# 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 T0547 numbered 1 through 611 Created new target T0547 from T0547.a2m # command:CPU_time= 5.898 sec, elapsed time= 7.899 sec. # command:# reading script from file all-templates.under # Reading fragments from alignment file # Attempting to read fragment alignments from file 2o0tA/T0547-2o0tA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2o0tA expands to /projects/compbio/data/pdb/2o0t.pdb.gz 2o0tA:# T0547 read from 2o0tA/T0547-2o0tA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2o0tA read from 2o0tA/T0547-2o0tA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2o0tA to template set # found chain 2o0tA in template set Warning: unaligning (T0547)I15 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (2o0tA)D19 Warning: unaligning (T0547)I16 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (2o0tA)D19 Warning: unaligning (T0547)L85 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2o0tA)A73 Warning: unaligning (T0547)V87 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2o0tA)A73 Warning: unaligning (T0547)I180 because of BadResidue code BAD_PEPTIDE in next template residue (2o0tA)L159 Warning: unaligning (T0547)G181 because of BadResidue code BAD_PEPTIDE at template residue (2o0tA)L159 Warning: unaligning (T0547)L351 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (2o0tA)D336 Warning: unaligning (T0547)K352 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (2o0tA)D336 Warning: unaligning (T0547)N459 because last residue in template chain is (2o0tA)R447 T0547 8 :IWGNENF 2o0tA 11 :VWPRNTT # choosing archetypes in rotamer library T0547 17 :KNGKVCI 2o0tA 20 :EVGVVCI T0547 27 :KKPAIIDIVKE 2o0tA 27 :AGIPLTQLAQE T0547 43 :YKGPLLLRFPHLIQKQIENIYGNF 2o0tA 38 :YGTPLFVIDEDDFRSRCRETAAAF T0547 77 :G 2o0tA 62 :G T0547 78 :GFNAVYP 2o0tA 64 :GANVHYA T0547 88 :NQYPGFVKNLVKLG 2o0tA 74 :FLCSEVARWISEEG T0547 106 :YGLEAGSKAELLLAMAYNNEGAPITVNGF 2o0tA 88 :LCLDVCTGGELAVALHASFPPERITLHGN T0547 135 :KDRELINIGF 2o0tA 118 :KSVSELTAAV T0547 148 :EMGHNIT 2o0tA 128 :KAGVGHI T0547 156 :TIEGLNELEAIIDIAKE 2o0tA 135 :VVDSMTEIERLDAIAGE T0547 174 :FKPKPN 2o0tA 152 :AGIVQD T0547 182 :LRVRLHSAGVGIWAKSGG 2o0tA 160 :VRLTVGVEAHTHEFISTA T0547 200 :INSKFGL 2o0tA 179 :EDQKFGL T0547 207 :TSTELIEAVNLLKENKLLEQFT 2o0tA 188 :ASGAAMAAVRRVFATDHLRLVG T0547 230 :IHFHLGSQITEIHPLKKALNEAGNIYTELR 2o0tA 210 :LHSHIGSQIFDVDGFELAAHRVIGLLRDVV T0547 260 :KMG 2o0tA 241 :EFG T0547 263 :AKNLKAINLGGGLAVEYSQFKNEK 2o0tA 247 :TAQIATVDLGGGLGISYLPSDDPP T0547 291 :TLREYANDVVFILKNIAEQKKDLEPDIFIESGRFVAANHAVLIAPVLELFSQE 2o0tA 271 :PIAELAAKLGTIVSDESTAVGLPTPKLVVEPGRAIAGPGTITLYEVGTVKDVD T0547 344 :YAE 2o0tA 329 :HRR T0547 348 :KLI 2o0tA 332 :YVS T0547 353 :K 2o0tA 337 :G T0547 354 :QNPKLIDELYDLYKSIKPSNALE 2o0tA 339 :MSDNIRTALYGAQYDVRLVSRVS T0547 377 :YLHDSIDHLESILTLFDLGY 2o0tA 366 :VPARLVGKHCESGDIIVRDT T0547 398 :DLQ 2o0tA 386 :WVP T0547 401 :DRSNAEILTHLITKKAILLLGDKQNPADLLAIQDE 2o0tA 390 :DIRPGDLVAVAATGAYCYSLSSRYNMVGRPAVVAV T0547 437 :QERYLVNFSLFQSMPDFWGLEQ 2o0tA 425 :HAGNARLVLRRETVDDLLSLEV Number of specific fragments extracted= 27 number of extra gaps= 3 total=27 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 2o0tA/T0547-2o0tA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0547 read from 2o0tA/T0547-2o0tA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2o0tA read from 2o0tA/T0547-2o0tA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2o0tA in template set Warning: unaligning (T0547)I23 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (2o0tA)D19 Warning: unaligning (T0547)N24 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (2o0tA)D19 Warning: unaligning (T0547)L85 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2o0tA)A73 Warning: unaligning (T0547)V87 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2o0tA)A73 Warning: unaligning (T0547)I180 because of BadResidue code BAD_PEPTIDE in next template residue (2o0tA)L159 Warning: unaligning (T0547)G181 because of BadResidue code BAD_PEPTIDE at template residue (2o0tA)L159 Warning: unaligning (T0547)L351 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (2o0tA)D336 Warning: unaligning (T0547)K352 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (2o0tA)D336 T0547 19 :GKVC 2o0tA 14 :RNTT T0547 25 :YEKKPAIIDIVKELRDDGYKGPLLLRFPHLIQKQIENIYGNF 2o0tA 20 :EVGVVCIAGIPLTQLAQEYGTPLFVIDEDDFRSRCRETAAAF T0547 76 :KGGFNAVYP 2o0tA 62 :GSGANVHYA T0547 88 :NQYPGFVKNLVKLG 2o0tA 74 :FLCSEVARWISEEG T0547 106 :YGLEAGSKAELLLAMAYNNEGAPITVNGFKDRE 2o0tA 88 :LCLDVCTGGELAVALHASFPPERITLHGNNKSV T0547 140 :INIGF 2o0tA 121 :SELTA T0547 146 :AAEMGHNI 2o0tA 126 :AVKAGVGH T0547 155 :LTIEGLNELEAIIDIAKE 2o0tA 134 :IVVDSMTEIERLDAIAGE T0547 174 :FKPKPN 2o0tA 152 :AGIVQD T0547 182 :LRVRLH 2o0tA 160 :VRLTVG T0547 188 :SAGVGIWAKSGGINSKFGLTST 2o0tA 167 :EAHTHEFISTAHEDQKFGLSVA T0547 210 :ELIEAVNLLKENKLL 2o0tA 191 :AAMAAVRRVFATDHL T0547 226 :QFTMIHFHLGSQITEIHPLKKALNEAGNIYTELRKMG 2o0tA 206 :RLVGLHSHIGSQIFDVDGFELAAHRVIGLLRDVVGEF T0547 263 :AKNLKAINLGGGLAVEY 2o0tA 247 :TAQIATVDLGGGLGISY T0547 282 :FKNEKSR 2o0tA 264 :LPSDDPP T0547 291 :TLREYANDVVFILKNIAEQKKDLEPDIFIESGRFVAANHAVLIAPVLELFSQ 2o0tA 271 :PIAELAAKLGTIVSDESTAVGLPTPKLVVEPGRAIAGPGTITLYEVGTVKDV T0547 343 :EYAENKLI 2o0tA 327 :TAHRRYVS T0547 353 :KQNPKLIDE 2o0tA 337 :GGMSDNIRT T0547 362 :LYDLYKSIKPS 2o0tA 347 :LYGAQYDVRLV T0547 373 :NALEYLHDSIDHLESILTLFDLGYVD 2o0tA 359 :RVSDAPPVPARLVGKHCESGDIIVRD T0547 399 :LQDRSNAEILTHLITKKAILLLGDKQNPAD 2o0tA 388 :PDDIRPGDLVAVAATGAYCYSLSSRYNMVG T0547 429 :L 2o0tA 419 :P T0547 536 :AIISINEKGYEVEG 2o0tA 420 :AVVAVHAGNARLVL T0547 582 :KLVNDKQKK 2o0tA 434 :RRETVDDLL Number of specific fragments extracted= 24 number of extra gaps= 3 total=51 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 2o0tA/T0547-2o0tA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0547 read from 2o0tA/T0547-2o0tA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2o0tA read from 2o0tA/T0547-2o0tA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2o0tA in template set Warning: unaligning (T0547)N24 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (2o0tA)D19 Warning: unaligning (T0547)Y25 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (2o0tA)D19 Warning: unaligning (T0547)L85 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2o0tA)A73 Warning: unaligning (T0547)V87 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2o0tA)A73 Warning: unaligning (T0547)I180 because of BadResidue code BAD_PEPTIDE in next template residue (2o0tA)L159 Warning: unaligning (T0547)G181 because of BadResidue code BAD_PEPTIDE at template residue (2o0tA)L159 Warning: unaligning (T0547)I350 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (2o0tA)D336 Warning: unaligning (T0547)L351 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (2o0tA)D336 T0547 22 :CI 2o0tA 16 :TT T0547 26 :EKK 2o0tA 20 :EVG T0547 29 :PAIIDIVKELRDDGYKGPLLLRFPHLIQKQIENIYGNF 2o0tA 24 :VCIAGIPLTQLAQEYGTPLFVIDEDDFRSRCRETAAAF T0547 76 :KGGFNAVYP 2o0tA 62 :GSGANVHYA T0547 88 :NQYPGFVKNLVKLG 2o0tA 74 :FLCSEVARWISEEG T0547 106 :YGLEAGSKAELLLAMAYNNEGAPITVNGFKDRELINIGFIAAEMG 2o0tA 88 :LCLDVCTGGELAVALHASFPPERITLHGNNKSVSELTAAVKAGVG T0547 154 :TLTIEGLNELEAIIDIAKE 2o0tA 133 :HIVVDSMTEIERLDAIAGE T0547 174 :FKPKPN 2o0tA 152 :AGIVQD T0547 182 :LRVRLHSAGVGI 2o0tA 160 :VRLTVGVEAHTH T0547 194 :WAKSGGINSKFGLTS 2o0tA 173 :FISTAHEDQKFGLSV T0547 209 :TELIEAVNLLKENK 2o0tA 190 :GAAMAAVRRVFATD T0547 224 :LEQFTMIHFHLGSQITEIHPLKKALNEAGNIYTELRKMG 2o0tA 204 :HLRLVGLHSHIGSQIFDVDGFELAAHRVIGLLRDVVGEF T0547 263 :AKNLKAINLGGGLAVEYSQFKNEKS 2o0tA 247 :TAQIATVDLGGGLGISYLPSDDPPP T0547 292 :LREYANDVVFILKNIAEQKKDLEPDIFIESGRFVAANHAVLIAPVLELFSQEY 2o0tA 272 :IAELAAKLGTIVSDESTAVGLPTPKLVVEPGRAIAGPGTITLYEVGTVKDVDV T0547 345 :AENKL 2o0tA 330 :RRYVS T0547 352 :KKQNPKLIDELYDLYKSIKPS 2o0tA 337 :GGMSDNIRTALYGAQYDVRLV T0547 373 :NALEYLHDSIDHLESILTLFDLGYVDLQDR 2o0tA 359 :RVSDAPPVPARLVGKHCESGDIIVRDTWVP T0547 403 :SNAEILTHLITKKAILLLGDKQNPADLLAIQDEVQERYLVNFSLFQSMPDFWGL 2o0tA 391 :IRPGDLVAVAATGAYCYSLSSRYNMVGRPAVVAVHAGNARLVLRRETVDDLLSL Number of specific fragments extracted= 18 number of extra gaps= 3 total=69 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 2qghA/T0547-2qghA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2qghA expands to /projects/compbio/data/pdb/2qgh.pdb.gz 2qghA:# T0547 read from 2qghA/T0547-2qghA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2qghA read from 2qghA/T0547-2qghA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2qghA to template set # found chain 2qghA in template set Warning: unaligning (T0547)A30 because first residue in template chain is (2qghA)N3 Warning: unaligning (T0547)S341 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (2qghA)N283 Warning: unaligning (T0547)Y344 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR at template residue (2qghA)N283 Warning: unaligning (T0547)L375 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (2qghA)E318 Warning: unaligning (T0547)Q437 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2qghA)K381 Warning: unaligning (T0547)R439 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2qghA)K381 Warning: unaligning (T0547)P461 because last residue in template chain is (2qghA)L402 T0547 31 :IIDIVKE 2qghA 4 :YEELFQT T0547 43 :YKGPLLLRFPHLIQKQIENIYGNF 2qghA 11 :HKTPFYLYDFDKIKQAFLNYKEAF T0547 75 :YKGGFNAVYPLKVNQYPGFVKNLVKLG 2qghA 35 :KGRKSLICYALKANSNLSILSLLAHLE T0547 106 :YGLEAGSKAELLLAMAYNNEGAPITVNGF 2qghA 62 :SGADCVSIGEIQRALKAGIKPYRIVFSGV T0547 135 :KDRELINIGF 2qghA 92 :KSAFEIEQAL T0547 148 :EMGHNIT 2qghA 102 :KLNILFL T0547 156 :TIEGLNELEAIIDIAKE 2qghA 109 :NVESFMELKTIETIAQS T0547 174 :FKPKPNIGLRVRLHSAGVGIWAKSGG 2qghA 126 :LGIKARISIRINPNIDAKTHPYISTG T0547 200 :INSKFGLTSTELIEAVNLLKENKLLEQFT 2qghA 153 :KENKFGVGEKEALEMFLWAKKSAFLEPVS T0547 230 :IHFHLGSQITEIHPLKKALNEAGNIYTELRKMGA 2qghA 182 :VHFHIGSQLLDLEPIIEASQKVAKIAKSLIALGI T0547 265 :NLKAINLGGGLAVEYSQFKNE 2qghA 216 :DLRFFDVGGGIGVSYENEETI T0547 291 :TLREYANDVVFI 2qghA 237 :KLYDYAQGILNA T0547 310 :KKDLEPDIFIESGRFVAANHAVLIAPVLELF 2qghA 249 :LQGLDLTIICEPGRSIVAESGELITQVLYEK T0547 345 :AE 2qghA 284 :KR T0547 348 :KLILKK 2qghA 286 :FVIVDA T0547 354 :QNPKLIDELYDLYKSIKPSNA 2qghA 293 :MNDFLRPSLYHAKHAIRVITP T0547 377 :YLHDSIDHLESILTLFDLGY 2qghA 320 :SPCDVVGPVCESSDTFLKDA T0547 398 :DLQDRSNAEILTHLITKKAILLLGDKQNPADLLAIQDEV 2qghA 340 :HLPELEPGDKIAIEKVGAYGSSMASQYNSRPKLLELALE T0547 441 :LVNFSLFQSMPDFWGLEQNF 2qghA 382 :IRVIRKREALEDLWRLEEEG Number of specific fragments extracted= 19 number of extra gaps= 0 total=88 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 2qghA/T0547-2qghA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0547 read from 2qghA/T0547-2qghA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2qghA read from 2qghA/T0547-2qghA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2qghA in template set Warning: unaligning (T0547)V35 because first residue in template chain is (2qghA)N3 Warning: unaligning (T0547)S341 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (2qghA)N283 Warning: unaligning (T0547)Y344 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR at template residue (2qghA)N283 Warning: unaligning (T0547)L375 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (2qghA)E318 Warning: unaligning (T0547)L378 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR at template residue (2qghA)E318 Warning: unaligning (T0547)E435 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2qghA)K381 Warning: unaligning (T0547)Q437 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2qghA)K381 T0547 36 :KELRDDGYKGPLLLRFPHLIQKQIENIYGNFN 2qghA 4 :YEELFQTHKTPFYLYDFDKIKQAFLNYKEAFK T0547 76 :KGGFNAVYPLKVNQYPGFVKNLVKLG 2qghA 36 :GRKSLICYALKANSNLSILSLLAHLE T0547 106 :YGLEAGSKAELLLAMAYNNEGAPITVNGFKDRE 2qghA 62 :SGADCVSIGEIQRALKAGIKPYRIVFSGVGKSA T0547 140 :INIGF 2qghA 95 :FEIEQ T0547 146 :AAEMGHNI 2qghA 100 :ALKLNILF T0547 155 :LTIEGLNELEAIIDIAKE 2qghA 108 :LNVESFMELKTIETIAQS T0547 174 :FKPKPNIGLRVRLH 2qghA 126 :LGIKARISIRINPN T0547 188 :SAGVGIWAKSGGINSKFGLTSTELIEAVNLLKENKLL 2qghA 141 :DAKTHPYISTGLKENKFGVGEKEALEMFLWAKKSAFL T0547 226 :QFTMIHFHLGSQITEIHPLKKALNEAGNIYTELRKMGA 2qghA 178 :EPVSVHFHIGSQLLDLEPIIEASQKVAKIAKSLIALGI T0547 265 :NLKAINLGGGLAVEYS 2qghA 216 :DLRFFDVGGGIGVSYE T0547 284 :NEKSR 2qghA 232 :NEETI T0547 291 :TLREYANDVVFIL 2qghA 237 :KLYDYAQGILNAL T0547 311 :KDLEPDIFIESGRFVAANHAVLIAPVLELF 2qghA 250 :QGLDLTIICEPGRSIVAESGELITQVLYEK T0547 346 :ENKLILKKQNPKLIDE 2qghA 284 :KRFVIVDAGMNDFLRP T0547 362 :LYDLYKSIKPSNA 2qghA 301 :LYHAKHAIRVITP T0547 379 :HDSIDHLESILTLFDLGYVD 2qghA 319 :ISPCDVVGPVCESSDTFLKD T0547 399 :LQDRSNAEILTHLITKKAILLLGDKQNPAD 2qghA 341 :LPELEPGDKIAIEKVGAYGSSMASQYNSRP T0547 429 :LLAIQD 2qghA 373 :LELALE T0547 438 :ERYLVNFSLFQSMPDFWGL 2qghA 382 :IRVIRKREALEDLWRLEEE Number of specific fragments extracted= 19 number of extra gaps= 0 total=107 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 2qghA/T0547-2qghA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0547 read from 2qghA/T0547-2qghA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2qghA read from 2qghA/T0547-2qghA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2qghA in template set Warning: unaligning (T0547)V35 because first residue in template chain is (2qghA)N3 Warning: unaligning (T0547)S341 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (2qghA)N283 Warning: unaligning (T0547)Y344 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR at template residue (2qghA)N283 Warning: unaligning (T0547)A374 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (2qghA)E318 Warning: unaligning (T0547)L378 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR at template residue (2qghA)E318 Warning: unaligning (T0547)N541 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2qghA)K381 Warning: unaligning (T0547)K543 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2qghA)K381 T0547 36 :KELRDDGYKGPLLLRFPHLIQKQIENIYGNFN 2qghA 4 :YEELFQTHKTPFYLYDFDKIKQAFLNYKEAFK T0547 76 :KGGFNAVYPLKVNQYPGFVKNLVKLG 2qghA 36 :GRKSLICYALKANSNLSILSLLAHLE T0547 106 :YGLEAGSKAELLLAMAYNNEGAPITVNGFKDRELINIGFIAAEMG 2qghA 62 :SGADCVSIGEIQRALKAGIKPYRIVFSGVGKSAFEIEQALKLNIL T0547 154 :TLTIEGLNELEAIIDIAKE 2qghA 107 :FLNVESFMELKTIETIAQS T0547 174 :FKPKPNIGLRVRLHSAGVGI 2qghA 126 :LGIKARISIRINPNIDAKTH T0547 194 :WAKSGGINSKFGLTSTELIEAVNLLKENK 2qghA 147 :YISTGLKENKFGVGEKEALEMFLWAKKSA T0547 224 :LEQFTMIHFHLGSQITEIHPLKKALNEAGNIYTELRKM 2qghA 176 :FLEPVSVHFHIGSQLLDLEPIIEASQKVAKIAKSLIAL T0547 263 :AKNLKAINLGGGLAVEYSQFKNEK 2qghA 214 :GIDLRFFDVGGGIGVSYENEETIK T0547 292 :LREYANDVV 2qghA 238 :LYDYAQGIL T0547 308 :EQKKDLEPDIFIESGRFVAANHAVLIAPVLELF 2qghA 247 :NALQGLDLTIICEPGRSIVAESGELITQVLYEK T0547 345 :AENKLILKKQNPKLIDELYDLYKSIKPS 2qghA 284 :KRFVIVDAGMNDFLRPSLYHAKHAIRVI T0547 373 :N 2qghA 313 :P T0547 379 :HDSIDHLESILTLFDLGYVDLQDR 2qghA 319 :ISPCDVVGPVCESSDTFLKDAHLP T0547 403 :SNAEILTHLITKKAILLLGDKQNPADLLA 2qghA 344 :LEPGDKIAIEKVGAYGSSMASQYNSRPKL T0547 535 :EAIISI 2qghA 373 :LELALE T0547 544 :GYEVEGIIEAQS 2qghA 382 :IRVIRKREALED Number of specific fragments extracted= 16 number of extra gaps= 0 total=123 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 1twiA/T0547-1twiA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1twiA expands to /projects/compbio/data/pdb/1twi.pdb.gz 1twiA:# T0547 read from 1twiA/T0547-1twiA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1twiA read from 1twiA/T0547-1twiA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1twiA to template set # found chain 1twiA in template set T0547 9 :WGNENFIIKNGKVCI 1twiA 16 :LGNDTVEIKDGRFFI T0547 27 :KKPAIIDIVKE 1twiA 31 :DGYDAIELAEK T0547 43 :YKGPLLLRFPHLIQKQIENIYGNFNKARKEFGYK 1twiA 42 :FGTPLYVMSEEQIKINYNRYIEAFKRWEEETGKE T0547 79 :FNAVYPLKVNQYPGFVKNLVKLG 1twiA 76 :FIVAYAYKANANLAITRLLAKLG T0547 106 :YGLEAGSKAELLLAMAYNNEGAPITVNGF 1twiA 99 :CGADVVSGGELYIAKLSNVPSKKIVFNGN T0547 135 :KDRELINIGF 1twiA 129 :KTKEEIIMGI T0547 148 :EMGHNIT 1twiA 139 :EANIRAF T0547 156 :TIEGLNELEAIIDIAKE 1twiA 146 :NVDSISELILINETAKE T0547 174 :FKPKPNIGLRVRLHSAGVGIWAKSGG 1twiA 163 :LGETANVAFRINPNVNPKTHPKISTG T0547 200 :INSKFGLTST 1twiA 190 :KKNKFGLDVE T0547 210 :ELIEAVNLLKENKLLEQFT 1twiA 202 :IAMKAIKMALEMEYVNVVG T0547 230 :IHFHLGSQITEIHPLKKALNEAGNIYTELRKMGA 1twiA 221 :VHCHIGSQLTDISPFIEETRKVMDFVVELKEEGI T0547 265 :NLKAINLGGGLAVEYSQFKNEK 1twiA 255 :EIEDVNLGGGLGIPYYKDKQIP T0547 291 :TLREYANDVVFILKNIAEQK 1twiA 277 :TQKDLADAIINTMLKYKDKV T0547 313 :LEPDIFIESGRFVAANHAVLIAPVLELFSQEYAE 1twiA 297 :EMPNLILEPGRSLVATAGYLLGKVHHIKETPVTK T0547 348 :KLILKK 1twiA 331 :WVMIDA T0547 354 :QNPKLIDELYDLYKSIKPSNALE 1twiA 338 :MNDMMRPAMYEAYHHIINCKVKN T0547 377 :YLHDSIDHLESILTLFDLGY 1twiA 363 :EVVSIAGGLCESSDVFGRDR T0547 398 :DLQDRSNAEILTHLITKKAILLLGDKQNPADLLAIQDEV 1twiA 383 :ELDKVEVGDVLAIFDVGAYGISMANNYNARGRPRMVLTS T0547 438 :ERYLVNFSLFQSMPDFWGLEQN 1twiA 422 :KKGVFLIRERETYADLIAKDIV T0547 465 :LD 1twiA 444 :PP Number of specific fragments extracted= 21 number of extra gaps= 0 total=144 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 1twiA/T0547-1twiA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0547 read from 1twiA/T0547-1twiA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1twiA read from 1twiA/T0547-1twiA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1twiA in template set T0547 12 :ENFIIKN 1twiA 19 :DTVEIKD T0547 27 :KKPAIIDIVKELRDDGYKGPLLLRFPHLIQKQIENIYGNFNKARKEFGYK 1twiA 26 :GRFFIDGYDAIELAEKFGTPLYVMSEEQIKINYNRYIEAFKRWEEETGKE T0547 79 :FNAVYPLKVNQYPGFVKNLVKLG 1twiA 76 :FIVAYAYKANANLAITRLLAKLG T0547 106 :YGLEAGSKAELLLAMAYNNEGAPITVNGFKDRE 1twiA 99 :CGADVVSGGELYIAKLSNVPSKKIVFNGNCKTK T0547 140 :INIGF 1twiA 132 :EEIIM T0547 146 :AAEMGHNI 1twiA 137 :GIEANIRA T0547 155 :LTIEGLNELEAIIDIAKE 1twiA 145 :FNVDSISELILINETAKE T0547 174 :FKPKPNIGLRVRLH 1twiA 163 :LGETANVAFRINPN T0547 188 :SAGVGIWAKSGGINSKFGLTST 1twiA 178 :NPKTHPKISTGLKKNKFGLDVE T0547 210 :ELIEAVNLLKENKLL 1twiA 202 :IAMKAIKMALEMEYV T0547 226 :QFTMIHFHLGSQITEIHPLKKALNEAGNIYTELRKMGA 1twiA 217 :NVVGVHCHIGSQLTDISPFIEETRKVMDFVVELKEEGI T0547 265 :NLKAINLGGGLAVEY 1twiA 255 :EIEDVNLGGGLGIPY T0547 282 :FKNEKSR 1twiA 270 :YKDKQIP T0547 291 :TLREYANDVVFILKNI 1twiA 277 :TQKDLADAIINTMLKY T0547 309 :QKKDLEPDIFIESGRFVAANHAVLIAPVLELFSQEY 1twiA 293 :KDKVEMPNLILEPGRSLVATAGYLLGKVHHIKETPV T0547 346 :ENKLILKKQNPKLIDE 1twiA 329 :TKWVMIDAGMNDMMRP T0547 362 :LYDLYKSIKPSNALE 1twiA 346 :MYEAYHHIINCKVKN T0547 378 :LHDSIDHLESILTLFDLGYVD 1twiA 361 :EKEVVSIAGGLCESSDVFGRD T0547 399 :LQDRSNAEILTHLITKKAILLLGDKQNPAD 1twiA 384 :LDKVEVGDVLAIFDVGAYGISMANNYNARG T0547 429 :L 1twiA 415 :P T0547 475 :S 1twiA 416 :R T0547 537 :IISINEKGYEVEG 1twiA 417 :MVLTSKKGVFLIR T0547 582 :KLVNDKQK 1twiA 430 :ERETYADL Number of specific fragments extracted= 23 number of extra gaps= 0 total=167 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 1twiA/T0547-1twiA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0547 read from 1twiA/T0547-1twiA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1twiA read from 1twiA/T0547-1twiA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1twiA in template set T0547 22 :CINYEKKPAIIDIVKELRDDGYKGPLLLRFPHLIQKQIENIYGNFNKARKEFGY 1twiA 21 :VEIKDGRFFIDGYDAIELAEKFGTPLYVMSEEQIKINYNRYIEAFKRWEEETGK T0547 78 :GFNAVYPLKVNQYPGFVKNLVKLG 1twiA 75 :EFIVAYAYKANANLAITRLLAKLG T0547 106 :YGLEAGSKAELLLAMAYNNEGAPITVNGFKDRELINIGFIAAEMG 1twiA 99 :CGADVVSGGELYIAKLSNVPSKKIVFNGNCKTKEEIIMGIEANIR T0547 154 :TLTIEGLNELEAIIDIAKE 1twiA 144 :AFNVDSISELILINETAKE T0547 174 :FKPKPNIGLRVRLHSAGVGI 1twiA 163 :LGETANVAFRINPNVNPKTH T0547 194 :WAKSGGINSKFGLTS 1twiA 184 :KISTGLKKNKFGLDV T0547 209 :TELIEAVNLLKENK 1twiA 201 :GIAMKAIKMALEME T0547 224 :LEQFTMIHFHLGSQITEIHPLKKALNEAGNIYTELRKM 1twiA 215 :YVNVVGVHCHIGSQLTDISPFIEETRKVMDFVVELKEE T0547 263 :AKNLKAINLGGGLAVEYSQFKNEKS 1twiA 253 :GIEIEDVNLGGGLGIPYYKDKQIPT T0547 292 :LREYANDVVFILKNI 1twiA 278 :QKDLADAIINTMLKY T0547 309 :QKKDLEPDIFIESGRFVAANHAVLIAPVLELFSQEYAENKLILKKQNPKLIDELYDLYKSIKPS 1twiA 293 :KDKVEMPNLILEPGRSLVATAGYLLGKVHHIKETPVTKWVMIDAGMNDMMRPAMYEAYHHIINC T0547 376 :E 1twiA 360 :N T0547 378 :LHDSIDHLESILTLFDLGYVDLQDR 1twiA 361 :EKEVVSIAGGLCESSDVFGRDRELD T0547 403 :SNAEILTHLITKKAILLLGDKQNPADLLAIQDEVQERYLVNFSLFQSMPDFWGL 1twiA 387 :VEVGDVLAIFDVGAYGISMANNYNARGRPRMVLTSKKGVFLIRERETYADLIAK Number of specific fragments extracted= 14 number of extra gaps= 0 total=181 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 2pljA/T0547-2pljA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2pljA expands to /projects/compbio/data/pdb/2plj.pdb.gz 2pljA:Skipped atom 865, because occupancy 0.5 <= existing 0.500 in 2pljA Skipped atom 867, because occupancy 0.500 <= existing 0.500 in 2pljA Skipped atom 869, because occupancy 0.500 <= existing 0.500 in 2pljA Skipped atom 871, because occupancy 0.500 <= existing 0.500 in 2pljA Skipped atom 1825, because occupancy 0.500 <= existing 0.500 in 2pljA Skipped atom 1827, because occupancy 0.500 <= existing 0.500 in 2pljA Skipped atom 1829, because occupancy 0.500 <= existing 0.500 in 2pljA Skipped atom 2313, because occupancy 0.500 <= existing 0.500 in 2pljA Skipped atom 2315, because occupancy 0.500 <= existing 0.500 in 2pljA Skipped atom 2317, because occupancy 0.500 <= existing 0.500 in 2pljA Skipped atom 2519, because occupancy 0.500 <= existing 0.500 in 2pljA # T0547 read from 2pljA/T0547-2pljA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2pljA read from 2pljA/T0547-2pljA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2pljA to template set # found chain 2pljA in template set Warning: unaligning (T0547)L186 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2pljA)S164 Warning: unaligning (T0547)N201 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2pljA)S164 Warning: unaligning (T0547)D486 because of BadResidue code BAD_PEPTIDE in next template residue (2pljA)V391 Warning: unaligning (T0547)G487 because of BadResidue code BAD_PEPTIDE at template residue (2pljA)V391 T0547 31 :IIDIVKE 2pljA 26 :IEASVEQ T0547 43 :YKGPLLLRFPHLIQKQIENIYGNF 2pljA 33 :FGAPLLLLDCDVIRQQYRALKNAL T0547 77 :GGFNAVYPLKVNQYPGFVKNLVKLG 2pljA 57 :PNVTLHYALKPLPHPVVVRTLLAEG T0547 106 :YGLEAGSKAELLLAMAYNNEGAPITV 2pljA 82 :ASFDLATTGEVELVASEGVPADLTIH T0547 132 :NGFKDRELINIGF 2pljA 109 :HPIKRDADIRDAL T0547 148 :EMGHNIT 2pljA 122 :AYGCNVF T0547 156 :TIEGLNELE 2pljA 129 :VVDNLNELE T0547 169 :IAKERFKP 2pljA 138 :KFKAYRDD T0547 178 :PNIGLRVR 2pljA 146 :VELLVRLS T0547 202 :SKFGLTSTELIEAVNLLKENK 2pljA 165 :KKFGCSPEQALVIIETAKEWN T0547 224 :LEQFT 2pljA 186 :IRIKG T0547 230 :IHFHLGSQITEIHPLKKALNEAGNIYTELRKMGAKNLKAINLGGGLAVEYSQFKN 2pljA 191 :LSFHVGSQTTNPNKYVEAIHTCRHVMEQVVERGLPALSTLDIGGGFPVNYTQQVM T0547 291 :TLREYANDVVFI 2pljA 246 :PIDQFCAPINEA T0547 307 :AEQKKD 2pljA 258 :LSLLPE T0547 314 :EPDIFIESGRFVAANHAVLIAPVLELFSQEYAE 2pljA 264 :TVHVLAEPGRFICAPAVTSVASVMGQAEREGQI T0547 348 :KLILKK 2pljA 297 :WYYLDD T0547 354 :QNPKLIDELYDLYKSI 2pljA 304 :IYGSFSGLMFDDARYP T0547 370 :KPSNALEYLHDSIDHLESILTLFDLGY 2pljA 323 :IKQGGELIPSVLSGPTCDSVDVIAENI T0547 398 :DLQDRSNAEILTHLITKKAILLLGDKQNPADLLA 2pljA 350 :LLPKLNNGDLVIGRTMGAYTSATATDFNFFKRAQ T0547 480 :DITCDS 2pljA 384 :TIALNE Number of specific fragments extracted= 20 number of extra gaps= 1 total=201 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 2pljA/T0547-2pljA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0547 read from 2pljA/T0547-2pljA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2pljA read from 2pljA/T0547-2pljA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2pljA in template set Warning: unaligning (T0547)L186 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2pljA)S164 Warning: unaligning (T0547)N201 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2pljA)S164 T0547 36 :KELRDDGYKGPLLLRFPHLIQKQIENIYGNF 2pljA 26 :IEASVEQFGAPLLLLDCDVIRQQYRALKNAL T0547 77 :GGFNAVYPLKVNQYPGFVKNLVKLG 2pljA 57 :PNVTLHYALKPLPHPVVVRTLLAEG T0547 106 :YGLEAGSKAELLLAMAYNNEGAPITVNGFKDRE 2pljA 82 :ASFDLATTGEVELVASEGVPADLTIHTHPIKRD T0547 140 :INIGF 2pljA 115 :ADIRD T0547 146 :AAEMGHNI 2pljA 120 :ALAYGCNV T0547 155 :LTIEGLNELE 2pljA 128 :FVVDNLNELE T0547 169 :IAKE 2pljA 138 :KFKA T0547 174 :FKPKPNIGLRVR 2pljA 142 :YRDDVELLVRLS T0547 202 :SKFGLTSTELIEAVNLLKENKL 2pljA 165 :KKFGCSPEQALVIIETAKEWNI T0547 226 :QFTMIHFHLGSQITEIHPLKKALNEAGNIYTELRKMGAKNLKAINLGGGLAVEY 2pljA 187 :RIKGLSFHVGSQTTNPNKYVEAIHTCRHVMEQVVERGLPALSTLDIGGGFPVNY T0547 283 :KNE 2pljA 241 :TQQ T0547 287 :SR 2pljA 244 :VM T0547 291 :TLREYANDVVFIL 2pljA 246 :PIDQFCAPINEAL T0547 308 :E 2pljA 259 :S T0547 310 :KKDLEPDIFIESGRFVAANHAVLIAPVLELFSQEY 2pljA 260 :LLPETVHVLAEPGRFICAPAVTSVASVMGQAEREG T0547 346 :ENKLILKKQNPKLIDELY 2pljA 295 :QIWYYLDDGIYGSFSGLM T0547 366 :YKSIKPS 2pljA 313 :FDDARYP T0547 373 :NALEYLHDSIDHLESILTLFDLGYVD 2pljA 323 :IKQGGELIPSVLSGPTCDSVDVIAEN T0547 399 :LQDRSNAEILTHLITKKAILLLGDKQNPAD 2pljA 351 :LPKLNNGDLVIGRTMGAYTSATATDFNFFK Number of specific fragments extracted= 19 number of extra gaps= 0 total=220 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 2pljA/T0547-2pljA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0547 read from 2pljA/T0547-2pljA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2pljA read from 2pljA/T0547-2pljA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2pljA in template set Warning: unaligning (T0547)E26 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2pljA)P16 Warning: unaligning (T0547)L186 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2pljA)S164 Warning: unaligning (T0547)N201 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2pljA)S164 T0547 27 :KKPAIIDIVKELRDDGYKGPLLLRFPHLIQKQIENIYGNFN 2pljA 17 :VLSAEEIHLIEASVEQFGAPLLLLDCDVIRQQYRALKNALP T0547 78 :GFNAVYPLKVNQYPGFVKNLVKLG 2pljA 58 :NVTLHYALKPLPHPVVVRTLLAEG T0547 106 :YGLEAGSKAELLLAMAYNNEGAPITVNGFKDRELINIGFIAAEMG 2pljA 82 :ASFDLATTGEVELVASEGVPADLTIHTHPIKRDADIRDALAYGCN T0547 154 :TLTIEGLNELEA 2pljA 127 :VFVVDNLNELEK T0547 170 :AKE 2pljA 139 :FKA T0547 174 :FKPKPNIGLRVR 2pljA 142 :YRDDVELLVRLS T0547 202 :SKFGLTSTELIEAVNLLKENK 2pljA 165 :KKFGCSPEQALVIIETAKEWN T0547 225 :EQFTMIHFHLGSQITEIHPLKKALNEAGNIYTELRKMGAKNLKAINLGGGLAVEYSQFKNEK 2pljA 186 :IRIKGLSFHVGSQTTNPNKYVEAIHTCRHVMEQVVERGLPALSTLDIGGGFPVNYTQQVMPI T0547 293 :REYANDVVFIL 2pljA 248 :DQFCAPINEAL T0547 309 :QKKDLEPDIFIESGRFVAANHAVLIAPVLELFSQEYAENKLILKKQNPKLIDELY 2pljA 259 :SLLPETVHVLAEPGRFICAPAVTSVASVMGQAEREGQIWYYLDDGIYGSFSGLMF T0547 367 :KSIKPS 2pljA 314 :DDARYP T0547 373 :NALEYLHDSIDHLESILTLFDLGYVDLQDR 2pljA 323 :IKQGGELIPSVLSGPTCDSVDVIAENILLP T0547 403 :SNAEILTHLITKKAILLLGDKQNPADLLA 2pljA 354 :LNNGDLVIGRTMGAYTSATATDFNFFKRA Number of specific fragments extracted= 13 number of extra gaps= 0 total=233 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 2p3eA/T0547-2p3eA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2p3eA expands to /projects/compbio/data/pdb/2p3e.pdb.gz 2p3eA:# T0547 read from 2p3eA/T0547-2p3eA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2p3eA read from 2p3eA/T0547-2p3eA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2p3eA to template set # found chain 2p3eA in template set Warning: unaligning (T0547)T156 because of BadResidue code BAD_PEPTIDE in next template residue (2p3eA)V129 Warning: unaligning (T0547)I157 because of BadResidue code BAD_PEPTIDE at template residue (2p3eA)V129 Warning: unaligning (T0547)L186 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2p3eA)S174 Warning: unaligning (T0547)S202 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2p3eA)S174 Warning: unaligning (T0547)H231 because of BadResidue code BAD_PEPTIDE in next template residue (2p3eA)C203 Warning: unaligning (T0547)F232 because of BadResidue code BAD_PEPTIDE at template residue (2p3eA)C203 Warning: unaligning (T0547)L313 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2p3eA)V272 Warning: unaligning (T0547)E376 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2p3eA)V339 Warning: unaligning (T0547)Y377 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2p3eA)V339 T0547 12 :ENFIIKNGKVCI 2p3eA 9 :PYLEYRDGELFI T0547 27 :KKPAIIDIVKE 2p3eA 21 :EGVSLKELAQT T0547 43 :YKGPLLLRFPHLIQKQIENIYGNF 2p3eA 32 :FGTPLYVYSSNFIKERFEAYRKAF T0547 77 :GGFNAVYPLKVNQYPGFVKNLVKLG 2p3eA 56 :PDALICYAVKANFNPHLVKLLGELG T0547 106 :YGLEAGSKAELLLAMAYNNEGAPITV 2p3eA 81 :AGADIVSGGELYLAKKAGIPPERIVY T0547 132 :NGFKDRELINIGF 2p3eA 108 :GVGKTEKELTDAV T0547 148 :EMGHNIT 2p3eA 121 :DSEILMF T0547 158 :EGLNELEAIIDIAKE 2p3eA 130 :ESRQELDVLNEIAGK T0547 174 :FKPKPNIGLRVR 2p3eA 145 :LGKKARIAIRVN T0547 203 :KFGLTSTELIEAVNLLKENKLLEQFT 2p3eA 175 :KFGVDIREAQKEYEYASKLENLEIVG T0547 230 :I 2p3eA 201 :I T0547 233 :HLGSQITEIHPLKKALNEAGNIYTELRKMGA 2p3eA 204 :HIGSQILDISPYREAVEKVVSLYESLTQKGF T0547 265 :NLKAINLGGGLAVEYSQFKNEK 2p3eA 235 :DIKYLDIGGGLGIKYKPEDKEP T0547 291 :TLREYANDV 2p3eA 257 :APQDLADLL T0547 314 :EPDIFIESGRFVAANHAVLIAPVLELFSQEYAE 2p3eA 273 :KAKIILEPGRSIMGNAGILITQVQFLKDKGSKH T0547 348 :KLILKK 2p3eA 306 :FIIVDA T0547 354 :QNPKLIDELYDLYKSIKPSNAL 2p3eA 313 :MNDLIRPSIYNAYHHIIPVETK T0547 378 :LHDSIDHLESILTLFDLGY 2p3eA 340 :VADIVGPICETGDFLALDR T0547 398 :DLQDRSNAEILTHLITKKAILLLGDKQNPADLLAIQDE 2p3eA 359 :EIEEVQRGEYLAVLSAGAYGFAMSSHYNMRPRAAEVLV T0547 437 :QERYLVNFSLFQSMPDFWGLEQ 2p3eA 397 :ENGSVKLIRKRENYDYIVEPSL Number of specific fragments extracted= 20 number of extra gaps= 2 total=253 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 2p3eA/T0547-2p3eA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0547 read from 2p3eA/T0547-2p3eA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2p3eA read from 2p3eA/T0547-2p3eA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2p3eA in template set Warning: unaligning (T0547)T156 because of BadResidue code BAD_PEPTIDE in next template residue (2p3eA)V129 Warning: unaligning (T0547)I157 because of BadResidue code BAD_PEPTIDE at template residue (2p3eA)V129 Warning: unaligning (T0547)L186 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2p3eA)S174 Warning: unaligning (T0547)S202 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2p3eA)S174 Warning: unaligning (T0547)H231 because of BadResidue code BAD_PEPTIDE in next template residue (2p3eA)C203 Warning: unaligning (T0547)F232 because of BadResidue code BAD_PEPTIDE at template residue (2p3eA)C203 Warning: unaligning (T0547)K310 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2p3eA)V272 Warning: unaligning (T0547)L313 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2p3eA)V272 Warning: unaligning (T0547)E376 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2p3eA)V339 Warning: unaligning (T0547)D380 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2p3eA)V339 T0547 23 :INYEKKPAIIDIVKELRDDGYKGPLLLRFPHLIQKQIENIYGNF 2p3eA 12 :EYRDGELFIEGVSLKELAQTFGTPLYVYSSNFIKERFEAYRKAF T0547 77 :GGFNAVYPLKVNQYPGFVKNLVKLG 2p3eA 56 :PDALICYAVKANFNPHLVKLLGELG T0547 106 :YGLEAGSKAELLLAMAYNNEGAPITVNGFKDRE 2p3eA 81 :AGADIVSGGELYLAKKAGIPPERIVYAGVGKTE T0547 140 :INIGF 2p3eA 114 :KELTD T0547 146 :AAEMGHNI 2p3eA 119 :AVDSEILM T0547 155 :L 2p3eA 127 :F T0547 158 :EGLNELEAIIDIAKE 2p3eA 130 :ESRQELDVLNEIAGK T0547 174 :FKPKPNIGLRVR 2p3eA 145 :LGKKARIAIRVN T0547 203 :KFGLTSTELIEAVNLLKENKLL 2p3eA 175 :KFGVDIREAQKEYEYASKLENL T0547 226 :QFTMI 2p3eA 197 :EIVGI T0547 233 :HLGSQITEIHPLKKALNEAGNIYTELRKMGA 2p3eA 204 :HIGSQILDISPYREAVEKVVSLYESLTQKGF T0547 265 :NLKAINLGGGLAVEY 2p3eA 235 :DIKYLDIGGGLGIKY T0547 282 :FKNEKSR 2p3eA 250 :KPEDKEP T0547 291 :TLREYANDV 2p3eA 257 :APQDLADLL T0547 314 :EPDIFIESGRFVAANHAVLIAPVLELFSQEY 2p3eA 273 :KAKIILEPGRSIMGNAGILITQVQFLKDKGS T0547 346 :ENKLILKKQNPKLIDE 2p3eA 304 :KHFIIVDAGMNDLIRP T0547 362 :LYDLYKSIKPSNAL 2p3eA 321 :IYNAYHHIIPVETK T0547 381 :SIDHLESILTLFDLGYVD 2p3eA 340 :VADIVGPICETGDFLALD T0547 399 :LQDRSNAEILTHLITKKAILLLGDKQNPAD 2p3eA 360 :IEEVQRGEYLAVLSAGAYGFAMSSHYNMRP T0547 429 :L 2p3eA 391 :A T0547 536 :AIISINEKGYEVEG 2p3eA 392 :AEVLVENGSVKLIR T0547 582 :KLVNDKQK 2p3eA 406 :KRENYDYI Number of specific fragments extracted= 22 number of extra gaps= 2 total=275 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 2p3eA/T0547-2p3eA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0547 read from 2p3eA/T0547-2p3eA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2p3eA read from 2p3eA/T0547-2p3eA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2p3eA in template set Warning: unaligning (T0547)T156 because of BadResidue code BAD_PEPTIDE in next template residue (2p3eA)V129 Warning: unaligning (T0547)I157 because of BadResidue code BAD_PEPTIDE at template residue (2p3eA)V129 Warning: unaligning (T0547)L186 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2p3eA)S174 Warning: unaligning (T0547)S202 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2p3eA)S174 Warning: unaligning (T0547)H231 because of BadResidue code BAD_PEPTIDE in next template residue (2p3eA)C203 Warning: unaligning (T0547)F232 because of BadResidue code BAD_PEPTIDE at template residue (2p3eA)C203 Warning: unaligning (T0547)K310 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2p3eA)V272 Warning: unaligning (T0547)L313 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2p3eA)V272 Warning: unaligning (T0547)E376 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2p3eA)V339 Warning: unaligning (T0547)D380 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2p3eA)V339 T0547 22 :CINYEKKPAIIDIVKELRDDGYKGPLLLRFPHLIQKQIENIYGNFN 2p3eA 11 :LEYRDGELFIEGVSLKELAQTFGTPLYVYSSNFIKERFEAYRKAFP T0547 78 :GFNAVYPLKVNQYPGFVKNLVKLG 2p3eA 57 :DALICYAVKANFNPHLVKLLGELG T0547 106 :YGLEAGSKAELLLAMAYNNEGAPITVNGFKDRELINIGFIAAEMG 2p3eA 81 :AGADIVSGGELYLAKKAGIPPERIVYAGVGKTEKELTDAVDSEIL T0547 154 :TL 2p3eA 126 :MF T0547 158 :EGLNELEAIIDIAKE 2p3eA 130 :ESRQELDVLNEIAGK T0547 174 :FKPKPNIGLRVR 2p3eA 145 :LGKKARIAIRVN T0547 203 :KFGLTSTELIEAVNLLKENK 2p3eA 175 :KFGVDIREAQKEYEYASKLE T0547 224 :LEQFTMI 2p3eA 195 :NLEIVGI T0547 233 :HLGSQITEIHPLKKALNEAGNIYTELRKM 2p3eA 204 :HIGSQILDISPYREAVEKVVSLYESLTQK T0547 263 :AKNLKAINLGGGLAVEYSQFKNEK 2p3eA 233 :GFDIKYLDIGGGLGIKYKPEDKEP T0547 291 :TLREYANDV 2p3eA 257 :APQDLADLL T0547 309 :Q 2p3eA 266 :K T0547 314 :EPDIFIESGRFVAANHAVLIAPVLELFSQEYAENKLILKKQNPKLIDELYDLYKSIKPSNAL 2p3eA 273 :KAKIILEPGRSIMGNAGILITQVQFLKDKGSKHFIIVDAGMNDLIRPSIYNAYHHIIPVETK T0547 381 :SIDHLESILTLFDLGYVDLQDR 2p3eA 340 :VADIVGPICETGDFLALDREIE T0547 403 :SNAEILTHLITKKAILLLGDKQNPADLLAIQDEVQERYLVNFSLFQSMPDFWGLEQ 2p3eA 363 :VQRGEYLAVLSAGAYGFAMSSHYNMRPRAAEVLVENGSVKLIRKRENYDYIVEPSL Number of specific fragments extracted= 15 number of extra gaps= 2 total=290 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 2j66A/T0547-2j66A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2j66A expands to /projects/compbio/data/pdb/2j66.pdb.gz 2j66A:# T0547 read from 2j66A/T0547-2j66A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2j66A read from 2j66A/T0547-2j66A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2j66A to template set # found chain 2j66A in template set Warning: unaligning (T0547)K27 because first residue in template chain is (2j66A)D4 Warning: unaligning (T0547)G190 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2j66A)T148 Warning: unaligning (T0547)I193 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2j66A)T148 Warning: unaligning (T0547)S280 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2j66A)E237 Warning: unaligning (T0547)K283 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2j66A)E237 Warning: unaligning (T0547)P356 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2j66A)P321 Warning: unaligning (T0547)S368 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2j66A)P321 Warning: unaligning (T0547)N373 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2j66A)L336 Warning: unaligning (T0547)Q458 because of BadResidue code TOO_FEW_ATOMS+NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2j66A)Q418 Warning: unaligning (T0547)N459 because of BadResidue code TOO_FEW_ATOMS+NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2j66A)Q418 T0547 28 :KPAIIDIVKE 2j66A 5 :QAEITALTKR T0547 43 :YKGPLLLRFPHLIQKQIENIYGNFN 2j66A 15 :FETPFYLYDGDFIEAHYRQLRSRTN T0547 77 :GGFNAVYPLKVNQYPGFVKNLVKLG 2j66A 40 :PAIQFYLSLKANNNIHLAKLFRQWG T0547 106 :YGLEAGSKAELLLAMAYNNEGAPITVNGF 2j66A 65 :LGVEVASAGELALARHAGFSAENIIFSGP T0547 135 :KDRELINIGF 2j66A 95 :KKRSELEIAV T0547 148 :EMGHNIT 2j66A 105 :QSGIYCI T0547 156 :TIEGLNELEAIIDIAKE 2j66A 112 :IAESVEELFYIEELAEK T0547 174 :FKPKPNIGLRVRLHSA 2j66A 129 :ENKTARVAIRINPDKS T0547 194 :WAKSGGINSKFGLTSTELIEAVNLLKENKLLEQFT 2j66A 149 :AIKMGGVPRQFGMDESMLDAVMDAVRSLQFTKFIG T0547 230 :IHFHLGSQITEIHPLKKALNEAGNIYTELR 2j66A 184 :IHVYTGTQNLNTDSIIESMKYTVDLGRNIY T0547 260 :KMGA 2j66A 215 :RYGI T0547 265 :NLKAINLGGGLAVEY 2j66A 219 :VCECINLGGGFGVPY T0547 284 :NEK 2j66A 238 :KAL T0547 291 :TLREYANDVVFILKNIAEQ 2j66A 241 :DIGKITRTVSDYVQEARDT T0547 311 :KDLEPDIFIESGRFVAANHAVLIAPVLELFSQEYAE 2j66A 260 :RFPQTTFIIESGRYLLAQAAVYVTEVLYRKASKGEV T0547 348 :KLILKK 2j66A 296 :FVIVDG T0547 354 :QN 2j66A 303 :MH T0547 369 :I 2j66A 322 :M T0547 377 :YLHDSIDHLESILTLFDLGY 2j66A 337 :EKVTIAGPLCTPEDCLGKDV T0547 398 :DLQDRSNAEILTHLITKKAILLLGD 2j66A 357 :HVPALYPGDLVCVLNSGAYGLSFSP T0547 423 :KQNPADLLAIQDEVQER 2j66A 383 :HFLGHPTPIEILKRNGS T0547 441 :LVNFSLFQSMPDFWGLE 2j66A 400 :YELIRRKGTADDIVATQ Number of specific fragments extracted= 22 number of extra gaps= 1 total=312 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 2j66A/T0547-2j66A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0547 read from 2j66A/T0547-2j66A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2j66A read from 2j66A/T0547-2j66A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2j66A in template set Warning: unaligning (T0547)I32 because first residue in template chain is (2j66A)D4 Warning: unaligning (T0547)G190 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2j66A)T148 Warning: unaligning (T0547)I193 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2j66A)T148 Warning: unaligning (T0547)N284 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2j66A)E237 Warning: unaligning (T0547)S287 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2j66A)E237 Warning: unaligning (T0547)I359 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2j66A)P321 Warning: unaligning (T0547)K370 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2j66A)P321 Warning: unaligning (T0547)H379 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2j66A)L336 T0547 33 :DIVKELRDDGYKGPLLLRFPHLIQKQIENIYGNF 2j66A 5 :QAEITALTKRFETPFYLYDGDFIEAHYRQLRSRT T0547 76 :KGGFNAVYPLKVNQYPGFVKNLVKLG 2j66A 39 :NPAIQFYLSLKANNNIHLAKLFRQWG T0547 106 :YGLEAGSKAELLLAMAYNNEGAPITVNGFKDRE 2j66A 65 :LGVEVASAGELALARHAGFSAENIIFSGPGKKR T0547 140 :INIGF 2j66A 98 :SELEI T0547 146 :AAEMGHNI 2j66A 103 :AVQSGIYC T0547 155 :LTIEGLNELEAIIDIAKE 2j66A 111 :IIAESVEELFYIEELAEK T0547 174 :FKPKPNIGLRVRLHSA 2j66A 129 :ENKTARVAIRINPDKS T0547 194 :WAKSGGINSKFGLTSTELIEAVNLLKENKLL 2j66A 149 :AIKMGGVPRQFGMDESMLDAVMDAVRSLQFT T0547 226 :QFTMIHFHLGSQITEIHPLKKALNEAGNIYTELRKMGAKNLKAINLGGGLAVEY 2j66A 180 :KFIGIHVYTGTQNLNTDSIIESMKYTVDLGRNIYERYGIVCECINLGGGFGVPY T0547 288 :RNYTLREYANDVVFILKNIAEQ 2j66A 238 :KALDIGKITRTVSDYVQEARDT T0547 311 :KDLEPDIFIESGRFVAANHAVLIAPVLELFSQEY 2j66A 260 :RFPQTTFIIESGRYLLAQAAVYVTEVLYRKASKG T0547 346 :ENKLILKKQNPK 2j66A 294 :EVFVIVDGGMHH T0547 358 :L 2j66A 308 :A T0547 371 :PS 2j66A 322 :ME T0547 380 :DSIDHLESILTLFDLGYVD 2j66A 337 :EKVTIAGPLCTPEDCLGKD T0547 399 :LQDRSNAEILTHLITKKAILLLGD 2j66A 358 :VPALYPGDLVCVLNSGAYGLSFSP T0547 423 :KQNPAD 2j66A 383 :HFLGHP T0547 429 :L 2j66A 390 :P T0547 536 :AIISINEKGYEVEG 2j66A 391 :IEILKRNGSYELIR T0547 582 :KLVNDKQKK 2j66A 405 :RKGTADDIV Number of specific fragments extracted= 20 number of extra gaps= 0 total=332 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 2j66A/T0547-2j66A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0547 read from 2j66A/T0547-2j66A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2j66A read from 2j66A/T0547-2j66A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2j66A in template set Warning: unaligning (T0547)G190 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2j66A)T148 Warning: unaligning (T0547)I193 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2j66A)T148 Warning: unaligning (T0547)S280 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2j66A)E237 Warning: unaligning (T0547)K283 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2j66A)E237 Warning: unaligning (T0547)D360 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2j66A)P321 Warning: unaligning (T0547)S372 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2j66A)P321 Warning: unaligning (T0547)H379 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2j66A)L336 Warning: unaligning (T0547)N459 because of BadResidue code TOO_FEW_ATOMS+NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2j66A)Q418 Warning: unaligning (T0547)F460 because of BadResidue code TOO_FEW_ATOMS+NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2j66A)Q418 T0547 33 :DIVKELRDDGYKGPLLLRFPHLIQKQIENIYGNF 2j66A 5 :QAEITALTKRFETPFYLYDGDFIEAHYRQLRSRT T0547 76 :KGGFNAVYPLKVNQYPGFVKNLVKLG 2j66A 39 :NPAIQFYLSLKANNNIHLAKLFRQWG T0547 106 :YGLEAGSKAELLLAMAYNNEGAPITVNGFKDRELINIGFIAAEMG 2j66A 65 :LGVEVASAGELALARHAGFSAENIIFSGPGKKRSELEIAVQSGIY T0547 154 :TLTIEGLNELEAIIDIAKE 2j66A 110 :CIIAESVEELFYIEELAEK T0547 174 :FKPKPNIGLRVRLHSA 2j66A 129 :ENKTARVAIRINPDKS T0547 194 :WAKSGGINSKFGLTSTELIEAVNLLKENK 2j66A 149 :AIKMGGVPRQFGMDESMLDAVMDAVRSLQ T0547 224 :LEQFTMIHFHLGSQITEIHPLKKALNEAGNIYTELRKMGAKNLKAINLGGGLAVEY 2j66A 178 :FTKFIGIHVYTGTQNLNTDSIIESMKYTVDLGRNIYERYGIVCECINLGGGFGVPY T0547 284 :NEKS 2j66A 238 :KALD T0547 292 :LREYANDVVFILKNIA 2j66A 242 :IGKITRTVSDYVQEAR T0547 309 :QKKDLEPDIFIESGRFVAANHAVLIAPVLELFSQEYAENKLILKKQNPKLI 2j66A 258 :DTRFPQTTFIIESGRYLLAQAAVYVTEVLYRKASKGEVFVIVDGGMHHHAA T0547 380 :DSIDHLESILTLFDLGYVDLQDR 2j66A 337 :EKVTIAGPLCTPEDCLGKDVHVP T0547 403 :SNAEILTHLITKKAILLLGDKQNPADLLAIQDEVQERYLVNFSLFQSMPDFWGLEQ 2j66A 361 :LYPGDLVCVLNSGAYGLSFSPVHFLGHPTPIEILKRNGSYELIRRKGTADDIVATQ Number of specific fragments extracted= 12 number of extra gaps= 1 total=344 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 1knwA/T0547-1knwA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1knwA expands to /projects/compbio/data/pdb/1knw.pdb.gz 1knwA:Skipped atom 1707, because occupancy 0.500 <= existing 0.500 in 1knwA Skipped atom 1709, because occupancy 0.500 <= existing 0.500 in 1knwA Skipped atom 1711, because occupancy 0.500 <= existing 0.500 in 1knwA Skipped atom 1713, because occupancy 0.500 <= existing 0.500 in 1knwA Skipped atom 1999, because occupancy 0.500 <= existing 0.500 in 1knwA Skipped atom 2003, because occupancy 0.500 <= existing 0.500 in 1knwA Skipped atom 2005, because occupancy 0.500 <= existing 0.500 in 1knwA Skipped atom 2007, because occupancy 0.500 <= existing 0.500 in 1knwA Skipped atom 2009, because occupancy 0.500 <= existing 0.500 in 1knwA Skipped atom 2011, because occupancy 0.500 <= existing 0.500 in 1knwA Skipped atom 2013, because occupancy 0.500 <= existing 0.500 in 1knwA # T0547 read from 1knwA/T0547-1knwA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1knwA read from 1knwA/T0547-1knwA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1knwA to template set # found chain 1knwA in template set Warning: unaligning (T0547)P461 because last residue in template chain is (1knwA)H422 T0547 30 :AIIDIVKE 1knwA 16 :NLLRLPAE T0547 43 :YKGPLLLRFPHLIQKQIENI 1knwA 24 :FGCPVWVYDAQIIRRQIAAL T0547 76 :KGGFNAVYPLKVNQYPGFVKNLVKLG 1knwA 44 :KQFDVVRFAQKACSNIHILRLMREQG T0547 106 :YGLEAGSKAELLLAMAYNNEG 1knwA 70 :VKVDSVSLGEIERALAAGYNP T0547 127 :APITVNGF 1knwA 95 :DDIVFTAD T0547 135 :KDRELINIGF 1knwA 104 :IDQATLERVS T0547 148 :EMGHN 1knwA 114 :ELQIP T0547 155 :LTIEGLNELEAIIDIAKE 1knwA 119 :VNAGSVDMLDQLGQVSPG T0547 178 :PNIGLRVRLHSAGVGIWAKSGG 1knwA 137 :HRVWLRVNPGFGHGHSQKTNTG T0547 200 :INSKFGLTSTELIEAVNLLKENK 1knwA 160 :ENSKHGIWYTDLPAALDVIQRHH T0547 224 :LEQFT 1knwA 183 :LQLVG T0547 230 :IHFHLGSQ 1knwA 188 :IHMHIGSG T0547 239 :TEIHPLKKALNEAGNIYTEL 1knwA 196 :VDYAHLEQVCGAMVRQVIEF T0547 262 :GA 1knwA 216 :GQ T0547 265 :NLKAINLGGGLAVEYSQFKNEK 1knwA 218 :DLQAISAGGGLSVPYQQGEEAV T0547 291 :TLREYANDVVFILKNIAEQKKD 1knwA 240 :DTEHYYGLWNAAREQIARHLGH T0547 314 :EPDIFIESGRFVAANHAVLIAPVLELFSQEYAE 1knwA 262 :PVKLEIEPGRFLVAQSGVLITQVRSVKQMGSRH T0547 348 :KLILKK 1knwA 295 :FVLVDA T0547 354 :QNPKLIDELYDLYKSI 1knwA 302 :FNDLMRPAMYGSYHHI T0547 370 :KPSNALE 1knwA 325 :RSLEHAP T0547 377 :YLHDSIDHLESILTLF 1knwA 333 :VETVVAGPLCESGDVF T0547 393 :DLGYVDLQDRSNAEILTHLITKKAILLLGDKQNPADLLAIQDEVQER 1knwA 355 :NVETRALPEVKAGDYLVLHDTGAYGASMSSNYNSRPLLPEVLFDNGQ T0547 441 :LVNFSLFQSMPDFWGLEQNF 1knwA 402 :ARLIRRRQTIEELLALELLH Number of specific fragments extracted= 23 number of extra gaps= 0 total=367 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 1knwA/T0547-1knwA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0547 read from 1knwA/T0547-1knwA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1knwA read from 1knwA/T0547-1knwA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1knwA in template set T0547 25 :YEKKPAIIDIVKELRDDGYKGPLLLRFPHLIQKQIEN 1knwA 6 :FSTDTDLTAENLLRLPAEFGCPVWVYDAQIIRRQIAA T0547 75 :YKGGFNAVYPLKVNQYPGFVKNLVKLG 1knwA 43 :LKQFDVVRFAQKACSNIHILRLMREQG T0547 106 :YGLEAGSKAELLLAMAYNNE 1knwA 70 :VKVDSVSLGEIERALAAGYN T0547 126 :GAPITVNGFKDRE 1knwA 94 :PDDIVFTADVIDQ T0547 140 :INIGF 1knwA 107 :ATLER T0547 146 :AAEMGHN 1knwA 112 :VSELQIP T0547 155 :LTIEGLNELEAIIDIAKE 1knwA 119 :VNAGSVDMLDQLGQVSPG T0547 178 :PNIGLRVRLH 1knwA 137 :HRVWLRVNPG T0547 188 :SAGVGIWAKSGGINSKFGLTSTELIEAVNLLKENKL 1knwA 148 :GHGHSQKTNTGGENSKHGIWYTDLPAALDVIQRHHL T0547 226 :QFTMIHFHLGSQ 1knwA 184 :QLVGIHMHIGSG T0547 239 :TEIHPLKKALNEAGNIYTEL 1knwA 196 :VDYAHLEQVCGAMVRQVIEF T0547 262 :GA 1knwA 216 :GQ T0547 265 :NLKAINLGGGLAVEY 1knwA 218 :DLQAISAGGGLSVPY T0547 282 :FKNEKSR 1knwA 233 :QQGEEAV T0547 291 :TLREYANDVVFILKNIAEQKKDL 1knwA 240 :DTEHYYGLWNAAREQIARHLGHP T0547 315 :PDIFIESGRFVAANHAVLIAPVLELFSQEY 1knwA 263 :VKLEIEPGRFLVAQSGVLITQVRSVKQMGS T0547 346 :ENKLILKKQNPKLIDE 1knwA 293 :RHFVLVDAGFNDLMRP T0547 362 :LYDLYKSIK 1knwA 310 :MYGSYHHIS T0547 371 :PSNALEYLHDSIDHLESILTLFDLGYVD 1knwA 324 :GRSLEHAPTVETVVAGPLCESGDVFTQQ T0547 399 :LQDRSNAEILTHLITKKAILLLGDKQNPAD 1knwA 361 :LPEVKAGDYLVLHDTGAYGASMSSNYNSRP T0547 429 :LL 1knwA 392 :LP T0547 537 :IISINEKGYEVEG 1knwA 394 :EVLFDNGQARLIR T0547 582 :KLVNDKQKK 1knwA 407 :RRQTIEELL Number of specific fragments extracted= 23 number of extra gaps= 0 total=390 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 1knwA/T0547-1knwA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0547 read from 1knwA/T0547-1knwA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1knwA read from 1knwA/T0547-1knwA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1knwA in template set Warning: unaligning (T0547)T473 because last residue in template chain is (1knwA)H422 T0547 26 :EKKPAIIDIVKELRDDGYKGPLLLRFPHLIQKQIEN 1knwA 7 :STDTDLTAENLLRLPAEFGCPVWVYDAQIIRRQIAA T0547 75 :YKGGFNAVYPLKVNQYPGFVKNLVKLG 1knwA 43 :LKQFDVVRFAQKACSNIHILRLMREQG T0547 106 :YGLEAGSKAELLLAMAYNNEGA 1knwA 70 :VKVDSVSLGEIERALAAGYNPQ T0547 128 :PITVNGFKDRELINIGFIAAEM 1knwA 96 :DIVFTADVIDQATLERVSELQI T0547 154 :TLTIEGLNELEAIIDIAKE 1knwA 118 :PVNAGSVDMLDQLGQVSPG T0547 178 :PNIGLRVRLHSAGVGI 1knwA 137 :HRVWLRVNPGFGHGHS T0547 194 :WAKSGGINSKFGLTSTELIEAVNLLKENK 1knwA 154 :KTNTGGENSKHGIWYTDLPAALDVIQRHH T0547 225 :EQFTMIHFHLGSQI 1knwA 183 :LQLVGIHMHIGSGV T0547 240 :EIHPLKKALNEAGNIYTEL 1knwA 197 :DYAHLEQVCGAMVRQVIEF T0547 263 :AKNLKAINLGGGLAVEYSQFKNEKS 1knwA 216 :GQDLQAISAGGGLSVPYQQGEEAVD T0547 292 :LREYANDVVFILKNIAEQKKD 1knwA 241 :TEHYYGLWNAAREQIARHLGH T0547 314 :EPDIFIESGRFVAANHAVLIAPVLELFSQEYAENKLILKKQNPKLIDELYDLYKSIKPS 1knwA 262 :PVKLEIEPGRFLVAQSGVLITQVRSVKQMGSRHFVLVDAGFNDLMRPAMYGSYHHISAL T0547 373 :NALEYLHDSIDHLESILTLFDLGYVDLQDR 1knwA 326 :SLEHAPTVETVVAGPLCESGDVFTQQEGGN T0547 403 :SNAEILTHLITKKAILLLGDKQNPADLLAIQDEVQERYLVNFSLFQSMPDFW 1knwA 364 :VKAGDYLVLHDTGAYGASMSSNYNSRPLLPEVLFDNGQARLIRRRQTIEELL T0547 467 :RLDEEP 1knwA 416 :ALELLH Number of specific fragments extracted= 15 number of extra gaps= 0 total=405 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 2yxxA/T0547-2yxxA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2yxxA expands to /projects/compbio/data/pdb/2yxx.pdb.gz 2yxxA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0547 read from 2yxxA/T0547-2yxxA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2yxxA read from 2yxxA/T0547-2yxxA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2yxxA to template set # found chain 2yxxA in template set T0547 30 :AIIDIVKE 2yxxA 3 :ILRKVAEI T0547 43 :YKGPLLLRFPHLIQKQIENIYGNFN 2yxxA 11 :HGTPTYVYFEETLRKRSRLVKEVFE T0547 77 :G 2yxxA 36 :G T0547 78 :GFNAVYPLKVNQYPGFVKNLVKLG 2yxxA 38 :NLLPTFAVKANNNPVLLKILREEG T0547 106 :YGLEAGSKAELLLAMAYNNEGAPITVNGF 2yxxA 62 :FGMDVVTKGELLAAKLAGVPSHTVVWNGN T0547 135 :KDRELINIGF 2yxxA 92 :KSRDQMEHFL T0547 148 :EMGHNIT 2yxxA 102 :REDVRIV T0547 156 :TIEGLNELEAIIDI 2yxxA 109 :NVDSFEEMEIWREL T0547 174 :FKPKPNIGLRVRLHSAGVGIWAKSGG 2yxxA 123 :NPEGVEYFIRVNPEVDAKTHPHISTG T0547 200 :INSKFGLTSTELIEAVNLLK 2yxxA 150 :KKHKFGIPLEDLDSFMERFR T0547 222 :K 2yxxA 170 :S T0547 224 :LEQFT 2yxxA 171 :MNIRG T0547 230 :IHFHLGSQITEIHPLKKALNEAGNIYTEL 2yxxA 176 :LHVHIGSQITRVEPFVEAFSKVVRASERY T0547 265 :NLKAINLGGGLAVEYSQFKN 2yxxA 205 :GFEEINIGGGWGINYSGEEL T0547 291 :TLREYANDV 2yxxA 225 :DLSSYREKV T0547 307 :AEQKK 2yxxA 234 :VPDLK T0547 313 :LEPDIFIESGRFVAANHAVLIAPVLELFSQEYAE 2yxxA 239 :RFKRVIVEIGRYIVAPSGYLLLRVVLVKRRHNKA T0547 348 :KLILKK 2yxxA 273 :FVVVDG T0547 354 :QNPKLIDELYDLYKSIKPSNALE 2yxxA 280 :MNVLIRPALYSAYHRIFVLGKQG T0547 377 :YLHDSIDHLESILTLFDLGYV 2yxxA 305 :MRADVVGPLCESGDVIAYDRE T0547 399 :LQDRSNAEILTHLITKKAILLLGDKQNPADLLAIQDEVQERYLVNFSLFQSMPDFWG 2yxxA 326 :LPEVEPGDIIAVENAGAYGYTMSNNYNSTTRPAEVLVRENGRISLIRRRETEMDIFK Number of specific fragments extracted= 21 number of extra gaps= 0 total=426 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 2yxxA/T0547-2yxxA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0547 read from 2yxxA/T0547-2yxxA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2yxxA read from 2yxxA/T0547-2yxxA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2yxxA in template set T0547 35 :VKELRDDGYKGPLLLRFPHLIQKQIENIYGNFN 2yxxA 3 :ILRKVAEIHGTPTYVYFEETLRKRSRLVKEVFE T0547 76 :KGGFNAVYPLKVNQYPGFVKNLVKLG 2yxxA 36 :GVNLLPTFAVKANNNPVLLKILREEG T0547 106 :YGLEAGSKAELLLAMAYNNEGAPITVNGFKDRE 2yxxA 62 :FGMDVVTKGELLAAKLAGVPSHTVVWNGNGKSR T0547 140 :INIGF 2yxxA 95 :DQMEH T0547 146 :AAEMGHNI 2yxxA 100 :FLREDVRI T0547 155 :LTIEGLNELEAIIDI 2yxxA 108 :VNVDSFEEMEIWREL T0547 174 :FKPKPNIGLRVRLH 2yxxA 123 :NPEGVEYFIRVNPE T0547 188 :SAGVGIWAKSGGINSKFGLTSTELIEAVNLL 2yxxA 138 :DAKTHPHISTGLKKHKFGIPLEDLDSFMERF T0547 221 :NKL 2yxxA 169 :RSM T0547 226 :QFTMIHFHLGSQITEIHPLKKALNEAGNIYTEL 2yxxA 172 :NIRGLHVHIGSQITRVEPFVEAFSKVVRASERY T0547 265 :NLKAINLGGGLAVEY 2yxxA 205 :GFEEINIGGGWGINY T0547 284 :NEKSR 2yxxA 220 :SGEEL T0547 291 :TLREYANDVV 2yxxA 225 :DLSSYREKVV T0547 308 :EQKK 2yxxA 235 :PDLK T0547 313 :LEPDIFIESGRFVAANHAVLIAPVLELFSQEY 2yxxA 239 :RFKRVIVEIGRYIVAPSGYLLLRVVLVKRRHN T0547 346 :ENKLILKKQNPKLIDE 2yxxA 271 :KAFVVVDGGMNVLIRP T0547 362 :LYDLYKSIKPSNALE 2yxxA 288 :LYSAYHRIFVLGKQG T0547 378 :LHDSIDHLESILTLFDLGYVD 2yxxA 303 :KEMRADVVGPLCESGDVIAYD T0547 399 :LQDRSNAEILTHLITKKAILLLGDKQNPAD 2yxxA 326 :LPEVEPGDIIAVENAGAYGYTMSNNYNSTT T0547 534 :TEAIISINEKGYEVEG 2yxxA 357 :PAEVLVRENGRISLIR T0547 582 :KLVNDKQK 2yxxA 373 :RRETEMDI Number of specific fragments extracted= 21 number of extra gaps= 0 total=447 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 2yxxA/T0547-2yxxA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0547 read from 2yxxA/T0547-2yxxA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2yxxA read from 2yxxA/T0547-2yxxA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2yxxA in template set T0547 36 :KELRDDGYKGPLLLRFPHLIQKQIENIYGNFN 2yxxA 4 :LRKVAEIHGTPTYVYFEETLRKRSRLVKEVFE T0547 76 :KGGFNAVYPLKVNQYPGFVKNLVKLG 2yxxA 36 :GVNLLPTFAVKANNNPVLLKILREEG T0547 106 :YGLEAGSKAELLLAMAYNNEGAPITVNGFKDRELINIGFIAAEMG 2yxxA 62 :FGMDVVTKGELLAAKLAGVPSHTVVWNGNGKSRDQMEHFLREDVR T0547 154 :TLTIEGLNELEAIIDI 2yxxA 107 :IVNVDSFEEMEIWREL T0547 174 :FKPKPNIGLRVRLHSAGVGI 2yxxA 123 :NPEGVEYFIRVNPEVDAKTH T0547 194 :WAKSGGINSKFGLTSTELIEAVNLL 2yxxA 144 :HISTGLKKHKFGIPLEDLDSFMERF T0547 221 :NK 2yxxA 169 :RS T0547 225 :EQFTMIHFHLGSQITEIHPLKKALNEAGNIYTEL 2yxxA 171 :MNIRGLHVHIGSQITRVEPFVEAFSKVVRASERY T0547 265 :NLKAINLGGGLAVEYSQFKNEKSR 2yxxA 205 :GFEEINIGGGWGINYSGEELDLSS T0547 295 :Y 2yxxA 229 :Y T0547 304 :KNIAEQKKDLEPDIFIESGRFVAANHAVLIAPVLELFSQEYAENKLILKKQNPKLIDELYDLYKSIKPS 2yxxA 230 :REKVVPDLKRFKRVIVEIGRYIVAPSGYLLLRVVLVKRRHNKAFVVVDGGMNVLIRPALYSAYHRIFVL T0547 375 :LEYLHDSIDHLESILTLFDLGYVDLQDR 2yxxA 300 :KQGKEMRADVVGPLCESGDVIAYDRELP T0547 403 :SNAEILTHLITKKAILLLGDKQNPADLLAIQDEVQERYLVNFSLFQSMPDFWGL 2yxxA 329 :VEPGDIIAVENAGAYGYTMSNNYNSTTRPAEVLVRENGRISLIRRRETEMDIFK Number of specific fragments extracted= 13 number of extra gaps= 0 total=460 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 2nvaA/T0547-2nvaA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2nvaA expands to /projects/compbio/data/pdb/2nva.pdb.gz 2nvaA:Skipped atom 2538, because occupancy 0.500 <= existing 0.500 in 2nvaA Skipped atom 2540, because occupancy 0.500 <= existing 0.500 in 2nvaA Skipped atom 2542, because occupancy 0.500 <= existing 0.500 in 2nvaA Skipped atom 2544, because occupancy 0.500 <= existing 0.500 in 2nvaA Skipped atom 2546, because occupancy 0.500 <= existing 0.500 in 2nvaA Skipped atom 2548, because occupancy 0.500 <= existing 0.500 in 2nvaA # T0547 read from 2nvaA/T0547-2nvaA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2nvaA read from 2nvaA/T0547-2nvaA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2nvaA to template set # found chain 2nvaA in template set Warning: unaligning (T0547)S280 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2nvaA)L226 Warning: unaligning (T0547)N284 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2nvaA)L226 T0547 29 :PAIIDIVKE 2nvaA 3 :SVVNNILKA T0547 40 :DDGYKGPLLLRFPHLIQKQIENIYGNF 2nvaA 12 :HPHQTKSFYVSSPKIVEDLIDQWTILF T0547 77 :GGFNAVYPLKVNQYPGFVKNLVKLG 2nvaA 39 :PRVTPHYAVKCNNDEVLLKTMCDKN T0547 106 :YGLEAGSKAELLLAMAYNNEGAPITV 2nvaA 64 :VNFDCASSSEIKKVIQIGVSPSRIIF T0547 132 :NGFKDRELINIGF 2nvaA 91 :HTMKTIDDLIFAK T0547 148 :EMGHNIT 2nvaA 104 :DQGVDIA T0547 156 :TIEGLNELEAIIDIAKE 2nvaA 111 :TFDSSFELDKIHTYHPN T0547 178 :PNIGLRVRLHSAGV 2nvaA 128 :CKMILRIRCDDPNA T0547 197 :SGGINSKFGLTSTELIEAVNLLKENK 2nvaA 142 :TVQLGNKFGANEDEIRHLLEYAKQLD T0547 224 :LEQFT 2nvaA 168 :IEVIG T0547 230 :IHFHLGSQITEIHPLKKALNEAGNIYTELRKMGA 2nvaA 173 :ISFHVGSGSRNPEAYYRAIKSSKEAFNEAISVGH T0547 265 :NLKAINLGGGLAVEY 2nvaA 207 :KPYILDIGGGLHADI T0547 285 :EK 2nvaA 227 :ST T0547 294 :EYANDVVFILKNIAEQ 2nvaA 229 :YMSDYINDAIKDFFPE T0547 313 :LEPDIFIESGRFVAANHAVLIAPVLELFSQEYAE 2nvaA 245 :DTVTIVAEPGRFFAEHYSVLATQVIGKRVRDGLY T0547 348 :KLILKK 2nvaA 279 :EYFFNE T0547 354 :QNPKLID 2nvaA 286 :TYGGFSN T0547 362 :LYDLYKSI 2nvaA 293 :VIFEKSVP T0547 370 :KPSNALE 2nvaA 307 :DVPDDEE T0547 377 :YLHDSIDHLESILTLFDLGY 2nvaA 315 :VPSVLYGCTCDGVDVINHNV T0547 398 :DLQDRSNAEILTHLITKKAILLLGDKQNPADLLAIQ 2nvaA 335 :ALPELHIGDWVYFPSWGAYTNVLTTSFNGFGEYDVY Number of specific fragments extracted= 21 number of extra gaps= 0 total=481 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 2nvaA/T0547-2nvaA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0547 read from 2nvaA/T0547-2nvaA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2nvaA read from 2nvaA/T0547-2nvaA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2nvaA in template set Warning: unaligning (T0547)F282 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2nvaA)L226 Warning: unaligning (T0547)K286 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2nvaA)L226 T0547 35 :VKELRDDGYKGPLLLRFPHLIQKQIENIYGNF 2nvaA 7 :NILKAHPHQTKSFYVSSPKIVEDLIDQWTILF T0547 77 :GGFNAVYPLKVNQYPGFVKNLVKLG 2nvaA 39 :PRVTPHYAVKCNNDEVLLKTMCDKN T0547 106 :YGLEAGSKAELLLAMAYNNEGAPITVNGFKDRE 2nvaA 64 :VNFDCASSSEIKKVIQIGVSPSRIIFAHTMKTI T0547 140 :INIGF 2nvaA 97 :DDLIF T0547 146 :AAEMGHNI 2nvaA 102 :AKDQGVDI T0547 155 :LTIEGLNELEAIIDIAKE 2nvaA 110 :ATFDSSFELDKIHTYHPN T0547 178 :PNIGLRVRLH 2nvaA 128 :CKMILRIRCD T0547 188 :SAGVGI 2nvaA 139 :PNATVQ T0547 200 :INSKFGLTSTELIEAVNLLKENKL 2nvaA 145 :LGNKFGANEDEIRHLLEYAKQLDI T0547 226 :QFTMIHFHLGSQITEIHPLKKALNEAGNIYTELRKMGA 2nvaA 169 :EVIGISFHVGSGSRNPEAYYRAIKSSKEAFNEAISVGH T0547 265 :NLKAINLGGGLAVEY 2nvaA 207 :KPYILDIGGGLHADI T0547 287 :SR 2nvaA 227 :ST T0547 294 :EYANDVVFILKNIAEQ 2nvaA 229 :YMSDYINDAIKDFFPE T0547 313 :LEPDIFIESGRFVAANHAVLIAPVLELFSQEY 2nvaA 245 :DTVTIVAEPGRFFAEHYSVLATQVIGKRVRDG T0547 346 :ENKLILKKQNPKLIDELYDLYKSIKPSNALEYLHD 2nvaA 277 :LYEYFFNESTYGGFSNVIFEKSVPTPQLLRDVPDD T0547 381 :SIDHLESILTLFDLGYVD 2nvaA 316 :PSVLYGCTCDGVDVINHN T0547 399 :LQDRSNAEILTHLITKKAILLLGDKQNPAD 2nvaA 336 :LPELHIGDWVYFPSWGAYTNVLTTSFNGFG Number of specific fragments extracted= 17 number of extra gaps= 0 total=498 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 2nvaA/T0547-2nvaA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0547 read from 2nvaA/T0547-2nvaA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2nvaA read from 2nvaA/T0547-2nvaA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2nvaA in template set Warning: unaligning (T0547)S280 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2nvaA)L226 Warning: unaligning (T0547)N284 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2nvaA)L226 T0547 34 :IVKELRDDGYKGPLLLRFPHLIQKQIENIYGNFN 2nvaA 6 :NNILKAHPHQTKSFYVSSPKIVEDLIDQWTILFP T0547 78 :GFNAVYPLKVNQYPGFVKNLVKLG 2nvaA 40 :RVTPHYAVKCNNDEVLLKTMCDKN T0547 106 :YGLEAGSKAELLLAMAYNNEGAPITVNGFKDRELINIGFIAAEMG 2nvaA 64 :VNFDCASSSEIKKVIQIGVSPSRIIFAHTMKTIDDLIFAKDQGVD T0547 154 :TLTIEGLNELEAIIDIAKE 2nvaA 109 :IATFDSSFELDKIHTYHPN T0547 178 :PNIGLRVRLHSAGVG 2nvaA 128 :CKMILRIRCDDPNAT T0547 198 :GGINSKFGLTSTELIEAVNLLKENK 2nvaA 143 :VQLGNKFGANEDEIRHLLEYAKQLD T0547 225 :EQFTMIHFHLGSQITEIHPLKKALNEAGNIYTELRKM 2nvaA 168 :IEVIGISFHVGSGSRNPEAYYRAIKSSKEAFNEAISV T0547 263 :AKNLKAINLGGGLAVEY 2nvaA 205 :GHKPYILDIGGGLHADI T0547 285 :EK 2nvaA 227 :ST T0547 294 :EYANDVVFILKN 2nvaA 229 :YMSDYINDAIKD T0547 309 :QKKDLEPDIFIESGRFVAANHAVLIAPVLELFSQEYAENKLILKKQNPKLIDELY 2nvaA 241 :FFPEDTVTIVAEPGRFFAEHYSVLATQVIGKRVRDGLYEYFFNESTYGGFSNVIF T0547 367 :KSIKPS 2nvaA 296 :EKSVPT T0547 373 :NALEYLHDSIDHLESILTLFDLGYVDLQDR 2nvaA 308 :VPDDEEYVPSVLYGCTCDGVDVINHNVALP T0547 403 :SNAEILTHLITKKAILLLGDKQNPADLL 2nvaA 339 :LHIGDWVYFPSWGAYTNVLTTSFNGFGE Number of specific fragments extracted= 14 number of extra gaps= 0 total=512 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 7odcA/T0547-7odcA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 7odcA expands to /projects/compbio/data/pdb/7odc.pdb.gz 7odcA:# T0547 read from 7odcA/T0547-7odcA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 7odcA read from 7odcA/T0547-7odcA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 7odcA to template set # found chain 7odcA in template set Warning: unaligning (T0547)Y43 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (7odcA)D36 Warning: unaligning (T0547)L186 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (7odcA)K169 Warning: unaligning (T0547)K203 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (7odcA)K169 Warning: unaligning (T0547)E343 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (7odcA)E311 Warning: unaligning (T0547)Y344 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (7odcA)E311 T0547 18 :NGKVCINYEKKPAIIDIVKELR 7odcA 7 :DEFDCHILDEGFTAKDILDQKI T0547 44 :KGPLLLRFPHLIQKQIENIYGNF 7odcA 37 :KDAFYVADLGDILKKHLRWLKAL T0547 77 :GGFNAVYPLKVNQYPGFVKNLVKLG 7odcA 60 :PRVTPFYAVKCNDSRAIVSTLAAIG T0547 106 :YGLEAGSKAELLLAMAYNNEGAPITVNGF 7odcA 85 :TGFDCASKTEIQLVQGLGVPAERVIYANP T0547 135 :KDRELINIGF 7odcA 115 :KQVSQIKYAA T0547 148 :EMGHNIT 7odcA 125 :SNGVQMM T0547 156 :TIEGLNELEAIIDIAKE 7odcA 132 :TFDSEIELMKVARAHPK T0547 178 :PNIGLRVR 7odcA 149 :AKLVLRIA T0547 204 :FGLTSTELIEAVNLLKENK 7odcA 170 :FGATLKTSRLLLERAKELN T0547 224 :LEQFT 7odcA 189 :IDVIG T0547 230 :IHFHLGSQITEIHPLKKALNEAGNIYTELRKMGA 7odcA 194 :VSFHVGSGCTDPDTFVQAVSDARCVFDMATEVGF T0547 265 :NLKAINLGGGLAVEY 7odcA 228 :SMHLLDIGGGFPGSE T0547 283 :KNEK 7odcA 243 :DTKL T0547 291 :TLREYANDVVFILKNIA 7odcA 247 :KFEEITSVINPALDKYF T0547 308 :EQKKD 7odcA 265 :SDSGV T0547 316 :DIFIESGRFVAANHAVLIAPVLELFSQ 7odcA 270 :RIIAEPGRYYVASAFTLAVNIIAKKTV T0547 345 :AENKLILKK 7odcA 312 :QTFMYYVND T0547 354 :QNPKLIDELYDLYK 7odcA 322 :VYGSFNCILYDHAH T0547 368 :SIKPSNALEYLHDSIDHLESILTLFDLGY 7odcA 342 :KRPKPDEKYYSSSIWGPTCDGLDRIVERC T0547 398 :DLQDRSNAEILTHLITKKAILLLGDKQNPADLLA 7odcA 371 :NLPEMHVGDWMLFENMGAYTVAAASTFNGFQRPN T0547 476 :ASIWD 7odcA 405 :IYYVM Number of specific fragments extracted= 21 number of extra gaps= 0 total=533 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 7odcA/T0547-7odcA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0547 read from 7odcA/T0547-7odcA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 7odcA read from 7odcA/T0547-7odcA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 7odcA in template set Warning: unaligning (T0547)Y43 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (7odcA)D36 Warning: unaligning (T0547)L186 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (7odcA)K169 Warning: unaligning (T0547)K203 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (7odcA)K169 Warning: unaligning (T0547)Y344 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (7odcA)E311 T0547 13 :NFIIKNGKVCINYEK 7odcA 3 :SFTKDEFDCHILDEG T0547 34 :IVKELRDD 7odcA 18 :FTAKDILD T0547 44 :KGPLLLRFPHLIQKQIENIYGNF 7odcA 37 :KDAFYVADLGDILKKHLRWLKAL T0547 77 :GGFNAVYPLKVNQYPGFVKNLVKLG 7odcA 60 :PRVTPFYAVKCNDSRAIVSTLAAIG T0547 106 :YGLEAGSKAELLLAMAYNNEGAPITVNGFKDRE 7odcA 85 :TGFDCASKTEIQLVQGLGVPAERVIYANPCKQV T0547 140 :INIGF 7odcA 118 :SQIKY T0547 146 :AAEMGHNI 7odcA 123 :AASNGVQM T0547 155 :LTIEGLNELEAIIDIAKE 7odcA 131 :MTFDSEIELMKVARAHPK T0547 178 :PNIGLRVR 7odcA 149 :AKLVLRIA T0547 204 :FGLTSTELIEAVNLLKENKL 7odcA 170 :FGATLKTSRLLLERAKELNI T0547 226 :QFTMIHFHLGSQITEIHPLKKALNEAGNIYTELRKMGA 7odcA 190 :DVIGVSFHVGSGCTDPDTFVQAVSDARCVFDMATEVGF T0547 265 :NLKAINLGGGLAVEY 7odcA 228 :SMHLLDIGGGFPGSE T0547 285 :EKSR 7odcA 243 :DTKL T0547 291 :TLREYANDVVFILKNIAEQK 7odcA 247 :KFEEITSVINPALDKYFPSD T0547 313 :LEPDIFIESGRFVAANHAVLIAPVLELFSQ 7odcA 267 :SGVRIIAEPGRYYVASAFTLAVNIIAKKTV T0547 345 :AENKLILKKQNPKLIDELYDLYKSIK 7odcA 312 :QTFMYYVNDGVYGSFNCILYDHAHVK T0547 371 :PSNALEYLHDSIDHLESILTLFDLGYVD 7odcA 342 :KRPKPDEKYYSSSIWGPTCDGLDRIVER T0547 399 :LQDRSNAEILTHLITKKAILLLGDKQNPADL 7odcA 372 :LPEMHVGDWMLFENMGAYTVAAASTFNGFQR Number of specific fragments extracted= 18 number of extra gaps= 0 total=551 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 7odcA/T0547-7odcA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0547 read from 7odcA/T0547-7odcA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 7odcA read from 7odcA/T0547-7odcA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 7odcA in template set Warning: unaligning (T0547)Y43 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (7odcA)D36 Warning: unaligning (T0547)L186 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (7odcA)K169 Warning: unaligning (T0547)K203 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (7odcA)K169 Warning: unaligning (T0547)E343 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (7odcA)E311 T0547 16 :IKNGKVCINYEKKPAIIDIVKELR 7odcA 5 :TKDEFDCHILDEGFTAKDILDQKI T0547 44 :KGPLLLRFPHLIQKQIENIYGNFN 7odcA 37 :KDAFYVADLGDILKKHLRWLKALP T0547 78 :GFNAVYPLKVNQYPGFVKNLVKLG 7odcA 61 :RVTPFYAVKCNDSRAIVSTLAAIG T0547 106 :YGLEAGSKAELLLAMAYNNEGAPITVNGFKDRELINIGFIAAEMG 7odcA 85 :TGFDCASKTEIQLVQGLGVPAERVIYANPCKQVSQIKYAASNGVQ T0547 154 :TLTIEGLNELEAIIDIAKE 7odcA 130 :MMTFDSEIELMKVARAHPK T0547 178 :PNIGLRVR 7odcA 149 :AKLVLRIA T0547 204 :FGLTSTELIEAVNLLKENK 7odcA 170 :FGATLKTSRLLLERAKELN T0547 225 :EQFTMIHFHLGSQITEIHPLKKALNEAGNIYTELRKM 7odcA 189 :IDVIGVSFHVGSGCTDPDTFVQAVSDARCVFDMATEV T0547 263 :AKNLKAINLGGGLAVEYSQ 7odcA 226 :GFSMHLLDIGGGFPGSEDT T0547 289 :NYTLREYANDVVFILKNIAE 7odcA 245 :KLKFEEITSVINPALDKYFP T0547 311 :KDLEPDIFIESGRFVAANHAVLIAPVLELFSQ 7odcA 265 :SDSGVRIIAEPGRYYVASAFTLAVNIIAKKTV T0547 344 :YAENKLILKKQNPKLIDELY 7odcA 312 :QTFMYYVNDGVYGSFNCILY T0547 368 :SIKPS 7odcA 333 :HAHVK T0547 373 :NALEYLHDSIDHLESILTLFDLGYVDLQDR 7odcA 344 :PKPDEKYYSSSIWGPTCDGLDRIVERCNLP T0547 403 :SNAEILTHLITKKAILLLGDKQNPADLL 7odcA 375 :MHVGDWMLFENMGAYTVAAASTFNGFQR T0547 474 :RSASIWDI 7odcA 403 :PNIYYVMS T0547 557 :LDTLEDL 7odcA 411 :RPMWQLM Number of specific fragments extracted= 17 number of extra gaps= 0 total=568 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 1tufA/T0547-1tufA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1tufA expands to /projects/compbio/data/pdb/1tuf.pdb.gz 1tufA:Bad short name: N1 for alphabet: pdb_atoms Bad short name: C2 for alphabet: pdb_atoms Bad short name: C2' for alphabet: pdb_atoms Bad short name: C3 for alphabet: pdb_atoms Bad short name: O3 for alphabet: pdb_atoms Bad short name: C4 for alphabet: pdb_atoms Bad short name: C4' for alphabet: pdb_atoms Bad short name: C5 for alphabet: pdb_atoms Bad short name: C6 for alphabet: pdb_atoms Bad short name: C5' for alphabet: pdb_atoms Bad short name: OP4 for alphabet: pdb_atoms Bad short name: P for alphabet: pdb_atoms Bad short name: OP1 for alphabet: pdb_atoms Bad short name: OP2 for alphabet: pdb_atoms Bad short name: OP3 for alphabet: pdb_atoms # T0547 read from 1tufA/T0547-1tufA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1tufA read from 1tufA/T0547-1tufA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1tufA to template set # found chain 1tufA in template set Warning: unaligning (T0547)L85 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1tufA)A84 Warning: unaligning (T0547)V87 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1tufA)A84 T0547 9 :WGNENFIIKNGKVCI 1tufA 16 :LGNDTVEIKDGRFFI T0547 27 :KKPAIIDIVKE 1tufA 31 :DGYDAIELAEK T0547 43 :YKGPLLLRFPHLIQKQIENIYGNFNKARKEFG 1tufA 42 :FGTPLYVMSEEQIKINYNRYIEAFKRWEEETG T0547 77 :GGFNAVYP 1tufA 74 :KEFIVAYA T0547 88 :NQYPGFVKNLVKLG 1tufA 85 :NANLAITRLLAKLG T0547 106 :YGLEAGSKAELLLAMAYNNEGAPITVNGF 1tufA 99 :CGADVVSGGELYIAKLSNVPSKKIVFNGN T0547 135 :KDRELINIGF 1tufA 129 :KTKEEIIMGI T0547 148 :EMGHNIT 1tufA 139 :EANIRAF T0547 156 :TIEGLNELEAIIDIAKE 1tufA 146 :NVDSISELILINETAKE T0547 174 :FKPKPNIGLRVRLHSAGVGIWAKSGG 1tufA 163 :LGETANVAFRINPNVNPKTHPKISTG T0547 200 :INSKFGLTS 1tufA 190 :KKNKFGLDV T0547 209 :TELIEAVNLLKENKLLEQFT 1tufA 201 :GIAMKAIKMALEMEYVNVVG T0547 230 :IHFHLGSQITEIHPLKKALNEAGNIYTELRKMGA 1tufA 221 :VHCHIGSQLTDISPFIEETRKVMDFVVELKEEGI T0547 265 :NLKAINLGGGLAVEYSQFKNEK 1tufA 255 :EIEDVNLGGGLGIPYYKDKQIP T0547 291 :TLREYANDVVFILKNI 1tufA 277 :TQKDLADAIINTMLKY T0547 309 :QKKDLEPDIFIESGRFVAANHAVLIAPVLELFSQEYAE 1tufA 293 :KDKVEMPNLILEPGRSLVATAGYLLGKVHHIKETPVTK T0547 348 :KLILKK 1tufA 331 :WVMIDA T0547 354 :QNPKLIDELYDLYKSIKPSNALE 1tufA 338 :MNDMMRPAMYEAYHHIINCKVKN T0547 377 :YLHDSIDHLESILTLFDLGY 1tufA 363 :EVVSIAGGLCESSDVFGRDR T0547 398 :DLQDRSNAEILTHLITKKAILLLGDKQNPADLLAIQDEVQER 1tufA 383 :ELDKVEVGDVLAIFDVGAYGISMANNYNARGRPRMVLTSKKG T0547 441 :LVNFSLFQSMPDFWGLE 1tufA 425 :VFLIRERETYADLIAKD T0547 462 :IMPLDR 1tufA 442 :IVPPHL Number of specific fragments extracted= 22 number of extra gaps= 0 total=590 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 1tufA/T0547-1tufA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0547 read from 1tufA/T0547-1tufA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1tufA read from 1tufA/T0547-1tufA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1tufA in template set Warning: unaligning (T0547)L85 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1tufA)A84 Warning: unaligning (T0547)V87 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1tufA)A84 T0547 23 :INYEKKPAIIDIVKELRDDGYKGPLLLRFPHLIQKQIENIYGNFNKARKEFGYK 1tufA 22 :EIKDGRFFIDGYDAIELAEKFGTPLYVMSEEQIKINYNRYIEAFKRWEEETGKE T0547 79 :FNAVYP 1tufA 76 :FIVAYA T0547 88 :NQYPGFVKNLVKLG 1tufA 85 :NANLAITRLLAKLG T0547 106 :YGLEAGSKAELLLAMAYNNEGAPITVNGFKDRE 1tufA 99 :CGADVVSGGELYIAKLSNVPSKKIVFNGNCKTK T0547 140 :INIGF 1tufA 132 :EEIIM T0547 146 :AAEMGHNI 1tufA 137 :GIEANIRA T0547 155 :LTIEGLNELEAIIDIAKE 1tufA 145 :FNVDSISELILINETAKE T0547 174 :FKPKPNIGLRVRLH 1tufA 163 :LGETANVAFRINPN T0547 188 :SAGVGIWAKSGGINSKFGLTST 1tufA 178 :NPKTHPKISTGLKKNKFGLDVE T0547 210 :ELIEAVNLLKENKLL 1tufA 202 :IAMKAIKMALEMEYV T0547 226 :QFTMIHFHLGSQITEIHPLKKALNEAGNIYTELRKMGA 1tufA 217 :NVVGVHCHIGSQLTDISPFIEETRKVMDFVVELKEEGI T0547 265 :NLKAINLGGGLAVEY 1tufA 255 :EIEDVNLGGGLGIPY T0547 282 :FKNEKSR 1tufA 270 :YKDKQIP T0547 291 :TLREYANDVVFILKNI 1tufA 277 :TQKDLADAIINTMLKY T0547 309 :QKKDLEPDIFIESGRFVAANHAVLIAPVLELFSQEY 1tufA 293 :KDKVEMPNLILEPGRSLVATAGYLLGKVHHIKETPV T0547 346 :ENKLILKKQNPKLIDE 1tufA 329 :TKWVMIDAGMNDMMRP T0547 362 :LYDLYKSIKPSNALE 1tufA 346 :MYEAYHHIINCKVKN T0547 378 :LHDSIDHLESILTLFDLGYVD 1tufA 361 :EKEVVSIAGGLCESSDVFGRD T0547 399 :LQDRSNAEILTHLITKKAILLLGDKQNPAD 1tufA 384 :LDKVEVGDVLAIFDVGAYGISMANNYNARG T0547 429 :L 1tufA 415 :P T0547 536 :AIISINEKGYEVEG 1tufA 416 :RMVLTSKKGVFLIR T0547 582 :KLVNDKQK 1tufA 430 :ERETYADL Number of specific fragments extracted= 22 number of extra gaps= 0 total=612 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 1tufA/T0547-1tufA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0547 read from 1tufA/T0547-1tufA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1tufA read from 1tufA/T0547-1tufA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1tufA in template set Warning: unaligning (T0547)L85 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1tufA)A84 Warning: unaligning (T0547)V87 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1tufA)A84 T0547 22 :CINYEKKPAIIDIVKELRDDGYKGPLLLRFPHLIQKQIENIYGNFNKARKE 1tufA 21 :VEIKDGRFFIDGYDAIELAEKFGTPLYVMSEEQIKINYNRYIEAFKRWEEE T0547 75 :YKGGFNAVYP 1tufA 72 :TGKEFIVAYA T0547 88 :NQYPGFVKNLVKLG 1tufA 85 :NANLAITRLLAKLG T0547 106 :YGLEAGSKAELLLAMAYNNEGAPITVNGFKDRELINIGFIAAEMG 1tufA 99 :CGADVVSGGELYIAKLSNVPSKKIVFNGNCKTKEEIIMGIEANIR T0547 154 :TLTIEGLNELEAIIDIAKE 1tufA 144 :AFNVDSISELILINETAKE T0547 174 :FKPKPNIGLRVRLHSAGVGI 1tufA 163 :LGETANVAFRINPNVNPKTH T0547 194 :WAKSGGINSKFGLTS 1tufA 184 :KISTGLKKNKFGLDV T0547 209 :TELIEAVNLLKENK 1tufA 201 :GIAMKAIKMALEME T0547 224 :LEQFTMIHFHLGSQITEIHPLKKALNEAGNIYTELRKM 1tufA 215 :YVNVVGVHCHIGSQLTDISPFIEETRKVMDFVVELKEE T0547 263 :AKNLKAINLGGGLAVEYSQFKNEKS 1tufA 253 :GIEIEDVNLGGGLGIPYYKDKQIPT T0547 292 :LREYANDVVFILKNI 1tufA 278 :QKDLADAIINTMLKY T0547 309 :QKKDLEPDIFIESGRFVAANHAVLIAPVLELFSQEYAENKLILKKQNPKLIDELYDLYKSIKPS 1tufA 293 :KDKVEMPNLILEPGRSLVATAGYLLGKVHHIKETPVTKWVMIDAGMNDMMRPAMYEAYHHIINC T0547 374 :ALE 1tufA 358 :VKN T0547 378 :LHDSIDHLESILTLFDLGYVDLQDR 1tufA 361 :EKEVVSIAGGLCESSDVFGRDRELD T0547 403 :SNAEILTHLITKKAILLLGDKQNPADLLAIQDEVQERYLVNFSLFQSMPDFWGL 1tufA 387 :VEVGDVLAIFDVGAYGISMANNYNARGRPRMVLTSKKGVFLIRERETYADLIAK T0547 469 :D 1tufA 441 :D Number of specific fragments extracted= 16 number of extra gaps= 0 total=628 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 3gwqA/T0547-3gwqA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 3gwqA expands to /projects/compbio/data/pdb/3gwq.pdb.gz 3gwqA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 128, because occupancy 0.500 <= existing 0.500 in 3gwqA Skipped atom 132, because occupancy 0.500 <= existing 0.500 in 3gwqA Skipped atom 134, because occupancy 0.500 <= existing 0.500 in 3gwqA Skipped atom 136, because occupancy 0.500 <= existing 0.500 in 3gwqA Skipped atom 138, because occupancy 0.500 <= existing 0.500 in 3gwqA Skipped atom 140, because occupancy 0.500 <= existing 0.500 in 3gwqA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 527, because occupancy 0.500 <= existing 0.500 in 3gwqA Skipped atom 531, because occupancy 0.500 <= existing 0.500 in 3gwqA Skipped atom 533, because occupancy 0.500 <= existing 0.500 in 3gwqA Skipped atom 535, because occupancy 0.500 <= existing 0.500 in 3gwqA Skipped atom 537, because occupancy 0.500 <= existing 0.500 in 3gwqA Skipped atom 539, because occupancy 0.500 <= existing 0.500 in 3gwqA Skipped atom 541, because occupancy 0.500 <= existing 0.500 in 3gwqA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 767, because occupancy 0.500 <= existing 0.500 in 3gwqA Skipped atom 771, because occupancy 0.500 <= existing 0.500 in 3gwqA Skipped atom 773, because occupancy 0.500 <= existing 0.500 in 3gwqA Skipped atom 775, because occupancy 0.500 <= existing 0.500 in 3gwqA Skipped atom 777, because occupancy 0.500 <= existing 0.500 in 3gwqA Skipped atom 779, because occupancy 0.500 <= existing 0.500 in 3gwqA Skipped atom 781, because occupancy 0.500 <= existing 0.500 in 3gwqA Skipped atom 783, because occupancy 0.500 <= existing 0.500 in 3gwqA Skipped atom 808, because occupancy 0.500 <= existing 0.500 in 3gwqA Skipped atom 812, because occupancy 0.500 <= existing 0.500 in 3gwqA Skipped atom 814, because occupancy 0.500 <= existing 0.500 in 3gwqA Skipped atom 816, because occupancy 0.500 <= existing 0.500 in 3gwqA Skipped atom 818, because occupancy 0.500 <= existing 0.500 in 3gwqA Skipped atom 820, because occupancy 0.500 <= existing 0.500 in 3gwqA Skipped atom 822, because occupancy 0.500 <= existing 0.500 in 3gwqA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 921, because occupancy 0.500 <= existing 0.500 in 3gwqA Skipped atom 925, because occupancy 0.500 <= existing 0.500 in 3gwqA Skipped atom 927, because occupancy 0.500 <= existing 0.500 in 3gwqA Skipped atom 929, because occupancy 0.500 <= existing 0.500 in 3gwqA Skipped atom 931, because occupancy 0.500 <= existing 0.500 in 3gwqA Skipped atom 933, because occupancy 0.500 <= existing 0.500 in 3gwqA Skipped atom 935, because occupancy 0.500 <= existing 0.500 in 3gwqA Skipped atom 937, because occupancy 0.500 <= existing 0.500 in 3gwqA Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 959, because occupancy 0.500 <= existing 0.500 in 3gwqA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 963, because occupancy 0.500 <= existing 0.500 in 3gwqA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 965, because occupancy 0.500 <= existing 0.500 in 3gwqA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 969, because occupancy 0.500 <= existing 0.500 in 3gwqA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 980, because occupancy 0.500 <= existing 0.500 in 3gwqA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 984, because occupancy 0.500 <= existing 0.500 in 3gwqA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 986, because occupancy 0.500 <= existing 0.500 in 3gwqA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 988, because occupancy 0.370 <= existing 0.380 in 3gwqA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 990, because occupancy 0.500 <= existing 0.500 in 3gwqA Skipped atom 1030, because occupancy 0.500 <= existing 0.500 in 3gwqA Skipped atom 1034, because occupancy 0.500 <= existing 0.500 in 3gwqA Skipped atom 1036, because occupancy 0.500 <= existing 0.500 in 3gwqA Skipped atom 1426, because occupancy 0.500 <= existing 0.500 in 3gwqA Skipped atom 1430, because occupancy 0.500 <= existing 0.500 in 3gwqA Skipped atom 1432, because occupancy 0.500 <= existing 0.500 in 3gwqA Skipped atom 1434, because occupancy 0.500 <= existing 0.500 in 3gwqA Skipped atom 1436, because occupancy 0.500 <= existing 0.500 in 3gwqA Skipped atom 1438, because occupancy 0.500 <= existing 0.500 in 3gwqA Skipped atom 1440, because occupancy 0.500 <= existing 0.500 in 3gwqA Skipped atom 1442, because occupancy 0.500 <= existing 0.500 in 3gwqA Skipped atom 1833, because occupancy 0.500 <= existing 0.500 in 3gwqA Skipped atom 1837, because occupancy 0.500 <= existing 0.500 in 3gwqA Skipped atom 1839, because occupancy 0.500 <= existing 0.500 in 3gwqA Skipped atom 1841, because occupancy 0.500 <= existing 0.500 in 3gwqA Skipped atom 1843, because occupancy 0.500 <= existing 0.500 in 3gwqA Skipped atom 1845, because occupancy 0.500 <= existing 0.500 in 3gwqA Skipped atom 1847, because occupancy 0.500 <= existing 0.500 in 3gwqA Skipped atom 1849, because occupancy 0.500 <= existing 0.500 in 3gwqA Skipped atom 1930, because occupancy 0.500 <= existing 0.500 in 3gwqA Skipped atom 1934, because occupancy 0.500 <= existing 0.500 in 3gwqA Skipped atom 1936, because occupancy 0.500 <= existing 0.500 in 3gwqA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 2588, because occupancy 0.500 <= existing 0.500 in 3gwqA Skipped atom 2592, because occupancy 0.500 <= existing 0.500 in 3gwqA Skipped atom 2594, because occupancy 0.500 <= existing 0.500 in 3gwqA Skipped atom 2596, because occupancy 0.500 <= existing 0.500 in 3gwqA Skipped atom 2598, because occupancy 0.500 <= existing 0.500 in 3gwqA Skipped atom 2600, because occupancy 0.500 <= existing 0.500 in 3gwqA Skipped atom 2602, because occupancy 0.500 <= existing 0.500 in 3gwqA Skipped atom 2604, because occupancy 0.500 <= existing 0.500 in 3gwqA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 3187, because occupancy 0.500 <= existing 0.500 in 3gwqA Skipped atom 3191, because occupancy 0.500 <= existing 0.500 in 3gwqA Skipped atom 3193, because occupancy 0.500 <= existing 0.500 in 3gwqA Skipped atom 3195, because occupancy 0.500 <= existing 0.500 in 3gwqA Skipped atom 3197, because occupancy 0.500 <= existing 0.500 in 3gwqA # T0547 read from 3gwqA/T0547-3gwqA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3gwqA read from 3gwqA/T0547-3gwqA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3gwqA to template set # found chain 3gwqA in template set Warning: unaligning (T0547)P335 because of BadResidue code BAD_PEPTIDE in next template residue (3gwqA)V318 Warning: unaligning (T0547)V336 because of BadResidue code BAD_PEPTIDE at template residue (3gwqA)V318 T0547 5 :GIDI 3gwqA 35 :EWNL T0547 39 :RDDGYKGPLLLRFPHLIQKQIENIYGNFNKA 3gwqA 39 :LNEDVSLPAAVLYADRVEHNLKWMQAFVAEY T0547 78 :GFNAVYPLKVNQYPGFVKNLVKLGK 3gwqA 70 :GVKLAPHGKTTMAPQLFRRQLETGA T0547 106 :YGLEAGSKAELLLAMAYNN 3gwqA 95 :WGITLATAHQVRAAYHGGV T0547 127 :APITVNGF 3gwqA 114 :SRVLMANQ T0547 135 :KDRELINIGFIAAE 3gwqA 123 :VGRRNMMMVAELLS T0547 149 :MGHNITLTIEGLNELEAIIDIAKE 3gwqA 138 :PEFEFFCLVDSVEGVEQLGEFFKS T0547 174 :FKPKPNIGLRV 3gwqA 162 :VNKQLQVLLEL T0547 187 :HSAGV 3gwqA 173 :GVPGG T0547 203 :KFGL 3gwqA 178 :RTGV T0547 207 :TSTELIEAVNLLKEN 3gwqA 183 :DAAQRNAVLEAITRY T0547 222 :KLLEQFT 3gwqA 199 :DTLKLAG T0547 230 :IHFHLG 3gwqA 206 :VELYEG T0547 237 :QITEIHPLKKALNEAGNIYTELRKMGAK 3gwqA 212 :VLKEEHEVREFLQSAVAVTRELVEQERF T0547 265 :NLKAINLGGGLAV 3gwqA 242 :APAVLSGAGSAWY T0547 293 :REYAND 3gwqA 255 :DVVAEE T0547 303 :LKNIAEQ 3gwqA 261 :FVKASET T0547 313 :LEPDIFIESGRFVAA 3gwqA 268 :GKVEVVLRPGCYLTH T0547 328 :NHAVLIA 3gwqA 310 :PALQLWA T0547 337 :LELFSQE 3gwqA 319 :QSIPEPD T0547 348 :KLILKK 3gwqA 326 :RAIIGL T0547 354 :QNPKLIDE 3gwqA 333 :KRDSAFDA T0547 367 :KSI 3gwqA 341 :GMP T0547 370 :KPSNALE 3gwqA 355 :APRDIAA T0547 377 :YLHDSIDHLES 3gwqA 363 :EGWEIFGLMDQ T0547 389 :LTLFDLG 3gwqA 374 :HAYLRIP T0547 398 :DLQDRSNAEILTHL 3gwqA 381 :AGADLKVGDMIAFD T0547 450 :MPDFWGLEQNFPI 3gwqA 395 :ISHPCLTFDKWRQ T0547 512 :GFFL 3gwqA 408 :VLVV T0547 542 :EKGYEVEGIIEA 3gwqA 412 :DPAYRVTEVIET Number of specific fragments extracted= 30 number of extra gaps= 1 total=658 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 3gwqA/T0547-3gwqA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0547 read from 3gwqA/T0547-3gwqA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3gwqA read from 3gwqA/T0547-3gwqA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3gwqA in template set Warning: unaligning (T0547)P335 because of BadResidue code BAD_PEPTIDE in next template residue (3gwqA)V318 Warning: unaligning (T0547)V336 because of BadResidue code BAD_PEPTIDE at template residue (3gwqA)V318 T0547 27 :KKPAIIDIVKELRDDGYKGPLLLRFPHLIQKQIENIYGNFNKA 3gwqA 27 :QLTDAARLEWNLLNEDVSLPAAVLYADRVEHNLKWMQAFVAEY T0547 78 :GFNAVYPLKVNQYPGFVKNLVKLGK 3gwqA 70 :GVKLAPHGKTTMAPQLFRRQLETGA T0547 106 :YGLEAGSKAELLLAMAYNNE 3gwqA 95 :WGITLATAHQVRAAYHGGVS T0547 128 :PITVNGFKDRE 3gwqA 115 :RVLMANQLVGR T0547 140 :INIGF 3gwqA 126 :RNMMM T0547 146 :AAEM 3gwqA 131 :VAEL T0547 150 :GHNITLTIEGLNELEAIIDIAKE 3gwqA 139 :EFEFFCLVDSVEGVEQLGEFFKS T0547 174 :FKPKPNIGLRVRLHS 3gwqA 162 :VNKQLQVLLELGVPG T0547 202 :SKFGLTS 3gwqA 177 :GRTGVRD T0547 209 :TELIEAVNLLKEN 3gwqA 185 :AQRNAVLEAITRY T0547 222 :KLL 3gwqA 199 :DTL T0547 226 :QFTMIHFHLGSQ 3gwqA 202 :KLAGVELYEGVL T0547 239 :TEIHPLKKALNEAGNIYTELRKMGAK 3gwqA 214 :KEEHEVREFLQSAVAVTRELVEQERF T0547 265 :NLKAINLGGGLAV 3gwqA 241 :RAPAVLSGAGSAW T0547 296 :ANDVVFILKNIAEQ 3gwqA 254 :YDVVAEEFVKASET T0547 313 :LEPDIFIESGRFV 3gwqA 268 :GKVEVVLRPGCYL T0547 328 :NHAVLIA 3gwqA 310 :PALQLWA T0547 337 :LELFSQ 3gwqA 319 :QSIPEP T0547 347 :NKLILKKQNPKLIDE 3gwqA 325 :DRAIIGLGKRDSAFD T0547 367 :KSIK 3gwqA 341 :GMPE T0547 377 :YLHD 3gwqA 359 :IAAS T0547 381 :SIDHLE 3gwqA 364 :GWEIFG T0547 388 :ILTLFDLGYVD 3gwqA 370 :LMDQHAYLRIP T0547 399 :LQDRSNAEILTHLITKKA 3gwqA 382 :GADLKVGDMIAFDISHPC T0547 417 :ILLLGD 3gwqA 401 :TFDKWR T0547 538 :ISINEKGYEVEGIIEAQ 3gwqA 408 :VLVVDPAYRVTEVIETF Number of specific fragments extracted= 26 number of extra gaps= 1 total=684 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 3gwqA/T0547-3gwqA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0547 read from 3gwqA/T0547-3gwqA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3gwqA read from 3gwqA/T0547-3gwqA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3gwqA in template set Warning: unaligning (T0547)P335 because of BadResidue code BAD_PEPTIDE in next template residue (3gwqA)V318 Warning: unaligning (T0547)V336 because of BadResidue code BAD_PEPTIDE at template residue (3gwqA)V318 T0547 39 :RDDGYKGPLLLRFPHLIQKQIENIYGNFNKA 3gwqA 39 :LNEDVSLPAAVLYADRVEHNLKWMQAFVAEY T0547 78 :GFNAVYPLKVNQYPGFVKNLVKLGK 3gwqA 70 :GVKLAPHGKTTMAPQLFRRQLETGA T0547 106 :YGLEAGSKAELLLAMAYNNE 3gwqA 95 :WGITLATAHQVRAAYHGGVS T0547 127 :APITVNGFKDRELINIGFIAAEMGH 3gwqA 115 :RVLMANQLVGRRNMMMVAELLSDPE T0547 152 :NITLTIEGLNELEAIIDIAKE 3gwqA 141 :EFFCLVDSVEGVEQLGEFFKS T0547 174 :FKPKPNIGLRVRLHSAGV 3gwqA 162 :VNKQLQVLLELGVPGGRT T0547 205 :GLTS 3gwqA 180 :GVRD T0547 209 :TELIEAVNLLKENKLLEQFTMIHFHLG 3gwqA 185 :AQRNAVLEAITRYPDTLKLAGVELYEG T0547 237 :QITEIHPLKKALNEAGNIYTELRKMGAKNLK 3gwqA 212 :VLKEEHEVREFLQSAVAVTRELVEQERFARA T0547 268 :AINLGGGLAV 3gwqA 244 :AVLSGAGSAW T0547 292 :LREYANDVVFI 3gwqA 254 :YDVVAEEFVKA T0547 307 :A 3gwqA 265 :S T0547 311 :KDLEPDIFIESGRFV 3gwqA 266 :ETGKVEVVLRPGCYL T0547 328 :NHAVLIA 3gwqA 310 :PALQLWA T0547 337 :LELFSQ 3gwqA 319 :QSIPEP T0547 345 :AENKLILKKQN 3gwqA 344 :EPARHYRPGNE T0547 373 :NALEYLHDSID 3gwqA 361 :ASEGWEIFGLM T0547 393 :DLGYVDLQDR 3gwqA 373 :QHAYLRIPAG T0547 403 :SNAEILTHLITKKAILLLGD 3gwqA 385 :LKVGDMIAFDISHPCLTFDK T0547 460 :F 3gwqA 405 :W T0547 508 :NY 3gwqA 406 :RQ T0547 538 :ISINEKGYEVEGIIE 3gwqA 408 :VLVVDPAYRVTEVIE Number of specific fragments extracted= 22 number of extra gaps= 1 total=706 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 2dy3A/T0547-2dy3A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2dy3A expands to /projects/compbio/data/pdb/2dy3.pdb.gz 2dy3A:# T0547 read from 2dy3A/T0547-2dy3A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2dy3A read from 2dy3A/T0547-2dy3A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2dy3A to template set # found chain 2dy3A in template set Warning: unaligning (T0547)Y43 because first residue in template chain is (2dy3A)M1 Warning: unaligning (T0547)G235 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2dy3A)E169 Warning: unaligning (T0547)P243 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2dy3A)E169 Warning: unaligning (T0547)E343 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (2dy3A)R265 Warning: unaligning (T0547)A345 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR at template residue (2dy3A)R265 T0547 44 :KGPLLLRFPHLIQKQIENIYGNF 2dy3A 2 :NLLTTKIDLDAIAHNTRVLKQMA T0547 77 :GGFNAVYPLKV 2dy3A 25 :GPAKLMAVVKA T0547 88 :NQYPGFVKNLVKLGK 2dy3A 40 :HGVEKVAPVIAAHGA T0547 106 :YGLEAGSKAELLLAMAYNNE 2dy3A 55 :DAFGVATLAEAMQLRDIGIS T0547 127 :APITVNGF 2dy3A 75 :QEVLCWIW T0547 135 :K 2dy3A 84 :P T0547 140 :INIGF 2dy3A 88 :FRAAI T0547 148 :EMGH 2dy3A 93 :DRNI T0547 153 :I 2dy3A 97 :D T0547 155 :LTIEGLNELEAIID 2dy3A 98 :LAVISPAHAKALIE T0547 173 :RFKPKPNIGLRVRLHSA 2dy3A 112 :TDAEHIRVSIKIDSGLH T0547 203 :KFGLTSTELIEAVNLLKENKLLEQFT 2dy3A 129 :RSGVDEQEWEGVFSALAAAPHIEVTG T0547 230 :IHFHL 2dy3A 155 :MFTHL T0547 244 :LKKALNEAGNIYTELRKMGA 2dy3A 170 :TDRQIIAFRRALALARKHGL T0547 265 :NLKAINLG 2dy3A 190 :ECPVNHVC T0547 291 :TLREYA 2dy3A 198 :NSPAFL T0547 306 :IAEQKK 2dy3A 204 :TRSDLH T0547 315 :PDI 2dy3A 210 :MEM T0547 319 :IESGRFVAA 2dy3A 213 :VRPGLAFYG T0547 328 :NHAVLIAPVLELFSQ 2dy3A 234 :PAMTWEAKVSVVKQI T0547 346 :ENKLILKK 2dy3A 266 :GFVAVVPA T0547 354 :QNPKLIDEL 2dy3A 275 :YADGMPRHA T0547 372 :SNALE 2dy3A 284 :QGKFS T0547 377 :YLHDSIDHLESILTLFDL 2dy3A 294 :LDYPQVGRVCMDQFVISL T0547 398 :DLQ 2dy3A 313 :DNP T0547 401 :DRSNAEILTHLITKKAILLLGDKQNPADLLAIQDEVQERY 2dy3A 317 :GVEAGAKAVIFGENGHDATDFAERLDTINYEVVCRPTGRT Number of specific fragments extracted= 26 number of extra gaps= 0 total=732 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 2dy3A/T0547-2dy3A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0547 read from 2dy3A/T0547-2dy3A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2dy3A read from 2dy3A/T0547-2dy3A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2dy3A in template set Warning: unaligning (T0547)Y43 because first residue in template chain is (2dy3A)M1 Warning: unaligning (T0547)G235 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2dy3A)E169 Warning: unaligning (T0547)A345 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR at template residue (2dy3A)R265 T0547 44 :KGPLLLRFPHLIQKQIENIYGNF 2dy3A 2 :NLLTTKIDLDAIAHNTRVLKQMA T0547 77 :GGFNAVYPLKVNQY 2dy3A 25 :GPAKLMAVVKANAY T0547 91 :PGFVKNLVKLGK 2dy3A 43 :EKVAPVIAAHGA T0547 106 :YGLEAGSKAELLLAMAYNNE 2dy3A 55 :DAFGVATLAEAMQLRDIGIS T0547 127 :APITVNGFKDR 2dy3A 75 :QEVLCWIWTPE T0547 140 :INIGF 2dy3A 86 :QDFRA T0547 146 :AAEMGH 2dy3A 91 :AIDRNI T0547 153 :I 2dy3A 97 :D T0547 155 :LTIEGLNELEAIID 2dy3A 98 :LAVISPAHAKALIE T0547 173 :RFKPKPNIGLRVRLH 2dy3A 112 :TDAEHIRVSIKIDSG T0547 188 :S 2dy3A 128 :H T0547 203 :KFGLTSTELIEAVNLLKENKLL 2dy3A 129 :RSGVDEQEWEGVFSALAAAPHI T0547 226 :QFTMIHFHL 2dy3A 151 :EVTGMFTHL T0547 244 :LKKALNEAGNIYTELRKMGA 2dy3A 170 :TDRQIIAFRRALALARKHGL T0547 265 :NLKAINLGGGLAVEY 2dy3A 190 :ECPVNHVCNSPAFLT T0547 282 :FKNEKSR 2dy3A 205 :RSDLHME T0547 318 :FIESGRFVAA 2dy3A 212 :MVRPGLAFYG T0547 328 :NHAVLIAPVLELFSQ 2dy3A 234 :PAMTWEAKVSVVKQI T0547 346 :ENKLILKKQNPKLIDE 2dy3A 266 :GFVAVVPAGYADGMPR T0547 364 :DLYKSIK 2dy3A 282 :HAQGKFS T0547 378 :LHDSIDHLESILTLFDLGYVD 2dy3A 292 :DGLDYPQVGRVCMDQFVISLG T0547 399 :LQDRSNAEILTHLITKKAILLLGDKQNPADLLAIQD 2dy3A 315 :PHGVEAGAKAVIFGENGHDATDFAERLDTINYEVVC Number of specific fragments extracted= 22 number of extra gaps= 0 total=754 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 2dy3A/T0547-2dy3A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0547 read from 2dy3A/T0547-2dy3A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2dy3A read from 2dy3A/T0547-2dy3A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2dy3A in template set Warning: unaligning (T0547)G235 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2dy3A)E169 Warning: unaligning (T0547)E240 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2dy3A)E169 Warning: unaligning (T0547)E343 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (2dy3A)R265 Warning: unaligning (T0547)P371 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR at template residue (2dy3A)R265 T0547 45 :GPLLLRFPHLIQKQIENIYGNFN 2dy3A 3 :LLTTKIDLDAIAHNTRVLKQMAG T0547 78 :GFNAVYPLKVNQY 2dy3A 26 :PAKLMAVVKANAY T0547 91 :PGFVKNLVKLGK 2dy3A 43 :EKVAPVIAAHGA T0547 106 :YGLEAGSKAELLLAMAYNNEGAPITVNGFKD 2dy3A 55 :DAFGVATLAEAMQLRDIGISQEVLCWIWTPE T0547 141 :NIGFIAAEM 2dy3A 88 :FRAAIDRNI T0547 154 :TLTIEGLNELEAIID 2dy3A 97 :DLAVISPAHAKALIE T0547 173 :RFKPKPNIGLRVRLHSA 2dy3A 112 :TDAEHIRVSIKIDSGLH T0547 203 :KFGLTSTELIEAVNLLKENK 2dy3A 129 :RSGVDEQEWEGVFSALAAAP T0547 224 :LEQFTMIHFHL 2dy3A 149 :HIEVTGMFTHL T0547 241 :IHPLKKALNEAGN 2dy3A 170 :TDRQIIAFRRALA T0547 257 :ELRKM 2dy3A 183 :LARKH T0547 263 :AKNL 2dy3A 188 :GLEC T0547 285 :EKSRNYTLREYA 2dy3A 192 :PVNHVCNSPAFL T0547 309 :QKKDLEPDIFI 2dy3A 204 :TRSDLHMEMVR T0547 321 :SGRFVAA 2dy3A 215 :PGLAFYG T0547 328 :NHAVLIAPVLELFSQ 2dy3A 234 :PAMTWEAKVSVVKQI T0547 397 :VDLQDRSNAEILTHL 2dy3A 277 :DGMPRHAQGKFSVTI T0547 438 :ERYLVNFSLFQSMPD 2dy3A 292 :DGLDYPQVGRVCMDQ T0547 536 :AIISINE 2dy3A 307 :FVISLGD T0547 543 :KGYEVEGIIEAQ 2dy3A 320 :AGAKAVIFGENG T0547 555 :SILDTLEDLDYDIHAI 2dy3A 333 :DATDFAERLDTINYEV Number of specific fragments extracted= 21 number of extra gaps= 0 total=775 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 1rcqA/T0547-1rcqA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1rcqA expands to /projects/compbio/data/pdb/1rcq.pdb.gz 1rcqA:Bad short name: CX for alphabet: pdb_atoms Bad short name: OQ1 for alphabet: pdb_atoms Bad short name: OQ2 for alphabet: pdb_atoms # T0547 read from 1rcqA/T0547-1rcqA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1rcqA read from 1rcqA/T0547-1rcqA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1rcqA to template set # found chain 1rcqA in template set Warning: unaligning (T0547)K44 because first residue in template chain is (1rcqA)M1 Warning: unaligning (T0547)G78 because of BadResidue code BAD_PEPTIDE in next template residue (1rcqA)A26 Warning: unaligning (T0547)F79 because of BadResidue code BAD_PEPTIDE at template residue (1rcqA)A26 Warning: unaligning (T0547)I167 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (1rcqA)R110 Warning: unaligning (T0547)D168 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (1rcqA)R110 Warning: unaligning (T0547)L182 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1rcqA)M123 Warning: unaligning (T0547)V184 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1rcqA)M123 Warning: unaligning (T0547)N221 because of BadResidue code BAD_PEPTIDE in next template residue (1rcqA)G148 Warning: unaligning (T0547)K222 because of BadResidue code BAD_PEPTIDE at template residue (1rcqA)G148 Warning: unaligning (T0547)E346 because of BadResidue code BAD_PEPTIDE in next template residue (1rcqA)R264 Warning: unaligning (T0547)N347 because of BadResidue code BAD_PEPTIDE at template residue (1rcqA)R264 T0547 45 :GPL 1rcqA 2 :RPA T0547 48 :LLRFPHLIQKQIENIYGNF 1rcqA 6 :ALIDLQALRHNYRLAREAT T0547 80 :NAVYPLKV 1rcqA 27 :RALAVIKA T0547 88 :NQYPGFVKNLVKLG 1rcqA 39 :HGAVRCAEALAAEA T0547 106 :YGLEAGSKAELLLAMAYNNEGAPITVNGFKDRELINIGF 1rcqA 53 :DGFAVACIEEGLELREAGIRQPILLLEGFFEASELELIV T0547 148 :EMG 1rcqA 92 :AHD T0547 153 :ITLTIEGLNELEAI 1rcqA 95 :FWCVVHCAWQLEAI T0547 174 :FKPKPNIG 1rcqA 113 :LARPLNVW T0547 185 :RLHS 1rcqA 124 :DSGM T0547 191 :V 1rcqA 128 :H T0547 203 :KFGLTSTELIEAVNLLKE 1rcqA 129 :RVGFFPEDFRAAHERLRA T0547 223 :LLEQFT 1rcqA 149 :KVAKIV T0547 230 :IHFHLG 1rcqA 155 :MMSHFS T0547 236 :SQITEIHPLKKALNEAGNIY 1rcqA 162 :ADELDCPRTEEQLAAFSAAS T0547 262 :GAK 1rcqA 183 :GLE T0547 269 :INLGG 1rcqA 188 :ISLRN T0547 292 :LREYA 1rcqA 193 :SPAVL T0547 306 :IAEQ 1rcqA 198 :GWPK T0547 313 :LEPDIFI 1rcqA 202 :VPSDWVR T0547 320 :ESGRFVAANHAVLIAPVLELFSQE 1rcqA 223 :HPLADRLRPVMTLESKVISVRDLP T0547 344 :YA 1rcqA 261 :RR T0547 348 :KLILKK 1rcqA 265 :IGVVAM T0547 354 :QNPKLIDE 1rcqA 272 :YADGYPRH T0547 371 :PSNALE 1rcqA 280 :AADGTL T0547 377 :YLHDSIDHLESILTLFDLGY 1rcqA 291 :KPGRLVGRVSMDMLTVDLTD T0547 399 :LQDRSNAEILTHLITKKAILLLGDKQNPAD 1rcqA 311 :HPQAGLGSRVELWGPNVPVGALAAQFGSIP T0547 557 :LDTLED 1rcqA 341 :YQLLCN Number of specific fragments extracted= 27 number of extra gaps= 4 total=802 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 1rcqA/T0547-1rcqA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0547 read from 1rcqA/T0547-1rcqA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1rcqA read from 1rcqA/T0547-1rcqA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1rcqA in template set Warning: unaligning (T0547)Y43 because first residue in template chain is (1rcqA)M1 Warning: unaligning (T0547)G78 because of BadResidue code BAD_PEPTIDE in next template residue (1rcqA)A26 Warning: unaligning (T0547)F79 because of BadResidue code BAD_PEPTIDE at template residue (1rcqA)A26 Warning: unaligning (T0547)I167 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (1rcqA)R110 Warning: unaligning (T0547)D168 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (1rcqA)R110 Warning: unaligning (T0547)L182 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1rcqA)M123 Warning: unaligning (T0547)V184 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1rcqA)M123 Warning: unaligning (T0547)N221 because of BadResidue code BAD_PEPTIDE in next template residue (1rcqA)G148 Warning: unaligning (T0547)K222 because of BadResidue code BAD_PEPTIDE at template residue (1rcqA)G148 Warning: unaligning (T0547)E346 because of BadResidue code BAD_PEPTIDE in next template residue (1rcqA)R264 Warning: unaligning (T0547)N347 because of BadResidue code BAD_PEPTIDE at template residue (1rcqA)R264 T0547 44 :KGPLLLRFPHLIQKQIENIYGNF 1rcqA 2 :RPARALIDLQALRHNYRLAREAT T0547 80 :NAVYPLKVNQ 1rcqA 27 :RALAVIKADA T0547 90 :YPGFVKNLVKLG 1rcqA 41 :AVRCAEALAAEA T0547 106 :YGLEAGSKAELLLAMAYNNEGAPITVNGFKDREL 1rcqA 53 :DGFAVACIEEGLELREAGIRQPILLLEGFFEASE T0547 142 :IGF 1rcqA 87 :LEL T0547 146 :AAEMG 1rcqA 90 :IVAHD T0547 153 :ITLTIEGLNELEAI 1rcqA 95 :FWCVVHCAWQLEAI T0547 173 :RFKPKPNIG 1rcqA 112 :SLARPLNVW T0547 185 :RLH 1rcqA 124 :DSG T0547 202 :SKFGLTSTELIEAVNLLKE 1rcqA 128 :HRVGFFPEDFRAAHERLRA T0547 223 :LL 1rcqA 149 :KV T0547 226 :QFTMIHFHLG 1rcqA 151 :AKIVMMSHFS T0547 236 :SQITEIHPLKKALNEAGNIY 1rcqA 162 :ADELDCPRTEEQLAAFSAAS T0547 261 :MGA 1rcqA 182 :QGL T0547 265 :NLK 1rcqA 185 :EGE T0547 269 :INLGGGLAVEY 1rcqA 188 :ISLRNSPAVLG T0547 282 :FKNEK 1rcqA 199 :WPKVP T0547 315 :PDI 1rcqA 204 :SDW T0547 319 :IESGRFVAA 1rcqA 207 :VRPGILLYG T0547 328 :NHAVLIAPVLELFSQ 1rcqA 231 :PVMTLESKVISVRDL T0547 343 :EY 1rcqA 261 :RR T0547 348 :KLILKKQNPKLIDE 1rcqA 265 :IGVVAMGYADGYPR T0547 362 :LYDLYK 1rcqA 280 :AADGTL T0547 378 :LHDSIDHLESILTLFDLGYVD 1rcqA 289 :DGKPGRLVGRVSMDMLTVDLT T0547 399 :LQDRSNAEILTHLITKKAILLLGDKQNPADLLAIQ 1rcqA 311 :HPQAGLGSRVELWGPNVPVGALAAQFGSIPYQLLC Number of specific fragments extracted= 25 number of extra gaps= 4 total=827 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 1rcqA/T0547-1rcqA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0547 read from 1rcqA/T0547-1rcqA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1rcqA read from 1rcqA/T0547-1rcqA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1rcqA in template set Warning: unaligning (T0547)G78 because of BadResidue code BAD_PEPTIDE in next template residue (1rcqA)A26 Warning: unaligning (T0547)F79 because of BadResidue code BAD_PEPTIDE at template residue (1rcqA)A26 Warning: unaligning (T0547)I167 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (1rcqA)R110 Warning: unaligning (T0547)D168 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (1rcqA)R110 Warning: unaligning (T0547)L182 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1rcqA)M123 Warning: unaligning (T0547)V184 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1rcqA)M123 Warning: unaligning (T0547)N221 because of BadResidue code BAD_PEPTIDE in next template residue (1rcqA)G148 Warning: unaligning (T0547)K222 because of BadResidue code BAD_PEPTIDE at template residue (1rcqA)G148 Warning: unaligning (T0547)I407 because of BadResidue code BAD_PEPTIDE in next template residue (1rcqA)R264 Warning: unaligning (T0547)L408 because of BadResidue code BAD_PEPTIDE at template residue (1rcqA)R264 T0547 45 :GPLLLRFPHLIQKQIENIYGNF 1rcqA 3 :PARALIDLQALRHNYRLAREAT T0547 80 :NAVYPLKV 1rcqA 27 :RALAVIKA T0547 88 :NQYPGFVKNLVKLG 1rcqA 39 :HGAVRCAEALAAEA T0547 106 :YGLEAGSKAELLLAMAYNNEGAPITVNGFKDREL 1rcqA 53 :DGFAVACIEEGLELREAGIRQPILLLEGFFEASE T0547 141 :NIGFIAAEM 1rcqA 87 :LELIVAHDF T0547 154 :TLTIEGLNELEAI 1rcqA 96 :WCVVHCAWQLEAI T0547 174 :FKPKPNIG 1rcqA 113 :LARPLNVW T0547 185 :RLHS 1rcqA 124 :DSGM T0547 202 :SKFGLTSTELIEAVNLLKE 1rcqA 128 :HRVGFFPEDFRAAHERLRA T0547 224 :LEQFTMIHFHLGS 1rcqA 149 :KVAKIVMMSHFSR T0547 237 :QITEIHPLKKALNEAGNIYT 1rcqA 163 :DELDCPRTEEQLAAFSAASQ T0547 263 :AKNLKAI 1rcqA 183 :GLEGEIS T0547 287 :S 1rcqA 192 :N T0547 304 :KNIAEQKKDLEPDIFI 1rcqA 193 :SPAVLGWPKVPSDWVR T0547 321 :SGRFVAA 1rcqA 209 :PGILLYG T0547 328 :NHAVLIAPVLELFSQEYAENK 1rcqA 231 :PVMTLESKVISVRDLPAGEPV T0547 396 :YVDLQ 1rcqA 252 :GYGAR T0547 403 :SNAE 1rcqA 259 :TERR T0547 409 :THLITKKAILLLGDKQNPADLLA 1rcqA 265 :IGVVAMGYADGYPRHAADGTLVF T0547 438 :ERYLVNFSLFQSMP 1rcqA 289 :DGKPGRLVGRVSMD T0547 535 :EAIISINE 1rcqA 303 :MLTVDLTD T0547 543 :KGYEVEGIIEAQSILDTLEDLD 1rcqA 316 :LGSRVELWGPNVPVGALAAQFG Number of specific fragments extracted= 22 number of extra gaps= 4 total=849 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 1xfcA/T0547-1xfcA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1xfcA expands to /projects/compbio/data/pdb/1xfc.pdb.gz 1xfcA:# T0547 read from 1xfcA/T0547-1xfcA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1xfcA read from 1xfcA/T0547-1xfcA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1xfcA to template set # found chain 1xfcA in template set Warning: unaligning (T0547)G45 because first residue in template chain is (1xfcA)L11 Warning: unaligning (T0547)H187 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (1xfcA)L138 Warning: unaligning (T0547)S188 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (1xfcA)L138 Warning: unaligning (T0547)A189 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (1xfcA)N139 Warning: unaligning (T0547)L234 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (1xfcA)P179 Warning: unaligning (T0547)T239 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR at template residue (1xfcA)P179 T0547 46 :PLLLRFPHLIQKQIENIYGNF 1xfcA 12 :AEAMVDLGAIEHNVRVLREHA T0547 77 :GGFNAVYPLKV 1xfcA 33 :GHAQLMAVVKA T0547 88 :NQYPGFVKNLVKLGK 1xfcA 48 :HGATRVAQTALGAGA T0547 106 :YGLEAGSKAELLLAMAYNNEGAPITVNGF 1xfcA 63 :AELGVATVDEALALRADGITAPVLAWLHP T0547 135 :KDRELI 1xfcA 95 :DFGPAL T0547 148 :EMGH 1xfcA 101 :LADV T0547 154 :TLTIEGLNELEAIIDIAKE 1xfcA 105 :QVAVSSLRQLDELLHAVRR T0547 174 :FKPKPNIGLRVRL 1xfcA 124 :TGRTATVTVKVDT T0547 203 :KFGLTST 1xfcA 140 :RNGVGPA T0547 210 :ELIEAVNLLKENKLLEQFT 1xfcA 150 :AMLTALRQAMAEDAVRLRG T0547 230 :IHFH 1xfcA 169 :LMSH T0547 240 :EIHPLKKALNEAGNIYTELRKMGA 1xfcA 180 :DDSINDVQAQRFTAFLAQAREQGV T0547 265 :NLKAINLG 1xfcA 204 :RFEVAHLS T0547 291 :TLREYA 1xfcA 212 :NSSATM T0547 309 :Q 1xfcA 221 :D T0547 313 :LEPDI 1xfcA 222 :LTFDL T0547 319 :IESGRFVAA 1xfcA 227 :VRPGIAVYG T0547 328 :NHAVLIAPVLELFSQE 1xfcA 249 :PAMTVKCAVALVKSIR T0547 344 :YAENKLILKK 1xfcA 279 :RDTNLALLPI T0547 354 :QNPKLIDELY 1xfcA 290 :YADGVFRSLG T0547 373 :NALE 1xfcA 300 :GRLE T0547 377 :YLHDSIDHLESILTLFDLGYVDL 1xfcA 309 :RRCPGVGRICMDQFMVDLGPGPL T0547 401 :DRSNAEILTHLITKKAILLL 1xfcA 332 :DVAEGDEAILFGPGIRGEPT T0547 516 :VGAYQEVLG 1xfcA 352 :AQDWADLVG T0547 554 :QSILDTL 1xfcA 361 :TIHYEVV Number of specific fragments extracted= 25 number of extra gaps= 1 total=874 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 1xfcA/T0547-1xfcA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0547 read from 1xfcA/T0547-1xfcA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1xfcA read from 1xfcA/T0547-1xfcA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1xfcA in template set Warning: unaligning (T0547)G45 because first residue in template chain is (1xfcA)L11 Warning: unaligning (T0547)H187 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (1xfcA)L138 Warning: unaligning (T0547)S188 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (1xfcA)N139 Warning: unaligning (T0547)L234 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (1xfcA)P179 Warning: unaligning (T0547)T239 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR at template residue (1xfcA)P179 T0547 46 :PLLLRFPHLIQKQIENIYGNF 1xfcA 12 :AEAMVDLGAIEHNVRVLREHA T0547 77 :GGFNAVYPLKVN 1xfcA 33 :GHAQLMAVVKAD T0547 89 :QYPGFVKNLVKLGK 1xfcA 49 :GATRVAQTALGAGA T0547 106 :YGLEAGSKAELLLAMAYNNEG 1xfcA 63 :AELGVATVDEALALRADGITA T0547 128 :PITVNGFKDRE 1xfcA 84 :PVLAWLHPPGI T0547 141 :NIGF 1xfcA 95 :DFGP T0547 146 :AAEMGH 1xfcA 99 :ALLADV T0547 153 :I 1xfcA 105 :Q T0547 155 :LTIEGLNELEAIIDIAKE 1xfcA 106 :VAVSSLRQLDELLHAVRR T0547 174 :FKPKPNIGLRVRL 1xfcA 124 :TGRTATVTVKVDT T0547 203 :KFGLTSTELIEAVNLLKE 1xfcA 140 :RNGVGPAQFPAMLTALRQ T0547 221 :NKLL 1xfcA 161 :EDAV T0547 226 :QFTMIHFH 1xfcA 165 :RLRGLMSH T0547 240 :EIHPLKKALNEAGNIYTELRKMGA 1xfcA 180 :DDSINDVQAQRFTAFLAQAREQGV T0547 265 :NLKAINLGGGLAVEY 1xfcA 204 :RFEVAHLSNSSATMA T0547 282 :FKNEKSR 1xfcA 219 :RPDLTFD T0547 318 :FIESGRFVAA 1xfcA 226 :LVRPGIAVYG T0547 328 :NHAVLIAPVLELFSQ 1xfcA 249 :PAMTVKCAVALVKSI T0547 343 :EYAENKLILKKQNPKLIDE 1xfcA 278 :PRDTNLALLPIGYADGVFR T0547 362 :LYD 1xfcA 298 :LGG T0547 376 :EYL 1xfcA 301 :RLE T0547 379 :HDSIDHLESILTLFDLGYVD 1xfcA 308 :GRRCPGVGRICMDQFMVDLG T0547 399 :LQ 1xfcA 329 :GP T0547 401 :DRSNAEILTHLITKKAILLLGDKQN 1xfcA 332 :DVAEGDEAILFGPGIRGEPTAQDWA T0547 426 :PADLLA 1xfcA 360 :GTIHYE Number of specific fragments extracted= 25 number of extra gaps= 2 total=899 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 1xfcA/T0547-1xfcA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0547 read from 1xfcA/T0547-1xfcA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1xfcA read from 1xfcA/T0547-1xfcA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1xfcA in template set Warning: unaligning (T0547)G45 because first residue in template chain is (1xfcA)L11 Warning: unaligning (T0547)H187 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (1xfcA)L138 Warning: unaligning (T0547)S188 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (1xfcA)L138 Warning: unaligning (T0547)A189 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (1xfcA)N139 Warning: unaligning (T0547)L234 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (1xfcA)P179 T0547 46 :PLLLRFPHLIQKQIENIYGNFN 1xfcA 12 :AEAMVDLGAIEHNVRVLREHAG T0547 78 :GFNAVYPLKVNQY 1xfcA 34 :HAQLMAVVKADGY T0547 91 :PGFVKNLVKLGK 1xfcA 51 :TRVAQTALGAGA T0547 106 :YGLEAGSKAELLLAMAYNNEGAPIT 1xfcA 63 :AELGVATVDEALALRADGITAPVLA T0547 132 :NGFKD 1xfcA 88 :WLHPP T0547 142 :IGFIAAEM 1xfcA 97 :GPALLADV T0547 154 :TLTIEGLNELEAIIDIAKE 1xfcA 105 :QVAVSSLRQLDELLHAVRR T0547 174 :FKPKPNIGLRVRL 1xfcA 124 :TGRTATVTVKVDT T0547 190 :GVG 1xfcA 140 :RNG T0547 206 :LTS 1xfcA 143 :VGP T0547 209 :TELIEAVNLLKENK 1xfcA 149 :PAMLTALRQAMAED T0547 224 :LEQFTMIHFH 1xfcA 163 :AVRLRGLMSH T0547 240 :EIHPLKKALNEAGNIYTELRKM 1xfcA 180 :DDSINDVQAQRFTAFLAQAREQ T0547 263 :AKNLKAINLG 1xfcA 202 :GVRFEVAHLS T0547 287 :S 1xfcA 212 :N T0547 292 :LREY 1xfcA 213 :SSAT T0547 303 :L 1xfcA 217 :M T0547 309 :QKKDLEPDIFI 1xfcA 218 :ARPDLTFDLVR T0547 321 :SGRFVAA 1xfcA 229 :PGIAVYG T0547 328 :NHAVLIAPVLELFSQEYAENK 1xfcA 249 :PAMTVKCAVALVKSIRAGEGV T0547 396 :YVDLQ 1xfcA 270 :SYGHT T0547 403 :SNAEILTHLITKKAILLLGDKQNPADLL 1xfcA 277 :APRDTNLALLPIGYADGVFRSLGGRLEV T0547 438 :ERYLVNFSLFQSMPD 1xfcA 307 :NGRRCPGVGRICMDQ T0547 477 :SIWDIT 1xfcA 322 :FMVDLG T0547 497 :LFLHDVDVE 1xfcA 328 :PGPLDVAEG T0547 534 :TEAIISINEKG 1xfcA 337 :DEAILFGPGIR T0547 555 :SILDTLEDLDYD 1xfcA 351 :TAQDWADLVGTI Number of specific fragments extracted= 27 number of extra gaps= 1 total=926 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 3llxA/T0547-3llxA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 3llxA expands to /projects/compbio/data/pdb/3llx.pdb.gz 3llxA:Skipped atom 41, because occupancy 0.500 <= existing 0.500 in 3llxA Skipped atom 43, because occupancy 0.500 <= existing 0.500 in 3llxA Skipped atom 45, because occupancy 0.500 <= existing 0.500 in 3llxA Skipped atom 47, because occupancy 0.500 <= existing 0.500 in 3llxA Skipped atom 49, because occupancy 0.500 <= existing 0.500 in 3llxA Skipped atom 51, because occupancy 0.500 <= existing 0.500 in 3llxA Skipped atom 53, because occupancy 0.500 <= existing 0.500 in 3llxA Skipped atom 55, because occupancy 0.500 <= existing 0.500 in 3llxA Skipped atom 159, because occupancy 0.500 <= existing 0.500 in 3llxA Skipped atom 161, because occupancy 0.500 <= existing 0.500 in 3llxA Skipped atom 163, because occupancy 0.500 <= existing 0.500 in 3llxA Skipped atom 165, because occupancy 0.500 <= existing 0.500 in 3llxA Skipped atom 167, because occupancy 0.500 <= existing 0.500 in 3llxA Skipped atom 169, because occupancy 0.500 <= existing 0.500 in 3llxA Skipped atom 171, because occupancy 0.500 <= existing 0.500 in 3llxA Skipped atom 173, because occupancy 0.500 <= existing 0.500 in 3llxA Skipped atom 175, because occupancy 0.500 <= existing 0.500 in 3llxA Skipped atom 177, because occupancy 0.500 <= existing 0.500 in 3llxA Skipped atom 179, because occupancy 0.500 <= existing 0.500 in 3llxA Skipped atom 181, because occupancy 0.500 <= existing 0.500 in 3llxA Skipped atom 183, because occupancy 0.500 <= existing 0.500 in 3llxA Skipped atom 185, because occupancy 0.500 <= existing 0.500 in 3llxA Skipped atom 187, because occupancy 0.500 <= existing 0.500 in 3llxA Skipped atom 189, because occupancy 0.500 <= existing 0.500 in 3llxA Skipped atom 191, because occupancy 0.500 <= existing 0.500 in 3llxA Skipped atom 202, because occupancy 0.400 <= existing 0.600 in 3llxA Skipped atom 204, because occupancy 0.400 <= existing 0.600 in 3llxA Skipped atom 206, because occupancy 0.400 <= existing 0.600 in 3llxA Skipped atom 208, because occupancy 0.400 <= existing 0.600 in 3llxA Skipped atom 210, because occupancy 0.400 <= existing 0.600 in 3llxA Skipped atom 212, because occupancy 0.400 <= existing 0.600 in 3llxA Skipped atom 267, because occupancy 0.500 <= existing 0.500 in 3llxA Skipped atom 269, because occupancy 0.500 <= existing 0.500 in 3llxA Skipped atom 271, because occupancy 0.500 <= existing 0.500 in 3llxA Skipped atom 273, because occupancy 0.500 <= existing 0.500 in 3llxA Skipped atom 275, because occupancy 0.500 <= existing 0.500 in 3llxA Skipped atom 277, because occupancy 0.500 <= existing 0.500 in 3llxA Skipped atom 279, because occupancy 0.500 <= existing 0.500 in 3llxA Skipped atom 281, because occupancy 0.500 <= existing 0.500 in 3llxA Skipped atom 283, because occupancy 0.500 <= existing 0.500 in 3llxA Skipped atom 336, because occupancy 0.500 <= existing 0.500 in 3llxA Skipped atom 338, because occupancy 0.500 <= existing 0.500 in 3llxA Skipped atom 340, because occupancy 0.500 <= existing 0.500 in 3llxA Skipped atom 342, because occupancy 0.500 <= existing 0.500 in 3llxA Skipped atom 344, because occupancy 0.500 <= existing 0.500 in 3llxA Skipped atom 346, because occupancy 0.500 <= existing 0.500 in 3llxA Skipped atom 348, because occupancy 0.500 <= existing 0.500 in 3llxA Skipped atom 350, because occupancy 0.500 <= existing 0.500 in 3llxA Skipped atom 352, because occupancy 0.500 <= existing 0.500 in 3llxA Skipped atom 354, because occupancy 0.500 <= existing 0.500 in 3llxA Bad short name: N1 for alphabet: pdb_atoms Bad short name: N1 for alphabet: pdb_atoms Bad short name: C2 for alphabet: pdb_atoms Bad short name: C2 for alphabet: pdb_atoms Bad short name: C2' for alphabet: pdb_atoms Bad short name: C2' for alphabet: pdb_atoms Bad short name: C3 for alphabet: pdb_atoms Bad short name: C3 for alphabet: pdb_atoms Bad short name: O3 for alphabet: pdb_atoms Bad short name: O3 for alphabet: pdb_atoms Bad short name: C4 for alphabet: pdb_atoms Bad short name: C4 for alphabet: pdb_atoms Bad short name: C4' for alphabet: pdb_atoms Bad short name: C4' for alphabet: pdb_atoms Bad short name: C5 for alphabet: pdb_atoms Bad short name: C5 for alphabet: pdb_atoms Bad short name: C6 for alphabet: pdb_atoms Bad short name: C6 for alphabet: pdb_atoms Bad short name: C5' for alphabet: pdb_atoms Bad short name: C5' for alphabet: pdb_atoms Bad short name: OP4 for alphabet: pdb_atoms Bad short name: OP4 for alphabet: pdb_atoms Bad short name: P for alphabet: pdb_atoms Bad short name: P for alphabet: pdb_atoms Bad short name: OP1 for alphabet: pdb_atoms Bad short name: OP1 for alphabet: pdb_atoms Bad short name: OP2 for alphabet: pdb_atoms Bad short name: OP2 for alphabet: pdb_atoms Bad short name: OP3 for alphabet: pdb_atoms Bad short name: OP3 for alphabet: pdb_atoms Skipped atom 455, because occupancy 0.300 <= existing 0.700 in 3llxA Skipped atom 457, because occupancy 0.300 <= existing 0.700 in 3llxA Skipped atom 459, because occupancy 0.300 <= existing 0.700 in 3llxA Skipped atom 461, because occupancy 0.300 <= existing 0.700 in 3llxA Skipped atom 463, because occupancy 0.300 <= existing 0.700 in 3llxA Skipped atom 465, because occupancy 0.300 <= existing 0.700 in 3llxA Skipped atom 467, because occupancy 0.300 <= existing 0.700 in 3llxA Skipped atom 469, because occupancy 0.300 <= existing 0.700 in 3llxA Skipped atom 548, because occupancy 0.200 <= existing 0.800 in 3llxA Skipped atom 550, because occupancy 0.200 <= existing 0.800 in 3llxA Skipped atom 552, because occupancy 0.200 <= existing 0.800 in 3llxA Skipped atom 554, because occupancy 0.200 <= existing 0.800 in 3llxA Skipped atom 556, because occupancy 0.200 <= existing 0.800 in 3llxA Skipped atom 558, because occupancy 0.200 <= existing 0.800 in 3llxA Skipped atom 560, because occupancy 0.200 <= existing 0.800 in 3llxA Skipped atom 562, because occupancy 0.200 <= existing 0.800 in 3llxA Skipped atom 590, because occupancy 0.500 <= existing 0.500 in 3llxA Skipped atom 592, because occupancy 0.500 <= existing 0.500 in 3llxA Skipped atom 594, because occupancy 0.500 <= existing 0.500 in 3llxA Skipped atom 596, because occupancy 0.500 <= existing 0.500 in 3llxA Skipped atom 598, because occupancy 0.500 <= existing 0.500 in 3llxA Skipped atom 600, because occupancy 0.500 <= existing 0.500 in 3llxA Skipped atom 602, because occupancy 0.500 <= existing 0.500 in 3llxA Skipped atom 825, because occupancy 0.500 <= existing 0.500 in 3llxA Skipped atom 827, because occupancy 0.500 <= existing 0.500 in 3llxA Skipped atom 829, because occupancy 0.500 <= existing 0.500 in 3llxA Skipped atom 831, because occupancy 0.500 <= existing 0.500 in 3llxA Skipped atom 833, because occupancy 0.500 <= existing 0.500 in 3llxA Skipped atom 835, because occupancy 0.500 <= existing 0.500 in 3llxA Skipped atom 837, because occupancy 0.500 <= existing 0.500 in 3llxA Skipped atom 839, because occupancy 0.500 <= existing 0.500 in 3llxA Skipped atom 841, because occupancy 0.500 <= existing 0.500 in 3llxA Skipped atom 871, because occupancy 0.400 <= existing 0.600 in 3llxA Skipped atom 873, because occupancy 0.400 <= existing 0.600 in 3llxA Skipped atom 875, because occupancy 0.400 <= existing 0.600 in 3llxA Skipped atom 877, because occupancy 0.400 <= existing 0.600 in 3llxA Skipped atom 879, because occupancy 0.400 <= existing 0.600 in 3llxA Skipped atom 881, because occupancy 0.400 <= existing 0.600 in 3llxA Skipped atom 883, because occupancy 0.400 <= existing 0.600 in 3llxA Skipped atom 885, because occupancy 0.400 <= existing 0.600 in 3llxA Skipped atom 898, because occupancy 0.500 <= existing 0.500 in 3llxA Skipped atom 900, because occupancy 0.500 <= existing 0.500 in 3llxA Skipped atom 902, because occupancy 0.500 <= existing 0.500 in 3llxA Skipped atom 904, because occupancy 0.500 <= existing 0.500 in 3llxA Skipped atom 906, because occupancy 0.500 <= existing 0.500 in 3llxA Skipped atom 908, because occupancy 0.500 <= existing 0.500 in 3llxA Skipped atom 910, because occupancy 0.500 <= existing 0.500 in 3llxA Skipped atom 912, because occupancy 0.500 <= existing 0.500 in 3llxA Skipped atom 914, because occupancy 0.500 <= existing 0.500 in 3llxA Skipped atom 916, because occupancy 0.500 <= existing 0.500 in 3llxA Skipped atom 918, because occupancy 0.500 <= existing 0.500 in 3llxA Skipped atom 920, because occupancy 0.500 <= existing 0.500 in 3llxA Skipped atom 922, because occupancy 0.500 <= existing 0.500 in 3llxA Skipped atom 924, because occupancy 0.500 <= existing 0.500 in 3llxA Skipped atom 926, because occupancy 0.500 <= existing 0.500 in 3llxA Skipped atom 928, because occupancy 0.500 <= existing 0.500 in 3llxA Skipped atom 930, because occupancy 0.500 <= existing 0.500 in 3llxA Skipped atom 932, because occupancy 0.500 <= existing 0.500 in 3llxA Skipped atom 954, because occupancy 0.500 <= existing 0.500 in 3llxA Skipped atom 956, because occupancy 0.500 <= existing 0.500 in 3llxA Skipped atom 958, because occupancy 0.500 <= existing 0.500 in 3llxA Skipped atom 960, because occupancy 0.500 <= existing 0.500 in 3llxA Skipped atom 962, because occupancy 0.500 <= existing 0.500 in 3llxA Skipped atom 964, because occupancy 0.500 <= existing 0.500 in 3llxA Skipped atom 966, because occupancy 0.500 <= existing 0.500 in 3llxA Skipped atom 968, because occupancy 0.500 <= existing 0.500 in 3llxA Skipped atom 1012, because occupancy 0.500 <= existing 0.500 in 3llxA Skipped atom 1014, because occupancy 0.500 <= existing 0.500 in 3llxA Skipped atom 1016, because occupancy 0.500 <= existing 0.500 in 3llxA Skipped atom 1018, because occupancy 0.500 <= existing 0.500 in 3llxA Skipped atom 1020, because occupancy 0.500 <= existing 0.500 in 3llxA Skipped atom 1022, because occupancy 0.500 <= existing 0.500 in 3llxA Skipped atom 1024, because occupancy 0.500 <= existing 0.500 in 3llxA Skipped atom 1026, because occupancy 0.500 <= existing 0.500 in 3llxA Skipped atom 1036, because occupancy 0.500 <= existing 0.500 in 3llxA Skipped atom 1038, because occupancy 0.500 <= existing 0.500 in 3llxA Skipped atom 1040, because occupancy 0.500 <= existing 0.500 in 3llxA Skipped atom 1042, because occupancy 0.500 <= existing 0.500 in 3llxA Skipped atom 1044, because occupancy 0.500 <= existing 0.500 in 3llxA Skipped atom 1046, because occupancy 0.500 <= existing 0.500 in 3llxA Skipped atom 1048, because occupancy 0.500 <= existing 0.500 in 3llxA Skipped atom 1245, because occupancy 0.300 <= existing 0.700 in 3llxA Skipped atom 1247, because occupancy 0.300 <= existing 0.700 in 3llxA Skipped atom 1249, because occupancy 0.300 <= existing 0.700 in 3llxA Skipped atom 1251, because occupancy 0.300 <= existing 0.700 in 3llxA Skipped atom 1253, because occupancy 0.300 <= existing 0.700 in 3llxA Skipped atom 1255, because occupancy 0.300 <= existing 0.700 in 3llxA Skipped atom 1257, because occupancy 0.300 <= existing 0.700 in 3llxA Skipped atom 1259, because occupancy 0.300 <= existing 0.700 in 3llxA Skipped atom 1261, because occupancy 0.400 <= existing 0.600 in 3llxA Skipped atom 1263, because occupancy 0.400 <= existing 0.600 in 3llxA Skipped atom 1265, because occupancy 0.400 <= existing 0.600 in 3llxA Skipped atom 1267, because occupancy 0.400 <= existing 0.600 in 3llxA Skipped atom 1269, because occupancy 0.400 <= existing 0.600 in 3llxA Skipped atom 1271, because occupancy 0.400 <= existing 0.600 in 3llxA Skipped atom 1273, because occupancy 0.400 <= existing 0.600 in 3llxA Skipped atom 1275, because occupancy 0.400 <= existing 0.600 in 3llxA Skipped atom 1277, because occupancy 0.400 <= existing 0.600 in 3llxA Skipped atom 1279, because occupancy 0.400 <= existing 0.600 in 3llxA Skipped atom 1308, because occupancy 0.500 <= existing 0.500 in 3llxA Skipped atom 1310, because occupancy 0.500 <= existing 0.500 in 3llxA Skipped atom 1312, because occupancy 0.500 <= existing 0.500 in 3llxA Skipped atom 1314, because occupancy 0.500 <= existing 0.500 in 3llxA Skipped atom 1316, because occupancy 0.500 <= existing 0.500 in 3llxA Skipped atom 1318, because occupancy 0.500 <= existing 0.500 in 3llxA Skipped atom 1320, because occupancy 0.500 <= existing 0.500 in 3llxA Skipped atom 1322, because occupancy 0.500 <= existing 0.500 in 3llxA Skipped atom 1324, because occupancy 0.500 <= existing 0.500 in 3llxA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 1666, because occupancy 0.500 <= existing 0.500 in 3llxA Skipped atom 1668, because occupancy 0.500 <= existing 0.500 in 3llxA Skipped atom 1670, because occupancy 0.500 <= existing 0.500 in 3llxA Skipped atom 1672, because occupancy 0.500 <= existing 0.500 in 3llxA Skipped atom 1674, because occupancy 0.500 <= existing 0.500 in 3llxA Skipped atom 1676, because occupancy 0.500 <= existing 0.500 in 3llxA Skipped atom 1678, because occupancy 0.500 <= existing 0.500 in 3llxA Skipped atom 1782, because occupancy 0.400 <= existing 0.600 in 3llxA Skipped atom 1784, because occupancy 0.400 <= existing 0.600 in 3llxA Skipped atom 1786, because occupancy 0.400 <= existing 0.600 in 3llxA Skipped atom 1788, because occupancy 0.400 <= existing 0.600 in 3llxA Skipped atom 1790, because occupancy 0.400 <= existing 0.600 in 3llxA Skipped atom 1792, because occupancy 0.400 <= existing 0.600 in 3llxA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 2055, because occupancy 0.500 <= existing 0.500 in 3llxA Skipped atom 2057, because occupancy 0.500 <= existing 0.500 in 3llxA Skipped atom 2059, because occupancy 0.500 <= existing 0.500 in 3llxA Skipped atom 2061, because occupancy 0.500 <= existing 0.500 in 3llxA Skipped atom 2063, because occupancy 0.500 <= existing 0.500 in 3llxA Skipped atom 2065, because occupancy 0.500 <= existing 0.500 in 3llxA Skipped atom 2067, because occupancy 0.500 <= existing 0.500 in 3llxA Skipped atom 2069, because occupancy 0.500 <= existing 0.500 in 3llxA Skipped atom 2071, because occupancy 0.500 <= existing 0.500 in 3llxA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 2168, because occupancy 0.200 <= existing 0.800 in 3llxA Skipped atom 2170, because occupancy 0.200 <= existing 0.800 in 3llxA Skipped atom 2172, because occupancy 0.200 <= existing 0.800 in 3llxA Skipped atom 2174, because occupancy 0.200 <= existing 0.800 in 3llxA Skipped atom 2176, because occupancy 0.200 <= existing 0.800 in 3llxA Skipped atom 2178, because occupancy 0.200 <= existing 0.800 in 3llxA Skipped atom 2180, because occupancy 0.200 <= existing 0.800 in 3llxA Skipped atom 2248, because occupancy 0.500 <= existing 0.500 in 3llxA Skipped atom 2250, because occupancy 0.500 <= existing 0.500 in 3llxA Skipped atom 2252, because occupancy 0.500 <= existing 0.500 in 3llxA Skipped atom 2254, because occupancy 0.500 <= existing 0.500 in 3llxA Skipped atom 2256, because occupancy 0.500 <= existing 0.500 in 3llxA Skipped atom 2258, because occupancy 0.500 <= existing 0.500 in 3llxA Skipped atom 2260, because occupancy 0.500 <= existing 0.500 in 3llxA Skipped atom 2262, because occupancy 0.500 <= existing 0.500 in 3llxA Skipped atom 2264, because occupancy 0.500 <= existing 0.500 in 3llxA Skipped atom 2275, because occupancy 0.400 <= existing 0.600 in 3llxA Skipped atom 2277, because occupancy 0.400 <= existing 0.600 in 3llxA Skipped atom 2279, because occupancy 0.400 <= existing 0.600 in 3llxA Skipped atom 2281, because occupancy 0.400 <= existing 0.600 in 3llxA Skipped atom 2283, because occupancy 0.400 <= existing 0.600 in 3llxA Skipped atom 2285, because occupancy 0.400 <= existing 0.600 in 3llxA Skipped atom 2287, because occupancy 0.400 <= existing 0.600 in 3llxA Skipped atom 2289, because occupancy 0.400 <= existing 0.600 in 3llxA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 2387, because occupancy 0.500 <= existing 0.500 in 3llxA Skipped atom 2389, because occupancy 0.500 <= existing 0.500 in 3llxA Skipped atom 2391, because occupancy 0.500 <= existing 0.500 in 3llxA Skipped atom 2393, because occupancy 0.500 <= existing 0.500 in 3llxA Skipped atom 2395, because occupancy 0.500 <= existing 0.500 in 3llxA Skipped atom 2397, because occupancy 0.500 <= existing 0.500 in 3llxA Skipped atom 2399, because occupancy 0.500 <= existing 0.500 in 3llxA Skipped atom 2401, because occupancy 0.500 <= existing 0.500 in 3llxA Skipped atom 2403, because occupancy 0.500 <= existing 0.500 in 3llxA Skipped atom 2405, because occupancy 0.500 <= existing 0.500 in 3llxA Skipped atom 2407, because occupancy 0.500 <= existing 0.500 in 3llxA Skipped atom 2439, because occupancy 0.300 <= existing 0.700 in 3llxA Skipped atom 2441, because occupancy 0.300 <= existing 0.700 in 3llxA Skipped atom 2443, because occupancy 0.300 <= existing 0.700 in 3llxA Skipped atom 2445, because occupancy 0.300 <= existing 0.700 in 3llxA Skipped atom 2545, because occupancy 0.400 <= existing 0.600 in 3llxA Skipped atom 2547, because occupancy 0.400 <= existing 0.600 in 3llxA Skipped atom 2549, because occupancy 0.400 <= existing 0.600 in 3llxA Skipped atom 2551, because occupancy 0.400 <= existing 0.600 in 3llxA Skipped atom 2553, because occupancy 0.400 <= existing 0.600 in 3llxA Skipped atom 2555, because occupancy 0.400 <= existing 0.600 in 3llxA Skipped atom 2557, because occupancy 0.400 <= existing 0.600 in 3llxA Skipped atom 2559, because occupancy 0.400 <= existing 0.600 in 3llxA Skipped atom 2573, because occupancy 0.500 <= existing 0.500 in 3llxA Skipped atom 2575, because occupancy 0.500 <= existing 0.500 in 3llxA Skipped atom 2577, because occupancy 0.500 <= existing 0.500 in 3llxA Skipped atom 2579, because occupancy 0.500 <= existing 0.500 in 3llxA Skipped atom 2581, because occupancy 0.500 <= existing 0.500 in 3llxA Skipped atom 2583, because occupancy 0.500 <= existing 0.500 in 3llxA Skipped atom 2585, because occupancy 0.500 <= existing 0.500 in 3llxA Skipped atom 2587, because occupancy 0.500 <= existing 0.500 in 3llxA Skipped atom 2589, because occupancy 0.500 <= existing 0.500 in 3llxA Skipped atom 2591, because occupancy 0.500 <= existing 0.500 in 3llxA Skipped atom 2593, because occupancy 0.500 <= existing 0.500 in 3llxA Skipped atom 2595, because occupancy 0.500 <= existing 0.500 in 3llxA Skipped atom 2597, because occupancy 0.500 <= existing 0.500 in 3llxA Skipped atom 2627, because occupancy 0.500 <= existing 0.500 in 3llxA Skipped atom 2629, because occupancy 0.500 <= existing 0.500 in 3llxA Skipped atom 2631, because occupancy 0.500 <= existing 0.500 in 3llxA Skipped atom 2633, because occupancy 0.500 <= existing 0.500 in 3llxA Skipped atom 2635, because occupancy 0.500 <= existing 0.500 in 3llxA Skipped atom 2637, because occupancy 0.500 <= existing 0.500 in 3llxA Skipped atom 2654, because occupancy 0.500 <= existing 0.500 in 3llxA Skipped atom 2656, because occupancy 0.500 <= existing 0.500 in 3llxA Skipped atom 2658, because occupancy 0.500 <= existing 0.500 in 3llxA Skipped atom 2660, because occupancy 0.500 <= existing 0.500 in 3llxA Skipped atom 2662, because occupancy 0.500 <= existing 0.500 in 3llxA Skipped atom 2664, because occupancy 0.500 <= existing 0.500 in 3llxA Skipped atom 2673, because occupancy 0.400 <= existing 0.600 in 3llxA Skipped atom 2675, because occupancy 0.400 <= existing 0.600 in 3llxA Skipped atom 2677, because occupancy 0.400 <= existing 0.600 in 3llxA Skipped atom 2679, because occupancy 0.400 <= existing 0.600 in 3llxA Skipped atom 2681, because occupancy 0.400 <= existing 0.600 in 3llxA Skipped atom 2683, because occupancy 0.400 <= existing 0.600 in 3llxA Skipped atom 2732, because occupancy 0.500 <= existing 0.500 in 3llxA Skipped atom 2734, because occupancy 0.500 <= existing 0.500 in 3llxA Skipped atom 2736, because occupancy 0.500 <= existing 0.500 in 3llxA Skipped atom 2738, because occupancy 0.500 <= existing 0.500 in 3llxA Skipped atom 2740, because occupancy 0.500 <= existing 0.500 in 3llxA Skipped atom 2742, because occupancy 0.500 <= existing 0.500 in 3llxA Skipped atom 2744, because occupancy 0.500 <= existing 0.500 in 3llxA Skipped atom 2746, because occupancy 0.500 <= existing 0.500 in 3llxA Skipped atom 2748, because occupancy 0.500 <= existing 0.500 in 3llxA Skipped atom 2789, because occupancy 0.300 <= existing 0.700 in 3llxA Skipped atom 2791, because occupancy 0.300 <= existing 0.700 in 3llxA Skipped atom 2793, because occupancy 0.300 <= existing 0.700 in 3llxA Skipped atom 2795, because occupancy 0.300 <= existing 0.700 in 3llxA Skipped atom 2797, because occupancy 0.300 <= existing 0.700 in 3llxA Skipped atom 2799, because occupancy 0.300 <= existing 0.700 in 3llxA Skipped atom 2801, because occupancy 0.300 <= existing 0.700 in 3llxA Skipped atom 2803, because occupancy 0.300 <= existing 0.700 in 3llxA Skipped atom 2805, because occupancy 0.300 <= existing 0.700 in 3llxA Skipped atom 2815, because occupancy 0.400 <= existing 0.600 in 3llxA Skipped atom 2817, because occupancy 0.400 <= existing 0.600 in 3llxA Skipped atom 2819, because occupancy 0.400 <= existing 0.600 in 3llxA Skipped atom 2821, because occupancy 0.400 <= existing 0.600 in 3llxA Skipped atom 2823, because occupancy 0.400 <= existing 0.600 in 3llxA Skipped atom 2825, because occupancy 0.400 <= existing 0.600 in 3llxA Skipped atom 2827, because occupancy 0.400 <= existing 0.600 in 3llxA Skipped atom 2829, because occupancy 0.400 <= existing 0.600 in 3llxA Skipped atom 2831, because occupancy 0.400 <= existing 0.600 in 3llxA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 2931, because occupancy 0.400 <= existing 0.600 in 3llxA Skipped atom 2933, because occupancy 0.400 <= existing 0.600 in 3llxA Skipped atom 2935, because occupancy 0.400 <= existing 0.600 in 3llxA Skipped atom 2937, because occupancy 0.400 <= existing 0.600 in 3llxA Skipped atom 2939, because occupancy 0.400 <= existing 0.600 in 3llxA Skipped atom 2941, because occupancy 0.400 <= existing 0.600 in 3llxA Skipped atom 2943, because occupancy 0.400 <= existing 0.600 in 3llxA Skipped atom 2945, because occupancy 0.400 <= existing 0.600 in 3llxA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 3015, because occupancy 0.500 <= existing 0.500 in 3llxA Skipped atom 3017, because occupancy 0.500 <= existing 0.500 in 3llxA Skipped atom 3019, because occupancy 0.500 <= existing 0.500 in 3llxA Skipped atom 3021, because occupancy 0.500 <= existing 0.500 in 3llxA Skipped atom 3023, because occupancy 0.500 <= existing 0.500 in 3llxA Skipped atom 3025, because occupancy 0.500 <= existing 0.500 in 3llxA Skipped atom 3027, because occupancy 0.500 <= existing 0.500 in 3llxA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 3108, because occupancy 0.400 <= existing 0.600 in 3llxA Skipped atom 3110, because occupancy 0.400 <= existing 0.600 in 3llxA Skipped atom 3112, because occupancy 0.400 <= existing 0.600 in 3llxA Skipped atom 3114, because occupancy 0.400 <= existing 0.600 in 3llxA Skipped atom 3116, because occupancy 0.400 <= existing 0.600 in 3llxA Skipped atom 3118, because occupancy 0.400 <= existing 0.600 in 3llxA Skipped atom 3120, because occupancy 0.400 <= existing 0.600 in 3llxA Skipped atom 3122, because occupancy 0.400 <= existing 0.600 in 3llxA # T0547 read from 3llxA/T0547-3llxA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3llxA read from 3llxA/T0547-3llxA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3llxA to template set # found chain 3llxA in template set Warning: unaligning (T0547)A81 because of BadResidue code BAD_PEPTIDE in next template residue (3llxA)R42 Warning: unaligning (T0547)V82 because of BadResidue code BAD_PEPTIDE at template residue (3llxA)R42 Warning: unaligning (T0547)L85 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (3llxA)T47 Warning: unaligning (T0547)V87 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (3llxA)T47 Warning: unaligning (T0547)L271 because of BadResidue code BAD_PEPTIDE in next template residue (3llxA)G215 Warning: unaligning (T0547)G272 because of BadResidue code BAD_PEPTIDE at template residue (3llxA)G215 Warning: unaligning (T0547)G273 because of BadResidue code BAD_PEPTIDE at template residue (3llxA)S216 Warning: unaligning (T0547)L339 because of BadResidue code BAD_PEPTIDE in next template residue (3llxA)N267 Warning: unaligning (T0547)F340 because of BadResidue code BAD_PEPTIDE at template residue (3llxA)N267 Warning: unaligning (T0547)K348 because of BadResidue code BAD_PEPTIDE in next template residue (3llxA)L273 Warning: unaligning (T0547)L349 because of BadResidue code BAD_PEPTIDE at template residue (3llxA)L273 Warning: unaligning (T0547)H384 because of BadResidue code BAD_PEPTIDE in next template residue (3llxA)S317 Warning: unaligning (T0547)L385 because of BadResidue code BAD_PEPTIDE at template residue (3llxA)S317 T0547 41 :DGYKGPLLLRFPHLIQKQIENIYGNFNK 3llxA 9 :AHPDTPYLLIDEAKLKSNINYLKQRVES T0547 77 :GGFN 3llxA 37 :LGSH T0547 83 :YP 3llxA 43 :PH T0547 88 :NQYPGFVKNL 3llxA 48 :LRTLEAAGYL T0547 101 :GK 3llxA 61 :KS T0547 106 :YGLEAGSKAELLLAMAYNNE 3llxA 63 :APATVSTLAEAEAYAKAGYT T0547 127 :APITV 3llxA 83 :DLLYA T0547 132 :NGF 3llxA 89 :GIA T0547 135 :KDRELINIGF 3llxA 93 :AKLKRVAALR T0547 148 :EMGHNITLTIEGLNELEAIIDIAKE 3llxA 103 :QQGINLHILLDNITQAQAVVDYAAE T0547 174 :FKPKPNIGLRVRL 3llxA 128 :FGQDFSVFIEIDS T0547 189 :AGV 3llxA 141 :DDH T0547 203 :KFGLTST 3llxA 144 :RGGIKPS T0547 213 :EAVNLLKENK 3llxA 153 :KLLTIAKTLG T0547 224 :LEQFT 3llxA 163 :EHFTG T0547 230 :IHFHLGS 3llxA 168 :LMTHAGG T0547 237 :QITEIHPLKKALNE 3llxA 177 :ACNTEQGLKNFAKQ T0547 251 :AGNIYTELRKMGA 3llxA 195 :VRIARNNLETAGI T0547 265 :NLKAIN 3llxA 208 :HCAITS T0547 274 :GLAVE 3llxA 217 :TPTAH T0547 306 :IAEQKKDLE 3llxA 222 :FGEDFSDIS T0547 318 :FIESGRFVAAN 3llxA 231 :EVRAGVYTTFD T0547 329 :HAVLIAPVLE 3llxA 256 :AMSVVTTVIG T0547 341 :SQEY 3llxA 268 :KEKN T0547 350 :ILKK 3llxA 274 :LTDS T0547 363 :YDLYKSIKPSNALE 3llxA 279 :WMALSRDSGTAGQN T0547 377 :YLHDSID 3llxA 309 :DGLCVNS T0547 386 :ESILTLFDLGYVDLQDRSNAEILTHLI 3llxA 318 :QEHGVIELSDAYQLEDFPVGHQLRIMP T0547 414 :KKAILLLGD 3llxA 345 :NHACATAAM T0547 423 :K 3llxA 355 :P T0547 440 :YL 3llxA 356 :VY T0547 481 :ITCDSDGEISYS 3llxA 358 :HVLMSDGSHNTW Number of specific fragments extracted= 32 number of extra gaps= 5 total=958 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 3llxA/T0547-3llxA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0547 read from 3llxA/T0547-3llxA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3llxA read from 3llxA/T0547-3llxA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3llxA in template set Warning: unaligning (T0547)A81 because of BadResidue code BAD_PEPTIDE in next template residue (3llxA)R42 Warning: unaligning (T0547)V82 because of BadResidue code BAD_PEPTIDE at template residue (3llxA)R42 Warning: unaligning (T0547)L85 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (3llxA)T47 Warning: unaligning (T0547)V87 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (3llxA)T47 Warning: unaligning (T0547)L271 because of BadResidue code BAD_PEPTIDE in next template residue (3llxA)G215 Warning: unaligning (T0547)G272 because of BadResidue code BAD_PEPTIDE at template residue (3llxA)G215 Warning: unaligning (T0547)G273 because of BadResidue code BAD_PEPTIDE at template residue (3llxA)S216 Warning: unaligning (T0547)L339 because of BadResidue code BAD_PEPTIDE in next template residue (3llxA)N267 Warning: unaligning (T0547)F340 because of BadResidue code BAD_PEPTIDE at template residue (3llxA)N267 Warning: unaligning (T0547)K348 because of BadResidue code BAD_PEPTIDE in next template residue (3llxA)L273 Warning: unaligning (T0547)L349 because of BadResidue code BAD_PEPTIDE at template residue (3llxA)L273 Warning: unaligning (T0547)I388 because of BadResidue code BAD_PEPTIDE in next template residue (3llxA)S317 Warning: unaligning (T0547)L391 because of BadResidue code BAD_PEPTIDE at template residue (3llxA)S317 T0547 39 :RDDGYKGPLLLRFPHLIQKQIENIYGNFNK 3llxA 7 :WIAHPDTPYLLIDEAKLKSNINYLKQRVES T0547 77 :GGFN 3llxA 37 :LGSH T0547 83 :YP 3llxA 43 :PH T0547 88 :NQYPGFVKNL 3llxA 48 :LRTLEAAGYL T0547 102 :KDYNYGLEAGSKAELLLAMAYNNEGAPITVNGFKDR 3llxA 59 :DSKSAPATVSTLAEAEAYAKAGYTDLLYAVGIAPAK T0547 139 :LINIGF 3llxA 95 :LKRVAA T0547 146 :AAEMGHNITLTIEGLNELEAIIDIAKE 3llxA 101 :LRQQGINLHILLDNITQAQAVVDYAAE T0547 174 :FKPKPNIGLRVRLHSA 3llxA 128 :FGQDFSVFIEIDSDDH T0547 203 :KFGLTST 3llxA 144 :RGGIKPS T0547 213 :EAVNLLKENKL 3llxA 153 :KLLTIAKTLGE T0547 226 :QFTMIHFHLGSQIT 3llxA 164 :HFTGLMTHAGGSYA T0547 240 :EIHPLKKA 3llxA 180 :TEQGLKNF T0547 248 :LNEAGNIYTELRKMGA 3llxA 192 :CDAVRIARNNLETAGI T0547 265 :NLKAIN 3llxA 208 :HCAITS T0547 274 :GLAVEY 3llxA 217 :TPTAHF T0547 282 :FKN 3llxA 223 :GED T0547 287 :S 3llxA 226 :F T0547 310 :KKDL 3llxA 227 :SDIS T0547 318 :FIESGRFVAAN 3llxA 231 :EVRAGVYTTFD T0547 329 :HAVLIAPVLE 3llxA 256 :AMSVVTTVIG T0547 341 :SQEY 3llxA 268 :KEKN T0547 350 :ILKKQNPKLIDE 3llxA 274 :LTDSGWMALSRD T0547 362 :L 3llxA 287 :G T0547 366 :YKSIKPSNAL 3llxA 288 :TAGQNRDFGY T0547 377 :YLHDSIDHLES 3llxA 305 :GSVLDGLCVNS T0547 392 :FDLGYVD 3llxA 318 :QEHGVIE T0547 399 :LQDRSNAEILTHLITKKAILL 3llxA 331 :LEDFPVGHQLRIMPNHACATA Number of specific fragments extracted= 27 number of extra gaps= 5 total=985 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 3llxA/T0547-3llxA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0547 read from 3llxA/T0547-3llxA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3llxA read from 3llxA/T0547-3llxA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3llxA in template set Warning: unaligning (T0547)A81 because of BadResidue code BAD_PEPTIDE in next template residue (3llxA)R42 Warning: unaligning (T0547)V82 because of BadResidue code BAD_PEPTIDE at template residue (3llxA)R42 Warning: unaligning (T0547)L85 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (3llxA)T47 Warning: unaligning (T0547)V87 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (3llxA)T47 Warning: unaligning (T0547)L271 because of BadResidue code BAD_PEPTIDE in next template residue (3llxA)G215 Warning: unaligning (T0547)G272 because of BadResidue code BAD_PEPTIDE at template residue (3llxA)G215 Warning: unaligning (T0547)G273 because of BadResidue code BAD_PEPTIDE at template residue (3llxA)S216 Warning: unaligning (T0547)L339 because of BadResidue code BAD_PEPTIDE in next template residue (3llxA)N267 Warning: unaligning (T0547)F340 because of BadResidue code BAD_PEPTIDE at template residue (3llxA)N267 Warning: unaligning (T0547)A345 because of BadResidue code BAD_PEPTIDE in next template residue (3llxA)L273 Warning: unaligning (T0547)K348 because of BadResidue code BAD_PEPTIDE at template residue (3llxA)L273 T0547 41 :DGYKGPLLLRFPHLIQKQIENIYGNFNKA 3llxA 9 :AHPDTPYLLIDEAKLKSNINYLKQRVESL T0547 78 :GFN 3llxA 38 :GSH T0547 83 :YP 3llxA 43 :PH T0547 88 :NQYPGFVKNL 3llxA 48 :LRTLEAAGYL T0547 101 :GKDYNYGLEAGSKAELLLAMAYNN 3llxA 58 :LDSKSAPATVSTLAEAEAYAKAGY T0547 127 :APITVNGFKDRELINIGFIAAEMGHNITLTIEGLNELEAIIDIAKE 3llxA 82 :TDLLYAVGIAPAKLKRVAALRQQGINLHILLDNITQAQAVVDYAAE T0547 174 :FKPKPNIGLRVRLHSAGVG 3llxA 128 :FGQDFSVFIEIDSDDHRGG T0547 206 :LTS 3llxA 147 :IKP T0547 209 :TELIEAVNLL 3llxA 152 :SKLLTIAKTL T0547 224 :LEQFTMIHFHLG 3llxA 162 :GEHFTGLMTHAG T0547 236 :SQITEIHPLKKALNEAGNIYTELRKM 3llxA 176 :YACNTEQGLKNFAKQECDAVRIARNN T0547 262 :GAKNLKAIN 3llxA 205 :AGIHCAITS T0547 291 :TLREYA 3llxA 241 :DLVMKN T0547 310 :KKDLEP 3llxA 247 :IGVCDF T0547 328 :NHAVLIAPVLE 3llxA 255 :IAMSVVTTVIG T0547 341 :SQEY 3llxA 268 :KEKN T0547 349 :LILKK 3llxA 274 :LTDSG T0547 363 :YDLYKSIKPS 3llxA 279 :WMALSRDSGT T0547 397 :VDLQDR 3llxA 327 :DAYQLE T0547 403 :SNAEILTHLITKKAILLLGD 3llxA 334 :FPVGHQLRIMPNHACATAAM T0547 533 :PTEAIISINEKGYEVEGIIEA 3llxA 354 :HPVYHVLMSDGSHNTWQRITG Number of specific fragments extracted= 21 number of extra gaps= 4 total=1006 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 1bd0A/T0547-1bd0A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1bd0A expands to /projects/compbio/data/pdb/1bd0.pdb.gz 1bd0A:# T0547 read from 1bd0A/T0547-1bd0A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1bd0A read from 1bd0A/T0547-1bd0A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1bd0A to template set # found chain 1bd0A in template set T0547 42 :GYKGPL 1bd0A 3 :DFHRDT T0547 48 :LLRFPHLIQKQIENIYGNFN 1bd0A 10 :AEVDLDAIYDNVENLRRLLP T0547 77 :GGFNAVYPLKV 1bd0A 30 :DDTHIMAVVKA T0547 88 :NQYPGFVKNLVKLGK 1bd0A 45 :HGDVQVARTALEAGA T0547 106 :YGLEAGSKAELLLAMAYNNE 1bd0A 60 :SRLAVAFLDEALALREKGIE T0547 127 :APITVNGFKDRELINIGF 1bd0A 80 :APILVLGASRPADAALAA T0547 148 :EMG 1bd0A 98 :QQR T0547 153 :ITLTIEGLNELEAIIDIAK 1bd0A 101 :IALTVFRSDWLEEASALYS T0547 174 :FKPKPNIGLRVRLH 1bd0A 120 :GPFPIHFHLKMDTG T0547 190 :GV 1bd0A 134 :MG T0547 203 :KFGL 1bd0A 136 :RLGV T0547 207 :TSTELIEAVNLLKENKLLEQFT 1bd0A 141 :DEEETKRIVALIERHPHFVLEG T0547 230 :IHFHLG 1bd0A 163 :LYTHFA T0547 236 :SQITEIHPLKKALNEAGNIYTEL 1bd0A 170 :ADEVNTDYFSYQYTRFLHMLEWL T0547 262 :G 1bd0A 193 :P T0547 264 :KNLKAINLGGGLAV 1bd0A 194 :SRPPLVHCANSAAS T0547 310 :KK 1bd0A 211 :PD T0547 313 :LEPDI 1bd0A 213 :RTFNM T0547 319 :IESGRFVAA 1bd0A 218 :VRFGIAMYG T0547 328 :NHAVLIAPVLELFSQE 1bd0A 243 :EAFSLHSRLVHVKKLQ T0547 344 :YAE 1bd0A 274 :EEW T0547 348 :KLILKK 1bd0A 277 :IGTIPI T0547 354 :QNPKLIDELY 1bd0A 284 :YADGWLRRLQ T0547 374 :ALE 1bd0A 294 :HFH T0547 377 :YLHDSIDHLES 1bd0A 302 :QKAPIVGRICM T0547 390 :TLFDLGY 1bd0A 313 :DQCMIRL T0547 399 :LQDRSNAEILTHLI 1bd0A 320 :PGPLPVGTKVTLIG T0547 413 :TKKAILLLGD 1bd0A 342 :IDDVARHLET T0547 428 :DLLAIQDEVQERYLVNFSL 1bd0A 352 :INYEVPCTISYRVPRIFFR T0547 543 :KGYEVEGI 1bd0A 371 :HKRIMEVR Number of specific fragments extracted= 30 number of extra gaps= 0 total=1036 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 1bd0A/T0547-1bd0A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0547 read from 1bd0A/T0547-1bd0A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1bd0A read from 1bd0A/T0547-1bd0A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1bd0A in template set Warning: unaligning (T0547)S555 because last residue in template chain is (1bd0A)G382 T0547 43 :YKGPLLLRFPHLIQKQIENIYGNFN 1bd0A 5 :HRDTWAEVDLDAIYDNVENLRRLLP T0547 77 :GGFNAVYPLKVN 1bd0A 30 :DDTHIMAVVKAN T0547 89 :QYPGFVKNLVKLGK 1bd0A 46 :GDVQVARTALEAGA T0547 106 :YGLEAGSKAELLLAMAYNNEG 1bd0A 60 :SRLAVAFLDEALALREKGIEA T0547 128 :PITVNGFKDRE 1bd0A 81 :PILVLGASRPA T0547 141 :NIGF 1bd0A 92 :DAAL T0547 146 :AAEMG 1bd0A 96 :AAQQR T0547 153 :ITLTIEGLNELEAIIDIAK 1bd0A 101 :IALTVFRSDWLEEASALYS T0547 174 :FKPKPNIGLRVRLH 1bd0A 120 :GPFPIHFHLKMDTG T0547 202 :SKFGLTS 1bd0A 135 :GRLGVKD T0547 209 :TELIEAVNLLKENKLL 1bd0A 143 :EETKRIVALIERHPHF T0547 226 :QFTMIHFHLGSQI 1bd0A 159 :VLEGLYTHFATAD T0547 239 :TEIHPLKKA 1bd0A 173 :VNTDYFSYQ T0547 252 :GNIYTELRKMGAKNLKAINLGGGLAVEY 1bd0A 182 :YTRFLHMLEWLPSRPPLVHCANSAASLR T0547 282 :FKNE 1bd0A 210 :FPDR T0547 287 :SR 1bd0A 214 :TF T0547 313 :L 1bd0A 216 :N T0547 318 :FIESGRFVAA 1bd0A 217 :MVRFGIAMYG T0547 328 :NHAVLIAPVLELFSQ 1bd0A 243 :EAFSLHSRLVHVKKL T0547 343 :EYAENKLILKKQNPKLIDE 1bd0A 272 :QTEEWIGTIPIGYADGWLR T0547 362 :LYDL 1bd0A 292 :LQHF T0547 378 :LHDSIDHLESILT 1bd0A 300 :DGQKAPIVGRICM T0547 393 :DLGYVDL 1bd0A 313 :DQCMIRL T0547 400 :QDRSNAEILTHLITKKAILL 1bd0A 321 :GPLPVGTKVTLIGRQGDEVI T0547 428 :DLLAIQDEVQERY 1bd0A 341 :SIDDVARHLETIN T0547 448 :QSM 1bd0A 354 :YEV T0547 453 :FWGLEQNFP 1bd0A 357 :PCTISYRVP T0547 537 :IISINEK 1bd0A 366 :RIFFRHK T0547 546 :EVEGIIEAQ 1bd0A 373 :RIMEVRNAI Number of specific fragments extracted= 29 number of extra gaps= 0 total=1065 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 1bd0A/T0547-1bd0A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0547 read from 1bd0A/T0547-1bd0A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1bd0A read from 1bd0A/T0547-1bd0A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1bd0A in template set T0547 44 :KGPLLLRFPHLIQKQIENIYGNF 1bd0A 6 :RDTWAEVDLDAIYDNVENLRRLL T0547 76 :KGGFNAVYPLKV 1bd0A 29 :PDDTHIMAVVKA T0547 88 :NQYPGFVKNLVKLGK 1bd0A 45 :HGDVQVARTALEAGA T0547 106 :YGLEAGSKAELLLAMAYNNEGAPITVNGFKDRE 1bd0A 60 :SRLAVAFLDEALALREKGIEAPILVLGASRPAD T0547 141 :NIGFIAAEM 1bd0A 93 :AALAAQQRI T0547 154 :TLTIEGLNELEAIIDIAK 1bd0A 102 :ALTVFRSDWLEEASALYS T0547 174 :FKPKPNIGLRVRLHSAGVGI 1bd0A 120 :GPFPIHFHLKMDTGMGRLGV T0547 207 :TSTELIEAVNLLKENK 1bd0A 141 :DEEETKRIVALIERHP T0547 224 :LEQFTMIHFHLGSQI 1bd0A 157 :HFVLEGLYTHFATAD T0547 239 :TEIHPLKKA 1bd0A 173 :VNTDYFSYQ T0547 252 :GNIYTELRKMGAKNLKAINLG 1bd0A 182 :YTRFLHMLEWLPSRPPLVHCA T0547 309 :QKKDLEPDIFI 1bd0A 209 :RFPDRTFNMVR T0547 321 :SGRFVAA 1bd0A 220 :FGIAMYG T0547 328 :NHAVLIAPVLELFSQEYAE 1bd0A 243 :EAFSLHSRLVHVKKLQPGE T0547 349 :LILKK 1bd0A 262 :KVSYG T0547 401 :DR 1bd0A 267 :AT T0547 403 :SNAEILTHLITKK 1bd0A 271 :AQTEEWIGTIPIG T0547 421 :GDKQNPADLLAIQDEVQERYLVNF 1bd0A 284 :YADGWLRRLQHFHVLVDGQKAPIV T0547 470 :EEPTRSASIWDIT 1bd0A 308 :GRICMDQCMIRLP T0547 501 :DVDVE 1bd0A 321 :GPLPV T0547 533 :PTEAIISINEKGYEV 1bd0A 326 :GTKVTLIGRQGDEVI T0547 555 :SILDTLEDLDY 1bd0A 341 :SIDDVARHLET Number of specific fragments extracted= 22 number of extra gaps= 0 total=1087 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 2vd8A/T0547-2vd8A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2vd8A expands to /projects/compbio/data/pdb/2vd8.pdb.gz 2vd8A:Skipped atom 187, because occupancy 0.500 <= existing 0.500 in 2vd8A Skipped atom 188, because occupancy 0.500 <= existing 0.500 in 2vd8A Skipped atom 189, because occupancy 0.500 <= existing 0.500 in 2vd8A Skipped atom 190, because occupancy 0.500 <= existing 0.500 in 2vd8A Skipped atom 191, because occupancy 0.500 <= existing 0.500 in 2vd8A Skipped atom 192, because occupancy 0.500 <= existing 0.500 in 2vd8A Skipped atom 193, because occupancy 0.500 <= existing 0.500 in 2vd8A Bad short name: CH1 for alphabet: pdb_atoms Bad short name: N1 for alphabet: pdb_atoms Bad short name: C2 for alphabet: pdb_atoms Bad short name: C2' for alphabet: pdb_atoms Bad short name: C3 for alphabet: pdb_atoms Bad short name: O3 for alphabet: pdb_atoms Bad short name: C4 for alphabet: pdb_atoms Bad short name: C4' for alphabet: pdb_atoms Bad short name: C5 for alphabet: pdb_atoms Bad short name: C6 for alphabet: pdb_atoms Bad short name: C5' for alphabet: pdb_atoms Bad short name: OP4 for alphabet: pdb_atoms Bad short name: P for alphabet: pdb_atoms Bad short name: OP1 for alphabet: pdb_atoms Bad short name: OP2 for alphabet: pdb_atoms Bad short name: OP3 for alphabet: pdb_atoms Bad short name: CH1 for alphabet: pdb_atoms Bad short name: CH1 for alphabet: pdb_atoms Bad short name: CH1 for alphabet: pdb_atoms Bad short name: CH1 for alphabet: pdb_atoms Bad short name: CH1 for alphabet: pdb_atoms Bad short name: CH1 for alphabet: pdb_atoms Bad short name: CH1 for alphabet: pdb_atoms Skipped atom 1226, because occupancy 0.500 <= existing 0.500 in 2vd8A Skipped atom 1227, because occupancy 0.500 <= existing 0.500 in 2vd8A Skipped atom 1228, because occupancy 0.500 <= existing 0.500 in 2vd8A Skipped atom 1229, because occupancy 0.500 <= existing 0.500 in 2vd8A Skipped atom 1230, because occupancy 0.500 <= existing 0.500 in 2vd8A Skipped atom 1231, because occupancy 0.500 <= existing 0.500 in 2vd8A Bad short name: CH1 for alphabet: pdb_atoms Bad short name: CH1 for alphabet: pdb_atoms Bad short name: CH1 for alphabet: pdb_atoms Bad short name: CH1 for alphabet: pdb_atoms Bad short name: CH1 for alphabet: pdb_atoms Bad short name: CH1 for alphabet: pdb_atoms Bad short name: CH1 for alphabet: pdb_atoms Bad short name: CH1 for alphabet: pdb_atoms Skipped atom 2601, because occupancy 0.500 <= existing 0.500 in 2vd8A Skipped atom 2602, because occupancy 0.500 <= existing 0.500 in 2vd8A Skipped atom 2603, because occupancy 0.500 <= existing 0.500 in 2vd8A Skipped atom 2604, because occupancy 0.500 <= existing 0.500 in 2vd8A Skipped atom 2605, because occupancy 0.500 <= existing 0.500 in 2vd8A Skipped atom 2606, because occupancy 0.500 <= existing 0.500 in 2vd8A Skipped atom 2607, because occupancy 0.500 <= existing 0.500 in 2vd8A Skipped atom 2608, because occupancy 0.500 <= existing 0.500 in 2vd8A Bad short name: CH1 for alphabet: pdb_atoms Skipped atom 2925, because occupancy 0.500 <= existing 0.500 in 2vd8A Skipped atom 2926, because occupancy 0.500 <= existing 0.500 in 2vd8A Skipped atom 2927, because occupancy 0.500 <= existing 0.500 in 2vd8A Skipped atom 2928, because occupancy 0.500 <= existing 0.500 in 2vd8A Skipped atom 2929, because occupancy 0.500 <= existing 0.500 in 2vd8A Skipped atom 2930, because occupancy 0.500 <= existing 0.500 in 2vd8A Skipped atom 2931, because occupancy 0.500 <= existing 0.500 in 2vd8A Bad short name: CH1 for alphabet: pdb_atoms # T0547 read from 2vd8A/T0547-2vd8A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2vd8A read from 2vd8A/T0547-2vd8A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2vd8A to template set # found chain 2vd8A in template set Warning: unaligning (T0547)I62 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2vd8A)E28 Warning: unaligning (T0547)G64 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2vd8A)E28 Warning: unaligning (T0547)L85 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2vd8A)G42 Warning: unaligning (T0547)V87 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2vd8A)G42 Warning: unaligning (T0547)V94 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2vd8A)I55 Warning: unaligning (T0547)N96 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2vd8A)I55 Warning: unaligning (T0547)G159 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2vd8A)E111 Warning: unaligning (T0547)N161 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2vd8A)E111 Warning: unaligning (T0547)I167 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2vd8A)L119 Warning: unaligning (T0547)I169 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2vd8A)L119 Warning: unaligning (T0547)P178 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2vd8A)Y128 Warning: unaligning (T0547)I180 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2vd8A)Y128 Warning: unaligning (T0547)S208 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2vd8A)E146 Warning: unaligning (T0547)E210 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2vd8A)E146 Warning: unaligning (T0547)L211 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2vd8A)G149 Warning: unaligning (T0547)E213 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2vd8A)G149 Warning: unaligning (T0547)V215 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2vd8A)S153 Warning: unaligning (T0547)L217 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2vd8A)S153 Warning: unaligning (T0547)K245 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2vd8A)Q183 Warning: unaligning (T0547)A247 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2vd8A)Q183 Warning: unaligning (T0547)L258 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2vd8A)E196 Warning: unaligning (T0547)K260 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2vd8A)E196 Warning: unaligning (T0547)L266 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2vd8A)F203 Warning: unaligning (T0547)A268 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2vd8A)F203 Warning: unaligning (T0547)A334 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2vd8A)V256 Warning: unaligning (T0547)V336 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2vd8A)V256 Warning: unaligning (T0547)E343 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2vd8A)G265 Warning: unaligning (T0547)Y344 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2vd8A)T278 Warning: unaligning (T0547)L378 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2vd8A)R308 Warning: unaligning (T0547)E406 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2vd8A)V334 Warning: unaligning (T0547)L408 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2vd8A)V334 Warning: unaligning (T0547)Q448 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2vd8A)V379 Warning: unaligning (T0547)M450 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2vd8A)V379 T0547 43 :YKGPLLLRFPHLIQKQIEN 2vd8A 7 :YRDTWVEVDLDAIYNNVTH T0547 65 :NFN 2vd8A 29 :FIP T0547 77 :GGFNAVYP 2vd8A 32 :SDVEIFAV T0547 88 :NQ 2vd8A 43 :NA T0547 90 :YPGF 2vd8A 49 :YVPV T0547 97 :LVKLGK 2vd8A 56 :ALEAGA T0547 106 :YGLEAGSKAELLLAMAYNNE 2vd8A 62 :TRLAVAFLDEALVLRRAGIT T0547 127 :APITVNGFKDRELINIGF 2vd8A 82 :APILVLGPSPPRDINVAA T0547 148 :EMG 2vd8A 100 :END T0547 153 :ITLTIE 2vd8A 103 :VALTVF T0547 162 :ELEAI 2vd8A 112 :WVDEA T0547 170 :AK 2vd8A 120 :WD T0547 174 :FKPK 2vd8A 122 :GSST T0547 181 :GLRVRLH 2vd8A 129 :HINFDSG T0547 190 :GV 2vd8A 136 :MG T0547 203 :KFGL 2vd8A 138 :RIGI T0547 207 :T 2vd8A 143 :E T0547 214 :A 2vd8A 150 :F T0547 218 :LKENKLLEQFT 2vd8A 154 :LEGAPFLELEG T0547 230 :IHFHLG 2vd8A 165 :VYTHFA T0547 236 :SQITEIHPL 2vd8A 172 :ADEVETSYF T0547 248 :LNEAGNIYTE 2vd8A 184 :YNTFLEQLSW T0547 261 :MGA 2vd8A 197 :FGV T0547 265 :N 2vd8A 200 :D T0547 269 :INLGGGLAVEYSQFKNEK 2vd8A 204 :VHTANSAATLRFQGITFN T0547 318 :FIESGRFVAA 2vd8A 222 :AVRIGIAMYG T0547 328 :NHAVLI 2vd8A 248 :PALSLH T0547 337 :LELFSQ 2vd8A 257 :AHIKQV T0547 345 :AENKLILKK 2vd8A 279 :EEWIATVAI T0547 354 :QNPKLIDELYD 2vd8A 289 :YADGWLRRLQG T0547 375 :LE 2vd8A 300 :FE T0547 379 :HDSIDHLES 2vd8A 309 :VPIVGRVTM T0547 395 :GYV 2vd8A 318 :DQF T0547 400 :QDRSNA 2vd8A 326 :CEVPLG T0547 409 :THLI 2vd8A 335 :TLIG T0547 413 :TKKAILLL 2vd8A 347 :ATEVAEYS T0547 426 :PADLLAIQDEVQERYLVNFSLF 2vd8A 355 :GTINYEIITTISFRVPRIFIRN T0547 451 :PDFWGLEQ 2vd8A 380 :VEVINYLN Number of specific fragments extracted= 38 number of extra gaps= 0 total=1125 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 2vd8A/T0547-2vd8A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0547 read from 2vd8A/T0547-2vd8A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2vd8A read from 2vd8A/T0547-2vd8A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2vd8A in template set Warning: unaligning (T0547)I62 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2vd8A)E28 Warning: unaligning (T0547)G64 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2vd8A)E28 Warning: unaligning (T0547)L85 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2vd8A)G42 Warning: unaligning (T0547)V87 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2vd8A)G42 Warning: unaligning (T0547)V94 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2vd8A)I55 Warning: unaligning (T0547)N96 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2vd8A)I55 Warning: unaligning (T0547)G159 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2vd8A)E111 Warning: unaligning (T0547)N161 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2vd8A)E111 Warning: unaligning (T0547)I167 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2vd8A)L119 Warning: unaligning (T0547)I169 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2vd8A)L119 Warning: unaligning (T0547)P178 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2vd8A)Y128 Warning: unaligning (T0547)I180 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2vd8A)Y128 Warning: unaligning (T0547)E210 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2vd8A)E146 Warning: unaligning (T0547)L211 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2vd8A)G149 Warning: unaligning (T0547)E213 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2vd8A)G149 Warning: unaligning (T0547)V215 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2vd8A)S153 Warning: unaligning (T0547)L217 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2vd8A)S153 Warning: unaligning (T0547)K245 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2vd8A)Q183 Warning: unaligning (T0547)A247 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2vd8A)Q183 Warning: unaligning (T0547)L258 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2vd8A)E196 Warning: unaligning (T0547)K260 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2vd8A)E196 Warning: unaligning (T0547)L266 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2vd8A)F203 Warning: unaligning (T0547)A268 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2vd8A)F203 Warning: unaligning (T0547)A334 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2vd8A)V256 Warning: unaligning (T0547)V336 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2vd8A)V256 Warning: unaligning (T0547)E343 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2vd8A)G265 Warning: unaligning (T0547)A345 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2vd8A)G265 Warning: unaligning (T0547)L351 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2vd8A)T278 Warning: unaligning (T0547)K353 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2vd8A)T278 Warning: unaligning (T0547)H379 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2vd8A)R308 Warning: unaligning (T0547)S381 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2vd8A)R308 Warning: unaligning (T0547)E406 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2vd8A)V334 Warning: unaligning (T0547)L408 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2vd8A)V334 T0547 43 :YKGPLLLRFPHLIQKQIEN 2vd8A 7 :YRDTWVEVDLDAIYNNVTH T0547 65 :NF 2vd8A 29 :FI T0547 76 :KGGFNAVYP 2vd8A 31 :PSDVEIFAV T0547 88 :N 2vd8A 43 :N T0547 89 :QYPGF 2vd8A 48 :DYVPV T0547 97 :LVKLGK 2vd8A 56 :ALEAGA T0547 106 :YGLEAGSKAELLLAMAYNNEG 2vd8A 62 :TRLAVAFLDEALVLRRAGITA T0547 128 :PITVNGFKDRE 2vd8A 83 :PILVLGPSPPR T0547 141 :NIGF 2vd8A 94 :DINV T0547 146 :AAEMG 2vd8A 98 :AAEND T0547 153 :ITLTIE 2vd8A 103 :VALTVF T0547 162 :ELEAI 2vd8A 112 :WVDEA T0547 170 :AK 2vd8A 120 :WD T0547 174 :FKPK 2vd8A 122 :GSST T0547 181 :GLRVRLH 2vd8A 129 :HINFDSG T0547 188 :S 2vd8A 137 :G T0547 203 :KFGLTS 2vd8A 138 :RIGIRE T0547 214 :A 2vd8A 150 :F T0547 218 :LKENKLL 2vd8A 154 :LEGAPFL T0547 226 :QFTMIHFHLG 2vd8A 161 :ELEGVYTHFA T0547 236 :SQITEIHPL 2vd8A 172 :ADEVETSYF T0547 248 :LNEAGNIYTE 2vd8A 184 :YNTFLEQLSW T0547 261 :MGA 2vd8A 197 :FGV T0547 265 :N 2vd8A 200 :D T0547 269 :INLGGGLAVEY 2vd8A 204 :VHTANSAATLR T0547 282 :FKNEKSR 2vd8A 215 :FQGITFN T0547 318 :FIESGRFVAA 2vd8A 222 :AVRIGIAMYG T0547 328 :NHAVLI 2vd8A 248 :PALSLH T0547 337 :LELFSQ 2vd8A 257 :AHIKQV T0547 346 :EN 2vd8A 266 :DG T0547 348 :KLI 2vd8A 273 :TYR T0547 354 :QN 2vd8A 279 :EE T0547 356 :PKLIDE 2vd8A 290 :ADGWLR T0547 374 :ALEYL 2vd8A 297 :LQGFE T0547 382 :IDHLESILT 2vd8A 309 :VPIVGRVTM T0547 393 :DLGYVD 2vd8A 318 :DQFMIH T0547 399 :LQDRSNA 2vd8A 325 :PCEVPLG T0547 409 :THLITKKAILLLGDKQN 2vd8A 335 :TLIGRQGDEYISATEVA T0547 426 :PADLLAIQ 2vd8A 355 :GTINYEII Number of specific fragments extracted= 39 number of extra gaps= 0 total=1164 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 2vd8A/T0547-2vd8A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0547 read from 2vd8A/T0547-2vd8A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2vd8A read from 2vd8A/T0547-2vd8A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2vd8A in template set Warning: unaligning (T0547)I62 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2vd8A)E28 Warning: unaligning (T0547)G64 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2vd8A)E28 Warning: unaligning (T0547)L85 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2vd8A)G42 Warning: unaligning (T0547)V87 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2vd8A)G42 Warning: unaligning (T0547)V94 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2vd8A)I55 Warning: unaligning (T0547)N96 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2vd8A)I55 Warning: unaligning (T0547)G159 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2vd8A)E111 Warning: unaligning (T0547)N161 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2vd8A)E111 Warning: unaligning (T0547)I167 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2vd8A)L119 Warning: unaligning (T0547)I169 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2vd8A)L119 Warning: unaligning (T0547)P178 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2vd8A)Y128 Warning: unaligning (T0547)I180 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2vd8A)Y128 Warning: unaligning (T0547)S208 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2vd8A)E146 Warning: unaligning (T0547)E210 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2vd8A)E146 Warning: unaligning (T0547)L211 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2vd8A)G149 Warning: unaligning (T0547)E213 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2vd8A)G149 Warning: unaligning (T0547)V215 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2vd8A)S153 Warning: unaligning (T0547)L217 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2vd8A)S153 Warning: unaligning (T0547)K245 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2vd8A)Q183 Warning: unaligning (T0547)A247 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2vd8A)Q183 Warning: unaligning (T0547)L258 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2vd8A)E196 Warning: unaligning (T0547)K260 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2vd8A)E196 Warning: unaligning (T0547)L266 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2vd8A)F203 Warning: unaligning (T0547)A268 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2vd8A)F203 Warning: unaligning (T0547)R288 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2vd8A)L246 Warning: unaligning (T0547)L313 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2vd8A)L246 Warning: unaligning (T0547)A334 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2vd8A)V256 Warning: unaligning (T0547)V336 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2vd8A)V256 Warning: unaligning (T0547)E343 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2vd8A)G265 Warning: unaligning (T0547)A345 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2vd8A)G265 Warning: unaligning (T0547)S403 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2vd8A)T278 Warning: unaligning (T0547)A405 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2vd8A)T278 Warning: unaligning (T0547)R439 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2vd8A)R308 Warning: unaligning (T0547)L441 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2vd8A)R308 Warning: unaligning (T0547)G544 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2vd8A)V334 Warning: unaligning (T0547)Y545 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2vd8A)V334 T0547 46 :PLLLRFPHLIQKQIEN 2vd8A 10 :TWVEVDLDAIYNNVTH T0547 65 :NF 2vd8A 29 :FI T0547 76 :KGGFNAVYP 2vd8A 31 :PSDVEIFAV T0547 88 :NQ 2vd8A 43 :NA T0547 90 :YPGF 2vd8A 49 :YVPV T0547 97 :LVKLGK 2vd8A 56 :ALEAGA T0547 106 :YGLEAGSKAELLLAMAYNNEGAPITVNGFKDR 2vd8A 62 :TRLAVAFLDEALVLRRAGITAPILVLGPSPPR T0547 140 :INIGFIAAEM 2vd8A 94 :DINVAAENDV T0547 154 :TLTIE 2vd8A 104 :ALTVF T0547 162 :ELEAI 2vd8A 112 :WVDEA T0547 170 :AK 2vd8A 120 :WD T0547 174 :FKPK 2vd8A 122 :GSST T0547 181 :GLRVRLHSAGVG 2vd8A 129 :HINFDSGMGRIG T0547 205 :GLT 2vd8A 141 :IRE T0547 214 :A 2vd8A 150 :F T0547 218 :LKENK 2vd8A 154 :LEGAP T0547 224 :LEQFTMIHFHLGSQ 2vd8A 159 :FLELEGVYTHFATA T0547 238 :ITEIHPL 2vd8A 174 :EVETSYF T0547 248 :LNEAGNIYTE 2vd8A 184 :YNTFLEQLSW T0547 261 :M 2vd8A 197 :F T0547 263 :AKN 2vd8A 198 :GVD T0547 269 :IN 2vd8A 204 :VH T0547 283 :KNEKS 2vd8A 239 :RPFLP T0547 314 :E 2vd8A 247 :E T0547 328 :NHAVLI 2vd8A 248 :PALSLH T0547 337 :LELFSQ 2vd8A 257 :AHIKQV T0547 346 :EN 2vd8A 266 :DG T0547 350 :ILKKQ 2vd8A 268 :ISYNV T0547 402 :R 2vd8A 273 :T T0547 406 :EILTHLITKK 2vd8A 279 :EEWIATVAIG T0547 417 :ILLLGDKQNPADLL 2vd8A 289 :YADGWLRRLQGFEV T0547 438 :E 2vd8A 305 :N T0547 442 :VNFSLFQSMP 2vd8A 309 :VPIVGRVTMD T0547 535 :EAIISI 2vd8A 319 :QFMIHL T0547 541 :NEK 2vd8A 329 :PLG T0547 546 :EVEGIIEAQ 2vd8A 335 :TLIGRQGDE T0547 555 :SILDTLEDLDYDI 2vd8A 346 :SATEVAEYSGTIN Number of specific fragments extracted= 37 number of extra gaps= 0 total=1201 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 1vfsA/T0547-1vfsA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1vfsA expands to /projects/compbio/data/pdb/1vfs.pdb.gz 1vfsA:Bad short name: CX for alphabet: pdb_atoms Bad short name: OQ1 for alphabet: pdb_atoms Bad short name: OQ2 for alphabet: pdb_atoms # T0547 read from 1vfsA/T0547-1vfsA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1vfsA read from 1vfsA/T0547-1vfsA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1vfsA to template set # found chain 1vfsA in template set Warning: unaligning (T0547)L182 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1vfsA)A130 Warning: unaligning (T0547)V184 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1vfsA)A130 T0547 45 :GPLLLRFPHLIQKQIENIYGNF 1vfsA 7 :RVYAEIDLDAVRANVRALRARA T0547 77 :GGFNAVYPLK 1vfsA 29 :PRSALMAVVK T0547 87 :VNQYPGFVKNLVKLGK 1vfsA 43 :GHGAVPCARAAQEAGA T0547 106 :YGLEAGSKAELLLAMAYNNE 1vfsA 59 :AWLGTATPEEALELRAAGIQ T0547 127 :APITVNGFKDRELINIGF 1vfsA 79 :GRIMCWLWTPGGPWREAI T0547 148 :EMGH 1vfsA 97 :ETDI T0547 154 :TLTIEGLNELEAIIDIAKE 1vfsA 101 :DVSVSGMWALDEVRAAARA T0547 174 :FKPKPNIG 1vfsA 120 :AGRTARIQ T0547 185 :RLHSA 1vfsA 131 :DTGLG T0547 203 :KFGLTSTELIEAVNLLKEN 1vfsA 136 :RNGCQPADWAELVGAAVAA T0547 222 :KLLEQFT 1vfsA 158 :GTVQVTG T0547 230 :IHFHLG 1vfsA 165 :VWSHFA T0547 236 :SQITEIHPLKKALNEAGNIYTELRKMGA 1vfsA 172 :ADEPGHPSIRLQLDAFRDMLAYAEKEGV T0547 265 :NLKAINLGGGLAV 1vfsA 200 :DPEVRHIANSPAT T0547 305 :NIAEQKKD 1vfsA 213 :LTLPETHF T0547 316 :DIF 1vfsA 221 :DLV T0547 320 :ESGRFVAA 1vfsA 224 :RTGLAVYG T0547 328 :NHAVLIAPVLELFSQE 1vfsA 248 :PAMTLRASLALVKTVP T0547 344 :YAE 1vfsA 279 :ETH T0547 348 :KLILKK 1vfsA 282 :LALVPA T0547 354 :QNPKLIDELY 1vfsA 289 :YADGIPRNAS T0547 373 :NALE 1vfsA 299 :GRGP T0547 377 :YLHDSIDHLE 1vfsA 308 :KIRRAAGRIA T0547 394 :LGYV 1vfsA 318 :MDQF T0547 398 :DLQDRSNAEILTHLITKKA 1vfsA 326 :GEDLAEAGDEAVILGDAER T0547 417 :ILLLGDKQNPADLLAIQDEVQER 1vfsA 348 :TAEDWAQAAHTIAYEIVTRIGGR Number of specific fragments extracted= 26 number of extra gaps= 0 total=1227 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 1vfsA/T0547-1vfsA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0547 read from 1vfsA/T0547-1vfsA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1vfsA read from 1vfsA/T0547-1vfsA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1vfsA in template set Warning: unaligning (T0547)K44 because first residue in template chain is (1vfsA)E3 Warning: unaligning (T0547)L182 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1vfsA)A130 Warning: unaligning (T0547)V184 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1vfsA)A130 T0547 45 :GP 1vfsA 4 :TP T0547 47 :LLLRFPHLIQKQIENIYGNF 1vfsA 9 :YAEIDLDAVRANVRALRARA T0547 77 :GGFNAVYPLKVN 1vfsA 29 :PRSALMAVVKSN T0547 89 :QYPGFVKNLVKLGK 1vfsA 45 :GAVPCARAAQEAGA T0547 106 :YGLEAGSKAELLLAMAYNNE 1vfsA 59 :AWLGTATPEEALELRAAGIQ T0547 127 :APITVNGFKDR 1vfsA 79 :GRIMCWLWTPG T0547 140 :INIGF 1vfsA 90 :GPWRE T0547 146 :AAEMGH 1vfsA 95 :AIETDI T0547 153 :I 1vfsA 101 :D T0547 155 :LTIEGLNELEAIIDIAKE 1vfsA 102 :VSVSGMWALDEVRAAARA T0547 174 :FKPKPNIG 1vfsA 120 :AGRTARIQ T0547 185 :RLH 1vfsA 131 :DTG T0547 188 :S 1vfsA 135 :G T0547 203 :KFGLTSTELIEAVNLLK 1vfsA 136 :RNGCQPADWAELVGAAV T0547 220 :ENKLL 1vfsA 156 :AEGTV T0547 226 :QFTMIHFHLGS 1vfsA 161 :QVTGVWSHFAC T0547 237 :QITEIHPLKKALNEAGNIYTELRKMGA 1vfsA 173 :DEPGHPSIRLQLDAFRDMLAYAEKEGV T0547 265 :NLKAINLGGGLAVEY 1vfsA 200 :DPEVRHIANSPATLT T0547 282 :FKNEKSR 1vfsA 215 :LPETHFD T0547 318 :FIESGRFVAA 1vfsA 222 :LVRTGLAVYG T0547 328 :NHAVLIAPVLELFSQ 1vfsA 248 :PAMTLRASLALVKTV T0547 343 :EYAENKLILK 1vfsA 277 :ESETHLALVP T0547 353 :KQ 1vfsA 291 :DG T0547 358 :LIDELYD 1vfsA 293 :IPRNASG T0547 376 :E 1vfsA 300 :R T0547 377 :YLHDSIDHLESILT 1vfsA 305 :VAGKIRRAAGRIAM T0547 393 :DLGYVD 1vfsA 319 :DQFVVD T0547 399 :LQDRSNAEILTHLITKKA 1vfsA 327 :EDLAEAGDEAVILGDAER T0547 426 :PAD 1vfsA 345 :GEP T0547 429 :LLAIQDEV 1vfsA 349 :AEDWAQAA T0547 553 :AQSILDTL 1vfsA 357 :HTIAYEIV Number of specific fragments extracted= 31 number of extra gaps= 0 total=1258 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 1vfsA/T0547-1vfsA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0547 read from 1vfsA/T0547-1vfsA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1vfsA read from 1vfsA/T0547-1vfsA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1vfsA in template set Warning: unaligning (T0547)L182 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1vfsA)A130 Warning: unaligning (T0547)V184 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1vfsA)A130 T0547 44 :KGPLLLRFPHLIQKQIENIYGNFN 1vfsA 6 :TRVYAEIDLDAVRANVRALRARAP T0547 78 :GFNAVYPLKVNQ 1vfsA 30 :RSALMAVVKSNA T0547 90 :YPGFVKNLVKLGK 1vfsA 46 :AVPCARAAQEAGA T0547 106 :YGLEAGSKAELLLAMAYNNEGAPITVNGFKD 1vfsA 59 :AWLGTATPEEALELRAAGIQGRIMCWLWTPG T0547 141 :NIGFIAAEM 1vfsA 92 :WREAIETDI T0547 154 :TLTIEGLNELEAIIDIAKE 1vfsA 101 :DVSVSGMWALDEVRAAARA T0547 174 :FKPKPNIG 1vfsA 120 :AGRTARIQ T0547 185 :RLHSA 1vfsA 131 :DTGLG T0547 203 :KFGLTSTELIEAVNLLKEN 1vfsA 136 :RNGCQPADWAELVGAAVAA T0547 222 :K 1vfsA 158 :G T0547 224 :LEQFTMIHFHLGS 1vfsA 159 :TVQVTGVWSHFAC T0547 237 :QITEIHPLKKALNEAGNIYTELRKM 1vfsA 173 :DEPGHPSIRLQLDAFRDMLAYAEKE T0547 263 :AKNLKAINLGG 1vfsA 198 :GVDPEVRHIAN T0547 304 :KNIAEQKKDLEPDIFI 1vfsA 209 :SPATLTLPETHFDLVR T0547 321 :SGRFVAA 1vfsA 225 :TGLAVYG T0547 328 :NHAVLIAPVLELFSQEYAENK 1vfsA 248 :PAMTLRASLALVKTVPAGHGV T0547 396 :YVDLQ 1vfsA 269 :SYGHH T0547 403 :SNAEILTHLITKK 1vfsA 276 :TESETHLALVPAG T0547 421 :GDKQNPAD 1vfsA 289 :YADGIPRN T0547 436 :VQERYLVNFS 1vfsA 297 :ASGRGPVLVA T0547 457 :EQNFPI 1vfsA 307 :GKIRRA T0547 530 :FT 1vfsA 313 :AG T0547 532 :HPTEAIISINE 1vfsA 317 :AMDQFVVDLGE T0547 543 :KGYEVEGIIEAQS 1vfsA 332 :AGDEAVILGDAER T0547 556 :ILDTLEDLDYD 1vfsA 349 :AEDWAQAAHTI Number of specific fragments extracted= 25 number of extra gaps= 0 total=1283 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 3co8A/T0547-3co8A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 3co8A expands to /projects/compbio/data/pdb/3co8.pdb.gz 3co8A:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0547 read from 3co8A/T0547-3co8A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3co8A read from 3co8A/T0547-3co8A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3co8A to template set # found chain 3co8A in template set Warning: unaligning (T0547)G235 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (3co8A)F178 Warning: unaligning (T0547)I241 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (3co8A)F178 T0547 44 :KGPLLLRFPHLIQKQIENIYGNF 3co8A 7 :RSTRIEFSKSSLAYNVQYTKQVS T0547 77 :GGFNAVYPLKV 3co8A 30 :GAKTLWLAVKS T0547 88 :NQYPGFVKNLVKLGK 3co8A 45 :HGLLQVSKIARECGV T0547 106 :YGLEAGSKAELLLAMAYNNE 3co8A 60 :DGLAVSVLDEGIAIRQAGID T0547 127 :APITVNGFKDRELINIGF 3co8A 80 :DFILILGPIDVKYAPIAS T0547 148 :EMGH 3co8A 98 :KYHF T0547 154 :TLTIEGLNELEAIIDIAKE 3co8A 102 :LTTVSSLDWLKSADKILGK T0547 176 :PKPNIGLRV 3co8A 121 :EKLSVNLAV T0547 187 :HSAGV 3co8A 130 :DTGMN T0547 203 :KFGL 3co8A 135 :RIGV T0547 207 :TSTELIEAVNLLKEN 3co8A 140 :SKKDLKDEIEFLQEH T0547 222 :KLLEQFT 3co8A 156 :DHFSYDG T0547 230 :IHFHL 3co8A 163 :IFTHF T0547 242 :HPL 3co8A 179 :QRQ T0547 252 :GNIYTELRKMGA 3co8A 182 :KNRWYELIDGLI T0547 265 :NLKAINLGG 3co8A 194 :MPRYVHVMN T0547 300 :VFILKNIAEQKK 3co8A 203 :SGAAMYHSKELP T0547 313 :LEPDIFI 3co8A 215 :GCNSIAR T0547 321 :SGRFVAAN 3co8A 222 :VGTVVYGV T0547 329 :HAVLIAPVLELFSQE 3co8A 245 :VFELKSALTFVKKIP T0547 344 :YAENKLILKK 3co8A 274 :RDTWIGTLPI T0547 354 :QNPKLIDELYD 3co8A 285 :YGDGWLAEYQD T0547 375 :LE 3co8A 296 :FQ T0547 377 :YLHDSIDHLES 3co8A 303 :QKCRQVGQIAM T0547 395 :GYV 3co8A 314 :DQM T0547 399 :LQDRSNAEILTHLITK 3co8A 321 :PHEYPIGTEVTLIGKS T0547 437 :QERYL 3co8A 337 :GKYEN T0547 555 :SILDTLEDLDY 3co8A 342 :TLYDLHKHSGV Number of specific fragments extracted= 28 number of extra gaps= 0 total=1311 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 3co8A/T0547-3co8A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0547 read from 3co8A/T0547-3co8A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3co8A read from 3co8A/T0547-3co8A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3co8A in template set Warning: unaligning (T0547)G235 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (3co8A)F178 T0547 44 :KGP 3co8A 6 :HRS T0547 47 :LLLRFPHLIQKQIENIYGNF 3co8A 10 :RIEFSKSSLAYNVQYTKQVS T0547 77 :GGFNAVYPLKVN 3co8A 30 :GAKTLWLAVKSN T0547 89 :QYPGFVKNLVKLGK 3co8A 46 :GLLQVSKIARECGV T0547 106 :YGLEAGSKAELLLAMAYNNEGAPITVNGFKDRE 3co8A 60 :DGLAVSVLDEGIAIRQAGIDDFILILGPIDVKY T0547 142 :IGF 3co8A 93 :API T0547 146 :AAEMG 3co8A 96 :ASKYH T0547 153 :ITLTIEGLNELEAIIDIA 3co8A 101 :FLTTVSSLDWLKSADKIL T0547 174 :FKPKPNIGLRVRLHS 3co8A 119 :GKEKLSVNLAVDTGM T0547 202 :SKFGLTS 3co8A 134 :NRIGVRS T0547 209 :TELIEAVNLLKEN 3co8A 142 :KDLKDEIEFLQEH T0547 222 :KLL 3co8A 156 :DHF T0547 226 :QFTMIHFHL 3co8A 159 :SYDGIFTHF T0547 249 :NEAGNIYTELRKMGA 3co8A 179 :QRQKNRWYELIDGLI T0547 265 :NLKAINLGG 3co8A 194 :MPRYVHVMN T0547 279 :Y 3co8A 208 :Y T0547 282 :FKNEKSR 3co8A 209 :HSKELPG T0547 314 :EPD 3co8A 216 :CNS T0547 318 :FIESGRFVAA 3co8A 219 :IARVGTVVYG T0547 328 :NHAVLIAPVLELFSQ 3co8A 244 :PVFELKSALTFVKKI T0547 343 :EYAENKLILK 3co8A 273 :SRDTWIGTLP T0547 353 :KQNPKLIDELY 3co8A 284 :GYGDGWLAEYQ T0547 376 :E 3co8A 295 :D T0547 377 :YLHDSIDHLESILT 3co8A 300 :IDGQKCRQVGQIAM T0547 393 :DLGYVD 3co8A 314 :DQMMVA T0547 399 :LQDRSNAEILTHL 3co8A 321 :PHEYPIGTEVTLI Number of specific fragments extracted= 26 number of extra gaps= 0 total=1337 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 3co8A/T0547-3co8A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0547 read from 3co8A/T0547-3co8A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3co8A read from 3co8A/T0547-3co8A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3co8A in template set Warning: unaligning (T0547)G235 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (3co8A)F178 T0547 45 :GPLLLRFPHLIQKQIENIYGNFN 3co8A 8 :STRIEFSKSSLAYNVQYTKQVSG T0547 78 :GFNAVYPLKVNQ 3co8A 31 :AKTLWLAVKSNA T0547 90 :YPGFVKNLVKLGK 3co8A 47 :LLQVSKIARECGV T0547 106 :YGLEAGSKAELLLAMAYNNEGAPITVNGFKDRE 3co8A 60 :DGLAVSVLDEGIAIRQAGIDDFILILGPIDVKY T0547 141 :NIGFIAAEM 3co8A 93 :APIASKYHF T0547 154 :TLTIEGLNELEAIIDIAKE 3co8A 102 :LTTVSSLDWLKSADKILGK T0547 176 :PKPNIGLRVRLHSAGVGI 3co8A 121 :EKLSVNLAVDTGMNRIGV T0547 206 :LTSTELIEAVNLLKENKLLEQFTMIHFHL 3co8A 139 :RSKKDLKDEIEFLQEHSDHFSYDGIFTHF T0547 245 :KKALNEAGN 3co8A 179 :QRQKNRWYE T0547 258 :LRKMGAKN 3co8A 188 :LIDGLIMP T0547 266 :LKAI 3co8A 197 :YVHV T0547 290 :YTLREYANDV 3co8A 201 :MNSGAAMYHS T0547 309 :QKKDLEPDIFI 3co8A 211 :KELPGCNSIAR T0547 321 :SGRFVAA 3co8A 222 :VGTVVYG T0547 328 :NHAVLIAPVLELFSQEYAENK 3co8A 244 :PVFELKSALTFVKKIPAGEGI T0547 351 :LKK 3co8A 265 :SYG T0547 399 :LQ 3co8A 268 :SK T0547 403 :SNAEILTHLITKKAILLLGDKQNPAD 3co8A 272 :TSRDTWIGTLPIGYGDGWLAEYQDFQ T0547 438 :ERYLVNFSLFQS 3co8A 301 :DGQKCRQVGQIA T0547 533 :PTEAIISI 3co8A 313 :MDQMMVAL T0547 541 :NEKG 3co8A 325 :PIGT T0547 545 :YEVEGIIEAQ 3co8A 330 :VTLIGKSGKY T0547 555 :SILDTLEDLDYD 3co8A 342 :TLYDLHKHSGVP Number of specific fragments extracted= 23 number of extra gaps= 0 total=1360 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 3kw3A/T0547-3kw3A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 3kw3A expands to /projects/compbio/data/pdb/3kw3.pdb.gz 3kw3A:Bad short name: N1 for alphabet: pdb_atoms Bad short name: C2 for alphabet: pdb_atoms Bad short name: C2' for alphabet: pdb_atoms Bad short name: C3 for alphabet: pdb_atoms Bad short name: O3 for alphabet: pdb_atoms Bad short name: C4 for alphabet: pdb_atoms Bad short name: C4' for alphabet: pdb_atoms Bad short name: C5 for alphabet: pdb_atoms Bad short name: C6 for alphabet: pdb_atoms Bad short name: C5' for alphabet: pdb_atoms Bad short name: OP4 for alphabet: pdb_atoms Bad short name: P for alphabet: pdb_atoms Bad short name: OP1 for alphabet: pdb_atoms Bad short name: OP2 for alphabet: pdb_atoms Bad short name: OP3 for alphabet: pdb_atoms Skipped atom 1176, because occupancy 0.500 <= existing 0.500 in 3kw3A Skipped atom 1180, because occupancy 0.500 <= existing 0.500 in 3kw3A Skipped atom 1182, because occupancy 0.500 <= existing 0.500 in 3kw3A Skipped atom 1184, because occupancy 0.500 <= existing 0.500 in 3kw3A Skipped atom 1186, because occupancy 0.500 <= existing 0.500 in 3kw3A Skipped atom 1188, because occupancy 0.500 <= existing 0.500 in 3kw3A # T0547 read from 3kw3A/T0547-3kw3A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3kw3A read from 3kw3A/T0547-3kw3A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3kw3A to template set # found chain 3kw3A in template set Warning: unaligning (T0547)G42 because first residue in template chain is (3kw3A)F13 Warning: unaligning (T0547)L85 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (3kw3A)A48 Warning: unaligning (T0547)V87 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (3kw3A)A48 Warning: unaligning (T0547)I153 because of BadResidue code BAD_PEPTIDE in next template residue (3kw3A)L113 Warning: unaligning (T0547)T156 because of BadResidue code BAD_PEPTIDE at template residue (3kw3A)L113 Warning: unaligning (T0547)Q342 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (3kw3A)P277 Warning: unaligning (T0547)Y344 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (3kw3A)P277 T0547 43 :YKGPLLLRFPHLIQKQIENIYGNF 3kw3A 14 :PATAIATIDVRAIVANYRTLAQHV T0547 77 :GGFNAVYP 3kw3A 38 :APTECSAV T0547 88 :NQYPGFVKNLVKLGK 3kw3A 53 :LGAHKIAPALYQAGC T0547 106 :YGLEAGSKAELLLAMAYNNEGAPITVNGFKDRELINIGF 3kw3A 68 :RTFFVAQIEEALQLKAVLPENVMIALLNGFPHKAEEFVA T0547 148 :EMGHN 3kw3A 107 :QSGII T0547 157 :IEGLNELEAIIDIAKE 3kw3A 114 :LNSWSTIEDWQTLCQK T0547 174 :FKPKPNIGLRVRLHS 3kw3A 130 :KNKKFPAIIQVDTNM T0547 191 :V 3kw3A 145 :S T0547 203 :KFGLTSTELIEAVN 3kw3A 146 :RLGLDKKELQKLIK T0547 220 :ENKLLEQFT 3kw3A 163 :IFEKAEIKY T0547 230 :IHFHLG 3kw3A 172 :ILSHLA T0547 236 :SQITEIHPLKKALNEAGNIYTE 3kw3A 179 :GEDASHSSNNKQLAAFKRVLAQ T0547 263 :AKNLKAI 3kw3A 201 :LPTCKVS T0547 275 :LAV 3kw3A 208 :FAN T0547 278 :EYSQFKNEK 3kw3A 236 :PHGKHPTPL T0547 327 :ANHAVLIAPVLELFS 3kw3A 245 :KAVVKVEAQVLQSRF T0547 345 :AE 3kw3A 278 :ST T0547 348 :KLILKK 3kw3A 280 :LATISI T0547 354 :QNPKLIDELYDLYKSIK 3kw3A 287 :YADGWPRILSNKGTVYF T0547 375 :LEYLHDSIDHLESILTLFDLGYV 3kw3A 304 :NGHKLPIVGHISMDSIIVDATDL T0547 399 :LQDRSNAEILTHLITKKAILLLGDKQNPA 3kw3A 327 :DKKPQRGDWVELIGPHQPLEKVSTDTNTI T0547 429 :LLAIQDEVQER 3kw3A 356 :PHEILTSLGKR Number of specific fragments extracted= 22 number of extra gaps= 1 total=1382 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 3kw3A/T0547-3kw3A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0547 read from 3kw3A/T0547-3kw3A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3kw3A read from 3kw3A/T0547-3kw3A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3kw3A in template set Warning: unaligning (T0547)G42 because first residue in template chain is (3kw3A)F13 Warning: unaligning (T0547)L85 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (3kw3A)A48 Warning: unaligning (T0547)V87 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (3kw3A)A48 Warning: unaligning (T0547)L155 because of BadResidue code BAD_PEPTIDE in next template residue (3kw3A)L113 Warning: unaligning (T0547)T156 because of BadResidue code BAD_PEPTIDE at template residue (3kw3A)L113 Warning: unaligning (T0547)Q342 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (3kw3A)P277 Warning: unaligning (T0547)A345 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (3kw3A)P277 T0547 43 :YKGPLLLRFPHLIQKQIENIYGNF 3kw3A 14 :PATAIATIDVRAIVANYRTLAQHV T0547 77 :GGFNAVYP 3kw3A 38 :APTECSAV T0547 88 :N 3kw3A 49 :N T0547 89 :QYPGFVKNLVKLGK 3kw3A 54 :GAHKIAPALYQAGC T0547 106 :YGLEAGSKAELLLAMAYNNEGAPITVNGFKDRE 3kw3A 68 :RTFFVAQIEEALQLKAVLPENVMIALLNGFPHK T0547 141 :NIGF 3kw3A 101 :AEEF T0547 146 :AAEMGH 3kw3A 105 :VAQSGI T0547 153 :I 3kw3A 111 :I T0547 157 :IEGLNELEAIIDIAKE 3kw3A 114 :LNSWSTIEDWQTLCQK T0547 174 :FKPKPNIGLRVRLH 3kw3A 130 :KNKKFPAIIQVDTN T0547 188 :S 3kw3A 145 :S T0547 203 :KFGLTSTELIEAVN 3kw3A 146 :RLGLDKKELQKLIK T0547 221 :NKLL 3kw3A 164 :FEKA T0547 226 :QFTMIHFHLGS 3kw3A 168 :EIKYILSHLAN T0547 237 :QITEIHPLKKALNEAGNIY 3kw3A 180 :EDASHSSNNKQLAAFKRVL T0547 261 :MGA 3kw3A 199 :AQL T0547 265 :NLKAINLGGGLAVE 3kw3A 202 :PTCKVSFANSGGIF T0547 282 :FKNEKSR 3kw3A 216 :LGSDFYF T0547 313 :L 3kw3A 223 :D T0547 318 :FIESGRFVAA 3kw3A 224 :LVRPGIALYG T0547 328 :NHAVLIAPVLELFS 3kw3A 246 :AVVKVEAQVLQSRF T0547 346 :ENKLILKKQ 3kw3A 278 :STLATISIG T0547 355 :NPKLIDELYDL 3kw3A 288 :ADGWPRILSNK T0547 377 :YLHDSIDHLESIL 3kw3A 303 :FNGHKLPIVGHIS T0547 392 :FDLGYVD 3kw3A 316 :MDSIIVD T0547 399 :LQDRSNAEILT 3kw3A 327 :DKKPQRGDWVE T0547 549 :GIIEAQSILDTLEDLDYDI 3kw3A 338 :LIGPHQPLEKVSTDTNTIP T0547 597 :YLFLN 3kw3A 357 :HEILT Number of specific fragments extracted= 28 number of extra gaps= 1 total=1410 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 3kw3A/T0547-3kw3A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0547 read from 3kw3A/T0547-3kw3A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3kw3A read from 3kw3A/T0547-3kw3A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3kw3A in template set Warning: unaligning (T0547)Y43 because first residue in template chain is (3kw3A)F13 Warning: unaligning (T0547)L85 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (3kw3A)A48 Warning: unaligning (T0547)V87 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (3kw3A)A48 Warning: unaligning (T0547)L155 because of BadResidue code BAD_PEPTIDE in next template residue (3kw3A)L113 Warning: unaligning (T0547)T156 because of BadResidue code BAD_PEPTIDE at template residue (3kw3A)L113 Warning: unaligning (T0547)Q342 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (3kw3A)P277 Warning: unaligning (T0547)E406 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (3kw3A)P277 T0547 44 :KGPLLL 3kw3A 14 :PATAIA T0547 50 :RFPHLIQKQIENIYGNFN 3kw3A 21 :IDVRAIVANYRTLAQHVA T0547 78 :GFNAVYP 3kw3A 39 :PTECSAV T0547 88 :NQY 3kw3A 49 :NAY T0547 91 :PGFVKNLVKLGK 3kw3A 56 :HKIAPALYQAGC T0547 106 :YGLEAGSKAELLLAMAYNNEGAPITVNGFKDRE 3kw3A 68 :RTFFVAQIEEALQLKAVLPENVMIALLNGFPHK T0547 141 :NIGFIAAEM 3kw3A 102 :EEFVAQSGI T0547 154 :T 3kw3A 111 :I T0547 157 :IEGLNELEAIIDIAKE 3kw3A 114 :LNSWSTIEDWQTLCQK T0547 174 :FKPKPNIGLRVRLHS 3kw3A 130 :KNKKFPAIIQVDTNM T0547 202 :SKFGLTSTELIEAVN 3kw3A 145 :SRLGLDKKELQKLIK T0547 221 :NK 3kw3A 164 :FE T0547 224 :LEQFTMIHFHLGS 3kw3A 166 :KAEIKYILSHLAN T0547 237 :QITEIHPLKKALNEAGNIY 3kw3A 180 :EDASHSSNNKQLAAFKRVL T0547 260 :KM 3kw3A 199 :AQ T0547 263 :AKNLK 3kw3A 201 :LPTCK T0547 328 :NHAVLIAPVLELFS 3kw3A 246 :AVVKVEAQVLQSRF T0547 407 :ILTHLITKKAI 3kw3A 278 :STLATISIGYA T0547 426 :PADLLA 3kw3A 289 :DGWPRI T0547 436 :VQERYLVNF 3kw3A 295 :LSNKGTVYF T0547 473 :TRSA 3kw3A 305 :GHKL T0547 488 :EISYSK 3kw3A 309 :PIVGHI T0547 532 :HPTEAIISINE 3kw3A 315 :SMDSIIVDATD T0547 543 :KGYEVEGIIEAQSILDTLEDLDYDI 3kw3A 332 :RGDWVELIGPHQPLEKVSTDTNTIP Number of specific fragments extracted= 24 number of extra gaps= 1 total=1434 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 3hurA/T0547-3hurA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 3hurA expands to /projects/compbio/data/pdb/3hur.pdb.gz 3hurA:# T0547 read from 3hurA/T0547-3hurA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3hurA read from 3hurA/T0547-3hurA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3hurA to template set # found chain 3hurA in template set Warning: unaligning (T0547)V131 because of BadResidue code BAD_PEPTIDE in next template residue (3hurA)L86 Warning: unaligning (T0547)N132 because of BadResidue code BAD_PEPTIDE at template residue (3hurA)L86 Warning: unaligning (T0547)G205 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (3hurA)F137 Warning: unaligning (T0547)L206 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3hurA)F137 T0547 42 :GYKGPL 3hurA 4 :AIHRPT T0547 48 :LLRFPHLIQKQIENIYGNF 3hurA 11 :VSVDLDAAAHNLQEIREWT T0547 77 :GGFNAVYPLKV 3hurA 30 :KAKKVYAVLKA T0547 88 :NQYPGFVKNLVKLGK 3hurA 45 :LGAIPLAKAFQETAS T0547 105 :NYGLEAGSKAELLLAMAYNNE 3hurA 60 :ADALIVSNLDEALELRQADLT T0547 127 :APIT 3hurA 81 :LPIW T0547 133 :GFKDRELINIGF 3hurA 87 :GAWDYSDLKLFI T0547 148 :EMG 3hurA 99 :DHD T0547 153 :ITLTIEGLNELE 3hurA 102 :IVITIPSLAWLQ T0547 174 :FKPKPNIGLRV 3hurA 118 :FEGTLKVSLAI T0547 187 :HSAGV 3hurA 129 :DTGMT T0547 203 :KF 3hurA 134 :RI T0547 207 :TSTELIEAVNLLKENKLLEQFT 3hurA 139 :KADEISAAKKIIDKNPQLDLFS T0547 230 :IHFHLGSQITEIHPLKKALNEAGNIYTELRK 3hurA 161 :VYTHFATADEAGEKSKAYFEEQLRRWQELTI T0547 261 :MGA 3hurA 193 :QGF T0547 265 :NLKAINLGGGLAV 3hurA 196 :DPSLFSMANSATC T0547 314 :EPDIF 3hurA 218 :SFAAI T0547 320 :ESGRFVAAN 3hurA 223 :RPGQLISGV T0547 329 :HAVLIAPVLELFSQE 3hurA 249 :IFSVCSEIADVRFVK T0547 344 :YAENKLILKK 3hurA 278 :EDGYVATLPF T0547 354 :QNPKLIDEL 3hurA 289 :YNDGWLRRM T0547 374 :AL 3hurA 299 :KS T0547 377 :YLHDSIDHLES 3hurA 307 :KRMPIIGRITM T0547 390 :TLFDLGY 3hurA 318 :DQTMVKL T0547 399 :LQDRSNAEILTHLITKKA 3hurA 325 :DRKYPIGTRVTLIGKDGG Number of specific fragments extracted= 25 number of extra gaps= 2 total=1459 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 3hurA/T0547-3hurA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0547 read from 3hurA/T0547-3hurA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3hurA read from 3hurA/T0547-3hurA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3hurA in template set Warning: unaligning (T0547)V131 because of BadResidue code BAD_PEPTIDE in next template residue (3hurA)L86 Warning: unaligning (T0547)N132 because of BadResidue code BAD_PEPTIDE at template residue (3hurA)L86 Warning: unaligning (T0547)G192 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (3hurA)F137 Warning: unaligning (T0547)I193 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3hurA)F137 T0547 43 :YKGPLLLRFPHLIQKQIENIYGNF 3hurA 6 :HRPTWVSVDLDAAAHNLQEIREWT T0547 77 :GGFNAVYPLKVNQY 3hurA 30 :KAKKVYAVLKADGY T0547 91 :PGFVKNLVKLGK 3hurA 48 :IPLAKAFQETAS T0547 105 :NYGLEAGSKAELLLAMAYNNE 3hurA 60 :ADALIVSNLDEALELRQADLT T0547 127 :APIT 3hurA 81 :LPIW T0547 133 :GFKDRELIN 3hurA 87 :GAWDYSDLK T0547 144 :F 3hurA 96 :L T0547 146 :AAEMG 3hurA 97 :FIDHD T0547 153 :ITLTIEGLNELE 3hurA 102 :IVITIPSLAWLQ T0547 174 :FKPKPNIGLRVRLH 3hurA 118 :FEGTLKVSLAIDTG T0547 189 :AGV 3hurA 133 :TRI T0547 194 :W 3hurA 138 :D T0547 207 :TSTELIEAVNLLKENKLL 3hurA 139 :KADEISAAKKIIDKNPQL T0547 226 :QFTMIHFHLGSQITEIHPLKKALNEAGNIYTELRKMGAKNLKAINLG 3hurA 157 :DLFSVYTHFATADEAGEKSKAYFEEQLRRWQELTINQGFDPSLFSMA T0547 310 :KKDLEPDI 3hurA 212 :HDDPRISF T0547 318 :FIESGRFVAA 3hurA 221 :AIRPGQLISG T0547 328 :NHAVLIAPVLELFSQ 3hurA 248 :RIFSVCSEIADVRFV T0547 343 :EYAENKLILK 3hurA 277 :PEDGYVATLP T0547 353 :KQNPKLIDE 3hurA 288 :GYNDGWLRR T0547 377 :YLHDSIDHLESI 3hurA 304 :INGKRMPIIGRI T0547 391 :LFDLGYVDL 3hurA 316 :TMDQTMVKL T0547 400 :QDRSNAEILTH 3hurA 326 :RKYPIGTRVTL Number of specific fragments extracted= 22 number of extra gaps= 2 total=1481 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 3hurA/T0547-3hurA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0547 read from 3hurA/T0547-3hurA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3hurA read from 3hurA/T0547-3hurA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3hurA in template set Warning: unaligning (T0547)T130 because of BadResidue code BAD_PEPTIDE in next template residue (3hurA)L86 Warning: unaligning (T0547)V131 because of BadResidue code BAD_PEPTIDE at template residue (3hurA)L86 Warning: unaligning (T0547)G192 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (3hurA)F137 Warning: unaligning (T0547)I193 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3hurA)F137 T0547 45 :GPLLLRFPHLIQKQIENIYGNFN 3hurA 8 :PTWVSVDLDAAAHNLQEIREWTK T0547 78 :GFNAVYPLKV 3hurA 31 :AKKVYAVLKA T0547 88 :NQYPGFVKNLVKLG 3hurA 45 :LGAIPLAKAFQETA T0547 104 :YNYGLEAGSKAELLLAMAYNNEGAPI 3hurA 59 :SADALIVSNLDEALELRQADLTLPIW T0547 132 :NGFKDRE 3hurA 87 :GAWDYSD T0547 141 :NIGFIAAEM 3hurA 94 :LKLFIDHDI T0547 154 :TLTIEGLNELE 3hurA 103 :VITIPSLAWLQ T0547 174 :FKPKPNIGLRVRLHSAGV 3hurA 118 :FEGTLKVSLAIDTGMTRI T0547 206 :LTSTELIEAVNLLKENK 3hurA 138 :DKADEISAAKKIIDKNP T0547 224 :LEQFTMIHFHLGSQITEIHPLKKALNEAGNIYTELRKMGAKN 3hurA 155 :QLDLFSVYTHFATADEAGEKSKAYFEEQLRRWQELTINQGFD T0547 287 :SR 3hurA 239 :KM T0547 310 :KKDLEPD 3hurA 241 :PPNLHLE T0547 328 :NHAVLIAPVLELFSQEYAENK 3hurA 248 :RIFSVCSEIADVRFVKKDQSL T0547 396 :YVDLQDRSNAEILTHLITKK 3hurA 269 :SYGASERMPEDGYVATLPFG T0547 421 :GDKQNPADLL 3hurA 289 :YNDGWLRRMQ T0547 439 :RYLVNF 3hurA 299 :KSSVII T0547 494 :DKPLFLHDVDVEKENYFLG 3hurA 305 :NGKRMPIIGRITMDQTMVK T0547 526 :KHNLFTHPTEAIISINEKG 3hurA 324 :LDRKYPIGTRVTLIGKDGG T0547 545 :YEVEGIIEAQS 3hurA 346 :TVEEVANYSHT Number of specific fragments extracted= 19 number of extra gaps= 2 total=1500 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 3e6eA/T0547-3e6eA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 3e6eA expands to /projects/compbio/data/pdb/3e6e.pdb.gz 3e6eA:# T0547 read from 3e6eA/T0547-3e6eA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3e6eA read from 3e6eA/T0547-3e6eA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3e6eA to template set # found chain 3e6eA in template set Warning: unaligning (T0547)S188 because of BadResidue code BAD_PEPTIDE in next template residue (3e6eA)G136 Warning: unaligning (T0547)A189 because of BadResidue code BAD_PEPTIDE at template residue (3e6eA)G136 Warning: unaligning (T0547)E220 because of BadResidue code BAD_PEPTIDE in next template residue (3e6eA)H158 Warning: unaligning (T0547)N221 because of BadResidue code BAD_PEPTIDE at template residue (3e6eA)H158 Warning: unaligning (T0547)K222 because of BadResidue code BAD_PEPTIDE at template residue (3e6eA)K159 Warning: unaligning (T0547)L223 because of BadResidue code BAD_PEPTIDE at template residue (3e6eA)E160 Warning: unaligning (T0547)Q400 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (3e6eA)E324 Warning: unaligning (T0547)D401 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3e6eA)E324 T0547 42 :GYKG 3e6eA 6 :HRPT T0547 47 :LLLRFPHLIQKQIENIYGNF 3e6eA 10 :RLHIDTQAITENVQKECQRL T0547 77 :G 3e6eA 30 :P T0547 78 :GFNAVYPLKV 3e6eA 32 :GTALFAVVKA T0547 88 :NQYPGFVKNLVKLGK 3e6eA 46 :HGAVESAKAAKKGGA T0547 106 :YGLEAGSKAELLLAMAYNNE 3e6eA 61 :TGFCVALLDEAIELREAGVQ T0547 127 :APITVNGFKDRELINIGF 3e6eA 81 :DPILILSVVDLAYVPLLI T0547 148 :EMGH 3e6eA 99 :QYDL T0547 153 :IT 3e6eA 103 :SV T0547 156 :TIEGLNELEAIIDIAKERFKPKPNIGLRV 3e6eA 105 :TVATQEWLEAALQQLTPESNTPLRVHLKV T0547 187 :H 3e6eA 134 :D T0547 190 :GV 3e6eA 137 :MG T0547 203 :KFGL 3e6eA 139 :RIGF T0547 207 :TSTELIEAVNLLK 3e6eA 144 :TPEETKQAVRFVQ T0547 224 :LEQFT 3e6eA 161 :FLWEG T0547 230 :IHFHLG 3e6eA 166 :IFTHFS T0547 236 :SQITEIHPLKKALNEAGNIYTEL 3e6eA 173 :ADEIDTSYFEKQAGRFKAVLAVL T0547 262 :GA 3e6eA 196 :EE T0547 265 :NLKAINLGG 3e6eA 198 :LPRYVHVSN T0547 292 :LREYA 3e6eA 207 :SATAL T0547 306 :IAEQ 3e6eA 212 :WHPD T0547 313 :LEPDIFI 3e6eA 216 :VPGNMIR T0547 321 :SGRFVAAN 3e6eA 223 :YGVAMYGL T0547 329 :HAVLIAPVLELFSQE 3e6eA 246 :ALRLTSELIHVKRLA T0547 344 :YAENKLILKK 3e6eA 275 :AEEWIGTVPI T0547 354 :QNPKLIDELYD 3e6eA 286 :YADGWLRHLQG T0547 375 :LE 3e6eA 297 :FT T0547 377 :YLHDSIDHLE 3e6eA 304 :KRCEIVGRVC T0547 394 :LGYV 3e6eA 314 :MDQC T0547 399 :L 3e6eA 322 :A T0547 402 :RSNAEILTHLITKK 3e6eA 325 :VPVGPVVTLVGKDG T0547 424 :QNPADLLAIQDEVQ 3e6eA 339 :NEENTLQMVAEKLE T0547 554 :QSILDTLED 3e6eA 353 :TIHYEVACT Number of specific fragments extracted= 33 number of extra gaps= 3 total=1533 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 3e6eA/T0547-3e6eA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0547 read from 3e6eA/T0547-3e6eA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3e6eA read from 3e6eA/T0547-3e6eA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3e6eA in template set Warning: unaligning (T0547)L186 because of BadResidue code BAD_PEPTIDE in next template residue (3e6eA)G136 Warning: unaligning (T0547)H187 because of BadResidue code BAD_PEPTIDE at template residue (3e6eA)G136 Warning: unaligning (T0547)E220 because of BadResidue code BAD_PEPTIDE in next template residue (3e6eA)H158 Warning: unaligning (T0547)N221 because of BadResidue code BAD_PEPTIDE at template residue (3e6eA)H158 Warning: unaligning (T0547)K222 because of BadResidue code BAD_PEPTIDE at template residue (3e6eA)K159 Warning: unaligning (T0547)L223 because of BadResidue code BAD_PEPTIDE at template residue (3e6eA)E160 Warning: unaligning (T0547)E542 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (3e6eA)E324 Warning: unaligning (T0547)K543 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3e6eA)E324 T0547 44 :KGPLLLRFPHLIQKQIENIYGNF 3e6eA 7 :RPTRLHIDTQAITENVQKECQRL T0547 76 :KGGFNAVYPLKVNQ 3e6eA 30 :PEGTALFAVVKANG T0547 90 :YPGFVKNLVKLGK 3e6eA 48 :AVESAKAAKKGGA T0547 106 :YGLEAGSKAELLLAMAYNNEGAPITVNGFKDRE 3e6eA 61 :TGFCVALLDEAIELREAGVQDPILILSVVDLAY T0547 142 :IGF 3e6eA 94 :VPL T0547 146 :AAEMGH 3e6eA 97 :LIQYDL T0547 153 :I 3e6eA 103 :S T0547 155 :LTIEGLNELEAIIDIAKERFKPKPNIGLRVR 3e6eA 104 :VTVATQEWLEAALQQLTPESNTPLRVHLKVD T0547 188 :SAGVG 3e6eA 138 :GRIGF T0547 206 :LTSTELIEAVNLLK 3e6eA 143 :LTPEETKQAVRFVQ T0547 224 :L 3e6eA 161 :F T0547 226 :QFTMIHFHLGS 3e6eA 162 :LWEGIFTHFST T0547 237 :QITEIHPL 3e6eA 174 :DEIDTSYF T0547 249 :NEAGNIYTELRKMGAKNLKAINLG 3e6eA 182 :EKQAGRFKAVLAVLEELPRYVHVS T0547 291 :TLREYA 3e6eA 206 :NSATAL T0547 306 :IAEQKK 3e6eA 212 :WHPDVP T0547 315 :PDI 3e6eA 218 :GNM T0547 319 :IESGRFVAA 3e6eA 221 :IRYGVAMYG T0547 328 :NHAVLIAPVLELFSQ 3e6eA 245 :PALRLTSELIHVKRL T0547 343 :EYAENKLILK 3e6eA 274 :EAEEWIGTVP T0547 486 :DGEISYSKDKP 3e6eA 288 :DGWLRHLQGFT T0547 500 :HD 3e6eA 310 :GR T0547 531 :THPTEAIISIN 3e6eA 312 :VCMDQCMIRLA T0547 544 :GYEVEGIIEAQ 3e6eA 328 :GPVVTLVGKDG T0547 555 :SILDTLEDLDYDI 3e6eA 343 :TLQMVAEKLETIH Number of specific fragments extracted= 25 number of extra gaps= 3 total=1558 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 3e6eA/T0547-3e6eA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0547 read from 3e6eA/T0547-3e6eA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3e6eA read from 3e6eA/T0547-3e6eA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3e6eA in template set Warning: unaligning (T0547)L186 because of BadResidue code BAD_PEPTIDE in next template residue (3e6eA)G136 Warning: unaligning (T0547)H187 because of BadResidue code BAD_PEPTIDE at template residue (3e6eA)G136 Warning: unaligning (T0547)E220 because of BadResidue code BAD_PEPTIDE in next template residue (3e6eA)H158 Warning: unaligning (T0547)N221 because of BadResidue code BAD_PEPTIDE at template residue (3e6eA)H158 Warning: unaligning (T0547)K222 because of BadResidue code BAD_PEPTIDE at template residue (3e6eA)K159 Warning: unaligning (T0547)L224 because of BadResidue code BAD_PEPTIDE at template residue (3e6eA)E160 Warning: unaligning (T0547)E542 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (3e6eA)E324 T0547 44 :KGPLLLRFPHLIQKQIENIYGNF 3e6eA 7 :RPTRLHIDTQAITENVQKECQRL T0547 76 :KGGFNAVYPLKVNQ 3e6eA 30 :PEGTALFAVVKANG T0547 90 :YPGFVKNLVKLGK 3e6eA 48 :AVESAKAAKKGGA T0547 106 :YGLEAGSKAELLLAMAYNNEGAPITVNGFKDRE 3e6eA 61 :TGFCVALLDEAIELREAGVQDPILILSVVDLAY T0547 141 :NIGFIAAEM 3e6eA 94 :VPLLIQYDL T0547 154 :TLTIEGLNELEAIIDIAKERFKPKPNIGLRVR 3e6eA 103 :SVTVATQEWLEAALQQLTPESNTPLRVHLKVD T0547 188 :SAGVGI 3e6eA 137 :MGRIGF T0547 207 :TSTELIEAVNLLK 3e6eA 144 :TPEETKQAVRFVQ T0547 225 :EQFTMIHFHLGSQI 3e6eA 161 :FLWEGIFTHFSTAD T0547 239 :TEIHPL 3e6eA 176 :IDTSYF T0547 249 :NEAGNIYTELRKMGAKNLKAINLGG 3e6eA 182 :EKQAGRFKAVLAVLEELPRYVHVSN T0547 292 :LREYA 3e6eA 207 :SATAL T0547 309 :QKKDLEPDIFI 3e6eA 212 :WHPDVPGNMIR T0547 321 :SGRFVAA 3e6eA 223 :YGVAMYG T0547 328 :NHAVLIAPVLELFSQEYAENK 3e6eA 245 :PALRLTSELIHVKRLAAGEGI T0547 351 :LKKQ 3e6eA 266 :GYGE T0547 402 :R 3e6eA 270 :T T0547 403 :SNAEILTHLITKK 3e6eA 273 :TEAEEWIGTVPIG T0547 421 :GDKQNPADLLAIQDEV 3e6eA 286 :YADGWLRHLQGFTVLV T0547 438 :ERYLVNFSLFQSMP 3e6eA 302 :NGKRCEIVGRVCMD T0547 535 :EAIISIN 3e6eA 316 :QCMIRLA T0547 543 :KG 3e6eA 327 :VG T0547 545 :YEVEGIIEAQ 3e6eA 331 :VTLVGKDGNE T0547 555 :SILDTLEDLDYD 3e6eA 343 :TLQMVAEKLETI Number of specific fragments extracted= 24 number of extra gaps= 3 total=1582 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 1hkvA/T0547-1hkvA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1hkvA expands to /projects/compbio/data/pdb/1hkv.pdb.gz 1hkvA:# T0547 read from 1hkvA/T0547-1hkvA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1hkvA read from 1hkvA/T0547-1hkvA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1hkvA to template set # found chain 1hkvA in template set Warning: unaligning (T0547)I15 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (1hkvA)D19 Warning: unaligning (T0547)I16 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (1hkvA)D19 Warning: unaligning (T0547)K17 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (1hkvA)E20 Warning: unaligning (T0547)N152 because of BadResidue code BAD_PEPTIDE in next template residue (1hkvA)H133 Warning: unaligning (T0547)I153 because of BadResidue code BAD_PEPTIDE at template residue (1hkvA)H133 Warning: unaligning (T0547)L275 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1hkvA)G260 Warning: unaligning (T0547)A276 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1hkvA)G260 Warning: unaligning (T0547)E308 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (1hkvA)A289 Warning: unaligning (T0547)Q309 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (1hkvA)A289 Warning: unaligning (T0547)L351 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (1hkvA)D336 Warning: unaligning (T0547)K352 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (1hkvA)D336 T0547 7 :DIWGNENF 1hkvA 10 :NVWPRNTT T0547 18 :NGKVCI 1hkvA 21 :VGVVCI T0547 27 :KKPAIIDIVKE 1hkvA 27 :AGIPLTQLAQE T0547 43 :YKGPLLLRFPHLIQKQIENIYGNFN 1hkvA 38 :YGTPLFVIDEDDFRSRCRETAAAFG T0547 77 :GGFNAVYPLKVNQYPGFVKNLVKLG 1hkvA 63 :SGANVHYAAKAFLCSEVARWISEEG T0547 106 :YGLEAGSKAELLLAMAYNNEGAPITVNGF 1hkvA 88 :LCLDVCTGGELAVALHASFPPERITLHGN T0547 135 :KDRELINIGF 1hkvA 118 :KSVSELTAAV T0547 148 :EMGH 1hkvA 128 :KAGV T0547 154 :T 1hkvA 134 :I T0547 156 :TIEGLNELEAIIDIAKE 1hkvA 135 :VVDSMTEIERLDAIAGE T0547 174 :FKPKPNIGLRVRLHSAGVGIWAKSGG 1hkvA 152 :AGIVQDVLVRLTVGVEAHTHEFISTA T0547 200 :INSKFGLTS 1hkvA 179 :EDQKFGLSV T0547 209 :TELIEAVNLLKENKLLEQFT 1hkvA 190 :GAAMAAVRRVFATDHLRLVG T0547 230 :IHFHLGSQITEIHPLKKALNEAGNIYTELR 1hkvA 210 :LHSHIGSQIFDVDGFELAAHRVIGLLRDVV T0547 260 :KMG 1hkvA 241 :EFG T0547 265 :NLKAINLGGG 1hkvA 249 :QIATVDLGGG T0547 277 :VEYSQFKNEK 1hkvA 261 :ISYLPSDDPP T0547 291 :TLREYANDVVFILKNIA 1hkvA 271 :PIAELAAKLGTIVSDES T0547 310 :KKDLEPDIFIESGRFVAANHAVLIAPVLELFSQE 1hkvA 290 :VGLPTPKLVVEPGRAIAGPGTITLYEVGTVKDVD T0547 344 :YAE 1hkvA 329 :HRR T0547 348 :KLI 1hkvA 332 :YVS T0547 353 :K 1hkvA 337 :G T0547 354 :QNPKLIDELYDLYKSIKPSNALE 1hkvA 339 :MSDNIRTALYGAQYDVRLVSRVS T0547 377 :YLHDSIDHLESILTLFDLGY 1hkvA 366 :VPARLVGKHCESGDIIVRDT T0547 398 :DLQ 1hkvA 386 :WVP T0547 401 :DRSNAEILTHLITKKAILLLGDKQNPADLLAIQDEV 1hkvA 390 :DIRPGDLVAVAATGAYCYSLSSRYNMVGRPAVVAVH T0547 438 :ERYLVNFSLFQSMPDFWGLE 1hkvA 426 :AGNARLVLRRETVDDLLSLE Number of specific fragments extracted= 27 number of extra gaps= 5 total=1609 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 1hkvA/T0547-1hkvA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0547 read from 1hkvA/T0547-1hkvA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1hkvA read from 1hkvA/T0547-1hkvA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1hkvA in template set Warning: unaligning (T0547)I23 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (1hkvA)D19 Warning: unaligning (T0547)N24 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (1hkvA)D19 Warning: unaligning (T0547)Y25 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (1hkvA)E20 Warning: unaligning (T0547)N152 because of BadResidue code BAD_PEPTIDE in next template residue (1hkvA)H133 Warning: unaligning (T0547)I153 because of BadResidue code BAD_PEPTIDE at template residue (1hkvA)H133 Warning: unaligning (T0547)L275 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1hkvA)G260 Warning: unaligning (T0547)A276 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1hkvA)G260 Warning: unaligning (T0547)E308 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (1hkvA)A289 Warning: unaligning (T0547)Q309 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (1hkvA)A289 Warning: unaligning (T0547)L351 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (1hkvA)D336 Warning: unaligning (T0547)K352 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (1hkvA)D336 T0547 19 :GKVC 1hkvA 14 :RNTT T0547 26 :EKKPAIIDIVKELRDDGYKGPLLLRFPHLIQKQIENIYGNFN 1hkvA 21 :VGVVCIAGIPLTQLAQEYGTPLFVIDEDDFRSRCRETAAAFG T0547 77 :GGFNAVYPLKVNQYPGFVKNLVKLG 1hkvA 63 :SGANVHYAAKAFLCSEVARWISEEG T0547 106 :YGLEAGSKAELLLAMAYNNEGAPITVNGFKDRE 1hkvA 88 :LCLDVCTGGELAVALHASFPPERITLHGNNKSV T0547 140 :INIGF 1hkvA 121 :SELTA T0547 146 :AAEMGH 1hkvA 126 :AVKAGV T0547 155 :LTIEGLNELEAIIDIAKE 1hkvA 134 :IVVDSMTEIERLDAIAGE T0547 174 :FKPKPNIGLRVRLH 1hkvA 152 :AGIVQDVLVRLTVG T0547 188 :SAGVGIWAKSGGINSKFGLTST 1hkvA 167 :EAHTHEFISTAHEDQKFGLSVA T0547 210 :ELIEAVNLLKENKLL 1hkvA 191 :AAMAAVRRVFATDHL T0547 226 :QFTMIHFHLGSQITEIHPLKKALNEAGNIYTELRKM 1hkvA 206 :RLVGLHSHIGSQIFDVDGFELAAHRVIGLLRDVVGE T0547 263 :AKNLKAINLGGG 1hkvA 247 :TAQIATVDLGGG T0547 277 :VEY 1hkvA 261 :ISY T0547 282 :FKNEKSR 1hkvA 264 :LPSDDPP T0547 291 :TLREYANDVVFILKNIA 1hkvA 271 :PIAELAAKLGTIVSDES T0547 310 :KKDLEPDIFIESGRFVAANHAVLIAPVLELFSQ 1hkvA 290 :VGLPTPKLVVEPGRAIAGPGTITLYEVGTVKDV T0547 343 :EYAENKLI 1hkvA 327 :TAHRRYVS T0547 353 :KQNPKLIDE 1hkvA 337 :GGMSDNIRT T0547 362 :LYDLYKSIKPSNAL 1hkvA 347 :LYGAQYDVRLVSRV T0547 376 :EYLHDSIDHLESILTLFDLGYVD 1hkvA 362 :DAPPVPARLVGKHCESGDIIVRD T0547 399 :LQDRSNAEILTHLITKKAILLLGDKQN 1hkvA 388 :PDDIRPGDLVAVAATGAYCYSLSSRYN T0547 426 :PA 1hkvA 417 :GR T0547 533 :PT 1hkvA 419 :PA T0547 537 :IISINEKGYEVEG 1hkvA 421 :VVAVHAGNARLVL T0547 582 :KLVNDKQKK 1hkvA 434 :RRETVDDLL Number of specific fragments extracted= 25 number of extra gaps= 5 total=1634 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 1hkvA/T0547-1hkvA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0547 read from 1hkvA/T0547-1hkvA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1hkvA read from 1hkvA/T0547-1hkvA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1hkvA in template set Warning: unaligning (T0547)I16 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (1hkvA)D19 Warning: unaligning (T0547)K17 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (1hkvA)D19 Warning: unaligning (T0547)N18 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (1hkvA)E20 Warning: unaligning (T0547)G150 because of BadResidue code BAD_PEPTIDE in next template residue (1hkvA)H133 Warning: unaligning (T0547)T154 because of BadResidue code BAD_PEPTIDE at template residue (1hkvA)H133 Warning: unaligning (T0547)L275 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1hkvA)G260 Warning: unaligning (T0547)A276 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1hkvA)G260 Warning: unaligning (T0547)E308 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (1hkvA)A289 Warning: unaligning (T0547)Q309 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (1hkvA)A289 Warning: unaligning (T0547)I350 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (1hkvA)D336 Warning: unaligning (T0547)L351 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (1hkvA)D336 T0547 14 :FI 1hkvA 16 :TT T0547 19 :GKVCIN 1hkvA 21 :VGVVCI T0547 27 :KKPAIIDIV 1hkvA 27 :AGIPLTQLA T0547 41 :DGYKGPLLLRFPHLIQKQIENIYGNF 1hkvA 36 :QEYGTPLFVIDEDDFRSRCRETAAAF T0547 76 :KGGFNAVYPLKVNQYPGFVKNLVKLG 1hkvA 62 :GSGANVHYAAKAFLCSEVARWISEEG T0547 106 :YGLEAGSKAELLLAMAYNNEGAPITVNGFKDRELINIGFIAAEM 1hkvA 88 :LCLDVCTGGELAVALHASFPPERITLHGNNKSVSELTAAVKAGV T0547 155 :LTIEGLNELEAIIDIAKE 1hkvA 134 :IVVDSMTEIERLDAIAGE T0547 174 :FKPKPNIGLRVRLHSAGVGI 1hkvA 152 :AGIVQDVLVRLTVGVEAHTH T0547 194 :WAKSGGINSKFGLTS 1hkvA 173 :FISTAHEDQKFGLSV T0547 209 :TELIEAVNLLKENK 1hkvA 190 :GAAMAAVRRVFATD T0547 224 :LEQFTMIHFHLGSQITEIHPLKKALNEAGNIYTELRKMG 1hkvA 204 :HLRLVGLHSHIGSQIFDVDGFELAAHRVIGLLRDVVGEF T0547 263 :AKNLKAINLGGG 1hkvA 247 :TAQIATVDLGGG T0547 277 :VEYSQFKNEKS 1hkvA 261 :ISYLPSDDPPP T0547 292 :LREYANDVVFILKNIA 1hkvA 272 :IAELAAKLGTIVSDES T0547 310 :KKDLEPDIFIESGRFVAANHAVLIAPVLELFSQEY 1hkvA 290 :VGLPTPKLVVEPGRAIAGPGTITLYEVGTVKDVDV T0547 345 :AENKL 1hkvA 330 :RRYVS T0547 352 :KKQNPKLIDELYDLYKSIKPS 1hkvA 337 :GGMSDNIRTALYGAQYDVRLV T0547 373 :NALEYLHDSIDHLESILTLFDLGYVDLQDR 1hkvA 359 :RVSDAPPVPARLVGKHCESGDIIVRDTWVP T0547 403 :SNAEILTHLITKKAILLLGDKQNPADLLAIQDEVQERYLVNFSLFQSMPDFWG 1hkvA 391 :IRPGDLVAVAATGAYCYSLSSRYNMVGRPAVVAVHAGNARLVLRRETVDDLLS Number of specific fragments extracted= 19 number of extra gaps= 5 total=1653 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 1d7kA/T0547-1d7kA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1d7kA expands to /projects/compbio/data/pdb/1d7k.pdb.gz 1d7kA:Bad short name: N1 for alphabet: pdb_atoms Bad short name: C2 for alphabet: pdb_atoms Bad short name: C2' for alphabet: pdb_atoms Bad short name: C3 for alphabet: pdb_atoms Bad short name: O3 for alphabet: pdb_atoms Bad short name: C4 for alphabet: pdb_atoms Bad short name: C4' for alphabet: pdb_atoms Bad short name: C5 for alphabet: pdb_atoms Bad short name: C6 for alphabet: pdb_atoms Bad short name: C5' for alphabet: pdb_atoms Bad short name: OP4 for alphabet: pdb_atoms Bad short name: P for alphabet: pdb_atoms Bad short name: OP1 for alphabet: pdb_atoms Bad short name: OP2 for alphabet: pdb_atoms Bad short name: OP3 for alphabet: pdb_atoms # T0547 read from 1d7kA/T0547-1d7kA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1d7kA read from 1d7kA/T0547-1d7kA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1d7kA to template set # found chain 1d7kA in template set Warning: unaligning (T0547)Y25 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (1d7kA)D15 Warning: unaligning (T0547)E26 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (1d7kA)D15 Warning: unaligning (T0547)K27 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (1d7kA)E16 Warning: unaligning (T0547)K28 because of BadResidue code BAD_PEPTIDE at template residue (1d7kA)G17 Warning: unaligning (T0547)P29 because of BadResidue code BAD_PEPTIDE at template residue (1d7kA)F18 Warning: unaligning (T0547)A30 because of BadResidue code BAD_PEPTIDE at template residue (1d7kA)T19 Warning: unaligning (T0547)E37 because of BadResidue code BAD_PEPTIDE in next template residue (1d7kA)K27 Warning: unaligning (T0547)L38 because of BadResidue code BAD_PEPTIDE at template residue (1d7kA)K27 Warning: unaligning (T0547)D40 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (1d7kA)E30 Warning: unaligning (T0547)D41 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (1d7kA)E30 Warning: unaligning (T0547)G42 because of BadResidue code TOO_FEW_ATOMS+BAD_PEPTIDE+HIGH_B_FACTOR at template residue (1d7kA)S34 Warning: unaligning (T0547)Y43 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (1d7kA)D36 Warning: unaligning (T0547)K44 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (1d7kA)D36 Warning: unaligning (T0547)G45 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (1d7kA)K37 Warning: unaligning (T0547)L48 because of BadResidue code BAD_PEPTIDE in next template residue (1d7kA)V42 Warning: unaligning (T0547)L49 because of BadResidue code BAD_PEPTIDE at template residue (1d7kA)V42 Warning: unaligning (T0547)G78 because of BadResidue code BAD_PEPTIDE in next template residue (1d7kA)V62 Warning: unaligning (T0547)F79 because of BadResidue code BAD_PEPTIDE at template residue (1d7kA)V62 Warning: unaligning (T0547)L85 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1d7kA)C70 Warning: unaligning (T0547)V87 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1d7kA)C70 Warning: unaligning (T0547)Y106 because of BadResidue code BAD_PEPTIDE in next template residue (1d7kA)G86 Warning: unaligning (T0547)G107 because of BadResidue code BAD_PEPTIDE at template residue (1d7kA)G86 Warning: unaligning (T0547)I167 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (1d7kA)R144 Warning: unaligning (T0547)D168 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (1d7kA)R144 Warning: unaligning (T0547)H187 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (1d7kA)D159 Warning: unaligning (T0547)S188 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (1d7kA)D159 Warning: unaligning (T0547)A189 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (1d7kA)S160 Warning: unaligning (T0547)G190 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (1d7kA)K161 Warning: unaligning (T0547)V191 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (1d7kA)A162 Warning: unaligning (T0547)S197 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (1d7kA)C164 Warning: unaligning (T0547)G198 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (1d7kA)C164 Warning: unaligning (T0547)G199 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (1d7kA)L166 Warning: unaligning (T0547)I200 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (1d7kA)L166 Warning: unaligning (T0547)G235 because of BadResidue code BAD_PEPTIDE in next template residue (1d7kA)S200 Warning: unaligning (T0547)S236 because of BadResidue code BAD_PEPTIDE at template residue (1d7kA)S200 Warning: unaligning (T0547)Q237 because of BadResidue code BAD_PEPTIDE in next template residue (1d7kA)C202 Warning: unaligning (T0547)I238 because of BadResidue code BAD_PEPTIDE at template residue (1d7kA)C202 Warning: unaligning (T0547)G262 because of BadResidue code BAD_PEPTIDE in next template residue (1d7kA)F227 Warning: unaligning (T0547)A263 because of BadResidue code BAD_PEPTIDE at template residue (1d7kA)F227 Warning: unaligning (T0547)Q309 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (1d7kA)D266 Warning: unaligning (T0547)K310 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (1d7kA)D266 Warning: unaligning (T0547)E314 because of BadResidue code BAD_PEPTIDE in next template residue (1d7kA)V269 Warning: unaligning (T0547)P315 because of BadResidue code BAD_PEPTIDE at template residue (1d7kA)V269 Warning: unaligning (T0547)Q342 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (1d7kA)L297 Warning: unaligning (T0547)E343 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (1d7kA)L297 Warning: unaligning (T0547)Y344 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR at template residue (1d7kA)E311 Warning: unaligning (T0547)K352 because of BadResidue code BAD_PEPTIDE in next template residue (1d7kA)D320 Warning: unaligning (T0547)K353 because of BadResidue code BAD_PEPTIDE at template residue (1d7kA)D320 Warning: unaligning (T0547)N373 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (1d7kA)R343 Warning: unaligning (T0547)A374 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (1d7kA)R343 Warning: unaligning (T0547)L375 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (1d7kA)P344 Warning: unaligning (T0547)E376 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (1d7kA)K345 Warning: unaligning (T0547)L378 because of BadResidue code BAD_PEPTIDE in next template residue (1d7kA)S353 Warning: unaligning (T0547)H379 because of BadResidue code BAD_PEPTIDE at template residue (1d7kA)S353 Warning: unaligning (T0547)S381 because of BadResidue code BAD_PEPTIDE in next template residue (1d7kA)W356 Warning: unaligning (T0547)I382 because of BadResidue code BAD_PEPTIDE at template residue (1d7kA)W356 Warning: unaligning (T0547)T390 because of BadResidue code BAD_PEPTIDE in next template residue (1d7kA)R365 Warning: unaligning (T0547)L391 because of BadResidue code BAD_PEPTIDE at template residue (1d7kA)R365 Warning: unaligning (T0547)G395 because of BadResidue code BAD_PEPTIDE in next template residue (1d7kA)C370 Warning: unaligning (T0547)Y396 because of BadResidue code BAD_PEPTIDE at template residue (1d7kA)C370 Warning: unaligning (T0547)A427 because of BadResidue code BAD_PEPTIDE in next template residue (1d7kA)Q401 Warning: unaligning (T0547)D428 because of BadResidue code BAD_PEPTIDE at template residue (1d7kA)Q401 T0547 24 :N 1d7kA 13 :F T0547 31 :IIDIVK 1d7kA 20 :AKDILD T0547 39 :R 1d7kA 28 :I T0547 46 :PL 1d7kA 39 :AF T0547 50 :RFPHLIQKQIENIYGNF 1d7kA 43 :ADLGDILKKHLRWLKAL T0547 77 :G 1d7kA 60 :P T0547 80 :NAVYP 1d7kA 63 :TPFYA T0547 88 :NQYPGFVKNLVKLG 1d7kA 71 :NDSKAIVKTLAATG T0547 108 :LEAGSKAELLLAMAYNNEGAPITV 1d7kA 87 :FDCASKTEIQLVQSLGVPPERIIY T0547 132 :NGFKDRELINIGF 1d7kA 112 :NPCKQVSQIKYAA T0547 148 :EMGHNIT 1d7kA 125 :NNGVQMM T0547 156 :TIEGLNELEAI 1d7kA 132 :TFDSEVELMKV T0547 169 :IAKE 1d7kA 145 :AHPK T0547 178 :PNIGLRVRL 1d7kA 149 :AKLVLRIAT T0547 201 :NSKFGLTSTELIEAVNLLKENK 1d7kA 167 :SVKFGATLRTSRLLLERAKELN T0547 224 :LEQFT 1d7kA 189 :IDVVG T0547 230 :IHFHL 1d7kA 194 :VSFHV T0547 239 :TEIHPLKKALNEAGNIYTELRKM 1d7kA 203 :TDPETFVQAISDARCVFDMGAEV T0547 265 :NLKAINLGGGLAV 1d7kA 228 :SMYLLDIGGGFPG T0547 281 :QFKNEK 1d7kA 241 :SEDVKL T0547 291 :TLREYANDVVFILKNIAE 1d7kA 247 :KFEEITGVINPALDKYFP T0547 313 :L 1d7kA 267 :S T0547 316 :DIFIESGRFVAANHAVLIAPVLELFS 1d7kA 270 :RIIAEPGRYYVASAFTLAVNIIAKKI T0547 345 :AENKLIL 1d7kA 312 :QTFMYYV T0547 354 :QNPKLIDELYDLYKS 1d7kA 322 :VYGSFNCILYDHAHV T0547 369 :IKPS 1d7kA 338 :PLLQ T0547 377 :Y 1d7kA 351 :Y T0547 380 :D 1d7kA 354 :S T0547 383 :DHLESIL 1d7kA 357 :GPTCDGL T0547 392 :FDL 1d7kA 366 :IVE T0547 398 :DLQDRSNAEILTHLITKKAILLLGDKQNP 1d7kA 371 :DLPEMHVGDWMLFENMGAYTVAAASTFNG T0547 429 :LLA 1d7kA 402 :RPT T0547 511 :LGFFL 1d7kA 405 :IYYVM T0547 585 :NDKQKKHILG 1d7kA 410 :SGPAWQLMQQ Number of specific fragments extracted= 34 number of extra gaps= 21 total=1687 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 1d7kA/T0547-1d7kA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0547 read from 1d7kA/T0547-1d7kA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1d7kA read from 1d7kA/T0547-1d7kA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1d7kA in template set Warning: unaligning (T0547)N24 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (1d7kA)D15 Warning: unaligning (T0547)Y25 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (1d7kA)D15 Warning: unaligning (T0547)E26 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (1d7kA)E16 Warning: unaligning (T0547)K27 because of BadResidue code BAD_PEPTIDE at template residue (1d7kA)G17 Warning: unaligning (T0547)P29 because of BadResidue code BAD_PEPTIDE at template residue (1d7kA)F18 Warning: unaligning (T0547)A30 because of BadResidue code BAD_PEPTIDE at template residue (1d7kA)T19 Warning: unaligning (T0547)E37 because of BadResidue code BAD_PEPTIDE in next template residue (1d7kA)K27 Warning: unaligning (T0547)L38 because of BadResidue code BAD_PEPTIDE at template residue (1d7kA)K27 Warning: unaligning (T0547)D40 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (1d7kA)E30 Warning: unaligning (T0547)D41 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (1d7kA)E30 Warning: unaligning (T0547)G42 because of BadResidue code TOO_FEW_ATOMS+BAD_PEPTIDE+HIGH_B_FACTOR at template residue (1d7kA)S34 Warning: unaligning (T0547)Y43 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (1d7kA)D36 Warning: unaligning (T0547)K44 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (1d7kA)D36 Warning: unaligning (T0547)L48 because of BadResidue code BAD_PEPTIDE in next template residue (1d7kA)V42 Warning: unaligning (T0547)L49 because of BadResidue code BAD_PEPTIDE at template residue (1d7kA)V42 Warning: unaligning (T0547)G78 because of BadResidue code BAD_PEPTIDE in next template residue (1d7kA)V62 Warning: unaligning (T0547)F79 because of BadResidue code BAD_PEPTIDE at template residue (1d7kA)V62 Warning: unaligning (T0547)L85 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1d7kA)C70 Warning: unaligning (T0547)V87 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1d7kA)C70 Warning: unaligning (T0547)Y106 because of BadResidue code BAD_PEPTIDE in next template residue (1d7kA)G86 Warning: unaligning (T0547)G107 because of BadResidue code BAD_PEPTIDE at template residue (1d7kA)G86 Warning: unaligning (T0547)I167 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (1d7kA)R144 Warning: unaligning (T0547)D168 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (1d7kA)R144 Warning: unaligning (T0547)H187 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (1d7kA)D159 Warning: unaligning (T0547)S188 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (1d7kA)D159 Warning: unaligning (T0547)A189 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (1d7kA)S160 Warning: unaligning (T0547)G190 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (1d7kA)K161 Warning: unaligning (T0547)V191 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (1d7kA)A162 Warning: unaligning (T0547)G192 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (1d7kA)C164 Warning: unaligning (T0547)I193 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (1d7kA)C164 Warning: unaligning (T0547)W194 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (1d7kA)L166 Warning: unaligning (T0547)I200 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (1d7kA)L166 Warning: unaligning (T0547)G235 because of BadResidue code BAD_PEPTIDE in next template residue (1d7kA)S200 Warning: unaligning (T0547)S236 because of BadResidue code BAD_PEPTIDE at template residue (1d7kA)S200 Warning: unaligning (T0547)Q237 because of BadResidue code BAD_PEPTIDE in next template residue (1d7kA)C202 Warning: unaligning (T0547)I238 because of BadResidue code BAD_PEPTIDE at template residue (1d7kA)C202 Warning: unaligning (T0547)G262 because of BadResidue code BAD_PEPTIDE in next template residue (1d7kA)F227 Warning: unaligning (T0547)A263 because of BadResidue code BAD_PEPTIDE at template residue (1d7kA)F227 Warning: unaligning (T0547)Q309 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (1d7kA)D266 Warning: unaligning (T0547)K310 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (1d7kA)D266 Warning: unaligning (T0547)E314 because of BadResidue code BAD_PEPTIDE in next template residue (1d7kA)V269 Warning: unaligning (T0547)P315 because of BadResidue code BAD_PEPTIDE at template residue (1d7kA)V269 Warning: unaligning (T0547)Q342 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (1d7kA)L297 Warning: unaligning (T0547)Y344 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR at template residue (1d7kA)E311 Warning: unaligning (T0547)K352 because of BadResidue code BAD_PEPTIDE in next template residue (1d7kA)D320 Warning: unaligning (T0547)K353 because of BadResidue code BAD_PEPTIDE at template residue (1d7kA)D320 Warning: unaligning (T0547)N373 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (1d7kA)P344 Warning: unaligning (T0547)A374 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (1d7kA)K345 Warning: unaligning (T0547)E376 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (1d7kA)E348 Warning: unaligning (T0547)Y377 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (1d7kA)E348 Warning: unaligning (T0547)S381 because of BadResidue code BAD_PEPTIDE in next template residue (1d7kA)S353 Warning: unaligning (T0547)I382 because of BadResidue code BAD_PEPTIDE at template residue (1d7kA)S353 Warning: unaligning (T0547)H384 because of BadResidue code BAD_PEPTIDE in next template residue (1d7kA)W356 Warning: unaligning (T0547)L385 because of BadResidue code BAD_PEPTIDE at template residue (1d7kA)W356 Warning: unaligning (T0547)D393 because of BadResidue code BAD_PEPTIDE in next template residue (1d7kA)R365 Warning: unaligning (T0547)L394 because of BadResidue code BAD_PEPTIDE at template residue (1d7kA)R365 Warning: unaligning (T0547)D398 because of BadResidue code BAD_PEPTIDE in next template residue (1d7kA)C370 Warning: unaligning (T0547)A427 because of BadResidue code BAD_PEPTIDE in next template residue (1d7kA)Q401 Warning: unaligning (T0547)D428 because of BadResidue code BAD_PEPTIDE at template residue (1d7kA)Q401 T0547 21 :VCI 1d7kA 11 :CHF T0547 31 :IIDIVK 1d7kA 20 :AKDILD T0547 39 :R 1d7kA 28 :I T0547 45 :GPL 1d7kA 38 :DAF T0547 50 :RFPHLIQKQIENIYGNF 1d7kA 43 :ADLGDILKKHLRWLKAL T0547 77 :G 1d7kA 60 :P T0547 80 :NAVYP 1d7kA 63 :TPFYA T0547 88 :NQYPGFVKNLVKLG 1d7kA 71 :NDSKAIVKTLAATG T0547 108 :LEAGSKAELLLAMAYNNEGAPITVNGFKDRE 1d7kA 87 :FDCASKTEIQLVQSLGVPPERIIYANPCKQV T0547 140 :INIGF 1d7kA 118 :SQIKY T0547 146 :AAEMGHNI 1d7kA 123 :AANNGVQM T0547 155 :LTIEGLNELEAI 1d7kA 131 :MTFDSEVELMKV T0547 169 :IAKE 1d7kA 145 :AHPK T0547 178 :PNIGLRVRL 1d7kA 149 :AKLVLRIAT T0547 201 :NSKFGLTSTELIEAVNLLKENKL 1d7kA 167 :SVKFGATLRTSRLLLERAKELNI T0547 226 :QFTMIHFHL 1d7kA 190 :DVVGVSFHV T0547 239 :TEIHPLKKALNEAGNIYTELRKM 1d7kA 203 :TDPETFVQAISDARCVFDMGAEV T0547 265 :NLKAINLGGGLA 1d7kA 228 :SMYLLDIGGGFP T0547 282 :FKNEKSR 1d7kA 240 :GSEDVKL T0547 291 :TLREYANDVVFILKNIAE 1d7kA 247 :KFEEITGVINPALDKYFP T0547 313 :L 1d7kA 267 :S T0547 316 :DIFIESGRFVAANHAVLIAPVLELFS 1d7kA 270 :RIIAEPGRYYVASAFTLAVNIIAKKI T0547 345 :AENKLIL 1d7kA 312 :QTFMYYV T0547 354 :QNPKLIDELYDLYKSIKPS 1d7kA 321 :GVYGSFNCILYDHAHVKPL T0547 375 :L 1d7kA 346 :P T0547 378 :LHD 1d7kA 349 :RYY T0547 383 :D 1d7kA 354 :S T0547 386 :ESILTLF 1d7kA 357 :GPTCDGL T0547 395 :GYV 1d7kA 366 :IVE T0547 399 :LQDRSNAEILTHLITKKAILLLGDKQNP 1d7kA 372 :LPEMHVGDWMLFENMGAYTVAAASTFNG T0547 472 :PTRSASIW 1d7kA 403 :PTIYYVMS T0547 568 :HAIMDILNE 1d7kA 411 :GPAWQLMQQ Number of specific fragments extracted= 32 number of extra gaps= 22 total=1719 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 1d7kA/T0547-1d7kA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0547 read from 1d7kA/T0547-1d7kA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1d7kA read from 1d7kA/T0547-1d7kA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1d7kA in template set Warning: unaligning (T0547)K27 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (1d7kA)E16 Warning: unaligning (T0547)K28 because of BadResidue code BAD_PEPTIDE at template residue (1d7kA)G17 Warning: unaligning (T0547)P29 because of BadResidue code BAD_PEPTIDE at template residue (1d7kA)F18 Warning: unaligning (T0547)A30 because of BadResidue code BAD_PEPTIDE at template residue (1d7kA)T19 Warning: unaligning (T0547)E37 because of BadResidue code BAD_PEPTIDE in next template residue (1d7kA)K27 Warning: unaligning (T0547)L38 because of BadResidue code BAD_PEPTIDE at template residue (1d7kA)K27 Warning: unaligning (T0547)D40 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (1d7kA)E30 Warning: unaligning (T0547)D41 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (1d7kA)E30 Warning: unaligning (T0547)G42 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (1d7kA)D36 Warning: unaligning (T0547)Y43 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (1d7kA)D36 Warning: unaligning (T0547)K44 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (1d7kA)K37 Warning: unaligning (T0547)L48 because of BadResidue code BAD_PEPTIDE in next template residue (1d7kA)V42 Warning: unaligning (T0547)L49 because of BadResidue code BAD_PEPTIDE at template residue (1d7kA)V42 Warning: unaligning (T0547)G78 because of BadResidue code BAD_PEPTIDE in next template residue (1d7kA)V62 Warning: unaligning (T0547)F79 because of BadResidue code BAD_PEPTIDE at template residue (1d7kA)V62 Warning: unaligning (T0547)L85 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1d7kA)C70 Warning: unaligning (T0547)V87 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1d7kA)C70 Warning: unaligning (T0547)Y106 because of BadResidue code BAD_PEPTIDE in next template residue (1d7kA)G86 Warning: unaligning (T0547)G107 because of BadResidue code BAD_PEPTIDE at template residue (1d7kA)G86 Warning: unaligning (T0547)I167 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (1d7kA)R144 Warning: unaligning (T0547)D168 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (1d7kA)R144 Warning: unaligning (T0547)H187 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (1d7kA)D159 Warning: unaligning (T0547)S188 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (1d7kA)D159 Warning: unaligning (T0547)A189 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (1d7kA)S160 Warning: unaligning (T0547)G190 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (1d7kA)K161 Warning: unaligning (T0547)V191 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (1d7kA)A162 Warning: unaligning (T0547)G192 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (1d7kA)C164 Warning: unaligning (T0547)G198 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (1d7kA)C164 Warning: unaligning (T0547)G199 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (1d7kA)L166 Warning: unaligning (T0547)I200 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (1d7kA)L166 Warning: unaligning (T0547)G235 because of BadResidue code BAD_PEPTIDE in next template residue (1d7kA)S200 Warning: unaligning (T0547)S236 because of BadResidue code BAD_PEPTIDE at template residue (1d7kA)S200 Warning: unaligning (T0547)Q237 because of BadResidue code BAD_PEPTIDE in next template residue (1d7kA)C202 Warning: unaligning (T0547)I238 because of BadResidue code BAD_PEPTIDE at template residue (1d7kA)C202 Warning: unaligning (T0547)A263 because of BadResidue code BAD_PEPTIDE in next template residue (1d7kA)F227 Warning: unaligning (T0547)K264 because of BadResidue code BAD_PEPTIDE at template residue (1d7kA)F227 Warning: unaligning (T0547)K311 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (1d7kA)D266 Warning: unaligning (T0547)D312 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (1d7kA)D266 Warning: unaligning (T0547)E314 because of BadResidue code BAD_PEPTIDE in next template residue (1d7kA)V269 Warning: unaligning (T0547)P315 because of BadResidue code BAD_PEPTIDE at template residue (1d7kA)V269 Warning: unaligning (T0547)Q342 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (1d7kA)L297 Warning: unaligning (T0547)E343 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR at template residue (1d7kA)E311 Warning: unaligning (T0547)L351 because of BadResidue code BAD_PEPTIDE in next template residue (1d7kA)D320 Warning: unaligning (T0547)K352 because of BadResidue code BAD_PEPTIDE at template residue (1d7kA)D320 Warning: unaligning (T0547)N373 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (1d7kA)P344 Warning: unaligning (T0547)A374 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (1d7kA)K345 Warning: unaligning (T0547)E376 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (1d7kA)E348 Warning: unaligning (T0547)Y377 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (1d7kA)E348 Warning: unaligning (T0547)S381 because of BadResidue code BAD_PEPTIDE in next template residue (1d7kA)S353 Warning: unaligning (T0547)I382 because of BadResidue code BAD_PEPTIDE at template residue (1d7kA)S353 Warning: unaligning (T0547)H384 because of BadResidue code BAD_PEPTIDE in next template residue (1d7kA)W356 Warning: unaligning (T0547)L385 because of BadResidue code BAD_PEPTIDE at template residue (1d7kA)W356 Warning: unaligning (T0547)D393 because of BadResidue code BAD_PEPTIDE in next template residue (1d7kA)R365 Warning: unaligning (T0547)L394 because of BadResidue code BAD_PEPTIDE at template residue (1d7kA)R365 Warning: unaligning (T0547)D398 because of BadResidue code BAD_PEPTIDE in next template residue (1d7kA)C370 Warning: unaligning (T0547)L399 because of BadResidue code BAD_PEPTIDE at template residue (1d7kA)C370 Warning: unaligning (T0547)D428 because of BadResidue code BAD_PEPTIDE in next template residue (1d7kA)Q401 Warning: unaligning (T0547)L429 because of BadResidue code BAD_PEPTIDE at template residue (1d7kA)Q401 T0547 31 :IIDIVK 1d7kA 20 :AKDILD T0547 39 :R 1d7kA 28 :I T0547 45 :GPL 1d7kA 38 :DAF T0547 50 :RFPHLIQKQIENIYGNFN 1d7kA 43 :ADLGDILKKHLRWLKALP T0547 80 :NAVYP 1d7kA 63 :TPFYA T0547 88 :NQYPGFVKNLVKLG 1d7kA 71 :NDSKAIVKTLAATG T0547 108 :LEAGSKAELLLAMAYNNEGAPITVNGFKDRELINIGFIAAEMG 1d7kA 87 :FDCASKTEIQLVQSLGVPPERIIYANPCKQVSQIKYAANNGVQ T0547 154 :TLTIEGLNELEAI 1d7kA 130 :MMTFDSEVELMKV T0547 169 :IAKE 1d7kA 145 :AHPK T0547 178 :PNIGLRVRL 1d7kA 149 :AKLVLRIAT T0547 201 :NSKFGLTSTELIEAVNLLKENK 1d7kA 167 :SVKFGATLRTSRLLLERAKELN T0547 225 :EQFTMIHFHL 1d7kA 189 :IDVVGVSFHV T0547 239 :TEIHPLKKALNEAGNIYTELRKM 1d7kA 203 :TDPETFVQAISDARCVFDMGAEV T0547 265 :NLKAINLGGGLAVEYSQ 1d7kA 228 :SMYLLDIGGGFPGSEDV T0547 289 :NYTLREYANDVVFILKNIA 1d7kA 245 :KLKFEEITGVINPALDKYF T0547 310 :K 1d7kA 264 :P T0547 313 :L 1d7kA 267 :S T0547 316 :DIFIESGRFVAANHAVLIAPVLELFS 1d7kA 270 :RIIAEPGRYYVASAFTLAVNIIAKKI T0547 344 :YAENKLI 1d7kA 312 :QTFMYYV T0547 353 :KQNPKLIDELY 1d7kA 321 :GVYGSFNCILY T0547 367 :KSIKPS 1d7kA 332 :DHAHVK T0547 375 :L 1d7kA 346 :P T0547 378 :LHD 1d7kA 349 :RYY T0547 383 :D 1d7kA 354 :S T0547 386 :ESILTLF 1d7kA 357 :GPTCDGL T0547 395 :GYV 1d7kA 366 :IVE T0547 400 :QDR 1d7kA 371 :DLP T0547 403 :SNAEILTHLITKKAILLLGDKQNPA 1d7kA 375 :MHVGDWMLFENMGAYTVAAASTFNG T0547 430 :L 1d7kA 402 :R T0547 475 :SASIWD 1d7kA 404 :TIYYVM T0547 572 :DILNERISNS 1d7kA 411 :GPAWQLMQQF Number of specific fragments extracted= 31 number of extra gaps= 22 total=1750 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 1w8gA/T0547-1w8gA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1w8gA expands to /projects/compbio/data/pdb/1w8g.pdb.gz 1w8gA:Skipped atom 62, because occupancy 0.500 <= existing 0.500 in 1w8gA Skipped atom 63, because occupancy 0.500 <= existing 0.500 in 1w8gA Skipped atom 64, because occupancy 0.500 <= existing 0.500 in 1w8gA Skipped atom 65, because occupancy 0.500 <= existing 0.500 in 1w8gA Skipped atom 66, because occupancy 0.500 <= existing 0.500 in 1w8gA Skipped atom 85, because occupancy 0.400 <= existing 0.600 in 1w8gA Skipped atom 86, because occupancy 0.400 <= existing 0.600 in 1w8gA Skipped atom 87, because occupancy 0.400 <= existing 0.600 in 1w8gA Skipped atom 88, because occupancy 0.400 <= existing 0.600 in 1w8gA Skipped atom 89, because occupancy 0.400 <= existing 0.600 in 1w8gA Skipped atom 90, because occupancy 0.400 <= existing 0.600 in 1w8gA Skipped atom 91, because occupancy 0.400 <= existing 0.600 in 1w8gA Skipped atom 92, because occupancy 0.400 <= existing 0.600 in 1w8gA Skipped atom 110, because occupancy 0.400 <= existing 0.600 in 1w8gA Skipped atom 111, because occupancy 0.400 <= existing 0.600 in 1w8gA Skipped atom 112, because occupancy 0.400 <= existing 0.600 in 1w8gA Skipped atom 113, because occupancy 0.400 <= existing 0.600 in 1w8gA Skipped atom 114, because occupancy 0.400 <= existing 0.600 in 1w8gA Skipped atom 151, because occupancy 0.500 <= existing 0.500 in 1w8gA Skipped atom 152, because occupancy 0.500 <= existing 0.500 in 1w8gA Skipped atom 153, because occupancy 0.500 <= existing 0.500 in 1w8gA Skipped atom 154, because occupancy 0.500 <= existing 0.500 in 1w8gA Skipped atom 387, because occupancy 0.400 <= existing 0.600 in 1w8gA Skipped atom 388, because occupancy 0.400 <= existing 0.600 in 1w8gA Skipped atom 389, because occupancy 0.400 <= existing 0.600 in 1w8gA Skipped atom 390, because occupancy 0.400 <= existing 0.600 in 1w8gA Skipped atom 391, because occupancy 0.400 <= existing 0.600 in 1w8gA Skipped atom 392, because occupancy 0.400 <= existing 0.600 in 1w8gA Skipped atom 393, because occupancy 0.400 <= existing 0.600 in 1w8gA Skipped atom 394, because occupancy 0.400 <= existing 0.600 in 1w8gA Skipped atom 404, because occupancy 0.500 <= existing 0.500 in 1w8gA Skipped atom 405, because occupancy 0.500 <= existing 0.500 in 1w8gA Skipped atom 406, because occupancy 0.500 <= existing 0.500 in 1w8gA Skipped atom 407, because occupancy 0.500 <= existing 0.500 in 1w8gA Skipped atom 408, because occupancy 0.500 <= existing 0.500 in 1w8gA Skipped atom 722, because occupancy 0.500 <= existing 0.500 in 1w8gA Skipped atom 723, because occupancy 0.500 <= existing 0.500 in 1w8gA Skipped atom 724, because occupancy 0.500 <= existing 0.500 in 1w8gA Skipped atom 725, because occupancy 0.500 <= existing 0.500 in 1w8gA Skipped atom 726, because occupancy 0.500 <= existing 0.500 in 1w8gA Skipped atom 727, because occupancy 0.500 <= existing 0.500 in 1w8gA Skipped atom 728, because occupancy 0.500 <= existing 0.500 in 1w8gA Skipped atom 870, because occupancy 0.500 <= existing 0.500 in 1w8gA Skipped atom 871, because occupancy 0.500 <= existing 0.500 in 1w8gA Skipped atom 872, because occupancy 0.500 <= existing 0.500 in 1w8gA Skipped atom 873, because occupancy 0.500 <= existing 0.500 in 1w8gA Skipped atom 874, because occupancy 0.500 <= existing 0.500 in 1w8gA Skipped atom 875, because occupancy 0.500 <= existing 0.500 in 1w8gA Skipped atom 876, because occupancy 0.500 <= existing 0.500 in 1w8gA Skipped atom 877, because occupancy 0.500 <= existing 0.500 in 1w8gA Skipped atom 898, because occupancy 0.500 <= existing 0.500 in 1w8gA Skipped atom 899, because occupancy 0.500 <= existing 0.500 in 1w8gA Skipped atom 900, because occupancy 0.500 <= existing 0.500 in 1w8gA Skipped atom 1546, because occupancy 0.400 <= existing 0.600 in 1w8gA Skipped atom 1547, because occupancy 0.400 <= existing 0.600 in 1w8gA Skipped atom 1548, because occupancy 0.400 <= existing 0.600 in 1w8gA Skipped atom 1549, because occupancy 0.400 <= existing 0.600 in 1w8gA Skipped atom 1550, because occupancy 0.400 <= existing 0.600 in 1w8gA Skipped atom 1551, because occupancy 0.400 <= existing 0.600 in 1w8gA Skipped atom 1552, because occupancy 0.400 <= existing 0.600 in 1w8gA # T0547 read from 1w8gA/T0547-1w8gA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1w8gA read from 1w8gA/T0547-1w8gA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1w8gA to template set # found chain 1w8gA in template set T0547 56 :QKQIENIYGNFNKARKEFGYKG 1w8gA 5 :AHNLAQVRDKISAAATRCGRSP T0547 78 :GFNAVYPLKVNQ 1w8gA 28 :EITLLAVSKTKP T0547 91 :PGFVKNLVKLGK 1w8gA 40 :ASAIAEAIDAGQ T0547 106 :YGLEAGSKAELLLAMA 1w8gA 52 :RQFGENYVQEGVDKIR T0547 122 :YNNEGAPITVNGFKDRELINIGF 1w8gA 72 :LGVTGLEWHFIGPLQSNKSRLVA T0547 148 :EM 1w8gA 95 :EH T0547 151 :HNITLTIEGLNELEAIIDIAKE 1w8gA 97 :FDWCHTIDRLRIATRLNDQRPA T0547 174 :FKPKPNIGLRVRLH 1w8gA 119 :ELPPLNVLIQINIS T0547 199 :GINSKFGLTSTELIEAVNLLKENKLLEQFT 1w8gA 133 :DENSKSGIQLAELDELAAAVAELPRLRLRG T0547 230 :IHFHLG 1w8gA 163 :LMAIPA T0547 237 :QITEIHPLKKALNEAGNIYTELRKMGA 1w8gA 169 :PESEYVRQFEVARQMAVAFAGLKTRYP T0547 265 :NLKAINLG 1w8gA 196 :HIDTLSLG T0547 281 :Q 1w8gA 206 :D T0547 291 :TLREYAND 1w8gA 207 :DMEAAIAA T0547 311 :KD 1w8gA 215 :GS T0547 316 :DIFI 1w8gA 217 :TMVR Number of specific fragments extracted= 16 number of extra gaps= 0 total=1766 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 1w8gA/T0547-1w8gA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0547 read from 1w8gA/T0547-1w8gA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1w8gA read from 1w8gA/T0547-1w8gA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1w8gA in template set T0547 55 :IQKQIENIYGNFNKARKEFGYKGGFNAVYPLKVNQYPGFVKNLVKLGK 1w8gA 4 :IAHNLAQVRDKISAAATRCGRSPEEITLLAVSKTKPASAIAEAIDAGQ T0547 106 :YGLEAGS 1w8gA 52 :RQFGENY T0547 113 :KAELLLAMAYNNEGAPITVNGFKDRE 1w8gA 63 :VDKIRHFQELGVTGLEWHFIGPLQSN T0547 141 :NIGF 1w8gA 89 :KSRL T0547 146 :AAEM 1w8gA 93 :VAEH T0547 151 :HNITLTIEGLNELEAIIDIAKE 1w8gA 97 :FDWCHTIDRLRIATRLNDQRPA T0547 174 :FKPKPNIGLRVRLHS 1w8gA 119 :ELPPLNVLIQINISD T0547 200 :INSKFGLTSTELIEAVNLLKENKLL 1w8gA 134 :ENSKSGIQLAELDELAAAVAELPRL T0547 226 :QFTMIHF 1w8gA 159 :RLRGLMA T0547 235 :GSQITEIHPLKKALNEAGNIYTELRKMGA 1w8gA 167 :PAPESEYVRQFEVARQMAVAFAGLKTRYP T0547 265 :NLKAINLG 1w8gA 196 :HIDTLSLG Number of specific fragments extracted= 11 number of extra gaps= 0 total=1777 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 1w8gA/T0547-1w8gA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0547 read from 1w8gA/T0547-1w8gA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1w8gA read from 1w8gA/T0547-1w8gA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1w8gA in template set T0547 55 :IQKQIENIYGNFNKARKEFGYKGG 1w8gA 4 :IAHNLAQVRDKISAAATRCGRSPE T0547 79 :FNAVYPLKVNQY 1w8gA 29 :ITLLAVSKTKPA T0547 92 :GFVKNLVKLG 1w8gA 41 :SAIAEAIDAG T0547 106 :YGL 1w8gA 51 :QRQ T0547 113 :KAELLLAMAYNNEGAPITVNGFKDRELINIGF 1w8gA 63 :VDKIRHFQELGVTGLEWHFIGPLQSNKSRLVA T0547 146 :AA 1w8gA 95 :EH T0547 151 :HNITLTIEGLNELEAIIDIAKE 1w8gA 97 :FDWCHTIDRLRIATRLNDQRPA T0547 174 :FKPKPNIGLRVRL 1w8gA 119 :ELPPLNVLIQINI T0547 198 :GGINSKFGLTSTELIEAVNLLKENK 1w8gA 132 :SDENSKSGIQLAELDELAAAVAELP T0547 224 :LEQFTMIHF 1w8gA 157 :RLRLRGLMA T0547 238 :ITEIHPLKKALNEAGNIYTELRKM 1w8gA 170 :ESEYVRQFEVARQMAVAFAGLKTR T0547 263 :AKNLKAINLG 1w8gA 194 :YPHIDTLSLG T0547 288 :RNYTLREYAND 1w8gA 204 :MSDDMEAAIAA T0547 314 :EPDIF 1w8gA 215 :GSTMV Number of specific fragments extracted= 14 number of extra gaps= 0 total=1791 Will force an alignment to be made, even if fragment is small Number of alignments=78 # command:CPU_time= 45.964 sec, elapsed time= 104.817 sec. # command:DEBUG: alignment library has 78 conformations DEBUG: current conformations has 0 conformations # in ExtractAlignmentsContacts extracting from alignment library using radius 8.000 separation >= 9 style evalue NUMB_ALIGNS: 78 # Adding 6852 constraints to all_contacts Done adding distance constraints # command:CPU_time= 46.445 sec, elapsed time= 105.341 sec. # command:Reading probabilities from T0547.t06.CB8-sep9.rdb Reading constraints from ConstraintSet all_contacts maxweight: 75.298 Optimizing... Probability sum: -1142.539, CN propb: -1142.539 weights: 0.242 constraints: 2086 # command:CPU_time= 1731.025 sec, elapsed time= 1791.277 sec. # command:Found ConstraintSet # PrintContacts align.constraints Number of constraints in align 2086 # command:Found ConstraintSet # PrintContacts align_bonus.constraints Number of constraints in align.bonus 2086 # command:Found ConstraintSet # PrintContacts rejected.constraints Number of constraints in rejected 4766 # command:Found ConstraintSet # PrintContacts rejected_bonus.constraints Number of constraints in rejected.bonus 4766 # 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= 1731.131 sec, elapsed time= 1792.392 sec. # command: