500 <= existing 0.500 in 2wjwA Skipped atom 1083, because occupancy 0.500 <= existing 0.500 in 2wjwA Skipped atom 1084, because occupancy 0.500 <= existing 0.500 in 2wjwA Skipped atom 1085, because occupancy 0.500 <= existing 0.500 in 2wjwA Skipped atom 1086, because occupancy 0.500 <= existing 0.500 in 2wjwA Skipped atom 1087, because occupancy 0.500 <= existing 0.500 in 2wjwA Skipped atom 1088, because occupancy 0.500 <= existing 0.500 in 2wjwA Skipped atom 1089, because occupancy 0.500 <= existing 0.500 in 2wjwA Skipped atom 1090, because occupancy 0.500 <= existing 0.500 in 2wjwA Skipped atom 1095, because occupancy 0.500 <= existing 0.500 in 2wjwA Skipped atom 1096, because occupancy 0.500 <= existing 0.500 in 2wjwA Skipped atom 1097, because occupancy 0.500 <= existing 0.500 in 2wjwA Skipped atom 1098, because occupancy 0.500 <= existing 0.500 in 2wjwA Skipped atom 1107, because occupancy 0.500 <= existing 0.500 in 2wjwA Skipped atom 1108, because occupancy 0.500 <= existing 0.500 in 2wjwA Skipped atom 1109, because occupancy 0.500 <= existing 0.500 in 2wjwA Skipped atom 1110, because occupancy 0.500 <= existing 0.500 in 2wjwA Skipped atom 1111, because occupancy 0.500 <= existing 0.500 in 2wjwA Skipped atom 1112, because occupancy 0.500 <= existing 0.500 in 2wjwA Skipped atom 1113, because occupancy 0.500 <= existing 0.500 in 2wjwA Skipped atom 1114, because occupancy 0.500 <= existing 0.500 in 2wjwA Skipped atom 1121, because occupancy 0.500 <= existing 0.500 in 2wjwA Skipped atom 1122, because occupancy 0.500 <= existing 0.500 in 2wjwA Skipped atom 1123, because occupancy 0.500 <= existing 0.500 in 2wjwA Skipped atom 1124, because occupancy 0.500 <= existing 0.500 in 2wjwA Skipped atom 1125, because occupancy 0.500 <= existing 0.500 in 2wjwA Skipped atom 1126, because occupancy 0.500 <= existing 0.500 in 2wjwA # T0528 read from 2wjwA/T0528-2wjwA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2wjwA read from 2wjwA/T0528-2wjwA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2wjwA to template set # found chain 2wjwA in template set Warning: unaligning (T0528)D17 because first residue in template chain is (2wjwA)N25 Warning: unaligning (T0528)E378 because last residue in template chain is (2wjwA)T398 T0528 18 :DLKIALIYGKTG 2wjwA 26 :SIQIGGLFPRGA T0528 36 :KQTETGLMMGLE 2wjwA 38 :DQEYSAFRVGMV T0528 49 :ATKGT 2wjwA 50 :QFSTS T0528 58 :GRKIVVITKD 2wjwA 55 :EFRLTPHIDN T0528 68 :DQSKPDLSKAALAEAYQD 2wjwA 66 :EVANSFAVTNAFCSQFSR T0528 87 :GADIAIGTSSSAAALADLPVAEENKKILIVEPAVAD 2wjwA 84 :GVYAIFGFYDKKSVNTITSFCGTLHVSFITPSFPTD T0528 127 :EK 2wjwA 120 :GT T0528 130 :NRYIFRTGRN 2wjwA 122 :HPFVIQMRPD T0528 143 :DAISNAVAIGKQG 2wjwA 132 :LKGALLSLIEYYQ T0528 156 :VTIATLA 2wjwA 146 :DKFAYLY T0528 164 :DYAFGRDGVAAFKEALAKTGATLATEEYVPTTTT 2wjwA 153 :DSDRGLSTLQAVLDSAAEKKWQVTAINVGNINND T0528 198 :DFTAVGQRLFDA 2wjwA 191 :MYRSLFQDLELK T0528 215 :GKKIIWVIWAGGG 2wjwA 203 :KERRVILDCERDK T0528 228 :DPLTKLQDMDPK 2wjwA 218 :DIVDQVITIGKH T0528 240 :RYGIELSTGGNILPALAAYKR 2wjwA 232 :GYHYIIANLGFTDGDLLKIQF T0528 261 :LPGMEGATYYYY 2wjwA 254 :GANVSGFQIVDY T0528 276 :KNPINEWLVTEHQKRFN 2wjwA 266 :DDSLVSKFIERWSTLEE T0528 293 :APPDFFTAGGFSAAMAVVTAVQKA 2wjwA 291 :TTIKYTSALTYDAVQVMTEAFRNL T0528 317 :KS 2wjwA 333 :NP T0528 320 :D 2wjwA 336 :V T0528 321 :TEKLIAAMEGMEFDTPKGKMVFRKEDHQALQSMYHFKVKVDPAVAWAVLEPVRELKI 2wjwA 341 :GVEIERALKQVQVEGLSGNIKFDQNGKRINYTINIMELKTNGPRKIGYWSEVDKMVV Number of specific fragments extracted= 21 number of extra gaps= 0 total=943 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 2wjwA/T0528-2wjwA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0528 read from 2wjwA/T0528-2wjwA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2wjwA read from 2wjwA/T0528-2wjwA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2wjwA in template set Warning: unaligning (T0528)D17 because first residue in template chain is (2wjwA)N25 T0528 18 :DLKIALIYGKTG 2wjwA 26 :SIQIGGLFPRGA T0528 36 :KQTETGLMMGLEYATKGT 2wjwA 38 :DQEYSAFRVGMVQFSTSE T0528 59 :RKIVVITKD 2wjwA 56 :FRLTPHIDN T0528 68 :DQSKPDLSKAALAEAY 2wjwA 66 :EVANSFAVTNAFCSQF T0528 85 :DDGADIAIGTSSSAAALADLPVAEENKKILIVEPAVAD 2wjwA 82 :SRGVYAIFGFYDKKSVNTITSFCGTLHVSFITPSFPTD T0528 127 :EKW 2wjwA 120 :GTH T0528 131 :RYIFRTGRNSSQDAISNAVA 2wjwA 123 :PFVIQMRPDLKGALLSLIEY T0528 154 :QGV 2wjwA 143 :YQW T0528 157 :TIATLAQD 2wjwA 147 :KFAYLYDS T0528 166 :AFGRDGVAAFKEALAKTGATLATEEYVPTTTT 2wjwA 155 :DRGLSTLQAVLDSAAEKKWQVTAINVGNINND T0528 198 :DFTAVGQRLFDA 2wjwA 191 :MYRSLFQDLELK T0528 213 :KP 2wjwA 203 :KE T0528 216 :KKIIWVIWAGGGDPLTK 2wjwA 205 :RRVILDCERDKVNDIVD T0528 233 :LQDMDP 2wjwA 223 :VITIGK T0528 240 :RYGIELSTGGNILPALA 2wjwA 235 :YIIANLGFTDGDLLKIQ T0528 259 :KRLPGMEGATYYYY 2wjwA 252 :FGGANVSGFQIVDY T0528 276 :KNPINEWLVTEHQKRFN 2wjwA 266 :DDSLVSKFIERWSTLEE T0528 293 :APPDFFTAGGFSAAMAVVTAVQKA 2wjwA 291 :TTIKYTSALTYDAVQVMTEAFRNL T0528 321 :TEKLIAAMEGMEFDTPKGKMVFRKEDHQALQSMYHFKVKVDPAVAWAVLEPV 2wjwA 341 :GVEIERALKQVQVEGLSGNIKFDQNGKRINYTINIMELKTNGPRKIGYWSEV Number of specific fragments extracted= 19 number of extra gaps= 0 total=962 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 2wjwA/T0528-2wjwA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0528 read from 2wjwA/T0528-2wjwA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2wjwA read from 2wjwA/T0528-2wjwA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2wjwA in template set Warning: unaligning (T0528)I377 because last residue in template chain is (2wjwA)T398 T0528 18 :DLKIALIYG 2wjwA 26 :SIQIGGLFP T0528 33 :AYAKQTETGLMMGLEYATKGTMTLDGRKIVV 2wjwA 35 :RGADQEYSAFRVGMVQFSTSEFRLTPHIDNL T0528 68 :DQSKPDLSKAALAEAYQD 2wjwA 66 :EVANSFAVTNAFCSQFSR T0528 87 :GADIAIGTSSSAAALADLPVAEENKKILIVEPAVA 2wjwA 84 :GVYAIFGFYDKKSVNTITSFCGTLHVSFITPSFPT T0528 126 :GEK 2wjwA 119 :DGT T0528 130 :NRYIFRTGRNSSQDAISNAVA 2wjwA 122 :HPFVIQMRPDLKGALLSLIEY T0528 154 :QGVTIATLAQD 2wjwA 144 :QWDKFAYLYDS T0528 166 :AFGRDGVAAFKEALAKTGATLATEEYVPTTT 2wjwA 155 :DRGLSTLQAVLDSAAEKKWQVTAINVGNINN T0528 197 :TDFTAVGQRL 2wjwA 190 :EMYRSLFQDL T0528 210 :LKDKPGKKIIWVIWAGGGDPLTKLQDMDP 2wjwA 200 :ELKKERRVILDCERDKVNDIVDQVITIGK T0528 239 :KRYGIELSTGGNILP 2wjwA 231 :KGYHYIIANLGFTDG T0528 256 :AAYKR 2wjwA 246 :DLLKI T0528 261 :LPGMEGATYYYYD 2wjwA 252 :FGGANVSGFQIVD T0528 275 :PKNPINEWLVTEHQKRFN 2wjwA 265 :YDDSLVSKFIERWSTLEE T0528 293 :APPDFFTAGGFSAAMAVVTAVQKA 2wjwA 291 :TTIKYTSALTYDAVQVMTEAFRNL T0528 317 :KS 2wjwA 333 :NP T0528 319 :TDTEKLIAAMEGMEFDTPKGKMVFRKEDHQALQSMYHFKVKVDPAVAWA 2wjwA 339 :GQGVEIERALKQVQVEGLSGNIKFDQNGKRINYTINIMELKTNGPRKIG T0528 368 :VLEPVRELK 2wjwA 389 :WSEVDKMVV Number of specific fragments extracted= 18 number of extra gaps= 0 total=980 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 3ckmA/T0528-3ckmA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 3ckmA expands to /projects/compbio/data/pdb/3ckm.pdb.gz 3ckmA:Skipped atom 155, because occupancy 0.400 <= existing 0.600 in 3ckmA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 635, because occupancy 0.300 <= existing 0.700 in 3ckmA Skipped atom 637, because occupancy 0.300 <= existing 0.700 in 3ckmA Skipped atom 639, because occupancy 0.300 <= existing 0.700 in 3ckmA Skipped atom 641, because occupancy 0.300 <= existing 0.700 in 3ckmA Skipped atom 643, because occupancy 0.300 <= existing 0.700 in 3ckmA Skipped atom 645, because occupancy 0.300 <= existing 0.700 in 3ckmA Skipped atom 647, because occupancy 0.300 <= existing 0.700 in 3ckmA Skipped atom 649, because occupancy 0.300 <= existing 0.700 in 3ckmA Skipped atom 827, because occupancy 0.500 <= existing 0.500 in 3ckmA Skipped atom 829, because occupancy 0.500 <= existing 0.500 in 3ckmA Skipped atom 831, because occupancy 0.500 <= existing 0.500 in 3ckmA Skipped atom 833, because occupancy 0.500 <= existing 0.500 in 3ckmA Skipped atom 835, because occupancy 0.500 <= existing 0.500 in 3ckmA Skipped atom 837, because occupancy 0.500 <= existing 0.500 in 3ckmA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1083, because occupancy 0.500 <= existing 0.500 in 3ckmA Skipped atom 1085, because occupancy 0.500 <= existing 0.500 in 3ckmA Skipped atom 1087, because occupancy 0.500 <= existing 0.500 in 3ckmA Skipped atom 1089, because occupancy 0.500 <= existing 0.500 in 3ckmA Skipped atom 1091, because occupancy 0.500 <= existing 0.500 in 3ckmA Skipped atom 1093, because occupancy 0.500 <= existing 0.500 in 3ckmA Skipped atom 1095, because occupancy 0.500 <= existing 0.500 in 3ckmA Skipped atom 1097, because occupancy 0.500 <= existing 0.500 in 3ckmA Skipped atom 1099, because occupancy 0.500 <= existing 0.500 in 3ckmA Skipped atom 1101, because occupancy 0.500 <= existing 0.500 in 3ckmA Skipped atom 1103, because occupancy 0.500 <= existing 0.500 in 3ckmA Skipped atom 1254, because occupancy 0.300 <= existing 0.700 in 3ckmA Skipped atom 1258, because occupancy 0.300 <= existing 0.700 in 3ckmA Skipped atom 1260, because occupancy 0.300 <= existing 0.700 in 3ckmA Skipped atom 1262, because occupancy 0.300 <= existing 0.700 in 3ckmA Skipped atom 1264, because occupancy 0.300 <= existing 0.700 in 3ckmA Skipped atom 1427, because occupancy 0.500 <= existing 0.500 in 3ckmA Skipped atom 1429, because occupancy 0.500 <= existing 0.500 in 3ckmA Skipped atom 1431, because occupancy 0.500 <= existing 0.500 in 3ckmA Skipped atom 1433, because occupancy 0.500 <= existing 0.500 in 3ckmA Skipped atom 1435, because occupancy 0.500 <= existing 0.500 in 3ckmA Skipped atom 1437, because occupancy 0.500 <= existing 0.500 in 3ckmA Skipped atom 1439, because occupancy 0.500 <= existing 0.500 in 3ckmA Skipped atom 1442, because occupancy 0.500 <= existing 0.500 in 3ckmA Skipped atom 1446, because occupancy 0.500 <= existing 0.500 in 3ckmA Skipped atom 1448, because occupancy 0.500 <= existing 0.500 in 3ckmA Skipped atom 1450, because occupancy 0.500 <= existing 0.500 in 3ckmA Skipped atom 1452, because occupancy 0.500 <= existing 0.500 in 3ckmA Skipped atom 1454, because occupancy 0.500 <= existing 0.500 in 3ckmA Skipped atom 1461, because occupancy 0.500 <= existing 0.500 in 3ckmA Skipped atom 1463, because occupancy 0.500 <= existing 0.500 in 3ckmA Skipped atom 1465, because occupancy 0.500 <= existing 0.500 in 3ckmA Skipped atom 1473, because occupancy 0.300 <= existing 0.700 in 3ckmA Skipped atom 1477, because occupancy 0.300 <= existing 0.700 in 3ckmA Skipped atom 1479, because occupancy 0.300 <= existing 0.700 in 3ckmA Skipped atom 1481, because occupancy 0.300 <= existing 0.700 in 3ckmA Skipped atom 1483, because occupancy 0.300 <= existing 0.700 in 3ckmA Skipped atom 1485, because occupancy 0.300 <= existing 0.700 in 3ckmA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 1651, because occupancy 0.500 <= existing 0.500 in 3ckmA Skipped atom 1655, because occupancy 0.500 <= existing 0.500 in 3ckmA Skipped atom 1657, because occupancy 0.500 <= existing 0.500 in 3ckmA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 2359, because occupancy 0.500 <= existing 0.500 in 3ckmA Skipped atom 2361, because occupancy 0.500 <= existing 0.500 in 3ckmA Skipped atom 2363, because occupancy 0.500 <= existing 0.500 in 3ckmA Skipped atom 2365, because occupancy 0.500 <= existing 0.500 in 3ckmA Skipped atom 2367, because occupancy 0.500 <= existing 0.500 in 3ckmA Skipped atom 2369, because occupancy 0.500 <= existing 0.500 in 3ckmA Skipped atom 2371, because occupancy 0.500 <= existing 0.500 in 3ckmA Skipped atom 2373, because occupancy 0.500 <= existing 0.500 in 3ckmA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0528 read from 3ckmA/T0528-3ckmA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3ckmA read from 3ckmA/T0528-3ckmA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3ckmA to template set # found chain 3ckmA in template set Warning: unaligning (T0528)A119 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (3ckmA)T346 Warning: unaligning (T0528)V120 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (3ckmA)T346 Warning: unaligning (T0528)G137 because of BadResidue code BAD_PEPTIDE in next template residue (3ckmA)L360 Warning: unaligning (T0528)R138 because of BadResidue code BAD_PEPTIDE at template residue (3ckmA)L360 Warning: unaligning (T0528)P214 because of BadResidue code BAD_PEPTIDE in next template residue (3ckmA)N431 Warning: unaligning (T0528)G215 because of BadResidue code BAD_PEPTIDE at template residue (3ckmA)N431 Warning: unaligning (T0528)A367 because last residue in template chain is (3ckmA)V574 T0528 20 :KIALIYGKTGPLEAYAKQTETGLMMGLE 3ckmA 258 :QIGLLLPLSGDGQILGTTIQSGFNDAKG T0528 58 :GRKIVVITKDDQSKP 3ckmA 286 :NSTIPVQVFDTSMNS T0528 76 :KAALAEAYQDDGADIAIGTSSSAAALADLPVAEE 3ckmA 301 :VQDIIAQAKQAGIKTLVGPLLKQNLDVILADPAQ T0528 110 :NKKILIVEP 3ckmA 336 :QGMDVLALN T0528 121 :ADQ 3ckmA 347 :PNS T0528 127 :EK 3ckmA 350 :RA T0528 130 :NRYIFRT 3ckmA 352 :IPQLCYY T0528 139 :NSSQDAISNAVAIGKQG 3ckmA 361 :SPEDEAESAANKMWNDG T0528 156 :VTIATLAQDYAFGRDGVAAFKEALAKTGATLATEEYVP 3ckmA 379 :RNPLVAMPQNDLGQRVGNAFNVRWQQLAGTDANIRYYN T0528 195 :TTTDFTAVGQRL 3ckmA 417 :LPADVTYFVQEN T0528 213 :K 3ckmA 429 :N T0528 216 :KKIIWVIWAGGG 3ckmA 432 :TTALYAVASPTE T0528 228 :DPLTKLQDMDPKRYGIELSTGGNILPAL 3ckmA 445 :AEMKGYLTNIVPNLAIYASSRASASATN T0528 256 :AAYKRLPGMEGATYYYYDIPKNPI 3ckmA 476 :DFIAQMNGVQFSDIPFFKDTNSPQ T0528 284 :VTEHQKRFNAPPDFF 3ckmA 500 :YQKLAKSTGGEYQLM T0528 299 :TAGGFSAAMAVVTAVQ 3ckmA 517 :YAMGADAWLLINQFNE T0528 324 :LIA 3ckmA 533 :LRQ T0528 329 :EGMEFDTPKGKMVFRK 3ckmA 537 :PGYRLSGLTGILSADT T0528 346 :DHQALQSMYHFKVKVDPAVAW 3ckmA 553 :NCNVERDMTWYQYQDGAIVPV Number of specific fragments extracted= 19 number of extra gaps= 3 total=999 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 3ckmA/T0528-3ckmA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0528 read from 3ckmA/T0528-3ckmA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3ckmA read from 3ckmA/T0528-3ckmA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3ckmA in template set Warning: unaligning (T0528)A119 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (3ckmA)T346 Warning: unaligning (T0528)V120 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (3ckmA)T346 Warning: unaligning (T0528)G137 because of BadResidue code BAD_PEPTIDE in next template residue (3ckmA)L360 Warning: unaligning (T0528)R138 because of BadResidue code BAD_PEPTIDE at template residue (3ckmA)L360 Warning: unaligning (T0528)D212 because of BadResidue code BAD_PEPTIDE in next template residue (3ckmA)N431 Warning: unaligning (T0528)K213 because of BadResidue code BAD_PEPTIDE at template residue (3ckmA)N431 Warning: unaligning (T0528)A367 because last residue in template chain is (3ckmA)V574 T0528 20 :KIALIYGKTGPLEAYAKQTETGLMMGL 3ckmA 258 :QIGLLLPLSGDGQILGTTIQSGFNDAK T0528 57 :DGRKIVVITKDDQSKP 3ckmA 285 :GNSTIPVQVFDTSMNS T0528 75 :SKAALAEAY 3ckmA 301 :VQDIIAQAK T0528 85 :DDGADIAIGTSSSAAALADLP 3ckmA 310 :QAGIKTLVGPLLKQNLDVILA T0528 106 :VAEENKKILIVEP 3ckmA 332 :PAQIQGMDVLALN T0528 121 :ADQITG 3ckmA 347 :PNSRAI T0528 131 :RYIFRT 3ckmA 353 :PQLCYY T0528 139 :NSSQDAISNAVAIGKQGV 3ckmA 361 :SPEDEAESAANKMWNDGV T0528 157 :TIATLAQDYAFGRDGVAAFKEALAKTGATLATEEYVPTTT 3ckmA 380 :NPLVAMPQNDLGQRVGNAFNVRWQQLAGTDANIRYYNLPA T0528 198 :DFTAVGQR 3ckmA 420 :DVTYFVQE T0528 210 :LK 3ckmA 428 :NN T0528 214 :P 3ckmA 432 :T T0528 216 :KKIIWVIWAGGGDPLTK 3ckmA 433 :TALYAVASPTELAEMKG T0528 233 :LQDMDP 3ckmA 451 :LTNIVP T0528 239 :KRYGIELSTGGNILPALAAYKRLPGMEGATYYYY 3ckmA 459 :AIYASSRASASATNTNTDFIAQMNGVQFSDIPFF T0528 273 :DI 3ckmA 494 :DT T0528 276 :KNPINEWLVTE 3ckmA 496 :NSPQYQKLAKS T0528 291 :FNAPP 3ckmA 507 :TGGEY T0528 296 :DFFTAGGFSAAMAVVTA 3ckmA 514 :MRLYAMGADAWLLINQF T0528 322 :EKLIA 3ckmA 531 :NELRQ T0528 329 :EGMEFDTPKGKMVFRK 3ckmA 537 :PGYRLSGLTGILSADT T0528 346 :DHQALQSMYHFKVKVDPAVAW 3ckmA 553 :NCNVERDMTWYQYQDGAIVPV Number of specific fragments extracted= 22 number of extra gaps= 3 total=1021 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 3ckmA/T0528-3ckmA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0528 read from 3ckmA/T0528-3ckmA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3ckmA read from 3ckmA/T0528-3ckmA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3ckmA in template set Warning: unaligning (T0528)V120 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (3ckmA)T346 Warning: unaligning (T0528)A121 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (3ckmA)T346 Warning: unaligning (T0528)G137 because of BadResidue code BAD_PEPTIDE in next template residue (3ckmA)L360 Warning: unaligning (T0528)R138 because of BadResidue code BAD_PEPTIDE at template residue (3ckmA)L360 Warning: unaligning (T0528)P214 because of BadResidue code BAD_PEPTIDE in next template residue (3ckmA)N431 Warning: unaligning (T0528)G215 because of BadResidue code BAD_PEPTIDE at template residue (3ckmA)N431 T0528 20 :KIALIYGKTGPLEAYAKQTETGLMMGL 3ckmA 258 :QIGLLLPLSGDGQILGTTIQSGFNDAK T0528 52 :GTMT 3ckmA 285 :GNST T0528 59 :RK 3ckmA 289 :IP T0528 63 :VITKD 3ckmA 291 :VQVFD T0528 68 :DQSK 3ckmA 297 :SMNS T0528 75 :SKAALAEAYQD 3ckmA 301 :VQDIIAQAKQA T0528 87 :GADIAIGTSSSAAALADLPVAEENKKILIVEPA 3ckmA 312 :GIKTLVGPLLKQNLDVILADPAQIQGMDVLALN T0528 122 :DQITG 3ckmA 347 :PNSRA T0528 130 :NRYIFRT 3ckmA 352 :IPQLCYY T0528 139 :NSSQDAISNAVAIGK 3ckmA 361 :SPEDEAESAANKMWN T0528 154 :QGVTIATLAQDYAFGRDGVAAFKEALAKTGATLATEEYVPTTT 3ckmA 377 :GVRNPLVAMPQNDLGQRVGNAFNVRWQQLAGTDANIRYYNLPA T0528 201 :AVGQRL 3ckmA 420 :DVTYFV T0528 210 :LKDK 3ckmA 426 :QENN T0528 216 :K 3ckmA 432 :T T0528 217 :KIIWVIWAGGGDPLTKLQDMDP 3ckmA 434 :ALYAVASPTELAEMKGYLTNIV T0528 239 :KRYGIELSTGGNILPA 3ckmA 457 :NLAIYASSRASASATN T0528 255 :LAAYKRLPGMEGATYYYYDIPKNPINEWL 3ckmA 475 :TDFIAQMNGVQFSDIPFFKDTNSPQYQKL T0528 288 :QKRFNA 3ckmA 504 :AKSTGG T0528 296 :DFFTAGGFSAAMAVVTAVQKA 3ckmA 510 :EYQLMRLYAMGADAWLLINQF T0528 322 :EKLIA 3ckmA 531 :NELRQ T0528 329 :EGMEFDTPKGKMVFR 3ckmA 537 :PGYRLSGLTGILSAD T0528 345 :EDHQALQSMYHFKVKVDPAVA 3ckmA 552 :TNCNVERDMTWYQYQDGAIVP T0528 377 :I 3ckmA 573 :V Number of specific fragments extracted= 23 number of extra gaps= 3 total=1044 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 3jpwA/T0528-3jpwA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 3jpwA expands to /projects/compbio/data/pdb/3jpw.pdb.gz 3jpwA:Skipped atom 889, because occupancy 0.390 <= existing 0.610 in 3jpwA Skipped atom 1609, because occupancy 0.460 <= existing 0.540 in 3jpwA Skipped atom 1613, because occupancy 0.460 <= existing 0.540 in 3jpwA Skipped atom 1615, because occupancy 0.460 <= existing 0.540 in 3jpwA Skipped atom 1617, because occupancy 0.460 <= existing 0.540 in 3jpwA Skipped atom 1619, because occupancy 0.460 <= existing 0.540 in 3jpwA Skipped atom 2468, because occupancy 0.320 <= existing 0.680 in 3jpwA # T0528 read from 3jpwA/T0528-3jpwA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3jpwA read from 3jpwA/T0528-3jpwA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3jpwA to template set # found chain 3jpwA in template set Warning: unaligning (T0528)A16 because first residue in template chain is (3jpwA)P32 Warning: unaligning (T0528)T196 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (3jpwA)S214 T0528 17 :DDLKIALIYGK 3jpwA 33 :PSIGIAVILVG T0528 29 :GPLEAY 3jpwA 51 :KDAHEK T0528 49 :ATKGTMTL 3jpwA 58 :DFHHLSVV T0528 59 :RKIVVITK 3jpwA 66 :PRVELVAM T0528 68 :DQSKPDLSKAALAEAYQDDGADIAIGTSSS 3jpwA 74 :NETDPKSIITRICDLMSDRKIQGVVFADDT T0528 98 :AAALADLPVAEENKKILIV 3jpwA 107 :AIAQILDFISAQTLTPILG T0528 117 :EPAVADQITGEKWNRYIFRTGRNSSQDAISNAVAIGKQG 3jpwA 127 :HGGSSMIMADKDESSMFFQFGPSIEQQASVMLNIMEEYD T0528 156 :VTIATLAQDYAFGRDGVAAFKEALAKT 3jpwA 167 :YIFSIVTTYFPGYQDFVNKIRSTIENS T0528 183 :GATLATEEYVPTT 3jpwA 196 :GWELEEVLLLDMS T0528 206 :LFDALKDK 3jpwA 216 :IQNQLKKL T0528 215 :GKKIIWVIWAGGG 3jpwA 224 :QSPIILLYCTKEE T0528 228 :DPLTKLQDMDPK 3jpwA 239 :YIFEVANSVGLT T0528 240 :RYGIELSTGGNIL 3jpwA 253 :GYTWIVPSLVAGD T0528 255 :LAAY 3jpwA 266 :TDTV T0528 259 :KR 3jpwA 271 :SE T0528 261 :LPGMEGATYYYY 3jpwA 274 :PTGLISVSYDEW T0528 276 :KNPINEWLV 3jpwA 286 :DYGLPARVR T0528 304 :SAAMAVVTAVQKA 3jpwA 295 :DGIAIITTAASDM T0528 317 :KS 3jpwA 327 :KR T0528 319 :TDTEKLIAAMEGMEFD 3jpwA 330 :YQSNMLNRYLINVTFE T0528 337 :KGKMVFRKEDHQALQSMYHFKVK 3jpwA 346 :GRDLSFSEDGYQMHPKLVIILLN T0528 360 :VDPAVAWAVLEPVR 3jpwA 370 :ERKWERVGKWKDKS T0528 375 :LKIE 3jpwA 384 :LQMK Number of specific fragments extracted= 23 number of extra gaps= 0 total=1067 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 3jpwA/T0528-3jpwA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0528 read from 3jpwA/T0528-3jpwA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3jpwA read from 3jpwA/T0528-3jpwA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3jpwA in template set Warning: unaligning (T0528)T196 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (3jpwA)S214 T0528 18 :DLKIALIYGKTG 3jpwA 34 :SIGIAVILVGTS T0528 52 :GTMTL 3jpwA 60 :HHLSV T0528 58 :GRKIVVITK 3jpwA 65 :VPRVELVAM T0528 68 :DQSKPDLSKAALAEAYQDDGA 3jpwA 74 :NETDPKSIITRICDLMSDRKI T0528 89 :DIAIGTSSSAAALADLPVAEENKKILIVEPAVADQIT 3jpwA 98 :VFADDTDQEAIAQILDFISAQTLTPILGIHGGSSMIM T0528 126 :GEK 3jpwA 138 :DES T0528 131 :RYIFRTGRNSSQDAISNAVAIGKQGV 3jpwA 141 :SMFFQFGPSIEQQASVMLNIMEEYDW T0528 157 :TIATLAQDYAFGRDGVAAFKEALAKTG 3jpwA 168 :IFSIVTTYFPGYQDFVNKIRSTIENSF T0528 184 :ATLATEEYVPTT 3jpwA 197 :WELEEVLLLDMS T0528 207 :FDALKD 3jpwA 217 :QNQLKK T0528 213 :KP 3jpwA 224 :QS T0528 216 :KKIIWVIWAGGGDPLTK 3jpwA 226 :PIILLYCTKEEATYIFE T0528 233 :LQDMDP 3jpwA 244 :ANSVGL T0528 239 :KRYGIEL 3jpwA 253 :GYTWIVP T0528 247 :TGGN 3jpwA 264 :GDTD T0528 254 :ALAA 3jpwA 268 :TVPS T0528 259 :KRLPGMEGATYYYYDIP 3jpwA 272 :EFPTGLISVSYDEWDYG T0528 279 :INE 3jpwA 289 :LPA T0528 297 :FFTAGGFSAAMAVVTAVQKAK 3jpwA 292 :RVRDGIAIITTAASDMLSEHS T0528 319 :TDTEKLIAAMEGMEF 3jpwA 330 :YQSNMLNRYLINVTF T0528 336 :PKGKMVFRKEDHQALQSMYHFKVK 3jpwA 345 :EGRDLSFSEDGYQMHPKLVIILLN T0528 360 :VDPAVAWAVLEPVR 3jpwA 370 :ERKWERVGKWKDKS Number of specific fragments extracted= 22 number of extra gaps= 0 total=1089 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 3jpwA/T0528-3jpwA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0528 read from 3jpwA/T0528-3jpwA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3jpwA read from 3jpwA/T0528-3jpwA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3jpwA in template set Warning: unaligning (T0528)T196 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (3jpwA)S214 Warning: unaligning (T0528)T200 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3jpwA)S214 T0528 68 :DQSKPDLSKAALAEAYQD 3jpwA 74 :NETDPKSIITRICDLMSD T0528 88 :ADIAIGTSSSAAALADLPVAEENKKILIVEPAVADQIT 3jpwA 97 :VVFADDTDQEAIAQILDFISAQTLTPILGIHGGSSMIM T0528 127 :EKWNRYIFRTGRNSSQDAISNAVAIGK 3jpwA 137 :KDESSMFFQFGPSIEQQASVMLNIMEE T0528 154 :QGVTIATLAQDYAFGRDGVAAFKEALAKT 3jpwA 165 :DWYIFSIVTTYFPGYQDFVNKIRSTIENS T0528 183 :GATLATEEYVPTT 3jpwA 196 :GWELEEVLLLDMS T0528 201 :AVGQRL 3jpwA 215 :KIQNQL T0528 210 :LKDKPGKKIIWVIWAGGGDPLTKLQDMDP 3jpwA 221 :KKLQSPIILLYCTKEEATYIFEVANSVGL T0528 239 :KRYGIELSTG 3jpwA 252 :YGYTWIVPSL T0528 250 :NILPALAAYKRLPGMEGATYYYYDIPK 3jpwA 262 :VAGDTDTVPSEFPTGLISVSYDEWDYG T0528 298 :FTAGGFSAAMAVVTAVQKA 3jpwA 289 :LPARVRDGIAIITTAASDM T0528 317 :KS 3jpwA 327 :KR T0528 319 :TDTEKLIAAMEGMEFDTPKGKMV 3jpwA 330 :YQSNMLNRYLINVTFEGRDLSFS T0528 344 :KEDHQALQSMYHFKVKVDPAVA 3jpwA 353 :EDGYQMHPKLVIILLNKERKWE T0528 366 :WAVLEPVRELKIEEMN 3jpwA 377 :GKWKDKSLQMKYYVWP Number of specific fragments extracted= 14 number of extra gaps= 0 total=1103 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 2liv/T0528-2liv-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2liv expands to /projects/compbio/data/pdb/2liv.pdb.gz 2liv:Warning: there is no chain 2liv will retry with 2livA # T0528 read from 2liv/T0528-2liv-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2liv read from 2liv/T0528-2liv-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2liv to template set # found chain 2liv in template set Warning: unaligning (T0528)D17 because first residue in template chain is (2liv)E1 Warning: unaligning (T0528)D18 because of BadResidue code BAD_PEPTIDE at template residue (2liv)D2 Warning: unaligning (T0528)Y25 because of BadResidue code BAD_PEPTIDE in next template residue (2liv)A10 Warning: unaligning (T0528)G26 because of BadResidue code BAD_PEPTIDE at template residue (2liv)A10 Warning: unaligning (T0528)K27 because of BadResidue code BAD_PEPTIDE in next template residue (2liv)S12 Warning: unaligning (T0528)T28 because of BadResidue code BAD_PEPTIDE at template residue (2liv)S12 Warning: unaligning (T0528)I64 because of BadResidue code BAD_PEPTIDE in next template residue (2liv)K48 Warning: unaligning (T0528)T65 because of BadResidue code BAD_PEPTIDE at template residue (2liv)K48 Warning: unaligning (T0528)D67 because of BadResidue code BAD_PEPTIDE in next template residue (2liv)D51 Warning: unaligning (T0528)D68 because of BadResidue code BAD_PEPTIDE at template residue (2liv)D51 Warning: unaligning (T0528)Q69 because of BadResidue code BAD_PEPTIDE in next template residue (2liv)C53 Warning: unaligning (T0528)S70 because of BadResidue code BAD_PEPTIDE at template residue (2liv)C53 Warning: unaligning (T0528)Y83 because of BadResidue code BAD_PEPTIDE in next template residue (2liv)N67 Warning: unaligning (T0528)Q84 because of BadResidue code BAD_PEPTIDE at template residue (2liv)N67 Warning: unaligning (T0528)G93 because of BadResidue code BAD_PEPTIDE in next template residue (2liv)H76 Warning: unaligning (T0528)T94 because of BadResidue code BAD_PEPTIDE at template residue (2liv)H76 Warning: unaligning (T0528)A99 because of BadResidue code BAD_PEPTIDE in next template residue (2liv)T82 Warning: unaligning (T0528)A100 because of BadResidue code BAD_PEPTIDE at template residue (2liv)T82 Warning: unaligning (T0528)T136 because of BadResidue code BAD_PEPTIDE in next template residue (2liv)T118 Warning: unaligning (T0528)G137 because of BadResidue code BAD_PEPTIDE at template residue (2liv)T118 Warning: unaligning (T0528)R138 because of BadResidue code BAD_PEPTIDE at template residue (2liv)G119 Warning: unaligning (T0528)I151 because of BadResidue code BAD_PEPTIDE in next template residue (2liv)L133 Warning: unaligning (T0528)G152 because of BadResidue code BAD_PEPTIDE at template residue (2liv)L133 Warning: unaligning (T0528)T182 because of BadResidue code BAD_PEPTIDE in next template residue (2liv)N166 Warning: unaligning (T0528)G183 because of BadResidue code BAD_PEPTIDE at template residue (2liv)N166 Warning: unaligning (T0528)A184 because of BadResidue code BAD_PEPTIDE in next template residue (2liv)N168 Warning: unaligning (T0528)T185 because of BadResidue code BAD_PEPTIDE at template residue (2liv)N168 Warning: unaligning (T0528)T188 because of BadResidue code BAD_PEPTIDE in next template residue (2liv)F172 Warning: unaligning (T0528)E189 because of BadResidue code BAD_PEPTIDE at template residue (2liv)F172 Warning: unaligning (T0528)F207 because of BadResidue code BAD_PEPTIDE in next template residue (2liv)K191 Warning: unaligning (T0528)D208 because of BadResidue code BAD_PEPTIDE at template residue (2liv)K191 Warning: unaligning (T0528)L252 because of BadResidue code BAD_PEPTIDE in next template residue (2liv)S232 Warning: unaligning (T0528)P253 because of BadResidue code BAD_PEPTIDE at template residue (2liv)S232 Warning: unaligning (T0528)K259 because of BadResidue code BAD_PEPTIDE in next template residue (2liv)E239 Warning: unaligning (T0528)R260 because of BadResidue code BAD_PEPTIDE at template residue (2liv)E239 Warning: unaligning (T0528)Y272 because of BadResidue code BAD_PEPTIDE in next template residue (2liv)D253 Warning: unaligning (T0528)D273 because of BadResidue code BAD_PEPTIDE at template residue (2liv)D253 Warning: unaligning (T0528)K276 because of BadResidue code BAD_PEPTIDE at template residue (2liv)Q254 Warning: unaligning (T0528)H287 because of BadResidue code BAD_PEPTIDE in next template residue (2liv)K266 Warning: unaligning (T0528)Q288 because of BadResidue code BAD_PEPTIDE at template residue (2liv)K266 Warning: unaligning (T0528)Q314 because of BadResidue code BAD_PEPTIDE in next template residue (2liv)Q293 Warning: unaligning (T0528)K317 because of BadResidue code BAD_PEPTIDE at template residue (2liv)Q293 Warning: unaligning (T0528)P336 because of BadResidue code BAD_PEPTIDE in next template residue (2liv)M313 Warning: unaligning (T0528)K337 because of BadResidue code BAD_PEPTIDE at template residue (2liv)M313 Warning: unaligning (T0528)A363 because of BadResidue code BAD_PEPTIDE in next template residue (2liv)T341 Warning: unaligning (T0528)V364 because of BadResidue code BAD_PEPTIDE at template residue (2liv)T341 T0528 19 :LKIALI 2liv 3 :IKVAVV T0528 29 :GPLEAYAKQTETGLMMGLE 2liv 13 :GPVAQYGDQEFTGAEQAVA T0528 49 :ATKGTMTLDGRKIVV 2liv 32 :DINAKGGIKGNKLQI T0528 66 :K 2liv 49 :Y T0528 71 :KPDLSKAALAEA 2liv 54 :DPKQAVAVANKV T0528 85 :D 2liv 68 :D T0528 87 :GADIAI 2liv 69 :GIKYVI T0528 95 :SSSA 2liv 77 :LCSS T0528 101 :LADLPVAEENKKILIVEPAVADQITGEK 2liv 83 :QPASDIYEDEGILMITPAATAPELTARG T0528 130 :NRYIFR 2liv 111 :YQLILR T0528 139 :NSSQDAISNAVA 2liv 120 :LDSDQGPTAAKY T0528 153 :K 2liv 134 :E T0528 154 :QG 2liv 136 :VK T0528 156 :VTIATLAQDYAFGRDGVAAFKEALAK 2liv 139 :QRIAIVHDKQQYGEGLARAVQDGLKK T0528 186 :LA 2liv 169 :VV T0528 190 :EYVPTTTTDFTAVGQRL 2liv 173 :DGITAGEKDFSTLVARL T0528 209 :A 2liv 192 :E T0528 215 :GKKIIWVIWAGGG 2liv 193 :NIDFVYYGGYHPE T0528 228 :DPLTKLQDMDP 2liv 208 :QILRQARAAGL T0528 240 :RYGIELSTGGNI 2liv 219 :KTQFMGPEGVAN T0528 254 :ALAAY 2liv 233 :LSNIA T0528 261 :LPGMEGATYYY 2liv 241 :AEGLLVTKPKN T0528 277 :NPINEWLVTE 2liv 255 :VPANKPIVDA T0528 289 :KRFNAPPDFFTAGGFSAAMAVVTAV 2liv 267 :AKKQDPSGAFVWTTYAALQSLQAGL T0528 318 :STDTEKLIAAMEGMEFDT 2liv 294 :SDDPAEIAKYLKANSVDT T0528 338 :GKMVFRKEDHQALQSMYHFKVKVDP 2liv 314 :GPLTWDEKGDLKGFEFGVFDWHANG T0528 365 :A 2liv 342 :D Number of specific fragments extracted= 27 number of extra gaps= 18 total=1130 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 2liv/T0528-2liv-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0528 read from 2liv/T0528-2liv-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2liv read from 2liv/T0528-2liv-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2liv in template set Warning: unaligning (T0528)D17 because first residue in template chain is (2liv)E1 Warning: unaligning (T0528)D18 because of BadResidue code BAD_PEPTIDE at template residue (2liv)D2 Warning: unaligning (T0528)Y25 because of BadResidue code BAD_PEPTIDE in next template residue (2liv)A10 Warning: unaligning (T0528)G26 because of BadResidue code BAD_PEPTIDE at template residue (2liv)A10 Warning: unaligning (T0528)K27 because of BadResidue code BAD_PEPTIDE in next template residue (2liv)S12 Warning: unaligning (T0528)T28 because of BadResidue code BAD_PEPTIDE at template residue (2liv)S12 Warning: unaligning (T0528)I64 because of BadResidue code BAD_PEPTIDE in next template residue (2liv)K48 Warning: unaligning (T0528)T65 because of BadResidue code BAD_PEPTIDE at template residue (2liv)K48 Warning: unaligning (T0528)D67 because of BadResidue code BAD_PEPTIDE in next template residue (2liv)D51 Warning: unaligning (T0528)D68 because of BadResidue code BAD_PEPTIDE at template residue (2liv)D51 Warning: unaligning (T0528)Q69 because of BadResidue code BAD_PEPTIDE in next template residue (2liv)C53 Warning: unaligning (T0528)S70 because of BadResidue code BAD_PEPTIDE at template residue (2liv)C53 Warning: unaligning (T0528)Y83 because of BadResidue code BAD_PEPTIDE in next template residue (2liv)N67 Warning: unaligning (T0528)D85 because of BadResidue code BAD_PEPTIDE at template residue (2liv)N67 Warning: unaligning (T0528)G93 because of BadResidue code BAD_PEPTIDE in next template residue (2liv)H76 Warning: unaligning (T0528)T94 because of BadResidue code BAD_PEPTIDE at template residue (2liv)H76 Warning: unaligning (T0528)A99 because of BadResidue code BAD_PEPTIDE in next template residue (2liv)T82 Warning: unaligning (T0528)A100 because of BadResidue code BAD_PEPTIDE at template residue (2liv)T82 Warning: unaligning (T0528)T136 because of BadResidue code BAD_PEPTIDE in next template residue (2liv)T118 Warning: unaligning (T0528)G137 because of BadResidue code BAD_PEPTIDE at template residue (2liv)T118 Warning: unaligning (T0528)R138 because of BadResidue code BAD_PEPTIDE at template residue (2liv)G119 Warning: unaligning (T0528)I151 because of BadResidue code BAD_PEPTIDE in next template residue (2liv)L133 Warning: unaligning (T0528)G152 because of BadResidue code BAD_PEPTIDE at template residue (2liv)L133 Warning: unaligning (T0528)T182 because of BadResidue code BAD_PEPTIDE in next template residue (2liv)N166 Warning: unaligning (T0528)G183 because of BadResidue code BAD_PEPTIDE at template residue (2liv)N166 Warning: unaligning (T0528)A184 because of BadResidue code BAD_PEPTIDE in next template residue (2liv)N168 Warning: unaligning (T0528)T185 because of BadResidue code BAD_PEPTIDE at template residue (2liv)N168 Warning: unaligning (T0528)T188 because of BadResidue code BAD_PEPTIDE in next template residue (2liv)F172 Warning: unaligning (T0528)E189 because of BadResidue code BAD_PEPTIDE at template residue (2liv)F172 Warning: unaligning (T0528)F207 because of BadResidue code BAD_PEPTIDE in next template residue (2liv)K191 Warning: unaligning (T0528)D208 because of BadResidue code BAD_PEPTIDE at template residue (2liv)K191 Warning: unaligning (T0528)G249 because of BadResidue code BAD_PEPTIDE in next template residue (2liv)S232 Warning: unaligning (T0528)N250 because of BadResidue code BAD_PEPTIDE at template residue (2liv)S232 Warning: unaligning (T0528)A256 because of BadResidue code BAD_PEPTIDE in next template residue (2liv)E239 Warning: unaligning (T0528)K259 because of BadResidue code BAD_PEPTIDE at template residue (2liv)E239 Warning: unaligning (T0528)Y272 because of BadResidue code BAD_PEPTIDE in next template residue (2liv)D253 Warning: unaligning (T0528)D273 because of BadResidue code BAD_PEPTIDE at template residue (2liv)D253 Warning: unaligning (T0528)K276 because of BadResidue code BAD_PEPTIDE at template residue (2liv)Q254 Warning: unaligning (T0528)H287 because of BadResidue code BAD_PEPTIDE in next template residue (2liv)K266 Warning: unaligning (T0528)Q288 because of BadResidue code BAD_PEPTIDE at template residue (2liv)K266 Warning: unaligning (T0528)Q314 because of BadResidue code BAD_PEPTIDE in next template residue (2liv)Q293 Warning: unaligning (T0528)K315 because of BadResidue code BAD_PEPTIDE at template residue (2liv)Q293 Warning: unaligning (T0528)P336 because of BadResidue code BAD_PEPTIDE in next template residue (2liv)M313 Warning: unaligning (T0528)K337 because of BadResidue code BAD_PEPTIDE at template residue (2liv)M313 Warning: unaligning (T0528)V364 because of BadResidue code BAD_PEPTIDE in next template residue (2liv)T341 Warning: unaligning (T0528)A365 because of BadResidue code BAD_PEPTIDE at template residue (2liv)T341 T0528 19 :LKIALI 2liv 3 :IKVAVV T0528 29 :GPLEAYAKQTETGLMMGLEYATKGTM 2liv 13 :GPVAQYGDQEFTGAEQAVADINAKGG T0528 56 :LDGRKIVV 2liv 39 :IKGNKLQI T0528 66 :K 2liv 49 :Y T0528 71 :KPDLSKAALAEA 2liv 54 :DPKQAVAVANKV T0528 86 :DGADIAI 2liv 68 :DGIKYVI T0528 95 :SSSA 2liv 77 :LCSS T0528 101 :LADLPVAEENKKILIVEPAVADQITGEKW 2liv 83 :QPASDIYEDEGILMITPAATAPELTARGY T0528 131 :RYIFR 2liv 112 :QLILR T0528 139 :NSSQDAISNAVA 2liv 120 :LDSDQGPTAAKY T0528 153 :KQ 2liv 134 :EK T0528 155 :GV 2liv 137 :KP T0528 157 :TIATLAQDYAFGRDGVAAFKEALAK 2liv 140 :RIAIVHDKQQYGEGLARAVQDGLKK T0528 186 :LA 2liv 169 :VV T0528 190 :EYVPTTTTDFTAVGQRL 2liv 173 :DGITAGEKDFSTLVARL T0528 209 :A 2liv 192 :E T0528 213 :KP 2liv 193 :NI T0528 216 :KKIIWVIWAGGGDPLTK 2liv 195 :DFVYYGGYHPEMGQILR T0528 233 :LQDMDP 2liv 213 :ARAAGL T0528 239 :KRYGIELSTG 2liv 221 :QFMGPEGVAN T0528 251 :ILPAL 2liv 233 :LSNIA T0528 260 :RLPGMEGATYYY 2liv 240 :SAEGLLVTKPKN T0528 277 :NPINEWLVTE 2liv 255 :VPANKPIVDA T0528 289 :KRFNAPPDFFTAGGFSAAMAVVTAV 2liv 267 :AKKQDPSGAFVWTTYAALQSLQAGL T0528 318 :STDTEKLIAAMEGMEFDT 2liv 294 :SDDPAEIAKYLKANSVDT T0528 338 :GKMVFRKEDHQALQSMYHFKVKVDPA 2liv 314 :GPLTWDEKGDLKGFEFGVFDWHANGT Number of specific fragments extracted= 26 number of extra gaps= 18 total=1156 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 2liv/T0528-2liv-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0528 read from 2liv/T0528-2liv-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2liv read from 2liv/T0528-2liv-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2liv in template set Warning: unaligning (T0528)D17 because first residue in template chain is (2liv)E1 Warning: unaligning (T0528)D18 because of BadResidue code BAD_PEPTIDE at template residue (2liv)D2 Warning: unaligning (T0528)Y25 because of BadResidue code BAD_PEPTIDE in next template residue (2liv)A10 Warning: unaligning (T0528)G26 because of BadResidue code BAD_PEPTIDE at template residue (2liv)A10 Warning: unaligning (T0528)K27 because of BadResidue code BAD_PEPTIDE in next template residue (2liv)S12 Warning: unaligning (T0528)T28 because of BadResidue code BAD_PEPTIDE at template residue (2liv)S12 Warning: unaligning (T0528)I64 because of BadResidue code BAD_PEPTIDE in next template residue (2liv)K48 Warning: unaligning (T0528)T65 because of BadResidue code BAD_PEPTIDE at template residue (2liv)K48 Warning: unaligning (T0528)D67 because of BadResidue code BAD_PEPTIDE in next template residue (2liv)D51 Warning: unaligning (T0528)D68 because of BadResidue code BAD_PEPTIDE at template residue (2liv)D51 Warning: unaligning (T0528)Q69 because of BadResidue code BAD_PEPTIDE in next template residue (2liv)C53 Warning: unaligning (T0528)S70 because of BadResidue code BAD_PEPTIDE at template residue (2liv)C53 Warning: unaligning (T0528)Y83 because of BadResidue code BAD_PEPTIDE in next template residue (2liv)N67 Warning: unaligning (T0528)Q84 because of BadResidue code BAD_PEPTIDE at template residue (2liv)N67 Warning: unaligning (T0528)G93 because of BadResidue code BAD_PEPTIDE in next template residue (2liv)H76 Warning: unaligning (T0528)T94 because of BadResidue code BAD_PEPTIDE at template residue (2liv)H76 Warning: unaligning (T0528)A99 because of BadResidue code BAD_PEPTIDE in next template residue (2liv)T82 Warning: unaligning (T0528)A100 because of BadResidue code BAD_PEPTIDE at template residue (2liv)T82 Warning: unaligning (T0528)T136 because of BadResidue code BAD_PEPTIDE in next template residue (2liv)T118 Warning: unaligning (T0528)G137 because of BadResidue code BAD_PEPTIDE at template residue (2liv)T118 Warning: unaligning (T0528)R138 because of BadResidue code BAD_PEPTIDE at template residue (2liv)G119 Warning: unaligning (T0528)I151 because of BadResidue code BAD_PEPTIDE in next template residue (2liv)L133 Warning: unaligning (T0528)G152 because of BadResidue code BAD_PEPTIDE at template residue (2liv)L133 Warning: unaligning (T0528)T182 because of BadResidue code BAD_PEPTIDE in next template residue (2liv)N166 Warning: unaligning (T0528)G183 because of BadResidue code BAD_PEPTIDE at template residue (2liv)N166 Warning: unaligning (T0528)A184 because of BadResidue code BAD_PEPTIDE in next template residue (2liv)N168 Warning: unaligning (T0528)T185 because of BadResidue code BAD_PEPTIDE at template residue (2liv)N168 Warning: unaligning (T0528)T188 because of BadResidue code BAD_PEPTIDE in next template residue (2liv)F172 Warning: unaligning (T0528)E189 because of BadResidue code BAD_PEPTIDE at template residue (2liv)F172 Warning: unaligning (T0528)L210 because of BadResidue code BAD_PEPTIDE in next template residue (2liv)K191 Warning: unaligning (T0528)K211 because of BadResidue code BAD_PEPTIDE at template residue (2liv)K191 Warning: unaligning (T0528)I251 because of BadResidue code BAD_PEPTIDE in next template residue (2liv)S232 Warning: unaligning (T0528)L252 because of BadResidue code BAD_PEPTIDE at template residue (2liv)S232 Warning: unaligning (T0528)Y258 because of BadResidue code BAD_PEPTIDE in next template residue (2liv)E239 Warning: unaligning (T0528)K259 because of BadResidue code BAD_PEPTIDE at template residue (2liv)E239 Warning: unaligning (T0528)Y272 because of BadResidue code BAD_PEPTIDE in next template residue (2liv)D253 Warning: unaligning (T0528)D273 because of BadResidue code BAD_PEPTIDE at template residue (2liv)D253 Warning: unaligning (T0528)K276 because of BadResidue code BAD_PEPTIDE at template residue (2liv)Q254 Warning: unaligning (T0528)H287 because of BadResidue code BAD_PEPTIDE in next template residue (2liv)K266 Warning: unaligning (T0528)Q288 because of BadResidue code BAD_PEPTIDE at template residue (2liv)K266 Warning: unaligning (T0528)Q314 because of BadResidue code BAD_PEPTIDE in next template residue (2liv)Q293 Warning: unaligning (T0528)K315 because of BadResidue code BAD_PEPTIDE at template residue (2liv)Q293 Warning: unaligning (T0528)P336 because of BadResidue code BAD_PEPTIDE in next template residue (2liv)M313 Warning: unaligning (T0528)K337 because of BadResidue code BAD_PEPTIDE at template residue (2liv)M313 Warning: unaligning (T0528)V364 because of BadResidue code BAD_PEPTIDE in next template residue (2liv)T341 Warning: unaligning (T0528)A365 because of BadResidue code BAD_PEPTIDE at template residue (2liv)T341 T0528 19 :LKIALI 2liv 3 :IKVAVV T0528 29 :GPLEAYAKQTETGLMMGLEYATKGTM 2liv 13 :GPVAQYGDQEFTGAEQAVADINAKGG T0528 56 :LDGRKIVV 2liv 39 :IKGNKLQI T0528 66 :K 2liv 49 :Y T0528 71 :KPDLSKAALAEA 2liv 54 :DPKQAVAVANKV T0528 85 :D 2liv 68 :D T0528 87 :GADIAI 2liv 69 :GIKYVI T0528 95 :SSSA 2liv 77 :LCSS T0528 101 :LADLPVAEENKKILIVEPAVADQITGEK 2liv 83 :QPASDIYEDEGILMITPAATAPELTARG T0528 130 :NRYIFR 2liv 111 :YQLILR T0528 139 :NSSQDAISNAVA 2liv 120 :LDSDQGPTAAKY T0528 153 :K 2liv 134 :E T0528 154 :QGVTIATLAQDYAFGRDGVAAFKEALAK 2liv 137 :KPQRIAIVHDKQQYGEGLARAVQDGLKK T0528 186 :LA 2liv 169 :VV T0528 190 :EYVPTTTTDFTAVGQRL 2liv 173 :DGITAGEKDFSTLVARL T0528 212 :DKPGKKIIWVIWAGGGDPLTKLQDMDPKRYGIELSTGGN 2liv 192 :ENIDFVYYGGYHPEMGQILRQARAAGLKTQFMGPEGVAN T0528 253 :PALAA 2liv 233 :LSNIA T0528 260 :RLPGMEGATYYY 2liv 240 :SAEGLLVTKPKN T0528 277 :NPINEWLVTE 2liv 255 :VPANKPIVDA T0528 289 :KRFNAPPDFFTAGGFSAAMAVVTAV 2liv 267 :AKKQDPSGAFVWTTYAALQSLQAGL T0528 318 :STDTEKLIAAMEGMEFDT 2liv 294 :SDDPAEIAKYLKANSVDT T0528 338 :GKMVFRKEDHQALQSMYHFKVKVDPA 2liv 314 :GPLTWDEKGDLKGFEFGVFDWHANGT T0528 366 :W 2liv 342 :D Number of specific fragments extracted= 23 number of extra gaps= 18 total=1179 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 2qh8A/T0528-2qh8A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2qh8A expands to /projects/compbio/data/pdb/2qh8.pdb.gz 2qh8A:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0528 read from 2qh8A/T0528-2qh8A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2qh8A read from 2qh8A/T0528-2qh8A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2qh8A to template set # found chain 2qh8A in template set Warning: unaligning (T0528)D17 because first residue in template chain is (2qh8A)K26 Warning: unaligning (T0528)T28 because of BadResidue code BAD_PEPTIDE in next template residue (2qh8A)H38 Warning: unaligning (T0528)G29 because of BadResidue code BAD_PEPTIDE at template residue (2qh8A)H38 T0528 18 :DLKIALIYGK 2qh8A 27 :TAKVAVSQIV T0528 33 :AYAKQTETGLMMGLE 2qh8A 39 :PALDATRQGLLDGLK T0528 49 :A 2qh8A 54 :A T0528 53 :TMTLDGRKIVVITKDDQSKPDLSKAALAEAYQD 2qh8A 55 :KGYEEGKNLEFDYKTAQGNPAIAVQIARQFVGE T0528 87 :GADIAIG 2qh8A 88 :NPDVLVG T0528 95 :SSSAAALADLPV 2qh8A 95 :IATPTAQALVSA T0528 109 :ENKKILIVEPAVAD 2qh8A 107 :TKTIPIVFTAVTDP T0528 123 :QITGEKWNRYIFRTGRNSSQDAISNAVAIGK 2qh8A 124 :KLVKQLEQPGKNVTGLSDLSPVEQHVELIKE T0528 154 :QG 2qh8A 157 :PN T0528 156 :VTIATLAQ 2qh8A 160 :KSIGVVYN T0528 164 :DYAFGRDGVAAFKEALAKTGATLAT 2qh8A 169 :GEANAVSLMELLKLSAAKHGIKLVE T0528 190 :EYVP 2qh8A 194 :ATAL T0528 195 :TTTDFTAVGQRL 2qh8A 198 :KSADVQSATQAI T0528 213 :KPGKKIIWVIWAGGG 2qh8A 210 :AEKSDVIYALIDNTV T0528 228 :DPLTKLQDMDPK 2qh8A 226 :SAIEGMIVAANQ T0528 240 :RYGIELST 2qh8A 239 :KTPVFGAA T0528 252 :LPALA 2qh8A 247 :TSYVE T0528 262 :PGMEGATYYYY 2qh8A 252 :RGAIASLGFDY T0528 299 :TAGGFSAAMAVVTAVQ 2qh8A 263 :YQIGVQTADYVAAILE T0528 317 :K 2qh8A 279 :G T0528 319 :T 2qh8A 280 :K T0528 329 :EGMEFDTPK 2qh8A 283 :GSLDVQVAK Number of specific fragments extracted= 22 number of extra gaps= 1 total=1201 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 2qh8A/T0528-2qh8A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0528 read from 2qh8A/T0528-2qh8A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2qh8A read from 2qh8A/T0528-2qh8A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2qh8A in template set Warning: unaligning (T0528)D17 because first residue in template chain is (2qh8A)K26 Warning: unaligning (T0528)T28 because of BadResidue code BAD_PEPTIDE in next template residue (2qh8A)H38 Warning: unaligning (T0528)G29 because of BadResidue code BAD_PEPTIDE at template residue (2qh8A)H38 T0528 18 :DLKIALIYGK 2qh8A 27 :TAKVAVSQIV T0528 30 :PL 2qh8A 39 :PA T0528 38 :TETGLMMGLEYATKGTMTL 2qh8A 41 :LDATRQGLLDGLKAKGYEE T0528 58 :GRKIVVITKDDQSKPDLSKAALAEAY 2qh8A 60 :GKNLEFDYKTAQGNPAIAVQIARQFV T0528 85 :DDGADIAIGTS 2qh8A 86 :GENPDVLVGIA T0528 97 :SAAALADLPV 2qh8A 97 :TPTAQALVSA T0528 110 :NKKILIVEPAVADQITG 2qh8A 108 :KTIPIVFTAVTDPVGAK T0528 127 :EKWNRYIFRTGRNSS 2qh8A 130 :EQPGKNVTGLSDLSP T0528 144 :AISNAVAIGKQ 2qh8A 145 :VEQHVELIKEI T0528 155 :GV 2qh8A 158 :NV T0528 157 :TIATLAQ 2qh8A 161 :SIGVVYN T0528 164 :DYAFGRDGVAAFKEALAKTGATLATEEYVPTTT 2qh8A 169 :GEANAVSLMELLKLSAAKHGIKLVEATALKSAD T0528 202 :VGQRLFDALK 2qh8A 202 :VQSATQAIAE T0528 213 :KP 2qh8A 212 :KS T0528 216 :KKIIWVIW 2qh8A 214 :DVIYALID T0528 224 :AGGGDPLTK 2qh8A 225 :ASAIEGMIV T0528 233 :LQDMDPKRYGIE 2qh8A 235 :ANQAKTPVFGAA T0528 249 :GN 2qh8A 247 :TS T0528 254 :ALA 2qh8A 249 :YVE T0528 262 :PGMEGATYYYY 2qh8A 252 :RGAIASLGFDY T0528 277 :NPINEWLVTEHQKRFN 2qh8A 263 :YQIGVQTADYVAAILE T0528 293 :APPDFF 2qh8A 285 :LDVQVA T0528 310 :VTAVQKAKSTDTEKLIA 2qh8A 299 :KTAAEQLGITIPEAVLA Number of specific fragments extracted= 23 number of extra gaps= 1 total=1224 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 2qh8A/T0528-2qh8A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0528 read from 2qh8A/T0528-2qh8A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2qh8A read from 2qh8A/T0528-2qh8A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2qh8A in template set Warning: unaligning (T0528)D17 because first residue in template chain is (2qh8A)K26 Warning: unaligning (T0528)T28 because of BadResidue code BAD_PEPTIDE in next template residue (2qh8A)H38 Warning: unaligning (T0528)G29 because of BadResidue code BAD_PEPTIDE at template residue (2qh8A)H38 T0528 18 :DLKIALIYGK 2qh8A 27 :TAKVAVSQIV T0528 30 :P 2qh8A 39 :P T0528 37 :QTETGLMMGLEYATKGTM 2qh8A 40 :ALDATRQGLLDGLKAKGY T0528 56 :LDGRKIVVITKDDQSKPDLSKAALAEAYQD 2qh8A 58 :EEGKNLEFDYKTAQGNPAIAVQIARQFVGE T0528 87 :GADIAIGT 2qh8A 88 :NPDVLVGI T0528 96 :SSAAALADLPV 2qh8A 96 :ATPTAQALVSA T0528 110 :NKKILIVEPAVADQIT 2qh8A 108 :KTIPIVFTAVTDPVGA T0528 126 :GEKWNRYIFRTGRNSS 2qh8A 129 :LEQPGKNVTGLSDLSP T0528 144 :AISNAVAIGK 2qh8A 145 :VEQHVELIKE T0528 154 :QGVTIATLAQ 2qh8A 158 :NVKSIGVVYN T0528 164 :DYAFGRDGVAAFKEALAKTGATLATEEY 2qh8A 169 :GEANAVSLMELLKLSAAKHGIKLVEATA T0528 194 :TTTTDFTAVGQRL 2qh8A 197 :LKSADVQSATQAI T0528 210 :L 2qh8A 210 :A T0528 212 :DKPGKKIIWVI 2qh8A 211 :EKSDVIYALID T0528 223 :WAGGGDPLTKLQDMDP 2qh8A 225 :ASAIEGMIVAANQAKT T0528 243 :IEL 2qh8A 242 :VFG T0528 249 :GNILPAL 2qh8A 245 :AATSYVE T0528 262 :PGMEGATYY 2qh8A 252 :RGAIASLGF T0528 273 :DI 2qh8A 261 :DY T0528 277 :NPINEWLVTEHQKRFN 2qh8A 263 :YQIGVQTADYVAAILE T0528 330 :GMEFDTPK 2qh8A 284 :SLDVQVAK T0528 338 :GKM 2qh8A 293 :SDL Number of specific fragments extracted= 22 number of extra gaps= 1 total=1246 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 1jx6A/T0528-1jx6A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1jx6A expands to /projects/compbio/data/pdb/1jx6.pdb.gz 1jx6A:# T0528 read from 1jx6A/T0528-1jx6A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1jx6A read from 1jx6A/T0528-1jx6A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1jx6A to template set # found chain 1jx6A in template set Warning: unaligning (T0528)E332 because last residue in template chain is (1jx6A)D364 T0528 15 :AADDLKIALIYGK 1jx6A 63 :TQRPIKISVVYPG T0528 28 :TG 1jx6A 78 :VS T0528 33 :AYAKQTETGLMMGLE 1jx6A 80 :DYWVRNIASFEKRLY T0528 49 :AT 1jx6A 95 :KL T0528 57 :D 1jx6A 97 :N T0528 58 :GRKIVVITKDDQSKPDLSKAALAEAYQD 1jx6A 99 :NYQLNQVFTRPNADIKQQSLSLMEALKS T0528 87 :GADIAIGTSSSAAALADLPVAEEN 1jx6A 127 :KSDYLIFTLDTTRHRKFVEHVLDS T0528 111 :KKILIVEPAVA 1jx6A 152 :NTKLILQNITT T0528 122 :DQITG 1jx6A 165 :REWDK T0528 130 :NRYIFRTGRNSSQDAISNAVAIGK 1jx6A 170 :HQPFLYVGFDHAEGSRELATEFGK T0528 154 :QG 1jx6A 195 :FP T0528 156 :VTIATL 1jx6A 199 :TYYSVL T0528 162 :AQDYAFGRDGVAAFKEALAKT 1jx6A 206 :FSEGYISDVRGDTFIHQVNRD T0528 183 :GATLATEEYVPTTTTDFTAVGQRLFDA 1jx6A 228 :NFELQSAYYTKATKQSGYDAAKASLAK T0528 213 :KPGKKIIWVIWAGGG 1jx6A 255 :HPDVDFIYACSTDVA T0528 228 :DPLTKLQDMDPKRYGIELSTGG 1jx6A 271 :GAVDALAELGREDIMINGWGGG T0528 252 :LPALAAYKR 1jx6A 293 :SAELDAIQK T0528 262 :PGMEGATYYYY 1jx6A 302 :GDLDITVMRMN T0528 299 :T 1jx6A 313 :D T0528 304 :SAAMAVVTAVQKA 1jx6A 314 :DTGIAMAEAIKWD T0528 317 :KSTDTEKL 1jx6A 345 :KADSPERI T0528 325 :IAAMEGM 1jx6A 356 :KKRAFRY Number of specific fragments extracted= 22 number of extra gaps= 0 total=1268 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 1jx6A/T0528-1jx6A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0528 read from 1jx6A/T0528-1jx6A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1jx6A read from 1jx6A/T0528-1jx6A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1jx6A in template set T0528 15 :AADDLKIALIYGKTGPLEAY 1jx6A 63 :TQRPIKISVVYPGQQVSDYW T0528 36 :KQTETGLMMGLEYA 1jx6A 83 :VRNIASFEKRLYKL T0528 53 :TMTL 1jx6A 97 :NINY T0528 60 :KIVVITKDDQSKPDLSKAALAEAY 1jx6A 101 :QLNQVFTRPNADIKQQSLSLMEAL T0528 85 :DDGADIAIGTSSSAAALADLP 1jx6A 125 :KSKSDYLIFTLDTTRHRKFVE T0528 106 :VAEENKKILIVEPAV 1jx6A 147 :VLDSTNTKLILQNIT T0528 121 :ADQITGE 1jx6A 164 :VREWDKH T0528 131 :RYIFRTGRNSSQDAISNAVAIGKQ 1jx6A 171 :QPFLYVGFDHAEGSRELATEFGKF T0528 155 :GVTIATLAQD 1jx6A 198 :HTYYSVLYFS T0528 165 :YAFGRDGVAAFKEALAKT 1jx6A 209 :GYISDVRGDTFIHQVNRD T0528 183 :GATLATEEYVPTTTTDFTAVGQRLFDA 1jx6A 228 :NFELQSAYYTKATKQSGYDAAKASLAK T0528 213 :KPGKKIIWVIWAGGGDPLTK 1jx6A 255 :HPDVDFIYACSTDVALGAVD T0528 233 :LQDMDP 1jx6A 276 :LAELGR T0528 239 :KRYGIELSTGGNILPALAA 1jx6A 283 :DIMINGWGGGSAELDAIQK T0528 259 :KRLPGMEGATY 1jx6A 302 :GDLDITVMRMN T0528 299 :TAGGFSAAMAVVT 1jx6A 313 :DDTGIAMAEAIKW T0528 327 :AMEGMEFDTP 1jx6A 326 :DLEDKPVPTV T0528 337 :KGKMVFRKE 1jx6A 338 :GDFEIVTKA Number of specific fragments extracted= 18 number of extra gaps= 0 total=1286 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 1jx6A/T0528-1jx6A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0528 read from 1jx6A/T0528-1jx6A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1jx6A read from 1jx6A/T0528-1jx6A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1jx6A in template set T0528 15 :AADDLKIALIY 1jx6A 63 :TQRPIKISVVY T0528 26 :G 1jx6A 75 :G T0528 27 :KTGP 1jx6A 77 :QVSD T0528 34 :YAKQTETGLMMGLEYA 1jx6A 81 :YWVRNIASFEKRLYKL T0528 53 :TM 1jx6A 97 :NI T0528 60 :KI 1jx6A 99 :NY T0528 62 :VVITKDDQSKPDLSKAALAEAYQD 1jx6A 103 :NQVFTRPNADIKQQSLSLMEALKS T0528 87 :GADIAIGTSSSAAALADLPVAEENKKILIVE 1jx6A 127 :KSDYLIFTLDTTRHRKFVEHVLDSTNTKLIL T0528 118 :PAVADQITGEK 1jx6A 161 :TTPVREWDKHQ T0528 132 :YIFRTGRNSSQDAISNAVAIGK 1jx6A 172 :PFLYVGFDHAEGSRELATEFGK T0528 154 :QGVTIATLAQD 1jx6A 197 :KHTYYSVLYFS T0528 165 :YAFGRDGVAAFKEALAKT 1jx6A 209 :GYISDVRGDTFIHQVNRD T0528 183 :GATLATEEYVPTTTTDFTAVGQRL 1jx6A 228 :NFELQSAYYTKATKQSGYDAAKAS T0528 210 :LKDKPGKKIIWVIWAGGGD 1jx6A 252 :LAKHPDVDFIYACSTDVAL T0528 229 :PLTKLQDMDP 1jx6A 272 :AVDALAELGR T0528 239 :KR 1jx6A 283 :DI T0528 242 :GIE 1jx6A 285 :MIN T0528 246 :STGGNILPALAAYKRL 1jx6A 288 :GWGGGSAELDAIQKGD T0528 264 :MEGATYYY 1jx6A 304 :LDITVMRM T0528 298 :FTAGGFSAAMAVVT 1jx6A 312 :NDDTGIAMAEAIKW T0528 327 :AMEGMEFDTPK 1jx6A 326 :DLEDKPVPTVY T0528 338 :GKMVFRKEDH 1jx6A 338 :GDFEIVTKAD Number of specific fragments extracted= 22 number of extra gaps= 0 total=1308 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 3lftA/T0528-3lftA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 3lftA expands to /projects/compbio/data/pdb/3lft.pdb.gz 3lftA:Skipped atom 155, because occupancy 0.500 <= existing 0.500 in 3lftA Skipped atom 159, because occupancy 0.500 <= existing 0.500 in 3lftA Skipped atom 161, because occupancy 0.500 <= existing 0.500 in 3lftA Skipped atom 163, because occupancy 0.500 <= existing 0.500 in 3lftA Skipped atom 165, because occupancy 0.500 <= existing 0.500 in 3lftA Skipped atom 167, because occupancy 0.500 <= existing 0.500 in 3lftA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 338, because occupancy 0.500 <= existing 0.500 in 3lftA Skipped atom 342, because occupancy 0.500 <= existing 0.500 in 3lftA Skipped atom 344, because occupancy 0.500 <= existing 0.500 in 3lftA Skipped atom 346, because occupancy 0.500 <= existing 0.500 in 3lftA Skipped atom 348, because occupancy 0.500 <= existing 0.500 in 3lftA Skipped atom 350, because occupancy 0.500 <= existing 0.500 in 3lftA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 577, because occupancy 0.500 <= existing 0.500 in 3lftA Skipped atom 581, because occupancy 0.500 <= existing 0.500 in 3lftA Skipped atom 583, because occupancy 0.500 <= existing 0.500 in 3lftA Skipped atom 598, because occupancy 0.500 <= existing 0.500 in 3lftA Skipped atom 602, because occupancy 0.500 <= existing 0.500 in 3lftA Skipped atom 604, because occupancy 0.500 <= existing 0.500 in 3lftA Skipped atom 606, because occupancy 0.500 <= existing 0.500 in 3lftA Skipped atom 608, because occupancy 0.500 <= existing 0.500 in 3lftA Skipped atom 610, because occupancy 0.500 <= existing 0.500 in 3lftA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 879, because occupancy 0.500 <= existing 0.500 in 3lftA Skipped atom 883, because occupancy 0.500 <= existing 0.500 in 3lftA Skipped atom 885, because occupancy 0.500 <= existing 0.500 in 3lftA Skipped atom 887, because occupancy 0.500 <= existing 0.500 in 3lftA Skipped atom 889, because occupancy 0.500 <= existing 0.500 in 3lftA Skipped atom 891, because occupancy 0.500 <= existing 0.500 in 3lftA Skipped atom 995, because occupancy 0.500 <= existing 0.500 in 3lftA Skipped atom 999, because occupancy 0.500 <= existing 0.500 in 3lftA Skipped atom 1001, because occupancy 0.500 <= existing 0.500 in 3lftA Skipped atom 1003, because occupancy 0.500 <= existing 0.500 in 3lftA Skipped atom 1277, because occupancy 0.500 <= existing 0.500 in 3lftA Skipped atom 1281, because occupancy 0.500 <= existing 0.500 in 3lftA Skipped atom 1283, because occupancy 0.500 <= existing 0.500 in 3lftA Skipped atom 1285, because occupancy 0.500 <= existing 0.500 in 3lftA Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 1352, because occupancy 0.500 <= existing 0.500 in 3lftA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 1356, because occupancy 0.500 <= existing 0.500 in 3lftA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1358, because occupancy 0.500 <= existing 0.500 in 3lftA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1360, because occupancy 0.500 <= existing 0.500 in 3lftA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1362, because occupancy 0.500 <= existing 0.500 in 3lftA Skipped atom 1372, because occupancy 0.500 <= existing 0.500 in 3lftA Skipped atom 1376, because occupancy 0.500 <= existing 0.500 in 3lftA Skipped atom 1378, because occupancy 0.500 <= existing 0.500 in 3lftA Skipped atom 1539, because occupancy 0.500 <= existing 0.500 in 3lftA Skipped atom 1543, because occupancy 0.500 <= existing 0.500 in 3lftA Skipped atom 1545, because occupancy 0.500 <= existing 0.500 in 3lftA Skipped atom 1577, because occupancy 0.500 <= existing 0.500 in 3lftA Skipped atom 1581, because occupancy 0.500 <= existing 0.500 in 3lftA Skipped atom 1583, because occupancy 0.500 <= existing 0.500 in 3lftA Skipped atom 1595, because occupancy 0.500 <= existing 0.500 in 3lftA Skipped atom 1599, because occupancy 0.500 <= existing 0.500 in 3lftA Skipped atom 1601, because occupancy 0.500 <= existing 0.500 in 3lftA Skipped atom 1603, because occupancy 0.500 <= existing 0.500 in 3lftA Skipped atom 1605, because occupancy 0.500 <= existing 0.500 in 3lftA Skipped atom 1607, because occupancy 0.500 <= existing 0.500 in 3lftA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 1739, because occupancy 0.500 <= existing 0.500 in 3lftA Skipped atom 1743, because occupancy 0.500 <= existing 0.500 in 3lftA Skipped atom 1745, because occupancy 0.500 <= existing 0.500 in 3lftA Skipped atom 1747, because occupancy 0.500 <= existing 0.500 in 3lftA Skipped atom 1749, because occupancy 0.500 <= existing 0.500 in 3lftA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0528 read from 3lftA/T0528-3lftA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3lftA read from 3lftA/T0528-3lftA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3lftA to template set # found chain 3lftA in template set Warning: unaligning (T0528)D17 because first residue in template chain is (3lftA)S49 Warning: unaligning (T0528)T28 because of BadResidue code BAD_PEPTIDE in next template residue (3lftA)H61 Warning: unaligning (T0528)G29 because of BadResidue code BAD_PEPTIDE at template residue (3lftA)H61 T0528 18 :DLKIALIYGK 3lftA 50 :NAKIGVLQFV T0528 33 :AYAKQTETGLMMGLE 3lftA 62 :PSLDLIYKGIQDGLA T0528 49 :A 3lftA 77 :E T0528 57 :DGRK 3lftA 78 :EGYK T0528 61 :IVVITKDDQSKPDLSKAALAEAYQD 3lftA 85 :VKIDFMNSEGDQSKVATMSKQLVAN T0528 87 :GADIAIG 3lftA 110 :GNDLVVG T0528 95 :SSSAAALADLPV 3lftA 117 :IATPAAQGLASA T0528 109 :ENKKILIVEPAVAD 3lftA 129 :TKDLPVIMAAITDP T0528 123 :QITGEK 3lftA 146 :NLVKDL T0528 129 :WNRYIFRTGRNS 3lftA 155 :GGNVTGVSDHNP T0528 144 :AISNAVAIGK 3lftA 167 :AQQQVELIKA T0528 155 :G 3lftA 180 :N T0528 156 :VTIATLAQ 3lftA 182 :KTIGALYS T0528 164 :DYAFGRDGVAAFKEALAKTGATLATEEY 3lftA 191 :SEDNSKTQVEEFKAYAEKAGLTVETFAV T0528 194 :TTTTDFTAVGQRL 3lftA 219 :PSTNEIASTVTVM T0528 213 :KPGKKIIWVIWAGGG 3lftA 232 :TSKVDAIWVPIDNTI T0528 228 :DPLTKLQDMDPK 3lftA 248 :SGFPTVVSSNQS T0528 240 :RYGIELSTGG 3lftA 261 :KKPIYPSATA T0528 257 :AYK 3lftA 271 :MVE T0528 262 :PGMEGATYYY 3lftA 274 :VGGLASVVID T0528 298 :FTAGGFSAAMAVVTAVQ 3lftA 284 :QHDLGVATGKMIVQVLK T0528 374 :ELKIEEMNI 3lftA 301 :GAKPADTPV Number of specific fragments extracted= 22 number of extra gaps= 1 total=1330 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 3lftA/T0528-3lftA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0528 read from 3lftA/T0528-3lftA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3lftA read from 3lftA/T0528-3lftA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3lftA in template set Warning: unaligning (T0528)D17 because first residue in template chain is (3lftA)S49 Warning: unaligning (T0528)T28 because of BadResidue code BAD_PEPTIDE in next template residue (3lftA)H61 Warning: unaligning (T0528)G29 because of BadResidue code BAD_PEPTIDE at template residue (3lftA)H61 T0528 18 :DLKIALIYGK 3lftA 50 :NAKIGVLQFV T0528 30 :PL 3lftA 62 :PS T0528 38 :TETGLMMGLEYATKGTMTL 3lftA 64 :LDLIYKGIQDGLAEEGYKD T0528 58 :G 3lftA 83 :D T0528 60 :KIVVITKDDQSKPDLSKAALAEAY 3lftA 84 :QVKIDFMNSEGDQSKVATMSKQLV T0528 85 :DDGADIAIGTSSSAAALA 3lftA 108 :ANGNDLVVGIATPAAQGL T0528 104 :LPV 3lftA 126 :ASA T0528 110 :NK 3lftA 129 :TK T0528 112 :KILIVEPAVADQIT 3lftA 133 :PVIMAAITDPIGAN T0528 126 :GEKWNRYIFRTGRNSSQDAISNAVAIG 3lftA 152 :KKPGGNVTGVSDHNPAQQQVELIKALT T0528 155 :GV 3lftA 180 :NV T0528 157 :TIATLAQ 3lftA 183 :TIGALYS T0528 164 :DYAFGRDGVAAFKEALAKTGATLATEEYVPTTT 3lftA 191 :SEDNSKTQVEEFKAYAEKAGLTVETFAVPSTNE T0528 203 :GQRLFDALKDKP 3lftA 224 :IASTVTVMTSKV T0528 216 :KKIIWVIW 3lftA 236 :DAIWVPID T0528 225 :GGGDPLTK 3lftA 248 :SGFPTVVS T0528 233 :LQDMDPKRYGIE 3lftA 257 :NQSSKKPIYPSA T0528 249 :GN 3lftA 269 :TA T0528 254 :ALA 3lftA 271 :MVE T0528 262 :PGMEGATYYYY 3lftA 274 :VGGLASVVIDQ T0528 277 :NPINEWLVTEHQKRFN 3lftA 285 :HDLGVATGKMIVQVLK T0528 293 :APPDFF 3lftA 307 :TPVNVF T0528 310 :VTAVQKAKSTDTEKLIA 3lftA 321 :KKIAQELGITIPESVLK Number of specific fragments extracted= 23 number of extra gaps= 1 total=1353 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 3lftA/T0528-3lftA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0528 read from 3lftA/T0528-3lftA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3lftA read from 3lftA/T0528-3lftA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3lftA in template set Warning: unaligning (T0528)D17 because first residue in template chain is (3lftA)S49 Warning: unaligning (T0528)T28 because of BadResidue code BAD_PEPTIDE in next template residue (3lftA)H61 Warning: unaligning (T0528)A35 because of BadResidue code BAD_PEPTIDE at template residue (3lftA)H61 T0528 18 :DLKIALIYGK 3lftA 50 :NAKIGVLQFV T0528 36 :KQTETGLMMGLEYATKGTM 3lftA 62 :PSLDLIYKGIQDGLAEEGY T0528 56 :LDG 3lftA 81 :KDD T0528 61 :IVVITKDDQSKPDLSKAALAEAYQD 3lftA 85 :VKIDFMNSEGDQSKVATMSKQLVAN T0528 87 :GADIAIGT 3lftA 110 :GNDLVVGI T0528 96 :SSAAALADLPV 3lftA 118 :ATPAAQGLASA T0528 110 :NK 3lftA 129 :TK T0528 112 :KILIVEPAVADQIT 3lftA 133 :PVIMAAITDPIGAN T0528 126 :GEKWNRYIFRTGRNSSQDAISNAVAIGKQGVTIATLAQ 3lftA 152 :KKPGGNVTGVSDHNPAQQQVELIKALTPNVKTIGALYS T0528 164 :DYAFGRDGVAAFKEALAKTGATLATEEYVP 3lftA 191 :SEDNSKTQVEEFKAYAEKAGLTVETFAVPS T0528 196 :TTDFTAVGQRL 3lftA 221 :TNEIASTVTVM T0528 211 :KDKPGKKI 3lftA 232 :TSKVDAIW T0528 220 :WVIWAGGGDPLTKLQDMDPKRYGIELSTG 3lftA 240 :VPIDNTIASGFPTVVSSNQSSKKPIYPSA T0528 251 :ILPAL 3lftA 269 :TAMVE T0528 262 :PGMEGATYY 3lftA 274 :VGGLASVVI T0528 273 :DI 3lftA 283 :DQ T0528 277 :NPINEWLVTEHQKRFN 3lftA 285 :HDLGVATGKMIVQVLK T0528 293 :APPD 3lftA 302 :AKPA T0528 335 :T 3lftA 306 :D Number of specific fragments extracted= 19 number of extra gaps= 1 total=1372 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 3lkvA/T0528-3lkvA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 3lkvA expands to /projects/compbio/data/pdb/3lkv.pdb.gz 3lkvA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0528 read from 3lkvA/T0528-3lkvA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3lkvA read from 3lkvA/T0528-3lkvA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3lkvA to template set # found chain 3lkvA in template set Warning: unaligning (T0528)D17 because first residue in template chain is (3lkvA)K26 Warning: unaligning (T0528)T28 because of BadResidue code BAD_PEPTIDE in next template residue (3lkvA)H38 Warning: unaligning (T0528)G29 because of BadResidue code BAD_PEPTIDE at template residue (3lkvA)H38 T0528 18 :DLKIALIYGK 3lkvA 27 :TAKVAVSQIV T0528 33 :AYAKQTETGLMMGLE 3lkvA 39 :PALDATRQGLLDGLK T0528 49 :A 3lkvA 54 :A T0528 53 :TMTLDGRKIVVITKDDQSKPDLSKAALAEAYQD 3lkvA 55 :KGYEEGKNLEFDYKTAQGNPAIAVQIARQFVGE T0528 87 :GADIAIG 3lkvA 88 :NPDVLVG T0528 95 :SSSAAALADLPV 3lkvA 95 :IATPTAQALVSA T0528 109 :ENKKILIVEPAVAD 3lkvA 107 :TKTIPIVFTAVTDP T0528 123 :QI 3lkvA 124 :KL T0528 125 :TGEKWNRYIFRTGR 3lkvA 128 :QLEQPGKNVTGLSD T0528 141 :SQDAISNAVAIGK 3lkvA 142 :LSPVEQHVELIKE T0528 154 :QG 3lkvA 157 :PN T0528 156 :VTIATLAQ 3lkvA 160 :KSIGVVYN T0528 164 :DYAFGRDGVAAFKEALAKTGATLATEEY 3lkvA 169 :GEANAVSLMELLKLSAAKHGIKLVEATA T0528 194 :TTTTDFTAVGQRLFD 3lkvA 197 :LKSADVQSATQAIAE T0528 215 :GKKIIWVIWAGGG 3lkvA 212 :KSDVIYALIDNTV T0528 228 :DPLTKLQDMDPK 3lkvA 226 :SAIEGMIVAANQ T0528 240 :RYGIELST 3lkvA 239 :KTPVFGAA T0528 252 :LPALA 3lkvA 247 :TSYVE T0528 262 :PGMEGATYYY 3lkvA 252 :RGAIASLGFD T0528 298 :FTAGGFSAAMAVVTAVQ 3lkvA 262 :YYQIGVQTADYVAAILE T0528 317 :K 3lkvA 279 :G T0528 329 :EGMEFDTPKG 3lkvA 283 :GSLDVQVAKG T0528 339 :KMV 3lkvA 294 :DLV Number of specific fragments extracted= 23 number of extra gaps= 1 total=1395 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 3lkvA/T0528-3lkvA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0528 read from 3lkvA/T0528-3lkvA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3lkvA read from 3lkvA/T0528-3lkvA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3lkvA in template set Warning: unaligning (T0528)D17 because first residue in template chain is (3lkvA)K26 Warning: unaligning (T0528)T28 because of BadResidue code BAD_PEPTIDE in next template residue (3lkvA)H38 Warning: unaligning (T0528)G29 because of BadResidue code BAD_PEPTIDE at template residue (3lkvA)H38 T0528 18 :DLKIALIYGK 3lkvA 27 :TAKVAVSQIV T0528 30 :PL 3lkvA 39 :PA T0528 38 :TETGLMMGLEYATKGTMTL 3lkvA 41 :LDATRQGLLDGLKAKGYEE T0528 58 :GRKIVVITKDDQSKPDLSKAALAEAY 3lkvA 60 :GKNLEFDYKTAQGNPAIAVQIARQFV T0528 85 :DDGADIAIGTSSS 3lkvA 86 :GENPDVLVGIATP T0528 99 :AALADLPV 3lkvA 99 :TAQALVSA T0528 111 :K 3lkvA 109 :T T0528 112 :KILIVEPAVADQIT 3lkvA 111 :PIVFTAVTDPVGAK T0528 126 :GEKWNRYIFRTGRNSS 3lkvA 129 :LEQPGKNVTGLSDLSP T0528 144 :AISNAVAIGKQ 3lkvA 145 :VEQHVELIKEI T0528 155 :GV 3lkvA 158 :NV T0528 157 :TIATLAQ 3lkvA 161 :SIGVVYN T0528 164 :DYAFGRDGVAAFKEALAKTGATLATEEYVPTTT 3lkvA 169 :GEANAVSLMELLKLSAAKHGIKLVEATALKSAD T0528 202 :VGQRLFDALK 3lkvA 202 :VQSATQAIAE T0528 213 :KP 3lkvA 212 :KS T0528 216 :KKIIWVIW 3lkvA 214 :DVIYALID T0528 225 :GGGDPLTK 3lkvA 226 :SAIEGMIV T0528 233 :LQDMDPKRYGIE 3lkvA 235 :ANQAKTPVFGAA T0528 252 :LPALA 3lkvA 247 :TSYVE T0528 262 :PGMEGATYYYY 3lkvA 252 :RGAIASLGFDY T0528 277 :NPINEWLVTEHQKRFN 3lkvA 263 :YQIGVQTADYVAAILE T0528 293 :APPDFF 3lkvA 285 :LDVQVA T0528 310 :VTAVQKAKSTDTEKLIA 3lkvA 299 :KTAAEQLGITIPEAVLA Number of specific fragments extracted= 23 number of extra gaps= 1 total=1418 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 3lkvA/T0528-3lkvA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0528 read from 3lkvA/T0528-3lkvA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3lkvA read from 3lkvA/T0528-3lkvA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3lkvA in template set Warning: unaligning (T0528)D17 because first residue in template chain is (3lkvA)K26 Warning: unaligning (T0528)T28 because of BadResidue code BAD_PEPTIDE in next template residue (3lkvA)H38 Warning: unaligning (T0528)G29 because of BadResidue code BAD_PEPTIDE at template residue (3lkvA)H38 T0528 18 :DLKIALIYGK 3lkvA 27 :TAKVAVSQIV T0528 36 :KQTETGLMMGLEYATKGTM 3lkvA 39 :PALDATRQGLLDGLKAKGY T0528 56 :LDGRKIVVITKDDQSKPDLSKAALAEAYQD 3lkvA 58 :EEGKNLEFDYKTAQGNPAIAVQIARQFVGE T0528 87 :GADIAIGT 3lkvA 88 :NPDVLVGI T0528 96 :SSAAALADLPV 3lkvA 96 :ATPTAQALVSA T0528 110 :NK 3lkvA 107 :TK T0528 112 :KILIVEPAVADQIT 3lkvA 110 :IPIVFTAVTDPVGA T0528 127 :EKWNR 3lkvA 130 :EQPGK T0528 132 :YIFRTGRNSSQDAISNAVAIGKQGVTIATLAQ 3lkvA 136 :VTGLSDLSPVEQHVELIKEILPNVKSIGVVYN T0528 164 :DYAFGRDGVAAFKEALAKTGATLATEEY 3lkvA 169 :GEANAVSLMELLKLSAAKHGIKLVEATA T0528 194 :TTTTDFTAVGQRL 3lkvA 197 :LKSADVQSATQAI T0528 210 :LK 3lkvA 210 :AE T0528 213 :KPGKKIIWVI 3lkvA 212 :KSDVIYALID T0528 225 :GGGDPLTKLQDMDP 3lkvA 227 :AIEGMIVAANQAKT T0528 243 :IEL 3lkvA 242 :VFG T0528 249 :GNILPAL 3lkvA 245 :AATSYVE T0528 262 :PGMEGATYYYY 3lkvA 252 :RGAIASLGFDY T0528 277 :NPINEWLVTEHQKRFN 3lkvA 263 :YQIGVQTADYVAAILE T0528 329 :EGMEFDTPK 3lkvA 283 :GSLDVQVAK T0528 338 :GKMV 3lkvA 293 :SDLV Number of specific fragments extracted= 20 number of extra gaps= 1 total=1438 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 3l49A/T0528-3l49A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 3l49A expands to /projects/compbio/data/pdb/3l49.pdb.gz 3l49A:Skipped atom 105, because occupancy 0.500 <= existing 0.500 in 3l49A Skipped atom 109, because occupancy 0.500 <= existing 0.500 in 3l49A Skipped atom 111, because occupancy 0.500 <= existing 0.500 in 3l49A Skipped atom 113, because occupancy 0.500 <= existing 0.500 in 3l49A Skipped atom 115, because occupancy 0.500 <= existing 0.500 in 3l49A Skipped atom 117, because occupancy 0.500 <= existing 0.500 in 3l49A Skipped atom 119, because occupancy 0.500 <= existing 0.500 in 3l49A Skipped atom 1666, because occupancy 0.500 <= existing 0.500 in 3l49A Skipped atom 1670, because occupancy 0.500 <= existing 0.500 in 3l49A Skipped atom 1672, because occupancy 0.500 <= existing 0.500 in 3l49A Skipped atom 1674, because occupancy 0.500 <= existing 0.500 in 3l49A Skipped atom 1676, because occupancy 0.500 <= existing 0.500 in 3l49A Skipped atom 1678, because occupancy 0.500 <= existing 0.500 in 3l49A Skipped atom 1680, because occupancy 0.500 <= existing 0.500 in 3l49A Skipped atom 1682, because occupancy 0.500 <= existing 0.500 in 3l49A # T0528 read from 3l49A/T0528-3l49A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3l49A read from 3l49A/T0528-3l49A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3l49A to template set # found chain 3l49A in template set Warning: unaligning (T0528)A16 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (3l49A)E30 Warning: unaligning (T0528)D17 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3l49A)E30 Warning: unaligning (T0528)E32 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (3l49A)D44 Warning: unaligning (T0528)A33 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3l49A)D44 Warning: unaligning (T0528)V116 because of BadResidue code BAD_PEPTIDE in next template residue (3l49A)V118 Warning: unaligning (T0528)E117 because of BadResidue code BAD_PEPTIDE at template residue (3l49A)V118 Warning: unaligning (T0528)S246 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (3l49A)D250 Warning: unaligning (T0528)T247 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3l49A)D250 T0528 18 :DLKIALIYGK 3l49A 31 :GKTIGITAIG T0528 30 :PL 3l49A 41 :TD T0528 34 :YAKQTETGLMMGLE 3l49A 45 :WDLKAYQAQIAEIE T0528 49 :A 3l49A 59 :R T0528 57 :DGRKI 3l49A 60 :LGGTA T0528 64 :ITKDDQSKPDLSKAALAEAYQD 3l49A 65 :IALDAGRNDQTQVSQIQTLIAQ T0528 87 :GADIA 3l49A 87 :KPDAI T0528 92 :IGTSSSAAALADLPVAEENKKILI 3l49A 93 :EQLGNLDVLNPWLQKINDAGIPLF T0528 118 :PAVADQI 3l49A 119 :DTATPHA T0528 133 :IFRTGRNSSQDAISNAVAIGK 3l49A 126 :INNTTSNNYSIGAELALQMVA T0528 154 :QG 3l49A 148 :LG T0528 156 :VTIATLAQ 3l49A 152 :GNVLVFNG T0528 164 :DYAFGRDGVAAFKEALAKT 3l49A 162 :SVPVCKIRYDQMKYVLEAF T0528 183 :GATLATEEYVP 3l49A 182 :DVKIIEPELRD T0528 194 :TTTTDFTAVGQRLFDALKDKPGKKIIWVIWAGGG 3l49A 196 :NTIQSAYSNVTDMLTKYPNEGDVGAIWACWDVPM T0528 228 :DPLTKLQDMDPKRYGIEL 3l49A 231 :GATQALQAAGRTDIRTYG T0528 248 :GG 3l49A 251 :GS T0528 252 :LPALAAYKRLPGMEGATYYYY 3l49A 253 :PEFVEMVADPESPAGAVAAQQ T0528 298 :FTAGGFSAAMAVVT 3l49A 274 :PSEIGKLAVQNVAR T0528 327 :AMEGMEFD 3l49A 288 :HLAGQEVK T0528 335 :TPKGKMVF 3l49A 299 :FAPAVLIT Number of specific fragments extracted= 21 number of extra gaps= 4 total=1459 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 3l49A/T0528-3l49A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0528 read from 3l49A/T0528-3l49A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3l49A read from 3l49A/T0528-3l49A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3l49A in template set Warning: unaligning (T0528)D17 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3l49A)E30 Warning: unaligning (T0528)A35 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (3l49A)D44 Warning: unaligning (T0528)K36 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3l49A)D44 Warning: unaligning (T0528)V116 because of BadResidue code BAD_PEPTIDE in next template residue (3l49A)V118 Warning: unaligning (T0528)E117 because of BadResidue code BAD_PEPTIDE at template residue (3l49A)V118 Warning: unaligning (T0528)L245 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (3l49A)D250 Warning: unaligning (T0528)S246 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3l49A)D250 T0528 18 :DLKIALIYGKTG 3l49A 31 :GKTIGITAIGTD T0528 37 :QTETGLMMGLEYATKGT 3l49A 45 :WDLKAYQAQIAEIERLG T0528 61 :IVVITKDDQSKPDLSKAALAEAYQDDGADIAIGTSSSAAALADLPVAEENKKILI 3l49A 62 :GTAIALDAGRNDQTQVSQIQTLIAQKPDAIIEQLGNLDVLNPWLQKINDAGIPLF T0528 118 :PAVAD 3l49A 119 :DTATP T0528 131 :RYIFRTGRNSSQDAISNAVAIGKQ 3l49A 124 :HAINNTTSNNYSIGAELALQMVAD T0528 155 :GV 3l49A 150 :GK T0528 157 :TIATLAQD 3l49A 153 :NVLVFNGF T0528 165 :YAFGRDGVAAFKEALAKT 3l49A 163 :VPVCKIRYDQMKYVLEAF T0528 183 :GATLATEEYVPTTTTDFTAVGQRLFDAL 3l49A 182 :DVKIIEPELRDVIPNTIQSAYSNVTDML T0528 211 :KDKP 3l49A 215 :EGDV T0528 216 :KKIIW 3l49A 219 :GAIWA T0528 224 :AGGGDPLTK 3l49A 226 :DVPMIGATQ T0528 233 :LQDMDP 3l49A 236 :LQAAGR T0528 239 :KRYGIE 3l49A 243 :DIRTYG T0528 247 :TGGNILPALAA 3l49A 251 :GSPEFVEMVAD T0528 262 :PGMEGATYYYYD 3l49A 262 :PESPAGAVAAQQ T0528 298 :FTAGGFSAAMAVVT 3l49A 274 :PSEIGKLAVQNVAR T0528 327 :AMEGMEFDTP 3l49A 288 :HLAGQEVKPF Number of specific fragments extracted= 18 number of extra gaps= 4 total=1477 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 3l49A/T0528-3l49A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0528 read from 3l49A/T0528-3l49A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3l49A read from 3l49A/T0528-3l49A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3l49A in template set Warning: unaligning (T0528)D17 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3l49A)E30 Warning: unaligning (T0528)P30 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (3l49A)D44 Warning: unaligning (T0528)K36 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3l49A)D44 Warning: unaligning (T0528)V116 because of BadResidue code BAD_PEPTIDE in next template residue (3l49A)V118 Warning: unaligning (T0528)E117 because of BadResidue code BAD_PEPTIDE at template residue (3l49A)V118 Warning: unaligning (T0528)L245 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (3l49A)D250 Warning: unaligning (T0528)S246 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3l49A)D250 Warning: unaligning (T0528)E345 because last residue in template chain is (3l49A)N309 T0528 18 :DLKIALIYGKTG 3l49A 31 :GKTIGITAIGTD T0528 37 :QTETGLMMGLEYATKGTM 3l49A 45 :WDLKAYQAQIAEIERLGG T0528 62 :VVITKDDQSKPDLSKAALAEAYQD 3l49A 63 :TAIALDAGRNDQTQVSQIQTLIAQ T0528 87 :GAD 3l49A 87 :KPD T0528 90 :IAIGTSSSAAALADLPVAEENKKILI 3l49A 91 :IIEQLGNLDVLNPWLQKINDAGIPLF T0528 118 :PAVAD 3l49A 119 :DTATP T0528 131 :RYIFRTGRNSSQDAISNAVAIGK 3l49A 124 :HAINNTTSNNYSIGAELALQMVA T0528 154 :QGVTIATLAQ 3l49A 150 :GKGNVLVFNG T0528 164 :DYAFGRDGVAAFKEALAKT 3l49A 162 :SVPVCKIRYDQMKYVLEAF T0528 183 :GATLATEEYVPTTTTDFTAVGQRLFDALKD 3l49A 182 :DVKIIEPELRDVIPNTIQSAYSNVTDMLTK T0528 213 :KPGKKIIWVIWAGGGD 3l49A 215 :EGDVGAIWACWDVPMI T0528 229 :PLTKLQDMDP 3l49A 232 :ATQALQAAGR T0528 239 :KRYGIE 3l49A 243 :DIRTYG T0528 247 :T 3l49A 251 :G T0528 251 :ILPALAAYKRLPGMEGATYY 3l49A 252 :SPEFVEMVADPESPAGAVAA T0528 272 :YD 3l49A 272 :QQ T0528 298 :FTAGGFSAAMAVVT 3l49A 274 :PSEIGKLAVQNVAR T0528 327 :AMEGMEFDT 3l49A 288 :HLAGQEVKP T0528 336 :PKGKMVFRK 3l49A 300 :APAVLITKE Number of specific fragments extracted= 19 number of extra gaps= 4 total=1496 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 2rjoA/T0528-2rjoA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2rjoA expands to /projects/compbio/data/pdb/2rjo.pdb.gz 2rjoA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0528 read from 2rjoA/T0528-2rjoA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2rjoA read from 2rjoA/T0528-2rjoA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2rjoA to template set # found chain 2rjoA in template set Warning: unaligning (T0528)A16 because first residue in template chain is (2rjoA)L38 T0528 17 :DDLKIALIYGK 2rjoA 39 :GQTTLACSFRS T0528 30 :PLEAYAKQTETGLMMGLE 2rjoA 50 :LTNPYYTAFNKGAQSFAK T0528 49 :AT 2rjoA 68 :SV T0528 58 :GRKI 2rjoA 70 :GLPY T0528 64 :ITKDDQSKPDLSKAALAEAYQDDG 2rjoA 74 :VPLTTEGSSEKGIADIRALLQKTG T0528 88 :ADIAIGTSSSAAALADLPVAEENKKILIVEPAVAD 2rjoA 100 :LVLNVDPNDSADARVIVEACSKAGAYVTTIWNKPK T0528 123 :QITGEK 2rjoA 137 :HPWDYN T0528 130 :NRYIFRTGRNSSQDAISNAVAIGK 2rjoA 143 :PNYVAHLSYDGVAYGEETATQLFK T0528 154 :QG 2rjoA 168 :MG T0528 156 :VTIATLAQ 2rjoA 172 :GGVVALGG T0528 164 :DYAFGRDGVAAFKEALAKT 2rjoA 182 :SNVPAIERKAGLDAALKKF T0528 183 :GATLATEEYVPTTTTDFTAVGQRLFDALKD 2rjoA 202 :GIQLLDFQVADWNSQKAFPIMQAWMTRFNS T0528 215 :GKKIIWVIWAGGG 2rjoA 232 :KIKGVWAANDDMA T0528 228 :DPLTKLQDMDPK 2rjoA 246 :GAIEALRAEGLA T0528 240 :RYGIELSTGG 2rjoA 259 :QIPVTGMDGT T0528 252 :LPALAAYK 2rjoA 269 :QPGLVAIK T0528 262 :PGMEGATYYYY 2rjoA 277 :SGELVASVDWD T0528 298 :FTAGGFSAAMAVVTAVQ 2rjoA 288 :PFWLGGIGLSMGLQAKE T0528 317 :KSTD 2rjoA 305 :KKID T0528 321 :TEKLIAAMEGMEFDTP 2rjoA 331 :VQDVIARAASPKAEWN Number of specific fragments extracted= 20 number of extra gaps= 0 total=1516 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 2rjoA/T0528-2rjoA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0528 read from 2rjoA/T0528-2rjoA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2rjoA read from 2rjoA/T0528-2rjoA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2rjoA in template set T0528 17 :DDLKIALIYG 2rjoA 39 :GQTTLACSFR T0528 27 :KTGPLEA 2rjoA 50 :LTNPYYT T0528 37 :QTETGLMMGLEYA 2rjoA 57 :AFNKGAQSFAKSV T0528 53 :TMT 2rjoA 70 :GLP T0528 63 :VITKDDQSKPDLSKAALAEAYQ 2rjoA 73 :YVPLTTEGSSEKGIADIRALLQ T0528 85 :DDGADIAIGTSSSAAALADLPVAEENKKILIVEPAVADQITGEKWNR 2rjoA 97 :GGNLVLNVDPNDSADARVIVEACSKAGAYVTTIWNKPKDLHPWDYNP T0528 132 :YIFRTGRNSSQDAISNAVAIGKQ 2rjoA 145 :YVAHLSYDGVAYGEETATQLFKS T0528 155 :GV 2rjoA 170 :GK T0528 157 :TIATLAQ 2rjoA 173 :GVVALGG T0528 164 :DYAFGRDGVAAFKEALAK 2rjoA 182 :SNVPAIERKAGLDAALKK T0528 182 :TGATLATEEYVPTTTTDFTAVGQRLFDALKDKP 2rjoA 201 :PGIQLLDFQVADWNSQKAFPIMQAWMTRFNSKI T0528 216 :KKIIWVI 2rjoA 234 :KGVWAAN T0528 227 :GDPLTK 2rjoA 244 :ALGAIE T0528 233 :LQDMDP 2rjoA 251 :LRAEGL T0528 239 :KRYGIELSTGGNILPALAA 2rjoA 259 :QIPVTGMDGTQPGLVAIKS T0528 259 :KRLPGMEGA 2rjoA 278 :GELVASVDW T0528 297 :FFTAGGFSAAMAVVTAV 2rjoA 287 :DPFWLGGIGLSMGLQAK Number of specific fragments extracted= 17 number of extra gaps= 0 total=1533 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 2rjoA/T0528-2rjoA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0528 read from 2rjoA/T0528-2rjoA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2rjoA read from 2rjoA/T0528-2rjoA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2rjoA in template set Warning: unaligning (T0528)A16 because first residue in template chain is (2rjoA)L38 T0528 17 :DDLKIALIYGK 2rjoA 39 :GQTTLACSFRS T0528 32 :EAYAKQTETGLMMGLEYA 2rjoA 52 :NPYYTAFNKGAQSFAKSV T0528 53 :TM 2rjoA 70 :GL T0528 62 :VVITKDDQSKPDLSKAALAEAYQD 2rjoA 72 :PYVPLTTEGSSEKGIADIRALLQK T0528 86 :DGADIAIGTSSSAAALADLPVAEENKKILIVEPAVAD 2rjoA 98 :GNLVLNVDPNDSADARVIVEACSKAGAYVTTIWNKPK T0528 127 :EK 2rjoA 135 :DL T0528 129 :WNRYIFRTGRNSSQDAISNAVAIGK 2rjoA 142 :NPNYVAHLSYDGVAYGEETATQLFK T0528 154 :QGVTIATLAQ 2rjoA 170 :GKGGVVALGG T0528 164 :DYAFGRDGVAAFKEALAKT 2rjoA 182 :SNVPAIERKAGLDAALKKF T0528 183 :GATLATEEYVPTTTTDFTAVGQRLFDALKDKPG 2rjoA 202 :GIQLLDFQVADWNSQKAFPIMQAWMTRFNSKIK T0528 218 :IIWVIWAGGGD 2rjoA 235 :GVWAANDDMAL T0528 229 :PLTKLQDMDPKRYGIELSTGGNILPALAAYKRL 2rjoA 247 :AIEALRAEGLAGQIPVTGMDGTQPGLVAIKSGE T0528 264 :MEGATYY 2rjoA 280 :LVASVDW T0528 297 :FFTAGGFSAAMAVVTAV 2rjoA 287 :DPFWLGGIGLSMGLQAK Number of specific fragments extracted= 14 number of extra gaps= 0 total=1547 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 1tlfA/T0528-1tlfA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1tlfA expands to /projects/compbio/data/pdb/1tlf.pdb.gz 1tlfA:# T0528 read from 1tlfA/T0528-1tlfA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1tlfA read from 1tlfA/T0528-1tlfA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1tlfA to template set # found chain 1tlfA in template set Warning: unaligning (T0528)D18 because first residue in template chain is (1tlfA)S61 T0528 19 :LKIALIYG 1tlfA 62 :LLIGVATS T0528 30 :PLE 1tlfA 70 :SLA T0528 33 :AYAKQTETGLMMGLE 1tlfA 74 :HAPSQIVAAIKSRAD T0528 49 :A 1tlfA 89 :Q T0528 57 :DGRKIVVI 1tlfA 90 :LGASVVVS T0528 66 :KDDQSKPDLSKAALAEAYQD 1tlfA 98 :MVERSGVEACKAAVHNLLAQ T0528 87 :GADIAIG 1tlfA 118 :RVSGLII T0528 94 :TSSSAAALADLPVAE 1tlfA 127 :PLDDQDAIAVEAACT T0528 111 :KKILIVEPAVAD 1tlfA 142 :NVPALFLDVSDQ T0528 130 :NR 1tlfA 154 :TP T0528 133 :IFRTGRNSSQDAISNAVAIGKQG 1tlfA 156 :INSIIFSHEDGTRLGVEHLVALG T0528 156 :VTIATLAQDYA 1tlfA 180 :QQIALLAGPLS T0528 167 :FGRDGVAAFKEALAKTGATLATEEYVPTTTTDFTAVGQRLFDA 1tlfA 193 :SARLRLAGWHKYLTRNQIQPIAEREGDWSAMSGFQQTMQMLNE T0528 215 :GK 1tlfA 236 :GI T0528 217 :KIIWVIWAGGG 1tlfA 240 :TAMLVANDQMA T0528 228 :DPLTKLQDMDPK 1tlfA 252 :GAMRAITESGLR T0528 240 :RYGIELSTGG 1tlfA 267 :DISVVGYDDT T0528 256 :AAYKR 1tlfA 277 :EDSSC T0528 261 :LPGMEGATY 1tlfA 283 :IPPLTTIKQ T0528 276 :KNPIN 1tlfA 292 :DFRLL T0528 281 :EWLVTEHQKRFN 1tlfA 298 :QTSVDRLLQLSQ T0528 293 :APPDF 1tlfA 311 :QAVKG Number of specific fragments extracted= 22 number of extra gaps= 0 total=1569 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 1tlfA/T0528-1tlfA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0528 read from 1tlfA/T0528-1tlfA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1tlfA read from 1tlfA/T0528-1tlfA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1tlfA in template set T0528 19 :LKIALIYG 1tlfA 62 :LLIGVATS T0528 27 :KTG 1tlfA 71 :LAL T0528 36 :KQTETGLMMGLEYATKGTM 1tlfA 74 :HAPSQIVAAIKSRADQLGA T0528 62 :VVITKD 1tlfA 93 :SVVVSM T0528 68 :DQSKPDLSKAALAEAY 1tlfA 100 :ERSGVEACKAAVHNLL T0528 85 :DDGADIAIGTSSSAAALADLPVAEENKKILIVEPAVAD 1tlfA 116 :AQRVSGLIINYPLDDQDAIAVEAACTNVPALFLDVSDQ T0528 124 :I 1tlfA 154 :T T0528 128 :KW 1tlfA 155 :PI T0528 134 :FRTGRNSSQDAISNAVAIGKQGV 1tlfA 157 :NSIIFSHEDGTRLGVEHLVALGH T0528 157 :TIATLAQ 1tlfA 181 :QIALLAG T0528 164 :DYAFGRDGVAAFKEALAKTGATLATEEYVPTTTTDFTAVGQRLFDA 1tlfA 190 :SSVSARLRLAGWHKYLTRNQIQPIAEREGDWSAMSGFQQTMQMLNE T0528 213 :KPGKKIIWVIWAGGGDPLTK 1tlfA 236 :GIVPTAMLVANDQMALGAMR T0528 233 :LQDMDP 1tlfA 257 :ITESGL T0528 241 :YGIELSTGGNIL 1tlfA 268 :ISVVGYDDTEDS T0528 259 :KRLPGMEGATYYY 1tlfA 280 :SCYIPPLTTIKQD T0528 276 :KNPINEWLVTEHQKRFN 1tlfA 293 :FRLLGQTSVDRLLQLSQ T0528 293 :APPD 1tlfA 312 :AVKG Number of specific fragments extracted= 17 number of extra gaps= 0 total=1586 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 1tlfA/T0528-1tlfA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0528 read from 1tlfA/T0528-1tlfA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1tlfA read from 1tlfA/T0528-1tlfA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1tlfA in template set Warning: unaligning (T0528)D18 because first residue in template chain is (1tlfA)S61 T0528 19 :LKIALIYG 1tlfA 62 :LLIGVATS T0528 27 :KTG 1tlfA 71 :LAL T0528 33 :AYAKQTETGLMMGLEY 1tlfA 74 :HAPSQIVAAIKSRADQ T0528 57 :DGRKIV 1tlfA 90 :LGASVV T0528 64 :ITKDDQSKPDLSKAALAEAYQD 1tlfA 96 :VSMVERSGVEACKAAVHNLLAQ T0528 87 :GADIAIGTSSSAAALADLPVAEENKKILIVEPAVA 1tlfA 118 :RVSGLIINYPLDDQDAIAVEAACTNVPALFLDVSD T0528 126 :GEK 1tlfA 153 :QTP T0528 133 :IFRTGRNSSQDAISNAVAIGK 1tlfA 156 :INSIIFSHEDGTRLGVEHLVA T0528 154 :QGVTIATLAQ 1tlfA 178 :GHQQIALLAG T0528 164 :DYAFGRDGVAAFKEALAKTGATLATEEYVPTTTTDFTAVGQRL 1tlfA 190 :SSVSARLRLAGWHKYLTRNQIQPIAEREGDWSAMSGFQQTMQM T0528 210 :LKDKPGKKIIWVIWAGGGD 1tlfA 233 :LNEGIVPTAMLVANDQMAL T0528 229 :PLTKLQDMDP 1tlfA 253 :AMRAITESGL T0528 239 :KRYGIELSTG 1tlfA 267 :DISVVGYDDT T0528 259 :KRLPGM 1tlfA 277 :EDSSCY T0528 265 :EGATYY 1tlfA 286 :LTTIKQ T0528 273 :DI 1tlfA 292 :DF T0528 277 :NPINEWLVTEHQKRFN 1tlfA 294 :RLLGQTSVDRLLQLSQ T0528 293 :APPD 1tlfA 311 :QAVK Number of specific fragments extracted= 18 number of extra gaps= 0 total=1604 Will force an alignment to be made, even if fragment is small Number of alignments=90 # command:CPU_time= 41.584 sec, elapsed time= 45.541 sec. # command:DEBUG: alignment library has 90 conformations DEBUG: current conformations has 0 conformations # in ExtractAlignmentsContacts extracting from alignment library using radius 8.000 separation >= 9 style evalue NUMB_ALIGNS: 90 # Adding 5082 constraints to all_contacts Done adding distance constraints # command:CPU_time= 41.852 sec, elapsed time= 45.827 sec. # command:Reading probabilities from T0528.t06.CB8-sep9.rdb Reading constraints from ConstraintSet all_contacts maxweight: 87.297 Optimizing... Probability sum: -666.977, CN propb: -666.977 weights: 0.414 constraints: 1056 # command:CPU_time= 963.443 sec, elapsed time= 967.591 sec. # command:Found ConstraintSet # PrintContacts align.constraints Number of constraints in align 1056 # command:Found ConstraintSet # PrintContacts align_bonus.constraints Number of constraints in align.bonus 1056 # command:Found ConstraintSet # PrintContacts rejected.constraints Number of constraints in rejected 4026 # command:Found ConstraintSet # PrintContacts rejected_bonus.constraints Number of constraints in rejected.bonus 4026 # command:Found ConstraintSet # PrintContacts noncontact.constraints Number of constraints in noncontact 0 # command:Found ConstraintSet # PrintContacts noncontact_bonus.constraints Number of constraints in noncontact.bonus 0 # command:CPU_time= 963.529 sec, elapsed time= 968.577 sec. # command: