# command:# Prefix for input files set to /projects/compbio/experiments/undertaker/atoms-inputs/ # command:# reading cullpdb_pc80_res1.2_R0.2_d070810_chains408.atoms.gz # #computed average backbone with maximum peptide_sq_deviance = 0.002 # computed average trans backbone unit from 1600 examples # computed average trans backbone unit before proline from 52 examples # trans (non-proline) backbone unit: # CA= -2.2097 1.0151 -0.0046 # O= -0.1488 2.2425 0.0020 # C= -0.6903 1.1357 0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4580 -0.0000 -0.0000 # cis backbone unit: # CA= -0.1462 2.4515 0.0018 # O= -2.0272 0.9713 0.0022 # C= -0.8006 1.0755 0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4659 0.0000 0.0000 # trans backbone unit before proline: # CA= -2.2063 1.0654 0.0002 # O= -0.1193 2.2442 0.0054 # C= -0.6842 1.1479 -0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4661 -0.0000 0.0000 # After reading cullpdb_pc80_res1.2_R0.2_d070810_chains408.atoms.gz have 408 chains in training database # Count of chains,residues,atoms: 408,82795,639989 # 81291 residues have no bad marker # 565 residues lack atoms needed to compute omega # 313 residues have cis peptide # number of each bad type: # NON_STANDARD_RESIDUE 1 # HAS_OXT 265 # TOO_MANY_ATOMS 0 # TOO_FEW_ATOMS 378 # HAS_UNKNOWN_ATOMS 0 # HAS_DUPLICATE_ATOMS 0 # CHAIN_BREAK_BEFORE 139 # NON_PLANAR_PEPTIDE 424 # BAD_PEPTIDE 803 # Note: may sum to more than number of residues, # because one residue may have multiple problems # command:# Reading rotamer library from dunbrack-40pc-3157.rot # command:# Prefix for input files set to /projects/compbio/experiments/undertaker/spots/ # command:# ReadAtomType exp-pdb.types Read AtomType exp-pdb with 49 types. # command:# ReadClashTable exp-pdb-2191-2symm.clash # Read ClashTable exp-pdb-2191-2symm checking bonds symmetric at MaxSep 2 # command:# command:# Prefix for input files set to # command:# Making conformation for sequence T0334 numbered 1 through 530 Created new target T0334 from T0334.a2m # command:CPU_time= 5.172 sec, elapsed time= 5.219 sec. # command:# reading script from file all-templates.under # Reading fragments from alignment file # Attempting to read fragment alignments from file 2aqjA/T0334-2aqjA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2aqjA expands to /projects/compbio/data/pdb/2aqj.pdb.gz 2aqjA:# T0334 read from 2aqjA/T0334-2aqjA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2aqjA read from 2aqjA/T0334-2aqjA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2aqjA to template set # found chain 2aqjA in template set Warning: unaligning (T0334)S2 because first residue in template chain is (2aqjA)N2 Warning: unaligning (T0334)V47 because of BadResidue code BAD_PEPTIDE in next template residue (2aqjA)G48 Warning: unaligning (T0334)G48 because of BadResidue code BAD_PEPTIDE at template residue (2aqjA)G48 Warning: unaligning (T0334)A81 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2aqjA)I82 Warning: unaligning (T0334)I82 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2aqjA)I82 Warning: unaligning (T0334)P376 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2aqjA)D366 Warning: unaligning (T0334)D377 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2aqjA)D366 Warning: unaligning (T0334)Q527 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2aqjA)R517 Warning: unaligning (T0334)H528 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2aqjA)R517 Warning: unaligning (T0334)G529 because last residue in template chain is (2aqjA)D518 T0334 3 :GKIDKILIVGGGTAGWMAASYLGKAL 2aqjA 3 :KPIKNIVIVGGGTAGWMAASYLVRAL # choosing archetypes in rotamer library T0334 29 :QGT 2aqjA 30 :QQA T0334 33 :DITLLQAPDIPTLG 2aqjA 33 :NITLIESAAIPRIG T0334 49 :EATIPNLQTAFFDFLGIPEDEWMRECNASYKV 2aqjA 49 :EATIPSLQKVFFDFLGIPEREWMPQVNGAFKA T0334 83 :KFINWRTAGEGT 2aqjA 83 :KFVNWRKSPDPS T0334 103 :GPDHFYHSFGLLKYHEQIPLSHYWFDRSYR 2aqjA 95 :RDDHFYHLFGNVPNCDGVPLTHYWLRKREQ T0334 152 :ANRSPRRLDGSKVTNYAWHF 2aqjA 125 :GFQQPMEYACYPQPGALDGK T0334 172 :DAHLVADFLRRFA 2aqjA 163 :DAHLVADFLKRWA T0334 186 :EKLGVRHVEDRVEHVQRDANGNIESVRTATGRVFDADLFVDCSGFRGLLINKAMEEPFLDMSDHLLNDSAVATQVPHDDDANGVEPFTSAIAMKSGWTWKIPMLGRFGTGYVYSSRFATEDEAVREFCEMWHLDP 2aqjA 176 :VERGVNRVVDEVVDVRLNNRGYISNLLTKEGRTLEADLFIDCSGMRGLLINQALKEPFIDMSDYLLCDSAVASAVPNDDARDGVEPYTSSIAMNSGWTWKIPMLGRFGSGYVFSSHFTSRDQATADFLKLWGLSD T0334 322 :TQPLNRIRFRVGRNRRAWVGNCVSIGTSSCFVEPLESTGIYFVYAALYQLVKHF 2aqjA 311 :NQPLNQIKFRVGRNKRAWVNNCVSIGLSSCFLEPLESTGIYFIYAALYQLVKHF T0334 378 :KSLNPVLTARFNREIETMFDDTRDFIQAHFYFSPRTDTPFWRANK 2aqjA 367 :TSFDPRLSDAFNAEIVHMFDDCRDFVQAHYFTTSRDDTPFWLANR T0334 423 :ELRLADGMQEKIDMYRAGMAINAP 2aqjA 413 :DLRLSDAIKEKVQRYKAGLPLTTT T0334 448 :SDDAQLYYGNFEEEFRNFWNNSNYYCVLAGLGLVPDAPSPRLAHMPQATESVDEVFGAVKDRQRNLLETLPSLHEFLRQ 2aqjA 437 :SFDDSTYYETFDYEFKNFWLNGNYYCIFAGLGMLPDRSLPLLQHRPESIEKAEAMFASIRREAERLRTSLPTNYDYLRS Number of specific fragments extracted= 13 number of extra gaps= 4 total=13 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 2aqjA/T0334-2aqjA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0334 read from 2aqjA/T0334-2aqjA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2aqjA read from 2aqjA/T0334-2aqjA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2aqjA in template set Warning: unaligning (T0334)S2 because first residue in template chain is (2aqjA)N2 Warning: unaligning (T0334)V47 because of BadResidue code BAD_PEPTIDE in next template residue (2aqjA)G48 Warning: unaligning (T0334)G48 because of BadResidue code BAD_PEPTIDE at template residue (2aqjA)G48 Warning: unaligning (T0334)P376 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2aqjA)D366 Warning: unaligning (T0334)D377 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2aqjA)D366 Warning: unaligning (T0334)Q527 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2aqjA)R517 Warning: unaligning (T0334)H528 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2aqjA)R517 Warning: unaligning (T0334)G529 because last residue in template chain is (2aqjA)D518 T0334 3 :GKIDKILIVGGGTAGWMAASYLGKALQGTADITLLQAPDIPTLG 2aqjA 3 :KPIKNIVIVGGGTAGWMAASYLVRALQQQANITLIESAAIPRIG T0334 49 :EATIPNLQTAFFDFLGIPEDEWM 2aqjA 49 :EATIPSLQKVFFDFLGIPEREWM T0334 96 :EARE 2aqjA 72 :PQVN T0334 100 :LDGGP 2aqjA 89 :KSPDP T0334 105 :DHFYHSFGLL 2aqjA 98 :HFYHLFGNVP T0334 120 :IPLSHYWFDRSYR 2aqjA 115 :THYWLRKREQGFQ T0334 142 :ACYKEPVILD 2aqjA 128 :QPMEYACYPQ T0334 152 :ANRSPRRLDGSKVTNYAWHFDAHLVADFLRRFAT 2aqjA 143 :GKLAPCLSDGTRQMSHAWHFDAHLVADFLKRWAV T0334 187 :KLGVRHVEDRVEHVQRDANGNIESVRTATGRVFDADLFVDCSGFRGLLINKAMEEPFLDMSDHLLNDSAVATQVPHDDDANGVEPFTSAIAMKSGWTWKIPMLGRFGTGYVYSSRFATEDEAVREFCEMWHLDPE 2aqjA 177 :ERGVNRVVDEVVDVRLNNRGYISNLLTKEGRTLEADLFIDCSGMRGLLINQALKEPFIDMSDYLLCDSAVASAVPNDDARDGVEPYTSSIAMNSGWTWKIPMLGRFGSGYVFSSHFTSRDQATADFLKLWGLSDN T0334 323 :QPLNRIRFRVGRNRRAWVGNCVSIGTSSCFVEPLESTGIYFVYAALYQLVKHF 2aqjA 312 :QPLNQIKFRVGRNKRAWVNNCVSIGLSSCFLEPLESTGIYFIYAALYQLVKHF T0334 378 :KSLNPVLTARFNREIETMFDDTRDFIQAHFYFSPRTDTPFWRANK 2aqjA 367 :TSFDPRLSDAFNAEIVHMFDDCRDFVQAHYFTTSRDDTPFWLANR T0334 423 :ELRLADGMQEKIDMYRAGMAINAPASDDAQLY 2aqjA 413 :DLRLSDAIKEKVQRYKAGLPLTTTSFDDSTYY T0334 456 :GNFEEEFRNFWNNSNYYCVLAGLGLVPDAPSPRLAHMPQATESVDEVFGAVKDRQRNLLETLPSLHEFLRQ 2aqjA 445 :ETFDYEFKNFWLNGNYYCIFAGLGMLPDRSLPLLQHRPESIEKAEAMFASIRREAERLRTSLPTNYDYLRS Number of specific fragments extracted= 13 number of extra gaps= 3 total=26 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 2aqjA/T0334-2aqjA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0334 read from 2aqjA/T0334-2aqjA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2aqjA read from 2aqjA/T0334-2aqjA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2aqjA in template set Warning: unaligning (T0334)S2 because first residue in template chain is (2aqjA)N2 Warning: unaligning (T0334)V47 because of BadResidue code BAD_PEPTIDE in next template residue (2aqjA)G48 Warning: unaligning (T0334)G48 because of BadResidue code BAD_PEPTIDE at template residue (2aqjA)G48 Warning: unaligning (T0334)A81 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2aqjA)I82 Warning: unaligning (T0334)I82 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2aqjA)I82 Warning: unaligning (T0334)P376 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2aqjA)D366 Warning: unaligning (T0334)D377 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2aqjA)D366 Warning: unaligning (T0334)L513 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2aqjA)R517 Warning: unaligning (T0334)L514 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2aqjA)R517 Warning: unaligning (T0334)E515 because last residue in template chain is (2aqjA)D518 T0334 3 :GKIDKILIVGGGTAGWMAASYLGKALQGTADITLLQAPDIPTLG 2aqjA 3 :KPIKNIVIVGGGTAGWMAASYLVRALQQQANITLIESAAIPRIG T0334 49 :EATIPNLQTAFFDFLGIPEDEWMRECNASYKV 2aqjA 49 :EATIPSLQKVFFDFLGIPEREWMPQVNGAFKA T0334 83 :KFINWRTAGEGTSEAREL 2aqjA 83 :KFVNWRKSPDPSRDDHFY T0334 101 :DGGPDHFYHSFGLLKYHEQIPLSHYWFDRSYRGKTV 2aqjA 105 :NVPNCDGVPLTHYWLRKREQGFQQPMEYACYPQPGA T0334 150 :LDANRSPRRLDGSKVTNYAWHFDAHLVADFLRRFATEKLGVRHVE 2aqjA 141 :LDGKLAPCLSDGTRQMSHAWHFDAHLVADFLKRWAVERGVNRVVD T0334 196 :RVEHVQRDANGNIESVRTATGRVFDADLFVDCSGFRGLLINKAMEEPFLDMSDHLLNDSAVATQVPHDDDANGVEPFTSAIAMKSGWTWKIPMLGRFGTGYVYSSRFATEDEAVREFCEMWHLDP 2aqjA 186 :EVVDVRLNNRGYISNLLTKEGRTLEADLFIDCSGMRGLLINQALKEPFIDMSDYLLCDSAVASAVPNDDARDGVEPYTSSIAMNSGWTWKIPMLGRFGSGYVFSSHFTSRDQATADFLKLWGLSD T0334 322 :TQPLNRIRFRVGRNRRAWVGNCVSIGTSSCFVEPLESTGIYFVYAALYQLVKHF 2aqjA 311 :NQPLNQIKFRVGRNKRAWVNNCVSIGLSSCFLEPLESTGIYFIYAALYQLVKHF T0334 378 :KSLNPVLTARFNREIETMFDDTRDFIQAHFYFSPRTDTPFWRANK 2aqjA 367 :TSFDPRLSDAFNAEIVHMFDDCRDFVQAHYFTTSRDDTPFWLANR T0334 423 :ELRLADGMQEKIDMYRAGMAINAPASDDA 2aqjA 413 :DLRLSDAIKEKVQRYKAGLPLTTTSFDDS T0334 452 :QLYYGNFEEEFRNFWNNSNYYCVLAGLGLVP 2aqjA 453 :NFWLNGNYYCIFAGLGMLPDRSLPLLQHRPE T0334 483 :DAPSPRLAHMPQATESVDEVFGAVKDRQRN 2aqjA 486 :EKAEAMFASIRREAERLRTSLPTNYDYLRS Number of specific fragments extracted= 11 number of extra gaps= 4 total=37 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 1pn0A/T0334-1pn0A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1pn0A expands to /projects/compbio/data/pdb/1pn0.pdb.gz 1pn0A:# T0334 read from 1pn0A/T0334-1pn0A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1pn0A read from 1pn0A/T0334-1pn0A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1pn0A to template set # found chain 1pn0A in template set Warning: unaligning (T0334)S2 because first residue in template chain is (1pn0A)T1 Warning: unaligning (T0334)S300 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1pn0A)T305 T0334 3 :GKID 1pn0A 2 :KYSE T0334 7 :KILIVGGGTAGWMAASYLGK 1pn0A 9 :DVLIVGAGPAGLMAARVLSE T0334 28 :L 1pn0A 29 :Y T0334 29 :QGT 1pn0A 34 :PDL T0334 33 :DITLLQAPD 1pn0A 37 :KVRIIDKRS T0334 42 :IPTLGVGEATIPNLQTAF 1pn0A 47 :KVYNGQADGLQCRTLESL T0334 61 :DFLGIPED 1pn0A 65 :KNLGLADK T0334 103 :GPDHFYHSFGLL 1pn0A 79 :DMSTIALYNPDE T0334 115 :KYHE 1pn0A 92 :GHIR T0334 152 :ANRSPRRLDGSKVTNYAWHFDAHLVADFLRRFATEKLG 1pn0A 96 :RTDRIPDTLPGISRYHQVVLHQGRIERRILDSIAEISD T0334 190 :VRHVED 1pn0A 136 :IKVERP T0334 196 :RVEHVQR 1pn0A 143 :IPEKMEI T0334 203 :DANGNIESVRTAT 1pn0A 156 :DPEAYPVTMTLRY T0334 216 :GR 1pn0A 211 :GE T0334 218 :VFDADLFVDCSGFRGLLI 1pn0A 215 :TVHCKYVIGCDGGHSWVR T0334 237 :KAMEEPFLDM 1pn0A 233 :RTLGFEMIGE T0334 247 :SD 1pn0A 245 :DY T0334 254 :SAVATQVPHDDDANGVEPFTSAIAMKSGWTWKIPM 1pn0A 247 :IWGVLDAVPASNFPDIRSRCAIHSAESGSIMIIPR T0334 289 :LGRFGTGYVYS 1pn0A 283 :NNLVRFYVQLQ T0334 306 :DEAVREFCEMWHLDP 1pn0A 310 :EVVIANAKKIFHPYT T0334 321 :ETQPLNRIRFRVGRNRRAWVG 1pn0A 329 :QLDWFTAYHIGQRVTEKFSKD T0334 342 :NCVSIGTSSCFVEPLESTGIYFVYAALYQLVKHFP 1pn0A 351 :RVFIAGDACHTHSPKAGQGMNTSMMDTYNLGWKLG T0334 377 :DKSLNPVLTARFNREIETMFDDTRDFIQAHFYFS 1pn0A 389 :TGRAKRDILKTYEEERQPFAQALIDFDHQFSRLF T0334 411 :PRTD 1pn0A 424 :GRPA T0334 427 :ADGMQEKIDMYRAGMAINA 1pn0A 438 :MDVFKEAFVKGNEFASGTA T0334 480 :LVPD 1pn0A 457 :INYD Number of specific fragments extracted= 26 number of extra gaps= 0 total=63 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 1pn0A/T0334-1pn0A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0334 read from 1pn0A/T0334-1pn0A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1pn0A read from 1pn0A/T0334-1pn0A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1pn0A in template set Warning: unaligning (T0334)S300 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1pn0A)T305 T0334 4 :KIDKILIVGGGTAGWMAASYLGKAL 1pn0A 6 :SYCDVLIVGAGPAGLMAARVLSEYV T0334 29 :QGTADITLLQAP 1pn0A 33 :KPDLKVRIIDKR T0334 41 :DIPTLGVGEATIPNLQTAF 1pn0A 46 :TKVYNGQADGLQCRTLESL T0334 61 :DFLGI 1pn0A 65 :KNLGL T0334 123 :SHYWFDRSYR 1pn0A 70 :ADKILSEAND T0334 136 :VEP 1pn0A 80 :MST T0334 141 :YACYKEPVILD 1pn0A 88 :PDENGHIRRTD T0334 154 :RSPRRLDGSKVTNYAW 1pn0A 99 :RIPDTLPGISRYHQVV T0334 171 :FDAHLVADFLRRFATEKLG 1pn0A 115 :LHQGRIERRILDSIAEISD T0334 190 :VRHVED 1pn0A 136 :IKVERP T0334 196 :RVEHVQR 1pn0A 143 :IPEKMEI T0334 203 :DANGNIESVRTA 1pn0A 156 :DPEAYPVTMTLR T0334 216 :G 1pn0A 211 :G T0334 217 :RVFDADLFVDCSGFRGLL 1pn0A 214 :ETVHCKYVIGCDGGHSWV T0334 236 :NKAMEEPFLDMSDH 1pn0A 232 :RRTLGFEMIGEQTD T0334 253 :DSAVATQVPHDDDANGVEPFTSAIAMKSGWTWKIPMLGR 1pn0A 246 :YIWGVLDAVPASNFPDIRSRCAIHSAESGSIMIIPRENN T0334 292 :FGTGYVYS 1pn0A 286 :VRFYVQLQ T0334 306 :DEAVREFCEMWHL 1pn0A 310 :EVVIANAKKIFHP T0334 322 :TQ 1pn0A 323 :YT T0334 324 :PLNRIRFRVGRNRRAWVG 1pn0A 332 :WFTAYHIGQRVTEKFSKD T0334 342 :NCVSIGTSSCFVEPLESTGIYFVYAALYQLVKHF 1pn0A 351 :RVFIAGDACHTHSPKAGQGMNTSMMDTYNLGWKL T0334 378 :KSLNPVLTARFNREIETMFDDTRDFIQAHFYFSPRTD 1pn0A 390 :GRAKRDILKTYEEERQPFAQALIDFDHQFSRLFSGRP T0334 481 :VPDAPSPRLAHMPQATESVDEVFG 1pn0A 427 :AKDVADEMGVSMDVFKEAFVKGNE Number of specific fragments extracted= 23 number of extra gaps= 0 total=86 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 1pn0A/T0334-1pn0A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0334 read from 1pn0A/T0334-1pn0A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1pn0A read from 1pn0A/T0334-1pn0A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1pn0A in template set Warning: unaligning (T0334)R301 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1pn0A)T305 T0334 5 :IDKILIVGGGTAGWMAASYLGKAL 1pn0A 7 :YCDVLIVGAGPAGLMAARVLSEYV T0334 29 :QGTADITLLQAPDIPTL 1pn0A 33 :KPDLKVRIIDKRSTKVY T0334 46 :GVGEATIPNLQTAF 1pn0A 51 :GQADGLQCRTLESL T0334 61 :DFLGI 1pn0A 65 :KNLGL T0334 68 :DEWMRECNASYKVAIKFINWRTAGEGTSEARELDGG 1pn0A 70 :ADKILSEANDMSTIALYNPDENGHIRRTDRIPDTLP T0334 162 :SKVTNYAWHFDAHLVADFLRRFATEK 1pn0A 106 :GISRYHQVVLHQGRIERRILDSIAEI T0334 188 :LGVRHVEDRVEHVQRDANGN 1pn0A 135 :RIKVERPLIPEKMEIDSSKA T0334 214 :ATGR 1pn0A 209 :EAGE T0334 218 :VFDADLFVDCSGFRGLLIN 1pn0A 215 :TVHCKYVIGCDGGHSWVRR T0334 238 :AMEEPFLDMSDHLLNDSAVATQV 1pn0A 234 :TLGFEMIGEQTDYIWGVLDAVPA T0334 264 :DDANGVEPFTSAIAMKSGWTWKIPMLGRFGTGYVYSS 1pn0A 257 :SNFPDIRSRCAIHSAESGSIMIIPRENNLVRFYVQLQ T0334 307 :EAVREFCEMWHLDP 1pn0A 311 :VVIANAKKIFHPYT T0334 325 :LNRIRFRVGRNRRAWV 1pn0A 325 :FDVQQLDWFTAYHIGQ T0334 341 :GNCVSIGTSSCFVEPLESTGIYFVYAALYQLVKHFP 1pn0A 350 :ERVFIAGDACHTHSPKAGQGMNTSMMDTYNLGWKLG T0334 377 :DKSLNPVLTARFNREIETMFDDTRDFIQAHFY 1pn0A 393 :KRDILKTYEEERQPFAQALIDFDHQFSRLFSG T0334 442 :AINAPASDDA 1pn0A 425 :RPAKDVADEM T0334 452 :QLYYGNFEEEFRNFWNNSNYYC 1pn0A 439 :DVFKEAFVKGNEFASGTAINYD Number of specific fragments extracted= 17 number of extra gaps= 0 total=103 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 1ryiA/T0334-1ryiA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1ryiA expands to /projects/compbio/data/pdb/1ryi.pdb.gz 1ryiA:Skipped atom 2303, because occupancy 0.5 <= existing 0.500 in 1ryiA Skipped atom 2305, because occupancy 0.500 <= existing 0.500 in 1ryiA Skipped atom 2307, because occupancy 0.500 <= existing 0.500 in 1ryiA Skipped atom 2309, because occupancy 0.500 <= existing 0.500 in 1ryiA Skipped atom 2311, because occupancy 0.500 <= existing 0.500 in 1ryiA Skipped atom 2313, because occupancy 0.500 <= existing 0.500 in 1ryiA Skipped atom 2315, because occupancy 0.500 <= existing 0.500 in 1ryiA Skipped atom 2317, because occupancy 0.500 <= existing 0.500 in 1ryiA Skipped atom 2319, because occupancy 0.500 <= existing 0.500 in 1ryiA Skipped atom 2321, because occupancy 0.500 <= existing 0.500 in 1ryiA Skipped atom 2323, because occupancy 0.500 <= existing 0.500 in 1ryiA # T0334 read from 1ryiA/T0334-1ryiA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ryiA read from 1ryiA/T0334-1ryiA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1ryiA to template set # found chain 1ryiA in template set Warning: unaligning (T0334)G3 because first residue in template chain is (1ryiA)M1 Warning: unaligning (T0334)F62 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1ryiA)A54 Warning: unaligning (T0334)L63 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1ryiA)A54 Warning: unaligning (T0334)I65 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1ryiA)E57 Warning: unaligning (T0334)P66 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1ryiA)E57 Warning: unaligning (T0334)Q201 because of BadResidue code BAD_PEPTIDE in next template residue (1ryiA)R179 Warning: unaligning (T0334)R202 because of BadResidue code BAD_PEPTIDE at template residue (1ryiA)R179 Warning: unaligning (T0334)G295 because of BadResidue code BAD_PEPTIDE in next template residue (1ryiA)A259 Warning: unaligning (T0334)Y296 because of BadResidue code BAD_PEPTIDE at template residue (1ryiA)A259 T0334 4 :KID 1ryiA 2 :KRH T0334 7 :KILIVGGGTAGWMAASYLGK 1ryiA 6 :EAVVIGGGIIGSAIAYYLAK T0334 29 :QGT 1ryiA 26 :ENK T0334 33 :DITLLQAP 1ryiA 29 :NTALFESG T0334 46 :GVGEATIPNLQTAFFD 1ryiA 37 :TMGGRTTSAAAGMLGA T0334 64 :G 1ryiA 55 :E T0334 67 :EDEWMRECNAS 1ryiA 58 :ERDAFFDFAMH T0334 115 :KYHE 1ryiA 75 :GLGE T0334 139 :FDYACYKEPVILDANRSPRRLDGSKVTNYAWHF 1ryiA 79 :ELYALSGVDIRQHNGGMFKLAFSEEDVLQLRQM T0334 172 :DAHLVADFLRRFA 1ryiA 149 :EPYFVCKAYVKAA T0334 186 :EKLGVRHVED 1ryiA 162 :KMLGAEIFEH T0334 196 :RVEHV 1ryiA 173 :PVLHV T0334 203 :DANG 1ryiA 180 :DGEA T0334 209 :ESVRTATG 1ryiA 184 :LFIKTPSG T0334 218 :VFDADLFVDCSGFRGLLINKAMEEP 1ryiA 192 :DVWANHVVVASGVWSGMFFKQLGLN T0334 247 :SDHLLNDSAVATQVPHDD 1ryiA 217 :NAFLPVKGECLSVWNDDI T0334 271 :PFTSAIAMKS 1ryiA 235 :PLTKTLYHDH T0334 283 :TWKIPM 1ryiA 245 :CYIVPR T0334 289 :LGRFGT 1ryiA 252 :SGRLVV T0334 297 :VYSSRFATE 1ryiA 260 :TMKPGDWSE T0334 306 :DEAVREFCEM 1ryiA 272 :LGGLESVMKK T0334 316 :WHLDPETQPLNRIRFRVGRNR 1ryiA 283 :KTMLPAIQNMKVDRFWAGLRP T0334 338 :AWVGNCVSIG 1ryiA 304 :GTKDGKPYIG T0334 348 :TSSCFVEPLESTGIYFVYAALYQLVKHFPDKSLNPVLTARF 1ryiA 319 :SRILFAAGHFRNGILLAPATGALISDLIMNKEVNQDWLHAF Number of specific fragments extracted= 24 number of extra gaps= 4 total=127 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 1ryiA/T0334-1ryiA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0334 read from 1ryiA/T0334-1ryiA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ryiA read from 1ryiA/T0334-1ryiA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1ryiA in template set Warning: unaligning (T0334)Q201 because of BadResidue code BAD_PEPTIDE in next template residue (1ryiA)R179 Warning: unaligning (T0334)R202 because of BadResidue code BAD_PEPTIDE at template residue (1ryiA)R179 Warning: unaligning (T0334)G295 because of BadResidue code BAD_PEPTIDE in next template residue (1ryiA)A259 Warning: unaligning (T0334)Y296 because of BadResidue code BAD_PEPTIDE at template residue (1ryiA)A259 T0334 1 :MSG 1ryiA 1 :MKR T0334 5 :IDKILIVGGGTAGWMAASYLGK 1ryiA 4 :HYEAVVIGGGIIGSAIAYYLAK T0334 30 :GTADITLLQAPDIPTLGVGEATIPNL 1ryiA 26 :ENKNTALFESGTMGGRTTSAAAGMLG T0334 76 :ASYKVAIKFINWRTAGEGTS 1ryiA 61 :AFFDFAMHSQRLYKGLGEEL T0334 96 :EARELDGGP 1ryiA 82 :ALSGVDIRQ T0334 105 :DHFYHSFGLLK 1ryiA 94 :GMFKLAFSEED T0334 123 :SHYWFDRS 1ryiA 105 :VLQLRQMD T0334 132 :RGKTVEPFDYACYKEP 1ryiA 113 :DLDSVSWYSKEEVLEK T0334 155 :SPRRLDGSK 1ryiA 129 :EPYASGDIF T0334 166 :NYAW 1ryiA 138 :GASF T0334 170 :HFDAHLVADFLRRFA 1ryiA 147 :HVEPYFVCKAYVKAA T0334 186 :EKLGVRHVED 1ryiA 162 :KMLGAEIFEH T0334 196 :RVEHV 1ryiA 173 :PVLHV T0334 203 :DANG 1ryiA 180 :DGEA T0334 209 :ESVRTATGR 1ryiA 184 :LFIKTPSGD T0334 219 :FDADLFVDCSGFRGLLINKAMEEPFLDMSDH 1ryiA 193 :VWANHVVVASGVWSGMFFKQLGLNNAFLPVK T0334 253 :DSAVATQVPH 1ryiA 224 :GECLSVWNDD T0334 266 :A 1ryiA 234 :I T0334 268 :GVEPFTSA 1ryiA 235 :PLTKTLYH T0334 279 :KSG 1ryiA 243 :DHC T0334 284 :WKIPMLGR 1ryiA 246 :YIVPRKSG T0334 292 :FGT 1ryiA 255 :LVV T0334 297 :VYSSRFATE 1ryiA 260 :TMKPGDWSE T0334 306 :DEAVREFCEMW 1ryiA 272 :LGGLESVMKKA T0334 317 :HLDPETQPLNRIRFRVGRNR 1ryiA 284 :TMLPAIQNMKVDRFWAGLRP T0334 338 :AWVGNCVSIG 1ryiA 304 :GTKDGKPYIG T0334 348 :TSSCFVEPLESTGIYFVYAALYQLVKHFPDKSLNPVLTARFN 1ryiA 319 :SRILFAAGHFRNGILLAPATGALISDLIMNKEVNQDWLHAFR Number of specific fragments extracted= 27 number of extra gaps= 2 total=154 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 1ryiA/T0334-1ryiA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0334 read from 1ryiA/T0334-1ryiA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ryiA read from 1ryiA/T0334-1ryiA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1ryiA in template set Warning: unaligning (T0334)S2 because first residue in template chain is (1ryiA)M1 Warning: unaligning (T0334)A50 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1ryiA)A54 Warning: unaligning (T0334)T51 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1ryiA)A54 Warning: unaligning (T0334)Q201 because of BadResidue code BAD_PEPTIDE in next template residue (1ryiA)R179 Warning: unaligning (T0334)R202 because of BadResidue code BAD_PEPTIDE at template residue (1ryiA)R179 Warning: unaligning (T0334)Y298 because of BadResidue code BAD_PEPTIDE in next template residue (1ryiA)A259 T0334 3 :GKIDKILIVGGGTAGWMAASYLGK 1ryiA 2 :KRHYEAVVIGGGIIGSAIAYYLAK T0334 30 :GTADITLLQAPDIPT 1ryiA 26 :ENKNTALFESGTMGG T0334 45 :LGVGE 1ryiA 48 :GMLGA T0334 52 :I 1ryiA 55 :E T0334 53 :PNLQTAF 1ryiA 64 :DFAMHSQ T0334 61 :DFLG 1ryiA 71 :RLYK T0334 66 :PEDEWMREC 1ryiA 75 :GLGEELYAL T0334 75 :NASYKVAIKFINWRTAGE 1ryiA 87 :DIRQHNGGMFKLAFSEED T0334 114 :LKYHEQIPLSHYWFDRS 1ryiA 105 :VLQLRQMDDLDSVSWYS T0334 141 :YACY 1ryiA 122 :KEEV T0334 154 :RSPRRLDGSKVTNYAW 1ryiA 126 :LEKEPYASGDIFGASF T0334 170 :HFDAHLVADFLRRFATEKLGVRHVEDRVEHV 1ryiA 147 :HVEPYFVCKAYVKAAKMLGAEIFEHTPVLHV T0334 203 :DANG 1ryiA 180 :DGEA T0334 209 :ESVRTAT 1ryiA 184 :LFIKTPS T0334 217 :RVFDADLFVDCSGFRGLLINKAMEEPFL 1ryiA 191 :GDVWANHVVVASGVWSGMFFKQLGLNNA T0334 249 :HLLN 1ryiA 219 :FLPV T0334 253 :DSAVATQV 1ryiA 224 :GECLSVWN T0334 268 :GVEPFTSAIAMKS 1ryiA 232 :DDIPLTKTLYHDH T0334 283 :TWKIPMLGRF 1ryiA 245 :CYIVPRKSGR T0334 295 :GYV 1ryiA 255 :LVV T0334 299 :SSRFATEDEAVREFCEMW 1ryiA 265 :DWSETPDLGGLESVMKKA T0334 317 :HLDPETQPLNRIRFRVGRNRRAWVGNCV 1ryiA 284 :TMLPAIQNMKVDRFWAGLRPGTKDGKPY T0334 345 :SIGTSSCFVEPLE 1ryiA 321 :ILFAAGHFRNGIL T0334 363 :FVYAALYQLVKHFPDKSLNPVLTARF 1ryiA 334 :LAPATGALISDLIMNKEVNQDWLHAF Number of specific fragments extracted= 24 number of extra gaps= 3 total=178 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 1ykjA/T0334-1ykjA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1ykjA expands to /projects/compbio/data/pdb/1ykj.pdb.gz 1ykjA:# T0334 read from 1ykjA/T0334-1ykjA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ykjA read from 1ykjA/T0334-1ykjA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1ykjA to template set # found chain 1ykjA in template set Warning: unaligning (T0334)I5 because first residue in template chain is (1ykjA)M1001 T0334 6 :D 1ykjA 1002 :K T0334 7 :KILIVGGGTAGWMAASYLGK 1ykjA 1004 :QVAIIGAGPSGLLLGQLLHK T0334 29 :QGT 1ykjA 1024 :AGI T0334 33 :DITLLQAPD 1ykjA 1027 :DNVILERQT T0334 52 :IPNLQTAF 1ykjA 1036 :PDYVLGRI T0334 61 :DFLG 1ykjA 1044 :RGGV T0334 69 :EWMRECNASYKVAIKFINW 1ykjA 1054 :DLLREAGVDRRMARDGLVH T0334 103 :GPDHFYHSFGLL 1ykjA 1073 :EGVEIAFAGQRR T0334 115 :KYHE 1ykjA 1087 :DLKR T0334 152 :ANRSPRRLD 1ykjA 1092 :SGGKTVTVY T0334 172 :DAHLVADFLRRFA 1ykjA 1101 :GQTEVTRDLMEAR T0334 186 :EKLGVRHVED 1ykjA 1114 :EACGATTVYQ T0334 196 :RVEHVQRDANGNIE 1ykjA 1125 :AEVRLHDLQGERPY T0334 211 :VRTA 1ykjA 1139 :VTFE T0334 215 :TGR 1ykjA 1144 :DGE T0334 218 :VFDADLFVDCSGFRGLLI 1ykjA 1149 :RLDCDYIAGCDGFHGISR T0334 237 :KAMEEPFLDM 1ykjA 1167 :QSIPAERLKV T0334 247 :SDHLLND 1ykjA 1178 :ERVYPFG T0334 254 :SAVATQVPHDD 1ykjA 1186 :LGLLADTPPVS T0334 271 :PFTSAIAMKSGWTWKIPM 1ykjA 1197 :HELIYANHPRGFALCSQR T0334 289 :LGR 1ykjA 1216 :ATR T0334 292 :FGTGYVYSSRFATEDEAVREFCEMWHLDP 1ykjA 1223 :VQVPLSEKVEDWSDERFWTELKARLPSEV T0334 321 :ETQPLNRIRFRVGRNRRAWVGNCVSIGTSSCFVEPLESTGIYFVYAALYQLVKHFP 1ykjA 1259 :PSLEKSIAPLRSFVVEPMQHGRLFLAGDAAHIVPPTGAKGLNLAASDVSTLYRLLL T0334 377 :DKSLNPVLTARFNREIETMFDDTRDFIQAHFYFSPRTDTP 1ykjA 1317 :YREGRGELLERYSAICLRRIWKAERFSWWMTSVLHRFPDT T0334 417 :FWR 1ykjA 1359 :FSQ T0334 504 :GAVKDRQRNLLETLPSLHEFLRQ 1ykjA 1362 :RIQQTELEYYLGSEAGLATIAEN Number of specific fragments extracted= 26 number of extra gaps= 0 total=204 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 1ykjA/T0334-1ykjA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0334 read from 1ykjA/T0334-1ykjA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ykjA read from 1ykjA/T0334-1ykjA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1ykjA in template set Warning: unaligning (T0334)K4 because first residue in template chain is (1ykjA)M1001 T0334 5 :IDKILIVGGGTAGWMAASYLGK 1ykjA 1002 :KTQVAIIGAGPSGLLLGQLLHK T0334 30 :GTADITLLQAPDI 1ykjA 1024 :AGIDNVILERQTP T0334 43 :PTLGVGEATIPNLQTAF 1ykjA 1040 :LGRIRGGVLEQGMVDLL T0334 61 :DFLGI 1ykjA 1057 :REAGV T0334 123 :SHYWFDRSYR 1ykjA 1062 :DRRMARDGLV T0334 136 :VEPFDYACYKEPVIL 1ykjA 1072 :HEGVEIAFAGQRRRI T0334 154 :RSPRRLDG 1ykjA 1087 :DLKRLSGG T0334 166 :NYAWHFDAHLVADFLRRFA 1ykjA 1095 :KTVTVYGQTEVTRDLMEAR T0334 186 :EKLGVRHVED 1ykjA 1114 :EACGATTVYQ T0334 196 :RVEHVQR 1ykjA 1125 :AEVRLHD T0334 203 :DANG 1ykjA 1133 :QGER T0334 209 :ESVRTA 1ykjA 1137 :PYVTFE T0334 215 :TG 1ykjA 1144 :DG T0334 217 :RVFDADLFVDCSGFRGLL 1ykjA 1148 :LRLDCDYIAGCDGFHGIS T0334 236 :NKAMEEP 1ykjA 1166 :RQSIPAE T0334 243 :FLDMSDHLLNDSAVAT 1ykjA 1174 :LKVFERVYPFGWLGLL T0334 264 :DDANGVEPFTSAIAMKSGWTWKIPMLGR 1ykjA 1190 :ADTPPVSHELIYANHPRGFALCSQRSAT T0334 292 :FGTGYVYSS 1ykjA 1219 :SRYYVQVPL T0334 301 :RFATEDEAVREFCEMW 1ykjA 1232 :EDWSDERFWTELKARL T0334 319 :DPETQPLNRIRFRVGRNRRAWVGNCVSIGTSSCFVEPLESTGIYFVYAALYQLVKHFPD 1ykjA 1257 :TGPSLEKSIAPLRSFVVEPMQHGRLFLAGDAAHIVPPTGAKGLNLAASDVSTLYRLLLK T0334 378 :KSLNPVLTARFNREIETMFDDTRDFIQAHFYFSPRTD 1ykjA 1318 :REGRGELLERYSAICLRRIWKAERFSWWMTSVLHRFP T0334 415 :TPFWR 1ykjA 1357 :DAFSQ T0334 504 :GAVKDRQRNLLETLPSLHEFLRQQH 1ykjA 1362 :RIQQTELEYYLGSEAGLATIAENYV Number of specific fragments extracted= 23 number of extra gaps= 0 total=227 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 1ykjA/T0334-1ykjA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0334 read from 1ykjA/T0334-1ykjA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ykjA read from 1ykjA/T0334-1ykjA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1ykjA in template set T0334 7 :KILIVGGGTAGWMAASYLGK 1ykjA 1004 :QVAIIGAGPSGLLLGQLLHK T0334 30 :GTADITLLQAPD 1ykjA 1024 :AGIDNVILERQT T0334 43 :PTL 1ykjA 1041 :GRI T0334 47 :VGEATIPNLQTAF 1ykjA 1044 :RGGVLEQGMVDLL T0334 61 :DFLGIP 1ykjA 1057 :REAGVD T0334 69 :EWMRE 1ykjA 1063 :RRMAR T0334 75 :NASYKVAIKFINWRTAGE 1ykjA 1068 :DGLVHEGVEIAFAGQRRR T0334 95 :SE 1ykjA 1086 :ID T0334 158 :RLDGS 1ykjA 1088 :LKRLS T0334 164 :VTNYAWHFDAHLVADFLRRFATEKLGVRHVEDRVEHVQRD 1ykjA 1093 :GGKTVTVYGQTEVTRDLMEAREACGATTVYQAAEVRLHDL T0334 204 :ANGNIESVRTATGR 1ykjA 1134 :GERPYVTFERDGER T0334 218 :VFDADLFVDCSGFRG 1ykjA 1149 :RLDCDYIAGCDGFHG T0334 241 :EPFLDMSDH 1ykjA 1166 :RQSIPAERL T0334 250 :LLNDSAVATQV 1ykjA 1180 :VYPFGWLGLLA T0334 265 :DANGVEPFTSAIAMKSGWTWKIPMLGRFGTGYVYS 1ykjA 1191 :DTPPVSHELIYANHPRGFALCSQRSATRSRYYVQV T0334 300 :SRFATEDEAVREFCEMW 1ykjA 1231 :VEDWSDERFWTELKARL T0334 318 :LDPETQPLNRIRFRVGRNRRAWVGNCVSIGTSSCFVEPLESTGIYFVYAALYQLVKHFP 1ykjA 1256 :VTGPSLEKSIAPLRSFVVEPMQHGRLFLAGDAAHIVPPTGAKGLNLAASDVSTLYRLLL T0334 377 :DKSLNPVLTARFNREIETMFDDTRDFIQAHFYFSPRT 1ykjA 1321 :RGELLERYSAICLRRIWKAERFSWWMTSVLHRFPDTD T0334 486 :SPRLAHMPQATESVDEVFGAVKDRQRNLL 1ykjA 1358 :AFSQRIQQTELEYYLGSEAGLATIAENYV Number of specific fragments extracted= 19 number of extra gaps= 0 total=246 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 1k0iA/T0334-1k0iA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1k0iA expands to /projects/compbio/data/pdb/1k0i.pdb.gz 1k0iA:Skipped atom 1267, because occupancy 0.500 <= existing 0.500 in 1k0iA Skipped atom 1269, because occupancy 0.500 <= existing 0.500 in 1k0iA Skipped atom 1271, because occupancy 0.500 <= existing 0.500 in 1k0iA Skipped atom 1273, because occupancy 0.500 <= existing 0.500 in 1k0iA Skipped atom 1275, because occupancy 0.500 <= existing 0.500 in 1k0iA Skipped atom 1277, because occupancy 0.500 <= existing 0.500 in 1k0iA Skipped atom 1753, because occupancy 0.500 <= existing 0.500 in 1k0iA Skipped atom 1755, because occupancy 0.500 <= existing 0.500 in 1k0iA Skipped atom 1757, because occupancy 0.500 <= existing 0.500 in 1k0iA Skipped atom 1759, because occupancy 0.500 <= existing 0.500 in 1k0iA Skipped atom 1761, because occupancy 0.500 <= existing 0.500 in 1k0iA Skipped atom 1763, because occupancy 0.500 <= existing 0.500 in 1k0iA Skipped atom 1765, because occupancy 0.500 <= existing 0.500 in 1k0iA Skipped atom 1767, because occupancy 0.500 <= existing 0.500 in 1k0iA Skipped atom 1769, because occupancy 0.500 <= existing 0.500 in 1k0iA Skipped atom 2745, because occupancy 0.500 <= existing 0.500 in 1k0iA Skipped atom 2747, because occupancy 0.500 <= existing 0.500 in 1k0iA Skipped atom 2749, because occupancy 0.500 <= existing 0.500 in 1k0iA Skipped atom 2751, because occupancy 0.500 <= existing 0.500 in 1k0iA Skipped atom 2753, because occupancy 0.500 <= existing 0.500 in 1k0iA Skipped atom 2755, because occupancy 0.500 <= existing 0.500 in 1k0iA Skipped atom 2757, because occupancy 0.500 <= existing 0.500 in 1k0iA Skipped atom 2759, because occupancy 0.500 <= existing 0.500 in 1k0iA Skipped atom 2768, because occupancy 0.500 <= existing 0.500 in 1k0iA Skipped atom 2770, because occupancy 0.500 <= existing 0.500 in 1k0iA Skipped atom 2772, because occupancy 0.500 <= existing 0.500 in 1k0iA Skipped atom 2774, because occupancy 0.500 <= existing 0.500 in 1k0iA Skipped atom 2776, because occupancy 0.500 <= existing 0.500 in 1k0iA Skipped atom 2778, because occupancy 0.500 <= existing 0.500 in 1k0iA Skipped atom 2982, because occupancy 0.500 <= existing 0.500 in 1k0iA Skipped atom 2984, because occupancy 0.500 <= existing 0.500 in 1k0iA Skipped atom 2986, because occupancy 0.500 <= existing 0.500 in 1k0iA Skipped atom 2988, because occupancy 0.500 <= existing 0.500 in 1k0iA Skipped atom 2990, because occupancy 0.500 <= existing 0.500 in 1k0iA Skipped atom 2992, because occupancy 0.500 <= existing 0.500 in 1k0iA Skipped atom 2994, because occupancy 0.500 <= existing 0.500 in 1k0iA Skipped atom 2996, because occupancy 0.500 <= existing 0.500 in 1k0iA # T0334 read from 1k0iA/T0334-1k0iA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1k0iA read from 1k0iA/T0334-1k0iA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1k0iA to template set # found chain 1k0iA in template set Warning: unaligning (T0334)I5 because first residue in template chain is (1k0iA)M1 T0334 6 :D 1k0iA 2 :K T0334 7 :KILIVGGGTAGWMAASYLGK 1k0iA 4 :QVAIIGAGPSGLLLGQLLHK T0334 29 :QGT 1k0iA 24 :AGI T0334 33 :DITLLQAPD 1k0iA 27 :DNVILERQT T0334 52 :IPNLQTAF 1k0iA 36 :PDYVLGRI T0334 61 :DFLGIPED 1k0iA 44 :RAGVLEQG T0334 69 :EWMRECNASYKVAIKFINW 1k0iA 54 :DLLREAGVDRRMARDGLVH T0334 103 :GPDHFYHSFGLL 1k0iA 73 :EGVEIAFAGQRR T0334 115 :KYHE 1k0iA 87 :DLKR T0334 152 :ANRSPRRLD 1k0iA 92 :SGGKTVTVY T0334 172 :DAHLVADFLRRFA 1k0iA 101 :GQTEVTRDLMEAR T0334 186 :EKLGVRHVED 1k0iA 114 :EACGATTVYQ T0334 196 :RVEHVQRDANGNIE 1k0iA 125 :AEVRLHDLQGERPY T0334 211 :VRTA 1k0iA 139 :VTFE T0334 215 :TGR 1k0iA 144 :DGE T0334 218 :VFDADLFVDCSGFRGLLI 1k0iA 149 :RLDCDYIAGCDGFHGISR T0334 237 :KAMEEPFLDM 1k0iA 167 :QSIPAERLKV T0334 247 :SDHLLND 1k0iA 178 :ERVYPFG T0334 254 :SAVATQVPHDD 1k0iA 186 :LGLLADTPPVS T0334 271 :PFTSAIAMKSGWTWKIPM 1k0iA 197 :HELIYANHPRGFALCSQR T0334 289 :LGR 1k0iA 216 :ATR T0334 292 :FGTGYVYSSRFATEDEAVREFCEMWHLDP 1k0iA 223 :VQVPLSEKVEDWSDERFWTELKARLPSEV T0334 321 :ETQPLNRIRFRVGRNRRAWVGNCVSIGTSSCFVEPLESTGIYFVYAALYQLVKHFP 1k0iA 259 :PSLEKSIAPLRSFVVEPMQHGRLFLAGDAAHIVPPTGAKGLNLAASDVSTLYRLLL T0334 377 :DKSLNPVLTARFNREIETMFDDTRDFIQAHFYFSPRTDTP 1k0iA 317 :YREGRGELLERYSAICLRRIWKAERFSWWMTSVLHRFPDT T0334 417 :FWR 1k0iA 359 :FSQ T0334 497 :ESVDEVFGAVKD 1k0iA 362 :RIQQTELEYYLG T0334 509 :RQRNLLE 1k0iA 377 :GLATIAE Number of specific fragments extracted= 27 number of extra gaps= 0 total=273 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 1k0iA/T0334-1k0iA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0334 read from 1k0iA/T0334-1k0iA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1k0iA read from 1k0iA/T0334-1k0iA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1k0iA in template set Warning: unaligning (T0334)K4 because first residue in template chain is (1k0iA)M1 T0334 5 :IDKILIVGGGTAGWMAASYLGKA 1k0iA 2 :KTQVAIIGAGPSGLLLGQLLHKA T0334 31 :TADITLLQAPDI 1k0iA 25 :GIDNVILERQTP T0334 43 :PTLGVGEATIPNLQTAF 1k0iA 40 :LGRIRAGVLEQGMVDLL T0334 61 :DFLGI 1k0iA 57 :REAGV T0334 123 :SHYWFDRSYR 1k0iA 62 :DRRMARDGLV T0334 136 :VEPFDYACYKEPVILD 1k0iA 72 :HEGVEIAFAGQRRRID T0334 155 :SPRRLDG 1k0iA 88 :LKRLSGG T0334 166 :NYAWHFDAHLVADFLRRFA 1k0iA 95 :KTVTVYGQTEVTRDLMEAR T0334 186 :EKLGVRHVED 1k0iA 114 :EACGATTVYQ T0334 196 :RVEHVQR 1k0iA 125 :AEVRLHD T0334 203 :DANG 1k0iA 133 :QGER T0334 209 :ESVRTA 1k0iA 137 :PYVTFE T0334 215 :TG 1k0iA 144 :DG T0334 217 :RVFDADLFVDCSGFRGLL 1k0iA 148 :LRLDCDYIAGCDGFHGIS T0334 236 :NKAMEEPFL 1k0iA 166 :RQSIPAERL T0334 245 :DMSDHLLNDSAVAT 1k0iA 176 :VFERVYPFGWLGLL T0334 264 :DDANGVEPFTSAIAMKSGWTWKIPMLGR 1k0iA 190 :ADTPPVSHELIYANHPRGFALCSQRSAT T0334 292 :FGTGYVYSS 1k0iA 219 :SQYYVQVPL T0334 301 :RFATEDEAVREFCEMW 1k0iA 232 :EDWSDERFWTELKARL T0334 324 :PLNRIRFRVGRNRRAWVGNCVSIGTSSCFVEPLESTGIYFVYAALYQLVKHFPD 1k0iA 262 :EKSIAPLRSFVVEPMQHGRLFLAGDAAHIVPPTGAKGLNLAASDVSTLYRLLLK T0334 378 :KSLNPVLTARFNREIETMFDDTRDFIQAHFY 1k0iA 318 :REGRGELLERYSAICLRRIWKAERFSWWMTS T0334 409 :FSPRTDTPFWR 1k0iA 351 :HRFPDTDAFSQ T0334 504 :GAVKDRQRNLLETLPSLHEFLR 1k0iA 362 :RIQQTELEYYLGSEAGLATIAE Number of specific fragments extracted= 23 number of extra gaps= 0 total=296 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 1k0iA/T0334-1k0iA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0334 read from 1k0iA/T0334-1k0iA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1k0iA read from 1k0iA/T0334-1k0iA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1k0iA in template set T0334 7 :KILIVGGGTAGWMAASYLGK 1k0iA 4 :QVAIIGAGPSGLLLGQLLHK T0334 30 :GTADITLLQAPD 1k0iA 24 :AGIDNVILERQT T0334 42 :IPTLGV 1k0iA 42 :RIRAGV T0334 51 :TIPNLQTAF 1k0iA 48 :LEQGMVDLL T0334 61 :DFLGIP 1k0iA 57 :REAGVD T0334 68 :DEWMRECNASYKVAIKFINWRT 1k0iA 63 :RRMARDGLVHEGVEIAFAGQRR T0334 155 :SPRRLDGSKVT 1k0iA 85 :RIDLKRLSGGK T0334 167 :YAWHFDAHLVADFLRRFATEKLGVRHVEDRVEHVQRDANGNIESVRTATGR 1k0iA 96 :TVTVYGQTEVTRDLMEAREACGATTVYQAAEVRLHDLQGERPYVTFERDGE T0334 218 :VFDADLFVDCSGFRG 1k0iA 149 :RLDCDYIAGCDGFHG T0334 241 :EPFLDMSDH 1k0iA 166 :RQSIPAERL T0334 250 :LLNDSAVATQV 1k0iA 180 :VYPFGWLGLLA T0334 265 :DANGVEPFTSAIAMKSGWTWKIPMLGRFGTGYVYS 1k0iA 191 :DTPPVSHELIYANHPRGFALCSQRSATRSQYYVQV T0334 300 :SRFATEDEAVREFCEMWHLD 1k0iA 231 :VEDWSDERFWTELKARLPSE T0334 320 :PETQPLNRIRFRVGRNRRAWVGNCVSIGTSSCFVEPLESTGIYFVYAALYQLVKHFP 1k0iA 258 :GPSLEKSIAPLRSFVVEPMQHGRLFLAGDAAHIVPPTGAKGLNLAASDVSTLYRLLL T0334 377 :DKSLNPVLTARFNREIETMFDDTRDFIQAHFYFSPRT 1k0iA 321 :RGELLERYSAICLRRIWKAERFSWWMTSVLHRFPDTD T0334 486 :SPRLAHMPQATESVDEVFGAVKDRQRNL 1k0iA 358 :AFSQRIQQTELEYYLGSEAGLATIAENY Number of specific fragments extracted= 16 number of extra gaps= 0 total=312 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 1pj5A/T0334-1pj5A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1pj5A expands to /projects/compbio/data/pdb/1pj5.pdb.gz 1pj5A:# T0334 read from 1pj5A/T0334-1pj5A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1pj5A read from 1pj5A/T0334-1pj5A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1pj5A to template set # found chain 1pj5A in template set Warning: unaligning (T0334)D6 because first residue in template chain is (1pj5A)T4 T0334 7 :KILIVGGGTAGWMAASYLGK 1pj5A 6 :RIVIIGAGIVGTNLADELVT T0334 29 :QGTADITLLQAPDI 1pj5A 26 :RGWNNITVLDQGPL T0334 46 :GVGEATIPNLQTAFFDFLGIPEDEWMRECNASYKVAIK 1pj5A 40 :NMPGGSTSHAPGLVFQTNPSKTMASFAKYTVEKLLSLT T0334 103 :GPDHFYHSFGLL 1pj5A 79 :DGVSCFNQVGGL T0334 115 :KYHEQIPLSHYWF 1pj5A 94 :TTETRLADLKRKL T0334 139 :FDYACYKEPVILDANRSPRRLDGSKVTNYAWHF 1pj5A 107 :GYAAAWGIEGRLLSPAECQELYPLLDGENILGG T0334 172 :DAHLVADFLRRFA 1pj5A 149 :SAARAVQLLIKRT T0334 186 :EKLGVRHVED 1pj5A 162 :ESAGVTYRGS T0334 196 :RVEHVQRDAN 1pj5A 173 :TVTGIEQSGG T0334 207 :NIESVRTATG 1pj5A 183 :RVTGVQTADG T0334 218 :VFDADLFVDCSGFRGLLINKAMEEP 1pj5A 193 :VIPADIVVSCAGFWGAKIGAMIGMA T0334 247 :SDHLLNDSAVATQVPHDDDANGVEPFTS 1pj5A 218 :VPLLPLAHQYVKTTPVPAQQGRNDQPNG T0334 275 :AIAMKSGWTWKIPMLGRFGTGYVYSSRFATE 1pj5A 250 :ILRHQDQDLYYREHGDRYGIGSYAHRPMPVD T0334 306 :DEAVREFCEMWHLDPETQPLNRIRFRVGRNR 1pj5A 306 :EDFLPAWEATKQLLPALADSEIEDGFNGIFS T0334 338 :AWVGNCVSIG 1pj5A 337 :FTPDGGPLLG T0334 348 :TSSCFVEP 1pj5A 352 :DGFYVAEA T0334 356 :LES 1pj5A 362 :VTH T0334 364 :VYAALYQLVKHFP 1pj5A 365 :SAGVAKAMAELLT T0334 378 :KSL 1pj5A 379 :GRS T0334 414 :DTP 1pj5A 382 :ETD T0334 427 :ADGMQEKI 1pj5A 400 :PEYVSETS T0334 435 :DMYRAGMAINAPASDDAQL 1pj5A 409 :QNFVEIYDVLHPLQPRLSP T0334 454 :YYGNFEEEFRNF 1pj5A 431 :RVSPFHARHKEL Number of specific fragments extracted= 23 number of extra gaps= 0 total=335 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 1pj5A/T0334-1pj5A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0334 read from 1pj5A/T0334-1pj5A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1pj5A read from 1pj5A/T0334-1pj5A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1pj5A in template set Warning: unaligning (T0334)I5 because first residue in template chain is (1pj5A)T4 T0334 6 :DKILIVGGGTAGWMAASYLGK 1pj5A 5 :PRIVIIGAGIVGTNLADELVT T0334 30 :GTA 1pj5A 26 :RGW T0334 33 :DITLLQAP 1pj5A 30 :NITVLDQG T0334 41 :DIPTLGVGEATI 1pj5A 40 :NMPGGSTSHAPG T0334 53 :PN 1pj5A 58 :PS T0334 57 :TAF 1pj5A 60 :KTM T0334 78 :YKVAIKFINWRTAGE 1pj5A 63 :ASFAKYTVEKLLSLT T0334 97 :ARELD 1pj5A 78 :EDGVS T0334 105 :DHFYHSFGLLKYHEQIPLSHYWFDRSYR 1pj5A 88 :GGLEVATTETRLADLKRKLGYAAAWGIE T0334 136 :VEPFDYACYKEPVI 1pj5A 116 :GRLLSPAECQELYP T0334 152 :ANRSPRRLDGSKVTNYAW 1pj5A 130 :LLDGENILGGLHVPSDGL T0334 171 :FDAHLVADFLRRFA 1pj5A 148 :ASAARAVQLLIKRT T0334 186 :EKLGVRHVED 1pj5A 162 :ESAGVTYRGS T0334 196 :RVEHVQR 1pj5A 173 :TVTGIEQ T0334 204 :ANGNIESVRTATG 1pj5A 180 :SGGRVTGVQTADG T0334 218 :VFDADLFVDCSGFRGLLINKAMEEPFLD 1pj5A 193 :VIPADIVVSCAGFWGAKIGAMIGMAVPL T0334 250 :LLNDSAVATQVPHDDDANGVE 1pj5A 221 :LPLAHQYVKTTPVPAQQGRND T0334 271 :PFTSA 1pj5A 249 :PILRH T0334 279 :KSGWTWKIPMLGRFGTGYVY 1pj5A 254 :QDQDLYYREHGDRYGIGSYA T0334 299 :SSRFATE 1pj5A 280 :DVDTLGA T0334 306 :DEAVREFCEMW 1pj5A 309 :LPAWEATKQLL T0334 320 :PETQPLNRIRFRVGRNR 1pj5A 320 :PALADSEIEDGFNGIFS T0334 338 :AWVGNCVSIG 1pj5A 337 :FTPDGGPLLG T0334 348 :TSSCFVEPLES 1pj5A 352 :DGFYVAEAVWV T0334 362 :YFVYAALYQLVKHFPD 1pj5A 363 :THSAGVAKAMAELLTT T0334 378 :KSLNPVLTARF 1pj5A 396 :VQLTPEYVSET T0334 399 :TRDFIQAHFYFSPRTDTP 1pj5A 407 :SQQNFVEIYDVLHPLQPR Number of specific fragments extracted= 27 number of extra gaps= 0 total=362 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 1pj5A/T0334-1pj5A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0334 read from 1pj5A/T0334-1pj5A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1pj5A read from 1pj5A/T0334-1pj5A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1pj5A in template set Warning: unaligning (T0334)I5 because first residue in template chain is (1pj5A)T4 T0334 6 :DKILIVGGGTAGWMAASYLGK 1pj5A 5 :PRIVIIGAGIVGTNLADELVT T0334 30 :GTAD 1pj5A 26 :RGWN T0334 34 :ITLLQAPDIPTLGVGEATIP 1pj5A 31 :ITVLDQGPLNMPGGSTSHAP T0334 55 :LQTAFFDFL 1pj5A 61 :TMASFAKYT T0334 68 :DEWMREC 1pj5A 70 :VEKLLSL T0334 75 :NASYKVAIKFINWRTAGEG 1pj5A 80 :GVSCFNQVGGLEVATTETR T0334 114 :LKYHEQIPLSHYWFDRSYRGKTVEPFDYA 1pj5A 99 :LADLKRKLGYAAAWGIEGRLLSPAECQEL T0334 156 :PRRLDGSKVTN 1pj5A 128 :YPLLDGENILG T0334 168 :AWHF 1pj5A 139 :GLHV T0334 172 :DAHLVADFLRRFATEKLGVRHVEDRVEHVQRDANG 1pj5A 149 :SAARAVQLLIKRTESAGVTYRGSTTVTGIEQSGGR T0334 208 :IESVRTATG 1pj5A 184 :VTGVQTADG T0334 218 :VFDADLFVDCSGFRGLLINKAMEEPFL 1pj5A 193 :VIPADIVVSCAGFWGAKIGAMIGMAVP T0334 249 :HLLNDSAVATQVPHD 1pj5A 220 :LLPLAHQYVKTTPVP T0334 264 :DDANGVEPFTSAIAMKSG 1pj5A 240 :NDQPNGARLPILRHQDQD T0334 283 :TWKIPMLGRFGTGYVY 1pj5A 258 :LYYREHGDRYGIGSYA T0334 307 :EAVREFCEMWHLDP 1pj5A 310 :PAWEATKQLLPALA T0334 322 :TQPL 1pj5A 324 :DSEI T0334 329 :RFRVGRNRRAWVGNCVSIGTS 1pj5A 328 :EDGFNGIFSFTPDGGPLLGES T0334 350 :SCFVEPLESTGIYFVYA 1pj5A 357 :AEAVWVTHSAGVAKAMA T0334 370 :QLVK 1pj5A 374 :ELLT T0334 374 :HF 1pj5A 392 :RF T0334 445 :APASDDAQLYYGNFEEEFRNFWNNSNYYCVLA 1pj5A 394 :EDVQLTPEYVSETSQQNFVEIYDVLHPLQPRL Number of specific fragments extracted= 22 number of extra gaps= 0 total=384 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 1el5A/T0334-1el5A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1el5A expands to /projects/compbio/data/pdb/1el5.pdb.gz 1el5A:Skipped atom 1482, because occupancy 0.500 <= existing 0.500 in 1el5A Skipped atom 1484, because occupancy 0.500 <= existing 0.500 in 1el5A Skipped atom 1486, because occupancy 0.500 <= existing 0.500 in 1el5A Skipped atom 1488, because occupancy 0.500 <= existing 0.500 in 1el5A Skipped atom 1490, because occupancy 0.500 <= existing 0.500 in 1el5A Skipped atom 1492, because occupancy 0.500 <= existing 0.500 in 1el5A Skipped atom 2799, because occupancy 0.500 <= existing 0.500 in 1el5A Skipped atom 2801, because occupancy 0.500 <= existing 0.500 in 1el5A Skipped atom 2803, because occupancy 0.500 <= existing 0.500 in 1el5A Skipped atom 2805, because occupancy 0.500 <= existing 0.500 in 1el5A Skipped atom 2807, because occupancy 0.500 <= existing 0.500 in 1el5A Skipped atom 2809, because occupancy 0.500 <= existing 0.500 in 1el5A # T0334 read from 1el5A/T0334-1el5A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1el5A read from 1el5A/T0334-1el5A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1el5A to template set # found chain 1el5A in template set Warning: unaligning (T0334)K4 because first residue in template chain is (1el5A)S1 T0334 5 :ID 1el5A 2 :TH T0334 7 :KILIVGGGTAGWMAASYLGK 1el5A 5 :DVIVVGAGSMGMAAGYQLAK T0334 29 :QGT 1el5A 25 :QGV T0334 33 :DITLLQAPD 1el5A 28 :KTLLVDAFD T0334 42 :IPTL 1el5A 38 :PHTN T0334 46 :GVGEATIPNLQTAF 1el5A 49 :RIIRHAYGEGREYV T0334 64 :GI 1el5A 63 :PL T0334 69 :EWMRECNAS 1el5A 70 :ELWYELEKE T0334 103 :GPDHFYHSFGLL 1el5A 79 :THHKIFTKTGVL T0334 115 :KYHEQIPLSHYW 1el5A 94 :PKGESAFVAETM T0334 139 :FDYACYKEPVILDANRSPRRLDGSKVTNYAWHF 1el5A 106 :EAAKEHSLTVDLLEGDEINKRWPGITVPENYNA T0334 172 :DAHLVADFLRRFA 1el5A 148 :FSENCIRAYRELA T0334 186 :EKLGVRHVED 1el5A 161 :EARGAKVLTH T0334 196 :RVEHVQRDAN 1el5A 172 :RVEDFDISPD T0334 207 :NIE 1el5A 182 :SVK T0334 211 :VRTATG 1el5A 185 :IETANG T0334 218 :VFDADLFVDCSGFRGLLINKAMEEPFLDM 1el5A 191 :SYTADKLIVSMGAWNSKLLSKLNLDIPLQ T0334 252 :NDSAVATQVPHDDDANGV 1el5A 222 :RQVVGFFESDESKYSNDI T0334 271 :PFTS 1el5A 240 :DFPG T0334 275 :AIAMKSGWTWKIPM 1el5A 245 :MVEVPNGIYYGFPS T0334 289 :LGR 1el5A 260 :GGC T0334 292 :FGTGYVYSSRFATE 1el5A 264 :LKLGYHTFGQKIDP T0334 306 :DEAVREFCEMWHLDPETQPLNRIRFRVGRNR 1el5A 288 :PEDESNLRAFLEEYMPGANGELKRGAVCMYT T0334 338 :AWVGNCVSIG 1el5A 319 :KTLDEHFIID T0334 348 :TSSCFVEPLESTGIYFVYAALYQLVKHFPDKS 1el5A 334 :SNVVIAAGFSGHGFKFSSGVGEVLSQLALTGK T0334 482 :PDAPSPRLAH 1el5A 366 :TEHDISIFSI Number of specific fragments extracted= 26 number of extra gaps= 0 total=410 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 1el5A/T0334-1el5A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0334 read from 1el5A/T0334-1el5A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1el5A read from 1el5A/T0334-1el5A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1el5A in template set Warning: unaligning (T0334)G3 because first residue in template chain is (1el5A)S1 T0334 4 :KIDKILIVGGGTAGWMAASYLGK 1el5A 2 :THFDVIVVGAGSMGMAAGYQLAK T0334 30 :GTADITLLQAPDI 1el5A 25 :QGVKTLLVDAFDP T0334 43 :PTLGVGE 1el5A 53 :HAYGEGR T0334 57 :TAF 1el5A 60 :EYV T0334 79 :KVAIKFINWRTAGE 1el5A 63 :PLALRSQELWYELE T0334 96 :EARELDGGP 1el5A 77 :KETHHKIFT T0334 105 :DHFYHSFGLLKYHEQIPLSHYWFDRSYR 1el5A 87 :TGVLVFGPKGESAFVAETMEAAKEHSLT T0334 136 :VEPFDYACYKEPVI 1el5A 115 :VDLLEGDEINKRWP T0334 152 :ANRSPRRLDGSKVTNYAW 1el5A 129 :GITVPENYNAIFEPNSGV T0334 171 :FDAHLVADFLRRFA 1el5A 147 :LFSENCIRAYRELA T0334 186 :EKLGVRHVED 1el5A 161 :EARGAKVLTH T0334 196 :RVEHVQRDANG 1el5A 172 :RVEDFDISPDS T0334 209 :ESVRTATG 1el5A 183 :VKIETANG T0334 218 :VFDADLFVDCSGFRGLLINKAMEEPFLDMSDH 1el5A 191 :SYTADKLIVSMGAWNSKLLSKLNLDIPLQPYR T0334 253 :DSAVATQVPHDDDANGVEPFTSAIAMKSGWTWKIPMLGR 1el5A 223 :QVVGFFESDESKYSNDIDFPGFMVEVPNGIYYGFPSFGG T0334 292 :FGTGYVY 1el5A 264 :LKLGYHT T0334 299 :SSRFATE 1el5A 276 :DPDTINR T0334 306 :DEAVREFCEMW 1el5A 288 :PEDESNLRAFL T0334 317 :HLDPET 1el5A 300 :EYMPGA T0334 324 :PLNRIRFRVGRNR 1el5A 306 :NGELKRGAVCMYT T0334 338 :AWVGNCVSIG 1el5A 319 :KTLDEHFIID T0334 348 :TSSCFVEPLESTGIYFVYAALYQLVKHFPDKSL 1el5A 334 :SNVVIAAGFSGHGFKFSSGVGEVLSQLALTGKT Number of specific fragments extracted= 22 number of extra gaps= 0 total=432 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 1el5A/T0334-1el5A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0334 read from 1el5A/T0334-1el5A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1el5A read from 1el5A/T0334-1el5A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1el5A in template set Warning: unaligning (T0334)G3 because first residue in template chain is (1el5A)S1 T0334 4 :KIDKILIVGGGTAGWMAASYLGK 1el5A 2 :THFDVIVVGAGSMGMAAGYQLAK T0334 30 :GTADITLLQAPDIPT 1el5A 25 :QGVKTLLVDAFDPPH T0334 45 :LGVGEATIPNLQTAF 1el5A 55 :YGEGREYVPLALRSQ T0334 61 :DFL 1el5A 70 :ELW T0334 68 :DEWMRECNASYKVAIKFINWRTAGEGTS 1el5A 73 :YELEKETHHKIFTKTGVLVFGPKGESAF T0334 110 :SFGLLKYHEQIPLSHYWFD 1el5A 101 :VAETMEAAKEHSLTVDLLE T0334 146 :EPVILDANRSPRRLDGSKV 1el5A 120 :GDEINKRWPGITVPENYNA T0334 168 :AWHFDAHLVADFLRRFATEKLGVRHVEDRVEHVQRDANG 1el5A 144 :SGVLFSENCIRAYRELAEARGAKVLTHTRVEDFDISPDS T0334 209 :ESVRTAT 1el5A 183 :VKIETAN T0334 217 :RVFDADLFVDCSGFRGL 1el5A 190 :GSYTADKLIVSMGAWNS T0334 237 :KA 1el5A 207 :KL T0334 246 :MSDH 1el5A 209 :LSKL T0334 250 :LLNDSAVATQVPHDDD 1el5A 218 :LQPYRQVVGFFESDES T0334 266 :ANGVEPFTSAIAMKSGWTWKIPMLGRFGTGYVYSS 1el5A 236 :SNDIDFPGFMVEVPNGIYYGFPSFGGCGLKLGYHT T0334 307 :EAVREFCEMWHLDPETQPLNRIRFRVGRNRRAW 1el5A 289 :EDESNLRAFLEEYMPGANGELKRGAVCMYTKTL T0334 340 :VGNCVSIGTSSCFVEP 1el5A 333 :HSNVVIAAGFSGHGFK T0334 357 :ESTG 1el5A 349 :FSSG T0334 367 :ALYQLVKHFPDKS 1el5A 353 :VGEVLSQLALTGK T0334 410 :SPRTDTPFWRANKELR 1el5A 366 :TEHDISIFSINRPALK Number of specific fragments extracted= 19 number of extra gaps= 0 total=451 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 1zmdA/T0334-1zmdA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1zmdA expands to /projects/compbio/data/pdb/1zmd.pdb.gz 1zmdA:Skipped atom 295, because occupancy 0.460 <= existing 0.540 in 1zmdA Skipped atom 297, because occupancy 0.460 <= existing 0.540 in 1zmdA Skipped atom 299, because occupancy 0.460 <= existing 0.540 in 1zmdA Skipped atom 301, because occupancy 0.460 <= existing 0.540 in 1zmdA Skipped atom 303, because occupancy 0.460 <= existing 0.540 in 1zmdA Skipped atom 305, because occupancy 0.460 <= existing 0.540 in 1zmdA Skipped atom 334, because occupancy 0.460 <= existing 0.540 in 1zmdA Skipped atom 336, because occupancy 0.460 <= existing 0.540 in 1zmdA Skipped atom 338, because occupancy 0.460 <= existing 0.540 in 1zmdA Skipped atom 340, because occupancy 0.460 <= existing 0.540 in 1zmdA Skipped atom 342, because occupancy 0.460 <= existing 0.540 in 1zmdA Skipped atom 344, because occupancy 0.460 <= existing 0.540 in 1zmdA Skipped atom 759, because occupancy 0.500 <= existing 0.500 in 1zmdA Skipped atom 761, because occupancy 0.500 <= existing 0.500 in 1zmdA Skipped atom 763, because occupancy 0.500 <= existing 0.500 in 1zmdA Skipped atom 765, because occupancy 0.500 <= existing 0.500 in 1zmdA Skipped atom 767, because occupancy 0.500 <= existing 0.500 in 1zmdA Skipped atom 769, because occupancy 0.500 <= existing 0.500 in 1zmdA Skipped atom 771, because occupancy 0.500 <= existing 0.500 in 1zmdA Skipped atom 773, because occupancy 0.500 <= existing 0.500 in 1zmdA Skipped atom 775, because occupancy 0.500 <= existing 0.500 in 1zmdA Skipped atom 777, because occupancy 0.500 <= existing 0.500 in 1zmdA # T0334 read from 1zmdA/T0334-1zmdA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1zmdA read from 1zmdA/T0334-1zmdA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1zmdA to template set # found chain 1zmdA in template set Warning: unaligning (T0334)G3 because first residue in template chain is (1zmdA)Q3 T0334 4 :KID 1zmdA 4 :PID T0334 7 :KILIVGGGTAGWMAASYLGK 1zmdA 8 :DVTVIGSGPGGYVAAIKAAQ T0334 29 :QGT 1zmdA 28 :LGF T0334 33 :DITLLQAPD 1zmdA 31 :KTVCIEKNE T0334 42 :IPTLGVGEATIPN 1zmdA 41 :LGGTCLNVGCIPS T0334 57 :TAFFDFLGIPED 1zmdA 54 :KALLNNSHYYHM T0334 69 :EWMRECNAS 1zmdA 69 :TDFASRGIE T0334 96 :EARELDGGPDHFYHSFGLL 1zmdA 154 :PFPGITIDEDTIVSSTGAL T0334 115 :KYHEQIPLSHYWFDRSYRG 1zmdA 176 :KVPEKMVVIGAGVIGVELG T0334 139 :FDYACYKEPVILD 1zmdA 195 :SVWQRLGADVTAV T0334 152 :ANRSPRRLD 1zmdA 209 :FLGHVGGVG T0334 172 :DAHLVADFLRRFA 1zmdA 218 :IDMEISKNFQRIL T0334 186 :EKLGVRHVED 1zmdA 231 :QKQGFKFKLN T0334 196 :RVEHVQRDANGNIE 1zmdA 242 :KVTGATKKSDGKID T0334 211 :VRTA 1zmdA 256 :VSIE T0334 215 :TGR 1zmdA 262 :SGG T0334 218 :VFDADLFVDCSGFRG 1zmdA 268 :VITCDVLLVCIGRRP T0334 233 :LLINKAMEEPFLD 1zmdA 286 :NLGLEELGIELDP T0334 247 :SDHLLNDSAVATQVPHDDDANGV 1zmdA 299 :RGRIPVNTRFQTKIPNIYAIGDV T0334 270 :EPFTSAIAM 1zmdA 352 :NCVPSVIYT T0334 280 :SGWTWKIPM 1zmdA 361 :HPEVAWVGK T0334 308 :AVREFCEM 1zmdA 370 :SEEQLKEE T0334 322 :TQPLNRIRFRVGRNR 1zmdA 378 :GIEYKVGKFPFAANS T0334 337 :RAWVGNCVSIG 1zmdA 398 :ADTDGMVKILG T0334 348 :TSSCFVEPLESTGIYFVYAALYQ 1zmdA 416 :LGAHILGPGAGEMVNEAALALEY T0334 414 :DTP 1zmdA 439 :GAS T0334 417 :FWRANK 1zmdA 445 :IARVCH T0334 423 :ELRLADGMQEKIDMYR 1zmdA 452 :HPTLSEAFREANLAAS Number of specific fragments extracted= 28 number of extra gaps= 0 total=479 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 1zmdA/T0334-1zmdA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0334 read from 1zmdA/T0334-1zmdA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1zmdA read from 1zmdA/T0334-1zmdA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1zmdA in template set Warning: unaligning (T0334)S2 because first residue in template chain is (1zmdA)Q3 T0334 3 :GKIDKILIVGGGTAGWMAASYLGKA 1zmdA 4 :PIDADVTVIGSGPGGYVAAIKAAQL T0334 31 :TADITLLQAP 1zmdA 29 :GFKTVCIEKN T0334 41 :DIPTLGVGEATIPN 1zmdA 40 :TLGGTCLNVGCIPS T0334 57 :TAF 1zmdA 54 :KAL T0334 60 :FDFLGI 1zmdA 71 :FASRGI T0334 74 :CNASYKVAIKFINWRTAGE 1zmdA 85 :LDKMMEQKSTAVKALTGGI T0334 96 :EARELDGGP 1zmdA 104 :AHLFKQNKV T0334 105 :DHFYHSFGL 1zmdA 124 :KNQVTATKA T0334 130 :SYR 1zmdA 149 :GSE T0334 136 :VEPFDYACYKEPVILD 1zmdA 152 :VTPFPGITIDEDTIVS T0334 152 :ANRSPRRLDGSKVTNYAW 1zmdA 171 :ALSLKKVPEKMVVIGAGV T0334 170 :HFD 1zmdA 217 :GID T0334 174 :HLVADFLRRFA 1zmdA 220 :MEISKNFQRIL T0334 186 :EKLGVRHVED 1zmdA 231 :QKQGFKFKLN T0334 196 :RVEHVQRDANGNI 1zmdA 242 :KVTGATKKSDGKI T0334 209 :ESVRTATG 1zmdA 256 :VSIEAASG T0334 217 :RVFDADLFVDCSGFRGLL 1zmdA 267 :EVITCDVLLVCIGRRPFT T0334 236 :N 1zmdA 288 :G T0334 237 :KAMEEPFLD 1zmdA 290 :EELGIELDP T0334 247 :SDHLLNDS 1zmdA 299 :RGRIPVNT T0334 259 :QVPHDDD 1zmdA 307 :RFQTKIP T0334 266 :ANGVE 1zmdA 344 :GGAVH T0334 271 :PFTSAIAMKSGWTWKIPM 1zmdA 352 :NCVPSVIYTHPEVAWVGK T0334 309 :VREFCEM 1zmdA 371 :EEQLKEE T0334 322 :TQPLNRIRFRVGRNRRA 1zmdA 378 :GIEYKVGKFPFAANSRA T0334 339 :WVGNCVSIG 1zmdA 400 :TDGMVKILG T0334 348 :TSSCFVEPLESTGIYFVYAALYQ 1zmdA 416 :LGAHILGPGAGEMVNEAALALEY T0334 371 :LVKHFPDKSLNPVL 1zmdA 445 :IARVCHAHPTLSEA T0334 399 :TRDFIQAHF 1zmdA 459 :FREANLAAS Number of specific fragments extracted= 29 number of extra gaps= 0 total=508 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 1zmdA/T0334-1zmdA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0334 read from 1zmdA/T0334-1zmdA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1zmdA read from 1zmdA/T0334-1zmdA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1zmdA in template set T0334 1 :MSGKIDKILIVGGGTAGWMAASYLGK 1zmdA 174 :LKKVPEKMVVIGAGVIGVELGSVWQR T0334 30 :GTADITLLQAPDI 1zmdA 200 :LGADVTAVEFLGH T0334 47 :VGE 1zmdA 213 :VGG T0334 63 :LGIPE 1zmdA 216 :VGIDM T0334 175 :LVADFLRRFATEKLGVRHVEDRVEHVQRDANGNIE 1zmdA 221 :EISKNFQRILQKQGFKFKLNTKVTGATKKSDGKID T0334 210 :SVRTATGR 1zmdA 257 :SIEAASGG T0334 218 :VFDADLFVDCSGFRG 1zmdA 268 :VITCDVLLVCIGRRP T0334 237 :KAMEEPFLDMS 1zmdA 290 :EELGIELDPRG T0334 285 :KIPMLGR 1zmdA 301 :RIPVNTR T0334 337 :RAWVGNCVSIGTSSCFVE 1zmdA 309 :QTKIPNIYAIGDVVAGPM T0334 357 :E 1zmdA 327 :L T0334 361 :IYFVYAALYQLVKHFPDKSLN 1zmdA 328 :AHKAEDEGIICVEGMAGGAVH Number of specific fragments extracted= 12 number of extra gaps= 0 total=520 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 1fohA/T0334-1fohA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1fohA expands to /projects/compbio/data/pdb/1foh.pdb.gz 1fohA:# T0334 read from 1fohA/T0334-1fohA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1fohA read from 1fohA/T0334-1fohA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1fohA to template set # found chain 1fohA in template set Warning: unaligning (T0334)S300 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1fohA)F307 T0334 3 :GKID 1fohA 2 :KYSE T0334 7 :KILIVGGGTAGWMAASYLGK 1fohA 9 :DVLIVGAGPAGLMAARVLSE T0334 28 :L 1fohA 29 :Y T0334 29 :QGT 1fohA 34 :PDL T0334 33 :DITLLQAPD 1fohA 37 :KVRIIDKRS T0334 42 :IPTLGVGEATIPNLQTAF 1fohA 47 :KVYNGQADGLQCRTLESL T0334 61 :DFLGIPED 1fohA 65 :KNLGLADK T0334 103 :GPDHFYHSFGLL 1fohA 79 :DMSTIALYNPDE T0334 115 :KYHE 1fohA 92 :GHIR T0334 152 :ANRSPRRLDGSKVTNYAWHFDAHLVADFLRRFATEKLG 1fohA 96 :RTDRIPDTLPGISRYHQVVLHQGRIERHILDSIAEISD T0334 190 :VRHVED 1fohA 136 :IKVERP T0334 196 :RVEHVQR 1fohA 143 :IPEKMEI T0334 203 :DANGNIESVRTA 1fohA 156 :DPEAYPVTMTLR T0334 216 :GR 1fohA 211 :GE T0334 218 :VFDADLFVDCSGFRGLLI 1fohA 215 :TVHCKYVIGCDGGHSWVR T0334 237 :KAMEEPFLDM 1fohA 233 :RTLGFEMIGE T0334 247 :SDHLLND 1fohA 245 :DYIWGVL T0334 254 :SAVATQVPHD 1fohA 253 :AVPASNFPDI T0334 270 :EPFTSAIAMKSGWTWKIPMLGRFGTGYVYS 1fohA 263 :RSRCAIHSAESGSIMIIPRENNLVRFYVQL T0334 306 :DEAVREFCEMWHLDP 1fohA 310 :EVVIANAKKIFHPYT T0334 321 :ETQPLNRIRFRVGRNRRAWVG 1fohA 329 :QLDWFTAYHIGQRVTEKFSKD T0334 342 :NCVSIGTSSCFVEPLESTGIYFVYAALYQLVKHFP 1fohA 351 :RVFIAGDACHTHSPKAGQGMNTSMMDTYNLGWKLG T0334 377 :DKSLNPVLTARFNREIETMFDDTRDFIQAHFYFS 1fohA 389 :TGRAKRDILKTYEEERHAFAQALIDFDHQFSRLF T0334 411 :PRT 1fohA 424 :GRP T0334 427 :ADGMQEKIDMYRAGMAINAP 1fohA 438 :MDVFKEAFVKGNEFASGTAI T0334 481 :VPD 1fohA 458 :NYD Number of specific fragments extracted= 26 number of extra gaps= 0 total=546 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 1fohA/T0334-1fohA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0334 read from 1fohA/T0334-1fohA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1fohA read from 1fohA/T0334-1fohA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1fohA in template set Warning: unaligning (T0334)S300 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1fohA)F307 T0334 5 :IDKILIVGGGTAGWMAASYLGKAL 1fohA 7 :YCDVLIVGAGPAGLMAARVLSEYV T0334 29 :QGTADITLLQAP 1fohA 33 :KPDLKVRIIDKR T0334 41 :DIPTLGVGEATIPNLQTAF 1fohA 46 :TKVYNGQADGLQCRTLESL T0334 61 :DFLGI 1fohA 65 :KNLGL T0334 123 :SHYWFDRSYR 1fohA 70 :ADKILSEAND T0334 136 :VEPF 1fohA 80 :MSTI T0334 141 :YACYKEPVILD 1fohA 88 :PDENGHIRRTD T0334 154 :RSPRRLDGSKVTNYAW 1fohA 99 :RIPDTLPGISRYHQVV T0334 171 :FDAHLVADFLRRFATEKLG 1fohA 115 :LHQGRIERHILDSIAEISD T0334 190 :VRHVED 1fohA 136 :IKVERP T0334 196 :RVEHVQR 1fohA 143 :IPEKMEI T0334 203 :DANGNIESVRTA 1fohA 156 :DPEAYPVTMTLR T0334 216 :G 1fohA 211 :G T0334 217 :RVFDADLFVDCSGFRGLL 1fohA 214 :ETVHCKYVIGCDGGHSWV T0334 236 :NKAMEEPFL 1fohA 232 :RRTLGFEMI T0334 245 :DMSDH 1fohA 243 :QTDYI T0334 253 :DSAVATQVP 1fohA 248 :WGVLDAVPA T0334 264 :DDANGVEPFTSAIAMKSGWTWKIPMLGRFGTGYVYS 1fohA 257 :SNFPDIRSRCAIHSAESGSIMIIPRENNLVRFYVQL T0334 306 :DEAVREFCEMWHL 1fohA 310 :EVVIANAKKIFHP T0334 322 :TQ 1fohA 323 :YT T0334 324 :PLNRIRFRVGRNRRAWVG 1fohA 332 :WFTAYHIGQRVTEKFSKD T0334 342 :NCVSIGTSSCFVEPLESTGIYFVYAALYQLVKHF 1fohA 351 :RVFIAGDACHTHSPKAGQGMNTSMMDTYNLGWKL T0334 378 :KSLNPVLTARFNREIETMFDDTRDFIQAHFYFSPRT 1fohA 390 :GRAKRDILKTYEEERHAFAQALIDFDHQFSRLFSGR T0334 480 :LVPDAPSPRLAHMPQATESVDEVFGA 1fohA 426 :PAKDVADEMGVSMDVFKEAFVKGNEF Number of specific fragments extracted= 24 number of extra gaps= 0 total=570 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 1fohA/T0334-1fohA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0334 read from 1fohA/T0334-1fohA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1fohA read from 1fohA/T0334-1fohA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1fohA in template set Warning: unaligning (T0334)S300 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1fohA)F307 T0334 4 :KIDKILIVGGGTAGWMAASYLGKAL 1fohA 6 :SYCDVLIVGAGPAGLMAARVLSEYV T0334 29 :QGTADITLLQAPDIPTL 1fohA 33 :KPDLKVRIIDKRSTKVY T0334 46 :GVGEATIPNLQTAF 1fohA 51 :GQADGLQCRTLESL T0334 61 :DFLGI 1fohA 65 :KNLGL T0334 68 :DEWMRECNASYKVAIKFINWRTAGEGTSEARELDG 1fohA 70 :ADKILSEANDMSTIALYNPDENGHIRRTDRIPDTL T0334 161 :GSKVTNYAWHFDAHLVADFLRRFATEKL 1fohA 105 :PGISRYHQVVLHQGRIERHILDSIAEIS T0334 189 :GVRHVEDRVEHVQRDANGN 1fohA 136 :IKVERPLIPEKMEIDSSKA T0334 217 :R 1fohA 208 :K T0334 218 :VFDADLFVDCSGFRGLLIN 1fohA 215 :TVHCKYVIGCDGGHSWVRR T0334 238 :AMEEPFLDMSDHLLNDSAVATQV 1fohA 234 :TLGFEMIGEQTDYIWGVLDAVPA T0334 264 :DDANGVEPFTSAIAMKSGWTWKIPMLGRFGTGYVYS 1fohA 257 :SNFPDIRSRCAIHSAESGSIMIIPRENNLVRFYVQL T0334 307 :EAVREFCEMWHLDP 1fohA 311 :VVIANAKKIFHPYT T0334 322 :T 1fohA 326 :D T0334 324 :PLNRIRFRVGRNRR 1fohA 332 :WFTAYHIGQRVTEK T0334 338 :AWVGNCVSIGTSSCFVEPLESTGIYFVYAALYQLVKHFP 1fohA 347 :SKDERVFIAGDACHTHSPKAGQGMNTSMMDTYNLGWKLG T0334 377 :DKSLNPVLTARFNREIETMFDDTRDFIQAHFYF 1fohA 393 :KRDILKTYEEERHAFAQALIDFDHQFSRLFSGR T0334 443 :INAPASDDA 1fohA 426 :PAKDVADEM T0334 452 :QLYYGNFEEEFRNFWNNSNYYCV 1fohA 439 :DVFKEAFVKGNEFASGTAINYDE Number of specific fragments extracted= 18 number of extra gaps= 0 total=588 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 1zk7A/T0334-1zk7A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1zk7A expands to /projects/compbio/data/pdb/1zk7.pdb.gz 1zk7A:# T0334 read from 1zk7A/T0334-1zk7A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1zk7A read from 1zk7A/T0334-1zk7A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1zk7A to template set # found chain 1zk7A in template set Warning: unaligning (T0334)G3 because first residue in template chain is (1zk7A)M1 T0334 4 :KID 1zk7A 2 :EPP T0334 7 :KILIVGGGTAGWMAASYLGK 1zk7A 6 :QVAVIGSGGAAMAAALKAVE T0334 29 :QGT 1zk7A 26 :QGA T0334 33 :DITLLQAPDIPTL 1zk7A 29 :QVTLIERGTIGGT T0334 46 :GVGEATIPN 1zk7A 66 :SPFDGGIAA T0334 61 :DFLGIPEDEWMRECNASYKVAIKFINWRTAGEGTS 1zk7A 75 :TVPTIDRSKLLAQQQARVDELRHAKYEGILGGNPA T0334 96 :EARELDGGPDHFYHSFGLL 1zk7A 152 :VPPIPGLKESPYWTSTEAL T0334 115 :KYHEQIPLSHYWFDRSYRG 1zk7A 174 :TIPERLAVIGSSVVALELA T0334 139 :FDYACYKEPVILDANRSPRRL 1zk7A 193 :QAFARLGSKVTVLARNTLFFR T0334 172 :DAHLVADFLRRFA 1zk7A 214 :EDPAIGEAVTAAF T0334 186 :EKLGVRHVED 1zk7A 227 :RAEGIEVLEH T0334 196 :RVEHVQRDANG 1zk7A 238 :QASQVAHMDGE T0334 209 :ESVRTATG 1zk7A 249 :FVLTTTHG T0334 218 :VFDADLFVDCSGFRG 1zk7A 257 :ELRADKLLVATGRTP T0334 233 :LLINKAMEEPFLD 1zk7A 275 :SLALDAAGVTVNA T0334 247 :SDHLLNDSAVATQVPHDDDANGV 1zk7A 288 :QGAIVIDQGMRTSNPNIYAAGDC T0334 270 :EPFTS 1zk7A 366 :DGIET T0334 275 :AIAMK 1zk7A 372 :SRTLT T0334 280 :SGWTWKIPMLGRFGTGYVY 1zk7A 391 :GFIKLVIEEGSHRLIGVQA T0334 338 :AWVG 1zk7A 410 :VAPE T0334 364 :VYAALYQLVKHFPDKSLNPVLT 1zk7A 414 :AGELIQTAALAIRNRMTVQELA T0334 463 :RNFWNNS 1zk7A 436 :DQLFPYL T0334 470 :NYYCVLAGLG 1zk7A 447 :GLKLAAQTFN Number of specific fragments extracted= 23 number of extra gaps= 0 total=611 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 1zk7A/T0334-1zk7A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0334 read from 1zk7A/T0334-1zk7A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1zk7A read from 1zk7A/T0334-1zk7A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1zk7A in template set T0334 1 :MSG 1zk7A 1 :MEP T0334 5 :IDKILIVGGGTAGWMAASYLGK 1zk7A 4 :PVQVAVIGSGGAAMAAALKAVE T0334 30 :GTADITLLQAPDIPTLGVGEATIPN 1zk7A 26 :QGAQVTLIERGTIGGTCVNVGCVPS T0334 57 :TAF 1zk7A 51 :KIM T0334 78 :YKVAIKFINWRTAGE 1zk7A 54 :IRAAHIAHLRRESPF T0334 101 :DGGPDHFYHSFGLLKY 1zk7A 69 :DGGIAATVPTIDRSKL T0334 117 :HEQIPLSHYWFDRS 1zk7A 86 :AQQQARVDELRHAK T0334 155 :SPRRLDGS 1zk7A 100 :YEGILGGN T0334 166 :NYAW 1zk7A 108 :PAIT T0334 171 :FDAHLVADFLRRFA 1zk7A 213 :REDPAIGEAVTAAF T0334 186 :EKLGVRHVED 1zk7A 227 :RAEGIEVLEH T0334 196 :RVEHVQRDANG 1zk7A 238 :QASQVAHMDGE T0334 209 :ESVRTATG 1zk7A 249 :FVLTTTHG T0334 218 :VFDADLFVDCSGFRGLL 1zk7A 257 :ELRADKLLVATGRTPNT T0334 236 :NKA 1zk7A 274 :RSL T0334 239 :MEEPFLDMSDHLLNDSAVATQVPH 1zk7A 336 :AALDLTAMPAVVFTDPQVATVGYS T0334 264 :DD 1zk7A 360 :EA T0334 266 :ANGVEPFTSAIAMKS 1zk7A 365 :HDGIETDSRTLTLDN T0334 281 :GWT 1zk7A 391 :GFI T0334 284 :WKIPMLGR 1zk7A 395 :LVIEEGSH T0334 292 :FGTGYVYSSRF 1zk7A 404 :LIGVQAVAPEA T0334 306 :DEAVREFCEMW 1zk7A 415 :GELIQTAALAI T0334 317 :HLDPET 1zk7A 437 :QLFPYL Number of specific fragments extracted= 23 number of extra gaps= 0 total=634 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 1zk7A/T0334-1zk7A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0334 read from 1zk7A/T0334-1zk7A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1zk7A read from 1zk7A/T0334-1zk7A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1zk7A in template set Warning: unaligning (T0334)S2 because first residue in template chain is (1zk7A)M1 T0334 3 :GKIDKILIVGGGTAGWMAASYLGK 1zk7A 2 :EPPVQVAVIGSGGAAMAAALKAVE T0334 30 :GTADITLLQAPDIP 1zk7A 26 :QGAQVTLIERGTIG T0334 49 :E 1zk7A 40 :G T0334 51 :TIPNLQTAFF 1zk7A 53 :MIRAAHIAHL T0334 64 :GIPEDEWMREC 1zk7A 78 :TIDRSKLLAQQ T0334 75 :NASYKVAIKFINWRTAGEGTSEAREL 1zk7A 116 :EARFKDDQSLTVRLNEGGERVVMFDR T0334 101 :DGGPDHF 1zk7A 151 :AVPPIPG T0334 117 :HEQIPLSHYWFDRSYRGKT 1zk7A 158 :LKESPYWTSTEALASDTIP T0334 137 :EPFDYACYKEPVILDANR 1zk7A 184 :SSVVALELAQAFARLGSK T0334 155 :S 1zk7A 206 :A T0334 158 :RLDGSKV 1zk7A 207 :RNTLFFR T0334 172 :DAHLVADFLRRFATEKLGVRHVEDRVEHVQRDANG 1zk7A 214 :EDPAIGEAVTAAFRAEGIEVLEHTQASQVAHMDGE T0334 209 :ESVRTAT 1zk7A 249 :FVLTTTH T0334 217 :RVFDADLFVDCSGF 1zk7A 256 :GELRADKLLVATGR T0334 240 :EEPFLDMSDH 1zk7A 272 :NTRSLALDAA T0334 321 :ETQPLNRIRFRVGR 1zk7A 284 :TVNAQGAIVIDQGM T0334 337 :RAWVGNCVSIGTSSCFVEP 1zk7A 298 :RTSNPNIYAAGDCTDQPQF T0334 361 :IYFVYAALYQLVKHFPDKSL 1zk7A 317 :VYVAAAAGTRAAINMTGGDA Number of specific fragments extracted= 18 number of extra gaps= 0 total=652 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 1c0pA/T0334-1c0pA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0334 read from 1c0pA/T0334-1c0pA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1c0pA read from 1c0pA/T0334-1c0pA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1c0pA in training set Warning: unaligning (T0334)D6 because of BadResidue code BAD_PEPTIDE in next template residue (1c0pA)K1005 Warning: unaligning (T0334)D61 because of BadResidue code BAD_PEPTIDE in next template residue (1c0pA)A1053 Warning: unaligning (T0334)F62 because of BadResidue code BAD_PEPTIDE at template residue (1c0pA)A1053 Warning: unaligning (T0334)E99 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1c0pA)L1104 Warning: unaligning (T0334)L100 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1c0pA)L1104 Warning: unaligning (T0334)V197 because of BadResidue code BAD_PEPTIDE in next template residue (1c0pA)T1163 Warning: unaligning (T0334)E198 because of BadResidue code BAD_PEPTIDE at template residue (1c0pA)T1163 Warning: unaligning (T0334)A204 because of BadResidue code BAD_PEPTIDE in next template residue (1c0pA)D1170 Warning: unaligning (T0334)N205 because of BadResidue code BAD_PEPTIDE at template residue (1c0pA)D1170 Warning: unaligning (T0334)L289 because of BadResidue code BAD_PEPTIDE in next template residue (1c0pA)G1230 Warning: unaligning (T0334)G290 because of BadResidue code BAD_PEPTIDE at template residue (1c0pA)G1230 Warning: unaligning (T0334)G295 because of BadResidue code BAD_PEPTIDE in next template residue (1c0pA)G1236 Warning: unaligning (T0334)Y296 because of BadResidue code BAD_PEPTIDE at template residue (1c0pA)G1236 Warning: unaligning (T0334)E321 because of BadResidue code BAD_PEPTIDE at template residue (1c0pA)T1271 T0334 2 :SGKI 1c0pA 1000 :MMHS T0334 7 :KILIVGGGTAGWMAASYLGK 1c0pA 1006 :RVVVLGSGVIGLSSALILAR T0334 29 :QGT 1c0pA 1026 :KGY T0334 33 :DITLLQAP 1c0pA 1029 :SVHILARD T0334 46 :GVGEATIPNLQTAFF 1c0pA 1037 :LPEDVSSQTFASPWA T0334 63 :LGIPED 1c0pA 1054 :NWTPFM T0334 69 :EWMRECNASYKVAIK 1c0pA 1065 :PRQAKWEESTFKKWV T0334 96 :EAR 1c0pA 1100 :EDG T0334 101 :DG 1c0pA 1105 :GH T0334 109 :HSFGLLKYHE 1c0pA 1107 :WYKDITPNYR T0334 152 :ANRSPRRLDGSKVTNYAWHF 1c0pA 1117 :PLPSSECPPGAIGVTYDTLS T0334 172 :DAHLVADFLRRFA 1c0pA 1138 :HAPKYCQYLAREL T0334 186 :EKLGVRHVEDR 1c0pA 1151 :QKLGATFERRT T0334 199 :HVQRD 1c0pA 1164 :SLEQA T0334 206 :G 1c0pA 1171 :G T0334 221 :ADLFVDCSGFRGLLI 1c0pA 1172 :ADLVVNATGLGAKSI T0334 239 :MEEPF 1c0pA 1187 :AGIDD T0334 247 :SDHLLND 1c0pA 1192 :QAAEPIR T0334 254 :SAVATQVP 1c0pA 1200 :QTVLVKSP T0334 270 :EPFTSAIAMKSGWTWKIPM 1c0pA 1209 :KRCTMDSSDPASPAYIIPR T0334 291 :RFGT 1c0pA 1231 :EVIC T0334 297 :VYSSRFATE 1c0pA 1237 :TYGVGDWDL T0334 306 :DEAVREFCEM 1c0pA 1249 :PETVQRILKH T0334 316 :WHLDP 1c0pA 1260 :LRLDP T0334 322 :TQPLNRIRFRVGRNR 1c0pA 1272 :IEGIEVLRHNVGLRP T0334 337 :RAWVG 1c0pA 1298 :RIVLP T0334 342 :NCVS 1c0pA 1324 :EVTL T0334 351 :CFVEPLESTGIYFVYAALYQLVKHF 1c0pA 1328 :VHAYGFSSAGYQQSWGAAEDVAQLV T0334 389 :NREIET 1c0pA 1353 :DEAFQR Number of specific fragments extracted= 29 number of extra gaps= 8 total=681 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 1c0pA/T0334-1c0pA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0334 read from 1c0pA/T0334-1c0pA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1c0pA read from 1c0pA/T0334-1c0pA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1c0pA in training set Warning: unaligning (T0334)I5 because of BadResidue code BAD_PEPTIDE in next template residue (1c0pA)K1005 Warning: unaligning (T0334)D6 because of BadResidue code BAD_PEPTIDE at template residue (1c0pA)K1005 Warning: unaligning (T0334)G48 because of BadResidue code BAD_PEPTIDE in next template residue (1c0pA)A1053 Warning: unaligning (T0334)E49 because of BadResidue code BAD_PEPTIDE at template residue (1c0pA)A1053 Warning: unaligning (T0334)Y116 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1c0pA)L1104 Warning: unaligning (T0334)H117 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1c0pA)L1104 Warning: unaligning (T0334)V197 because of BadResidue code BAD_PEPTIDE in next template residue (1c0pA)T1163 Warning: unaligning (T0334)E198 because of BadResidue code BAD_PEPTIDE at template residue (1c0pA)T1163 Warning: unaligning (T0334)N205 because of BadResidue code BAD_PEPTIDE at template residue (1c0pA)D1170 Warning: unaligning (T0334)G290 because of BadResidue code BAD_PEPTIDE in next template residue (1c0pA)G1230 Warning: unaligning (T0334)R291 because of BadResidue code BAD_PEPTIDE at template residue (1c0pA)G1230 Warning: unaligning (T0334)G295 because of BadResidue code BAD_PEPTIDE in next template residue (1c0pA)G1236 Warning: unaligning (T0334)Y296 because of BadResidue code BAD_PEPTIDE at template residue (1c0pA)G1236 Warning: unaligning (T0334)L318 because of BadResidue code BAD_PEPTIDE in next template residue (1c0pA)T1271 Warning: unaligning (T0334)D319 because of BadResidue code BAD_PEPTIDE at template residue (1c0pA)T1271 T0334 1 :MSGK 1c0pA 1000 :MMHS T0334 7 :KILIVGGGTAGWMAASYLGK 1c0pA 1006 :RVVVLGSGVIGLSSALILAR T0334 30 :GTADITLLQAPDI 1c0pA 1026 :KGYSVHILARDLP T0334 43 :P 1c0pA 1049 :P T0334 46 :GV 1c0pA 1050 :WA T0334 50 :ATIPN 1c0pA 1054 :NWTPF T0334 60 :FDFLGI 1c0pA 1059 :MTLTDG T0334 75 :NASYKVAIKFINWRTAGE 1c0pA 1065 :PRQAKWEESTFKKWVELV T0334 101 :DGGP 1c0pA 1083 :PTGH T0334 105 :DHFYHSFGLLK 1c0pA 1092 :GTRRFAQNEDG T0334 141 :YACYKEPVILD 1c0pA 1105 :GHWYKDITPNY T0334 152 :ANRSPRRLDGSKVTN 1c0pA 1117 :PLPSSECPPGAIGVT T0334 170 :HFDAHLVADFLRRFA 1c0pA 1136 :SVHAPKYCQYLAREL T0334 186 :EKLGVRHVEDR 1c0pA 1151 :QKLGATFERRT T0334 199 :HVQRD 1c0pA 1164 :SLEQA T0334 206 :G 1c0pA 1171 :G T0334 221 :ADLFVDCSG 1c0pA 1172 :ADLVVNATG T0334 236 :NKAMEEPFLDMSDHLLN 1c0pA 1181 :LGAKSIAGIDDQAAEPI T0334 253 :DSAVATQVPH 1c0pA 1199 :GQTVLVKSPC T0334 270 :EPFTSAIAMKSGWTWKIPML 1c0pA 1209 :KRCTMDSSDPASPAYIIPRP T0334 292 :FGT 1c0pA 1232 :VIC T0334 297 :VYSSRFATE 1c0pA 1237 :TYGVGDWDL T0334 306 :DEAVREFCEMW 1c0pA 1249 :PETVQRILKHC T0334 317 :H 1c0pA 1269 :D T0334 320 :PETQ 1c0pA 1272 :IEGI T0334 324 :PLNRIRFRVG 1c0pA 1295 :EAERIVLPLD T0334 343 :CVSIG 1c0pA 1325 :VTLVH T0334 353 :VEPLESTGIYFVYAALYQLVKHFP 1c0pA 1330 :AYGFSSAGYQQSWGAAEDVAQLVD T0334 386 :ARFNR 1c0pA 1354 :EAFQR Number of specific fragments extracted= 29 number of extra gaps= 8 total=710 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 1c0pA/T0334-1c0pA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0334 read from 1c0pA/T0334-1c0pA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1c0pA read from 1c0pA/T0334-1c0pA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1c0pA in training set Warning: unaligning (T0334)I5 because of BadResidue code BAD_PEPTIDE in next template residue (1c0pA)K1005 Warning: unaligning (T0334)D6 because of BadResidue code BAD_PEPTIDE at template residue (1c0pA)K1005 Warning: unaligning (T0334)G48 because of BadResidue code BAD_PEPTIDE in next template residue (1c0pA)A1053 Warning: unaligning (T0334)E49 because of BadResidue code BAD_PEPTIDE at template residue (1c0pA)A1053 Warning: unaligning (T0334)T94 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1c0pA)L1104 Warning: unaligning (T0334)S95 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1c0pA)L1104 Warning: unaligning (T0334)V197 because of BadResidue code BAD_PEPTIDE in next template residue (1c0pA)T1163 Warning: unaligning (T0334)E198 because of BadResidue code BAD_PEPTIDE at template residue (1c0pA)T1163 Warning: unaligning (T0334)A204 because of BadResidue code BAD_PEPTIDE in next template residue (1c0pA)D1170 Warning: unaligning (T0334)N205 because of BadResidue code BAD_PEPTIDE at template residue (1c0pA)D1170 Warning: unaligning (T0334)G290 because of BadResidue code BAD_PEPTIDE in next template residue (1c0pA)G1230 Warning: unaligning (T0334)R291 because of BadResidue code BAD_PEPTIDE at template residue (1c0pA)G1230 Warning: unaligning (T0334)Y298 because of BadResidue code BAD_PEPTIDE in next template residue (1c0pA)G1236 Warning: unaligning (T0334)H317 because of BadResidue code BAD_PEPTIDE in next template residue (1c0pA)T1271 Warning: unaligning (T0334)L318 because of BadResidue code BAD_PEPTIDE at template residue (1c0pA)T1271 Warning: unaligning (T0334)N342 because of BadResidue code BAD_PEPTIDE in next template residue (1c0pA)S1316 T0334 1 :MSGK 1c0pA 1000 :MMHS T0334 7 :KILIVGGGTAGWMAASYLGK 1c0pA 1006 :RVVVLGSGVIGLSSALILAR T0334 30 :GTADITLLQAP 1c0pA 1026 :KGYSVHILARD T0334 41 :DIPTLGV 1c0pA 1045 :TFASPWA T0334 50 :ATI 1c0pA 1054 :NWT T0334 53 :PNLQTAFFDF 1c0pA 1065 :PRQAKWEEST T0334 68 :DEWMREC 1c0pA 1075 :FKKWVEL T0334 75 :NASYKVAIKF 1c0pA 1087 :AMWLKGTRRF T0334 88 :RTAGEG 1c0pA 1097 :AQNEDG T0334 96 :EARELDGGP 1c0pA 1105 :GHWYKDITP T0334 149 :ILDANRSPRRLDGSKVTNY 1c0pA 1114 :NYRPLPSSECPPGAIGVTY T0334 168 :AWHFDAHLVADFLRRFATEKLGV 1c0pA 1134 :TLSVHAPKYCQYLARELQKLGAT T0334 192 :HVEDR 1c0pA 1157 :FERRT T0334 199 :HVQRD 1c0pA 1164 :SLEQA T0334 206 :G 1c0pA 1171 :G T0334 221 :ADLFVDCSGFRG 1c0pA 1172 :ADLVVNATGLGA T0334 239 :MEEPFLDMSDHLLNDSAVATQV 1c0pA 1184 :KSIAGIDDQAAEPIRGQTVLVK T0334 267 :NGVEPFTSAIAMKSGWTWKIPML 1c0pA 1206 :SPCKRCTMDSSDPASPAYIIPRP T0334 295 :GYV 1c0pA 1232 :VIC T0334 299 :SSRFATEDEAVREFCEMW 1c0pA 1242 :DWDLSVNPETVQRILKHC T0334 319 :DPET 1c0pA 1272 :IEGI T0334 324 :PLNRIRFRVGRNRRAWVG 1c0pA 1297 :ERIVLPLDRTKSPLSLGR T0334 343 :CVSIGTSSCFV 1c0pA 1324 :EVTLVHAYGFS T0334 358 :ST 1c0pA 1335 :SA T0334 364 :VYAALYQLVKH 1c0pA 1337 :GYQQSWGAAED T0334 388 :FNREIETMFDD 1c0pA 1348 :VAQLVDEAFQR Number of specific fragments extracted= 26 number of extra gaps= 9 total=736 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 1ng4A/T0334-1ng4A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1ng4A expands to /projects/compbio/data/pdb/1ng4.pdb.gz 1ng4A:# T0334 read from 1ng4A/T0334-1ng4A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ng4A read from 1ng4A/T0334-1ng4A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1ng4A to template set # found chain 1ng4A in template set Warning: unaligning (T0334)G3 because first residue in template chain is (1ng4A)M1 Warning: unaligning (T0334)G295 because of BadResidue code BAD_PEPTIDE in next template residue (1ng4A)A259 Warning: unaligning (T0334)Y296 because of BadResidue code BAD_PEPTIDE at template residue (1ng4A)A259 Warning: unaligning (T0334)V297 because of BadResidue code BAD_PEPTIDE at template residue (1ng4A)T260 T0334 4 :KID 1ng4A 2 :KRH T0334 7 :KILIVGGGTAGWMAASYLGK 1ng4A 6 :EAVVIGGGIIGSAIAYYLAK T0334 29 :QGT 1ng4A 26 :ENK T0334 33 :DITLLQAP 1ng4A 29 :NTALFESG T0334 46 :GVGEATIPNLQTAFFDFLGIPEDEWMRECNAS 1ng4A 37 :TMGGRTTSAAAGMLGAHAECEERDAFFDFAMH T0334 115 :KYHE 1ng4A 75 :GLGE T0334 139 :FDYACYKEPVILDANRSPRRLDGSKVTNYAWHF 1ng4A 79 :ELYALSGVDIRQHNGGMFKLAFSEEDVLQLRQM T0334 172 :DAHLVADFLRRFA 1ng4A 149 :EPYFVCKAYVKAA T0334 186 :EKLGVRHVED 1ng4A 162 :KMLGAEIFEH T0334 196 :RVEHVQRDANG 1ng4A 173 :PVLHVERDGEA T0334 209 :ESVRTATG 1ng4A 184 :LFIKTPSG T0334 218 :VFDADLFVDCSGFRGLLINKAMEEP 1ng4A 192 :DVWANHVVVASGVWSGMFFKQLGLN T0334 247 :SDHLLNDSAVATQVPHDD 1ng4A 217 :NAFLPVKGECLSVWNDDI T0334 271 :PFTSAIAMKS 1ng4A 235 :PLTKTLYHDH T0334 283 :TWKIPM 1ng4A 245 :CYIVPR T0334 289 :LGRFGT 1ng4A 252 :SGRLVV T0334 298 :YSSRFATE 1ng4A 261 :MKPGDWSE T0334 306 :DEAVREFCEM 1ng4A 272 :LGGLESVMKK T0334 316 :WHLDPETQPLNRIRFRVGRNR 1ng4A 283 :KTMLPPIQNMKVDRFWAGLRP T0334 338 :AWVGNCVSIG 1ng4A 304 :GTKDGKPYIG T0334 348 :TSSCFVEPLESTGIYFVYAALYQLVKHFPDKSLNPVLTARF 1ng4A 319 :SRILFAAGHFRNGILLAPATGALISDLIMNKEVNQDWLHAF Number of specific fragments extracted= 21 number of extra gaps= 1 total=757 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 1ng4A/T0334-1ng4A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0334 read from 1ng4A/T0334-1ng4A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ng4A read from 1ng4A/T0334-1ng4A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1ng4A in template set Warning: unaligning (T0334)G295 because of BadResidue code BAD_PEPTIDE in next template residue (1ng4A)A259 Warning: unaligning (T0334)Y296 because of BadResidue code BAD_PEPTIDE at template residue (1ng4A)A259 Warning: unaligning (T0334)V297 because of BadResidue code BAD_PEPTIDE at template residue (1ng4A)T260 T0334 1 :MSG 1ng4A 1 :MKR T0334 5 :IDKILIVGGGTAGWMAASYLGK 1ng4A 4 :HYEAVVIGGGIIGSAIAYYLAK T0334 30 :GTADITLLQAPDIPTLGVGEATIPNL 1ng4A 26 :ENKNTALFESGTMGGRTTSAAAGMLG T0334 61 :DFLGIPED 1ng4A 52 :AHAECEER T0334 75 :NASYKVAIKFINWRTAGEGTS 1ng4A 60 :DAFFDFAMHSQRLYKGLGEEL T0334 96 :EARELDGGP 1ng4A 82 :ALSGVDIRQ T0334 105 :DHFYHSFGLLK 1ng4A 94 :GMFKLAFSEED T0334 123 :SHYWFDRS 1ng4A 105 :VLQLRQMD T0334 132 :RGKTVEPFDYACYKEPV 1ng4A 113 :DLDSVSWYSKEEVLEKE T0334 156 :PRRLDGSK 1ng4A 130 :PYASGDIF T0334 166 :NYA 1ng4A 138 :GAS T0334 170 :HFDAHLVADFLRRFA 1ng4A 147 :HVEPYFVCKAYVKAA T0334 186 :EKLGVRHVED 1ng4A 162 :KMLGAEIFEH T0334 196 :RVEHVQRDANG 1ng4A 173 :PVLHVERDGEA T0334 209 :ESVRTATGR 1ng4A 184 :LFIKTPSGD T0334 219 :FDADLFVDCSGFRGLLINKAMEEPFLDMSDH 1ng4A 193 :VWANHVVVASGVWSGMFFKQLGLNNAFLPVK T0334 253 :DSAVATQVPH 1ng4A 224 :GECLSVWNDD T0334 266 :A 1ng4A 234 :I T0334 268 :GVEPFTSA 1ng4A 235 :PLTKTLYH T0334 279 :KSG 1ng4A 243 :DHC T0334 284 :WKIPMLGR 1ng4A 246 :YIVPRKSG T0334 292 :FGT 1ng4A 255 :LVV T0334 298 :YSSRFATE 1ng4A 261 :MKPGDWSE T0334 306 :DEAVREFCEMW 1ng4A 272 :LGGLESVMKKA T0334 317 :HLDPETQPLNRIRFRVGRNR 1ng4A 284 :TMLPPIQNMKVDRFWAGLRP T0334 338 :AWVGNCVSIG 1ng4A 304 :GTKDGKPYIG T0334 348 :TSSCFVEPLESTGIYFVYAALYQLVKHFPDKSLNPVLTARFN 1ng4A 319 :SRILFAAGHFRNGILLAPATGALISDLIMNKEVNQDWLHAFR Number of specific fragments extracted= 27 number of extra gaps= 1 total=784 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 1ng4A/T0334-1ng4A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0334 read from 1ng4A/T0334-1ng4A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ng4A read from 1ng4A/T0334-1ng4A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1ng4A in template set Warning: unaligning (T0334)S2 because first residue in template chain is (1ng4A)M1 Warning: unaligning (T0334)Y298 because of BadResidue code BAD_PEPTIDE in next template residue (1ng4A)A259 T0334 3 :GKIDKILIVGGGTAGWMAASYLGK 1ng4A 2 :KRHYEAVVIGGGIIGSAIAYYLAK T0334 30 :GTADITLLQAPDIPT 1ng4A 26 :ENKNTALFESGTMGG T0334 45 :LGVGEATI 1ng4A 48 :GMLGAHAE T0334 53 :PNLQTAFFDFLG 1ng4A 63 :FDFAMHSQRLYK T0334 66 :PEDEWMREC 1ng4A 75 :GLGEELYAL T0334 75 :NASYKVAIKFINWRTAGE 1ng4A 87 :DIRQHNGGMFKLAFSEED T0334 114 :LKYHEQIPLSHYWFDRSY 1ng4A 105 :VLQLRQMDDLDSVSWYSK T0334 142 :ACY 1ng4A 123 :EEV T0334 154 :RSPRRLDGSKVTNYAW 1ng4A 126 :LEKEPYASGDIFGASF T0334 170 :HFDAHLVADFLRRFATEKLGVRHVEDRVEHVQRDANG 1ng4A 147 :HVEPYFVCKAYVKAAKMLGAEIFEHTPVLHVERDGEA T0334 209 :ESVRTAT 1ng4A 184 :LFIKTPS T0334 217 :RVFDADLFVDCSGFRGLLINKAMEEPFL 1ng4A 191 :GDVWANHVVVASGVWSGMFFKQLGLNNA T0334 249 :HLLN 1ng4A 219 :FLPV T0334 253 :DSAVATQV 1ng4A 224 :GECLSVWN T0334 268 :GVEPFTSAIAMKS 1ng4A 232 :DDIPLTKTLYHDH T0334 283 :TWKIPMLGRF 1ng4A 245 :CYIVPRKSGR T0334 295 :GYV 1ng4A 255 :LVV T0334 299 :SSRFATEDEAVREFCEMW 1ng4A 265 :DWSETPDLGGLESVMKKA T0334 317 :HLDPETQPLNRIRFRVGRNRRAWVGNCVS 1ng4A 284 :TMLPPIQNMKVDRFWAGLRPGTKDGKPYI T0334 346 :IGTSSCFVEPLE 1ng4A 322 :LFAAGHFRNGIL T0334 363 :FVYAALYQLVKHFPDKSLNPVLTARF 1ng4A 334 :LAPATGALISDLIMNKEVNQDWLHAF Number of specific fragments extracted= 21 number of extra gaps= 1 total=805 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 1s3eA/T0334-1s3eA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1s3eA expands to /projects/compbio/data/pdb/1s3e.pdb.gz 1s3eA:Skipped atom 1352, because occupancy 0.400 <= existing 0.600 in 1s3eA # T0334 read from 1s3eA/T0334-1s3eA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1s3eA read from 1s3eA/T0334-1s3eA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1s3eA to template set # found chain 1s3eA in template set Warning: unaligning (T0334)I5 because first residue in template chain is (1s3eA)N3 Warning: unaligning (T0334)D508 because last residue in template chain is (1s3eA)I501 T0334 6 :D 1s3eA 4 :K T0334 7 :KILIVGGGTAGWMAASYLGK 1s3eA 6 :DVVVVGGGISGMAAAKLLHD T0334 29 :QGT 1s3eA 26 :SGL T0334 33 :DITLLQAPD 1s3eA 29 :NVVVLEARD T0334 42 :IPTL 1s3eA 39 :VGGR T0334 46 :GVGEATIPNLQTAF 1s3eA 56 :LGGSYVGPTQNRIL T0334 139 :FDYACYKEPVILD 1s3eA 70 :RLAKELGLETYKV T0334 152 :ANRSPRRLDGSKVTNYAWHF 1s3eA 84 :EVERLIHHVKGKSYPFRGPF T0334 172 :DAHLVADFLRRFA 1s3eA 213 :GSGQVSERIMDLL T0334 186 :EK 1s3eA 226 :GD T0334 191 :RHVED 1s3eA 228 :RVKLE T0334 196 :RVEHVQRDANG 1s3eA 234 :PVIYIDQTREN T0334 209 :ESVRTATGRVFDADLFVDCSG 1s3eA 245 :VLVETLNHEMYEAKYVISAIP T0334 233 :LLINKAMEEPFLDM 1s3eA 266 :PTLGMKIHFNPPLP T0334 247 :SDHLLND 1s3eA 286 :ITRVPLG T0334 254 :SAVATQVPHDDDANG 1s3eA 295 :IKCIVYYKEPFWRKK T0334 271 :PFTS 1s3eA 310 :DYCG T0334 275 :AIAMK 1s3eA 315 :MIIDG T0334 280 :SGWTWKIPM 1s3eA 323 :PVAYTLDDT T0334 289 :LGRFGTGYVYSSRFATE 1s3eA 335 :GNYAAIMGFILAHKARK T0334 306 :DEAVREFCEM 1s3eA 358 :EERLKKLCEL T0334 316 :WHLDPETQPLNRIRF 1s3eA 372 :LGSLEALEPVHYEEK T0334 337 :RAWVGNCVSIG 1s3eA 415 :RQPVDRIYFAG T0334 348 :TSSCFVEPLESTGIYFVYAALYQLVKHFP 1s3eA 427 :ETATHWSGYMEGAVEAGERAAREILHAMG T0334 377 :DKSLN 1s3eA 459 :EDEIW T0334 443 :INAPASDDAQLYYGNFEEEFRNFWNN 1s3eA 464 :QSEPESVDVPAQPITTTFLERHLPSV T0334 497 :ESVDEVFGAVK 1s3eA 490 :PGLLRLIGLTT Number of specific fragments extracted= 27 number of extra gaps= 0 total=832 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 1s3eA/T0334-1s3eA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0334 read from 1s3eA/T0334-1s3eA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1s3eA read from 1s3eA/T0334-1s3eA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1s3eA in template set Warning: unaligning (T0334)G3 because first residue in template chain is (1s3eA)N3 T0334 5 :IDKILIVGGGTAGWMAASYLGK 1s3eA 4 :KCDVVVVGGGISGMAAAKLLHD T0334 30 :GTADITLLQAP 1s3eA 26 :SGLNVVVLEAR T0334 41 :DI 1s3eA 38 :RV T0334 43 :PTLGVGEATIPNLQTAF 1s3eA 56 :LGGSYVGPTQNRILRLA T0334 61 :DFLGI 1s3eA 73 :KELGL T0334 96 :EARELDGGP 1s3eA 78 :ETYKVNEVE T0334 105 :DHFYHSFGLL 1s3eA 94 :GKSYPFRGPF T0334 119 :QIPLSHYWFDR 1s3eA 115 :HNNFWRTMDDM T0334 141 :YACYKEPVILDANRSPRR 1s3eA 126 :GREIPSDAPWKAPLAEEW T0334 170 :HFDAHLVADFLRRFA 1s3eA 211 :VGGSGQVSERIMDLL T0334 186 :EKL 1s3eA 226 :GDR T0334 192 :HVED 1s3eA 229 :VKLE T0334 196 :RVEHVQRDANG 1s3eA 234 :PVIYIDQTREN T0334 209 :ESVRTATGRVFDADLFVDCSG 1s3eA 245 :VLVETLNHEMYEAKYVISAIP T0334 236 :NKA 1s3eA 266 :PTL T0334 239 :MEEPFL 1s3eA 274 :FNPPLP T0334 245 :DMSDHLLNDSAVATQVPHDDDANGVEPFTSAIAMKS 1s3eA 286 :ITRVPLGSVIKCIVYYKEPFWRKKDYCGTMIIDGEE T0334 281 :GWTWKIPMLGR 1s3eA 325 :AYTLDDTKPEG T0334 292 :FGTGYVYSSRFATE 1s3eA 338 :AAIMGFILAHKARK T0334 306 :DEAVREFCEMW 1s3eA 358 :EERLKKLCELY T0334 317 :HL 1s3eA 373 :GS T0334 320 :PETQPLNRIRFRVGRNRRA 1s3eA 375 :LEALEPVHYEEKNWCEEQY T0334 339 :WVGNCVSIG 1s3eA 417 :PVDRIYFAG T0334 348 :TSSCFVEPLESTGIYFVYAALYQLVKHFPD 1s3eA 427 :ETATHWSGYMEGAVEAGERAAREILHAMGK T0334 378 :KSLN 1s3eA 460 :DEIW T0334 411 :PRTDTP 1s3eA 464 :QSEPES T0334 477 :GLGLVPDAPSPRLAHMP 1s3eA 471 :DVPAQPITTTFLERHLP T0334 503 :FGAVKDRQRNLL 1s3eA 489 :VPGLLRLIGLTT Number of specific fragments extracted= 28 number of extra gaps= 0 total=860 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 1s3eA/T0334-1s3eA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0334 read from 1s3eA/T0334-1s3eA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1s3eA read from 1s3eA/T0334-1s3eA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1s3eA in template set Warning: unaligning (T0334)K4 because first residue in template chain is (1s3eA)N3 T0334 5 :IDKILIVGGGTAGWMAASYLGK 1s3eA 4 :KCDVVVVGGGISGMAAAKLLHD T0334 30 :GTADITLLQ 1s3eA 26 :SGLNVVVLE T0334 39 :APDIPT 1s3eA 36 :RDRVGG T0334 45 :LGVGEA 1s3eA 54 :VDLGGS T0334 51 :TIPNLQTAF 1s3eA 64 :TQNRILRLA T0334 61 :DFLGIP 1s3eA 73 :KELGLE T0334 76 :ASYKVAIKF 1s3eA 83 :NEVERLIHH T0334 87 :WRTAGEGTSEARELDGGPDHFYHSFGLLKYHEQIP 1s3eA 92 :VKGKSYPFRGPFPPVWNPITYLDHNNFWRTMDDMG T0334 122 :LSHYWFDRSYRGKTVEPFDYACYKEP 1s3eA 147 :TMKELLDKLCWTESAKQLATLFVNLC T0334 148 :VILDANRSPRRLDGSKVTNYAWHFDAHLVADFLRRFA 1s3eA 189 :VKQCGGTTRIISTTNGGQERKFVGGSGQVSERIMDLL T0334 191 :RHVEDRVEHVQRDANG 1s3eA 229 :VKLERPVIYIDQTREN T0334 209 :ESVRTATGRVFDADLFVDCSGFRG 1s3eA 245 :VLVETLNHEMYEAKYVISAIPPTL T0334 233 :LLINKAMEEP 1s3eA 280 :MMRNQMITRV T0334 243 :FLDMSDHLLNDSAV 1s3eA 303 :EPFWRKKDYCGTMI T0334 257 :ATQV 1s3eA 327 :TLDD T0334 264 :DDANGVEPFTSAIAMK 1s3eA 331 :TKPEGNYAAIMGFILA T0334 303 :ATEDEAVREFCEMWH 1s3eA 355 :LTKEERLKKLCELYA T0334 318 :LDPETQPLNRIRF 1s3eA 373 :GSLEALEPVHYEE T0334 331 :RVGRNRRAW 1s3eA 403 :PPGILTQYG T0334 341 :GNCVSIGT 1s3eA 419 :DRIYFAGT T0334 349 :SSCFVEPLESTGIYFVYAALYQLVKHFP 1s3eA 428 :TATHWSGYMEGAVEAGERAAREILHAMG T0334 448 :SDDAQLYYG 1s3eA 457 :IPEDEIWQS T0334 469 :SNYYCVLAGLGLVPDAPSPR 1s3eA 466 :EPESVDVPAQPITTTFLERH T0334 489 :LAHMPQATESVD 1s3eA 489 :VPGLLRLIGLTT Number of specific fragments extracted= 24 number of extra gaps= 0 total=884 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 1q1rA/T0334-1q1rA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1q1rA expands to /projects/compbio/data/pdb/1q1r.pdb.gz 1q1rA:# T0334 read from 1q1rA/T0334-1q1rA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1q1rA read from 1q1rA/T0334-1q1rA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1q1rA to template set # found chain 1q1rA in template set Warning: unaligning (T0334)K4 because first residue in template chain is (1q1rA)N2 T0334 5 :ID 1q1rA 3 :AN T0334 7 :KILIVGGGTAGWMAASYLGK 1q1rA 6 :NVVIVGTGLAGVEVAFGLRA T0334 29 :QGTA 1q1rA 26 :SGWE T0334 33 :DITLLQAPD 1q1rA 31 :NIRLVGDAT T0334 42 :IPTLGVGEATIPNLQTAFFDFLGIPEDEWMRECNASYKVAIKFINWRTAGEGTS 1q1rA 41 :IPHHLPPLSKAYLAGKATAESLYLRTPDAYAAQNIQLLGGTQVTAINRDRQQVI T0334 96 :EARELDG 1q1rA 116 :PLPVASG T0334 103 :GPDHFYHSFGLL 1q1rA 126 :KANNFRYLRTLE T0334 115 :KYHEQIPLSHYWFDRSYRG 1q1rA 147 :IADNRLVVIGGGYIGLEVA T0334 139 :FDYACYKEPVILD 1q1rA 166 :ATAIKANMHVTLL T0334 152 :ANRSPRRLD 1q1rA 180 :TAARVLERV T0334 172 :DAHLVADFLRRFA 1q1rA 189 :TAPPVSAFYEHLH T0334 186 :EKLGVRHVED 1q1rA 202 :REAGVDIRTG T0334 196 :RVEHVQRDANG 1q1rA 213 :QVCGFEMSTDQ T0334 207 :NIESVRTATGRVFDADLFVDCSGFRG 1q1rA 225 :KVTAVLCEDGTRLPADLVIAGIGLIP T0334 233 :LLINKAMEEPF 1q1rA 252 :CELASAAGLQV T0334 247 :SDHLLNDSAVATQVPHDDDANGV 1q1rA 263 :DNGIVINEHMQTSDPLIMAVGDC T0334 270 :EPFTSAIAMKSGWTWKIPM 1q1rA 325 :AAPWFWSDQYEIGLKMVGL T0334 289 :LGRFGTGYVYSSRFATE 1q1rA 345 :EGYDRIIVRGSLAQPDF T0334 306 :DEAVREFCEM 1q1rA 380 :PVEFNQSKQI T0334 316 :WHLDP 1q1rA 391 :TDRLP T0334 321 :ETQP 1q1rA 404 :ESVP T0334 499 :VDEVFGAVKDRQRN 1q1rA 408 :LKEIIAAAKAELSS Number of specific fragments extracted= 22 number of extra gaps= 0 total=906 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 1q1rA/T0334-1q1rA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0334 read from 1q1rA/T0334-1q1rA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1q1rA read from 1q1rA/T0334-1q1rA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1q1rA in template set T0334 5 :IDKILIVGGGTAGWMAASYLGK 1q1rA 4 :NDNVVIVGTGLAGVEVAFGLRA T0334 30 :GTA 1q1rA 26 :SGW T0334 33 :DITLLQAPDIPTLGVGEA 1q1rA 31 :NIRLVGDATVIPHHLPPL T0334 55 :LQ 1q1rA 49 :SK T0334 96 :EARELDGGPDHFYHSF 1q1rA 51 :AYLAGKATAESLYLRT T0334 123 :SHYWFDRS 1q1rA 67 :PDAYAAQN T0334 136 :VEPFDYACYKEPVILD 1q1rA 75 :IQLLGGTQVTAINRDR T0334 152 :ANRSPRRLDGSKVTNYAW 1q1rA 114 :PRPLPVASGAVGKANNFR T0334 170 :HFDAHLVADFLRRFA 1q1rA 187 :RVTAPPVSAFYEHLH T0334 186 :EKLGVRHVED 1q1rA 202 :REAGVDIRTG T0334 196 :RVEHVQRDANGN 1q1rA 213 :QVCGFEMSTDQQ T0334 208 :IESVRTATGRVFDADLFVDCSGFRGL 1q1rA 226 :VTAVLCEDGTRLPADLVIAGIGLIPN T0334 235 :INKAMEEPFLD 1q1rA 254 :LASAAGLQVDN T0334 246 :MSDHLLNDSAVATQVPH 1q1rA 276 :DPLIMAVGDCARFHSQL T0334 264 :DD 1q1rA 293 :YD T0334 266 :ANGVEPFTSAIAMKSGWTWKIPMLGR 1q1rA 321 :PRDEAAPWFWSDQYEIGLKMVGLSEG T0334 292 :FGTGYVYSSRFATE 1q1rA 348 :DRIIVRGSLAQPDF T0334 306 :DEAVREFCEMW 1q1rA 380 :PVEFNQSKQII T0334 317 :HLDP 1q1rA 392 :DRLP T0334 335 :NRR 1q1rA 396 :VEP T0334 373 :KHFPD 1q1rA 399 :NLLGD T0334 378 :KSLNPVLTARFNREIET 1q1rA 405 :SVPLKEIIAAAKAELSS Number of specific fragments extracted= 22 number of extra gaps= 0 total=928 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 1q1rA/T0334-1q1rA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0334 read from 1q1rA/T0334-1q1rA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1q1rA read from 1q1rA/T0334-1q1rA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1q1rA in template set T0334 6 :DKILIVGGGTAGWMAASYLGK 1q1rA 150 :NRLVVIGGGYIGLEVAATAIK T0334 30 :GTADITLLQAPDI 1q1rA 171 :ANMHVTLLDTAAR T0334 46 :GVGEATIPNLQTAF 1q1rA 184 :VLERVTAPPVSAFY T0334 181 :RRFATEKLGVRHVEDRVEHVQRDANGN 1q1rA 198 :EHLHREAGVDIRTGTQVCGFEMSTDQQ T0334 208 :IESVRTATGRVFDADLFVDCSGF 1q1rA 226 :VTAVLCEDGTRLPADLVIAGIGL T0334 231 :RGLLI 1q1rA 251 :NCELA T0334 237 :KAMEEP 1q1rA 256 :SAAGLQ T0334 292 :FGTGYVYSSRFA 1q1rA 262 :VDNGIVINEHMQ T0334 338 :AWVGNCVSIGTSSCFVEPLE 1q1rA 274 :TSDPLIMAVGDCARFHSQLY T0334 358 :STGIYFVYAALYQLVKHFPDKSLNPV 1q1rA 299 :IESVPNALEQARKIAAILCGKVPRDE T0334 405 :AHFYFSP 1q1rA 362 :SVFYLQG T0334 425 :RLADGMQEKIDMYRAGMAINAPASDDAQL 1q1rA 378 :NRPVEFNQSKQIITDRLPVEPNLLGDESV T0334 491 :HMPQATESVDEVFGA 1q1rA 407 :PLKEIIAAAKAELSS Number of specific fragments extracted= 13 number of extra gaps= 0 total=941 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 1pbe/T0334-1pbe-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1pbe expands to /projects/compbio/data/pdb/1pbe.pdb.gz 1pbe:Warning: there is no chain 1pbe will retry with 1pbeA # T0334 read from 1pbe/T0334-1pbe-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1pbe read from 1pbe/T0334-1pbe-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1pbe to template set # found chain 1pbe in template set Warning: unaligning (T0334)I5 because first residue in template chain is (1pbe)M1 Warning: unaligning (T0334)L188 because of BadResidue code BAD_PEPTIDE in next template residue (1pbe)G117 Warning: unaligning (T0334)G189 because of BadResidue code BAD_PEPTIDE at template residue (1pbe)G117 Warning: unaligning (T0334)N205 because of BadResidue code BAD_PEPTIDE in next template residue (1pbe)E135 Warning: unaligning (T0334)G206 because of BadResidue code BAD_PEPTIDE at template residue (1pbe)E135 Warning: unaligning (T0334)R331 because of BadResidue code BAD_PEPTIDE in next template residue (1pbe)S270 Warning: unaligning (T0334)V332 because of BadResidue code BAD_PEPTIDE at template residue (1pbe)S270 Warning: unaligning (T0334)F402 because of BadResidue code BAD_PEPTIDE in next template residue (1pbe)S343 Warning: unaligning (T0334)I403 because of BadResidue code BAD_PEPTIDE at template residue (1pbe)S343 Warning: unaligning (T0334)F417 because of BadResidue code BAD_PEPTIDE in next template residue (1pbe)S360 Warning: unaligning (T0334)W418 because of BadResidue code BAD_PEPTIDE at template residue (1pbe)S360 T0334 6 :D 1pbe 2 :K T0334 7 :KILIVGGGTAGWMAASYLGK 1pbe 4 :QVAIIGAGPSGLLLGQLLHK T0334 29 :QGT 1pbe 24 :AGI T0334 33 :DITLLQAPD 1pbe 27 :DNVILERQT T0334 52 :I 1pbe 36 :P T0334 57 :TAFFDFLGIPE 1pbe 37 :DYVLGRIRAGV T0334 69 :EWMRECNASYKVAIKFINW 1pbe 54 :DLLREAGVDRRMARDGLVH T0334 103 :GPDHFYHSFGLL 1pbe 73 :EGVEIAFAGQRR T0334 115 :KYHE 1pbe 87 :DLKR T0334 152 :ANRSPRRLD 1pbe 92 :SGGKTVTVY T0334 172 :DAHLVADFLRRFA 1pbe 101 :GQTEVTRDLMEAR T0334 186 :EK 1pbe 114 :EA T0334 190 :VRHVED 1pbe 118 :ATTVYQ T0334 196 :RVEHVQRDA 1pbe 125 :AEVRLHDLQ T0334 207 :NIE 1pbe 136 :RPY T0334 211 :VRTA 1pbe 139 :VTFE T0334 215 :TGR 1pbe 144 :DGE T0334 218 :VFDADLFVDCSGFRGLLI 1pbe 149 :RLDCDYIAGCDGFHGISR T0334 237 :KAMEEPFLDM 1pbe 167 :QSIPAERLKV T0334 247 :SDHLLND 1pbe 178 :ERVYPFG T0334 254 :SAVATQVPHDD 1pbe 186 :LGLLADTPPVS T0334 271 :PFTSAIAMKSGWTWKIPM 1pbe 197 :HELIYANHPRGFALCSQR T0334 289 :LGR 1pbe 216 :ATR T0334 292 :FGTGYVYSSRFATEDEAVREFCEMWHLDP 1pbe 223 :VQVPLTEKVEDWSDERFWTELKARLPAEV T0334 321 :ETQPLNRIRF 1pbe 259 :PSLEKSIAPL T0334 333 :GRNRRAWVGNCVSIGTSSCFVEPLESTGIYFVYAALYQLVKHFP 1pbe 271 :FVVEPMQHGRLFLAGDAAHIVPPTGAKGLNLAASDVSTLYRLLL T0334 377 :DKSLNPVLTARFNREIETMFDDTRD 1pbe 317 :YREGRGELLERYSAICLRRIWKAER T0334 404 :QAHFYFSPRTDTP 1pbe 344 :WWMTSVLHRFPDT T0334 419 :R 1pbe 361 :Q T0334 508 :DRQRNLLETLPSLHEFLRQ 1pbe 362 :RIQQTELEYYLGSEAGLAT Number of specific fragments extracted= 30 number of extra gaps= 5 total=971 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 1pbe/T0334-1pbe-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0334 read from 1pbe/T0334-1pbe-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1pbe read from 1pbe/T0334-1pbe-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1pbe in template set Warning: unaligning (T0334)K4 because first residue in template chain is (1pbe)M1 Warning: unaligning (T0334)L188 because of BadResidue code BAD_PEPTIDE in next template residue (1pbe)G117 Warning: unaligning (T0334)G189 because of BadResidue code BAD_PEPTIDE at template residue (1pbe)G117 Warning: unaligning (T0334)N205 because of BadResidue code BAD_PEPTIDE in next template residue (1pbe)E135 Warning: unaligning (T0334)G206 because of BadResidue code BAD_PEPTIDE at template residue (1pbe)E135 Warning: unaligning (T0334)R331 because of BadResidue code BAD_PEPTIDE in next template residue (1pbe)S270 Warning: unaligning (T0334)V332 because of BadResidue code BAD_PEPTIDE at template residue (1pbe)S270 Warning: unaligning (T0334)F402 because of BadResidue code BAD_PEPTIDE in next template residue (1pbe)S343 Warning: unaligning (T0334)I403 because of BadResidue code BAD_PEPTIDE at template residue (1pbe)S343 Warning: unaligning (T0334)F417 because of BadResidue code BAD_PEPTIDE in next template residue (1pbe)S360 Warning: unaligning (T0334)W418 because of BadResidue code BAD_PEPTIDE at template residue (1pbe)S360 T0334 5 :IDKILIVGGGTAGWMAASYLGK 1pbe 2 :KTQVAIIGAGPSGLLLGQLLHK T0334 30 :GTADITLLQAPDI 1pbe 24 :AGIDNVILERQTP T0334 43 :PTLGVGEATIPNLQTAF 1pbe 40 :LGRIRAGVLEQGMVDLL T0334 61 :DFLGI 1pbe 57 :REAGV T0334 123 :SHYWFDRSYR 1pbe 62 :DRRMARDGLV T0334 136 :VEPFDYACYKEPVILD 1pbe 72 :HEGVEIAFAGQRRRID T0334 155 :SPRRLDG 1pbe 88 :LKRLSGG T0334 166 :NYAWHFDAHLVADFLRRFA 1pbe 95 :KTVTVYGQTEVTRDLMEAR T0334 186 :EK 1pbe 114 :EA T0334 190 :VRHVED 1pbe 118 :ATTVYQ T0334 196 :RVEHVQRDA 1pbe 125 :AEVRLHDLQ T0334 207 :N 1pbe 136 :R T0334 209 :ESVRTA 1pbe 137 :PYVTFE T0334 215 :TG 1pbe 144 :DG T0334 217 :RVFDADLFVDCSGFRGLL 1pbe 148 :LRLDCDYIAGCDGFHGIS T0334 236 :NKAMEEPFL 1pbe 166 :RQSIPAERL T0334 245 :DMSDHLLNDSAVAT 1pbe 176 :VFERVYPFGWLGLL T0334 264 :DDANGVEPFTSAIAMKSGWTWKIPMLGR 1pbe 190 :ADTPPVSHELIYANHPRGFALCSQRSAT T0334 292 :FGTGYVYSS 1pbe 219 :SRYYVQVPL T0334 301 :RFATEDEAVREFCEMW 1pbe 232 :EDWSDERFWTELKARL T0334 318 :LDPETQPLNRIRF 1pbe 256 :VTGPSLEKSIAPL T0334 333 :GRNRRAWVGNCVSIGTSSCFVEPLESTGIYFVYAALYQLVKHFPD 1pbe 271 :FVVEPMQHGRLFLAGDAAHIVPPTGAKGLNLAASDVSTLYRLLLK T0334 378 :KSLNPVLTARFNREIETMFDDTRD 1pbe 318 :REGRGELLERYSAICLRRIWKAER T0334 404 :QAHFYFSPRTD 1pbe 344 :WWMTSVLHRFP T0334 415 :TP 1pbe 357 :DA T0334 419 :R 1pbe 361 :Q T0334 428 :DGMQEKIDMYR 1pbe 362 :RIQQTELEYYL Number of specific fragments extracted= 27 number of extra gaps= 5 total=998 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 1pbe/T0334-1pbe-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0334 read from 1pbe/T0334-1pbe-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1pbe read from 1pbe/T0334-1pbe-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1pbe in template set Warning: unaligning (T0334)K187 because of BadResidue code BAD_PEPTIDE in next template residue (1pbe)G117 Warning: unaligning (T0334)L188 because of BadResidue code BAD_PEPTIDE at template residue (1pbe)G117 Warning: unaligning (T0334)A204 because of BadResidue code BAD_PEPTIDE in next template residue (1pbe)E135 Warning: unaligning (T0334)N205 because of BadResidue code BAD_PEPTIDE at template residue (1pbe)E135 Warning: unaligning (T0334)R331 because of BadResidue code BAD_PEPTIDE in next template residue (1pbe)S270 Warning: unaligning (T0334)V332 because of BadResidue code BAD_PEPTIDE at template residue (1pbe)S270 Warning: unaligning (T0334)D398 because of BadResidue code BAD_PEPTIDE in next template residue (1pbe)S343 Warning: unaligning (T0334)T399 because of BadResidue code BAD_PEPTIDE at template residue (1pbe)S343 Warning: unaligning (T0334)G429 because of BadResidue code BAD_PEPTIDE in next template residue (1pbe)S360 Warning: unaligning (T0334)M430 because of BadResidue code BAD_PEPTIDE at template residue (1pbe)S360 T0334 7 :KILIVGGGTAGWMAASYLGK 1pbe 4 :QVAIIGAGPSGLLLGQLLHK T0334 30 :GTADITLLQAPD 1pbe 24 :AGIDNVILERQT T0334 43 :PTLGVGE 1pbe 41 :GRIRAGV T0334 51 :TIPNLQTAF 1pbe 48 :LEQGMVDLL T0334 61 :DFLGIP 1pbe 57 :REAGVD T0334 69 :EWMRECNASY 1pbe 63 :RRMARDGLVH T0334 79 :KVAIKF 1pbe 74 :GVEIAF T0334 90 :AGEGTSEA 1pbe 80 :AGQRRRID T0334 158 :RLDGSKV 1pbe 88 :LKRLSGG T0334 166 :NYAWHFDAHLVADFLRRFATE 1pbe 95 :KTVTVYGQTEVTRDLMEAREA T0334 189 :GVRHVEDRVEHVQRD 1pbe 118 :ATTVYQAAEVRLHDL T0334 206 :GNIESVRTATGR 1pbe 136 :RPYVTFERDGER T0334 218 :VFDADLFVDCSGFRGLLIN 1pbe 149 :RLDCDYIAGCDGFHGISRQ T0334 243 :FLDMSDH 1pbe 168 :SIPAERL T0334 250 :LLNDSAVATQV 1pbe 180 :VYPFGWLGLLA T0334 265 :DANGVEPFTSAIAMKSGWTWKIPMLGRFGTGYVYS 1pbe 191 :DTPPVSHELIYANHPRGFALCSQRSATRSRYYVQV T0334 300 :SRFATEDEAVREFCEMW 1pbe 231 :VEDWSDERFWTELKARL T0334 318 :LDPETQPLNRIRF 1pbe 256 :VTGPSLEKSIAPL T0334 333 :GRNRRAWVGNCVSIGTSSCFVEPLESTGIYFVYAALYQLVKHFP 1pbe 271 :FVVEPMQHGRLFLAGDAAHIVPPTGAKGLNLAASDVSTLYRLLL T0334 377 :DKSLNPVLTARFNREIETMFD 1pbe 321 :RGELLERYSAICLRRIWKAER T0334 400 :RDFIQAHFYFSPRT 1pbe 344 :WWMTSVLHRFPDTD T0334 428 :D 1pbe 358 :A T0334 431 :QE 1pbe 361 :QR T0334 505 :AVKDRQRNLLETLPSLHEFLRQQ 1pbe 363 :IQQTELEYYLGSEAGLATIAENY Number of specific fragments extracted= 24 number of extra gaps= 5 total=1022 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 1p2hA/T0334-1p2hA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1p2hA expands to /projects/compbio/data/pdb/1p2h.pdb.gz 1p2hA:# T0334 read from 1p2hA/T0334-1p2hA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1p2hA read from 1p2hA/T0334-1p2hA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1p2hA to template set # found chain 1p2hA in template set Warning: unaligning (T0334)P66 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1p2hA)W176 Warning: unaligning (T0334)E67 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1p2hA)W176 Warning: unaligning (T0334)R98 because of BadResidue code BAD_PEPTIDE in next template residue (1p2hA)A225 Warning: unaligning (T0334)E99 because of BadResidue code BAD_PEPTIDE at template residue (1p2hA)A225 Warning: unaligning (T0334)R334 because of BadResidue code BAD_PEPTIDE in next template residue (1p2hA)H504 Warning: unaligning (T0334)N335 because of BadResidue code BAD_PEPTIDE at template residue (1p2hA)H504 T0334 3 :GKID 1p2hA 122 :APHD T0334 7 :KILIVGGGTAGWMAASYLGK 1p2hA 128 :DVVVVGSGGAGFSAAISATD T0334 29 :QGT 1p2hA 148 :SGA T0334 33 :DITLLQAPD 1p2hA 151 :KVILIEKEP T0334 42 :IPTL 1p2hA 161 :IGGN T0334 57 :TAFFDFLGI 1p2hA 166 :KLAAGGMNA T0334 68 :DEWMRECNASYKVAIKFINWRTAGEGTS 1p2hA 177 :TDQQKAKKITDSPELMFEDTMKGGQNIN T0334 96 :EA 1p2hA 222 :WM T0334 100 :LDGGPDHFYHSFGLL 1p2hA 226 :MGADLTDVGMMGGAS T0334 115 :KYHE 1p2hA 246 :RPTG T0334 152 :AN 1p2hA 251 :AG T0334 172 :DAHLVADFLRRFA 1p2hA 253 :VGAHVVQVLYDNA T0334 186 :EKLGVRHVED 1p2hA 266 :VKRNIDLRMN T0334 196 :RVEHVQRDANGNIESVRTA 1p2hA 277 :RGIEVLKDDKGTVKGILVK T0334 215 :T 1p2hA 297 :M T0334 216 :GR 1p2hA 299 :KG T0334 218 :VFDADLFVDCSGFRG 1p2hA 303 :WVKADAVILATGGFA T0334 233 :LLINKAM 1p2hA 321 :ERVAKLD T0334 264 :DDANGVEPFTSAIAMK 1p2hA 328 :PSLKGFISTNQPGAVG T0334 280 :SGWTWKIPM 1p2hA 359 :MQYIQAHPT T0334 289 :LGR 1p2hA 371 :KGG T0334 292 :FGTGYVYSSRFATE 1p2hA 383 :NGAILVNREGKRFV T0334 306 :DEAVREFCEM 1p2hA 462 :TETVARYNSL T0334 316 :WHLDP 1p2hA 473 :SSGKD T0334 321 :ETQPLNRIRF 1p2hA 490 :NEGNYYAIEV T0334 336 :R 1p2hA 505 :H T0334 337 :RAWVGNCVSIGTSSCFVEP 1p2hA 523 :KQVIPGLYGAGEVTGGVHG T0334 356 :LESTGIYFVYAALYQLVKHFP 1p2hA 545 :LGGNAISDIITFGRLAGEEAA Number of specific fragments extracted= 28 number of extra gaps= 3 total=1050 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 1p2hA/T0334-1p2hA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0334 read from 1p2hA/T0334-1p2hA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1p2hA read from 1p2hA/T0334-1p2hA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1p2hA in template set Warning: unaligning (T0334)W87 because of BadResidue code BAD_PEPTIDE in next template residue (1p2hA)S219 Warning: unaligning (T0334)R88 because of BadResidue code BAD_PEPTIDE at template residue (1p2hA)S219 Warning: unaligning (T0334)F127 because of BadResidue code BAD_PEPTIDE in next template residue (1p2hA)A225 Warning: unaligning (T0334)D128 because of BadResidue code BAD_PEPTIDE at template residue (1p2hA)A225 T0334 4 :KIDKILIVGGGTAGWMAASYLGK 1p2hA 125 :DTVDVVVVGSGGAGFSAAISATD T0334 30 :GTADITLLQAPDIPTLGVGEATI 1p2hA 148 :SGAKVILIEKEPVIGGNAKLAAG T0334 57 :TAF 1p2hA 178 :DQQ T0334 61 :DFLGI 1p2hA 181 :KAKKI T0334 66 :PEDEWMRECNA 1p2hA 188 :SPELMFEDTMK T0334 77 :SYKVAIKFIN 1p2hA 208 :LVKVLSSHSK T0334 123 :SHYW 1p2hA 220 :VDWM T0334 129 :RSYR 1p2hA 226 :MGAD T0334 144 :YKEPVI 1p2hA 230 :LTDVGM T0334 152 :ANRSPRRL 1p2hA 236 :MGGASVNR T0334 162 :SKVTNYAW 1p2hA 244 :AHRPTGGA T0334 171 :FDAHLVADFLRRFAT 1p2hA 252 :GVGAHVVQVLYDNAV T0334 187 :KLGVRHVED 1p2hA 267 :KRNIDLRMN T0334 196 :RVEHVQRDANGNIESVRTA 1p2hA 277 :RGIEVLKDDKGTVKGILVK T0334 215 :TG 1p2hA 299 :KG T0334 217 :RVFDADLFVDCSGFRGL 1p2hA 302 :YWVKADAVILATGGFAK T0334 234 :L 1p2hA 323 :V T0334 236 :NKAM 1p2hA 324 :AKLD T0334 244 :LDMSDHLLNDS 1p2hA 328 :PSLKGFISTNQ T0334 267 :NGVE 1p2hA 339 :PGAV T0334 271 :PFTSAIAMKSGWTWKIPM 1p2hA 350 :ENAGGALKDMQYIQAHPT T0334 289 :LGRFGT 1p2hA 371 :KGGVMV T0334 295 :GYVYSSRFATE 1p2hA 384 :GAILVNREGKR T0334 306 :DEAVREFCEMW 1p2hA 459 :KALTETVARYN T0334 317 :HLDPETQ 1p2hA 475 :GKDTDFE T0334 324 :PLNRIRFRVG 1p2hA 493 :NYYAIEVTPG T0334 334 :RNRRAWVGNCVSIG 1p2hA 520 :NAKKQVIPGLYGAG T0334 348 :TSSCFVEPLESTGIYFVYAALYQLVKHF 1p2hA 537 :GGVHGANRLGGNAISDIITFGRLAGEEA Number of specific fragments extracted= 28 number of extra gaps= 2 total=1078 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 1p2hA/T0334-1p2hA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0334 read from 1p2hA/T0334-1p2hA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1p2hA read from 1p2hA/T0334-1p2hA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1p2hA in template set Warning: unaligning (T0334)Y141 because of BadResidue code BAD_PEPTIDE in next template residue (1p2hA)S219 Warning: unaligning (T0334)A142 because of BadResidue code BAD_PEPTIDE at template residue (1p2hA)S219 Warning: unaligning (T0334)P147 because of BadResidue code BAD_PEPTIDE in next template residue (1p2hA)A225 Warning: unaligning (T0334)V148 because of BadResidue code BAD_PEPTIDE at template residue (1p2hA)A225 Warning: unaligning (T0334)R334 because of BadResidue code BAD_PEPTIDE in next template residue (1p2hA)H504 Warning: unaligning (T0334)N335 because of BadResidue code BAD_PEPTIDE at template residue (1p2hA)H504 T0334 5 :IDKILIVGGGTAGWMAASYLGK 1p2hA 126 :TVDVVVVGSGGAGFSAAISATD T0334 30 :GTADITLLQAPDI 1p2hA 148 :SGAKVILIEKEPV T0334 45 :LGVGEATI 1p2hA 161 :IGGNAKLA T0334 69 :EWMRECNASY 1p2hA 178 :DQQKAKKITD T0334 106 :HFYHSFGLLKYHEQIPLSHYWFDRSY 1p2hA 188 :SPELMFEDTMKGGQNINDPALVKVLS T0334 137 :EPFD 1p2hA 214 :SHSK T0334 143 :CYKE 1p2hA 220 :VDWM T0334 149 :ILDANRSPRRLDGSKVTN 1p2hA 226 :MGADLTDVGMMGGASVNR T0334 169 :WHF 1p2hA 244 :AHR T0334 172 :DAHLVADFLRRFATEKLGVRHVEDRVEHVQRDANGNIESVRT 1p2hA 253 :VGAHVVQVLYDNAVKRNIDLRMNTRGIEVLKDDKGTVKGILV T0334 214 :ATGR 1p2hA 297 :MYKG T0334 218 :VFDADLFVDCSGFRG 1p2hA 303 :WVKADAVILATGGFA T0334 233 :LLINK 1p2hA 322 :RVAKL T0334 243 :FLDMSDHLLND 1p2hA 327 :DPSLKGFISTN T0334 307 :EAVREFCEMWHLDP 1p2hA 463 :ETVARYNSLVSSGK T0334 322 :TQ 1p2hA 477 :DT T0334 324 :PLNRIRFRVG 1p2hA 493 :NYYAIEVTPG T0334 336 :RRA 1p2hA 505 :HTM T0334 339 :WVGNCVSIGTSSCFVEP 1p2hA 525 :VIPGLYGAGEVTGGVHG T0334 356 :LESTGIYFVYAALYQLVKHFPD 1p2hA 545 :LGGNAISDIITFGRLAGEEAAK Number of specific fragments extracted= 20 number of extra gaps= 3 total=1098 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 1gesA/T0334-1gesA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1gesA expands to /projects/compbio/data/pdb/1ges.pdb.gz 1gesA:Skipped atom 2956, because occupancy 0.500 <= existing 0.500 in 1gesA # T0334 read from 1gesA/T0334-1gesA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1gesA read from 1gesA/T0334-1gesA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1gesA to template set # found chain 1gesA in template set Warning: unaligning (T0334)I5 because first residue in template chain is (1gesA)K3 Warning: unaligning (T0334)H124 because of BadResidue code BAD_PEPTIDE in next template residue (1gesA)A175 Warning: unaligning (T0334)Y125 because of BadResidue code BAD_PEPTIDE at template residue (1gesA)A175 Warning: unaligning (T0334)W126 because of BadResidue code BAD_PEPTIDE at template residue (1gesA)G176 Warning: unaligning (T0334)F127 because of BadResidue code BAD_PEPTIDE at template residue (1gesA)Y177 T0334 6 :D 1gesA 4 :H T0334 7 :KILIVGGGTAGWMAASYLGK 1gesA 6 :DYIAIGGGSGGIASINRAAM T0334 29 :QGT 1gesA 26 :YGQ T0334 33 :DITLLQAPDIPTL 1gesA 29 :KCALIEAKELGGT T0334 46 :GVGEATIPNLQTAFFDFLGIPEDEWMRECNAS 1gesA 78 :KFNWETLIASRTAYIDRIHTSYENVLGKNNVD T0334 96 :EARELDG 1gesA 142 :RPSHPDI T0334 103 :GPDHFYHSFGLL 1gesA 150 :GVEYGIDSDGFF T0334 115 :KYHEQIPLS 1gesA 165 :ALPERVAVV T0334 128 :DRSYRG 1gesA 178 :IGVELG T0334 139 :FDYACYKEPVILD 1gesA 184 :GVINGLGAKTHLF T0334 152 :ANRSPRRL 1gesA 198 :MFDAPLPS T0334 172 :DAHLVADFLRRFA 1gesA 206 :FDPMISETLVEVM T0334 186 :EKLGVRHVED 1gesA 219 :NAEGPQLHTN T0334 196 :RVEHVQRDANGN 1gesA 230 :IPKAVVKNTDGS T0334 209 :ESVRTATGRVFDADLFVDCSGFRG 1gesA 242 :LTLELEDGRSETVDCLIWAIGREP T0334 233 :LLINKAMEEPFLD 1gesA 269 :NINLEAAGVKTNE T0334 247 :SDHLLNDSAVA 1gesA 282 :KGYIVVDKYQN T0334 338 :AWVGNCVSIGTSSCF 1gesA 293 :TNIEGIYAVGDNTGA T0334 358 :STGIYFVYAALYQLVKHFP 1gesA 308 :VELTPVAVAAGRRLSERLF T0334 377 :DKSLNPVL 1gesA 329 :KPDEHLDY T0334 385 :TARFNREI 1gesA 356 :EPQAREQY T0334 414 :DTP 1gesA 364 :GDD T0334 417 :FWRANKELRL 1gesA 378 :MYTAVTTHRQ T0334 427 :ADGMQEKIDMYRAGMA 1gesA 413 :DEMLQGFAVALKMGAT Number of specific fragments extracted= 24 number of extra gaps= 1 total=1122 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 1gesA/T0334-1gesA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0334 read from 1gesA/T0334-1gesA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1gesA read from 1gesA/T0334-1gesA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1gesA in template set Warning: unaligning (T0334)K4 because first residue in template chain is (1gesA)K3 T0334 5 :IDKILIVGGGTAGWMAASYLGK 1gesA 4 :HYDYIAIGGGSGGIASINRAAM T0334 30 :GTADITLLQAPDIPTLGVGEATIPN 1gesA 26 :YGQKCALIEAKELGGTCVNVGCVPK T0334 57 :TAF 1gesA 51 :KVM T0334 78 :YKVAIKFINW 1gesA 54 :WHAAQIREAI T0334 96 :EARELDGGP 1gesA 64 :HMYGPDYGF T0334 106 :HFYHSFGLL 1gesA 74 :TTINKFNWE T0334 115 :KYHEQI 1gesA 91 :YIDRIH T0334 121 :PLSHYWFDRSYRG 1gesA 98 :SYENVLGKNNVDV T0334 134 :KTVEPFDYA 1gesA 113 :GFARFVDAK T0334 152 :ANRSPRRLDGS 1gesA 141 :GRPSHPDIPGV T0334 166 :NYAW 1gesA 152 :EYGI T0334 170 :HFD 1gesA 205 :SFD T0334 174 :HLVADFLRRFA 1gesA 208 :PMISETLVEVM T0334 186 :EKLGVRHVED 1gesA 219 :NAEGPQLHTN T0334 196 :RVEHVQRDANGN 1gesA 230 :IPKAVVKNTDGS T0334 209 :ESVRTATGRVFDADLFVDCSGFRGL 1gesA 242 :LTLELEDGRSETVDCLIWAIGREPA T0334 236 :NKAMEEPFL 1gesA 272 :LEAAGVKTN T0334 246 :MSDHLLND 1gesA 281 :EKGYIVVD T0334 264 :DD 1gesA 289 :KY T0334 266 :ANGVE 1gesA 329 :KPDEH T0334 271 :PFTSAIAMKSGWTWKIPM 1gesA 337 :SNIPTVVFSHPPIGTVGL T0334 309 :VREFCEMWH 1gesA 356 :EPQAREQYG T0334 320 :PETQPLNRIRFRVG 1gesA 365 :DDQVKVYKSSFTAM T0334 334 :RNRRA 1gesA 386 :RQPCR T0334 346 :IG 1gesA 396 :VG T0334 378 :KSLNPVLTARFNREIETMFD 1gesA 409 :GFGMDEMLQGFAVALKMGAT T0334 434 :IDMYRAGMAINAPASDDAQ 1gesA 429 :KKDFDNTVAIHPTAAEEFV Number of specific fragments extracted= 27 number of extra gaps= 0 total=1149 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 1gesA/T0334-1gesA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0334 read from 1gesA/T0334-1gesA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1gesA read from 1gesA/T0334-1gesA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1gesA in template set Warning: unaligning (T0334)G12 because of BadResidue code BAD_PEPTIDE in next template residue (1gesA)A175 Warning: unaligning (T0334)G13 because of BadResidue code BAD_PEPTIDE at template residue (1gesA)A175 Warning: unaligning (T0334)G14 because of BadResidue code BAD_PEPTIDE at template residue (1gesA)G176 Warning: unaligning (T0334)T15 because of BadResidue code BAD_PEPTIDE at template residue (1gesA)Y177 T0334 5 :IDKILIV 1gesA 167 :PERVAVV T0334 16 :AGWMAASYLGK 1gesA 178 :IGVELGGVING T0334 30 :GTADITLLQAPDIPTL 1gesA 189 :LGAKTHLFEMFDAPLP T0334 50 :ATIPNLQTAF 1gesA 205 :SFDPMISETL T0334 181 :RRFATEKLGVRHVEDRVEHVQRDANGN 1gesA 215 :VEVMNAEGPQLHTNAIPKAVVKNTDGS T0334 209 :ESVRTATGRVFDADLFVDCSGF 1gesA 242 :LTLELEDGRSETVDCLIWAIGR T0334 237 :KAMEEPFLD 1gesA 273 :EAAGVKTNE T0334 294 :TGYVYSSRFAT 1gesA 282 :KGYIVVDKYQN T0334 338 :AWVGNCVSIGTSSCFVEPL 1gesA 293 :TNIEGIYAVGDNTGAVELT T0334 362 :YFVYAALYQLVKHFP 1gesA 312 :PVAVAAGRRLSERLF T0334 378 :K 1gesA 328 :N Number of specific fragments extracted= 11 number of extra gaps= 1 total=1160 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 1f8rA/T0334-1f8rA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1f8rA expands to /projects/compbio/data/pdb/1f8r.pdb.gz 1f8rA:# T0334 read from 1f8rA/T0334-1f8rA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1f8rA read from 1f8rA/T0334-1f8rA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1f8rA to template set # found chain 1f8rA in template set T0334 3 :GKID 1f8rA 30 :TSNP T0334 7 :KILIVGGGTAGWMAASYLGK 1f8rA 35 :HVVIVGAGMAGLSAAYVLAG T0334 29 :QGT 1f8rA 55 :AGH T0334 33 :DITLLQAPD 1f8rA 58 :QVTVLEASE T0334 42 :IPTL 1f8rA 68 :PGGR T0334 69 :EWMRECNAS 1f8rA 100 :EYIRKFDLR T0334 96 :EARELDGGPDHFYHSFGLL 1f8rA 109 :LNEFSQENDNAWYFIKNIR T0334 115 :KYHE 1f8rA 136 :DPGL T0334 152 :ANRSPRRLDGSKVTNYAWHF 1f8rA 141 :KYPVKPSEAGKSAGQLYEES T0334 172 :DAHLVADFLRRFA 1f8rA 239 :GMDKLPTAMYRDI T0334 186 :EK 1f8rA 252 :QD T0334 191 :RHVED 1f8rA 254 :KVHFN T0334 196 :RVEHVQRDANG 1f8rA 260 :QVIKIQQNDQK T0334 209 :ESVRTA 1f8rA 271 :VTVVYE T0334 215 :TGR 1f8rA 279 :SKE T0334 218 :VFDADLFVDCS 1f8rA 284 :SVTADYVIVCT T0334 231 :RGLLI 1f8rA 295 :TSRAV T0334 237 :KAMEEPFLDM 1f8rA 300 :RLIKFNPPLL T0334 247 :SDHLLNDSAVATQVPHDDDANGVEPFTSAIAMKSGWTWKIPM 1f8rA 319 :VHYRSGTKIFLTCTTKFWEDDGIHGGKSTTDLPSRFIYYPNH T0334 289 :LGRFGTGYVYSSRFATE 1f8rA 364 :NGVGVIIAYGIGDDANF T0334 306 :DEAVREFCEM 1f8rA 387 :KDCADIVFND T0334 316 :WHLDP 1f8rA 400 :IHQLP T0334 321 :ETQPLNRIRF 1f8rA 411 :FCYPSVIQKW T0334 331 :R 1f8rA 426 :A T0334 337 :RAWVGNCVSIGTSSCFVEPLESTGIYFVYAALYQLVKH 1f8rA 446 :TASQGRIYFAGEYTAQAHGWIDSTIKSGLRAARDVNLA Number of specific fragments extracted= 25 number of extra gaps= 0 total=1185 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 1f8rA/T0334-1f8rA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0334 read from 1f8rA/T0334-1f8rA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1f8rA read from 1f8rA/T0334-1f8rA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1f8rA in template set T0334 3 :GKIDKILIVGGGTAGWMAASYLGK 1f8rA 31 :SNPKHVVIVGAGMAGLSAAYVLAG T0334 30 :GTADITLLQAP 1f8rA 55 :AGHQVTVLEAS T0334 41 :DI 1f8rA 67 :RP T0334 45 :LGVGEATIPNLQTAF 1f8rA 88 :PMRLPEKHRIVREYI T0334 61 :DFLGI 1f8rA 103 :RKFDL T0334 96 :EARELDGGPDHFYHSFG 1f8rA 108 :RLNEFSQENDNAWYFIK T0334 123 :SHYWFDR 1f8rA 130 :VGEVKKD T0334 141 :YACYKEPVI 1f8rA 137 :PGLLKYPVK T0334 152 :ANRS 1f8rA 146 :PSEA T0334 173 :AHLVADFLRRFA 1f8rA 240 :MDKLPTAMYRDI T0334 186 :EKL 1f8rA 252 :QDK T0334 192 :HVED 1f8rA 255 :VHFN T0334 196 :RVEHVQRDANG 1f8rA 260 :QVIKIQQNDQK T0334 209 :ESVRTA 1f8rA 271 :VTVVYE T0334 215 :TG 1f8rA 279 :SK T0334 217 :RVFDADLFVDCS 1f8rA 283 :PSVTADYVIVCT T0334 231 :RGLL 1f8rA 295 :TSRA T0334 236 :NKA 1f8rA 299 :VRL T0334 239 :MEEPFLDM 1f8rA 304 :FNPPLLPK T0334 250 :LLNDSAVATQVPHDDDANGVEPFTSAIAMKSGWTWKIPM 1f8rA 321 :YRSGTKIFLTCTTKFWEDDGIHGGKSTTDLPSRFIYYPN T0334 289 :LGR 1f8rA 363 :TNG T0334 292 :FGTGYVYSSRFATE 1f8rA 367 :GVIIAYGIGDDANF T0334 306 :DEAVREFCEMW 1f8rA 387 :KDCADIVFNDL T0334 317 :HLDPETQ 1f8rA 402 :QLPKKDI T0334 328 :IRFRVG 1f8rA 413 :YPSVIQ T0334 337 :RA 1f8rA 419 :KW T0334 339 :WVGNCVSIGTSSCFVEPLESTGIYFVYAALYQLVKH 1f8rA 448 :SQGRIYFAGEYTAQAHGWIDSTIKSGLRAARDVNLA Number of specific fragments extracted= 27 number of extra gaps= 0 total=1212 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 1f8rA/T0334-1f8rA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0334 read from 1f8rA/T0334-1f8rA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1f8rA read from 1f8rA/T0334-1f8rA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1f8rA in template set Warning: unaligning (T0334)D377 because last residue in template chain is (1f8rA)N486 T0334 3 :GKIDKILIVGGGTAGWMAASYLGK 1f8rA 31 :SNPKHVVIVGAGMAGLSAAYVLAG T0334 30 :GTADITLLQAPDIPT 1f8rA 55 :AGHQVTVLEASERPG T0334 45 :LGVGEATI 1f8rA 84 :ANLGPMRL T0334 53 :PNLQTAFFDFLGIPE 1f8rA 95 :HRIVREYIRKFDLRL T0334 73 :ECNASYKVAIKFINWRTA 1f8rA 111 :EFSQENDNAWYFIKNIRK T0334 91 :GEGTSEARELDGGPDHFYHSFGLLKYHEQIPLSHYWFDRSYRGKTVEPFDYACYKEPVILDANRSPRRLDGSKVTNYAWHFDAHLVADF 1f8rA 135 :KDPGLLKYPVKPSEAGKSAGQLYEESLGKVVEELKRTNCSYILNKYDTYSTKEYLIKEGDLSPGAVDMIGDLLNEDSGYYVSFIESLKH T0334 180 :LRRFATEKLG 1f8rA 243 :LPTAMYRDIQ T0334 191 :RHVEDRVEHVQRDANGNIESVRTATGR 1f8rA 255 :VHFNAQVIKIQQNDQKVTVVYETLSKE T0334 218 :VFDADLFVDCSGFRG 1f8rA 284 :SVTADYVIVCTTSRA T0334 238 :AMEEPFLD 1f8rA 299 :VRLIKFNP T0334 246 :MSDHLLNDSAVATQVPHDDDANGVEPFTSAIAMKSGWTWKIPMLGR 1f8rA 317 :RSVHYRSGTKIFLTCTTKFWEDDGIHGGKSTTDLPSRFIYYPNHNF T0334 292 :FGTGYVYSS 1f8rA 366 :VGVIIAYGI T0334 301 :RFATEDEAVREFCEMWHLDPETQ 1f8rA 382 :QALDFKDCADIVFNDLSLIHQLP T0334 324 :PLNRIRFRVGRNRRAW 1f8rA 427 :MGGITTFTPYQFQHFS T0334 340 :VGNCVSIGTSSCFVEPLESTGIYFVYAALYQLVKHFP 1f8rA 449 :QGRIYFAGEYTAQAHGWIDSTIKSGLRAARDVNLASE Number of specific fragments extracted= 15 number of extra gaps= 0 total=1227 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 1fecA/T0334-1fecA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1fecA expands to /projects/compbio/data/pdb/1fec.pdb.gz 1fecA:Skipped atom 370, because occupancy 0.500 <= existing 0.500 in 1fecA Skipped atom 372, because occupancy 0.500 <= existing 0.500 in 1fecA Skipped atom 632, because occupancy 0.500 <= existing 0.500 in 1fecA Skipped atom 634, because occupancy 0.500 <= existing 0.500 in 1fecA Skipped atom 636, because occupancy 0.500 <= existing 0.500 in 1fecA Skipped atom 638, because occupancy 0.500 <= existing 0.500 in 1fecA Skipped atom 640, because occupancy 0.500 <= existing 0.500 in 1fecA Skipped atom 1589, because occupancy 0.500 <= existing 0.500 in 1fecA Skipped atom 1591, because occupancy 0.500 <= existing 0.500 in 1fecA Skipped atom 1593, because occupancy 0.500 <= existing 0.500 in 1fecA Skipped atom 1600, because occupancy 0.500 <= existing 0.500 in 1fecA Skipped atom 1602, because occupancy 0.500 <= existing 0.500 in 1fecA Skipped atom 1604, because occupancy 0.500 <= existing 0.500 in 1fecA Skipped atom 1606, because occupancy 0.500 <= existing 0.500 in 1fecA Skipped atom 1608, because occupancy 0.500 <= existing 0.500 in 1fecA Skipped atom 1610, because occupancy 0.500 <= existing 0.500 in 1fecA Skipped atom 1612, because occupancy 0.500 <= existing 0.500 in 1fecA Skipped atom 1614, because occupancy 0.500 <= existing 0.500 in 1fecA Skipped atom 1616, because occupancy 0.500 <= existing 0.500 in 1fecA Skipped atom 1618, because occupancy 0.500 <= existing 0.500 in 1fecA Skipped atom 1620, because occupancy 0.500 <= existing 0.500 in 1fecA Skipped atom 1622, because occupancy 0.500 <= existing 0.500 in 1fecA Skipped atom 1624, because occupancy 0.500 <= existing 0.500 in 1fecA Skipped atom 1626, because occupancy 0.500 <= existing 0.500 in 1fecA Skipped atom 1628, because occupancy 0.500 <= existing 0.500 in 1fecA Skipped atom 1630, because occupancy 0.500 <= existing 0.500 in 1fecA Skipped atom 1632, because occupancy 0.500 <= existing 0.500 in 1fecA Skipped atom 1634, because occupancy 0.500 <= existing 0.500 in 1fecA Skipped atom 1636, because occupancy 0.500 <= existing 0.500 in 1fecA Skipped atom 1638, because occupancy 0.500 <= existing 0.500 in 1fecA Skipped atom 1640, because occupancy 0.500 <= existing 0.500 in 1fecA Skipped atom 1642, because occupancy 0.500 <= existing 0.500 in 1fecA Skipped atom 1644, because occupancy 0.500 <= existing 0.500 in 1fecA Skipped atom 1646, because occupancy 0.500 <= existing 0.500 in 1fecA Skipped atom 1724, because occupancy 0.500 <= existing 0.500 in 1fecA Skipped atom 1726, because occupancy 0.500 <= existing 0.500 in 1fecA Skipped atom 1728, because occupancy 0.500 <= existing 0.500 in 1fecA Skipped atom 1730, because occupancy 0.500 <= existing 0.500 in 1fecA Skipped atom 1853, because occupancy 0.500 <= existing 0.500 in 1fecA Skipped atom 1855, because occupancy 0.500 <= existing 0.500 in 1fecA Skipped atom 1857, because occupancy 0.500 <= existing 0.500 in 1fecA Skipped atom 1859, because occupancy 0.500 <= existing 0.500 in 1fecA Skipped atom 1861, because occupancy 0.500 <= existing 0.500 in 1fecA Skipped atom 2566, because occupancy 0.500 <= existing 0.500 in 1fecA Skipped atom 2568, because occupancy 0.500 <= existing 0.500 in 1fecA Skipped atom 2570, because occupancy 0.500 <= existing 0.500 in 1fecA Skipped atom 2572, because occupancy 0.500 <= existing 0.500 in 1fecA Skipped atom 3406, because occupancy 0.500 <= existing 0.500 in 1fecA Skipped atom 3408, because occupancy 0.500 <= existing 0.500 in 1fecA # T0334 read from 1fecA/T0334-1fecA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1fecA read from 1fecA/T0334-1fecA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1fecA to template set # found chain 1fecA in template set T0334 5 :ID 1fecA 2 :RA T0334 7 :KILIVGGGTAGWMAASYLGK 1fecA 5 :DLVVIGAGSGGLEAGWNAAS T0334 28 :LQGT 1fecA 25 :LHKK T0334 33 :DITLLQAPD 1fecA 29 :RVAVIDLQK T0334 42 :IPTL 1fecA 39 :HGPP T0334 46 :GVGEATIPN 1fecA 75 :SAGFGWELD T0334 60 :FDFLGIPEDEWMRECNASYKVAIKFINWRTAGEGTS 1fecA 84 :RESVRPNWKALIAAKNKAVSGINDSYEGMFADTEGL T0334 96 :EARELDG 1fecA 162 :WPQHLGI T0334 103 :GPDHFYHSFGLL 1fecA 170 :GDDLCITSNEAF T0334 115 :KYHEQIPLSHYWFDRSYRGKTV 1fecA 185 :EAPKRALCVGGGYISIEFAGIF T0334 139 :FDYACYKEPVILD 1fecA 207 :NAYKARGGQVDLA T0334 152 :ANRSPRRL 1fecA 221 :RGDMILRG T0334 172 :DAHLVADFLRRFA 1fecA 229 :FDSELRKQLTEQL T0334 186 :EKLGVRHVED 1fecA 242 :RANGINVRTH T0334 196 :RVEHVQRDANGN 1fecA 253 :NPAKVTKNADGT T0334 209 :ESVRTATGRVFDADLFVDCSGF 1fecA 265 :RHVVFESGAEADYDVVMLAIGR T0334 231 :RG 1fecA 289 :RS T0334 233 :LLI 1fecA 293 :LQL T0334 237 :KAMEEPFLD 1fecA 296 :EKAGVEVAK T0334 247 :SDHLLNDSAVATQVPHDDDANGV 1fecA 305 :NGAIKVDAYSKTNVDNIYAIGDV T0334 281 :GWTWKIPM 1fecA 410 :FMVRIVTN T0334 289 :LGRFGTGYVYSSRFATE 1fecA 420 :DGEVLGVHMLGDSSPEI T0334 306 :DEAVREFCEMWHLDP 1fecA 438 :QSVAICLKMGAKISD T0334 321 :ETQPLNRIRFRVGRNR 1fecA 469 :SMRTPAYFYEKGKRVE Number of specific fragments extracted= 24 number of extra gaps= 0 total=1251 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 1fecA/T0334-1fecA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0334 read from 1fecA/T0334-1fecA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1fecA read from 1fecA/T0334-1fecA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1fecA in template set T0334 4 :KIDKILIVGGGTAGWMAASYLGKA 1fecA 2 :RAYDLVVIGAGSGGLEAGWNAASL T0334 30 :GTADITLLQAP 1fecA 26 :HKKRVAVIDLQ T0334 41 :DI 1fecA 38 :HH T0334 43 :PTLGVGEATIPNLQTAF 1fecA 41 :PPHYAALGGTCVNVGCV T0334 73 :ECNASYKVAIKFINWRTA 1fecA 58 :PKKLMVTGANYMDTIRES T0334 96 :EARELDGGPDHFYHSFGLL 1fecA 76 :AGFGWELDRESVRPNWKAL T0334 115 :KYHEQIPLSHYWFDR 1fecA 101 :AVSGINDSYEGMFAD T0334 159 :LDGSKVT 1fecA 116 :TEGLTFH T0334 166 :NYAW 1fecA 124 :GFGA T0334 170 :HFD 1fecA 228 :GFD T0334 174 :HLVADFLRRFA 1fecA 231 :SELRKQLTEQL T0334 186 :EKLGVRHVED 1fecA 242 :RANGINVRTH T0334 196 :RVEHVQRDANG 1fecA 253 :NPAKVTKNADG T0334 208 :IESVRTATGRVFDADLFVDCSGFRGL 1fecA 264 :TRHVVFESGAEADYDVVMLAIGRVPR T0334 234 :LIN 1fecA 292 :TLQ T0334 237 :KAMEEPFL 1fecA 296 :EKAGVEVA T0334 246 :MSDHLLNDSAV 1fecA 304 :KNGAIKVDAYS T0334 279 :KS 1fecA 406 :TY T0334 281 :GWTWKIPM 1fecA 410 :FMVRIVTN T0334 289 :LGR 1fecA 419 :ADG T0334 292 :FGTGYVYSSRFATE 1fecA 423 :VLGVHMLGDSSPEI T0334 306 :DEAVREFCEMW 1fecA 438 :QSVAICLKMGA T0334 323 :QPL 1fecA 461 :PTS Number of specific fragments extracted= 23 number of extra gaps= 0 total=1274 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 1fecA/T0334-1fecA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0334 read from 1fecA/T0334-1fecA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1fecA read from 1fecA/T0334-1fecA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1fecA in template set T0334 5 :IDKILIVGGGTAGWMAASYLGKALQGTADITLLQAPDI 1fecA 187 :PKRALCVGGGYISIEFAGIFNAYKARGGQVDLAYRGDM T0334 51 :TI 1fecA 225 :IL T0334 63 :LGIP 1fecA 227 :RGFD T0334 174 :HLVADFLRRFATEKLGVRHVEDRVEHVQRDANGN 1fecA 231 :SELRKQLTEQLRANGINVRTHENPAKVTKNADGT T0334 209 :ESVRTATGRVFDADLFVDCSGF 1fecA 265 :RHVVFESGAEADYDVVMLAIGR T0334 244 :LDMSDHLLNDS 1fecA 287 :VPRSQTLQLEK T0334 321 :ETQPLNRIRFRVG 1fecA 301 :EVAKNGAIKVDAY T0334 336 :RRAWVGNCVSIGTSSCFVEPL 1fecA 314 :SKTNVDNIYAIGDVTDRVMLT T0334 362 :YFVYAALYQLVKHFP 1fecA 335 :PVAINEGAAFVDTVF Number of specific fragments extracted= 9 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 1chuA/T0334-1chuA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1chuA expands to /projects/compbio/data/pdb/1chu.pdb.gz 1chuA:# T0334 read from 1chuA/T0334-1chuA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1chuA read from 1chuA/T0334-1chuA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1chuA to template set # found chain 1chuA in template set Warning: unaligning (T0334)S2 because first residue in template chain is (1chuA)N2 Warning: unaligning (T0334)P40 because of BadResidue code BAD_PEPTIDE in next template residue (1chuA)P40 Warning: unaligning (T0334)G46 because of BadResidue code BAD_PEPTIDE at template residue (1chuA)P40 Warning: unaligning (T0334)G48 because of BadResidue code BAD_PEPTIDE in next template residue (1chuA)E43 Warning: unaligning (T0334)E49 because of BadResidue code BAD_PEPTIDE at template residue (1chuA)E43 Warning: unaligning (T0334)L63 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1chuA)F57 Warning: unaligning (T0334)E118 because of BadResidue code BAD_PEPTIDE in next template residue (1chuA)S92 Warning: unaligning (T0334)Q119 because of BadResidue code BAD_PEPTIDE at template residue (1chuA)S92 Warning: unaligning (T0334)P147 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1chuA)T142 Warning: unaligning (T0334)D172 because of BadResidue code BAD_PEPTIDE at template residue (1chuA)L144 Warning: unaligning (T0334)V193 because of BadResidue code BAD_PEPTIDE in next template residue (1chuA)E158 Warning: unaligning (T0334)E194 because of BadResidue code BAD_PEPTIDE at template residue (1chuA)E158 Warning: unaligning (T0334)M288 because of BadResidue code BAD_PEPTIDE in next template residue (1chuA)G274 Warning: unaligning (T0334)L289 because of BadResidue code BAD_PEPTIDE at template residue (1chuA)G274 Warning: unaligning (T0334)S300 because of BadResidue code BAD_PEPTIDE in next template residue (1chuA)H315 Warning: unaligning (T0334)R301 because of BadResidue code BAD_PEPTIDE at template residue (1chuA)H315 Warning: unaligning (T0334)A303 because of BadResidue code BAD_PEPTIDE in next template residue (1chuA)A318 Warning: unaligning (T0334)T304 because of BadResidue code BAD_PEPTIDE at template residue (1chuA)A318 Warning: unaligning (T0334)E357 because of BadResidue code BAD_PEPTIDE in next template residue (1chuA)S389 Warning: unaligning (T0334)S358 because of BadResidue code BAD_PEPTIDE at template residue (1chuA)S389 Warning: unaligning (T0334)T516 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1chuA)F481 Warning: unaligning (T0334)L517 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1chuA)F481 T0334 3 :GKID 1chuA 3 :TLPE T0334 7 :KILIVGGGTAGWMAASYLG 1chuA 10 :DVLIIGSGAAGLSLALRLA T0334 29 :QGT 1chuA 29 :DQH T0334 33 :DITLLQA 1chuA 32 :QVIVLSK T0334 47 :V 1chuA 41 :V T0334 64 :GIPED 1chuA 58 :DETDS T0334 69 :EWMRECNAS 1chuA 65 :SHVEDTLIA T0334 104 :PDHFYHSFGLL 1chuA 74 :GAGICDRHAVE T0334 115 :KYH 1chuA 88 :SNA T0334 120 :IP 1chuA 93 :CV T0334 139 :FDYACYKE 1chuA 95 :QWLIDQGV T0334 173 :AHLVA 1chuA 145 :VSKAL T0334 186 :EKLGVRH 1chuA 150 :NHPNIRV T0334 195 :D 1chuA 159 :R T0334 196 :RVEHVQR 1chuA 161 :NAVDLIV T0334 203 :DANG 1chuA 173 :LPGT T0334 207 :NIESVRTA 1chuA 178 :RVVGAWVW T0334 216 :GR 1chuA 190 :ET T0334 218 :VFDADLFVDCSGFRGLLINKAMEEPFLDM 1chuA 194 :TCHAKAVVLATGGASKVYQYTTNPDISSG T0334 247 :SDHLLNDSAV 1chuA 239 :EFNQFHPTAL T0334 264 :DDANG 1chuA 249 :YHPQA T0334 271 :PFTS 1chuA 254 :RNFL T0334 275 :AIAMKSGWTWKIP 1chuA 260 :EALRGEGAYLKRP T0334 290 :GR 1chuA 275 :TR T0334 292 :FGTGYVYS 1chuA 306 :ADCMFLDI T0334 302 :F 1chuA 316 :K T0334 305 :E 1chuA 319 :D T0334 306 :DEAVREFCEM 1chuA 326 :PMIYEKLLGL T0334 317 :HLDPETQPLNRIRFRVGRNR 1chuA 336 :GIDLTQEPVPIVPAAHYTCG T0334 337 :RAWVGNCVSIGTSSCF 1chuA 364 :RTDVEGLYAIGEVSYT T0334 353 :VEP 1chuA 381 :LHG T0334 356 :L 1chuA 387 :M T0334 359 :TGIYFVYAALYQLVKHFP 1chuA 390 :NSLLECLVYGWSAAEDIT T0334 377 :DKSLNPVLTARFNREIETMFDDTRDF 1chuA 425 :SRVENPDERVVIQHNWHELRLFMWDY T0334 478 :LG 1chuA 451 :VG T0334 489 :LAHMPQATESVDEVFGAVKDRQRNLLE 1chuA 453 :IVRTTKRLERALRRITMLQQEIDEYYA T0334 518 :PSLHEFLR 1chuA 482 :RVSNNLLE Number of specific fragments extracted= 37 number of extra gaps= 10 total=1320 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 1chuA/T0334-1chuA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0334 read from 1chuA/T0334-1chuA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1chuA read from 1chuA/T0334-1chuA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1chuA in template set Warning: unaligning (T0334)P40 because of BadResidue code BAD_PEPTIDE in next template residue (1chuA)P40 Warning: unaligning (T0334)D41 because of BadResidue code BAD_PEPTIDE at template residue (1chuA)P40 Warning: unaligning (T0334)P43 because of BadResidue code BAD_PEPTIDE in next template residue (1chuA)E43 Warning: unaligning (T0334)T44 because of BadResidue code BAD_PEPTIDE at template residue (1chuA)E43 Warning: unaligning (T0334)I65 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1chuA)F57 Warning: unaligning (T0334)T89 because of BadResidue code BAD_PEPTIDE in next template residue (1chuA)S92 Warning: unaligning (T0334)A90 because of BadResidue code BAD_PEPTIDE at template residue (1chuA)S92 Warning: unaligning (T0334)R132 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1chuA)T142 Warning: unaligning (T0334)V193 because of BadResidue code BAD_PEPTIDE in next template residue (1chuA)E158 Warning: unaligning (T0334)E194 because of BadResidue code BAD_PEPTIDE at template residue (1chuA)E158 Warning: unaligning (T0334)G290 because of BadResidue code BAD_PEPTIDE in next template residue (1chuA)G274 Warning: unaligning (T0334)R291 because of BadResidue code BAD_PEPTIDE at template residue (1chuA)G274 Warning: unaligning (T0334)S300 because of BadResidue code BAD_PEPTIDE in next template residue (1chuA)H315 Warning: unaligning (T0334)R301 because of BadResidue code BAD_PEPTIDE at template residue (1chuA)H315 Warning: unaligning (T0334)A303 because of BadResidue code BAD_PEPTIDE in next template residue (1chuA)A318 Warning: unaligning (T0334)T304 because of BadResidue code BAD_PEPTIDE at template residue (1chuA)A318 Warning: unaligning (T0334)E357 because of BadResidue code BAD_PEPTIDE in next template residue (1chuA)S389 Warning: unaligning (T0334)S358 because of BadResidue code BAD_PEPTIDE at template residue (1chuA)S389 Warning: unaligning (T0334)T516 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1chuA)F481 Warning: unaligning (T0334)L517 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1chuA)F481 T0334 5 :IDKILIVGGGTAGWMAASYLG 1chuA 8 :SCDVLIIGSGAAGLSLALRLA T0334 30 :GTADITLLQA 1chuA 29 :DQHQVIVLSK T0334 42 :I 1chuA 41 :V T0334 66 :PEDE 1chuA 58 :DETD T0334 70 :WMRECNASYK 1chuA 63 :IDSHVEDTLI T0334 80 :VAIKFINWR 1chuA 82 :AVEFVASNA T0334 91 :G 1chuA 93 :C T0334 123 :SHYWFDRSY 1chuA 94 :VQWLIDQGV T0334 183 :FATEKLGVRH 1chuA 147 :KALNHPNIRV T0334 195 :D 1chuA 159 :R T0334 196 :RVEHVQR 1chuA 161 :NAVDLIV T0334 203 :DANGNIESVR 1chuA 174 :PGTRRVVGAW T0334 213 :TATG 1chuA 186 :NRNK T0334 217 :RVFDADLFVDCSGFRGLL 1chuA 193 :ETCHAKAVVLATGGASKV T0334 236 :NKA 1chuA 211 :YQY T0334 239 :MEEPFLDMSDHLLNDSAV 1chuA 231 :AGCRVANLEFNQFHPTAL T0334 261 :PHDDDANGVEPFTSA 1chuA 249 :YHPQARNFLLTEALR T0334 279 :KSG 1chuA 264 :GEG T0334 284 :WKIPML 1chuA 267 :AYLKRP T0334 292 :FGT 1chuA 276 :RFM T0334 295 :GYVYS 1chuA 309 :MFLDI T0334 302 :F 1chuA 316 :K T0334 305 :E 1chuA 319 :D T0334 306 :DEAVREFCEM 1chuA 326 :PMIYEKLLGL T0334 317 :HLDPETQPLNRIRFRVG 1chuA 336 :GIDLTQEPVPIVPAAHY T0334 339 :WVGNCVSIG 1chuA 366 :DVEGLYAIG T0334 348 :TSSCFVEPL 1chuA 379 :TGLHGANRM T0334 359 :TGIYFVYAALYQLVKHFPD 1chuA 390 :NSLLECLVYGWSAAEDITR T0334 378 :KSLNPVLTARFNREIETMFDDTRDF 1chuA 426 :RVENPDERVVIQHNWHELRLFMWDY T0334 442 :AINA 1chuA 452 :GIVR T0334 492 :MPQATESVDEVFGAVKDRQRNLLE 1chuA 456 :TTKRLERALRRITMLQQEIDEYYA T0334 518 :PSLHEFLRQQ 1chuA 482 :RVSNNLLELR Number of specific fragments extracted= 32 number of extra gaps= 9 total=1352 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 1chuA/T0334-1chuA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0334 read from 1chuA/T0334-1chuA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1chuA read from 1chuA/T0334-1chuA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1chuA in template set Warning: unaligning (T0334)P40 because of BadResidue code BAD_PEPTIDE in next template residue (1chuA)P40 Warning: unaligning (T0334)D41 because of BadResidue code BAD_PEPTIDE at template residue (1chuA)P40 Warning: unaligning (T0334)P43 because of BadResidue code BAD_PEPTIDE in next template residue (1chuA)E43 Warning: unaligning (T0334)T44 because of BadResidue code BAD_PEPTIDE at template residue (1chuA)E43 Warning: unaligning (T0334)I65 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1chuA)F57 Warning: unaligning (T0334)D140 because of BadResidue code BAD_PEPTIDE in next template residue (1chuA)S92 Warning: unaligning (T0334)Y141 because of BadResidue code BAD_PEPTIDE at template residue (1chuA)S92 Warning: unaligning (T0334)P156 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1chuA)T142 Warning: unaligning (T0334)H192 because of BadResidue code BAD_PEPTIDE in next template residue (1chuA)E158 Warning: unaligning (T0334)V193 because of BadResidue code BAD_PEPTIDE at template residue (1chuA)E158 Warning: unaligning (T0334)I276 because of BadResidue code BAD_PEPTIDE in next template residue (1chuA)A228 Warning: unaligning (T0334)A277 because of BadResidue code BAD_PEPTIDE at template residue (1chuA)A228 Warning: unaligning (T0334)E357 because of BadResidue code BAD_PEPTIDE in next template residue (1chuA)S389 Warning: unaligning (T0334)S358 because of BadResidue code BAD_PEPTIDE at template residue (1chuA)S389 Warning: unaligning (T0334)S379 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1chuA)H414 Warning: unaligning (T0334)P411 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1chuA)H414 Warning: unaligning (T0334)T413 because of BadResidue code BAD_PEPTIDE in next template residue (1chuA)S417 Warning: unaligning (T0334)D414 because of BadResidue code BAD_PEPTIDE at template residue (1chuA)S417 Warning: unaligning (T0334)T415 because of BadResidue code BAD_PEPTIDE at template residue (1chuA)T418 Warning: unaligning (T0334)T516 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1chuA)F481 T0334 5 :IDKILIVGGGTAGWMAASYLG 1chuA 8 :SCDVLIIGSGAAGLSLALRLA T0334 30 :GTADITLLQA 1chuA 29 :DQHQVIVLSK T0334 42 :I 1chuA 41 :V T0334 66 :PEDEWMREC 1chuA 58 :DETDSIDSH T0334 114 :LKYHEQIPLSHYWFDR 1chuA 68 :EDTLIAGAGICDRHAV T0334 133 :GKTVEPF 1chuA 84 :EFVASNA T0334 142 :ACYKEPVIL 1chuA 93 :CVQWLIDQG T0334 155 :S 1chuA 102 :V T0334 183 :FATEK 1chuA 147 :KALNH T0334 188 :LGVR 1chuA 153 :NIRV T0334 194 :EDRVEHVQRD 1chuA 159 :RTNAVDLIVS T0334 204 :ANGN 1chuA 175 :GTRR T0334 208 :IESVRTATGR 1chuA 181 :GAWVWNRNKE T0334 218 :VFDADLFVDCSGFRG 1chuA 194 :TCHAKAVVLATGGAS T0334 248 :DHL 1chuA 209 :KVY T0334 261 :PHDDDANGVEPFTSA 1chuA 212 :QYTTNPDISSGDGIA T0334 278 :MKSGWTWKIPMLGRFGTGYVYSSR 1chuA 229 :WRAGCRVANLEFNQFHPTALYHPQ T0334 302 :FATED 1chuA 257 :LLTEA T0334 307 :EAVREFCEMWHLDPETQ 1chuA 323 :QHFPMIYEKLLGLGIDL T0334 324 :PLNRIRFRVGRN 1chuA 342 :EPVPIVPAAHYT T0334 338 :AWV 1chuA 354 :CGG T0334 341 :GNCVSIGTSS 1chuA 368 :EGLYAIGEVS T0334 351 :CFVEPL 1chuA 382 :HGANRM T0334 359 :TGIYFVYAALYQLVKHFPDK 1chuA 390 :NSLLECLVYGWSAAEDITRR T0334 412 :R 1chuA 415 :D T0334 416 :PFWRANKELRLADGMQEKIDMYRA 1chuA 419 :LPPWDESRVENPDERVVIQHNWHE T0334 458 :FEEEFRNFWNNSNY 1chuA 443 :LRLFMWDYVGIVRT T0334 493 :PQATESVDEVFGAVKDRQRNLLE 1chuA 457 :TKRLERALRRITMLQQEIDEYYA Number of specific fragments extracted= 28 number of extra gaps= 8 total=1380 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 1nhs/T0334-1nhs-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1nhs expands to /projects/compbio/data/pdb/1nhs.pdb.gz 1nhs:Warning: there is no chain 1nhs will retry with 1nhsA # T0334 read from 1nhs/T0334-1nhs-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1nhs read from 1nhs/T0334-1nhs-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1nhs to template set # found chain 1nhs in template set Warning: unaligning (T0334)D101 because of BadResidue code BAD_PEPTIDE in next template residue (1nhs)K123 Warning: unaligning (T0334)G102 because of BadResidue code BAD_PEPTIDE at template residue (1nhs)K123 Warning: unaligning (T0334)G103 because of BadResidue code BAD_PEPTIDE at template residue (1nhs)D124 Warning: unaligning (T0334)P104 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1nhs)L125 T0334 7 :KILIVGGGTAGWMAASYLGK 1nhs 2 :KVIVLGSSHGGYEAVEELLN T0334 28 :L 1nhs 22 :L T0334 29 :QGT 1nhs 24 :PDA T0334 33 :DITLLQAPD 1nhs 27 :EIQWYEKGD T0334 42 :IPTLGVG 1nhs 37 :ISFLCCG T0334 57 :TAFFDFLGIPED 1nhs 44 :MQLYLEGKVKDV T0334 69 :EWMRECNASYKVAIKFINWRTAGEGTS 1nhs 64 :EKMESRGVNVFSNTEITAIQPKEHQVT T0334 96 :EAREL 1nhs 117 :ELDIP T0334 105 :DHFYHSFGLL 1nhs 126 :DNIYLMRGRQ T0334 115 :KYHEQIPLSHYWFDRSYRG 1nhs 147 :PEVNNVVVIGSGYIGIEAA T0334 139 :FDYACYKEPVILD 1nhs 166 :EAFAKAGKKVTVI T0334 152 :ANRSPRRLD 1nhs 180 :ILDRPLGVY T0334 172 :DAHLVADFLRRFA 1nhs 189 :LDKEFTDVLTEEM T0334 186 :EKLGVRHVED 1nhs 202 :EANNITIATG T0334 196 :RVEHV 1nhs 213 :TVERY T0334 203 :DANGNIESVRTATG 1nhs 218 :EGDGRVQKVVTDKN T0334 218 :VFDADLFVDCSGFRG 1nhs 232 :AYDADLVVVAVGVRP T0334 233 :LLINKAMEEPF 1nhs 249 :AWLKGTLELHP T0334 247 :SDHLLNDSAVATQVPHDDDANGV 1nhs 260 :NGLIKTDEYMRTSEPDVFAVGDA T0334 270 :EPF 1nhs 323 :VQG T0334 275 :AIAMKSGWTWKIPML 1nhs 328 :GLAVFDYKFASTGIN T0334 306 :DEAVREF 1nhs 343 :EVMAQKL T0334 322 :TQPLNRIRFRVGRNRRAWVG 1nhs 350 :GKETKAVTVVEDYLMDFNPD T0334 342 :NCVSIG 1nhs 388 :GAQLMS T0334 378 :KSLNPVLTARFNREIE 1nhs 394 :KADLTANINAISLAIQ T0334 414 :DTPFWRANKELRL 1nhs 410 :AKMTIEDLAYADF Number of specific fragments extracted= 26 number of extra gaps= 1 total=1406 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 1nhs/T0334-1nhs-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0334 read from 1nhs/T0334-1nhs-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1nhs read from 1nhs/T0334-1nhs-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1nhs in template set Warning: unaligning (T0334)D6 because first residue in template chain is (1nhs)M1 Warning: unaligning (T0334)L159 because of BadResidue code BAD_PEPTIDE in next template residue (1nhs)K123 Warning: unaligning (T0334)D160 because of BadResidue code BAD_PEPTIDE at template residue (1nhs)K123 Warning: unaligning (T0334)G161 because of BadResidue code BAD_PEPTIDE at template residue (1nhs)D124 Warning: unaligning (T0334)S162 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1nhs)L125 T0334 7 :KILIVGGGTAGWMAASYLGKA 1nhs 2 :KVIVLGSSHGGYEAVEELLNL T0334 29 :QGTADITLLQAPDIPTL 1nhs 23 :HPDAEIQWYEKGDFISF T0334 46 :GVG 1nhs 41 :CCG T0334 55 :LQTAF 1nhs 44 :MQLYL T0334 123 :SHYWFDRS 1nhs 63 :GEKMESRG T0334 136 :VEPFDYACYKEPVILD 1nhs 71 :VNVFSNTEITAIQPKE T0334 152 :ANRSPRR 1nhs 115 :PFELDIP T0334 166 :NYAW 1nhs 126 :DNIY T0334 170 :HFD 1nhs 188 :YLD T0334 174 :HLVADFLRRFA 1nhs 191 :KEFTDVLTEEM T0334 186 :EKLGVRHVED 1nhs 202 :EANNITIATG T0334 196 :RVEHVQ 1nhs 213 :TVERYE T0334 204 :ANGNIESVRTATG 1nhs 219 :GDGRVQKVVTDKN T0334 218 :VFDADLFVDCSGFRGLL 1nhs 232 :AYDADLVVVAVGVRPNT T0334 236 :NKAMEE 1nhs 249 :AWLKGT T0334 242 :PFLD 1nhs 256 :ELHP T0334 247 :SDHLLNDSAVAT 1nhs 260 :NGLIKTDEYMRT T0334 263 :DDD 1nhs 272 :SEP T0334 268 :GVE 1nhs 319 :PFP T0334 271 :PFTSAIAMKSGWTWKIPM 1nhs 324 :QGSSGLAVFDYKFASTGI T0334 310 :REFCEMWHL 1nhs 343 :EVMAQKLGK T0334 324 :PLNRIRFRVGRNRRAWVG 1nhs 352 :ETKAVTVVEDYLMDFNPD Number of specific fragments extracted= 22 number of extra gaps= 1 total=1428 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 1nhs/T0334-1nhs-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0334 read from 1nhs/T0334-1nhs-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1nhs read from 1nhs/T0334-1nhs-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1nhs in template set T0334 2 :SGKIDKILIVGGGTAGWMAASYLGK 1nhs 146 :DPEVNNVVVIGSGYIGIEAAEAFAK T0334 30 :GTADITLLQAPDIP 1nhs 171 :AGKKVTVIDILDRP T0334 63 :LGI 1nhs 185 :LGV T0334 101 :D 1nhs 188 :Y T0334 172 :DAHLVADFLRRFATEKLGVRHVEDRVEHVQ 1nhs 189 :LDKEFTDVLTEEMEANNITIATGETVERYE T0334 204 :ANGNIESVRT 1nhs 219 :GDGRVQKVVT T0334 215 :TGRVFDADLFVDCSGFR 1nhs 229 :DKNAYDADLVVVAVGVR T0334 258 :TQVPH 1nhs 246 :PNTAW T0334 316 :WHLDPETQPLNRIRFRVGR 1nhs 251 :LKGTLELHPNGLIKTDEYM T0334 337 :RAWVGNCVSIGTSS 1nhs 270 :RTSEPDVFAVGDAT T0334 361 :IYFVYAALYQLVKHFPDK 1nhs 299 :ATNARKQGRFAVKNLEEP Number of specific fragments extracted= 11 number of extra gaps= 0 total=1439 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 1xhcA/T0334-1xhcA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1xhcA expands to /projects/compbio/data/pdb/1xhc.pdb.gz 1xhcA:Skipped atom 303, because occupancy 0.350 <= existing 0.650 in 1xhcA Skipped atom 305, because occupancy 0.350 <= existing 0.650 in 1xhcA Skipped atom 307, because occupancy 0.350 <= existing 0.650 in 1xhcA Skipped atom 309, because occupancy 0.350 <= existing 0.650 in 1xhcA # T0334 read from 1xhcA/T0334-1xhcA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1xhcA read from 1xhcA/T0334-1xhcA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1xhcA to template set # found chain 1xhcA in template set Warning: unaligning (T0334)A90 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1xhcA)R82 Warning: unaligning (T0334)G91 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1xhcA)R82 Warning: unaligning (T0334)E92 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1xhcA)K83 Warning: unaligning (T0334)Y125 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1xhcA)G144 Warning: unaligning (T0334)W126 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1xhcA)G144 Warning: unaligning (T0334)L356 because of BadResidue code BAD_PEPTIDE in next template residue (1xhcA)I268 Warning: unaligning (T0334)E357 because of BadResidue code BAD_PEPTIDE at template residue (1xhcA)I268 T0334 7 :KILIVGGGTAGWMAASYLG 1xhcA 2 :KVVIVGNGPGGFELAKQLS T0334 29 :QGT 1xhcA 21 :QTY T0334 33 :DITLLQAPDIPTLGVG 1xhcA 24 :EVTVIDKEPVPYYSKP T0334 57 :TAFFDFLGIPED 1xhcA 40 :MLSHYIAGFIPR T0334 69 :EWMRECNASYKVAIKFINWRT 1xhcA 60 :DWYRKRGIEIRLAEEAKLIDR T0334 93 :GTS 1xhcA 84 :VVI T0334 96 :EARELDG 1xhcA 107 :EPQIKGK T0334 105 :DHFYHSFGLL 1xhcA 114 :EYLLTLRTIF T0334 115 :KYHEQIPLSH 1xhcA 133 :ENSGEAIIIG T0334 127 :FDRSYRG 1xhcA 145 :FIGLELA T0334 139 :FDYACYKEPVILD 1xhcA 152 :GNLAEAGYHVKLI T0334 152 :ANRSPRR 1xhcA 166 :RGAMFLG T0334 172 :DAHLVADFLRRFA 1xhcA 173 :LDEELSNMIKDML T0334 186 :EKLGVRHVED 1xhcA 186 :EETGVKFFLN T0334 196 :RVEHV 1xhcA 197 :ELLEA T0334 203 :DANG 1xhcA 202 :NEEG T0334 211 :VRTATG 1xhcA 206 :VLTNSG T0334 218 :VFDADLFVDCSGFRG 1xhcA 212 :FIEGKVKICAIGIVP T0334 233 :LLINKAMEEPF 1xhcA 228 :VDLARRSGIHT T0334 247 :SDHLLNDSAVA 1xhcA 239 :GRGILIDDNFR T0334 338 :AWVGNCVSIGTSSCF 1xhcA 250 :TSAKDVYAIGDCAEY T0334 354 :EP 1xhcA 265 :SG T0334 358 :STGIYFVYAALYQLVKHFPDKSLN 1xhcA 269 :AGTAKAAMEQARVLADILKGEPRR Number of specific fragments extracted= 23 number of extra gaps= 3 total=1462 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 1xhcA/T0334-1xhcA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0334 read from 1xhcA/T0334-1xhcA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1xhcA read from 1xhcA/T0334-1xhcA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1xhcA in template set Warning: unaligning (T0334)D6 because first residue in template chain is (1xhcA)S1 Warning: unaligning (T0334)A142 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1xhcA)R82 Warning: unaligning (T0334)C143 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1xhcA)R82 Warning: unaligning (T0334)P355 because of BadResidue code BAD_PEPTIDE in next template residue (1xhcA)I268 Warning: unaligning (T0334)L356 because of BadResidue code BAD_PEPTIDE at template residue (1xhcA)I268 T0334 7 :KILIVGGGTAGW 1xhcA 2 :KVVIVGNGPGGF T0334 23 :YLGKALQGTADITLLQAPDIPTLG 1xhcA 14 :ELAKQLSQTYEVTVIDKEPVPYYS T0334 52 :IPNLQTAF 1xhcA 38 :KPMLSHYI T0334 63 :LGI 1xhcA 46 :AGF T0334 92 :EGTSEARELD 1xhcA 49 :IPRNRLFPYS T0334 123 :SHYWFDRSYRG 1xhcA 59 :LDWYRKRGIEI T0334 134 :KTVEPFDY 1xhcA 73 :EEAKLIDR T0334 145 :KEPVILD 1xhcA 89 :KGEVPYD T0334 152 :ANRSPRRLDG 1xhcA 105 :AREPQIKGKE T0334 167 :YAW 1xhcA 115 :YLL T0334 170 :HFD 1xhcA 172 :GLD T0334 174 :HLVADFLRRFA 1xhcA 175 :EELSNMIKDML T0334 186 :EKLGVRHVED 1xhcA 186 :EETGVKFFLN T0334 196 :RVEHV 1xhcA 197 :ELLEA T0334 204 :ANG 1xhcA 202 :NEE T0334 210 :SVRTATGR 1xhcA 205 :GVLTNSGF T0334 219 :FDADLFVDCSGFRGLL 1xhcA 213 :IEGKVKICAIGIVPNV T0334 235 :INKAMEEP 1xhcA 230 :LARRSGIH T0334 246 :MSDH 1xhcA 238 :TGRG T0334 258 :TQV 1xhcA 242 :ILI T0334 278 :MKSG 1xhcA 245 :DDNF T0334 287 :P 1xhcA 249 :R T0334 338 :AWVGNCVSIGTSSCFVE 1xhcA 250 :TSAKDVYAIGDCAEYSG T0334 357 :EST 1xhcA 269 :AGT T0334 361 :IYFVYAALYQLVKHFPDKSLN 1xhcA 272 :AKAAMEQARVLADILKGEPRR Number of specific fragments extracted= 25 number of extra gaps= 2 total=1487 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 1xhcA/T0334-1xhcA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0334 read from 1xhcA/T0334-1xhcA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1xhcA read from 1xhcA/T0334-1xhcA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1xhcA in template set Warning: unaligning (T0334)D6 because first residue in template chain is (1xhcA)S1 Warning: unaligning (T0334)A90 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1xhcA)R82 Warning: unaligning (T0334)G91 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1xhcA)R82 Warning: unaligning (T0334)E92 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1xhcA)K83 Warning: unaligning (T0334)L356 because of BadResidue code BAD_PEPTIDE in next template residue (1xhcA)I268 Warning: unaligning (T0334)E357 because of BadResidue code BAD_PEPTIDE at template residue (1xhcA)I268 T0334 7 :KILIVGGGTAG 1xhcA 2 :KVVIVGNGPGG T0334 22 :SYLGKALQGTADITLLQAPDIPTLG 1xhcA 13 :FELAKQLSQTYEVTVIDKEPVPYYS T0334 52 :IPNLQTAF 1xhcA 38 :KPMLSHYI T0334 63 :LGI 1xhcA 46 :AGF T0334 66 :PE 1xhcA 50 :PR T0334 68 :DEWMRECNASYKVAIKFINWRT 1xhcA 59 :LDWYRKRGIEIRLAEEAKLIDR T0334 93 :GTSEAREL 1xhcA 84 :VVITEKGE T0334 101 :DGGPDH 1xhcA 106 :REPQIK T0334 119 :QIPLSHYWFDRSYRGKTVEPFD 1xhcA 112 :GKEYLLTLRTIFDADRIKESIE T0334 141 :YACYKEPVILDANRSPRRLDGSKVTNY 1xhcA 147 :GLELAGNLAEAGYHVKLIHRGAMFLGL T0334 173 :AHLVADFLRRFATEKLGVRHVEDRVEHVQ 1xhcA 174 :DEELSNMIKDMLEETGVKFFLNSELLEAN T0334 204 :ANG 1xhcA 203 :EEG T0334 211 :VRTAT 1xhcA 206 :VLTNS T0334 217 :RVFDADLFVDCSGF 1xhcA 211 :GFIEGKVKICAIGI T0334 258 :TQV 1xhcA 225 :VPN T0334 274 :SAIAMKSGW 1xhcA 228 :VDLARRSGI T0334 291 :RFGTGYVYSSRF 1xhcA 237 :HTGRGILIDDNF T0334 337 :RAWVGNCVSIGTSSCF 1xhcA 249 :RTSAKDVYAIGDCAEY T0334 355 :P 1xhcA 266 :G T0334 358 :STGIYFVYAALYQLVKHFPDKSL 1xhcA 269 :AGTAKAAMEQARVLADILKGEPR Number of specific fragments extracted= 20 number of extra gaps= 2 total=1507 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 3grs/T0334-3grs-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 3grs expands to /projects/compbio/data/pdb/3grs.pdb.gz 3grs:Warning: there is no chain 3grs will retry with 3grsA # T0334 read from 3grs/T0334-3grs-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3grs read from 3grs/T0334-3grs-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3grs to template set # found chain 3grs in template set Warning: unaligning (T0334)F62 because of BadResidue code BAD_PEPTIDE in next template residue (3grs)G92 Warning: unaligning (T0334)L63 because of BadResidue code BAD_PEPTIDE at template residue (3grs)G92 Warning: unaligning (T0334)G64 because of BadResidue code BAD_PEPTIDE at template residue (3grs)K93 Warning: unaligning (T0334)L100 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (3grs)Q167 Warning: unaligning (T0334)D101 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (3grs)Q167 T0334 5 :ID 3grs 19 :AS T0334 7 :KILIVGGGTAGWMAASYLGK 3grs 22 :DYLVIGGGSGGLASARRAAE T0334 29 :QGT 3grs 42 :LGA T0334 33 :DITLLQAPDIPTL 3grs 45 :RAAVVESHKLGGT T0334 46 :GVGEATIPN 3grs 81 :DHADYGFPS T0334 61 :D 3grs 90 :C T0334 65 :IPEDEWMRECNASYKVAIKFINWRTAGEGTS 3grs 94 :FNWRVIKEKRDAYVSRLNAIYQNNLTKSHIE T0334 96 :EARE 3grs 162 :TPHE T0334 102 :G 3grs 168 :I T0334 103 :GPDHFYHSFGLL 3grs 170 :GASLGITSDGFF T0334 115 :KYHEQIPLSHYWFDRSYRG 3grs 185 :ELPGRSVIVGAGYIAVEMA T0334 139 :FDYACYKEPVILD 3grs 204 :GILSALGSKTSLM T0334 152 :ANRSPRRL 3grs 218 :RHDKVLRS T0334 172 :DAHLVADFLRRFA 3grs 226 :FDSMISTNCTEEL T0334 186 :EKLGVRHVED 3grs 239 :ENAGVEVLKF T0334 196 :RVEHVQRDANG 3grs 250 :QVKEVKKTLSG T0334 209 :ESVRTA 3grs 261 :LEVSMV T0334 215 :TGR 3grs 270 :PGR T0334 218 :VF 3grs 278 :MI T0334 220 :DADLFVDCSGFRG 3grs 281 :DVDCLLWAIGRVP T0334 233 :LLI 3grs 298 :LSL T0334 237 :KAMEEPFLD 3grs 301 :NKLGIQTDD T0334 247 :SDHLLNDSAVATQV 3grs 310 :KGHIIVDEFQNTNV T0334 341 :GNCVSIGTSSCF 3grs 324 :KGIYAVGDVCGK T0334 358 :STGIYFVYAALYQLVKHFP 3grs 336 :ALLTPVAIAAGRKLAHRLF T0334 377 :DKSLN 3grs 357 :KEDSK Number of specific fragments extracted= 26 number of extra gaps= 2 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 3grs/T0334-3grs-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0334 read from 3grs/T0334-3grs-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3grs read from 3grs/T0334-3grs-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3grs in template set Warning: unaligning (T0334)P104 because of BadResidue code BAD_PEPTIDE in next template residue (3grs)G92 Warning: unaligning (T0334)D105 because of BadResidue code BAD_PEPTIDE at template residue (3grs)G92 Warning: unaligning (T0334)H106 because of BadResidue code BAD_PEPTIDE at template residue (3grs)K93 Warning: unaligning (T0334)R157 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (3grs)Q167 Warning: unaligning (T0334)R158 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (3grs)Q167 T0334 5 :IDKILIVGGGTAGWMAASYLGKA 3grs 20 :SYDYLVIGGGSGGLASARRAAEL T0334 31 :TADITLLQAPDIPTLGVGEATIPN 3grs 43 :GARAAVVESHKLGGTCVNVGCVPK T0334 57 :TAF 3grs 67 :KVM T0334 78 :YKVAIKFINWRTA 3grs 70 :WNTAVHSEFMHDH T0334 96 :EARELDGG 3grs 83 :ADYGFPSC T0334 107 :FYHSFGLLKYHEQIPLSHYWFDRSYRGKTVEPFD 3grs 94 :FNWRVIKEKRDAYVSRLNAIYQNNLTKSHIEIIR T0334 144 :YKEPVILD 3grs 128 :GHAAFTSD T0334 152 :ANRSP 3grs 161 :STPHE T0334 159 :LDGS 3grs 168 :IPGA T0334 166 :NYAW 3grs 172 :SLGI T0334 170 :HFD 3grs 225 :SFD T0334 174 :HLVADFLRRFA 3grs 228 :SMISTNCTEEL T0334 186 :EKLGVRHVED 3grs 239 :ENAGVEVLKF T0334 196 :RVEHVQRDANGNIESVRTA 3grs 250 :QVKEVKKTLSGLEVSMVTA T0334 215 :TG 3grs 270 :PG T0334 217 :RVFD 3grs 277 :TMIP T0334 221 :ADLFVDCSGFRGLL 3grs 282 :VDCLLWAIGRVPNT T0334 236 :NKA 3grs 296 :KDL T0334 239 :MEEPFLDMSDH 3grs 303 :LGIQTDDKGHI T0334 251 :LND 3grs 314 :IVD T0334 264 :DD 3grs 317 :EF T0334 266 :ANGVE 3grs 357 :KEDSK T0334 271 :PFTSAIAMKSGWTWKIPM 3grs 365 :NNIPTVVFSHPPIGTVGL T0334 309 :VREFCEMWH 3grs 384 :EDEAIHKYG T0334 320 :P 3grs 393 :I T0334 323 :QPLNRIRFRVGRNRRAWVGN 3grs 394 :ENVKTYSTSFTPMYHAVTKR T0334 343 :CVSIG 3grs 417 :CVMKM T0334 358 :STGIYF 3grs 430 :VVGIHM T0334 378 :KSLNPVLTARFNREIETMFD 3grs 437 :GLGCDEMLQGFAVAVKMGAT T0334 434 :IDMYRAGMAINAPASDDAQL 3grs 457 :KADFDNTVAIHPTSSEELVT Number of specific fragments extracted= 30 number of extra gaps= 2 total=1563 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 3grs/T0334-3grs-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0334 read from 3grs/T0334-3grs-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3grs read from 3grs/T0334-3grs-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3grs in template set Warning: unaligning (T0334)G103 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (3grs)Q167 Warning: unaligning (T0334)P104 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (3grs)Q167 T0334 5 :IDKILIVGGGTAGWMAASYLGK 3grs 20 :SYDYLVIGGGSGGLASARRAAE T0334 30 :GTADITLLQAPDIP 3grs 42 :LGARAAVVESHKLG T0334 51 :TIPNLQTAFFDFL 3grs 69 :MWNTAVHSEFMHD T0334 65 :IPE 3grs 94 :FNW T0334 68 :DEWMRECNASYKVA 3grs 115 :QNNLTKSHIEIIRG T0334 84 :FINWRTAGEGTS 3grs 129 :HAAFTSDPKPTI T0334 96 :EARELDG 3grs 159 :MPSTPHE T0334 105 :DHFYHSFGLLKYHEQIPLSHYWFDRSY 3grs 168 :IPGASLGITSDGFFQLEELPGRSVIVG T0334 135 :TVEPFDYACYKEPVILD 3grs 195 :AGYIAVEMAGILSALGS T0334 154 :RSPRRLDGSKVTN 3grs 212 :KTSLMIRHDKVLR T0334 172 :DAHLVADFLRRFATEKLGVRHVEDRVEHVQRDANGNIESVRTA 3grs 226 :FDSMISTNCTEELENAGVEVLKFSQVKEVKKTLSGLEVSMVTA T0334 215 :TGR 3grs 270 :PGR T0334 218 :VF 3grs 278 :MI T0334 220 :DADLFVDCSGF 3grs 281 :DVDCLLWAIGR T0334 338 :AWVGNCVSIGTSSCFVEP 3grs 321 :TNVKGIYAVGDVCGKALL T0334 361 :IYFVYAALYQLVKHFP 3grs 339 :TPVAIAAGRKLAHRLF Number of specific fragments extracted= 16 number of extra gaps= 1 total=1579 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 1b5qA/T0334-1b5qA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1b5qA expands to /projects/compbio/data/pdb/1b5q.pdb.gz 1b5qA:# T0334 read from 1b5qA/T0334-1b5qA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1b5qA read from 1b5qA/T0334-1b5qA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1b5qA to template set # found chain 1b5qA in template set Warning: unaligning (T0334)A238 because of BadResidue code BAD_PEPTIDE in next template residue (1b5qA)D274 Warning: unaligning (T0334)M239 because of BadResidue code BAD_PEPTIDE at template residue (1b5qA)D274 Warning: unaligning (T0334)F375 because of BadResidue code BAD_PEPTIDE in next template residue (1b5qA)Q459 Warning: unaligning (T0334)P376 because of BadResidue code BAD_PEPTIDE at template residue (1b5qA)Q459 Warning: unaligning (T0334)L380 because last residue in template chain is (1b5qA)C463 T0334 7 :KILIVGGGTAGWMAASYLGK 1b5qA 6 :RVIVVGAGMSGISAAKRLSE T0334 29 :QGTADITLLQAPD 1b5qA 26 :AGITDLLILEATD T0334 42 :IPTL 1b5qA 40 :IGGR T0334 46 :GVGEATIPNLQTAFFDFLGIPED 1b5qA 83 :RNFRSDFDYLAQNVYKEDGGVYD T0334 69 :EWMR 1b5qA 111 :KRIE T0334 172 :DAHLVADFLRRFA 1b5qA 115 :LADSVEEMGEKLS T0334 186 :EKL 1b5qA 128 :ATL T0334 189 :GVR 1b5qA 225 :KIV T0334 192 :HVED 1b5qA 231 :LQLN T0334 196 :RVEHVQRDANG 1b5qA 236 :VVREIKYSPGG T0334 209 :ESVRTATGRVFDADLFVDCSG 1b5qA 247 :VTVKTEDNSVYSADYVMVSAS T0334 233 :LLINK 1b5qA 268 :LGVLQ T0334 240 :EEPFLDM 1b5qA 275 :LIQFKPK T0334 247 :SDHLLNDSAVATQVP 1b5qA 292 :QFDMAVYTKIFLKFP T0334 262 :HDDDANGVEPFTSAIAMK 1b5qA 308 :KFWPEGKGREFFLYASSR T0334 280 :SGWTWKIPM 1b5qA 328 :YYGVWQEFE T0334 292 :FGTGYVYSSRFATE 1b5qA 343 :NVLLVTVTDEESRR T0334 306 :DEAVREFCEM 1b5qA 363 :EQTKAEIMQV T0334 316 :WHLDP 1b5qA 374 :RKMFP T0334 321 :ETQPLNRIRF 1b5qA 381 :DVPDATDILV T0334 331 :RVGRNRRAWVG 1b5qA 399 :YKGTFSNWPVG T0334 342 :NCVSIGTSSCF 1b5qA 424 :RVYFTGEHTSE T0334 353 :VEPLESTGIYFVYAALYQLVKH 1b5qA 436 :YNGYVHGAYLSGIDSAEILINC T0334 377 :DKS 1b5qA 460 :KKM Number of specific fragments extracted= 24 number of extra gaps= 2 total=1603 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 1b5qA/T0334-1b5qA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0334 read from 1b5qA/T0334-1b5qA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1b5qA read from 1b5qA/T0334-1b5qA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1b5qA in template set Warning: unaligning (T0334)T185 because of BadResidue code BAD_PEPTIDE in next template residue (1b5qA)Q215 Warning: unaligning (T0334)E186 because of BadResidue code BAD_PEPTIDE at template residue (1b5qA)Q215 Warning: unaligning (T0334)A238 because of BadResidue code BAD_PEPTIDE in next template residue (1b5qA)D274 Warning: unaligning (T0334)L380 because last residue in template chain is (1b5qA)C463 T0334 7 :KILIVGGGTAGWMAASYLGK 1b5qA 6 :RVIVVGAGMSGISAAKRLSE T0334 30 :GTA 1b5qA 26 :AGI T0334 33 :DITLLQAP 1b5qA 30 :DLLILEAT T0334 41 :DI 1b5qA 39 :HI T0334 44 :T 1b5qA 67 :G T0334 53 :PNLQTAF 1b5qA 70 :NPIWPIV T0334 65 :IPEDEWMRECNASYKVAIKFINWRTAGE 1b5qA 104 :YDEDYVQKRIELADSVEEMGEKLSATLH T0334 114 :LKYHEQIPLSHYWFDRSYRGKTV 1b5qA 132 :ASGRDDMSILAMQRLNEHQPNGP T0334 150 :LD 1b5qA 155 :AT T0334 152 :ANRSPRR 1b5qA 171 :FAEPPRV T0334 163 :KVTNYAW 1b5qA 178 :TSLQNTV T0334 170 :HFDAHLVADFLRRFA 1b5qA 199 :VADQRGYEAVVYYLA T0334 187 :KLGV 1b5qA 216 :YLKT T0334 192 :HVED 1b5qA 231 :LQLN T0334 196 :RVEHVQRDANG 1b5qA 236 :VVREIKYSPGG T0334 209 :ESVRTATGRVFDADLFVDCSG 1b5qA 247 :VTVKTEDNSVYSADYVMVSAS T0334 231 :RGL 1b5qA 268 :LGV T0334 236 :NK 1b5qA 271 :LQ T0334 239 :MEEPFLDMSDH 1b5qA 278 :FKPKLPTWKVR T0334 250 :LLNDSAVATQVPHDDDANGVEPFTSAIAMKS 1b5qA 295 :MAVYTKIFLKFPRKFWPEGKGREFFLYASSR T0334 281 :GWTWKIPM 1b5qA 329 :YGVWQEFE T0334 289 :LGR 1b5qA 340 :PDA T0334 292 :FGTGY 1b5qA 344 :VLLVT T0334 298 :YSSRFATE 1b5qA 349 :VTDEESRR T0334 306 :DEAVREFCEMW 1b5qA 363 :EQTKAEIMQVL T0334 317 :HLDPETQ 1b5qA 375 :KMFPGKD T0334 324 :PLNRIRFRVGRNRRA 1b5qA 384 :DATDILVPRWWSDRF T0334 339 :WVGNCVSIG 1b5qA 421 :PVGRVYFTG T0334 350 :SCFVEPLEST 1b5qA 430 :EHTSEHYNGY T0334 361 :IYFVYAALYQLVKHFPD 1b5qA 440 :VHGAYLSGIDSAEILIN T0334 378 :KS 1b5qA 461 :KM Number of specific fragments extracted= 31 number of extra gaps= 2 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 1b5qA/T0334-1b5qA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0334 read from 1b5qA/T0334-1b5qA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1b5qA read from 1b5qA/T0334-1b5qA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1b5qA in template set Warning: unaligning (T0334)T185 because of BadResidue code BAD_PEPTIDE in next template residue (1b5qA)Q215 Warning: unaligning (T0334)E186 because of BadResidue code BAD_PEPTIDE at template residue (1b5qA)Q215 Warning: unaligning (T0334)A238 because of BadResidue code BAD_PEPTIDE in next template residue (1b5qA)D274 Warning: unaligning (T0334)M239 because of BadResidue code BAD_PEPTIDE at template residue (1b5qA)D274 Warning: unaligning (T0334)F375 because of BadResidue code BAD_PEPTIDE in next template residue (1b5qA)Q459 Warning: unaligning (T0334)P376 because of BadResidue code BAD_PEPTIDE at template residue (1b5qA)Q459 Warning: unaligning (T0334)L380 because last residue in template chain is (1b5qA)C463 T0334 7 :KILIVGGGTAGWMAASYLGK 1b5qA 6 :RVIVVGAGMSGISAAKRLSE T0334 30 :GTAD 1b5qA 26 :AGIT T0334 34 :ITLLQAPDI 1b5qA 31 :LLILEATDH T0334 47 :VGEATI 1b5qA 40 :IGGRMH T0334 74 :CNASYKVAIKFINWRTAGE 1b5qA 50 :AGINVELGANWVEGVNGGK T0334 93 :GTSEARELDGGPDHFYHSFGLLKYHEQIPLSHYWFDRSYRGKTVEP 1b5qA 92 :LAQNVYKEDGGVYDEDYVQKRIELADSVEEMGEKLSATLHASGRDD T0334 139 :FDYACYKEPVILDANRSPR 1b5qA 140 :ILAMQRLNEHQPNGPATPV T0334 158 :RLDGSKVTNYAWHFDAHLVA 1b5qA 171 :FAEPPRVTSLQNTVPLATFS T0334 178 :DFLRRFA 1b5qA 207 :AVVYYLA T0334 187 :KLGV 1b5qA 216 :YLKT T0334 191 :RHVEDRVEHVQRDANG 1b5qA 231 :LQLNKVVREIKYSPGG T0334 209 :ESVRTATGRVFDADLFVDCSGF 1b5qA 247 :VTVKTEDNSVYSADYVMVSASL T0334 232 :GLL 1b5qA 269 :GVL T0334 237 :K 1b5qA 272 :Q T0334 240 :EEPFLD 1b5qA 275 :LIQFKP T0334 246 :MSDH 1b5qA 282 :LPTW T0334 250 :LLNDSAVATQVPHDDDANGVEPFTSA 1b5qA 296 :AVYTKIFLKFPRKFWPEGKGREFFLY T0334 277 :AM 1b5qA 322 :AS T0334 289 :LGRFGTGYVYSSRFATED 1b5qA 324 :SRRGYYGVWQEFEKQYPD T0334 307 :EAVREFCEMW 1b5qA 364 :QTKAEIMQVL T0334 317 :HLDP 1b5qA 378 :PGKD T0334 322 :TQ 1b5qA 382 :VP T0334 324 :PLNRIRF 1b5qA 387 :DILVPRW T0334 331 :RVGRNRRAW 1b5qA 399 :YKGTFSNWP T0334 341 :GNCVSIG 1b5qA 423 :GRVYFTG T0334 348 :TSSCFVEPLESTGIYFVYAALYQLVKH 1b5qA 431 :HTSEHYNGYVHGAYLSGIDSAEILINC T0334 377 :DKS 1b5qA 460 :KKM Number of specific fragments extracted= 27 number of extra gaps= 3 total=1661 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 1jnrA/T0334-1jnrA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1jnrA expands to /projects/compbio/data/pdb/1jnr.pdb.gz 1jnrA:Skipped atom 709, because occupancy 0.250 <= existing 0.250 in 1jnrA Skipped atom 711, because occupancy 0.250 <= existing 0.250 in 1jnrA Skipped atom 713, because occupancy 0.250 <= existing 0.250 in 1jnrA Skipped atom 715, because occupancy 0.250 <= existing 0.250 in 1jnrA Skipped atom 717, because occupancy 0.250 <= existing 0.250 in 1jnrA Skipped atom 719, because occupancy 0.250 <= existing 0.250 in 1jnrA Skipped atom 721, because occupancy 0.250 <= existing 0.250 in 1jnrA Skipped atom 1926, because occupancy 0.070 <= existing 0.070 in 1jnrA Skipped atom 1928, because occupancy 0.070 <= existing 0.070 in 1jnrA Skipped atom 1930, because occupancy 0.070 <= existing 0.070 in 1jnrA Skipped atom 1932, because occupancy 0.070 <= existing 0.070 in 1jnrA Skipped atom 2626, because occupancy 0.070 <= existing 0.070 in 1jnrA Skipped atom 2628, because occupancy 0.070 <= existing 0.070 in 1jnrA Skipped atom 2630, because occupancy 0.070 <= existing 0.070 in 1jnrA Skipped atom 2632, because occupancy 0.070 <= existing 0.070 in 1jnrA Skipped atom 2758, because occupancy 0.070 <= existing 0.070 in 1jnrA Skipped atom 2760, because occupancy 0.070 <= existing 0.070 in 1jnrA Skipped atom 2762, because occupancy 0.070 <= existing 0.070 in 1jnrA Skipped atom 2764, because occupancy 0.070 <= existing 0.070 in 1jnrA Skipped atom 2766, because occupancy 0.070 <= existing 0.070 in 1jnrA Skipped atom 2906, because occupancy 0.250 <= existing 0.250 in 1jnrA Skipped atom 2908, because occupancy 0.250 <= existing 0.250 in 1jnrA Skipped atom 2910, because occupancy 0.250 <= existing 0.250 in 1jnrA Skipped atom 2912, because occupancy 0.250 <= existing 0.250 in 1jnrA Skipped atom 3140, because occupancy 0.070 <= existing 0.070 in 1jnrA Skipped atom 3142, because occupancy 0.070 <= existing 0.070 in 1jnrA Skipped atom 3144, because occupancy 0.070 <= existing 0.070 in 1jnrA Skipped atom 3146, because occupancy 0.070 <= existing 0.070 in 1jnrA Skipped atom 4300, because occupancy 0.070 <= existing 0.070 in 1jnrA Skipped atom 4302, because occupancy 0.070 <= existing 0.070 in 1jnrA Skipped atom 4304, because occupancy 0.070 <= existing 0.070 in 1jnrA Skipped atom 4306, because occupancy 0.070 <= existing 0.070 in 1jnrA Skipped atom 5152, because occupancy 0.250 <= existing 0.250 in 1jnrA Skipped atom 5154, because occupancy 0.250 <= existing 0.250 in 1jnrA Skipped atom 5156, because occupancy 0.250 <= existing 0.250 in 1jnrA Skipped atom 5158, because occupancy 0.250 <= existing 0.250 in 1jnrA # T0334 read from 1jnrA/T0334-1jnrA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1jnrA read from 1jnrA/T0334-1jnrA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1jnrA to template set # found chain 1jnrA in template set T0334 4 :KID 1jnrA 17 :PTE T0334 7 :KILIVGGGTAGWMAASYLGKAL 1jnrA 24 :DILIIGGGFSGCGAAYEAAYWA T0334 29 :QGT 1jnrA 48 :GGL T0334 33 :DITLLQAP 1jnrA 51 :KVTLVEKA T0334 46 :GVGEATIPNLQTAFFDFLGIPED 1jnrA 59 :AVERSGAVAQGLSAINTYIDLTG T0334 115 :KYHEQIPLSHYWFDRSYRGKTVEP 1jnrA 82 :RSERQNTLEDYVRYVTLDMMGLAR T0334 139 :FDYACYKEPVILD 1jnrA 121 :HLFEKWGLPIWKT T0334 152 :AN 1jnrA 135 :DG T0334 155 :SPRRLDGSKVTNYAWH 1jnrA 137 :KYVREGQWQIMIHGES T0334 172 :DAHLVADFLRRFA 1jnrA 153 :YKPIIAEAAKMAV T0334 186 :EK 1jnrA 166 :GE T0334 191 :R 1jnrA 168 :E T0334 192 :HVED 1jnrA 170 :IYER T0334 196 :RVEHVQRDANG 1jnrA 175 :FIFELLKDNND T0334 207 :NIESVRTA 1jnrA 188 :AVAGAVGF T0334 215 :TGR 1jnrA 198 :REP T0334 218 :VFDADLFVDCSGF 1jnrA 204 :VFKAKAVILATGG T0334 231 :R 1jnrA 367 :V T0334 233 :LLINKAMEEPFLD 1jnrA 370 :ALLWACQNIDPQE T0334 248 :DHLLNDSAV 1jnrA 383 :QPSEAAPAE T0334 271 :PFTS 1jnrA 392 :PYIM T0334 288 :M 1jnrA 397 :S T0334 289 :LGRFGTGYVYSSRFATE 1jnrA 399 :SGEAGFWVCGPEDLMPE T0334 307 :EA 1jnrA 416 :EY T0334 313 :CEMWHLDP 1jnrA 418 :AKLFPLKY T0334 337 :RAWVGNCVSIGTSSCF 1jnrA 428 :MTTVKGLFAIGDCAGA T0334 353 :VEPLESTGIYFVYAALYQLVKHFP 1jnrA 445 :PHKFSSGSFTEGRIAAKAAVRFIL T0334 377 :DKSLNPVLTARFNREIETMFDDTRDF 1jnrA 473 :NPEIDDAVVEELKKKAYAPMERFMQY T0334 424 :LRL 1jnrA 499 :KDL T0334 427 :ADGMQEKIDMYRAGMAINAPAS 1jnrA 515 :WQGLVRLQKIMDEYAAGIATIY T0334 500 :DEVFGAVKDRQRNLLETLPS 1jnrA 540 :EKMLQRALELLAFLKEDLEK Number of specific fragments extracted= 31 number of extra gaps= 0 total=1692 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 1jnrA/T0334-1jnrA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0334 read from 1jnrA/T0334-1jnrA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1jnrA read from 1jnrA/T0334-1jnrA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1jnrA in template set T0334 5 :IDKILIVGGGTAGWMAASYLGKAL 1jnrA 22 :ETDILIIGGGFSGCGAAYEAAYWA T0334 29 :QGTADITLLQAPDI 1jnrA 47 :LGGLKVTLVEKAAV T0334 43 :PTLGVGEATIPNLQTAF 1jnrA 80 :TGRSERQNTLEDYVRYV T0334 60 :FDFLGIP 1jnrA 98 :LDMMGLA T0334 77 :SYKVAIKFINWRTAG 1jnrA 105 :REDLVADYARHVDGT T0334 123 :SHYWFDRSYR 1jnrA 120 :VHLFEKWGLP T0334 136 :V 1jnrA 130 :I T0334 141 :YACYKEPVI 1jnrA 131 :WKTPDGKYV T0334 163 :KVTNYAWHF 1jnrA 140 :REGQWQIMI T0334 173 :AHLVADFLRRFA 1jnrA 154 :KPIIAEAAKMAV T0334 189 :G 1jnrA 166 :G T0334 192 :HVED 1jnrA 170 :IYER T0334 196 :RVEHVQRDANGN 1jnrA 175 :FIFELLKDNNDP T0334 208 :IESVR 1jnrA 189 :VAGAV T0334 213 :TA 1jnrA 195 :FS T0334 215 :TG 1jnrA 198 :RE T0334 217 :RVFDADLFVDCSGFRGLL 1jnrA 203 :YVFKAKAVILATGGATLL T0334 243 :FLDMSDH 1jnrA 221 :FRPRSTG T0334 264 :DDANGVEPFTSAIAM 1jnrA 228 :EAAGRTWYAIFDTGS T0334 281 :GWTW 1jnrA 252 :AMLT T0334 285 :KIPMLGR 1jnrA 263 :PFRFKDG T0334 292 :FGT 1jnrA 271 :GPV T0334 306 :DEAVREFCEMW 1jnrA 348 :KKKLKHIYEEA T0334 317 :HLDPETQ 1jnrA 377 :NIDPQEQ T0334 329 :RFRVGRNRRA 1jnrA 384 :PSEAAPAEPY T0334 339 :WVGNCVSIGTSSCFVEPLESTGIYF 1jnrA 430 :TVKGLFAIGDCAGANPHKFSSGSFT T0334 364 :VYAALYQLVKHFPD 1jnrA 456 :GRIAAKAAVRFILE T0334 378 :KSLNPVLTARF 1jnrA 474 :PEIDDAVVEEL T0334 396 :FDDTRDFIQAHFYFSPRTDTP 1jnrA 485 :KKKAYAPMERFMQYKDLSTAD T0334 417 :FW 1jnrA 514 :PW T0334 428 :DGMQEKIDMYRAGMAINAP 1jnrA 516 :QGLVRLQKIMDEYAAGIAT T0334 491 :HM 1jnrA 535 :IY T0334 493 :PQATESVDEVFGAVKDRQ 1jnrA 540 :EKMLQRALELLAFLKEDL Number of specific fragments extracted= 33 number of extra gaps= 0 total=1725 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 1jnrA/T0334-1jnrA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0334 read from 1jnrA/T0334-1jnrA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1jnrA read from 1jnrA/T0334-1jnrA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1jnrA in template set T0334 7 :KILIVGGGTAGWMAASYLGKAL 1jnrA 24 :DILIIGGGFSGCGAAYEAAYWA T0334 29 :QGTADITLLQAPDIPTLGV 1jnrA 47 :LGGLKVTLVEKAAVERSGA T0334 78 :YKVAIKFINW 1jnrA 66 :VAQGLSAINT T0334 94 :TSEARELDGGPDHFYHSFGLLKYHEQIPLSHYWFD 1jnrA 76 :YIDLTGRSERQNTLEDYVRYVTLDMMGLAREDLVA T0334 134 :KTVEPFDYACYKEPVILDANRSPRRLDGSKVTNYAWHF 1jnrA 111 :DYARHVDGTVHLFEKWGLPIWKTPDGKYVREGQWQIMI T0334 172 :DAHLVADFLRRFA 1jnrA 153 :YKPIIAEAAKMAV T0334 191 :RHVEDRVEHVQRDANGN 1jnrA 170 :IYERVFIFELLKDNNDP T0334 208 :IESVRTATGR 1jnrA 192 :AVGFSVREPK T0334 218 :VFDADLFVDCSGFRGL 1jnrA 204 :VFKAKAVILATGGATL T0334 260 :VPHDDDANGVEPFT 1jnrA 220 :LFRPRSTGEAAGRT T0334 338 :AWVGNCVSIGTSSCFVEPLESTG 1jnrA 429 :TTVKGLFAIGDCAGANPHKFSSG T0334 361 :IYFVYAALYQLVKHFP 1jnrA 453 :FTEGRIAAKAAVRFIL T0334 377 :DKSLNPVLTARFNREIETMFDDTRDF 1jnrA 473 :NPEIDDAVVEELKKKAYAPMERFMQY T0334 441 :MAINAPASDDAQLY 1jnrA 499 :KDLSTADDVNPEYI T0334 457 :NFEEEFRNFWNNSNYYCVLAGLGL 1jnrA 513 :LPWQGLVRLQKIMDEYAAGIATIY T0334 481 :V 1jnrA 539 :N T0334 493 :PQATESVDEVFGAVKDRQR 1jnrA 540 :EKMLQRALELLAFLKEDLE Number of specific fragments extracted= 17 number of extra gaps= 0 total=1742 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 1rsgA/T0334-1rsgA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1rsgA expands to /projects/compbio/data/pdb/1rsg.pdb.gz 1rsgA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0334 read from 1rsgA/T0334-1rsgA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1rsgA read from 1rsgA/T0334-1rsgA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1rsgA to template set # found chain 1rsgA in template set Warning: unaligning (T0334)K4 because first residue in template chain is (1rsgA)P6 Warning: unaligning (T0334)Q323 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1rsgA)A427 Warning: unaligning (T0334)V340 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1rsgA)V460 T0334 5 :ID 1rsgA 7 :AK T0334 7 :KILIVGGGTAGWMAASYLGK 1rsgA 10 :KVIIIGAGIAGLKAASTLHQ T0334 29 :QGTADITLLQAPD 1rsgA 30 :NGIQDCLVLEARD T0334 42 :IPTL 1rsgA 44 :VGGR T0334 46 :GVGEATIPNLQTAFFDFLGIPEDEWMRECNAS 1rsgA 53 :GYQGRKYDIGASWHHDTLTNPLFLEEAQLSLN T0334 103 :GPDHFYHSFGLL 1rsgA 86 :GRTRFVFDDDNF T0334 115 :KYHE 1rsgA 102 :EERG T0334 152 :ANRSPRRL 1rsgA 106 :RVDHDKEL T0334 172 :DAHLVADFLRRFA 1rsgA 114 :LLEIVDNEMSKFA T0334 186 :EKL 1rsgA 127 :ELE T0334 189 :GVR 1rsgA 211 :SFP T0334 192 :HVED 1rsgA 217 :LKLS T0334 196 :RVEHVQRDANGNIE 1rsgA 222 :EVKSITREPSKNVT T0334 211 :VRTATGRVFDADLFVDCSG 1rsgA 236 :VNCEDGTVYNADYVIITVP T0334 233 :LLINKAMEEPFLDMSDHLLNDSAV 1rsgA 255 :QSVLNLSVQPEKNLRGRIEFQPPL T0334 271 :PFTSAIAMK 1rsgA 279 :KPVIQDAFD T0334 280 :SGWTWKIPM 1rsgA 355 :SQPLFFVNL T0334 289 :LGRFGTGYVYSSRFATE 1rsgA 367 :TGVASFMMLMQAPLTNH T0334 306 :DEAVREFCEMWHLDP 1rsgA 392 :ERLFSFFQPVLNKIM T0334 324 :PLNRIRF 1rsgA 428 :NKPVLRN T0334 337 :RAW 1rsgA 452 :ACF T0334 342 :NCVSIGTSSCF 1rsgA 473 :RIRFAGEHTIM T0334 353 :VEPL 1rsgA 485 :GAGC T0334 361 :IYFVYAALYQLVKHFP 1rsgA 489 :AYGAWESGRREATRIS Number of specific fragments extracted= 24 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 1rsgA/T0334-1rsgA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0334 read from 1rsgA/T0334-1rsgA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1rsgA read from 1rsgA/T0334-1rsgA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1rsgA in template set Warning: unaligning (T0334)G268 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1rsgA)S350 Warning: unaligning (T0334)D319 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1rsgA)A427 T0334 4 :KIDKILIVGGGTAGWMAASYLGK 1rsgA 7 :AKKKVIIIGAGIAGLKAASTLHQ T0334 30 :GTA 1rsgA 30 :NGI T0334 33 :DITLLQAP 1rsgA 34 :DCLVLEAR T0334 41 :DI 1rsgA 43 :RV T0334 47 :VGEATIPNLQTAF 1rsgA 67 :HDTLTNPLFLEEA T0334 123 :SHYWFDR 1rsgA 146 :MKYLLQR T0334 136 :VEPFD 1rsgA 153 :RQFLT T0334 141 :YACYKEPVILD 1rsgA 168 :CRYLELWHGLD T0334 152 :ANRSPRRLDGSKVTNYA 1rsgA 181 :LLSAKDTYFGHQGRNAF T0334 170 :HFDAHLVADFLR 1rsgA 198 :ALNYDSVVQRIA T0334 186 :EKLG 1rsgA 210 :QSFP T0334 192 :HVED 1rsgA 217 :LKLS T0334 196 :RVEHVQRDANGN 1rsgA 222 :EVKSITREPSKN T0334 209 :ESVRTATGRVFDADLFVDCS 1rsgA 234 :VTVNCEDGTVYNADYVIITV T0334 230 :FRGLL 1rsgA 254 :PQSVL T0334 236 :NKAMEEP 1rsgA 259 :NLSVQPE T0334 243 :FLDMSDHLLNDSAVAT 1rsgA 286 :FDKIHFGALGKVIFEF T0334 264 :DD 1rsgA 302 :EE T0334 269 :VE 1rsgA 351 :VT T0334 278 :MKSGWTWKIPM 1rsgA 353 :CWSQPLFFVNL T0334 289 :LGR 1rsgA 366 :STG T0334 292 :FGTGYVYSSRFATE 1rsgA 370 :ASFMMLMQAPLTNH T0334 306 :DEAVREFCEMW 1rsgA 392 :ERLFSFFQPVL T0334 317 :HL 1rsgA 417 :GM T0334 326 :NRIRFRVGRNRRA 1rsgA 428 :NKPVLRNIIVSNW T0334 339 :WVGNCVSIG 1rsgA 470 :QDSRIRFAG T0334 348 :TSSCF 1rsgA 484 :DGAGC T0334 361 :IYFVYAALYQLV 1rsgA 489 :AYGAWESGRREA T0334 386 :ARFNREIETM 1rsgA 501 :TRISDLLKLE Number of specific fragments extracted= 29 number of extra gaps= 0 total=1795 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 1rsgA/T0334-1rsgA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0334 read from 1rsgA/T0334-1rsgA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1rsgA read from 1rsgA/T0334-1rsgA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1rsgA in template set Warning: unaligning (T0334)G3 because first residue in template chain is (1rsgA)P6 Warning: unaligning (T0334)A97 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1rsgA)D138 Warning: unaligning (T0334)D105 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1rsgA)D138 T0334 4 :KIDKILIVGGGTAGWMAASYLGK 1rsgA 7 :AKKKVIIIGAGIAGLKAASTLHQ T0334 30 :GTAD 1rsgA 30 :NGIQ T0334 34 :ITLLQ 1rsgA 35 :CLVLE T0334 39 :APDIPT 1rsgA 41 :RDRVGG T0334 45 :LGVGEA 1rsgA 59 :YDIGAS T0334 51 :T 1rsgA 71 :T T0334 53 :PNLQTAF 1rsgA 72 :NPLFLEE T0334 68 :DEWMREC 1rsgA 79 :AQLSLND T0334 75 :NAS 1rsgA 94 :DDN T0334 78 :YKVAIKFINWRTAGEGTS 1rsgA 98 :IYIDEERGRVDHDKELLL T0334 96 :E 1rsgA 129 :E T0334 106 :HFYHSFGLLKYHEQIPLSHY 1rsgA 139 :CSFFQLVMKYLLQRRQFLTN T0334 138 :PFDYACYKEP 1rsgA 159 :DQIRYLPQLC T0334 148 :VILDANRSPRR 1rsgA 174 :WHGLDWKLLSA T0334 159 :LDGSKVTNYAWHFDAHLVADFLRR 1rsgA 187 :TYFGHQGRNAFALNYDSVVQRIAQ T0334 191 :RHVEDRVEHVQRDANGN 1rsgA 217 :LKLSCEVKSITREPSKN T0334 209 :ESVRTATGRVFDADLFVDC 1rsgA 234 :VTVNCEDGTVYNADYVIIT T0334 230 :FRGLLINKAMEEP 1rsgA 253 :VPQSVLNLSVQPE T0334 243 :FLDMSDHLLNDSAVATQVPHDDDAN 1rsgA 285 :AFDKIHFGALGKVIFEFEECCWSNE T0334 293 :GTGYVYSSR 1rsgA 310 :SSKIVTLAN T0334 303 :ATED 1rsgA 319 :STNE T0334 307 :EAVREFCEMW 1rsgA 461 :DMVVAMSNGQ T0334 340 :VGNCV 1rsgA 471 :DSRIR T0334 348 :TSSCFVEPLESTGIYFVYAALYQLV 1rsgA 476 :FAGEHTIMDGAGCAYGAWESGRREA Number of specific fragments extracted= 24 number of extra gaps= 0 total=1819 Will force an alignment to be made, even if fragment is small Number of alignments=78 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1mo9A/T0334-1mo9A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1mo9A expands to /projects/compbio/data/pdb/1mo9.pdb.gz 1mo9A:# T0334 read from 1mo9A/T0334-1mo9A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1mo9A read from 1mo9A/T0334-1mo9A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1mo9A to template set # found chain 1mo9A in template set T0334 2 :SGKID 1mo9A 39 :NDPRE T0334 7 :KILIVGGGTAGWMAASYLGK 1mo9A 45 :DAIFIGGGAAGRFGSAYLRA T0334 29 :QGT 1mo9A 65 :MGG T0334 33 :DITLLQAPD 1mo9A 68 :RQLIVDRWP T0334 42 :IPTL 1mo9A 78 :LGGS T0334 46 :GVGEATIP 1mo9A 106 :FSGQYWFP T0334 61 :DFLGIPED 1mo9A 114 :DMTEKVVG T0334 69 :EWMRECNASYKVAIKFINWRTAGEGTS 1mo9A 124 :EVVDLFRAGRNGPHGIMNFQSKEQLNL T0334 96 :EARELDGGPDHFYHSFGLL 1mo9A 188 :TLDVPGVNAKGVFDHATLV T0334 115 :KYHEQIPLSHYWFDRSYRG 1mo9A 212 :EPGSTVVVVGGSKTAVEYG T0334 139 :FDYACYKEPVILD 1mo9A 231 :CFFNATGRRTVML T0334 152 :ANRSPRRL 1mo9A 245 :RTEPLKLI T0334 172 :DAHLVADFLRRFA 1mo9A 253 :KDNETRAYVLDRM T0334 186 :EKLGVRHVED 1mo9A 266 :KEQGMEIISG T0334 196 :RVEHVQRDANGNIESVRTA 1mo9A 277 :NVTRIEEDANGRVQAVVAM T0334 215 :TGR 1mo9A 298 :NGE T0334 218 :VFDADLFVDCSGFRG 1mo9A 302 :RIETDFVFLGLGEQP T0334 233 :LLINKAMEEPFLD 1mo9A 319 :AELAKILGLDLGP T0334 247 :SDHLLNDSAVATQVPHDDDANGV 1mo9A 332 :KGEVLVNEYLQTSVPNVYAVGDL T0334 270 :EPFTS 1mo9A 410 :AGHEI T0334 275 :AIAMK 1mo9A 416 :TIKMP T0334 280 :SGWTWKIPMLGRFGTGYVYSSRFATE 1mo9A 451 :GFQKIVIDAKTRKVLGAHHVGYGAKD T0334 306 :DEAVREFCE 1mo9A 479 :QYLNVLIKQ T0334 378 :KSLNPVL 1mo9A 488 :GLTVDEL Number of specific fragments extracted= 24 number of extra gaps= 0 total=1843 Will force an alignment to be made, even if fragment is small Number of alignments=79 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1mo9A/T0334-1mo9A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0334 read from 1mo9A/T0334-1mo9A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1mo9A read from 1mo9A/T0334-1mo9A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1mo9A in template set Warning: unaligning (T0334)T413 because of BadResidue code BAD_PEPTIDE in next template residue (1mo9A)L502 Warning: unaligning (T0334)D414 because of BadResidue code BAD_PEPTIDE at template residue (1mo9A)L502 T0334 2 :SGKIDKILIVGGGTAGWMAASYLGK 1mo9A 40 :DPREYDAIFIGGGAAGRFGSAYLRA T0334 30 :GTADITLLQAPDIPTLGVGEA 1mo9A 65 :MGGRQLIVDRWPFLGGSCPHN T0334 52 :IPNLQTAFFDFL 1mo9A 86 :ACVPHHLFSDCA T0334 78 :YKVAIKFINWRTAGEGTS 1mo9A 98 :AELMLARTFSGQYWFPDM T0334 113 :LLKYHEQIPLSHYWFDR 1mo9A 116 :TEKVVGIKEVVDLFRAG T0334 170 :HFDAHLVADFLRRFA 1mo9A 251 :LIKDNETRAYVLDRM T0334 186 :EKLGVRHVED 1mo9A 266 :KEQGMEIISG T0334 196 :RVEHVQRDANGNIESVR 1mo9A 277 :NVTRIEEDANGRVQAVV T0334 213 :TATG 1mo9A 296 :TPNG T0334 217 :RVFDADLFVDCSG 1mo9A 301 :MRIETDFVFLGLG T0334 230 :FRGLLINKAMEEPFLD 1mo9A 316 :PRSAELAKILGLDLGP T0334 247 :SDHLLNDSAVATQV 1mo9A 332 :KGEVLVNEYLQTSV T0334 264 :D 1mo9A 346 :P T0334 266 :ANGVE 1mo9A 376 :MGEKI T0334 271 :PFTSAIAMKSGWTWKIPML 1mo9A 385 :KNYPDFLHTHYEVSFLGMG T0334 290 :GRFGTGYVYSSRFATE 1mo9A 411 :GHEIVTIKMPPDTENG T0334 318 :LDPETQPLNRIR 1mo9A 442 :FGKGTAHMSGFQ T0334 330 :FRVGRNR 1mo9A 457 :IDAKTRK T0334 338 :AW 1mo9A 464 :VL T0334 342 :NCVSIGTSS 1mo9A 466 :GAHHVGYGA T0334 382 :PVLTARFNREIETMF 1mo9A 475 :KDAFQYLNVLIKQGL T0334 403 :IQAHFYFSPR 1mo9A 491 :VDELGDMDEL T0334 415 :TP 1mo9A 503 :NP T0334 519 :SLHEFLRQQHG 1mo9A 506 :HFIQLSRLRAG Number of specific fragments extracted= 24 number of extra gaps= 1 total=1867 Will force an alignment to be made, even if fragment is small Number of alignments=80 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1mo9A/T0334-1mo9A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0334 read from 1mo9A/T0334-1mo9A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1mo9A read from 1mo9A/T0334-1mo9A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1mo9A in template set T0334 5 :IDKILIVGGGTAGWMAASYLGK 1mo9A 214 :GSTVVVVGGSKTAVEYGCFFNA T0334 30 :GTADITLLQAPDI 1mo9A 236 :TGRRTVMLVRTEP T0334 62 :FLGIPEDE 1mo9A 249 :LKLIKDNE T0334 176 :VADFLRRFATEKLGVRHVEDRVEHVQRDANGNIESVR 1mo9A 257 :TRAYVLDRMKEQGMEIISGSNVTRIEEDANGRVQAVV T0334 213 :TATGR 1mo9A 296 :TPNGE T0334 218 :VFDADLFVDCSGF 1mo9A 302 :RIETDFVFLGLGE T0334 231 :RG 1mo9A 317 :RS T0334 310 :REFCEMWHLDPETQPLNRIRFR 1mo9A 319 :AELAKILGLDLGPKGEVLVNEY T0334 336 :RRAWVGNCVSIGTSSCFVE 1mo9A 341 :LQTSVPNVYAVGDLIGGPM T0334 361 :IYFVYAALYQLVKHFPDKS 1mo9A 361 :MFKARKSGCYAARNVMGEK Number of specific fragments extracted= 10 number of extra gaps= 0 total=1877 Will force an alignment to be made, even if fragment is small Number of alignments=81 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2cvjA/T0334-2cvjA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2cvjA expands to /projects/compbio/data/pdb/2cvj.pdb.gz 2cvjA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0334 read from 2cvjA/T0334-2cvjA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2cvjA read from 2cvjA/T0334-2cvjA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2cvjA to template set # found chain 2cvjA in template set Warning: unaligning (T0334)D6 because first residue in template chain is (2cvjA)M1 T0334 7 :KILIVGGGTAGWMAASYLGK 2cvjA 3 :DVIVVGGGPSGLSAALFLAR T0334 29 :QGT 2cvjA 23 :AGL T0334 33 :DITLLQAP 2cvjA 26 :KVLVLDGG T0334 96 :EARELDG 2cvjA 34 :RSKVKGV T0334 115 :KYHE 2cvjA 42 :RVPN T0334 152 :ANRSPRRL 2cvjA 46 :YPGLLDEP T0334 172 :DAHLVADFLRRFA 2cvjA 54 :SGEELLRRLEAHA T0334 186 :EKLGVRHVEDRVEHVQRDAN 2cvjA 67 :RRYGAEVRPGVVKGVRDMGG T0334 207 :N 2cvjA 87 :V T0334 209 :ESVRTATG 2cvjA 88 :FEVETEEG T0334 218 :VFDADLFVDCSG 2cvjA 96 :VEKAERLLLCTH T0334 231 :RGLLINKAMEEPFL 2cvjA 108 :KDPTLPSLLGLTRR T0334 247 :SDHLLNDSAVA 2cvjA 122 :GAYIDTDEGGR T0334 338 :AWVGNCVSIGTSSCFVEPLESTGIYFVYAALYQLVKHFPDKSLN 2cvjA 133 :TSYPRVYAAGVARGKVPGHAIISAGDGAYVAVHLVSDLRGEPYK Number of specific fragments extracted= 14 number of extra gaps= 0 total=1891 Will force an alignment to be made, even if fragment is small Number of alignments=82 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2cvjA/T0334-2cvjA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0334 read from 2cvjA/T0334-2cvjA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2cvjA read from 2cvjA/T0334-2cvjA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2cvjA in template set T0334 6 :DKILIVGGGTAGWMAASYLGK 2cvjA 2 :WDVIVVGGGPSGLSAALFLAR T0334 30 :GTADITLLQAPDIP 2cvjA 23 :AGLKVLVLDGGRSK T0334 62 :FLGI 2cvjA 37 :VKGV T0334 137 :EPFD 2cvjA 41 :SRVP T0334 154 :RSP 2cvjA 45 :NYP T0334 161 :GSKVT 2cvjA 48 :GLLDE T0334 171 :FDAHLVADFLRRFA 2cvjA 53 :PSGEELLRRLEAHA T0334 186 :EKLGVRHVEDRVEHVQRDANG 2cvjA 67 :RRYGAEVRPGVVKGVRDMGGV T0334 209 :ESVRTATG 2cvjA 88 :FEVETEEG T0334 218 :VFDADLFVDCSGFRGLL 2cvjA 96 :VEKAERLLLCTHKDPTL T0334 236 :NKAMEEPFLD 2cvjA 113 :PSLLGLTRRG T0334 249 :H 2cvjA 123 :A T0334 272 :FTSA 2cvjA 124 :YIDT T0334 279 :KSG 2cvjA 128 :DEG T0334 336 :RRAWVGNCVSIGTSSCFVEPLESTGIYFVYAALYQLVKHFPDKSLN 2cvjA 131 :GRTSYPRVYAAGVARGKVPGHAIISAGDGAYVAVHLVSDLRGEPYK Number of specific fragments extracted= 15 number of extra gaps= 0 total=1906 Will force an alignment to be made, even if fragment is small Number of alignments=83 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2cvjA/T0334-2cvjA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0334 read from 2cvjA/T0334-2cvjA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2cvjA read from 2cvjA/T0334-2cvjA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2cvjA in template set T0334 7 :KILIVGGGTAGWMAASYLGK 2cvjA 3 :DVIVVGGGPSGLSAALFLAR T0334 30 :GTADITLLQAPDI 2cvjA 23 :AGLKVLVLDGGRS T0334 61 :DFLGIP 2cvjA 36 :KVKGVS T0334 154 :RSPRRLDGSKVTN 2cvjA 42 :RVPNYPGLLDEPS T0334 173 :AHLVADFLRRFATEKLGVRHVE 2cvjA 55 :GEELLRRLEAHARRYGAEVRPG T0334 196 :RVEHVQRDANG 2cvjA 77 :VVKGVRDMGGV T0334 209 :ESVRTAT 2cvjA 88 :FEVETEE T0334 217 :RVFDADLFVDCSGFRGLLIN 2cvjA 95 :GVEKAERLLLCTHKDPTLPS T0334 238 :AMEEPF 2cvjA 115 :LLGLTR T0334 326 :NRIRFRVGRNRRAWVGNCVSIGTSSCFVEPLESTGIYFVYAALYQLVKHFPDKSLN 2cvjA 121 :RGAYIDTDEGGRTSYPRVYAAGVARGKVPGHAIISAGDGAYVAVHLVSDLRGEPYK Number of specific fragments extracted= 10 number of extra gaps= 0 total=1916 Will force an alignment to be made, even if fragment is small Number of alignments=84 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1w4xA/T0334-1w4xA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1w4xA expands to /projects/compbio/data/pdb/1w4x.pdb.gz 1w4xA:Skipped atom 2639, because occupancy 0.500 <= existing 0.500 in 1w4xA Skipped atom 2641, because occupancy 0.500 <= existing 0.500 in 1w4xA Skipped atom 2643, because occupancy 0.500 <= existing 0.500 in 1w4xA Skipped atom 2645, because occupancy 0.500 <= existing 0.500 in 1w4xA Skipped atom 2647, because occupancy 0.500 <= existing 0.500 in 1w4xA Skipped atom 2649, because occupancy 0.500 <= existing 0.500 in 1w4xA # T0334 read from 1w4xA/T0334-1w4xA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1w4xA read from 1w4xA/T0334-1w4xA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1w4xA to template set # found chain 1w4xA in template set T0334 3 :GKI 1w4xA 13 :PPE T0334 7 :KILIVGGGTAGWMAASYLGK 1w4xA 18 :DVLVVGAGFSGLYALYRLRE T0334 29 :QGT 1w4xA 38 :LGR T0334 33 :DITLLQAPD 1w4xA 41 :SVHVIETAG T0334 46 :GVGEATIP 1w4xA 50 :DVGGVWYW T0334 57 :TAF 1w4xA 58 :NRY T0334 61 :DFLGIPED 1w4xA 61 :PGARCDIE T0334 103 :GPDHFYHSFGLL 1w4xA 70 :IEYCYSFSEEVL T0334 116 :YHE 1w4xA 83 :EWN T0334 152 :ANRSPR 1w4xA 86 :WTERYA T0334 172 :DAHLVADFLRRFA 1w4xA 92 :SQPEILRYINFVA T0334 186 :EKLGVR 1w4xA 105 :DKFDLR T0334 192 :HVED 1w4xA 113 :ITFH T0334 196 :RVEHVQRDANGNIESVRTATGRVFDADLFVDCSGFRG 1w4xA 118 :TVTAAAFDEATNTWTVDTNHGDRIRARYLIMASGQLS T0334 233 :LLI 1w4xA 156 :PQL T0334 261 :PHDDDANGVEPFTS 1w4xA 159 :PNFPGLKDFAGNLY T0334 275 :AIAMKSGWTW 1w4xA 175 :GNWPHEPVDF T0334 289 :LGR 1w4xA 185 :SGQ T0334 292 :FGTGYVYSSRFATE 1w4xA 219 :PHFAVPARNAPLDP T0334 306 :DEAVREFCEM 1w4xA 271 :EELVETLERY T0334 316 :WHLDP 1w4xA 282 :QEGGP T0334 321 :ETQPLNRIRFRVGRNR 1w4xA 349 :NRDNVHLVDTLSAPIE T0334 337 :RAWVGNCVSI 1w4xA 425 :TAGFPNLFFI T0334 350 :SCFVEPLESTGIYFVYAA 1w4xA 435 :AGPGSPSALSNMLVSIEQ T0334 395 :MFDDTRDFIQAHFY 1w4xA 453 :HVEWVTDHIAYMFK T0334 422 :KEL 1w4xA 467 :NGL T0334 427 :ADGMQEKIDMYRAGM 1w4xA 476 :LEKEDEWVEHVNEIA T0334 442 :AINAPASDDAQLYYGNFE 1w4xA 500 :SWYTGANVPGKPRVFMLY T0334 489 :L 1w4xA 518 :V T0334 497 :ESVD 1w4xA 519 :GGFH T0334 505 :AVKDRQRNLLE 1w4xA 523 :RYRQICDEVAA Number of specific fragments extracted= 31 number of extra gaps= 0 total=1947 Will force an alignment to be made, even if fragment is small Number of alignments=85 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1w4xA/T0334-1w4xA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0334 read from 1w4xA/T0334-1w4xA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1w4xA read from 1w4xA/T0334-1w4xA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1w4xA in template set T0334 3 :GKIDKILIVGGGTAGWMAASYLGKA 1w4xA 14 :PEEVDVLVVGAGFSGLYALYRLREL T0334 31 :TADITLLQAP 1w4xA 39 :GRSVHVIETA T0334 41 :DIPT 1w4xA 50 :DVGG T0334 57 :TAF 1w4xA 54 :VWY T0334 128 :DRSYR 1w4xA 57 :WNRYP T0334 141 :YACYKEPVILD 1w4xA 62 :GARCDIESIEY T0334 152 :ANRSPRRLDGSKVTNY 1w4xA 74 :YSFSEEVLQEWNWTER T0334 169 :W 1w4xA 90 :Y T0334 171 :FDAHLVADFLRRFA 1w4xA 91 :ASQPEILRYINFVA T0334 186 :EKLG 1w4xA 105 :DKFD T0334 192 :HVED 1w4xA 113 :ITFH T0334 196 :RVEHVQRDANGNIESVRTATGRVFDADLFVDCSGFRG 1w4xA 118 :TVTAAAFDEATNTWTVDTNHGDRIRARYLIMASGQLS T0334 243 :FLDMSDH 1w4xA 155 :VPQLPNF T0334 264 :DDANGVEPFTSAIA 1w4xA 162 :PGLKDFAGNLYHTG T0334 278 :MKS 1w4xA 177 :WPH T0334 333 :GRNR 1w4xA 180 :EPVD T0334 338 :AWVGNCVSIG 1w4xA 184 :FSGQRVGVIG T0334 362 :YFVYAALYQLVKHFPD 1w4xA 196 :SSGIQVSPQIAKQAAE T0334 378 :KSLNPVLTARFNREIETMFDDTRD 1w4xA 228 :APLDPEFLADLKKRYAEFREESRN T0334 440 :GM 1w4xA 252 :TP T0334 478 :LGLVPDAPSPRLAHMPQ 1w4xA 254 :GGTHRYQGPKSALEVSD T0334 497 :ESVDEVFGAVKDR 1w4xA 271 :EELVETLERYWQE Number of specific fragments extracted= 22 number of extra gaps= 0 total=1969 Will force an alignment to be made, even if fragment is small Number of alignments=86 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1w4xA/T0334-1w4xA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0334 read from 1w4xA/T0334-1w4xA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1w4xA read from 1w4xA/T0334-1w4xA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1w4xA in template set T0334 3 :GKIDKILIVGGGTAGWMAASYLGK 1w4xA 14 :PEEVDVLVVGAGFSGLYALYRLRE T0334 30 :GTADITLLQ 1w4xA 38 :LGRSVHVIE T0334 39 :APDIPT 1w4xA 48 :AGDVGG T0334 57 :TAF 1w4xA 54 :VWY T0334 64 :GI 1w4xA 57 :WN T0334 78 :YKVAIK 1w4xA 59 :RYPGAR T0334 103 :GPDHFY 1w4xA 65 :CDIESI T0334 130 :S 1w4xA 71 :E T0334 149 :ILDANRSPRRLDGSKVTNY 1w4xA 72 :YCYSFSEEVLQEWNWTERY T0334 171 :FDAHLVADFLRRFATEKLGV 1w4xA 91 :ASQPEILRYINFVADKFDLR T0334 191 :RHVEDRVEHVQRDANGNIESVRTATGRVFDADLFVDCSGFRG 1w4xA 113 :ITFHTTVTAAAFDEATNTWTVDTNHGDRIRARYLIMASGQLS T0334 240 :EEPFLDMSDHLLNDSAVATQ 1w4xA 155 :VPQLPNFPGLKDFAGNLYHT T0334 262 :HDDDANGVE 1w4xA 175 :GNWPHEPVD T0334 271 :PF 1w4xA 186 :GQ T0334 342 :NCVSIG 1w4xA 188 :RVGVIG T0334 356 :LESTGIYFVYAALYQL 1w4xA 194 :TGSSGIQVSPQIAKQA T0334 378 :KSLNPVLTARFNREIETMFDDTR 1w4xA 228 :APLDPEFLADLKKRYAEFREESR T0334 410 :SPRTDTP 1w4xA 256 :THRYQGP T0334 424 :LR 1w4xA 263 :KS T0334 426 :LADGMQEKIDMYRAGMAI 1w4xA 269 :SDEELVETLERYWQEGGP T0334 471 :YYCVLAGLGLVPDAPSPR 1w4xA 287 :DILAAYRDILRDRDANER T0334 492 :MPQATESVDEVFGAVKDRQRNL 1w4xA 305 :VAEFIRNKIRNTVRDPEVAERL Number of specific fragments extracted= 22 number of extra gaps= 0 total=1991 Will force an alignment to be made, even if fragment is small Number of alignments=87 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2bs3A/T0334-2bs3A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2bs3A expands to /projects/compbio/data/pdb/2bs3.pdb.gz 2bs3A:Skipped atom 10, because occupancy 0.500 <= existing 0.500 in 2bs3A Skipped atom 12, because occupancy 0.500 <= existing 0.500 in 2bs3A Skipped atom 14, because occupancy 0.500 <= existing 0.500 in 2bs3A Skipped atom 16, because occupancy 0.500 <= existing 0.500 in 2bs3A Skipped atom 18, because occupancy 0.500 <= existing 0.500 in 2bs3A Skipped atom 20, because occupancy 0.500 <= existing 0.500 in 2bs3A Skipped atom 22, because occupancy 0.500 <= existing 0.500 in 2bs3A Skipped atom 24, because occupancy 0.500 <= existing 0.500 in 2bs3A Skipped atom 26, because occupancy 0.500 <= existing 0.500 in 2bs3A Skipped atom 35, because occupancy 0.500 <= existing 0.500 in 2bs3A Skipped atom 37, because occupancy 0.500 <= existing 0.500 in 2bs3A Skipped atom 39, because occupancy 0.500 <= existing 0.500 in 2bs3A Skipped atom 41, because occupancy 0.500 <= existing 0.500 in 2bs3A Skipped atom 43, because occupancy 0.500 <= existing 0.500 in 2bs3A Skipped atom 45, because occupancy 0.500 <= existing 0.500 in 2bs3A Skipped atom 47, because occupancy 0.500 <= existing 0.500 in 2bs3A Skipped atom 49, because occupancy 0.500 <= existing 0.500 in 2bs3A Skipped atom 51, because occupancy 0.500 <= existing 0.500 in 2bs3A Skipped atom 867, because occupancy 0.500 <= existing 0.500 in 2bs3A Skipped atom 869, because occupancy 0.500 <= existing 0.500 in 2bs3A Skipped atom 871, because occupancy 0.500 <= existing 0.500 in 2bs3A Skipped atom 873, because occupancy 0.500 <= existing 0.500 in 2bs3A Skipped atom 875, because occupancy 0.500 <= existing 0.500 in 2bs3A Skipped atom 877, because occupancy 0.500 <= existing 0.500 in 2bs3A Skipped atom 879, because occupancy 0.500 <= existing 0.500 in 2bs3A Skipped atom 881, because occupancy 0.500 <= existing 0.500 in 2bs3A Skipped atom 883, because occupancy 0.500 <= existing 0.500 in 2bs3A Skipped atom 885, because occupancy 0.500 <= existing 0.500 in 2bs3A Skipped atom 887, because occupancy 0.500 <= existing 0.500 in 2bs3A Skipped atom 1072, because occupancy 0.500 <= existing 0.500 in 2bs3A Skipped atom 1074, because occupancy 0.500 <= existing 0.500 in 2bs3A Skipped atom 1076, because occupancy 0.500 <= existing 0.500 in 2bs3A Skipped atom 1078, because occupancy 0.500 <= existing 0.500 in 2bs3A Skipped atom 1080, because occupancy 0.500 <= existing 0.500 in 2bs3A Skipped atom 1082, because occupancy 0.500 <= existing 0.500 in 2bs3A Skipped atom 1084, because occupancy 0.500 <= existing 0.500 in 2bs3A Skipped atom 1086, because occupancy 0.500 <= existing 0.500 in 2bs3A Skipped atom 1088, because occupancy 0.500 <= existing 0.500 in 2bs3A Skipped atom 1090, because occupancy 0.500 <= existing 0.500 in 2bs3A Skipped atom 1092, because occupancy 0.500 <= existing 0.500 in 2bs3A Skipped atom 2077, because occupancy 0.500 <= existing 0.500 in 2bs3A Skipped atom 2079, because occupancy 0.500 <= existing 0.500 in 2bs3A Skipped atom 2081, because occupancy 0.500 <= existing 0.500 in 2bs3A Skipped atom 2083, because occupancy 0.500 <= existing 0.500 in 2bs3A Skipped atom 2085, because occupancy 0.500 <= existing 0.500 in 2bs3A Skipped atom 2087, because occupancy 0.500 <= existing 0.500 in 2bs3A Skipped atom 2089, because occupancy 0.500 <= existing 0.500 in 2bs3A Skipped atom 2091, because occupancy 0.500 <= existing 0.500 in 2bs3A Skipped atom 2093, because occupancy 0.500 <= existing 0.500 in 2bs3A Skipped atom 2095, because occupancy 0.500 <= existing 0.500 in 2bs3A Skipped atom 2097, because occupancy 0.500 <= existing 0.500 in 2bs3A # T0334 read from 2bs3A/T0334-2bs3A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2bs3A read from 2bs3A/T0334-2bs3A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2bs3A to template set # found chain 2bs3A in template set Warning: unaligning (T0334)I5 because first residue in template chain is (2bs3A)M1 Warning: unaligning (T0334)F352 because of BadResidue code BAD_PEPTIDE in next template residue (2bs3A)D398 T0334 6 :D 2bs3A 2 :K T0334 7 :KILIVGGGTAGWMAASYLGK 2bs3A 7 :DSLVIGGGLAGLRAAVATQQ T0334 29 :QGT 2bs3A 27 :KGL T0334 33 :DITLLQAP 2bs3A 30 :STIVLSLI T0334 46 :GVGEATIPNLQTAFFDFLGIPED 2bs3A 38 :PVKRSHSAAAQGGMQASLGNSKM T0334 100 :LDG 2bs3A 61 :SDG T0334 115 :KYHE 2bs3A 65 :NEDL T0334 122 :LSHYWFDRSYRGKTV 2bs3A 69 :HFMDTVKGSDWGCDQ T0334 139 :FDYACYKEPVILD 2bs3A 98 :RELAAWGVPWTRI T0334 152 :ANRSPRRLDGSKVTNYAWHF 2bs3A 112 :KGDRMAIINAQKTTITEEDF T0334 172 :DAHLVADFLRRFA 2bs3A 156 :TGHTMLFAVANEC T0334 186 :EKLGVRHVED 2bs3A 169 :LKLGVSIQDR T0334 196 :RVEHVQRDAN 2bs3A 180 :EAIALIHQDG T0334 207 :NIESVRTAT 2bs3A 190 :KCYGAVVRD T0334 216 :GR 2bs3A 202 :GD T0334 218 :VFDADLFVDCSGFRGLLINKAMEEPFLDM 2bs3A 206 :AYVAKGTLIATGGYGRIYKNTTNAVVCEG T0334 247 :SDHLLNDSAVATQVPHDDDANGVEPFTSAIAMKSG 2bs3A 243 :TGIAQLGNMEAVQFHPTPLFPSGILLTEGCRGDGG T0334 285 :KIPM 2bs3A 278 :ILRD T0334 289 :LGR 2bs3A 283 :DGH T0334 292 :FGTGYVYSSRFATE 2bs3A 323 :GQHLWLDISILGRK T0334 306 :DEAVREFCEMWHLDPETQPLNRIRFRVGRNRRAWVG 2bs3A 343 :RDVQEICEYFAGIDPAEKWAPVLPMQHYSMGGIRTD T0334 342 :NCVSIGTSSC 2bs3A 387 :GLFSAGEAAC T0334 353 :VEP 2bs3A 399 :MHG T0334 356 :LESTGIYFVYAALYQLVKHFP 2bs3A 405 :LGGNSVSEAVVAGMIVGEYFA T0334 377 :DKSLNPVLTARFNREIETMF 2bs3A 436 :ETKTLEKFVKGQEAYMKSLV T0334 397 :DDTRDFIQAHFYFS 2bs3A 465 :KIKNRMKDVMDDNV T0334 411 :PRTDTP 2bs3A 480 :IFRDGP T0334 417 :FWRA 2bs3A 487 :LEKA T0334 427 :ADGMQEKIDMYRAG 2bs3A 491 :VKELEELYKKSKNV T0334 450 :DAQLYYGNFEEEFRNFWNNSNYYCVLAG 2bs3A 505 :GIKNKRLHANPELEEAYRVPMMLKVALC T0334 478 :LGL 2bs3A 583 :LDV T0334 481 :VPDAPSPRLAHMPQ 2bs3A 587 :EMEIAPGYRGYGAK T0334 495 :ATESVDEVFGAVKDRQRNLLETLPSLHEFLRQQHG 2bs3A 605 :ENPLSVKRQEEIDKIQSELEAAGKDRHAIQEALMP Number of specific fragments extracted= 33 number of extra gaps= 1 total=2024 Will force an alignment to be made, even if fragment is small Number of alignments=88 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2bs3A/T0334-2bs3A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0334 read from 2bs3A/T0334-2bs3A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2bs3A read from 2bs3A/T0334-2bs3A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2bs3A in template set T0334 5 :IDKILIVGGGTAGWMAASYLGK 2bs3A 5 :YCDSLVIGGGLAGLRAAVATQQ T0334 30 :GTADITLLQAPDI 2bs3A 27 :KGLSTIVLSLIPV T0334 43 :PTLGVGEATIPN 2bs3A 47 :AQGGMQASLGNS T0334 60 :FDFLGIPEDEWMRECNAS 2bs3A 59 :KMSDGDNEDLHFMDTVKG T0334 78 :YKVAIKFINWRTAG 2bs3A 83 :QKVARMFVNTAPKA T0334 123 :SHYWFDRSYR 2bs3A 97 :IRELAAWGVP T0334 136 :VEPFDYACYKEPVILD 2bs3A 107 :WTRIHKGDRMAIINAQ T0334 152 :ANRSPRRLDGSKVTNYAW 2bs3A 126 :ITEEDFRHGLIHSRDFGG T0334 170 :HFDAHLVADFLRRFAT 2bs3A 154 :DATGHTMLFAVANECL T0334 187 :KLGVRHVED 2bs3A 170 :KLGVSIQDR T0334 196 :RVEHVQR 2bs3A 180 :EAIALIH T0334 204 :ANGNIESVR 2bs3A 187 :QDGKCYGAV T0334 213 :TATG 2bs3A 199 :LVTG T0334 217 :RVFDADLFVDCSGFRGLL 2bs3A 205 :IAYVAKGTLIATGGYGRI T0334 239 :M 2bs3A 241 :L T0334 246 :MSDH 2bs3A 242 :ETGI T0334 250 :LLNDSAVATQV 2bs3A 248 :LGNMEAVQFHP T0334 275 :AIAMKSGWTW 2bs3A 259 :TPLFPSGILL T0334 285 :KIPMLGRFGT 2bs3A 278 :ILRDVDGHRF T0334 295 :GYVYSSRFATE 2bs3A 325 :HLWLDISILGR T0334 306 :DEAVREFCEMWHLDPETQPLNRIRFRVGRNRRA 2bs3A 343 :RDVQEICEYFAGIDPAEKWAPVLPMQHYSMGGI T0334 339 :WVGNCVSIGTSS 2bs3A 384 :KLKGLFSAGEAA T0334 351 :CFVEPLESTGIYFVYAALYQLVKHFPD 2bs3A 400 :HGFNRLGGNSVSEAVVAGMIVGEYFAE T0334 378 :KSLNPVLTARFNREIETMFD 2bs3A 437 :TKTLEKFVKGQEAYMKSLVE T0334 410 :SPRT 2bs3A 457 :SKGT T0334 424 :LRLADGMQEKIDMYRAGMAINAP 2bs3A 461 :EDVFKIKNRMKDVMDDNVGIFRD T0334 448 :SDDAQLYYGNFEEEFRNFWN 2bs3A 484 :GPHLEKAVKELEELYKKSKN T0334 471 :YYCVLAG 2bs3A 530 :ALCVAKG T0334 478 :LGLVPDA 2bs3A 545 :GAHNRED T0334 488 :RLAHM 2bs3A 584 :DVNEM T0334 493 :PQ 2bs3A 600 :KG T0334 496 :TESVDEVFGAVKDRQRNLLETLPSLHEFLRQQHG 2bs3A 606 :NPLSVKRQEEIDKIQSELEAAGKDRHAIQEALMP Number of specific fragments extracted= 32 number of extra gaps= 0 total=2056 Will force an alignment to be made, even if fragment is small Number of alignments=89 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2bs3A/T0334-2bs3A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0334 read from 2bs3A/T0334-2bs3A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2bs3A read from 2bs3A/T0334-2bs3A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2bs3A in template set Warning: unaligning (T0334)F352 because of BadResidue code BAD_PEPTIDE in next template residue (2bs3A)D398 T0334 4 :KIDKILIVGGGTAGWMAASYLGK 2bs3A 4 :QYCDSLVIGGGLAGLRAAVATQQ T0334 30 :GTADITLLQAPDIPTLGVGEATI 2bs3A 27 :KGLSTIVLSLIPVKRSHSAAAQG T0334 53 :PNLQTAF 2bs3A 68 :LHFMDTV T0334 61 :DFLGIP 2bs3A 75 :KGSDWG T0334 68 :DEWMRECNAS 2bs3A 97 :IRELAAWGVP T0334 87 :WRTAGEGTSEARELDGGPD 2bs3A 107 :WTRIHKGDRMAIINAQKTT T0334 150 :LDANRSPRRLDGSKVTNYAWHF 2bs3A 130 :DFRHGLIHSRDFGGTKKWRTCY T0334 172 :DAHLVADFLRRFATEKLGVRHVEDRVEHVQRDANGN 2bs3A 156 :TGHTMLFAVANECLKLGVSIQDRKEAIALIHQDGKC T0334 208 :IESVRTATGR 2bs3A 194 :AVVRDLVTGD T0334 218 :VFDADLFVDCSGFRG 2bs3A 206 :AYVAKGTLIATGGYG T0334 248 :DHLLND 2bs3A 221 :RIYKNT T0334 264 :DDANGVEPFTSAIAMKSG 2bs3A 227 :TNAVVCEGTGTAIALETG T0334 307 :EAVREFCEMWHLDP 2bs3A 344 :DVQEICEYFAGIDP T0334 322 :TQPLNRIRF 2bs3A 358 :AEKWAPVLP T0334 331 :RVGRNRRAWVGNCVSIGTSSC 2bs3A 376 :RTDYRGEAKLKGLFSAGEAAC T0334 353 :VEPLESTGIYFVYAALYQLVKHFP 2bs3A 402 :FNRLGGNSVSEAVVAGMIVGEYFA T0334 377 :DKSLNPVLTARFNREIETMFD 2bs3A 436 :ETKTLEKFVKGQEAYMKSLVE T0334 410 :SPRTD 2bs3A 457 :SKGTE T0334 425 :RLADGMQEKIDMYRAGMAI 2bs3A 462 :DVFKIKNRMKDVMDDNVGI T0334 479 :GLVPDAPSPRLAHMPQATESV 2bs3A 481 :FRDGPHLEKAVKELEELYKKS Number of specific fragments extracted= 20 number of extra gaps= 1 total=2076 Will force an alignment to be made, even if fragment is small Number of alignments=90 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1kdgA/T0334-1kdgA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1kdgA expands to /projects/compbio/data/pdb/1kdg.pdb.gz 1kdgA:Skipped atom 858, because occupancy 0.500 <= existing 0.500 in 1kdgA Skipped atom 1621, because occupancy 0.500 <= existing 0.500 in 1kdgA Skipped atom 1623, because occupancy 0.500 <= existing 0.500 in 1kdgA Skipped atom 1625, because occupancy 0.500 <= existing 0.500 in 1kdgA Skipped atom 1960, because occupancy 0.500 <= existing 0.500 in 1kdgA Skipped atom 2493, because occupancy 0.500 <= existing 0.500 in 1kdgA Skipped atom 2495, because occupancy 0.500 <= existing 0.500 in 1kdgA Skipped atom 2497, because occupancy 0.500 <= existing 0.500 in 1kdgA # T0334 read from 1kdgA/T0334-1kdgA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1kdgA read from 1kdgA/T0334-1kdgA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1kdgA to template set # found chain 1kdgA in template set Warning: unaligning (T0334)I5 because first residue in template chain is (1kdgA)T215 Warning: unaligning (T0334)L380 because last residue in template chain is (1kdgA)P755 T0334 6 :D 1kdgA 216 :P T0334 7 :KILIVGGGTAGWMAASYLGK 1kdgA 218 :DYIIVGAGPGGIIAADRLSE T0334 29 :QGT 1kdgA 238 :AGK T0334 33 :DITLLQAPDIPTLGVGEATIP 1kdgA 241 :KVLLLERGGPSTKQTGGTYVA T0334 57 :TAFFDFLGIPED 1kdgA 262 :PWATSSGLTKFD T0334 96 :EARELDG 1kdgA 274 :IPGLFES T0334 103 :GPDHFYHSFGLLKYHEQIPLSHYWFDRSYRGKTVEP 1kdgA 284 :DSNPFWWCKDITVFAGCLVGGGTSVNGALYWYPNDG T0334 139 :FDYACYKEP 1kdgA 368 :QLLKGQGYN T0334 172 :DAHLVADFLRRFA 1kdgA 403 :RAGPVATYLQTAL T0334 186 :EKLGVRHVED 1kdgA 416 :ARPNFTFKTN T0334 196 :RVEHVQRDAN 1kdgA 427 :MVSNVVRNGS T0334 207 :NIESVRTAT 1kdgA 437 :QILGVQTND T0334 218 :VFDA 1kdgA 453 :FIPV T0334 222 :DLFVDCSGFRG 1kdgA 460 :GRVILSAGAFG T0334 233 :LLINKAMEEPFLDM 1kdgA 472 :SRILFQSGIGPTDM T0334 254 :SAVATQVPHDDDANGVEPFTSAIAMK 1kdgA 502 :QNQWINLPVGMNAQDNPSINLVFTHP T0334 280 :SGWTWKIPM 1kdgA 563 :PKLNFWRAY T0334 289 :LGR 1kdgA 575 :DGF T0334 294 :TGYVYSSRFATE 1kdgA 581 :AQGTVRPGAASV T0334 306 :DEAVREFCEM 1kdgA 639 :PVDKTVLLQA T0334 316 :WHLDP 1kdgA 650 :HDVVS T0334 321 :ETQPLNRIRF 1kdgA 658 :SIPGLTMITP T0334 342 :NCVSIGTSSCFVEPL 1kdgA 716 :NLFIVDAGIIPHLPT T0334 358 :STGIYFVYAALYQLVKHFP 1kdgA 731 :GNPQGTLMSAAEQAAAKIL T0334 377 :DKS 1kdgA 752 :AGG Number of specific fragments extracted= 25 number of extra gaps= 0 total=2101 Will force an alignment to be made, even if fragment is small Number of alignments=91 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1kdgA/T0334-1kdgA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0334 read from 1kdgA/T0334-1kdgA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1kdgA read from 1kdgA/T0334-1kdgA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1kdgA in template set Warning: unaligning (T0334)K4 because first residue in template chain is (1kdgA)T215 T0334 5 :IDKILIVGGGTAGWMAASYLGK 1kdgA 216 :PYDYIIVGAGPGGIIAADRLSE T0334 30 :GTADITLLQAPDI 1kdgA 238 :AGKKVLLLERGGP T0334 46 :GVGEATIPNL 1kdgA 255 :TGGTYVAPWA T0334 61 :DFLGI 1kdgA 265 :TSSGL T0334 87 :WRTAGEGTSEARELDGGP 1kdgA 270 :TKFDIPGLFESLFTDSNP T0334 106 :HFYHSFG 1kdgA 293 :DITVFAG T0334 129 :RSY 1kdgA 302 :VGG T0334 141 :YACYKEPVILD 1kdgA 305 :GTSVNGALYWY T0334 154 :RSPRR 1kdgA 316 :PNDGD T0334 159 :LDGSKVTNYAW 1kdgA 322 :SSSVGWPSSWT T0334 170 :HFDAHLVADFLRRFA 1kdgA 401 :GKRAGPVATYLQTAL T0334 186 :EKLGVRHVED 1kdgA 416 :ARPNFTFKTN T0334 196 :RVEHVQR 1kdgA 427 :MVSNVVR T0334 204 :ANGNIESVRTA 1kdgA 434 :NGSQILGVQTN T0334 215 :T 1kdgA 447 :T T0334 217 :RVFDAD 1kdgA 452 :GFIPVT T0334 223 :LFVDCSGFRGLL 1kdgA 461 :RVILSAGAFGTS T0334 236 :NKA 1kdgA 473 :RIL T0334 243 :FLDMSDH 1kdgA 499 :LPPQNQW T0334 250 :LLN 1kdgA 508 :LPV T0334 253 :DSAVATQVPHDDD 1kdgA 519 :SINLVFTHPSIDA T0334 266 :ANGVE 1kdgA 539 :WSNPR T0334 271 :PFTSAIAMKSGWTW 1kdgA 555 :SGVFAGASPKLNFW T0334 285 :KIPMLGR 1kdgA 570 :AYSGSDG T0334 292 :FGTGYVYSSRFATE 1kdgA 579 :RYAQGTVRPGAASV T0334 306 :DEAVREFCEMW 1kdgA 639 :PVDKTVLLQAL T0334 317 :HLDPETQ 1kdgA 657 :GSIPGLT T0334 324 :PLNRIRFRVGRNRRAWVGNC 1kdgA 690 :WVSSTTIGSSPQSAVVDSNV T0334 344 :VSIGTSSCFVEPLESTGIYFVYAALYQLVKHFPD 1kdgA 717 :LFIVDAGIIPHLPTGNPQGTLMSAAEQAAAKILA T0334 378 :KSL 1kdgA 752 :AGG Number of specific fragments extracted= 30 number of extra gaps= 0 total=2131 Will force an alignment to be made, even if fragment is small Number of alignments=92 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1kdgA/T0334-1kdgA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0334 read from 1kdgA/T0334-1kdgA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1kdgA read from 1kdgA/T0334-1kdgA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1kdgA in template set Warning: unaligning (T0334)K4 because first residue in template chain is (1kdgA)T215 T0334 5 :IDKILIVGGGTAGWMAASYLGK 1kdgA 216 :PYDYIIVGAGPGGIIAADRLSE T0334 30 :GTADITLLQAPDIPTLGVGEATIPNLQ 1kdgA 238 :AGKKVLLLERGGPSTKQTGGTYVAPWA T0334 61 :DFLGI 1kdgA 265 :TSSGL T0334 76 :ASYKVAIKFINWRTAGEGTSEAREL 1kdgA 270 :TKFDIPGLFESLFTDSNPFWWCKDI T0334 101 :DGGPDHFYHSFGLLKYHEQIPLSHYWFD 1kdgA 325 :VGWPSSWTNHAPYTSKLSSRLPSTDHPS T0334 130 :SYRGKTVEPFDYACYKEPVILDANRSPRRLDGSKVTNY 1kdgA 353 :TDGQRYLEQSFNVVSQLLKGQGYNQATINDNPNYKDHV T0334 168 :AWHF 1kdgA 395 :AFDF T0334 172 :DAHLVADFLRRFATEKLGVRHVEDRVEHVQRDANG 1kdgA 403 :RAGPVATYLQTALARPNFTFKTNVMVSNVVRNGSQ T0334 208 :IESVRTATGR 1kdgA 438 :ILGVQTNDPT T0334 218 :VFDAD 1kdgA 453 :FIPVT T0334 223 :LFVDCSGFRG 1kdgA 461 :RVILSAGAFG T0334 233 :LLINKAMEEP 1kdgA 484 :DMIQTVQSNP T0334 293 :GTGYVYSSRFAT 1kdgA 519 :SINLVFTHPSID T0334 307 :EAVREFCEMWHLDPETQ 1kdgA 671 :QTLEEYVDAYDPATMNS T0334 338 :AWVGNCVSI 1kdgA 712 :FGTNNLFIV T0334 348 :TSSCFVEPLESTGIYFVYAALYQLVKHFPDK 1kdgA 721 :DAGIIPHLPTGNPQGTLMSAAEQAAAKILAL Number of specific fragments extracted= 16 number of extra gaps= 0 total=2147 Will force an alignment to be made, even if fragment is small Number of alignments=93 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2fjbA/T0334-2fjbA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2fjbA expands to /projects/compbio/data/pdb/2fjb.pdb.gz 2fjbA:Skipped atom 1920, because occupancy 0.500 <= existing 0.500 in 2fjbA Skipped atom 1922, because occupancy 0.500 <= existing 0.500 in 2fjbA Skipped atom 1924, because occupancy 0.500 <= existing 0.500 in 2fjbA Skipped atom 1926, because occupancy 0.500 <= existing 0.500 in 2fjbA Skipped atom 2576, because occupancy 0.500 <= existing 0.500 in 2fjbA Skipped atom 2578, because occupancy 0.500 <= existing 0.500 in 2fjbA Skipped atom 2580, because occupancy 0.500 <= existing 0.500 in 2fjbA Skipped atom 2582, because occupancy 0.500 <= existing 0.500 in 2fjbA Skipped atom 2624, because occupancy 0.500 <= existing 0.500 in 2fjbA Skipped atom 2626, because occupancy 0.500 <= existing 0.500 in 2fjbA Skipped atom 2628, because occupancy 0.500 <= existing 0.500 in 2fjbA Skipped atom 2630, because occupancy 0.500 <= existing 0.500 in 2fjbA Skipped atom 3129, because occupancy 0.500 <= existing 0.500 in 2fjbA Skipped atom 3131, because occupancy 0.500 <= existing 0.500 in 2fjbA Skipped atom 3133, because occupancy 0.500 <= existing 0.500 in 2fjbA Skipped atom 3135, because occupancy 0.500 <= existing 0.500 in 2fjbA Skipped atom 4289, because occupancy 0.500 <= existing 0.500 in 2fjbA Skipped atom 4291, because occupancy 0.500 <= existing 0.500 in 2fjbA Skipped atom 4293, because occupancy 0.500 <= existing 0.500 in 2fjbA Skipped atom 4295, because occupancy 0.500 <= existing 0.500 in 2fjbA Skipped atom 5141, because occupancy 0.500 <= existing 0.500 in 2fjbA Skipped atom 5143, because occupancy 0.500 <= existing 0.500 in 2fjbA Skipped atom 5145, because occupancy 0.500 <= existing 0.500 in 2fjbA Skipped atom 5147, because occupancy 0.500 <= existing 0.500 in 2fjbA # T0334 read from 2fjbA/T0334-2fjbA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2fjbA read from 2fjbA/T0334-2fjbA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2fjbA to template set # found chain 2fjbA in template set T0334 4 :KID 2fjbA 17 :PTE T0334 7 :KILIVGGGTAGWMAASYLGKAL 2fjbA 24 :DILIIGGGFSGCGAAYEAAYWA T0334 29 :QGT 2fjbA 48 :GGL T0334 33 :DITLLQAP 2fjbA 51 :KVTLVEKA T0334 46 :GVGEATIPNLQTAFFDFLGIPED 2fjbA 59 :AVERSGAVAQGLSAINTYIDLTG T0334 115 :KYHEQIPLSHYWFDRSYRGKTVEP 2fjbA 82 :RSERQNTLEDYVRYVTLDMMGLAR T0334 139 :FDYACYKEPVILD 2fjbA 121 :HLFEKWGLPIWKT T0334 152 :ANRSPRRLD 2fjbA 135 :DGKYVREGQ T0334 162 :SKVTNYAWH 2fjbA 144 :WQIMIHGES T0334 172 :DAHLVADFLRRFA 2fjbA 153 :YKPIIAEAAKMAV T0334 186 :EK 2fjbA 166 :GE T0334 191 :R 2fjbA 168 :E T0334 192 :HVED 2fjbA 170 :IYER T0334 196 :RVEHVQRDANG 2fjbA 175 :FIFELLKDKND T0334 207 :NIESVRTA 2fjbA 188 :AVAGAVGF T0334 215 :TGR 2fjbA 198 :REP T0334 218 :VFDADLFVDCSGF 2fjbA 204 :VFKAKAVILATGG T0334 231 :R 2fjbA 367 :V T0334 233 :LLINKAMEEPFL 2fjbA 370 :ALLWACQNIDPQ T0334 247 :SDHLLNDSAV 2fjbA 382 :EQPSEAAPAE T0334 271 :PFTS 2fjbA 392 :PYIM T0334 287 :PMLGRFGTGYVYSSRFATEDEAV 2fjbA 396 :GSHSGEAGFWVCGPEDLMPEEYA T0334 314 :EMWHLDP 2fjbA 419 :KLFPLKY T0334 337 :RAWVGNCVSIGTSSCF 2fjbA 428 :MTTVKGLFAIGDCAGA T0334 353 :VEPLESTGIYFVYAALYQLVKHFP 2fjbA 445 :PHKFSSGSFTEGRIAAKAAVRFIL T0334 377 :DKSLNPVLTARFNREIETMFDDTRDF 2fjbA 473 :NPEIDDAVVEELKKKAYAPMERFMQY T0334 424 :LRL 2fjbA 499 :KDL T0334 427 :ADGMQEKIDMYRAGMAINAPAS 2fjbA 515 :WQGLVRLQKIMDEYAAGIATIY T0334 500 :DEVFGAVKDRQRNLLETLPS 2fjbA 540 :EKMLQRALELLAFLKEDLEK Number of specific fragments extracted= 29 number of extra gaps= 0 total=2176 Will force an alignment to be made, even if fragment is small Number of alignments=94 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2fjbA/T0334-2fjbA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0334 read from 2fjbA/T0334-2fjbA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2fjbA read from 2fjbA/T0334-2fjbA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2fjbA in template set T0334 5 :IDKILIVGGGTAGWMAASYLGKAL 2fjbA 22 :ETDILIIGGGFSGCGAAYEAAYWA T0334 29 :QGTADITLLQAPDI 2fjbA 47 :LGGLKVTLVEKAAV T0334 43 :PTLGVGEATIPNLQTAF 2fjbA 80 :TGRSERQNTLEDYVRYV T0334 60 :FDFLGIP 2fjbA 98 :LDMMGLA T0334 77 :SYKVAIKFINWRTAG 2fjbA 105 :REDLVADYARHVDGT T0334 123 :SHYWFDRSYR 2fjbA 120 :VHLFEKWGLP T0334 136 :V 2fjbA 130 :I T0334 141 :YACYKEPVI 2fjbA 131 :WKTPDGKYV T0334 163 :KVTNYAWHF 2fjbA 140 :REGQWQIMI T0334 173 :AHLVADFLRRFA 2fjbA 154 :KPIIAEAAKMAV T0334 189 :G 2fjbA 166 :G T0334 192 :HVED 2fjbA 170 :IYER T0334 196 :RVEHVQRDANGN 2fjbA 175 :FIFELLKDKNDP T0334 208 :IESVR 2fjbA 189 :VAGAV T0334 213 :TA 2fjbA 195 :FS T0334 215 :TG 2fjbA 198 :RE T0334 217 :RVFDADLFVDCSGFRGLL 2fjbA 203 :YVFKAKAVILATGGATLL T0334 243 :FLDMSDH 2fjbA 221 :FRPRSTG T0334 264 :DDANGVEPFTSAIAM 2fjbA 228 :EAAGRTWYAIFDTGS T0334 279 :KSGWTW 2fjbA 250 :AGAMLT T0334 285 :KIPM 2fjbA 261 :FIPF T0334 289 :LGR 2fjbA 267 :KDG T0334 292 :FGT 2fjbA 271 :GPV T0334 299 :SSRFATE 2fjbA 305 :PYGAAQP T0334 306 :DEAVREFCEMW 2fjbA 348 :KKKLKHIYEEA T0334 317 :HLDPETQ 2fjbA 377 :NIDPQEQ T0334 329 :RFRVGRNRRA 2fjbA 384 :PSEAAPAEPY T0334 339 :WVGNCVSIGTSSCFVEPLESTGIYF 2fjbA 430 :TVKGLFAIGDCAGANPHKFSSGSFT T0334 364 :VYAALYQLVKHFPD 2fjbA 456 :GRIAAKAAVRFILE T0334 378 :KSLNPVLTARF 2fjbA 474 :PEIDDAVVEEL T0334 396 :FDDTRDFIQAHFYFSPRTDTP 2fjbA 485 :KKKAYAPMERFMQYKDLSTAD T0334 417 :FW 2fjbA 514 :PW T0334 428 :DGMQEKIDMYRAGMAINAPA 2fjbA 516 :QGLVRLQKIMDEYAAGIATI T0334 500 :DEVFGAVKDRQRNLLET 2fjbA 540 :EKMLQRALELLAFLKED Number of specific fragments extracted= 34 number of extra gaps= 0 total=2210 Will force an alignment to be made, even if fragment is small Number of alignments=95 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2fjbA/T0334-2fjbA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0334 read from 2fjbA/T0334-2fjbA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2fjbA read from 2fjbA/T0334-2fjbA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2fjbA in template set T0334 7 :KILIVGGGTAGWMAASYLGKAL 2fjbA 24 :DILIIGGGFSGCGAAYEAAYWA T0334 29 :QGTADITLLQAPDIPTLGV 2fjbA 47 :LGGLKVTLVEKAAVERSGA T0334 78 :YKVAIKFINW 2fjbA 66 :VAQGLSAINT T0334 94 :TSEARELDGGPDHFYHSFGLLKYHEQIPLSHYWFD 2fjbA 76 :YIDLTGRSERQNTLEDYVRYVTLDMMGLAREDLVA T0334 134 :KTVEPFDYACYKEPVILDANRSPRRLDGSKVTNYAWHF 2fjbA 111 :DYARHVDGTVHLFEKWGLPIWKTPDGKYVREGQWQIMI T0334 172 :DAHLVADFLRRFA 2fjbA 153 :YKPIIAEAAKMAV T0334 191 :RHVEDRVEHVQRDANGN 2fjbA 170 :IYERVFIFELLKDKNDP T0334 208 :IESVRTATGR 2fjbA 192 :AVGFSVREPK T0334 218 :VFDADLFVDCSGFRGL 2fjbA 204 :VFKAKAVILATGGATL T0334 260 :VPHDDDANGVEPFTS 2fjbA 220 :LFRPRSTGEAAGRTW T0334 338 :AWVGNCVSIGTSSCFVEPLESTG 2fjbA 429 :TTVKGLFAIGDCAGANPHKFSSG T0334 361 :IYFVYAALYQLVKHFP 2fjbA 453 :FTEGRIAAKAAVRFIL T0334 377 :DKSLNPVLTARFNREIETMFDDTRDF 2fjbA 473 :NPEIDDAVVEELKKKAYAPMERFMQY T0334 441 :MAINAPASDDAQLY 2fjbA 499 :KDLSTADDVNPEYI T0334 457 :NFEEEFRNFWNNSNYYCVLAGLGL 2fjbA 513 :LPWQGLVRLQKIMDEYAAGIATIY T0334 481 :V 2fjbA 539 :N T0334 493 :PQATESVDEVFGAVKDRQ 2fjbA 540 :EKMLQRALELLAFLKEDL Number of specific fragments extracted= 17 number of extra gaps= 0 total=2227 Will force an alignment to be made, even if fragment is small Number of alignments=96 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1trb/T0334-1trb-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1trb expands to /projects/compbio/data/pdb/1trb.pdb.gz 1trb:Warning: there is no chain 1trb will retry with 1trbA # T0334 read from 1trb/T0334-1trb-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1trb read from 1trb/T0334-1trb-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1trb to template set # found chain 1trb in template set Warning: unaligning (T0334)L188 because of BadResidue code BAD_PEPTIDE in next template residue (1trb)N198 Warning: unaligning (T0334)G189 because of BadResidue code BAD_PEPTIDE at template residue (1trb)N198 Warning: unaligning (T0334)A214 because of BadResidue code BAD_PEPTIDE in next template residue (1trb)D224 Warning: unaligning (T0334)T215 because of BadResidue code BAD_PEPTIDE in next template residue (1trb)N227 Warning: unaligning (T0334)G216 because of BadResidue code BAD_PEPTIDE at template residue (1trb)N227 Warning: unaligning (T0334)S379 because last residue in template chain is (1trb)L316 T0334 4 :KID 1trb 2 :TTK T0334 7 :KILIVGGGTAGWMAASYLGK 1trb 7 :KLLILGSGPAGYTAAVYAAR T0334 29 :QGT 1trb 27 :ANL T0334 33 :DITLLQAPD 1trb 30 :QPVLITGME T0334 47 :VGEATIPN 1trb 39 :KGGQLTTT T0334 57 :TAFFDFLGIPED 1trb 47 :TEVENWPGDPND T0334 69 :EWMRECNASYKVAIKFINWRTAGEGTS 1trb 70 :EHATKFETEIIFDHINKVDLQNRPFRL T0334 96 :EARELDGGPDHFYHSFGLLKYHEQIPLSHYWFDRSYRG 1trb 124 :EEAFKGRGVSACATSDGFFYRNQKVAVIGGGNTAVEEA T0334 139 :FDYACYKEPVILD 1trb 162 :LYLSNIASEVHLI T0334 152 :ANRSPR 1trb 176 :RRDGFR T0334 172 :DAHLVADFLRRFA 1trb 182 :AEKILIKRLMDKV T0334 186 :EK 1trb 195 :EN T0334 190 :VRHVED 1trb 199 :IILHTN T0334 196 :RVEHVQRDANG 1trb 206 :TLEEVTGDQMG T0334 208 :IESVRT 1trb 217 :VTGVRL T0334 217 :R 1trb 228 :S T0334 218 :VFDADLFVDCSGFRG 1trb 233 :SLDVAGLFVAIGHSP T0334 233 :LLINKAMEEP 1trb 250 :AIFEGQLELE T0334 247 :SDHLLND 1trb 260 :NGYIKVQ T0334 261 :PHDD 1trb 267 :SGIH T0334 333 :GRNRRAWVGNCVSIGTSSCFVEPLESTGIYFVYAALYQLVKHFP 1trb 271 :GNATQTSIPGVFAAGDVMDHIYRQAITSAGTGCMAALDAERYLD T0334 378 :K 1trb 315 :G Number of specific fragments extracted= 22 number of extra gaps= 3 total=2249 Will force an alignment to be made, even if fragment is small Number of alignments=97 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1trb/T0334-1trb-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0334 read from 1trb/T0334-1trb-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1trb read from 1trb/T0334-1trb-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1trb in template set Warning: unaligning (T0334)H317 because of BadResidue code BAD_PEPTIDE in next template residue (1trb)D224 Warning: unaligning (T0334)L318 because of BadResidue code BAD_PEPTIDE at template residue (1trb)D224 Warning: unaligning (T0334)D319 because of BadResidue code BAD_PEPTIDE at template residue (1trb)T225 Warning: unaligning (T0334)P320 because of BadResidue code BAD_PEPTIDE in next template residue (1trb)N227 Warning: unaligning (T0334)E321 because of BadResidue code BAD_PEPTIDE at template residue (1trb)N227 Warning: unaligning (T0334)Q323 because of BadResidue code BAD_PEPTIDE in next template residue (1trb)N230 Warning: unaligning (T0334)P324 because of BadResidue code BAD_PEPTIDE at template residue (1trb)N230 T0334 4 :KIDKILIVGGGTAGWMAASYLGK 1trb 4 :KHSKLLILGSGPAGYTAAVYAAR T0334 30 :GTADITLLQAPDIPT 1trb 27 :ANLQPVLITGMEKGG T0334 53 :P 1trb 42 :Q T0334 141 :YACYKEPVI 1trb 43 :LTTTTEVEN T0334 155 :SPRRLDG 1trb 52 :WPGDPND T0334 171 :FDAHLVADFLRRFA 1trb 59 :LTGPLLMERMHEHA T0334 186 :EKLGVRHVEDRVEHVQRDANG 1trb 73 :TKFETEIIFDHINKVDLQNRP T0334 209 :ESVRTATGR 1trb 94 :FRLNGDNGE T0334 219 :FDADLFVDCSGFR 1trb 103 :YTCDALIIATGAS T0334 236 :NKAMEEP 1trb 116 :ARYLGLP T0334 245 :DMSDH 1trb 127 :FKGRG T0334 250 :LLN 1trb 133 :SAC T0334 272 :FTSA 1trb 140 :GFFY T0334 279 :KSGWTWKIPMLG 1trb 144 :RNQKVAVIGGGN T0334 291 :R 1trb 166 :N T0334 292 :FGTGYVYSSRFATE 1trb 169 :SEVHLIHRRDGFRA T0334 306 :DEAVREFCEMW 1trb 184 :KILIKRLMDKV T0334 322 :T 1trb 228 :S T0334 325 :LNRIRFRVG 1trb 231 :IESLDVAGL T0334 339 :WVGNCVSIGTSSCFVEPLESTGIYFVYAALYQLVKHFPD 1trb 277 :SIPGVFAAGDVMDHIYRQAITSAGTGCMAALDAERYLDG Number of specific fragments extracted= 20 number of extra gaps= 2 total=2269 Will force an alignment to be made, even if fragment is small Number of alignments=98 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1trb/T0334-1trb-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0334 read from 1trb/T0334-1trb-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1trb read from 1trb/T0334-1trb-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1trb in template set Warning: unaligning (T0334)K378 because last residue in template chain is (1trb)L316 T0334 6 :DKILIVGGGTAGWMAASYLGK 1trb 6 :SKLLILGSGPAGYTAAVYAAR T0334 30 :GTADITLLQAPDI 1trb 27 :ANLQPVLITGMEK T0334 48 :GEA 1trb 40 :GGQ T0334 78 :YKVAIKFINWRTAGEGT 1trb 43 :LTTTTEVENWPGDPNDL T0334 172 :DAHLVADFLRRFATEKLGVRHVE 1trb 60 :TGPLLMERMHEHATKFETEIIFD T0334 196 :RVEHVQRDANG 1trb 83 :HINKVDLQNRP T0334 209 :ESVRT 1trb 94 :FRLNG T0334 215 :TGRVFDADLFVDCSGF 1trb 99 :DNGEYTCDALIIATGA T0334 299 :SSRFATED 1trb 115 :SARYLGLP T0334 327 :RIRFRVGRNRRAWVGNCVSIGTSSCFVEPLESTGIYFVYAALYQLVKHFPD 1trb 265 :VQSGIHGNATQTSIPGVFAAGDVMDHIYRQAITSAGTGCMAALDAERYLDG Number of specific fragments extracted= 10 number of extra gaps= 0 total=2279 Will force an alignment to be made, even if fragment is small Number of alignments=99 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1m6iA/T0334-1m6iA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1m6iA expands to /projects/compbio/data/pdb/1m6i.pdb.gz 1m6iA:# T0334 read from 1m6iA/T0334-1m6iA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1m6iA read from 1m6iA/T0334-1m6iA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1m6iA to template set # found chain 1m6iA in template set T0334 5 :ID 1m6iA 130 :SH T0334 7 :KILIVGGGTAGWMAASYLGK 1m6iA 133 :PFLLIGGGTAAFAAARSIRA T0334 28 :L 1m6iA 153 :R T0334 29 :QGT 1m6iA 155 :PGA T0334 33 :DITLLQAPD 1m6iA 158 :RVLIVSEDP T0334 42 :IPTL 1m6iA 168 :LPYM T0334 139 :FDYACYKEPVILD 1m6iA 321 :RKARALGTEVIQL T0334 152 :ANRSPRRLD 1m6iA 335 :PEKGNMGKI T0334 172 :DAHLVADFLRRFA 1m6iA 344 :LPEYLSNWTMEKV T0334 186 :EKLGVRHVED 1m6iA 357 :RREGVKVMPN T0334 196 :RVEHVQRDANG 1m6iA 368 :IVQSVGVSSGK T0334 209 :ESVRTATGRVFDADLFVDCSGFRG 1m6iA 379 :LLIKLKDGRKVETDHIVAAVGLEP T0334 233 :LLINKAMEEPFLDMSDHLLNDSAV 1m6iA 404 :VELAKTGGLEIDSDFGGFRVNAEL T0334 338 :AWVGNCVSIGTSSCF 1m6iA 428 :QARSNIWVAGDAACF T0334 363 :FVYAALYQLVKHFPDKSLN 1m6iA 457 :HAVVSGRLAGENMTGAAKP Number of specific fragments extracted= 15 number of extra gaps= 0 total=2294 Will force an alignment to be made, even if fragment is small Number of alignments=100 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1m6iA/T0334-1m6iA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0334 read from 1m6iA/T0334-1m6iA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1m6iA read from 1m6iA/T0334-1m6iA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1m6iA in template set Warning: unaligning (T0334)N326 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1m6iA)Y560 T0334 4 :KIDKILIVGGGTAGWMAASYLGK 1m6iA 130 :SHVPFLLIGGGTAAFAAARSIRA T0334 28 :LQGTADITLLQAPDIPTLGVGEAT 1m6iA 153 :RDPGARVLIVSEDPELPYMRPPLS T0334 56 :QTAF 1m6iA 177 :KELW T0334 62 :FLGI 1m6iA 270 :IDRA T0334 67 :EDEWMR 1m6iA 274 :GAEVKS T0334 73 :ECNASYKVAIK 1m6iA 289 :DFRSLEKISRE T0334 84 :FINWRTA 1m6iA 312 :GSELACA T0334 122 :LSHYWFDRSYR 1m6iA 319 :LGRKARALGTE T0334 170 :HFDAHLVADFLRRFA 1m6iA 342 :KILPEYLSNWTMEKV T0334 186 :EKLGVRHVED 1m6iA 357 :RREGVKVMPN T0334 196 :RVEHVQRDANG 1m6iA 368 :IVQSVGVSSGK T0334 209 :ESVRTATGRVFDADLFVDCSGFRGLL 1m6iA 379 :LLIKLKDGRKVETDHIVAAVGLEPNV T0334 235 :INKAMEEPFLDMSDH 1m6iA 406 :LAKTGGLEIDSDFGG T0334 266 :ANGVE 1m6iA 473 :AKPYW T0334 272 :FTSAIA 1m6iA 480 :SMFWSD T0334 278 :MKSGWTWKIPMLGR 1m6iA 487 :GPDVGYEAIGLVDS T0334 292 :FGTGYVYSS 1m6iA 502 :LPTVGVFAK T0334 301 :RFATE 1m6iA 513 :AQDNP T0334 327 :RIRFRVGRNRRAWV 1m6iA 561 :GKGVIFYLRDKVVV T0334 342 :NCVSIG 1m6iA 575 :GIVLWN T0334 398 :DTRDFIQAHFYFSPR 1m6iA 584 :RMPIARKIIKDGEQH T0334 483 :DAPSPRLAH 1m6iA 599 :EDLNEVAKL Number of specific fragments extracted= 22 number of extra gaps= 0 total=2316 Will force an alignment to be made, even if fragment is small Number of alignments=101 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1m6iA/T0334-1m6iA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0334 read from 1m6iA/T0334-1m6iA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1m6iA read from 1m6iA/T0334-1m6iA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1m6iA in template set T0334 5 :IDKILIVGGGTAGWMAASYLGKAL 1m6iA 300 :VKSITIIGGGFLGSELACALGRKA T0334 29 :QGTADITLLQAPDI 1m6iA 325 :ALGTEVIQLFPEKG T0334 46 :GVGEATIPNLQTAF 1m6iA 339 :NMGKILPEYLSNWT T0334 181 :RRFATEKLGVRHVEDRVEHVQRDANG 1m6iA 353 :MEKVRREGVKVMPNAIVQSVGVSSGK T0334 209 :ESVRTATGRVFDADLFVDCSGF 1m6iA 379 :LLIKLKDGRKVETDHIVAAVGL T0334 235 :INKAMEEPFLDMSDH 1m6iA 406 :LAKTGGLEIDSDFGG T0334 297 :VYSSRFA 1m6iA 421 :FRVNAEL T0334 338 :AWVGNCVSIGTSSCFVE 1m6iA 428 :QARSNIWVAGDAACFYD T0334 359 :TGIYFVYAALYQLVKHFPDKS 1m6iA 453 :EHHDHAVVSGRLAGENMTGAA Number of specific fragments extracted= 9 number of extra gaps= 0 total=2325 Will force an alignment to be made, even if fragment is small Number of alignments=102 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2bryA/T0334-2bryA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2bryA expands to /projects/compbio/data/pdb/2bry.pdb.gz 2bryA:Skipped atom 81, because occupancy 0.400 <= existing 0.600 in 2bryA Skipped atom 83, because occupancy 0.400 <= existing 0.600 in 2bryA Skipped atom 85, because occupancy 0.400 <= existing 0.600 in 2bryA Skipped atom 140, because occupancy 0.500 <= existing 0.500 in 2bryA Skipped atom 142, because occupancy 0.500 <= existing 0.500 in 2bryA Skipped atom 522, because occupancy 0.400 <= existing 0.600 in 2bryA Skipped atom 524, because occupancy 0.400 <= existing 0.600 in 2bryA Skipped atom 976, because occupancy 0.400 <= existing 0.600 in 2bryA Skipped atom 978, because occupancy 0.400 <= existing 0.600 in 2bryA Skipped atom 980, because occupancy 0.400 <= existing 0.600 in 2bryA Skipped atom 1362, because occupancy 0.400 <= existing 0.600 in 2bryA Skipped atom 1364, because occupancy 0.400 <= existing 0.600 in 2bryA Skipped atom 1366, because occupancy 0.400 <= existing 0.600 in 2bryA Skipped atom 1656, because occupancy 0.500 <= existing 0.500 in 2bryA Skipped atom 1658, because occupancy 0.500 <= existing 0.500 in 2bryA Skipped atom 1908, because occupancy 0.400 <= existing 0.600 in 2bryA Skipped atom 1910, because occupancy 0.400 <= existing 0.600 in 2bryA Skipped atom 1912, because occupancy 0.400 <= existing 0.600 in 2bryA Skipped atom 3017, because occupancy 0.400 <= existing 0.600 in 2bryA Skipped atom 3019, because occupancy 0.400 <= existing 0.600 in 2bryA Skipped atom 3021, because occupancy 0.400 <= existing 0.600 in 2bryA Skipped atom 3297, because occupancy 0.400 <= existing 0.600 in 2bryA Skipped atom 3299, because occupancy 0.400 <= existing 0.600 in 2bryA Skipped atom 3301, because occupancy 0.400 <= existing 0.600 in 2bryA # T0334 read from 2bryA/T0334-2bryA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2bryA read from 2bryA/T0334-2bryA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2bryA to template set # found chain 2bryA in template set T0334 6 :D 2bryA 84 :N T0334 7 :KILIVGGGTAGWMAASYLGK 2bryA 86 :KCLVVGAGPCGLRAAVELAL T0334 29 :QGT 2bryA 106 :LGA T0334 33 :DITLLQAPD 2bryA 109 :RVVLVEKRI T0334 46 :GVGEATIPNLQTAF 2bryA 118 :KFSRHNVLHLWPFT T0334 69 :EWMRECNAS 2bryA 133 :HDLRALGAK T0334 109 :HSFGLL 2bryA 142 :KFYGRF T0334 152 :ANRSPRRL 2bryA 148 :CTGTLDHI T0334 172 :DAHLVADFLRRFA 2bryA 156 :SIRQLQLLLLKVA T0334 186 :EKLGVRHVED 2bryA 169 :LLLGVEIHWG T0334 196 :RVEHVQR 2bryA 180 :KFTGLQP T0334 203 :DANG 2bryA 190 :KGSG T0334 209 :ESVRTATGR 2bryA 194 :WRAQLQPNP T0334 218 :VFDADLFVDCSGF 2bryA 208 :SYEFDVLISAAGG T0334 231 :RGLLINKAMEEPFLD 2bryA 269 :FFQSLLKATGIDLEN T0334 284 :WKIPMLGRFGTGYVYSSRFATE 2bryA 284 :IVYYKDETHYFVMTAKKQCLLR T0334 306 :DEAVREFCEM 2bryA 328 :EALQRFARAA T0334 316 :WHLDP 2bryA 340 :FATHG T0334 321 :ETQPLNRIRFRVGRNR 2bryA 357 :GRPDVAAFDFTSMMRA T0334 337 :RAWVGNCVSIG 2bryA 379 :QEKHGARLLLG T0334 348 :TSSCFVEPLESTGIYFVYAALYQLVKHFP 2bryA 393 :DCLVEPFWPLGTGVARGFLAAFDAAWMVK T0334 377 :DKSLNPVLTAR 2bryA 425 :EGAGPLEVLAE T0334 434 :IDMYRAGMAINAPASD 2bryA 436 :RESLYQLLSQTSPENM T0334 450 :DAQLYYGNFEEEFRN 2bryA 454 :NVAQYGLDPATRYPN T0334 482 :PDAPSPRLAHMPQ 2bryA 469 :LNLRAVTPNQVQD Number of specific fragments extracted= 25 number of extra gaps= 0 total=2350 Will force an alignment to be made, even if fragment is small Number of alignments=103 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2bryA/T0334-2bryA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0334 read from 2bryA/T0334-2bryA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2bryA read from 2bryA/T0334-2bryA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2bryA in template set Warning: unaligning (T0334)M278 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2bryA)Y265 T0334 6 :DKILIVGGGTAGWMAASYLGKA 2bryA 85 :TKCLVVGAGPCGLRAAVELALL T0334 31 :TADITLLQAP 2bryA 107 :GARVVLVEKR T0334 41 :DIPTLGVGEA 2bryA 118 :KFSRHNVLHL T0334 52 :IPNLQTAF 2bryA 128 :WPFTIHDL T0334 61 :DFLGI 2bryA 136 :RALGA T0334 124 :HYW 2bryA 141 :KKF T0334 155 :SPRRLDG 2bryA 144 :YGRFCTG T0334 166 :NYAW 2bryA 151 :TLDH T0334 171 :FDAHLVADFLRRFAT 2bryA 155 :ISIRQLQLLLLKVAL T0334 187 :KLGVRHVED 2bryA 170 :LLGVEIHWG T0334 196 :RVEHVQR 2bryA 180 :KFTGLQP T0334 203 :DANGNIESVRTATG 2bryA 188 :PRKGSGWRAQLQPN T0334 217 :R 2bryA 208 :S T0334 219 :FDADLFVDCSG 2bryA 209 :YEFDVLISAAG T0334 239 :MEEPFLDMS 2bryA 220 :GKFVPEGFT T0334 248 :DHLLNDSAVATQVPHDDD 2bryA 234 :GKLAIGITANFVNGRTVE T0334 279 :KS 2bryA 266 :NQ T0334 281 :GWTWKIPM 2bryA 282 :ENIVYYKD T0334 291 :R 2bryA 290 :E T0334 292 :FGTGYVYS 2bryA 292 :HYFVMTAK T0334 300 :SRFATE 2bryA 306 :LGVLRQ T0334 306 :DEAVREFCEMW 2bryA 328 :EALQRFARAAA T0334 317 :HLDPETQPLNRIRFRVGRNRRA 2bryA 353 :QDARGRPDVAAFDFTSMMRAES T0334 339 :WVGNCVSIG 2bryA 381 :KHGARLLLG T0334 348 :TSSCFVEPLE 2bryA 391 :VGDCLVEPFW T0334 358 :STGIYFVYAALYQLVKHF 2bryA 403 :GTGVARGFLAAFDAAWMV T0334 378 :KSLNP 2bryA 425 :EGAGP T0334 397 :DDTRDFIQAHFYFSPR 2bryA 430 :LEVLAERESLYQLLSQ T0334 480 :LVPDAPSPRLAHM 2bryA 446 :TSPENMHRNVAQY Number of specific fragments extracted= 29 number of extra gaps= 0 total=2379 Will force an alignment to be made, even if fragment is small Number of alignments=104 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2bryA/T0334-2bryA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0334 read from 2bryA/T0334-2bryA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2bryA read from 2bryA/T0334-2bryA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2bryA in template set T0334 7 :KILIVGGGTAGWMAASYLGK 2bryA 86 :KCLVVGAGPCGLRAAVELAL T0334 30 :GTADITLLQAP 2bryA 106 :LGARVVLVEKR T0334 41 :DIPTLGVG 2bryA 118 :KFSRHNVL T0334 50 :ATIPNLQTAF 2bryA 126 :HLWPFTIHDL T0334 61 :DFLGI 2bryA 136 :RALGA T0334 68 :DEW 2bryA 141 :KKF T0334 98 :RELD 2bryA 144 :YGRF T0334 161 :GSKVTN 2bryA 148 :CTGTLD T0334 170 :HFDAHLVADFLRRFATEKLGVRHVEDRVEHVQRD 2bryA 154 :HISIRQLQLLLLKVALLLGVEIHWGVKFTGLQPP T0334 204 :ANGNIESVRTATGR 2bryA 189 :RKGSGWRAQLQPNP T0334 218 :VFDADLFVDCSGF 2bryA 208 :SYEFDVLISAAGG T0334 240 :EEPFLDMS 2bryA 221 :KFVPEGFT T0334 248 :DHLLNDSAVATQVPHD 2bryA 234 :GKLAIGITANFVNGRT T0334 307 :EAVREFCEMW 2bryA 328 :EALQRFARAA T0334 317 :HLDPETQPLNRIRFRVGRNR 2bryA 353 :QDARGRPDVAAFDFTSMMRA T0334 337 :RAWVGNCVSIGTSS 2bryA 379 :QEKHGARLLLGLVG T0334 351 :CFVEP 2bryA 394 :CLVEP T0334 356 :LESTGIYFVYAALYQLVKHFPDKSLNPVL 2bryA 405 :GVARGFLAAFDAAWMVKRWAEGAGPLEVL T0334 400 :RDFIQAHFYF 2bryA 434 :AERESLYQLL T0334 466 :WNNSNYYCVLAGLGL 2bryA 444 :SQTSPENMHRNVAQY Number of specific fragments extracted= 20 number of extra gaps= 0 total=2399 Will force an alignment to be made, even if fragment is small Number of alignments=105 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3ladA/T0334-3ladA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 3ladA expands to /projects/compbio/data/pdb/3lad.pdb.gz 3ladA:# T0334 read from 3ladA/T0334-3ladA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3ladA read from 3ladA/T0334-3ladA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3ladA to template set # found chain 3ladA in template set Warning: unaligning (T0334)K4 because first residue in template chain is (3ladA)S1 Warning: unaligning (T0334)I5 because of BadResidue code BAD_PEPTIDE at template residue (3ladA)Q2 Warning: unaligning (T0334)D6 because of BadResidue code BAD_PEPTIDE at template residue (3ladA)K3 Warning: unaligning (T0334)V47 because of BadResidue code BAD_PEPTIDE in next template residue (3ladA)V83 Warning: unaligning (T0334)G48 because of BadResidue code BAD_PEPTIDE at template residue (3ladA)V83 Warning: unaligning (T0334)E49 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (3ladA)A84 Warning: unaligning (T0334)F219 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (3ladA)A268 Warning: unaligning (T0334)D220 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (3ladA)A268 Warning: unaligning (T0334)C227 because of BadResidue code BAD_PEPTIDE in next template residue (3ladA)V276 Warning: unaligning (T0334)S228 because of BadResidue code BAD_PEPTIDE at template residue (3ladA)V276 Warning: unaligning (T0334)K237 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (3ladA)D289 Warning: unaligning (T0334)A238 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (3ladA)D289 Warning: unaligning (T0334)M239 because of BadResidue code BAD_PEPTIDE at template residue (3ladA)S290 T0334 7 :KILIVGGGTAGWMAASYLGK 3ladA 5 :DVIVIGAGPGGYVAAIKSAQ T0334 29 :QGT 3ladA 25 :LGL T0334 33 :DITLLQAPD 3ladA 28 :KTALIEKYK T0334 42 :IPTL 3ladA 38 :KEGK T0334 46 :G 3ladA 81 :G T0334 50 :ATIPNLQTAFFDFLGI 3ladA 85 :IDVPTMIARKDQIVRN T0334 69 :EWMRECNASYKVAIKFI 3ladA 107 :SLIKANGVTLFEGHGKL T0334 96 :EARELDGGPDHFYHSFGLL 3ladA 156 :EIPPAPVDQDVIVDSTGAL T0334 115 :KYHEQIPLSHYWFDRSYRG 3ladA 178 :NVPGKLGVIGAGVIGLELG T0334 139 :FDYACYKEPVILD 3ladA 197 :SVWARLGAEVTVL T0334 152 :ANRSPRRL 3ladA 211 :AMDKFLPA T0334 172 :DAHLVADFLRRFA 3ladA 219 :VDEQVAKEAQKIL T0334 186 :EKLGVRHVED 3ladA 232 :TKQGLKILLG T0334 196 :RVEHVQRDAN 3ladA 243 :RVTGTEVKNK T0334 207 :NIE 3ladA 253 :QVT T0334 211 :VRTAT 3ladA 256 :VKFVD T0334 216 :GR 3ladA 263 :GE T0334 218 :V 3ladA 266 :S T0334 221 :ADLFVD 3ladA 269 :FDKLIV T0334 229 :GFRG 3ladA 277 :GRRP T0334 233 :LLIN 3ladA 284 :DLLA T0334 240 :EEPFLD 3ladA 291 :GVTLDE T0334 247 :SDHLLNDSAVATQVPHDDDANGV 3ladA 297 :RGFIYVDDYCATSVPGVYAIGDV T0334 270 :EPFTS 3ladA 375 :EGVAI T0334 275 :AIAMK 3ladA 381 :VGVFP T0334 280 :SGWTWKIPM 3ladA 400 :GFVKVIADA T0334 289 :LGRFGTGYVYSSR 3ladA 410 :TDRVLGVHVIGPS T0334 364 :VYAALYQLVKHFP 3ladA 423 :AAELVQQGAIAME T0334 377 :DKSLNPVLTARF 3ladA 449 :AHPALSEALHEA Number of specific fragments extracted= 29 number of extra gaps= 4 total=2428 Will force an alignment to be made, even if fragment is small Number of alignments=106 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3ladA/T0334-3ladA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0334 read from 3ladA/T0334-3ladA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3ladA read from 3ladA/T0334-3ladA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3ladA in template set Warning: unaligning (T0334)K4 because of BadResidue code BAD_PEPTIDE at template residue (3ladA)Q2 Warning: unaligning (T0334)I5 because of BadResidue code BAD_PEPTIDE at template residue (3ladA)K3 Warning: unaligning (T0334)F219 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (3ladA)A268 Warning: unaligning (T0334)D220 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (3ladA)A268 Warning: unaligning (T0334)C227 because of BadResidue code BAD_PEPTIDE in next template residue (3ladA)V276 Warning: unaligning (T0334)S228 because of BadResidue code BAD_PEPTIDE at template residue (3ladA)V276 Warning: unaligning (T0334)L234 because of BadResidue code BAD_PEPTIDE in next template residue (3ladA)T283 Warning: unaligning (T0334)N236 because of BadResidue code BAD_PEPTIDE at template residue (3ladA)T283 Warning: unaligning (T0334)D253 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (3ladA)P360 Warning: unaligning (T0334)S254 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (3ladA)P360 Warning: unaligning (T0334)A255 because of BadResidue code BAD_PEPTIDE at template residue (3ladA)E361 T0334 6 :DKILIVGGGTAGWMAASYLGKA 3ladA 4 :FDVIVIGAGPGGYVAAIKSAQL T0334 31 :TADITLLQA 3ladA 26 :GLKTALIEK T0334 40 :PDIPTLGVGEATIPNLQTAF 3ladA 40 :GKTALGGTCLNVGCIPSKAL T0334 66 :PEDEWMRECNASY 3ladA 86 :DVPTMIARKDQIV T0334 79 :KVAIKFINWRTAGE 3ladA 100 :NLTGGVASLIKANG T0334 104 :P 3ladA 114 :V T0334 105 :DHFYHSFGLLKYHEQIPLSHYWFDRSYR 3ladA 126 :GKKVEVTAADGSSQVLDTENVILASGSK T0334 136 :VEPFDYACYKEPVILD 3ladA 154 :PVEIPPAPVDQDVIVD T0334 152 :ANRSPRRLDGSKVTN 3ladA 173 :ALDFQNVPGKLGVIG T0334 170 :HFD 3ladA 218 :AVD T0334 174 :HLVADFLRRFA 3ladA 221 :EQVAKEAQKIL T0334 186 :EKLGVRHVED 3ladA 232 :TKQGLKILLG T0334 196 :RVEHVQRDANGNIESVRTATG 3ladA 243 :RVTGTEVKNKQVTVKFVDAEG T0334 217 :RV 3ladA 265 :KS T0334 221 :ADLFVD 3ladA 269 :FDKLIV T0334 229 :GFRGL 3ladA 277 :GRRPV T0334 237 :KA 3ladA 284 :DL T0334 239 :MEEPFLDMSDHLLN 3ladA 345 :AQMNYDLIPAVIYT T0334 256 :VATQVPHDDDA 3ladA 362 :IAGVGKTEQAL T0334 267 :NGVEPFTSAIAMKS 3ladA 375 :EGVAINVGVFPFAA T0334 281 :GWTWKIPMLGR 3ladA 400 :GFVKVIADAKT T0334 292 :FGTGYVYSSRFA 3ladA 413 :VLGVHVIGPSAA T0334 307 :EAVREFCE 3ladA 425 :ELVQQGAI Number of specific fragments extracted= 23 number of extra gaps= 5 total=2451 Will force an alignment to be made, even if fragment is small Number of alignments=107 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3ladA/T0334-3ladA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0334 read from 3ladA/T0334-3ladA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3ladA read from 3ladA/T0334-3ladA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3ladA in template set Warning: unaligning (T0334)F219 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (3ladA)A268 Warning: unaligning (T0334)D220 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (3ladA)A268 Warning: unaligning (T0334)C227 because of BadResidue code BAD_PEPTIDE in next template residue (3ladA)V276 Warning: unaligning (T0334)S228 because of BadResidue code BAD_PEPTIDE at template residue (3ladA)V276 Warning: unaligning (T0334)H262 because of BadResidue code BAD_PEPTIDE in next template residue (3ladA)T283 Warning: unaligning (T0334)D263 because of BadResidue code BAD_PEPTIDE at template residue (3ladA)T283 Warning: unaligning (T0334)G268 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (3ladA)D289 Warning: unaligning (T0334)V269 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (3ladA)D289 Warning: unaligning (T0334)E270 because of BadResidue code BAD_PEPTIDE at template residue (3ladA)S290 T0334 3 :GKIDKILIVGGGTAGWMAASYLGK 3ladA 178 :NVPGKLGVIGAGVIGLELGSVWAR T0334 30 :GTADITLLQAPDIPT 3ladA 202 :LGAEVTVLEAMDKFL T0334 63 :LGIP 3ladA 217 :PAVD T0334 174 :HLVADFLRRFATEKLGVRHVEDRVEHVQRDANGNIESVRTATGR 3ladA 221 :EQVAKEAQKILTKQGLKILLGARVTGTEVKNKQVTVKFVDAEGE T0334 218 :V 3ladA 266 :S T0334 221 :ADLFVD 3ladA 269 :FDKLIV T0334 229 :GF 3ladA 277 :GR T0334 258 :TQV 3ladA 279 :RPV T0334 264 :DDAN 3ladA 284 :DLLA T0334 271 :PFTS 3ladA 291 :GVTL T0334 292 :FGTGYVYSSRFAT 3ladA 295 :DERGFIYVDDYCA T0334 338 :AWVGNCVSIGTSSCFVE 3ladA 308 :TSVPGVYAIGDVVRGAM T0334 360 :GIYFVYAALYQLVKHFPDKSL 3ladA 325 :LAHKASEEGVVVAERIAGHKA Number of specific fragments extracted= 13 number of extra gaps= 4 total=2464 Will force an alignment to be made, even if fragment is small Number of alignments=108 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1fl2A/T0334-1fl2A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1fl2A expands to /projects/compbio/data/pdb/1fl2.pdb.gz 1fl2A:# T0334 read from 1fl2A/T0334-1fl2A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1fl2A read from 1fl2A/T0334-1fl2A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1fl2A to template set # found chain 1fl2A in template set Warning: unaligning (T0334)D220 because of BadResidue code BAD_PEPTIDE in next template residue (1fl2A)L442 Warning: unaligning (T0334)A221 because of BadResidue code BAD_PEPTIDE at template residue (1fl2A)L442 T0334 7 :KILIVGGGTAGWMAASYLGK 1fl2A 214 :DVLIVGSGPAGAAAAIYSAR T0334 29 :QGT 1fl2A 234 :KGI T0334 33 :DITLLQAP 1fl2A 237 :RTGLMGER T0334 42 :IPTL 1fl2A 245 :FGGQ T0334 46 :GVGEATIPNLQTAF 1fl2A 260 :SVPKTEGQKLAGAL T0334 68 :DEWMRECNASYKVAIKFINWRTAGEGTS 1fl2A 274 :KVHVDEYDVDVIDSQSASKLIPAAVEGG T0334 96 :EARELDG 1fl2A 328 :NMNVPGE T0334 103 :GPDHFYHSFGLL 1fl2A 338 :RTKGVTYCPHCD T0334 115 :KYHEQIPLSHYWFDRSYRG 1fl2A 353 :FKGKRVAVIGGGNSGVEAA T0334 139 :FDYACYKEPVILDANRSPRRL 1fl2A 372 :IDLAGIVEHVTLLEFAPEMKA T0334 172 :DAHL 1fl2A 393 :DQVL T0334 181 :RRFATEKLGVRHVED 1fl2A 397 :QDKLRSLKNVDIILN T0334 196 :RVEHVQRDAN 1fl2A 413 :QTTEVKGDGS T0334 207 :NIESVRTA 1fl2A 423 :KVVGLEYR T0334 216 :GR 1fl2A 435 :GD T0334 218 :VF 1fl2A 439 :NI T0334 222 :DLFVDCSGFRG 1fl2A 443 :AGIFVQIGLLP T0334 233 :LLINKAMEEPF 1fl2A 456 :NWLEGAVERNR T0334 247 :SDHLLNDSAVA 1fl2A 467 :MGEIIIDAKCE T0334 338 :AWVGNCVSIGTSSCFVEPLESTGIYFVYAALYQLVKHFP 1fl2A 478 :TNVKGVFAAGDCTTVPYKQIIIATGEGAKASLSAFDYLI Number of specific fragments extracted= 20 number of extra gaps= 1 total=2484 Will force an alignment to be made, even if fragment is small Number of alignments=109 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1fl2A/T0334-1fl2A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0334 read from 1fl2A/T0334-1fl2A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1fl2A read from 1fl2A/T0334-1fl2A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1fl2A in template set Warning: unaligning (T0334)R329 because of BadResidue code BAD_PEPTIDE in next template residue (1fl2A)L442 Warning: unaligning (T0334)F330 because of BadResidue code BAD_PEPTIDE at template residue (1fl2A)L442 T0334 6 :DKILIVGGGTAGWMAASYLGK 1fl2A 213 :YDVLIVGSGPAGAAAAIYSAR T0334 30 :GTADITLLQAP 1fl2A 234 :KGIRTGLMGER T0334 130 :S 1fl2A 246 :G T0334 141 :YACYKEPVILDANRSPR 1fl2A 247 :GQILDTVDIENYISVPK T0334 171 :FDAHLVADFLRRFA 1fl2A 264 :TEGQKLAGALKVHV T0334 186 :EKLGVRHVED 1fl2A 278 :DEYDVDVIDS T0334 196 :RVEHVQRDA 1fl2A 289 :SASKLIPAA T0334 205 :NGNIESVRTATGRVFDADLFVDCSG 1fl2A 299 :EGGLHQIETASGAVLKARSIIVATG T0334 236 :NKAMEEPFLDMSDHLLN 1fl2A 324 :AKWRNMNVPGEDQYRTK T0334 254 :S 1fl2A 341 :G T0334 269 :VE 1fl2A 342 :VT T0334 271 :PFTSA 1fl2A 346 :PHCDG T0334 287 :PM 1fl2A 351 :PL T0334 289 :LGR 1fl2A 354 :KGK T0334 292 :FGT 1fl2A 358 :VAV T0334 295 :GYVYSSRFATE 1fl2A 382 :TLLEFAPEMKA T0334 306 :DEAVREFCEMW 1fl2A 394 :QVLQDKLRSLK T0334 320 :PETQPLNRI 1fl2A 432 :RVSGDIHNI T0334 331 :RVG 1fl2A 443 :AGI T0334 334 :RNRRA 1fl2A 451 :LLPNT T0334 339 :WVGNCVSIGTSSCFVEPLESTGIYFVYAALYQLVKHFPD 1fl2A 479 :NVKGVFAAGDCTTVPYKQIIIATGEGAKASLSAFDYLIR Number of specific fragments extracted= 21 number of extra gaps= 1 total=2505 Will force an alignment to be made, even if fragment is small Number of alignments=110 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1fl2A/T0334-1fl2A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0334 read from 1fl2A/T0334-1fl2A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1fl2A read from 1fl2A/T0334-1fl2A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1fl2A in template set T0334 7 :KILIVGGGTAGWMAASYLGK 1fl2A 214 :DVLIVGSGPAGAAAAIYSAR T0334 30 :GTADITLLQAP 1fl2A 234 :KGIRTGLMGER T0334 47 :VGEAT 1fl2A 245 :FGGQI T0334 79 :KVAIKFINWRTAGEGT 1fl2A 250 :LDTVDIENYISVPKTE T0334 173 :AHLVADFLRRFATEKLGVRHVEDRVEHVQRDA 1fl2A 266 :GQKLAGALKVHVDEYDVDVIDSQSASKLIPAA T0334 205 :NGNIESVRTATGRVFDADLFVDCSGF 1fl2A 299 :EGGLHQIETASGAVLKARSIIVATGA T0334 240 :EEP 1fl2A 325 :KWR T0334 259 :QVPHDDDAN 1fl2A 328 :NMNVPGEDQ T0334 292 :FGTGYVYS 1fl2A 338 :RTKGVTYC T0334 300 :SRFA 1fl2A 350 :GPLF T0334 339 :WVGNCVSIGTS 1fl2A 354 :KGKRVAVIGGG T0334 362 :YFVYAALYQLVKHFP 1fl2A 365 :NSGVEAAIDLAGIVE T0334 421 :NKELRLADGMQEKID 1fl2A 387 :APEMKADQVLQDKLR Number of specific fragments extracted= 13 number of extra gaps= 0 total=2518 Will force an alignment to be made, even if fragment is small Number of alignments=111 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1rp0A/T0334-1rp0A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1rp0A expands to /projects/compbio/data/pdb/1rp0.pdb.gz 1rp0A:Skipped atom 308, because occupancy 0.330 <= existing 0.330 in 1rp0A Skipped atom 309, because occupancy 0.330 <= existing 0.330 in 1rp0A Skipped atom 311, because occupancy 0.330 <= existing 0.330 in 1rp0A Skipped atom 312, because occupancy 0.330 <= existing 0.330 in 1rp0A Skipped atom 527, because occupancy 0.200 <= existing 0.800 in 1rp0A Skipped atom 789, because occupancy 0.300 <= existing 0.700 in 1rp0A Skipped atom 791, because occupancy 0.300 <= existing 0.700 in 1rp0A Skipped atom 793, because occupancy 0.300 <= existing 0.700 in 1rp0A Skipped atom 795, because occupancy 0.300 <= existing 0.700 in 1rp0A Skipped atom 925, because occupancy 0.500 <= existing 0.500 in 1rp0A Skipped atom 927, because occupancy 0.500 <= existing 0.500 in 1rp0A Skipped atom 929, because occupancy 0.500 <= existing 0.500 in 1rp0A Skipped atom 931, because occupancy 0.500 <= existing 0.500 in 1rp0A Skipped atom 938, because occupancy 0.500 <= existing 0.500 in 1rp0A Skipped atom 1324, because occupancy 0.450 <= existing 0.550 in 1rp0A Skipped atom 1326, because occupancy 0.450 <= existing 0.550 in 1rp0A Skipped atom 1328, because occupancy 0.450 <= existing 0.550 in 1rp0A # T0334 read from 1rp0A/T0334-1rp0A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1rp0A read from 1rp0A/T0334-1rp0A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1rp0A to template set # found chain 1rp0A in template set Warning: unaligning (T0334)P53 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1rp0A)G82 Warning: unaligning (T0334)N54 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1rp0A)G82 Warning: unaligning (T0334)L356 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1rp0A)F256 Warning: unaligning (T0334)E357 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1rp0A)F256 T0334 6 :D 1rp0A 39 :E T0334 7 :KILIVGGGTAGWMAASYLGK 1rp0A 41 :DVVVVGAGSAGLSAAYEISK T0334 29 :QGT 1rp0A 62 :PNV T0334 33 :DITLLQAPD 1rp0A 65 :QVAIIEQSV T0334 46 :GVGEATI 1rp0A 74 :SPGGGAW T0334 57 :TAF 1rp0A 83 :GQL T0334 104 :PDHFYHSFGLL 1rp0A 86 :FSAMIVRKPAH T0334 139 :FDYACYKEPV 1rp0A 97 :LFLDEIGVAY T0334 152 :ANRSPRRLD 1rp0A 108 :EQDTYVVVK T0334 172 :DAHLVADFLRRFATEKLGVRHVED 1rp0A 117 :HAALFTSTIMSKLLARPNVKLFNA T0334 196 :RVEHVQRDAN 1rp0A 142 :AAEDLIVKGN T0334 207 :NIESVRTAT 1rp0A 152 :RVGGVVTNW T0334 218 :VFDADLFVDCSGFRG 1rp0A 177 :VMEAKIVVSSCGHDG T0334 233 :LLINKAMEEPFL 1rp0A 196 :TGVKRLKSIGMI T0334 270 :EPFTSA 1rp0A 208 :DHVPGM T0334 306 :DEAVREFCEMWH 1rp0A 219 :NTAEDAIVRLTR T0334 338 :AWVGNCVSIG 1rp0A 231 :EVVPGMIVTG T0334 348 :TSSCFVEP 1rp0A 247 :DGAPRMGP T0334 358 :STGIYFVYAALYQLVKHFP 1rp0A 257 :GAMMISGQKAGQLALKALG T0334 377 :DK 1rp0A 281 :DG Number of specific fragments extracted= 20 number of extra gaps= 2 total=2538 Will force an alignment to be made, even if fragment is small Number of alignments=112 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1rp0A/T0334-1rp0A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0334 read from 1rp0A/T0334-1rp0A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1rp0A read from 1rp0A/T0334-1rp0A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1rp0A in template set Warning: unaligning (T0334)L356 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1rp0A)F256 Warning: unaligning (T0334)E357 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1rp0A)F256 T0334 5 :IDKILIVGGGTAGWMAASYLGKA 1rp0A 39 :ETDVVVVGAGSAGLSAAYEISKN T0334 30 :GTADITLLQAP 1rp0A 62 :PNVQVAIIEQS T0334 41 :DIPTLG 1rp0A 74 :SPGGGA T0334 52 :IPNLQTAF 1rp0A 92 :RKPAHLFL T0334 61 :DFLGI 1rp0A 100 :DEIGV T0334 130 :S 1rp0A 105 :A T0334 136 :VEPFD 1rp0A 106 :YDEQD T0334 166 :NYAWHFDAHLVADFLRRFATEKLGVRHVED 1rp0A 111 :TYVVVKHAALFTSTIMSKLLARPNVKLFNA T0334 196 :RVEHVQRDANG 1rp0A 142 :AAEDLIVKGNR T0334 208 :IESVRTAT 1rp0A 153 :VGGVVTNW T0334 217 :RVFDADLFVDCSGFR 1rp0A 176 :NVMEAKIVVSSCGHD T0334 232 :GLL 1rp0A 196 :TGV T0334 236 :NKAMEEPFL 1rp0A 199 :KRLKSIGMI T0334 267 :NGVEPFTSA 1rp0A 208 :DHVPGMKAL T0334 304 :TEDEAVREFCEM 1rp0A 217 :DMNTAEDAIVRL T0334 336 :RRAWVGNCVSIG 1rp0A 229 :TREVVPGMIVTG T0334 348 :TSSCFVEP 1rp0A 247 :DGAPRMGP T0334 358 :STGIYFVYAALYQLVKHFP 1rp0A 257 :GAMMISGQKAGQLALKALG Number of specific fragments extracted= 18 number of extra gaps= 1 total=2556 Will force an alignment to be made, even if fragment is small Number of alignments=113 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1rp0A/T0334-1rp0A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0334 read from 1rp0A/T0334-1rp0A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1rp0A read from 1rp0A/T0334-1rp0A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1rp0A in template set Warning: unaligning (T0334)T51 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1rp0A)G82 Warning: unaligning (T0334)I52 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1rp0A)G82 Warning: unaligning (T0334)L356 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1rp0A)F256 Warning: unaligning (T0334)E357 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1rp0A)F256 T0334 7 :KILIVGGGTAGWMAASYLGK 1rp0A 41 :DVVVVGAGSAGLSAAYEISK T0334 29 :QGTADITLLQAPDIPTLGV 1rp0A 61 :NPNVQVAIIEQSVSPGGGA T0334 50 :A 1rp0A 80 :W T0334 53 :PNLQ 1rp0A 93 :KPAH T0334 69 :EWMRECNASY 1rp0A 97 :LFLDEIGVAY T0334 88 :RTAGEGTS 1rp0A 107 :DEQDTYVV T0334 171 :F 1rp0A 115 :V T0334 172 :DAHLVADFLRRFATEK 1rp0A 117 :HAALFTSTIMSKLLAR T0334 188 :LGVRHVEDRVEHVQRDANG 1rp0A 134 :NVKLFNAVAAEDLIVKGNR T0334 208 :IESVRT 1rp0A 153 :VGGVVT T0334 214 :ATGR 1rp0A 167 :HHTQ T0334 218 :VFDADLFVDCSGFRG 1rp0A 177 :VMEAKIVVSSCGHDG T0334 233 :LLINKAMEEPFL 1rp0A 196 :TGVKRLKSIGMI T0334 264 :DDANGVE 1rp0A 208 :DHVPGMK T0334 307 :EAVREFCEMW 1rp0A 220 :TAEDAIVRLT T0334 337 :RAWVGNCVSIG 1rp0A 230 :REVVPGMIVTG T0334 348 :TSSCFVEP 1rp0A 247 :DGAPRMGP T0334 358 :STGIYFVYAALYQLVKHFP 1rp0A 257 :GAMMISGQKAGQLALKALG Number of specific fragments extracted= 18 number of extra gaps= 2 total=2574 Will force an alignment to be made, even if fragment is small Number of alignments=114 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2fbwA/T0334-2fbwA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2fbwA expands to /projects/compbio/data/pdb/2fbw.pdb.gz 2fbwA:# T0334 read from 2fbwA/T0334-2fbwA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2fbwA read from 2fbwA/T0334-2fbwA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2fbwA to template set # found chain 2fbwA in template set Warning: unaligning (T0334)F352 because of BadResidue code BAD_PEPTIDE in next template residue (2fbwA)S402 T0334 7 :KILIVGGGTAGWMAASYLGK 2fbwA 20 :DAVVVGAGGAGLRAAFGLSE T0334 29 :QGT 2fbwA 40 :AGF T0334 33 :DITLLQAP 2fbwA 43 :NTACVTKL T0334 46 :GVGEATIPNLQTAFFDFLGIPED 2fbwA 51 :FPTRSHTVAAQGGINAALGNMED T0334 76 :ASYKVAIKFINW 2fbwA 74 :DNWRWHFYDTVK T0334 103 :GPDHFYHSFGLL 2fbwA 86 :GSDWLGDQDAIH T0334 115 :KYHEQI 2fbwA 102 :QAPAAV T0334 139 :FDYACYKEP 2fbwA 108 :IELENYGMP T0334 148 :VILD 2fbwA 125 :IYQR T0334 152 :ANRSPRRLDGSKVTNYAWHF 2fbwA 130 :FGGQSLQFGKGGQAHRCCCV T0334 172 :DAHLVADFLRRFA 2fbwA 153 :TGHSLLHTLYGRS T0334 186 :EKLGVRHVED 2fbwA 166 :LRYDTSYFVE T0334 196 :RVEHVQRDAN 2fbwA 177 :FALDLLMENG T0334 207 :NIESVRTA 2fbwA 187 :ECRGVIAL T0334 215 :TGR 2fbwA 198 :DGT T0334 218 :VFDADLFVDCSGF 2fbwA 203 :RFRAKNTVIATGG T0334 233 :LLINKAMEEPFL 2fbwA 234 :TAMVTRAGLPCQ T0334 271 :PFTSAIAMK 2fbwA 246 :DLEFVQFHP T0334 280 :SGWTWKIPMLGR 2fbwA 271 :EGGILINSQGER T0334 292 :FGTGYVYSSRFATE 2fbwA 317 :EKDHVYLQLHHLPP T0334 306 :DEAVREFCEMWHLDPETQPLNRIRFRVGRNR 2fbwA 338 :PGISETAMIFAGVDVTKEPIPVLPTVHYNMG T0334 337 :RAWVGNCVSIGTSSC 2fbwA 386 :DKVVPGLYACGEAAS T0334 353 :VEP 2fbwA 403 :VHG T0334 356 :LESTGIYFVYAALYQLVKHFP 2fbwA 409 :LGANSLLDLVVFGRACALTIA T0334 377 :DKSLNPVLTARFNREI 2fbwA 442 :KPNAGEESVANLDKLR T0334 393 :ETMFDDTRDFIQAHFYFSPR 2fbwA 466 :SEARLNMQKTMQSHAAVFRT T0334 496 :TESVDEVFGAVKDRQRNLLE 2fbwA 486 :GSILQEGCEKLSQIYRDLAH T0334 516 :TLPSLHEFLR 2fbwA 512 :GIVWNTDLVE Number of specific fragments extracted= 28 number of extra gaps= 1 total=2602 Will force an alignment to be made, even if fragment is small Number of alignments=115 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2fbwA/T0334-2fbwA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0334 read from 2fbwA/T0334-2fbwA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2fbwA read from 2fbwA/T0334-2fbwA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2fbwA in template set Warning: unaligning (T0334)T348 because of BadResidue code BAD_PEPTIDE in next template residue (2fbwA)S402 Warning: unaligning (T0334)S349 because of BadResidue code BAD_PEPTIDE at template residue (2fbwA)S402 T0334 4 :KIDKILIVGGGTAGWMAASYLGK 2fbwA 17 :HEFDAVVVGAGGAGLRAAFGLSE T0334 30 :GTADITLLQAPDIPTLGVGEATI 2fbwA 40 :AGFNTACVTKLFPTRSHTVAAQG T0334 53 :PNLQTAFFDFLGI 2fbwA 78 :WHFYDTVKGSDWL T0334 71 :MRECNASYKVAIKF 2fbwA 93 :QDAIHYMTEQAPAA T0334 123 :SHYWFDRSYR 2fbwA 107 :VIELENYGMP T0334 136 :VEPFDYACYKEPVILD 2fbwA 117 :FSRTEEGKIYQRAFGG T0334 155 :SPR 2fbwA 135 :LQF T0334 160 :DGSKVTNYAWHF 2fbwA 138 :GKGGQAHRCCCV T0334 172 :DAHLVADFLRRFA 2fbwA 153 :TGHSLLHTLYGRS T0334 186 :EKLGVRHVED 2fbwA 166 :LRYDTSYFVE T0334 196 :RVEHVQR 2fbwA 177 :FALDLLM T0334 204 :ANGNIESVR 2fbwA 184 :ENGECRGVI T0334 213 :TATG 2fbwA 196 :IEDG T0334 217 :RVFDADLFVDCSGFR 2fbwA 202 :HRFRAKNTVIATGGY T0334 236 :NKA 2fbwA 217 :GRT T0334 239 :MEEPFLDMSDHLLNDSAV 2fbwA 240 :AGLPCQDLEFVQFHPTGI T0334 264 :DD 2fbwA 258 :YG T0334 267 :NGVEPF 2fbwA 310 :EGRGCG T0334 279 :KSGWTWKIPML 2fbwA 316 :PEKDHVYLQLH T0334 302 :FATE 2fbwA 327 :HLPP T0334 306 :DEAVREFCEMWHLDPETQ 2fbwA 338 :PGISETAMIFAGVDVTKE T0334 327 :RIRFRVG 2fbwA 356 :PIPVLPT T0334 339 :WVGNCVSIG 2fbwA 388 :VVPGLYACG T0334 350 :SCFVEPLESTGIYFVYAALYQLVKHFPD 2fbwA 403 :VHGANRLGANSLLDLVVFGRACALTIAE T0334 378 :KSLNPVLTARFNREIE 2fbwA 443 :PNAGEESVANLDKLRF T0334 394 :TMFDDTRDFIQAHFYFS 2fbwA 467 :EARLNMQKTMQSHAAVF T0334 445 :AP 2fbwA 484 :RT T0334 496 :TESVDEVFGAVKDRQR 2fbwA 486 :GSILQEGCEKLSQIYR Number of specific fragments extracted= 28 number of extra gaps= 1 total=2630 Will force an alignment to be made, even if fragment is small Number of alignments=116 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2fbwA/T0334-2fbwA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0334 read from 2fbwA/T0334-2fbwA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2fbwA read from 2fbwA/T0334-2fbwA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2fbwA in template set T0334 7 :KILIVGGGTAGWMAASYLGK 2fbwA 20 :DAVVVGAGGAGLRAAFGLSE T0334 30 :GTADITLLQAPDIPTLGV 2fbwA 40 :AGFNTACVTKLFPTRSHT T0334 77 :SYKVAIKFI 2fbwA 58 :VAAQGGINA T0334 97 :ARELDGGPDHFYHSFGLLKYHEQIPLSHYWFD 2fbwA 67 :ALGNMEDDNWRWHFYDTVKGSDWLGDQDAIHY T0334 138 :PFDYACYKEPVILDANRSPRRLDGSKVTNYAWH 2fbwA 99 :MTEQAPAAVIELENYGMPFSRTEEGKIYQRAFG T0334 171 :F 2fbwA 149 :V T0334 172 :DAHLVADFLRRFATEKLGVRHVEDRVEHVQRDANGN 2fbwA 153 :TGHSLLHTLYGRSLRYDTSYFVEYFALDLLMENGEC T0334 208 :IESVRTATGR 2fbwA 191 :VIALCIEDGT T0334 218 :VFDADLFVDCSGFRG 2fbwA 203 :RFRAKNTVIATGGYG T0334 247 :SDHLLNDS 2fbwA 218 :RTYFSCTS T0334 307 :EAVREFCEMWHLDPETQ 2fbwA 335 :TRLPGISETAMIFAGVD T0334 336 :RRAWVGNCVSIGTSS 2fbwA 385 :EDKVVPGLYACGEAA T0334 351 :CFVEPLESTGIYFVYAALYQLVKHFP 2fbwA 404 :HGANRLGANSLLDLVVFGRACALTIA T0334 377 :DKSLNPVLTARFNREI 2fbwA 442 :KPNAGEESVANLDKLR T0334 422 :K 2fbwA 460 :D T0334 423 :ELRLADGMQEKIDMYRAGMAI 2fbwA 462 :TIRTSEARLNMQKTMQSHAAV T0334 479 :GLVPDAPSPRLAHMPQATE 2fbwA 483 :FRTGSILQEGCEKLSQIYR Number of specific fragments extracted= 17 number of extra gaps= 0 total=2647 Will force an alignment to be made, even if fragment is small Number of alignments=117 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1vdc/T0334-1vdc-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1vdc expands to /projects/compbio/data/pdb/1vdc.pdb.gz 1vdc:Warning: there is no chain 1vdc will retry with 1vdcA # T0334 read from 1vdc/T0334-1vdc-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1vdc read from 1vdc/T0334-1vdc-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1vdc to template set # found chain 1vdc in template set Warning: unaligning (T0334)G206 because of BadResidue code BAD_PEPTIDE in next template residue (1vdc)D216 Warning: unaligning (T0334)V506 because last residue in template chain is (1vdc)I316 T0334 5 :ID 1vdc 2 :ET T0334 7 :KILIVGGGTAGWMAASYLGK 1vdc 7 :RLCIVGSGPAAHTAAIYAAR T0334 29 :QGT 1vdc 27 :AEL T0334 33 :DITLLQAPDIPTLGVGEATIPN 1vdc 30 :KPLLFEGWMANDIAPGGQLTTT T0334 57 :TAFFDFLGIPED 1vdc 47 :TDVENFPGFPEG T0334 69 :EWMRECNAS 1vdc 70 :KQSERFGTT T0334 96 :EARELDG 1vdc 118 :RLSFVGS T0334 103 :GPDHFYHSFGLL 1vdc 126 :EVLGGFWNRGIS T0334 115 :KYHEQIPLSHYWFDRSYRG 1vdc 143 :FRNKPLAVIGGGDSAMEEA T0334 139 :FDYACYKEPVILD 1vdc 162 :NFLTKYGSKVYII T0334 152 :ANRSPRR 1vdc 176 :RRDAFRA T0334 172 :DAHL 1vdc 183 :SKIM T0334 181 :RRFATEKLGVRHVED 1vdc 187 :QQRALSNPKIDVIWN T0334 196 :RVEHVQRDAN 1vdc 203 :SVVEAYGDGE T0334 207 :NIESVRTAT 1vdc 217 :VLGGLKVKN T0334 216 :GR 1vdc 229 :GD T0334 218 :VFDADLFVDCSGFRG 1vdc 233 :DLKVSGLFFAIGHEP T0334 233 :LLI 1vdc 250 :KFL T0334 247 :SDHLLNDSAVATQVP 1vdc 253 :DGGVELDSDGYVVTK T0334 289 :LGRFG 1vdc 267 :PGTTQ T0334 338 :AWVGNCVSIGTSSCFVEP 1vdc 276 :TSVPGVFAAGDVQDKKYR T0334 360 :GIYFVYAALYQLV 1vdc 294 :QAITAAGTGCMAA T0334 497 :ESVDEVFGA 1vdc 307 :LDAEHYLQE Number of specific fragments extracted= 23 number of extra gaps= 1 total=2670 Will force an alignment to be made, even if fragment is small Number of alignments=118 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1vdc/T0334-1vdc-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0334 read from 1vdc/T0334-1vdc-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1vdc read from 1vdc/T0334-1vdc-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1vdc in template set Warning: unaligning (T0334)E321 because of BadResidue code BAD_PEPTIDE in next template residue (1vdc)D216 Warning: unaligning (T0334)T322 because of BadResidue code BAD_PEPTIDE at template residue (1vdc)D216 Warning: unaligning (T0334)V506 because last residue in template chain is (1vdc)I316 T0334 5 :IDKILIVGGGTAGWMAASYLGK 1vdc 5 :NTRLCIVGSGPAAHTAAIYAAR T0334 30 :GTADITLLQAPDIPTLGVGEATIP 1vdc 27 :AELKPLLFEGWMANDIAPGGQLTT T0334 144 :YKEPVI 1vdc 46 :TTDVEN T0334 155 :SPRRLDG 1vdc 52 :FPGFPEG T0334 171 :FDAHLVADFLRRFA 1vdc 59 :ILGVELTDKFRKQS T0334 186 :EKLGVRHVEDRVEHVQR 1vdc 73 :ERFGTTIFTETVTKVDF T0334 204 :ANGN 1vdc 90 :SSKP T0334 209 :ESVRTATG 1vdc 94 :FKLFTDSK T0334 218 :VFDADLFVDCSGFR 1vdc 102 :AILADAVILAIGAV T0334 236 :NKAMEEPFLDMSDHLLNDSAV 1vdc 116 :AKRLSFVGSGEVLGGFWNRGI T0334 272 :FTSAIAMKSG 1vdc 133 :SACAVCDGAA T0334 287 :PM 1vdc 141B:PI T0334 289 :LGR 1vdc 144 :RNK T0334 292 :FGT 1vdc 148 :LAV T0334 295 :GYVYSSRFATE 1vdc 172 :YIIHRRDAFRA T0334 306 :DEAVREFCEMW 1vdc 184 :KIMQQRALSNP T0334 319 :DP 1vdc 213 :GE T0334 323 :Q 1vdc 217 :V T0334 324 :PLNRIRFRVG 1vdc 228 :TGDVSDLKVS T0334 339 :WVGNCVSIGTSSCFVEPL 1vdc 277 :SVPGVFAAGDVQDKKYRQ T0334 361 :IYFVYAALYQLV 1vdc 295 :AITAAGTGCMAA T0334 497 :ESVDEVFGA 1vdc 307 :LDAEHYLQE Number of specific fragments extracted= 22 number of extra gaps= 1 total=2692 Will force an alignment to be made, even if fragment is small Number of alignments=119 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1vdc/T0334-1vdc-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0334 read from 1vdc/T0334-1vdc-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1vdc read from 1vdc/T0334-1vdc-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1vdc in template set Warning: unaligning (T0334)K378 because last residue in template chain is (1vdc)I316 T0334 7 :KILIVGGGTAGWMAASYLGK 1vdc 7 :RLCIVGSGPAAHTAAIYAAR T0334 30 :GTADITLLQAPDIPTLGVGEATI 1vdc 27 :AELKPLLFEGWMANDIAPGGQLT T0334 80 :VAIKFINWRTAGEGT 1vdc 45 :TTTDVENFPGFPEGI T0334 172 :DAHLVADFLRRFATEKLGVRHVE 1vdc 60 :LGVELTDKFRKQSERFGTTIFTE T0334 196 :RVEHVQRDANG 1vdc 83 :TVTKVDFSSKP T0334 209 :ESVRTAT 1vdc 94 :FKLFTDS T0334 217 :RVFDADLFVDCSGF 1vdc 101 :KAILADAVILAIGA T0334 256 :VATQVPHDDDANGVEPFTS 1vdc 115 :VAKRLSFVGSGEVLGGFWN T0334 329 :RFRVGRN 1vdc 264 :VTKPGTT T0334 337 :RAWVGNCVSIGTSSCFVEPLESTGIYFVYAALYQLVKHFPD 1vdc 275 :QTSVPGVFAAGDVQDKKYRQAITAAGTGCMAALDAEHYLQE Number of specific fragments extracted= 10 number of extra gaps= 0 total=2702 Will force an alignment to be made, even if fragment is small Number of alignments=120 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1fcdA/T0334-1fcdA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1fcdA expands to /projects/compbio/data/pdb/1fcd.pdb.gz 1fcdA:# T0334 read from 1fcdA/T0334-1fcdA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1fcdA read from 1fcdA/T0334-1fcdA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1fcdA to template set # found chain 1fcdA in template set Warning: unaligning (T0334)P40 because of BadResidue code BAD_PEPTIDE in next template residue (1fcdA)T37 Warning: unaligning (T0334)D41 because of BadResidue code BAD_PEPTIDE at template residue (1fcdA)T37 Warning: unaligning (T0334)I52 because of BadResidue code BAD_PEPTIDE in next template residue (1fcdA)L44 Warning: unaligning (T0334)P53 because of BadResidue code BAD_PEPTIDE at template residue (1fcdA)L44 Warning: unaligning (T0334)L250 because of BadResidue code BAD_PEPTIDE in next template residue (1fcdA)P275 Warning: unaligning (T0334)L251 because of BadResidue code BAD_PEPTIDE at template residue (1fcdA)P275 Warning: unaligning (T0334)I346 because of BadResidue code BAD_PEPTIDE in next template residue (1fcdA)G293 Warning: unaligning (T0334)G347 because of BadResidue code BAD_PEPTIDE at template residue (1fcdA)G293 Warning: unaligning (T0334)T348 because of BadResidue code BAD_PEPTIDE at template residue (1fcdA)D294 Warning: unaligning (T0334)V353 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1fcdA)P300 T0334 7 :KILIVGGGTAGWMAASYLGK 1fcdA 4 :KVVVVGGGTGGATAAKYIKL T0334 28 :L 1fcdA 24 :A T0334 29 :QGT 1fcdA 26 :PSI T0334 33 :DITLLQA 1fcdA 29 :EVTLIEP T0334 46 :GVG 1fcdA 38 :DYY T0334 50 :AT 1fcdA 41 :TC T0334 54 :N 1fcdA 45 :S T0334 57 :TAF 1fcdA 46 :NEV T0334 61 :DFLGIPED 1fcdA 49 :IGGDRKLE T0334 69 :EWM 1fcdA 63 :DGL T0334 186 :EKLGVRHVEDRVEHV 1fcdA 66 :RAHGIQVVHDSATGI T0334 203 :DANG 1fcdA 81 :DPDK T0334 209 :ESVRTATGRVFDADLFVDCSGF 1fcdA 85 :KLVKTAGGAEFGYDRCVVAPGI T0334 231 :RGLLINKAMEEPFL 1fcdA 257 :RAGKIAQIAGLTND T0334 247 :SDH 1fcdA 271 :AGW T0334 252 :ND 1fcdA 276 :VD T0334 254 :SAVAT 1fcdA 279 :KTFES T0334 338 :AWVGNCVS 1fcdA 284 :SIHKGIHV T0334 349 :SSCF 1fcdA 295 :ASIA T0334 354 :EPLESTGIYFVYAALYQLV 1fcdA 301 :MPKSGYSANSQGKVAAAAV T0334 418 :WRANKELRL 1fcdA 320 :VVLLKGEEP T0334 427 :AD 1fcdA 377 :PD T0334 497 :ESVDEVFGAVKDRQRNLLETL 1fcdA 379 :WVLEREVQYAYSWYNNIVHDT Number of specific fragments extracted= 23 number of extra gaps= 5 total=2725 Will force an alignment to be made, even if fragment is small Number of alignments=121 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1fcdA/T0334-1fcdA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0334 read from 1fcdA/T0334-1fcdA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1fcdA read from 1fcdA/T0334-1fcdA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1fcdA in template set Warning: unaligning (T0334)P40 because of BadResidue code BAD_PEPTIDE in next template residue (1fcdA)T37 Warning: unaligning (T0334)D41 because of BadResidue code BAD_PEPTIDE at template residue (1fcdA)T37 Warning: unaligning (T0334)V47 because of BadResidue code BAD_PEPTIDE in next template residue (1fcdA)L44 Warning: unaligning (T0334)N54 because of BadResidue code BAD_PEPTIDE at template residue (1fcdA)L44 Warning: unaligning (T0334)T273 because of BadResidue code BAD_PEPTIDE in next template residue (1fcdA)K129 Warning: unaligning (T0334)S274 because of BadResidue code BAD_PEPTIDE at template residue (1fcdA)K129 Warning: unaligning (T0334)K279 because of BadResidue code BAD_PEPTIDE in next template residue (1fcdA)E132 Warning: unaligning (T0334)S280 because of BadResidue code BAD_PEPTIDE at template residue (1fcdA)E132 Warning: unaligning (T0334)Y298 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1fcdA)P155 Warning: unaligning (T0334)S299 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1fcdA)P155 Warning: unaligning (T0334)T304 because of BadResidue code BAD_PEPTIDE in next template residue (1fcdA)C161 Warning: unaligning (T0334)E305 because of BadResidue code BAD_PEPTIDE at template residue (1fcdA)C161 Warning: unaligning (T0334)T322 because of BadResidue code BAD_PEPTIDE in next template residue (1fcdA)N214 Warning: unaligning (T0334)Q323 because of BadResidue code BAD_PEPTIDE at template residue (1fcdA)N214 Warning: unaligning (T0334)I328 because of BadResidue code BAD_PEPTIDE in next template residue (1fcdA)P275 Warning: unaligning (T0334)R329 because of BadResidue code BAD_PEPTIDE at template residue (1fcdA)P275 Warning: unaligning (T0334)I346 because of BadResidue code BAD_PEPTIDE in next template residue (1fcdA)G293 Warning: unaligning (T0334)G347 because of BadResidue code BAD_PEPTIDE at template residue (1fcdA)G293 Warning: unaligning (T0334)T348 because of BadResidue code BAD_PEPTIDE at template residue (1fcdA)D294 Warning: unaligning (T0334)V353 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1fcdA)P300 Warning: unaligning (T0334)E354 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1fcdA)P300 T0334 5 :IDKILIVGGGTAGWMAASYLGK 1fcdA 2 :GRKVVVVGGGTGGATAAKYIKL T0334 28 :LQGTADITLLQA 1fcdA 24 :ADPSIEVTLIEP T0334 42 :IPTLG 1fcdA 38 :DYYTC T0334 55 :LQTAF 1fcdA 45 :SNEVI T0334 141 :YACYKEPVI 1fcdA 50 :GGDRKLESI T0334 166 :NYAW 1fcdA 59 :KHGY T0334 182 :RFA 1fcdA 63 :DGL T0334 186 :EKLGVRHVEDRVEHV 1fcdA 66 :RAHGIQVVHDSATGI T0334 203 :DANG 1fcdA 81 :DPDK T0334 209 :ESVRTATGRVFDADLFVDCSGF 1fcdA 85 :KLVKTAGGAEFGYDRCVVAPGI T0334 244 :L 1fcdA 107 :E T0334 245 :DMSDH 1fcdA 109 :IYDKI T0334 253 :DS 1fcdA 114 :EG T0334 261 :PHDDDANGVEPF 1fcdA 116 :YSEEAAAKLPHA T0334 275 :A 1fcdA 130 :A T0334 288 :MLGRFGTGYV 1fcdA 144 :MADGGTVVIA T0334 300 :SRFA 1fcdA 156 :AAPF T0334 306 :DEAVREFCEMWHL 1fcdA 198 :SQFSKGWERLYGF T0334 320 :PE 1fcdA 211 :GT T0334 324 :PLNR 1fcdA 270 :DAGW T0334 330 :FRVGRNRRAWVGNCVS 1fcdA 276 :VDIKTFESSIHKGIHV T0334 349 :SSCF 1fcdA 295 :ASIA T0334 355 :PLESTGIYF 1fcdA 302 :PKSGYSANS T0334 364 :VYAALYQLVKHFPD 1fcdA 312 :GKVAAAAVVVLLKG T0334 409 :FSPRTDTP 1fcdA 371 :VTPVDAPD T0334 497 :ESVDEVFGAVKDRQRNLLETL 1fcdA 379 :WVLEREVQYAYSWYNNIVHDT Number of specific fragments extracted= 26 number of extra gaps= 10 total=2751 Will force an alignment to be made, even if fragment is small Number of alignments=122 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1fcdA/T0334-1fcdA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0334 read from 1fcdA/T0334-1fcdA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1fcdA read from 1fcdA/T0334-1fcdA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1fcdA in template set Warning: unaligning (T0334)P40 because of BadResidue code BAD_PEPTIDE in next template residue (1fcdA)T37 Warning: unaligning (T0334)D41 because of BadResidue code BAD_PEPTIDE at template residue (1fcdA)T37 Warning: unaligning (T0334)V47 because of BadResidue code BAD_PEPTIDE in next template residue (1fcdA)L44 Warning: unaligning (T0334)N54 because of BadResidue code BAD_PEPTIDE at template residue (1fcdA)L44 Warning: unaligning (T0334)I328 because of BadResidue code BAD_PEPTIDE in next template residue (1fcdA)P275 Warning: unaligning (T0334)R329 because of BadResidue code BAD_PEPTIDE at template residue (1fcdA)P275 Warning: unaligning (T0334)I346 because of BadResidue code BAD_PEPTIDE in next template residue (1fcdA)G293 Warning: unaligning (T0334)G347 because of BadResidue code BAD_PEPTIDE at template residue (1fcdA)G293 Warning: unaligning (T0334)T348 because of BadResidue code BAD_PEPTIDE at template residue (1fcdA)D294 Warning: unaligning (T0334)C351 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1fcdA)P300 Warning: unaligning (T0334)F352 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1fcdA)P300 T0334 5 :IDKILIVGGGTAGWMAASYLGK 1fcdA 2 :GRKVVVVGGGTGGATAAKYIKL T0334 28 :LQGTADITLLQA 1fcdA 24 :ADPSIEVTLIEP T0334 42 :IPTLG 1fcdA 38 :DYYTC T0334 55 :LQTA 1fcdA 45 :SNEV T0334 148 :VILDANRSPRRLDGSK 1fcdA 49 :IGGDRKLESIKHGYDG T0334 184 :ATEKLGVRHVE 1fcdA 65 :LRAHGIQVVHD T0334 196 :RVEHVQ 1fcdA 76 :SATGID T0334 204 :ANG 1fcdA 82 :PDK T0334 209 :ESVRTATGRVFDADLFVDCSGF 1fcdA 85 :KLVKTAGGAEFGYDRCVVAPGI T0334 258 :TQVPHD 1fcdA 107 :ELIYDK T0334 300 :SRFATED 1fcdA 113 :IEGYSEE T0334 322 :TQPLNR 1fcdA 268 :TNDAGW T0334 330 :FRVGRNRRAWVGNCVS 1fcdA 276 :VDIKTFESSIHKGIHV T0334 349 :S 1fcdA 295 :A T0334 350 :S 1fcdA 298 :A T0334 353 :VEPLESTGIYFVYAALYQLVKHFPDKSLN 1fcdA 301 :MPKSGYSANSQGKVAAAAVVVLLKGEEPG T0334 407 :FYFSPRTDT 1fcdA 353 :YRPNADGSA T0334 467 :NNSNYYCVLAGLGLVPDAPSPRLAHMPQATESVDEV 1fcdA 363 :ESVPDSGGVTPVDAPDWVLEREVQYAYSWYNNIVHD Number of specific fragments extracted= 18 number of extra gaps= 5 total=2769 Will force an alignment to be made, even if fragment is small Number of alignments=123 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1cj3A/T0334-1cj3A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1cj3A expands to /projects/compbio/data/pdb/1cj3.pdb.gz 1cj3A:# T0334 read from 1cj3A/T0334-1cj3A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1cj3A read from 1cj3A/T0334-1cj3A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1cj3A to template set # found chain 1cj3A in template set Warning: unaligning (T0334)I5 because first residue in template chain is (1cj3A)M1 T0334 6 :D 1cj3A 2 :K T0334 7 :KILIVGGGTAGWMAASYLGK 1cj3A 4 :QVAIIGAGPSGLLLGQLLHK T0334 29 :QGT 1cj3A 24 :AGI T0334 33 :DITLLQAPD 1cj3A 27 :DNVILERQT T0334 52 :IPNLQ 1cj3A 36 :PDEVL T0334 61 :DFLGIPED 1cj3A 41 :GRIRAGVL T0334 69 :EWMRECNASYKVAIKFINW 1cj3A 54 :DLLREAGVDRRMARDGLVH T0334 103 :GPDHFYHSFGLL 1cj3A 73 :EGVEIAFAGQRR T0334 115 :KYHE 1cj3A 87 :DLKR T0334 152 :ANRSPRRLD 1cj3A 92 :SGGKTVTVY T0334 172 :DAHLVADFLRRFA 1cj3A 101 :GQTEVTRDLMEAR T0334 186 :EKLGVRHVED 1cj3A 114 :EASGATTVYQ T0334 196 :RVEHVQRDANGNIE 1cj3A 125 :AEVRLHDLQGERPY T0334 211 :VRTA 1cj3A 139 :VTFE T0334 215 :TGR 1cj3A 144 :DGE T0334 218 :VFDADLFVDCSGFRGLLI 1cj3A 149 :RLDCDYIAGCDGFHGISR T0334 237 :KAMEEPFLDM 1cj3A 167 :QSIPAERLKV T0334 247 :SDHLLND 1cj3A 178 :ERVYPFG T0334 254 :SAVATQVPHDD 1cj3A 186 :LGLLADTPPVS T0334 271 :PFTSAIAMKSGWTWKIPM 1cj3A 197 :HELIYANHPRGFALCSQR T0334 289 :LGR 1cj3A 216 :ATR T0334 292 :FGTGYVYSSRFATEDEAVREFCEM 1cj3A 223 :VQVPLTEKVEDWSDERFWTELKAR T0334 317 :HLDP 1cj3A 248 :PAEV T0334 321 :ETQPLNRIRFRVGRNRRAWVGNCVSIGTSSCFVEPLESTGIYFVYAALYQLVKHFP 1cj3A 259 :PSLEKSIAPLRSFVVEPMQHGRLFLAGDAAHIVPPTGAKGLNLAASDVSTLYRLLL T0334 377 :DKSLNPVLTARFNREIETMFDDTRDFIQAHFYFSPRTDTP 1cj3A 317 :YREGRGELLERYSAICLRRIWKAERFSWWMTSVLHRFPDT T0334 417 :FWR 1cj3A 359 :FSQ T0334 508 :DRQRNLLETLPSLHEFLRQ 1cj3A 362 :RIQQTELEYYLGSEAGLAT Number of specific fragments extracted= 27 number of extra gaps= 0 total=2796 Will force an alignment to be made, even if fragment is small Number of alignments=124 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1cj3A/T0334-1cj3A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0334 read from 1cj3A/T0334-1cj3A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1cj3A read from 1cj3A/T0334-1cj3A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1cj3A in template set Warning: unaligning (T0334)K4 because first residue in template chain is (1cj3A)M1 T0334 5 :IDKILIVGGGTAGWMAASYLGK 1cj3A 2 :KTQVAIIGAGPSGLLLGQLLHK T0334 30 :GTADITLLQAPDI 1cj3A 24 :AGIDNVILERQTP T0334 43 :PTLGVGEATIPNLQTAF 1cj3A 40 :LGRIRAGVLEQGMVDLL T0334 61 :DFLGI 1cj3A 57 :REAGV T0334 123 :SHYWFDRSYR 1cj3A 62 :DRRMARDGLV T0334 136 :VEPFDYACYKEPVILD 1cj3A 72 :HEGVEIAFAGQRRRID T0334 155 :SPRRLDG 1cj3A 88 :LKRLSGG T0334 166 :NYAWHFDAHLVADFLRRFA 1cj3A 95 :KTVTVYGQTEVTRDLMEAR T0334 186 :EKLGVRHVED 1cj3A 114 :EASGATTVYQ T0334 196 :RVEHVQR 1cj3A 125 :AEVRLHD T0334 203 :DANG 1cj3A 133 :QGER T0334 209 :ESVRTA 1cj3A 137 :PYVTFE T0334 215 :TG 1cj3A 144 :DG T0334 217 :RVFDADLFVDCSGFRGLL 1cj3A 148 :LRLDCDYIAGCDGFHGIS T0334 236 :NKAMEEPFL 1cj3A 166 :RQSIPAERL T0334 245 :DMSDHLLNDSAVAT 1cj3A 176 :VFERVYPFGWLGLL T0334 264 :DDANGVEPFTSAIAMKSGWTWKIPMLGR 1cj3A 190 :ADTPPVSHELIYANHPRGFALCSQRSAT T0334 292 :FGTGYVYSS 1cj3A 219 :SRYYVQVPL T0334 301 :RFATEDEAVREFCEMW 1cj3A 232 :EDWSDERFWTELKARL T0334 318 :L 1cj3A 254 :K T0334 322 :TQ 1cj3A 255 :LV T0334 324 :PLNRIRFRVGRNRRAWVGNCVSIGTSSCFVEPLESTGIYFVYAALYQLVKHFPD 1cj3A 262 :EKSIAPLRSFVVEPMQHGRLFLAGDAAHIVPPTGAKGLNLAASDVSTLYRLLLK T0334 378 :KSLNPVLTARFNREIETMFDDTRDFIQAHFY 1cj3A 318 :REGRGELLERYSAICLRRIWKAERFSWWMTS T0334 409 :FSPRTDTPFWR 1cj3A 351 :HRFPDTDAFSQ T0334 504 :GAVKDRQRNLLETLPSLHEFL 1cj3A 362 :RIQQTELEYYLGSEAGLATIA Number of specific fragments extracted= 25 number of extra gaps= 0 total=2821 Will force an alignment to be made, even if fragment is small Number of alignments=125 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1cj3A/T0334-1cj3A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0334 read from 1cj3A/T0334-1cj3A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1cj3A read from 1cj3A/T0334-1cj3A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1cj3A in template set T0334 7 :KILIVGGGTAGWMAASYLGK 1cj3A 4 :QVAIIGAGPSGLLLGQLLHK T0334 30 :GTADITLLQAPD 1cj3A 24 :AGIDNVILERQT T0334 43 :PTLGVGE 1cj3A 41 :GRIRAGV T0334 51 :TIPNLQTAF 1cj3A 48 :LEQGMVDLL T0334 61 :DFLGIP 1cj3A 57 :REAGVD T0334 68 :D 1cj3A 63 :R T0334 70 :WMRECNASY 1cj3A 64 :RMARDGLVH T0334 79 :KVAIKFINWRT 1cj3A 74 :GVEIAFAGQRR T0334 95 :SE 1cj3A 85 :RI T0334 157 :RRLDGSKVT 1cj3A 87 :DLKRLSGGK T0334 167 :YAWHFDAHLVADFLRRFATEKLGVRHVE 1cj3A 96 :TVTVYGQTEVTRDLMEAREASGATTVYQ T0334 197 :VEHVQRD 1cj3A 124 :AAEVRLH T0334 204 :ANGNIESVRTATGR 1cj3A 134 :GERPYVTFERDGER T0334 218 :VFDADLFVDCSGFRGLLINK 1cj3A 149 :RLDCDYIAGCDGFHGISRQS T0334 244 :LDMSDH 1cj3A 169 :IPAERL T0334 250 :LLNDSAVATQV 1cj3A 180 :VYPFGWLGLLA T0334 265 :DANGVEPFTSAIAMKSGWTWKIPMLGRFGTGYVYS 1cj3A 191 :DTPPVSHELIYANHPRGFALCSQRSATRSRYYVQV T0334 300 :SRFATEDEAVREFCEMW 1cj3A 231 :VEDWSDERFWTELKARL T0334 318 :LDPETQPLNRIRFRVGRNRRAWVGNCVSIGTSSCFVEPLESTGIYFVYAALYQLVKHFP 1cj3A 256 :VTGPSLEKSIAPLRSFVVEPMQHGRLFLAGDAAHIVPPTGAKGLNLAASDVSTLYRLLL T0334 377 :DKSLNPVLTARFNREIETMFDDTRDFIQAHFYFSPR 1cj3A 321 :RGELLERYSAICLRRIWKAERFSWWMTSVLHRFPDT T0334 481 :VPDAPS 1cj3A 357 :DAFSQR T0334 505 :AVKDRQRNLLETLPSLHEFLRQQ 1cj3A 363 :IQQTELEYYLGSEAGLATIAENY Number of specific fragments extracted= 22 number of extra gaps= 0 total=2843 Will force an alignment to be made, even if fragment is small Number of alignments=126 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1bgj/T0334-1bgj-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1bgj expands to /projects/compbio/data/pdb/1bgj.pdb.gz 1bgj:Warning: there is no chain 1bgj will retry with 1bgjA # T0334 read from 1bgj/T0334-1bgj-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1bgj read from 1bgj/T0334-1bgj-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1bgj to template set # found chain 1bgj in template set Warning: unaligning (T0334)I5 because first residue in template chain is (1bgj)M1 T0334 6 :D 1bgj 2 :K T0334 7 :KILIVGGGTAGWMAASYLGK 1bgj 4 :QVAIIGAGPSGLLLGQLLHK T0334 29 :QGT 1bgj 24 :AGI T0334 33 :DITLLQAPD 1bgj 27 :DNVILERQT T0334 52 :IPNLQTAF 1bgj 36 :PDYVLGRI T0334 61 :DFLGIPED 1bgj 44 :RAGVLEQG T0334 69 :EWMRECNASYKVAIKFINW 1bgj 54 :DLLREAGVDRRMARDGLVH T0334 103 :GPDHFYHSFGLL 1bgj 73 :EGVEIAFAGQRR T0334 115 :KYHE 1bgj 87 :DLKR T0334 152 :ANRSPRRLD 1bgj 92 :SGGKTVTVY T0334 172 :DAHLVADFLRRFA 1bgj 101 :GQTEVTRDLMEAR T0334 186 :EKLGVRHVED 1bgj 114 :EASGATTVYQ T0334 196 :RVEHVQRDANGNIE 1bgj 125 :AEVRLHDLQGERPY T0334 211 :VRTA 1bgj 139 :VTFE T0334 215 :TGR 1bgj 144 :DGE T0334 218 :VFDADLFVDCSGFRGLLI 1bgj 149 :RLDCDYIAGCDGFRGISR T0334 237 :KAMEEPFLDM 1bgj 167 :QSIPAERLKV T0334 247 :SDHLLND 1bgj 178 :ERVYPFG T0334 254 :SAVATQVPHDD 1bgj 186 :LGLLADTPPVS T0334 271 :PFTSAIAMKSGWTWKIPM 1bgj 197 :HELIYANHPRGFALCSQR T0334 289 :LGR 1bgj 216 :ATR T0334 292 :FGTGYVYSSRFATEDEAVREFCEM 1bgj 223 :VQVPLTEKVEDWSDERFWTELKAR T0334 317 :HLDP 1bgj 248 :PAEV T0334 321 :ETQPLNRIRFRVGRNRRAWVGNCVSIGTSSCFVEPLESTGIYFVYAALYQLVKHFP 1bgj 259 :PSLEKSIAPLRSFVVEPMQHGRLFLAGDAAHIVPPTGAKGLNLAASDVSTLYRLLL T0334 377 :DKSLNPVLTARFNREIETMFDDTRDFIQAHFYFSPRTDTP 1bgj 317 :YREGRGELLERYSAICLRRIWKAERFSWWMTSVLHRFPDT T0334 417 :FWRANKELRL 1bgj 359 :FSQRIQQTEL T0334 427 :ADGMQEKIDMY 1bgj 375 :EAGLATIAENY Number of specific fragments extracted= 27 number of extra gaps= 0 total=2870 Will force an alignment to be made, even if fragment is small Number of alignments=127 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1bgj/T0334-1bgj-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0334 read from 1bgj/T0334-1bgj-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1bgj read from 1bgj/T0334-1bgj-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1bgj in template set Warning: unaligning (T0334)K4 because first residue in template chain is (1bgj)M1 T0334 5 :IDKILIVGGGTAGWMAASYLGK 1bgj 2 :KTQVAIIGAGPSGLLLGQLLHK T0334 30 :GTADITLLQAPDI 1bgj 24 :AGIDNVILERQTP T0334 43 :PTLGVGEATIPNLQTAF 1bgj 40 :LGRIRAGVLEQGMVDLL T0334 61 :DFLGI 1bgj 57 :REAGV T0334 123 :SHYWFDRSYR 1bgj 62 :DRRMARDGLV T0334 139 :FDYAC 1bgj 72 :HEGVE T0334 144 :YKEPVILD 1bgj 80 :AGQRRRID T0334 155 :SPRRLDG 1bgj 88 :LKRLSGG T0334 166 :NYAWHFDAHLVADFLRRFA 1bgj 95 :KTVTVYGQTEVTRDLMEAR T0334 186 :EKLGVRHVED 1bgj 114 :EASGATTVYQ T0334 196 :RVEHVQR 1bgj 125 :AEVRLHD T0334 203 :DANG 1bgj 133 :QGER T0334 209 :ESVRTA 1bgj 137 :PYVTFE T0334 215 :TG 1bgj 144 :DG T0334 217 :RVFDADLFVDCSGFRGLL 1bgj 148 :LRLDCDYIAGCDGFRGIS T0334 236 :NKAMEEPFL 1bgj 166 :RQSIPAERL T0334 245 :DMSDHLLNDSAVAT 1bgj 176 :VFERVYPFGWLGLL T0334 264 :DDANGVEPFTSAIAMKSGWTWKIPMLGR 1bgj 190 :ADTPPVSHELIYANHPRGFALCSQRSAT T0334 292 :FGTGYVYSS 1bgj 219 :SRYYVQVPL T0334 301 :RFATEDEAVREFCEMW 1bgj 232 :EDWSDERFWTELKARL T0334 317 :HL 1bgj 254 :KL T0334 323 :Q 1bgj 256 :V T0334 324 :PLNRIRFRVGRNRRAWVGNCVSIGTSSCFVEPLESTGIYFVYAALYQLVKHFPD 1bgj 262 :EKSIAPLRSFVVEPMQHGRLFLAGDAAHIVPPTGAKGLNLAASDVSTLYRLLLK T0334 378 :KSLNPVLTARFNREIETMFDDTRDFIQAHFYFSPRTD 1bgj 318 :REGRGELLERYSAICLRRIWKAERFSWWMTSVLHRFP T0334 415 :TPFWR 1bgj 357 :DAFSQ T0334 504 :GAVKDRQRNLLETLPSLHEFLRQQH 1bgj 362 :RIQQTELEYYLGSEAGLATIAENYV Number of specific fragments extracted= 26 number of extra gaps= 0 total=2896 Will force an alignment to be made, even if fragment is small Number of alignments=128 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1bgj/T0334-1bgj-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0334 read from 1bgj/T0334-1bgj-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1bgj read from 1bgj/T0334-1bgj-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1bgj in template set T0334 7 :KILIVGGGTAGWMAASYLGK 1bgj 4 :QVAIIGAGPSGLLLGQLLHK T0334 30 :GTADITLLQAPD 1bgj 24 :AGIDNVILERQT T0334 42 :IPTLGVGE 1bgj 40 :LGRIRAGV T0334 51 :TIPNLQTAF 1bgj 48 :LEQGMVDLL T0334 61 :DFLGIP 1bgj 57 :REAGVD T0334 68 :DEWMRECNASYKVAIKF 1bgj 63 :RRMARDGLVHEGVEIAF T0334 90 :AGEGTSEA 1bgj 80 :AGQRRRID T0334 158 :RLDGSKVTN 1bgj 88 :LKRLSGGKT T0334 168 :AWHFDAHLVADFLRRFATEKLGVRHVEDRVEHVQR 1bgj 97 :VTVYGQTEVTRDLMEAREASGATTVYQAAEVRLHD T0334 204 :ANGNIESVRTATGR 1bgj 134 :GERPYVTFERDGER T0334 218 :VFDADLFVDCSGFRGLLIN 1bgj 149 :RLDCDYIAGCDGFRGISRQ T0334 243 :FLDMSDH 1bgj 168 :SIPAERL T0334 250 :LLNDSAVATQV 1bgj 180 :VYPFGWLGLLA T0334 265 :DANGVEPFTSAIAMKSGWTWKIPMLGRFGTGYVYS 1bgj 191 :DTPPVSHELIYANHPRGFALCSQRSATRSRYYVQV T0334 300 :SRFATEDEAVREFCEMW 1bgj 231 :VEDWSDERFWTELKARL T0334 318 :LDPETQPLNRIRFRVGRNRRAWVGNCVSIGTSSCFVEPLESTGIYFVYAALYQLVKHFP 1bgj 256 :VTGPSLEKSIAPLRSFVVEPMQHGRLFLAGDAAHIVPPTGAKGLNLAASDVSTLYRLLL T0334 377 :DKSLNPVLTARFNREIETMFDDTRDFIQAHFYFSPRT 1bgj 321 :RGELLERYSAICLRRIWKAERFSWWMTSVLHRFPDTD T0334 486 :SPRLAH 1bgj 358 :AFSQRI T0334 506 :VKDRQRNLLETLPSLHEFLRQQ 1bgj 364 :QQTELEYYLGSEAGLATIAENY Number of specific fragments extracted= 19 number of extra gaps= 0 total=2915 Will force an alignment to be made, even if fragment is small Number of alignments=129 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1kssA/T0334-1kssA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1kssA expands to /projects/compbio/data/pdb/1kss.pdb.gz 1kssA:# T0334 read from 1kssA/T0334-1kssA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1kssA read from 1kssA/T0334-1kssA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1kssA to template set # found chain 1kssA in template set Warning: unaligning (T0334)P66 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1kssA)W176 Warning: unaligning (T0334)E67 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1kssA)W176 T0334 3 :GKID 1kssA 122 :APHD T0334 7 :KILIVGGGTAGWMAASYLGK 1kssA 128 :DVVVVGSGGAGFSAAISATD T0334 29 :QGT 1kssA 148 :SGA T0334 33 :DITLLQAPD 1kssA 151 :KVILIEKEP T0334 42 :IPTL 1kssA 161 :IGGN T0334 59 :FFDFLGI 1kssA 168 :AAGGMNA T0334 68 :DEWMRECNASYKVAIKFINWRTAGEGTS 1kssA 177 :TDQQKAKKITDSPELMFEDTMKGGQNIN T0334 96 :EARELDGGPDHFYHSFGLL 1kssA 222 :WMTAMGADLTDVGMMGGAS T0334 115 :KYHE 1kssA 246 :RPTG T0334 152 :AN 1kssA 251 :AG T0334 172 :DAHLVADFLRRFA 1kssA 253 :VGAHVVQVLYDNA T0334 186 :EKLGVRHVED 1kssA 266 :VKRNIDLRMN T0334 196 :RVEHVQRDANGNIESVRTA 1kssA 277 :RGIEVLKDDKGTVKGILVK T0334 215 :T 1kssA 297 :M T0334 216 :GR 1kssA 299 :KG T0334 218 :VFDADLFVDCSGF 1kssA 303 :WVKADAVILATGG T0334 280 :SGWTWKIPM 1kssA 359 :MQYIQAHPT T0334 289 :LGR 1kssA 371 :KGG T0334 292 :FGTGYVYSSRFATE 1kssA 383 :NGAILVNREGKRFV T0334 306 :DEAVREFCEM 1kssA 462 :TETVARYNSL T0334 316 :WHLDPETQPLNRIRF 1kssA 473 :SSGKDTDFERPNLPR T0334 331 :RVGRNR 1kssA 500 :TPGVHA T0334 337 :RAWVGNCVSIGTSSCFVEP 1kssA 523 :KQVIPGLYGAGEVTGGVHG T0334 356 :LESTGIYFVYAALYQLVKHFP 1kssA 545 :LGGNAISDIITFGRLAGEEAA Number of specific fragments extracted= 24 number of extra gaps= 1 total=2939 Will force an alignment to be made, even if fragment is small Number of alignments=130 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1kssA/T0334-1kssA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0334 read from 1kssA/T0334-1kssA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1kssA read from 1kssA/T0334-1kssA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1kssA in template set T0334 4 :KIDKILIVGGGTAGWMAASYLGK 1kssA 125 :DTVDVVVVGSGGAGFSAAISATD T0334 30 :GTADITLLQAPDIPTLGVGEATI 1kssA 148 :SGAKVILIEKEPVIGGNAKLAAG T0334 57 :TAF 1kssA 178 :DQQ T0334 61 :DFLGI 1kssA 181 :KAKKI T0334 66 :PEDEWMRECNA 1kssA 188 :SPELMFEDTMK T0334 77 :SYKVAIKFINWR 1kssA 208 :LVKVLSSHSKDS T0334 123 :SHYWFDRSYR 1kssA 220 :VDWMTAMGAD T0334 141 :YACYKEPVI 1kssA 230 :LTDVGMMGG T0334 155 :SPRRL 1kssA 239 :ASVNR T0334 162 :SKVTNYAW 1kssA 244 :AHRPTGGA T0334 171 :FDAHLVADFLRRFAT 1kssA 252 :GVGAHVVQVLYDNAV T0334 187 :KLGVRHVED 1kssA 267 :KRNIDLRMN T0334 196 :RVEHVQRDANGNIESVRTA 1kssA 277 :RGIEVLKDDKGTVKGILVK T0334 215 :TG 1kssA 299 :KG T0334 217 :RVFDADLFVDCSGFRGL 1kssA 302 :YWVKADAVILATGGFAK T0334 234 :L 1kssA 323 :V T0334 236 :NKA 1kssA 324 :AKL T0334 246 :MSDHLLNDS 1kssA 330 :LKGFISTNQ T0334 267 :NGVE 1kssA 339 :PGAV T0334 272 :FTSAIAMKSGWTWKIPM 1kssA 351 :NAGGALKDMQYIQAHPT T0334 289 :LGRFGT 1kssA 371 :KGGVMV T0334 295 :GYVYSSRFATE 1kssA 384 :GAILVNREGKR T0334 306 :DEAVREFCEMW 1kssA 459 :KALTETVARYN T0334 317 :HLDPETQ 1kssA 475 :GKDTDFE T0334 324 :PLNRIRFRVG 1kssA 493 :NYYAIEVTPG T0334 334 :RNRRAWVGNCVSIG 1kssA 520 :NAKKQVIPGLYGAG T0334 348 :TSSCFVEPLESTGIYFVYAALYQLVKHF 1kssA 537 :GGVHGANRLGGNAISDIITFGRLAGEEA Number of specific fragments extracted= 27 number of extra gaps= 0 total=2966 Will force an alignment to be made, even if fragment is small Number of alignments=131 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1kssA/T0334-1kssA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0334 read from 1kssA/T0334-1kssA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1kssA read from 1kssA/T0334-1kssA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1kssA in template set Warning: unaligning (T0334)K378 because of BadResidue code BAD_PEPTIDE in next template residue (1kssA)S568 T0334 4 :KIDKILIVGGGTAGWMAASYLGK 1kssA 125 :DTVDVVVVGSGGAGFSAAISATD T0334 30 :GTADITLLQAPD 1kssA 148 :SGAKVILIEKEP T0334 44 :TLGVGEATI 1kssA 160 :VIGGNAKLA T0334 57 :TAF 1kssA 178 :DQQ T0334 61 :DFLGI 1kssA 181 :KAKKI T0334 66 :PEDEWMR 1kssA 188 :SPELMFE T0334 113 :LLKYHEQIPLSHYWFDRSY 1kssA 195 :DTMKGGQNINDPALVKVLS T0334 137 :EPFDYACYKEPVILDANRSPRRLDGSKVTN 1kssA 214 :SHSKDSVDWMTAMGADLTDVGMMGGASVNR T0334 169 :WHF 1kssA 244 :AHR T0334 172 :DAHLVADFLRRFATEKLGVRHVEDRVEHVQRDANGNIESVRT 1kssA 253 :VGAHVVQVLYDNAVKRNIDLRMNTRGIEVLKDDKGTVKGILV T0334 214 :ATGR 1kssA 297 :MYKG T0334 218 :VFDADLFVDCSGFRG 1kssA 303 :WVKADAVILATGGFA T0334 233 :LLINK 1kssA 322 :RVAKL T0334 243 :FLDMSDHLLND 1kssA 327 :DPSLKGFISTN T0334 307 :EAVREFCEMWHLDP 1kssA 463 :ETVARYNSLVSSGK T0334 322 :TQ 1kssA 477 :DT T0334 324 :PLNRIRFRVGRNRRA 1kssA 493 :NYYAIEVTPGVHATM T0334 339 :WVGNCVSIGTSSCFVEP 1kssA 525 :VIPGLYGAGEVTGGVHG T0334 356 :LESTGIYFVYAALYQLVKHFPD 1kssA 545 :LGGNAISDIITFGRLAGEEAAK Number of specific fragments extracted= 19 number of extra gaps= 1 total=2985 Will force an alignment to be made, even if fragment is small Number of alignments=132 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1e39A/T0334-1e39A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1e39A expands to /projects/compbio/data/pdb/1e39.pdb.gz 1e39A:# T0334 read from 1e39A/T0334-1e39A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1e39A read from 1e39A/T0334-1e39A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1e39A to template set # found chain 1e39A in template set Warning: unaligning (T0334)P66 because of BadResidue code BAD_PEPTIDE in next template residue (1e39A)W176 Warning: unaligning (T0334)E67 because of BadResidue code BAD_PEPTIDE at template residue (1e39A)W176 Warning: unaligning (T0334)N207 because of BadResidue code BAD_PEPTIDE in next template residue (1e39A)V289 Warning: unaligning (T0334)I208 because of BadResidue code BAD_PEPTIDE at template residue (1e39A)V289 T0334 3 :GKID 1e39A 122 :APHD T0334 7 :KILIVGGGTAGWMAASYLGK 1e39A 128 :DVVVVGSGGAGFSAAISATD T0334 29 :QGT 1e39A 148 :SGA T0334 33 :DITLLQAPD 1e39A 151 :KVILIEKEP T0334 42 :IPTL 1e39A 161 :IGGN T0334 59 :FFDFLGI 1e39A 168 :AAGGMNA T0334 68 :DEWMRECNASYKVAIKFINWRTAGEGTS 1e39A 177 :TDQQKAKKITDSPELMFEDTMKGGQNIN T0334 96 :EARELDGGPDHFYHSFGLL 1e39A 222 :WMTAMGADLTDVGMMGGAS T0334 115 :KYHE 1e39A 246 :RPTG T0334 152 :AN 1e39A 251 :AG T0334 172 :DAHLVADFLRRFA 1e39A 253 :VGAHVVQVLYDNA T0334 186 :EKLGVRHVED 1e39A 266 :VKRNIDLRMN T0334 196 :RVEHVQRDANG 1e39A 277 :RGIEVLKDDKG T0334 209 :ESVRTA 1e39A 290 :KGILVK T0334 215 :T 1e39A 297 :M T0334 216 :GR 1e39A 299 :KG T0334 218 :VFDADLFVDCSGFRG 1e39A 303 :WVKADAVILATGGFA T0334 233 :LLINKAM 1e39A 321 :ERVAKLD T0334 264 :DDANGVEPFTSAIAMK 1e39A 328 :PSLKGFISTNQPGAVG T0334 280 :SGWTWKIPM 1e39A 359 :MQYIQAAPT T0334 289 :LGR 1e39A 371 :KGG T0334 292 :FGTGYVYSSRFATE 1e39A 383 :NGAILVNREGKRFV T0334 306 :DEAVREFCEM 1e39A 462 :TETVARYNSL T0334 316 :WHLDPETQPLNRIRF 1e39A 473 :SSGKDTDFERPNLPR T0334 331 :RVGRNR 1e39A 503 :VHHTMG T0334 337 :RAWVGNCVSIGTSSCFVEP 1e39A 523 :KQVIPGLYGAGEVTGGVHG T0334 356 :LESTGIYFVYAALYQLVKHFP 1e39A 545 :LGGNAISDIITFGRLAGEEAA Number of specific fragments extracted= 27 number of extra gaps= 2 total=3012 Will force an alignment to be made, even if fragment is small Number of alignments=133 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1e39A/T0334-1e39A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0334 read from 1e39A/T0334-1e39A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1e39A read from 1e39A/T0334-1e39A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1e39A in template set Warning: unaligning (T0334)N207 because of BadResidue code BAD_PEPTIDE in next template residue (1e39A)V289 Warning: unaligning (T0334)I208 because of BadResidue code BAD_PEPTIDE at template residue (1e39A)V289 T0334 4 :KIDKILIVGGGTAGWMAASYLGK 1e39A 125 :DTVDVVVVGSGGAGFSAAISATD T0334 30 :GTADITLLQAPDIPTLGVGEATI 1e39A 148 :SGAKVILIEKEPVIGGNAKLAAG T0334 57 :TAF 1e39A 178 :DQQ T0334 61 :DFLGI 1e39A 181 :KAKKI T0334 66 :PEDEWMREC 1e39A 188 :SPELMFEDT T0334 75 :NASYKVAIKFINWR 1e39A 206 :PALVKVLSSHSKDS T0334 123 :SHYWFDRSYR 1e39A 220 :VDWMTAMGAD T0334 144 :YKEPVI 1e39A 230 :LTDVGM T0334 152 :ANRSPRRL 1e39A 236 :MGGASVNR T0334 162 :SKVTNYAW 1e39A 244 :AHRPTGGA T0334 171 :FDAHLVADFLRRFAT 1e39A 252 :GVGAHVVQVLYDNAV T0334 187 :KLGVRHVED 1e39A 267 :KRNIDLRMN T0334 196 :RVEHVQRDANG 1e39A 277 :RGIEVLKDDKG T0334 209 :ESVRTA 1e39A 290 :KGILVK T0334 215 :TG 1e39A 299 :KG T0334 217 :RVFDADLFVDCSGFRGL 1e39A 302 :YWVKADAVILATGGFAK T0334 234 :L 1e39A 323 :V T0334 236 :NKAM 1e39A 324 :AKLD T0334 244 :LDMSDHLLNDS 1e39A 328 :PSLKGFISTNQ T0334 267 :NGVE 1e39A 339 :PGAV T0334 273 :TSAIAMKSGWTWKIPM 1e39A 352 :AGGALKDMQYIQAAPT T0334 289 :LGRFGT 1e39A 371 :KGGVMV T0334 295 :GYVYSSRFATE 1e39A 384 :GAILVNREGKR T0334 306 :DEAVREFCEMW 1e39A 462 :TETVARYNSLV T0334 317 :HLDPETQ 1e39A 475 :GKDTDFE T0334 324 :PLNRIRFRVG 1e39A 493 :NYYAIEVTPG T0334 334 :RNRRAWVGNCVSIG 1e39A 520 :NAKKQVIPGLYGAG T0334 348 :TSSCFVEPLESTGIYFVYAALYQLVKHF 1e39A 537 :GGVHGANRLGGNAISDIITFGRLAGEEA Number of specific fragments extracted= 28 number of extra gaps= 1 total=3040 Will force an alignment to be made, even if fragment is small Number of alignments=134 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1e39A/T0334-1e39A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0334 read from 1e39A/T0334-1e39A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1e39A read from 1e39A/T0334-1e39A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1e39A in template set Warning: unaligning (T0334)N207 because of BadResidue code BAD_PEPTIDE in next template residue (1e39A)V289 Warning: unaligning (T0334)I208 because of BadResidue code BAD_PEPTIDE at template residue (1e39A)V289 T0334 4 :KIDKILIVGGGTAGWMAASYLGK 1e39A 125 :DTVDVVVVGSGGAGFSAAISATD T0334 30 :GTADITLLQAPD 1e39A 148 :SGAKVILIEKEP T0334 44 :TLGVGEATI 1e39A 160 :VIGGNAKLA T0334 57 :TAF 1e39A 178 :DQQ T0334 61 :DFLGI 1e39A 181 :KAKKI T0334 66 :PEDE 1e39A 188 :SPEL T0334 110 :SFGLLKYHEQIPLSHYWFDRSY 1e39A 192 :MFEDTMKGGQNINDPALVKVLS T0334 137 :EPFDYACYKEPVILDANRSPRRLDGSKVTN 1e39A 214 :SHSKDSVDWMTAMGADLTDVGMMGGASVNR T0334 169 :WHF 1e39A 244 :AHR T0334 172 :DAHLVADFLRRFATEKLGVRHVEDRVEHVQRDANG 1e39A 253 :VGAHVVQVLYDNAVKRNIDLRMNTRGIEVLKDDKG T0334 209 :ESVRT 1e39A 290 :KGILV T0334 214 :ATGR 1e39A 297 :MYKG T0334 218 :VFDADLFVDCSGFRG 1e39A 303 :WVKADAVILATGGFA T0334 233 :LLINK 1e39A 322 :RVAKL T0334 243 :FLDMSDHLLND 1e39A 327 :DPSLKGFISTN T0334 307 :EAVREFCEMWHLDP 1e39A 463 :ETVARYNSLVSSGK T0334 322 :TQ 1e39A 477 :DT T0334 324 :PLNRIRFRVGRNRRA 1e39A 493 :NYYAIEVTPGVHHTM T0334 339 :WVGNCVSIGTSSCFVEP 1e39A 525 :VIPGLYGAGEVTGGVHG T0334 356 :LESTGIYFVYAALYQLVKHFPD 1e39A 545 :LGGNAISDIITFGRLAGEEAAK Number of specific fragments extracted= 20 number of extra gaps= 1 total=3060 Will force an alignment to be made, even if fragment is small Number of alignments=135 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1q9iA/T0334-1q9iA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1q9iA expands to /projects/compbio/data/pdb/1q9i.pdb.gz 1q9iA:# T0334 read from 1q9iA/T0334-1q9iA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1q9iA read from 1q9iA/T0334-1q9iA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1q9iA to template set # found chain 1q9iA in template set Warning: unaligning (T0334)I42 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1q9iA)G162 Warning: unaligning (T0334)P43 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1q9iA)G162 Warning: unaligning (T0334)P66 because of BadResidue code BAD_PEPTIDE in next template residue (1q9iA)W176 Warning: unaligning (T0334)E67 because of BadResidue code BAD_PEPTIDE at template residue (1q9iA)W176 T0334 3 :GKID 1q9iA 122 :APHD T0334 7 :KILIVGGGTAGWMAASYLGK 1q9iA 128 :DVVVVGSGGAGFSAAISATD T0334 29 :QGT 1q9iA 148 :SGA T0334 33 :DITLLQAPD 1q9iA 151 :KVILIEKEP T0334 44 :TL 1q9iA 163 :GN T0334 59 :FFDFLGI 1q9iA 168 :AAGGMNA T0334 68 :DEWMRECNASYKVAIKFINWRTAGEGTS 1q9iA 177 :TDQQKAKKITDSPELMFEDTMKGGQNIN T0334 96 :EARELDGGPDHFYHSFGLL 1q9iA 222 :WMTAMGADLTDVGMMGGAS T0334 115 :KYHE 1q9iA 246 :RPTG T0334 152 :AN 1q9iA 251 :CG T0334 172 :DAHLVADFLRRFA 1q9iA 253 :VGAHVVQVLYDNA T0334 186 :EKLGVRHVED 1q9iA 266 :VKRNIDLRMN T0334 196 :RVEHVQRDANGNIESVRTA 1q9iA 277 :RGIEVLKDDKGTVKGILVK T0334 215 :T 1q9iA 297 :M T0334 216 :GR 1q9iA 299 :KG T0334 218 :VFDADLFVDCSGFRG 1q9iA 303 :WVKADAVILATGGFA T0334 233 :LLINKAM 1q9iA 321 :ERVAKLD T0334 264 :DDANGVEPFTSAIAMK 1q9iA 328 :PSLKGFISTNQPGAVG T0334 280 :SGWTWKIPM 1q9iA 359 :MQYIQAHPT T0334 289 :LGR 1q9iA 371 :KGG T0334 292 :FGTGYVYSSRFATE 1q9iA 383 :NGAILVNREGKRFV T0334 306 :DEAVREFCEM 1q9iA 462 :TETVARYNSL T0334 316 :WHLDPETQPLNRIRF 1q9iA 473 :SSGKDTDFERPNLPR T0334 331 :RVGRNR 1q9iA 503 :VHHTMG T0334 337 :RAWVGNCVSIGTSSCFVEP 1q9iA 523 :KQVIPGLYGAGEVTGGVHG T0334 356 :LESTGIYFVYAALYQLVKHFP 1q9iA 545 :LGGNAISDIITFGRLAGEEAA Number of specific fragments extracted= 26 number of extra gaps= 2 total=3086 Will force an alignment to be made, even if fragment is small Number of alignments=136 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1q9iA/T0334-1q9iA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0334 read from 1q9iA/T0334-1q9iA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1q9iA read from 1q9iA/T0334-1q9iA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1q9iA in template set Warning: unaligning (T0334)P43 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1q9iA)G162 Warning: unaligning (T0334)T44 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1q9iA)G162 T0334 4 :KIDKILIVGGGTAGWMAASYLGK 1q9iA 125 :DTVDVVVVGSGGAGFSAAISATD T0334 30 :GTADITLLQAPDI 1q9iA 148 :SGAKVILIEKEPV T0334 45 :LGVGEATI 1q9iA 163 :GNAKLAAG T0334 57 :TAF 1q9iA 178 :DQQ T0334 61 :DFLGI 1q9iA 181 :KAKKI T0334 66 :PEDEWMRECNA 1q9iA 188 :SPELMFEDTMK T0334 77 :SYKVAIKFINWR 1q9iA 208 :LVKVLSSHSKDS T0334 123 :SHYWFDRSYR 1q9iA 220 :VDWMTAMGAD T0334 141 :YACYKEPVI 1q9iA 230 :LTDVGMMGG T0334 155 :SPRRL 1q9iA 239 :ASVNR T0334 162 :SKVTNYAW 1q9iA 244 :AHRPTGGC T0334 171 :FDAHLVADFLRRFAT 1q9iA 252 :GVGAHVVQVLYDNAV T0334 187 :KLGVRHVED 1q9iA 267 :KRNIDLRMN T0334 196 :RVEHVQRDANGNIESVRTA 1q9iA 277 :RGIEVLKDDKGTVKGILVK T0334 215 :TG 1q9iA 299 :KG T0334 217 :RVFDADLFVDCSGFRGL 1q9iA 302 :YWVKADAVILATGGFAK T0334 234 :L 1q9iA 323 :V T0334 236 :NKAM 1q9iA 324 :AKLD T0334 244 :LDMSDHLLNDS 1q9iA 328 :PSLKGFISTNQ T0334 267 :NGVE 1q9iA 339 :PGAV T0334 271 :PFTSAIAMKSGWTWKIPM 1q9iA 350 :ENAGGALKDMQYIQAHPT T0334 289 :LGRFGT 1q9iA 371 :KGGVMV T0334 295 :GYVYSSRFATE 1q9iA 384 :GAILVNREGKR T0334 306 :DEAVREFCEMW 1q9iA 459 :KALTETVARYN T0334 317 :HLDPETQ 1q9iA 475 :GKDTDFE T0334 324 :PLNRIRFRVG 1q9iA 493 :NYYAIEVTPG T0334 334 :RNRRAWVGNCVSIG 1q9iA 520 :NAKKQVIPGLYGAG T0334 348 :TSSCFVEPLESTGIYFVYAALYQLVKHF 1q9iA 537 :GGVHGANRLGGNAISDIITFGRLAGEEA Number of specific fragments extracted= 28 number of extra gaps= 1 total=3114 Will force an alignment to be made, even if fragment is small Number of alignments=137 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1q9iA/T0334-1q9iA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0334 read from 1q9iA/T0334-1q9iA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1q9iA read from 1q9iA/T0334-1q9iA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1q9iA in template set Warning: unaligning (T0334)L45 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1q9iA)G162 Warning: unaligning (T0334)G46 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1q9iA)G162 T0334 5 :IDKILIVGGGTAGWMAASYLGK 1q9iA 126 :TVDVVVVGSGGAGFSAAISATD T0334 30 :GTADITLLQAPDI 1q9iA 148 :SGAKVILIEKEPV T0334 47 :VGEATI 1q9iA 163 :GNAKLA T0334 53 :P 1q9iA 178 :D T0334 58 :AF 1q9iA 179 :QQ T0334 61 :DFLGIPE 1q9iA 181 :KAKKITD T0334 68 :DEW 1q9iA 189 :PEL T0334 110 :SFGLLKYHEQIPLSHYWFDRSY 1q9iA 192 :MFEDTMKGGQNINDPALVKVLS T0334 137 :EPFDYACYKEPVILDANRSPRRLDGSKVT 1q9iA 214 :SHSKDSVDWMTAMGADLTDVGMMGGASVN T0334 168 :AWHF 1q9iA 243 :RAHR T0334 172 :DAHLVADFLRRFATEKLGVRHVEDRVEHVQRDANGNIESVRT 1q9iA 253 :VGAHVVQVLYDNAVKRNIDLRMNTRGIEVLKDDKGTVKGILV T0334 214 :ATGR 1q9iA 297 :MYKG T0334 218 :VFDADLFVDCSGFRG 1q9iA 303 :WVKADAVILATGGFA T0334 233 :LLINK 1q9iA 322 :RVAKL T0334 243 :FLDMSDHLLND 1q9iA 327 :DPSLKGFISTN T0334 307 :EAVREFCEMWHLDP 1q9iA 463 :ETVARYNSLVSSGK T0334 322 :TQ 1q9iA 477 :DT T0334 324 :PLNRIRFRVGRNRRA 1q9iA 493 :NYYAIEVTPGVHHTM T0334 339 :WVGNCVSIGTSSCFVEP 1q9iA 525 :VIPGLYGAGEVTGGVHG T0334 356 :LESTGIYFVYAALYQLVKHFPD 1q9iA 545 :LGGNAISDIITFGRLAGEEAAK Number of specific fragments extracted= 20 number of extra gaps= 1 total=3134 Will force an alignment to be made, even if fragment is small Number of alignments=138 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1an9A/T0334-1an9A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1an9A expands to /projects/compbio/data/pdb/1an9.pdb.gz 1an9A:# T0334 read from 1an9A/T0334-1an9A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1an9A read from 1an9A/T0334-1an9A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1an9A to template set # found chain 1an9A in template set Warning: unaligning (T0334)Q29 because of BadResidue code BAD_PEPTIDE in next template residue (1an9A)P29 Warning: unaligning (T0334)G30 because of BadResidue code BAD_PEPTIDE at template residue (1an9A)P29 T0334 7 :KILIVGGGTAGWMAASYLGKAL 1an9A 2 :RVVVIGAGVIGLSTALCIHERY T0334 31 :T 1an9A 30 :L T0334 33 :DITLLQAP 1an9A 31 :DVKVYADR T0334 46 :GVGEATIPNLQTAFFDFLGIPED 1an9A 39 :FTPFTTTDVAAGLWQPYTSEPSN T0334 70 :WMREC 1an9A 63 :QEANW T0334 115 :KYHE 1an9A 70 :QTFN T0334 139 :FDYACYKEP 1an9A 74 :YLLSHIGSP T0334 148 :VILD 1an9A 94 :GYNL T0334 152 :ANRSPRRLDGSKVTNYAWHF 1an9A 99 :REAVPDPYWKDMVLGFRKLT T0334 172 :DAHLVADFLRRFA 1an9A 140 :EGRKYLQWLTERL T0334 186 :EKLGVRHVEDRVE 1an9A 153 :TERGVKFFLRKVE T0334 203 :DAN 1an9A 172 :RGG T0334 221 :ADLFVDCSGFRGLLI 1an9A 175 :ADVIINCTGVWAGVL T0334 239 :MEEPFLDM 1an9A 190 :QPDPLLQP T0334 247 :SDHLLND 1an9A 200 :GQIIKVD T0334 280 :SGWTWKIPMLGRFGTGYVYSSRFATE 1an9A 224 :YNSPYIIPGLQAVTLGGTFQVGNWNE T0334 306 :DEAVREFCEM 1an9A 253 :IQDHNTIWEG T0334 316 :WHLDPETQPLNRIRFRVGRNR 1an9A 264 :CRLEPTLKDAKIVGEYTGFRP T0334 337 :RAWVG 1an9A 295 :QLRFG T0334 342 :NCVSIGT 1an9A 302 :NTEVIHN T0334 354 :EPLESTGIYFVYAALYQLVKH 1an9A 309 :YGHGGYGLTIHWGCALEVAKL T0334 434 :IDMYRAG 1an9A 330 :FGKVLEE Number of specific fragments extracted= 22 number of extra gaps= 1 total=3156 Will force an alignment to be made, even if fragment is small Number of alignments=139 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1an9A/T0334-1an9A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0334 read from 1an9A/T0334-1an9A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1an9A read from 1an9A/T0334-1an9A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1an9A in template set Warning: unaligning (T0334)D6 because first residue in template chain is (1an9A)M1 Warning: unaligning (T0334)G30 because of BadResidue code BAD_PEPTIDE in next template residue (1an9A)P29 Warning: unaligning (T0334)T31 because of BadResidue code BAD_PEPTIDE at template residue (1an9A)P29 T0334 7 :KILIVGGGTAGWMAASYLGKALQ 1an9A 2 :RVVVIGAGVIGLSTALCIHERYH T0334 32 :ADITLLQAPDIPTLG 1an9A 30 :LDVKVYADRFTPFTT T0334 47 :VGEATIPN 1an9A 47 :VAAGLWQP T0334 61 :DFLGIPEDEWMRECNASYKVAI 1an9A 55 :YTSEPSNPQEANWNQQTFNYLL T0334 96 :EARELDGGP 1an9A 77 :SHIGSPNAA T0334 105 :DHFYHSFGLLKYHEQ 1an9A 93 :SGYNLFREAVPDPYW T0334 141 :YACYKEPVI 1an9A 108 :KDMVLGFRK T0334 154 :RSPRRLDGSKVTNYAW 1an9A 117 :LTPRELDMFPDYRYGW T0334 170 :HFDAHLVADFLRRFA 1an9A 138 :ILEGRKYLQWLTERL T0334 186 :EKLGVRHVEDRVEH 1an9A 153 :TERGVKFFLRKVES T0334 205 :NG 1an9A 173 :GG T0334 221 :ADLFVDCSGFRGLLI 1an9A 175 :ADVIINCTGVWAGVL T0334 244 :LDMSDH 1an9A 190 :QPDPLL T0334 250 :LLNDSAVATQV 1an9A 197 :PGRGQIIKVDA T0334 267 :NGVEPFTSAIAMKS 1an9A 208 :PWLKNFIITHDLER T0334 281 :GWTWKIPMLGRFGTGYVYSSRFATE 1an9A 225 :NSPYIIPGLQAVTLGGTFQVGNWNE T0334 306 :DEAVREFCEMW 1an9A 253 :IQDHNTIWEGC T0334 317 :HLDPETQPLNRIRFRVG 1an9A 265 :RLEPTLKDAKIVGEYTG T0334 334 :RNRRAWVG 1an9A 292 :EREQLRFG T0334 342 :NCVSIG 1an9A 302 :NTEVIH T0334 353 :VEPLESTGIYFVYAALYQLVKHF 1an9A 308 :NYGHGGYGLTIHWGCALEVAKLF T0334 382 :PVLTAR 1an9A 331 :GKVLEE Number of specific fragments extracted= 22 number of extra gaps= 1 total=3178 Will force an alignment to be made, even if fragment is small Number of alignments=140 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1an9A/T0334-1an9A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0334 read from 1an9A/T0334-1an9A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1an9A read from 1an9A/T0334-1an9A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1an9A in template set Warning: unaligning (T0334)G30 because of BadResidue code BAD_PEPTIDE in next template residue (1an9A)P29 Warning: unaligning (T0334)T31 because of BadResidue code BAD_PEPTIDE at template residue (1an9A)P29 T0334 7 :KILIVGGGTAGWMAASYLGKAL 1an9A 2 :RVVVIGAGVIGLSTALCIHERY T0334 29 :Q 1an9A 27 :L T0334 32 :ADITLLQAPDIPT 1an9A 30 :LDVKVYADRFTPF T0334 48 :GEATI 1an9A 48 :AAGLW T0334 53 :PNLQTAFFDFLGI 1an9A 69 :QQTFNYLLSHIGS T0334 75 :NASYKVAIKFINWRTAGEGTSEARELDGGP 1an9A 87 :MGLTPVSGYNLFREAVPDPYWKDMVLGFRK T0334 154 :RSPRRLDGSKVTNYAW 1an9A 117 :LTPRELDMFPDYRYGW T0334 170 :HFDAHLVADFLRRFATEKLGVRHVED 1an9A 138 :ILEGRKYLQWLTERLTERGVKFFLRK T0334 197 :VEH 1an9A 164 :VES T0334 205 :NG 1an9A 173 :GG T0334 221 :ADLFVDCSGFRGLLI 1an9A 175 :ADVIINCTGVWAGVL T0334 245 :DMSDHLLNDSAVATQVPHD 1an9A 190 :QPDPLLQPGRGQIIKVDAP T0334 268 :GVEPFTSAIAMKSGWT 1an9A 209 :WLKNFIITHDLERGIY T0334 284 :WKIPMLGRFGTGYVYSSRFATED 1an9A 228 :YIIPGLQAVTLGGTFQVGNWNEI T0334 307 :EAVREFCEMW 1an9A 254 :QDHNTIWEGC T0334 317 :HLDPETQPLNRIRFRVGR 1an9A 265 :RLEPTLKDAKIVGEYTGF T0334 335 :NRRAWV 1an9A 293 :REQLRF T0334 341 :GNCVSIGTSSC 1an9A 301 :SNTEVIHNYGH T0334 357 :ESTGIYFVYAALYQLVKHFP 1an9A 312 :GGYGLTIHWGCALEVAKLFG Number of specific fragments extracted= 19 number of extra gaps= 1 total=3197 Will force an alignment to be made, even if fragment is small Number of alignments=141 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1y0pA/T0334-1y0pA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1y0pA expands to /projects/compbio/data/pdb/1y0p.pdb.gz 1y0pA:# T0334 read from 1y0pA/T0334-1y0pA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1y0pA read from 1y0pA/T0334-1y0pA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1y0pA to template set # found chain 1y0pA in template set Warning: unaligning (T0334)I34 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1y0pA)I153 Warning: unaligning (T0334)T35 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1y0pA)I153 Warning: unaligning (T0334)I42 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1y0pA)G162 Warning: unaligning (T0334)P43 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1y0pA)G162 Warning: unaligning (T0334)P66 because of BadResidue code BAD_PEPTIDE in next template residue (1y0pA)W176 Warning: unaligning (T0334)E67 because of BadResidue code BAD_PEPTIDE at template residue (1y0pA)W176 T0334 3 :GKID 1y0pA 122 :APHD T0334 7 :KILIVGGGTAGWMAASYLGK 1y0pA 128 :DVVVVGSGGAGFSAAISATD T0334 29 :QGT 1y0pA 148 :SGA T0334 33 :D 1y0pA 151 :K T0334 36 :LLQAPD 1y0pA 154 :LIEKEP T0334 44 :TL 1y0pA 163 :GN T0334 59 :FFDFLGI 1y0pA 168 :AAGGMNA T0334 68 :DEWMRECNASYKVAIKFINWRTAGEGTS 1y0pA 177 :TDQQKAKKITDSPELMFEDTMKGGQNIN T0334 96 :EARELDGGPDHFYHSFGLL 1y0pA 222 :WMTAMGADLTDVGMMGGAS T0334 115 :KYHE 1y0pA 246 :RPTG T0334 152 :AN 1y0pA 251 :AG T0334 172 :DAHLVADFLRRFA 1y0pA 253 :VGAHVVQVLYDNA T0334 186 :EKLGVRHVED 1y0pA 266 :VKRNIDLRMN T0334 196 :RVEHVQRDANGNIESVRTA 1y0pA 277 :RGIEVLKDDKGTVKGILVK T0334 215 :T 1y0pA 297 :M T0334 216 :GR 1y0pA 299 :KG T0334 218 :VFDADLFVDCSGFRG 1y0pA 303 :WVKADAVILATGGFA T0334 233 :LLINKAM 1y0pA 321 :ERVAKLD T0334 264 :DDANGVEPFTSAIAMK 1y0pA 328 :PSLKGFISTNQPGAVG T0334 280 :SGWTWKIPM 1y0pA 359 :MQYIQAHPT T0334 289 :LGR 1y0pA 371 :KGG T0334 292 :FGTGYVYSSRFATE 1y0pA 383 :NGAILVNREGKRFV T0334 306 :DEAVREFCEM 1y0pA 462 :TETVARYNSL T0334 316 :WHLDPETQPLNRIRF 1y0pA 473 :SSGKDTDFERPNLPR T0334 331 :RVGRNR 1y0pA 503 :VHHTMG T0334 337 :RAWVGNCVSIGTSSCFVEP 1y0pA 523 :KQVIPGLYGAGEVTGGVHG T0334 356 :LESTGIYFVYAALYQLVKHF 1y0pA 545 :LGGNAISDIITFGRLAGEEA Number of specific fragments extracted= 27 number of extra gaps= 3 total=3224 Will force an alignment to be made, even if fragment is small Number of alignments=142 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1y0pA/T0334-1y0pA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0334 read from 1y0pA/T0334-1y0pA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1y0pA read from 1y0pA/T0334-1y0pA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1y0pA in template set Warning: unaligning (T0334)I34 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1y0pA)I153 Warning: unaligning (T0334)T35 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1y0pA)I153 Warning: unaligning (T0334)P43 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1y0pA)G162 Warning: unaligning (T0334)T44 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1y0pA)G162 T0334 4 :KIDKILIVGGGTAGWMAASYLGK 1y0pA 125 :DTVDVVVVGSGGAGFSAAISATD T0334 30 :GTAD 1y0pA 148 :SGAK T0334 36 :LLQAPDI 1y0pA 154 :LIEKEPV T0334 45 :LGVGEATI 1y0pA 163 :GNAKLAAG T0334 57 :TAF 1y0pA 178 :DQQ T0334 61 :DFLGI 1y0pA 181 :KAKKI T0334 66 :PEDEWMRECNA 1y0pA 188 :SPELMFEDTMK T0334 77 :SYKVAIKFINWR 1y0pA 208 :LVKVLSSHSKDS T0334 123 :SHYWFDRSYR 1y0pA 220 :VDWMTAMGAD T0334 141 :YACYKEPVI 1y0pA 230 :LTDVGMMGG T0334 155 :SPRR 1y0pA 239 :ASVN T0334 162 :SKVTNYAW 1y0pA 244 :AHRPTGGA T0334 171 :FDAHLVADFLRRFAT 1y0pA 252 :GVGAHVVQVLYDNAV T0334 187 :KLGVRHVED 1y0pA 267 :KRNIDLRMN T0334 196 :RVEHVQRDANGNIESVRTA 1y0pA 277 :RGIEVLKDDKGTVKGILVK T0334 215 :TG 1y0pA 299 :KG T0334 217 :RVFDADLFVDCSGFRGL 1y0pA 302 :YWVKADAVILATGGFAK T0334 234 :L 1y0pA 323 :V T0334 236 :NKAM 1y0pA 324 :AKLD T0334 244 :LDMSDHLLNDS 1y0pA 328 :PSLKGFISTNQ T0334 267 :NGVE 1y0pA 339 :PGAV T0334 271 :PFTSAIAMKSGWTWKIPM 1y0pA 350 :ENAGGALKDMQYIQAHPT T0334 289 :LGRFGT 1y0pA 371 :KGGVMV T0334 295 :GYVYSSRFATE 1y0pA 384 :GAILVNREGKR T0334 306 :DEAVREFCEMW 1y0pA 459 :KALTETVARYN T0334 317 :HLDPETQ 1y0pA 475 :GKDTDFE T0334 324 :PLNRIRFRVG 1y0pA 493 :NYYAIEVTPG T0334 334 :RNRRAWVGNCVSIG 1y0pA 520 :NAKKQVIPGLYGAG T0334 348 :TSSCFVEPLESTGIYFVYAALYQLVKHF 1y0pA 537 :GGVHGANRLGGNAISDIITFGRLAGEEA Number of specific fragments extracted= 29 number of extra gaps= 2 total=3253 Will force an alignment to be made, even if fragment is small Number of alignments=143 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1y0pA/T0334-1y0pA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0334 read from 1y0pA/T0334-1y0pA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1y0pA read from 1y0pA/T0334-1y0pA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1y0pA in template set Warning: unaligning (T0334)I34 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1y0pA)I153 Warning: unaligning (T0334)T35 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1y0pA)I153 Warning: unaligning (T0334)L45 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1y0pA)G162 Warning: unaligning (T0334)G46 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1y0pA)G162 T0334 5 :IDKILIVGGGTAGWMAASYLGK 1y0pA 126 :TVDVVVVGSGGAGFSAAISATD T0334 30 :GTAD 1y0pA 148 :SGAK T0334 36 :LLQAPD 1y0pA 154 :LIEKEP T0334 44 :T 1y0pA 160 :V T0334 47 :VGEATI 1y0pA 163 :GNAKLA T0334 58 :AF 1y0pA 179 :QQ T0334 61 :DFLGI 1y0pA 181 :KAKKI T0334 66 :PEDEWMRE 1y0pA 188 :SPELMFED T0334 114 :LKYHEQIPLSHYWFDRSY 1y0pA 196 :TMKGGQNINDPALVKVLS T0334 137 :EPFDYACYKEPVILDANRSPRRLDGSKVT 1y0pA 214 :SHSKDSVDWMTAMGADLTDVGMMGGASVN T0334 168 :AWHF 1y0pA 243 :RAHR T0334 172 :DAHLVADFLRRFATEKLGVRHVEDRVEHVQRDANGNIESVRT 1y0pA 253 :VGAHVVQVLYDNAVKRNIDLRMNTRGIEVLKDDKGTVKGILV T0334 214 :ATGR 1y0pA 297 :MYKG T0334 218 :VFDADLFVDCSGFRG 1y0pA 303 :WVKADAVILATGGFA T0334 233 :LLINK 1y0pA 322 :RVAKL T0334 243 :FLDMSDHLLND 1y0pA 327 :DPSLKGFISTN T0334 307 :EAVREFCEMWHLDP 1y0pA 463 :ETVARYNSLVSSGK T0334 322 :TQ 1y0pA 477 :DT T0334 324 :PLNRIRFRVGRNRRA 1y0pA 493 :NYYAIEVTPGVHHTM T0334 339 :WVGNCVSIGTSSCFVEP 1y0pA 525 :VIPGLYGAGEVTGGVHG T0334 356 :LESTGIYFVYAALYQLVKHFP 1y0pA 545 :LGGNAISDIITFGRLAGEEAA Number of specific fragments extracted= 21 number of extra gaps= 2 total=3274 Will force an alignment to be made, even if fragment is small Number of alignments=144 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ojaA/T0334-1ojaA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1ojaA expands to /projects/compbio/data/pdb/1oja.pdb.gz 1ojaA:# T0334 read from 1ojaA/T0334-1ojaA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ojaA read from 1ojaA/T0334-1ojaA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1ojaA to template set # found chain 1ojaA in template set Warning: unaligning (T0334)I5 because first residue in template chain is (1ojaA)N3 Warning: unaligning (T0334)D508 because last residue in template chain is (1ojaA)I501 T0334 6 :D 1ojaA 4 :K T0334 7 :KILIVGGGTAGWMAASYLGK 1ojaA 6 :DVVVVGGGISGMAAAKLLHD T0334 29 :QGT 1ojaA 26 :SGL T0334 33 :DITLLQAPD 1ojaA 29 :NVVVLEARD T0334 42 :IPTL 1ojaA 39 :VGGR T0334 46 :GVGEATIPNLQTAF 1ojaA 56 :LGGSYVGPTQNRIL T0334 139 :FDYACYKEPVILD 1ojaA 70 :RLAKELGLETYKV T0334 152 :ANRSPRRLDGSKVTNYAWHF 1ojaA 84 :EVERLIHHVKGKSYPFRGPF T0334 172 :DAHLVADFLRRFA 1ojaA 213 :GSGQVSERIMDLL T0334 186 :EK 1ojaA 226 :GD T0334 191 :RHVED 1ojaA 228 :RVKLE T0334 196 :RVEHVQRDANG 1ojaA 234 :PVIYIDQTREN T0334 209 :ESVRTATGRVFDADLFVDCSG 1ojaA 245 :VLVETLNHEMYEAKYVISAIP T0334 233 :LLINKAMEEPFLDM 1ojaA 266 :PTLGMKIHFNPPLP T0334 247 :SDHLLND 1ojaA 286 :ITRVPLG T0334 254 :SAVATQVPHDDDANG 1ojaA 295 :IKCIVYYKEPFWRKK T0334 271 :PFTS 1ojaA 310 :DYCG T0334 275 :AIAMK 1ojaA 315 :MIIDG T0334 280 :SGWTWKIPM 1ojaA 323 :PVAYTLDDT T0334 289 :LGRFGTGYVYSSRFATE 1ojaA 335 :GNYAAIMGFILAHKARK T0334 306 :DEAVREFCEM 1ojaA 358 :EERLKKLCEL T0334 316 :WHLDPETQPLNRIRF 1ojaA 372 :LGSLEALEPVHYEEK T0334 337 :RAWVGNCVSIG 1ojaA 415 :RQPVDRIYFAG T0334 348 :TSSCFVEPLESTGIYFVYAALYQLVKHFP 1ojaA 427 :ETATHWSGYMEGAVEAGERAAREILHAMG T0334 377 :DKSLN 1ojaA 459 :EDEIW T0334 443 :INAPASDDAQLYYGNFEEEFRNFWNN 1ojaA 464 :QSEPESVDVPAQPITTTFLERHLPSV T0334 497 :ESVDEVFGAVK 1ojaA 490 :PGLLRLIGLTT Number of specific fragments extracted= 27 number of extra gaps= 0 total=3301 Will force an alignment to be made, even if fragment is small Number of alignments=145 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ojaA/T0334-1ojaA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0334 read from 1ojaA/T0334-1ojaA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ojaA read from 1ojaA/T0334-1ojaA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1ojaA in template set Warning: unaligning (T0334)G3 because first residue in template chain is (1ojaA)N3 T0334 5 :IDKILIVGGGTAGWMAASYLGK 1ojaA 4 :KCDVVVVGGGISGMAAAKLLHD T0334 30 :GTADITLLQAP 1ojaA 26 :SGLNVVVLEAR T0334 41 :DI 1ojaA 38 :RV T0334 43 :PTLGVGEATIPNLQTAF 1ojaA 56 :LGGSYVGPTQNRILRLA T0334 61 :DFLGI 1ojaA 73 :KELGL T0334 96 :EARELDGGP 1ojaA 78 :ETYKVNEVE T0334 105 :DHFYHSFGLL 1ojaA 94 :GKSYPFRGPF T0334 118 :EQIPLSHYWFDR 1ojaA 114 :DHNNFWRTMDDM T0334 141 :YACYKEPVILDANRSPRR 1ojaA 126 :GREIPSDAPWKAPLAEEW T0334 170 :HFDAHLVADFLRRFA 1ojaA 211 :VGGSGQVSERIMDLL T0334 186 :EKL 1ojaA 226 :GDR T0334 192 :HVED 1ojaA 229 :VKLE T0334 196 :RVEHVQRDANG 1ojaA 234 :PVIYIDQTREN T0334 209 :ESVRTATGRVFDADLFVDCSG 1ojaA 245 :VLVETLNHEMYEAKYVISAIP T0334 236 :NKA 1ojaA 266 :PTL T0334 239 :MEEPFL 1ojaA 274 :FNPPLP T0334 246 :MSDHLLNDSAVATQVPHDDDANGV 1ojaA 287 :TRVPLGSVIKCIVYYKEPFWRKKD T0334 271 :PFTSAIAMKS 1ojaA 311 :YCGTMIIDGE T0334 281 :GWTWKIPMLGR 1ojaA 325 :AYTLDDTKPEG T0334 292 :FGTGYVYSSRFATE 1ojaA 338 :AAIMGFILAHKARK T0334 306 :DEAVREFCEMW 1ojaA 358 :EERLKKLCELY T0334 317 :HL 1ojaA 373 :GS T0334 320 :PETQPLNRIRFRVGRNRRA 1ojaA 375 :LEALEPVHYEEKNWCEEQY T0334 339 :WVGNCVSIG 1ojaA 417 :PVDRIYFAG T0334 348 :TSSCFVEPLESTGIYFVYAALYQLVKHFPD 1ojaA 427 :ETATHWSGYMEGAVEAGERAAREILHAMGK T0334 378 :KSLNP 1ojaA 460 :DEIWQ T0334 412 :RTDT 1ojaA 465 :SEPE T0334 478 :LGLVPDAPSPRLAHMPQ 1ojaA 472 :VPAQPITTTFLERHLPS T0334 503 :FGAVKDRQRNLL 1ojaA 489 :VPGLLRLIGLTT Number of specific fragments extracted= 29 number of extra gaps= 0 total=3330 Will force an alignment to be made, even if fragment is small Number of alignments=146 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ojaA/T0334-1ojaA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0334 read from 1ojaA/T0334-1ojaA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ojaA read from 1ojaA/T0334-1ojaA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1ojaA in template set Warning: unaligning (T0334)K4 because first residue in template chain is (1ojaA)N3 T0334 5 :IDKILIVGGGTAGWMAASYLGK 1ojaA 4 :KCDVVVVGGGISGMAAAKLLHD T0334 30 :GTADITLLQ 1ojaA 26 :SGLNVVVLE T0334 39 :APDIPT 1ojaA 36 :RDRVGG T0334 45 :LGVGEA 1ojaA 54 :VDLGGS T0334 51 :TIPNLQTAF 1ojaA 64 :TQNRILRLA T0334 61 :DFLGIP 1ojaA 73 :KELGLE T0334 77 :SYKVAI 1ojaA 79 :TYKVNE T0334 83 :KFINWRTAGEGTSEARELDGGPDHFYHSFGLLKYHEQI 1ojaA 88 :LIHHVKGKSYPFRGPFPPVWNPITYLDHNNFWRTMDDM T0334 121 :PLSHYWFDRSYRGKTVEPFDYACYKEP 1ojaA 146 :MTMKELLDKLCWTESAKQLATLFVNLC T0334 148 :VILDANRSPRRLDGSKVTNYAWHFDAHLVADFLRRFA 1ojaA 189 :VKQCGGTTRIISTTNGGQERKFVGGSGQVSERIMDLL T0334 191 :RHVEDRVEHVQRDANG 1ojaA 229 :VKLERPVIYIDQTREN T0334 209 :ESVRTATGRVFDADLFVDCSGFRG 1ojaA 245 :VLVETLNHEMYEAKYVISAIPPTL T0334 233 :LLINKAMEEP 1ojaA 280 :MMRNQMITRV T0334 243 :FLDMSDHLLNDSAV 1ojaA 303 :EPFWRKKDYCGTMI T0334 257 :ATQV 1ojaA 327 :TLDD T0334 264 :DDANGVEPFTSAIAMK 1ojaA 331 :TKPEGNYAAIMGFILA T0334 301 :RFATEDEAVREFCEMWH 1ojaA 353 :ARLTKEERLKKLCELYA T0334 318 :LDPETQPLNRIRF 1ojaA 373 :GSLEALEPVHYEE T0334 331 :RVGRNRRAWV 1ojaA 403 :PPGILTQYGR T0334 341 :GNCVSIGT 1ojaA 419 :DRIYFAGT T0334 349 :SSCFVEPLESTGIYFVYAALYQLVKHFP 1ojaA 428 :TATHWSGYMEGAVEAGERAAREILHAMG T0334 448 :SDDAQLYY 1ojaA 457 :IPEDEIWQ T0334 468 :NSNYYCVLAGLGLVPDAPSPR 1ojaA 465 :SEPESVDVPAQPITTTFLERH T0334 489 :LAHMPQATESVD 1ojaA 489 :VPGLLRLIGLTT Number of specific fragments extracted= 24 number of extra gaps= 0 total=3354 Will force an alignment to be made, even if fragment is small Number of alignments=147 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2phh/T0334-2phh-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2phh expands to /projects/compbio/data/pdb/2phh.pdb.gz 2phh:Warning: there is no chain 2phh will retry with 2phhA # T0334 read from 2phh/T0334-2phh-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2phh read from 2phh/T0334-2phh-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2phh to template set # found chain 2phh in template set Warning: unaligning (T0334)I5 because first residue in template chain is (2phh)M1 Warning: unaligning (T0334)D61 because of BadResidue code BAD_PEPTIDE in next template residue (2phh)A45 Warning: unaligning (T0334)F62 because of BadResidue code BAD_PEPTIDE at template residue (2phh)A45 Warning: unaligning (T0334)L188 because of BadResidue code BAD_PEPTIDE in next template residue (2phh)G117 Warning: unaligning (T0334)G189 because of BadResidue code BAD_PEPTIDE at template residue (2phh)G117 Warning: unaligning (T0334)T215 because of BadResidue code BAD_PEPTIDE in next template residue (2phh)G145 Warning: unaligning (T0334)G216 because of BadResidue code BAD_PEPTIDE at template residue (2phh)G145 Warning: unaligning (T0334)H406 because of BadResidue code BAD_PEPTIDE in next template residue (2phh)T347 Warning: unaligning (T0334)F407 because of BadResidue code BAD_PEPTIDE at template residue (2phh)T347 T0334 6 :D 2phh 2 :K T0334 7 :KILIVGGGTAGWMAASYLGK 2phh 4 :QVAIIGAGPSGLLLGQLLHK T0334 29 :QGT 2phh 24 :AGI T0334 33 :DITLLQAPD 2phh 27 :DNVILERQT T0334 52 :IPNLQTAF 2phh 36 :PDYVLGRI T0334 63 :LG 2phh 46 :GV T0334 69 :EWMRECNAS 2phh 54 :DLLREAGVD T0334 139 :FDYACYKEP 2phh 63 :RRMARDGLV T0334 148 :VILD 2phh 77 :IAFA T0334 152 :ANRSPRRLDGSKVTNYAWH 2phh 82 :QRRRIDLKRLSGGKTVTVY T0334 172 :DAHLVADFLRRFA 2phh 101 :GQTEVTRDLMEAR T0334 186 :EK 2phh 114 :EA T0334 190 :VRHVED 2phh 118 :ATTVYQ T0334 196 :RVEHVQRDANGNIE 2phh 125 :AEVRLHDLQGERPY T0334 211 :VRTA 2phh 139 :VTFE T0334 217 :R 2phh 146 :E T0334 218 :VFDADLFVDCSGFRGLLI 2phh 149 :RLDCDYIAGCDGFHGISR T0334 237 :KAMEEPFLDM 2phh 167 :QSIPAERLKV T0334 247 :SDHLLND 2phh 178 :ERVYPFG T0334 254 :SAVATQVPHDD 2phh 186 :LGLLADTPPVS T0334 271 :PFTSAIAMKSGWTWKIPM 2phh 197 :HELIYANHPRGFALCSQR T0334 289 :LGR 2phh 216 :ATR T0334 292 :FGTGYVYSSRFATEDEAVREFCEM 2phh 223 :VQVPLTEKVEDWSDERFWTELKAR T0334 316 :WHLD 2phh 249 :AEVA T0334 321 :ETQPLNRIRFRVGRNRRAWVGNCVSIGTSSCFVEPLESTGIYFVYAALYQLVKHFP 2phh 259 :PSLEKSIAPLRSFVVEPMQHGRLFLAGDAAHIVPPTGAKGLNLAASDVSTLYRLLL T0334 378 :KSLNPVLTARFNREIETMFDDTRDFIQA 2phh 318 :REGRGELLERYSAICLRRIWKAERFSWW T0334 408 :YFSPRTDTP 2phh 348 :SVLHRFPDT T0334 417 :FW 2phh 359 :FS T0334 507 :KDRQRNLLETLPSLHEFLRQ 2phh 361 :QRIQQTELEYYLGSEAGLAT Number of specific fragments extracted= 29 number of extra gaps= 4 total=3383 Will force an alignment to be made, even if fragment is small Number of alignments=148 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2phh/T0334-2phh-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0334 read from 2phh/T0334-2phh-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2phh read from 2phh/T0334-2phh-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2phh in template set Warning: unaligning (T0334)K4 because first residue in template chain is (2phh)M1 Warning: unaligning (T0334)V47 because of BadResidue code BAD_PEPTIDE in next template residue (2phh)A45 Warning: unaligning (T0334)G48 because of BadResidue code BAD_PEPTIDE at template residue (2phh)A45 Warning: unaligning (T0334)F139 because of BadResidue code BAD_PEPTIDE in next template residue (2phh)E76 Warning: unaligning (T0334)D140 because of BadResidue code BAD_PEPTIDE at template residue (2phh)E76 Warning: unaligning (T0334)L188 because of BadResidue code BAD_PEPTIDE in next template residue (2phh)G117 Warning: unaligning (T0334)G189 because of BadResidue code BAD_PEPTIDE at template residue (2phh)G117 Warning: unaligning (T0334)T215 because of BadResidue code BAD_PEPTIDE in next template residue (2phh)G145 Warning: unaligning (T0334)G216 because of BadResidue code BAD_PEPTIDE at template residue (2phh)G145 Warning: unaligning (T0334)H406 because of BadResidue code BAD_PEPTIDE in next template residue (2phh)T347 Warning: unaligning (T0334)F407 because of BadResidue code BAD_PEPTIDE at template residue (2phh)T347 T0334 5 :IDKILIVGGGTAGWMAASYLGKA 2phh 2 :KTQVAIIGAGPSGLLLGQLLHKA T0334 31 :TADITLLQAPDI 2phh 25 :GIDNVILERQTP T0334 43 :PTLG 2phh 40 :LGRI T0334 49 :EATIPNLQTAF 2phh 46 :GVLEQGMVDLL T0334 61 :DFLGI 2phh 57 :REAGV T0334 123 :SHYWFDRSYR 2phh 62 :DRRMARDGLV T0334 136 :VEP 2phh 72 :HEG T0334 141 :YACYKEPVILD 2phh 77 :IAFAGQRRRID T0334 155 :SPRRLDG 2phh 88 :LKRLSGG T0334 166 :NYAWHFDAHLVADFLRRFA 2phh 95 :KTVTVYGQTEVTRDLMEAR T0334 186 :EK 2phh 114 :EA T0334 190 :VRHVED 2phh 118 :ATTVYQ T0334 196 :RVEHVQR 2phh 125 :AEVRLHD T0334 203 :DANG 2phh 133 :QGER T0334 209 :ESVRTA 2phh 137 :PYVTFE T0334 217 :RVFDADLFVDCSGFRGLL 2phh 148 :LRLDCDYIAGCDGFHGIS T0334 236 :NKAMEEPFL 2phh 166 :RQSIPAERL T0334 245 :DMSDHLL 2phh 176 :VFERVYP T0334 253 :DSAVATQV 2phh 183 :FGWLGLLA T0334 265 :DANGVEPFTSAIAMKSGWTWKIPMLGR 2phh 191 :DTPPVSHELIYANHPRGFALCSQRSAT T0334 292 :FGTGYVYSS 2phh 219 :SRYYVQVPL T0334 301 :RFATEDEAVREFCEMW 2phh 232 :EDWSDERFWTELKARL T0334 321 :ETQ 2phh 254 :KLV T0334 324 :PLNRIRFRVGRNRRAWVGNCVSIGTSSCFVEPLESTGIYFVYAALYQLVKHFPD 2phh 262 :EKSIAPLRSFVVEPMQHGRLFLAGDAAHIVPPTGAKGLNLAASDVSTLYRLLLK T0334 378 :KSLNPVLTARFNREIETMFDDTRDFIQA 2phh 318 :REGRGELLERYSAICLRRIWKAERFSWW T0334 408 :YFSPRTD 2phh 348 :SVLHRFP T0334 415 :TPFWR 2phh 357 :DAFSQ T0334 428 :DGMQEKIDMYRAG 2phh 362 :RIQQTELEYYLGS Number of specific fragments extracted= 28 number of extra gaps= 5 total=3411 Will force an alignment to be made, even if fragment is small Number of alignments=149 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2phh/T0334-2phh-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0334 read from 2phh/T0334-2phh-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2phh read from 2phh/T0334-2phh-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2phh in template set Warning: unaligning (T0334)G46 because of BadResidue code BAD_PEPTIDE in next template residue (2phh)A45 Warning: unaligning (T0334)V47 because of BadResidue code BAD_PEPTIDE at template residue (2phh)A45 Warning: unaligning (T0334)A81 because of BadResidue code BAD_PEPTIDE in next template residue (2phh)E76 Warning: unaligning (T0334)I82 because of BadResidue code BAD_PEPTIDE at template residue (2phh)E76 Warning: unaligning (T0334)K187 because of BadResidue code BAD_PEPTIDE in next template residue (2phh)G117 Warning: unaligning (T0334)L188 because of BadResidue code BAD_PEPTIDE at template residue (2phh)G117 Warning: unaligning (T0334)A214 because of BadResidue code BAD_PEPTIDE in next template residue (2phh)G145 Warning: unaligning (T0334)T215 because of BadResidue code BAD_PEPTIDE at template residue (2phh)G145 Warning: unaligning (T0334)F402 because of BadResidue code BAD_PEPTIDE in next template residue (2phh)T347 Warning: unaligning (T0334)I403 because of BadResidue code BAD_PEPTIDE at template residue (2phh)T347 T0334 7 :KILIVGGGTAGWMAASYLGK 2phh 4 :QVAIIGAGPSGLLLGQLLHK T0334 30 :GTADITLLQAPD 2phh 24 :AGIDNVILERQT T0334 43 :PTL 2phh 41 :GRI T0334 48 :GE 2phh 46 :GV T0334 51 :TIPNLQTAF 2phh 48 :LEQGMVDLL T0334 61 :DFLGIP 2phh 57 :REAGVD T0334 69 :EWMRECNASYKV 2phh 63 :RRMARDGLVHEG T0334 83 :KFI 2phh 77 :IAF T0334 90 :AGEGTSE 2phh 80 :AGQRRRI T0334 157 :RRLDGSKVT 2phh 87 :DLKRLSGGK T0334 167 :YAWHFDAHLVADFLRRFATE 2phh 96 :TVTVYGQTEVTRDLMEAREA T0334 189 :GVRHVE 2phh 118 :ATTVYQ T0334 195 :DRVEHVQRDANGNIESVRT 2phh 125 :AEVRLHDLQGERPYVTFER T0334 216 :GR 2phh 146 :ER T0334 218 :VFDADLFVDCSGFRG 2phh 149 :RLDCDYIAGCDGFHG T0334 241 :EPFLDMSDH 2phh 166 :RQSIPAERL T0334 250 :LLNDSAVATQV 2phh 180 :VYPFGWLGLLA T0334 265 :DANGVEPFTSAIAMKSGWTWKIPMLGRFGTGYVYS 2phh 191 :DTPPVSHELIYANHPRGFALCSQRSATRSRYYVQV T0334 300 :SRFATEDEAVREFCEMW 2phh 231 :VEDWSDERFWTELKARL T0334 318 :LDPETQPLNRIRFRVGRNRRAWVGNCVSIGTSSCFVEPLESTGIYFVYAALYQLVKHFP 2phh 256 :VTGPSLEKSIAPLRSFVVEPMQHGRLFLAGDAAHIVPPTGAKGLNLAASDVSTLYRLLL T0334 377 :DKSLNPVLTARFNREIETMFDDTRD 2phh 321 :RGELLERYSAICLRRIWKAERFSWW T0334 404 :QAHFYFSPRT 2phh 348 :SVLHRFPDTD T0334 428 :DGMQE 2phh 358 :AFSQR T0334 505 :AVKDRQRNLLETLPSLHEFLRQQ 2phh 363 :IQQTELEYYLGSEAGLATIAENY Number of specific fragments extracted= 24 number of extra gaps= 5 total=3435 Will force an alignment to be made, even if fragment is small Number of alignments=150 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1nhp/T0334-1nhp-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1nhp expands to /projects/compbio/data/pdb/1nhp.pdb.gz 1nhp:Warning: there is no chain 1nhp will retry with 1nhpA # T0334 read from 1nhp/T0334-1nhp-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1nhp read from 1nhp/T0334-1nhp-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1nhp to template set # found chain 1nhp in template set Warning: unaligning (T0334)G103 because of BadResidue code BAD_PEPTIDE in next template residue (1nhp)L125 Warning: unaligning (T0334)P104 because of BadResidue code BAD_PEPTIDE at template residue (1nhp)L125 T0334 7 :KILIVGGGTAGWMAASYLGK 1nhp 2 :KVIVLGSSHGGYEAVEELLN T0334 28 :L 1nhp 22 :L T0334 29 :QGT 1nhp 24 :PDA T0334 33 :DITLLQAPD 1nhp 27 :EIQWYEKGD T0334 47 :VGEATIPNL 1nhp 36 :FISFLSAGM T0334 57 :TAFFDFLGIPED 1nhp 45 :QLYLEGKVKDVN T0334 69 :EWMRECNASYKVAIKFINWRTAGEGTS 1nhp 64 :EKMESRGVNVFSNTEITAIQPKEHQVT T0334 96 :EARELDG 1nhp 117 :ELDIPGK T0334 105 :DHFYHSFGLL 1nhp 126 :DNIYLMRGRQ T0334 115 :KYHEQIPLSHYWFDRSYRG 1nhp 147 :PEVNNVVVIGSGYIGIEAA T0334 139 :FDYACYKEPVILD 1nhp 166 :EAFAKAGKKVTVI T0334 152 :ANRSPRRLD 1nhp 180 :ILDRPLGVY T0334 172 :DAHLVADFLRRFA 1nhp 189 :LDKEFTDVLTEEM T0334 186 :EKLGVRHVED 1nhp 202 :EANNITIATG T0334 196 :RVEHV 1nhp 213 :TVERY T0334 203 :DANGNIESVRTATG 1nhp 218 :EGDGRVQKVVTDKN T0334 218 :VFDADLFVDCSGFRG 1nhp 232 :AYDADLVVVAVGVRP T0334 233 :LLINKAMEEPF 1nhp 249 :AWLKGTLELHP T0334 247 :SDHLLNDSAVATQV 1nhp 260 :NGLIKTDEYMRTSE T0334 341 :GNCVSIGTSSCF 1nhp 274 :PDVFAVGDATLI T0334 353 :VEP 1nhp 287 :YNP T0334 356 :LESTGIYFVYAALYQLVKHFPDKSLN 1nhp 294 :VNIALATNARKQGRFAVKNLEEPVKP Number of specific fragments extracted= 22 number of extra gaps= 1 total=3457 Will force an alignment to be made, even if fragment is small Number of alignments=151 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1nhp/T0334-1nhp-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0334 read from 1nhp/T0334-1nhp-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1nhp read from 1nhp/T0334-1nhp-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1nhp in template set Warning: unaligning (T0334)D6 because first residue in template chain is (1nhp)M1 Warning: unaligning (T0334)G161 because of BadResidue code BAD_PEPTIDE in next template residue (1nhp)L125 Warning: unaligning (T0334)S162 because of BadResidue code BAD_PEPTIDE at template residue (1nhp)L125 T0334 7 :KILIVGGGTAGWMAASYLGKA 1nhp 2 :KVIVLGSSHGGYEAVEELLNL T0334 29 :QGTADITLLQAPDIPTLG 1nhp 23 :HPDAEIQWYEKGDFISFL T0334 52 :IPNLQTAF 1nhp 41 :SAGMQLYL T0334 123 :SHYWFDRS 1nhp 63 :GEKMESRG T0334 136 :VEPFDYACYKEPVILD 1nhp 71 :VNVFSNTEITAIQPKE T0334 152 :ANRSPRRLD 1nhp 115 :PFELDIPGK T0334 166 :NYAW 1nhp 126 :DNIY T0334 170 :HFD 1nhp 188 :YLD T0334 174 :HLVADFLRRFA 1nhp 191 :KEFTDVLTEEM T0334 186 :EKLGVRHVED 1nhp 202 :EANNITIATG T0334 196 :RVEHVQ 1nhp 213 :TVERYE T0334 204 :ANGNIESVRTATG 1nhp 219 :GDGRVQKVVTDKN T0334 218 :VFDADLFVDCSGFRGLL 1nhp 232 :AYDADLVVVAVGVRPNT T0334 236 :NKAMEE 1nhp 249 :AWLKGT T0334 242 :PFLD 1nhp 256 :ELHP T0334 247 :SDHLLNDSAVAT 1nhp 260 :NGLIKTDEYMRT T0334 263 :DDD 1nhp 272 :SEP T0334 267 :NGVE 1nhp 318 :KPFP T0334 271 :PFTSAIAMKSGWTWKIPM 1nhp 324 :QGSSGLAVFDYKFASTGI T0334 310 :REFCEMWHL 1nhp 343 :EVMAQKLGK T0334 324 :PLNRIRFRVG 1nhp 352 :ETKAVTVVED Number of specific fragments extracted= 21 number of extra gaps= 1 total=3478 Will force an alignment to be made, even if fragment is small Number of alignments=152 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1nhp/T0334-1nhp-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0334 read from 1nhp/T0334-1nhp-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1nhp read from 1nhp/T0334-1nhp-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1nhp in template set T0334 2 :SGKIDKILIVGGGTAGWMAASYLGK 1nhp 146 :DPEVNNVVVIGSGYIGIEAAEAFAK T0334 30 :GTADITLLQAPDIP 1nhp 171 :AGKKVTVIDILDRP T0334 63 :LGI 1nhp 185 :LGV T0334 171 :FDAHLVADFLRRFATEKLGVRHVEDRVEHVQ 1nhp 188 :YLDKEFTDVLTEEMEANNITIATGETVERYE T0334 204 :ANGNIESVRT 1nhp 219 :GDGRVQKVVT T0334 215 :TGRVFDADLFVDCSGFR 1nhp 229 :DKNAYDADLVVVAVGVR T0334 258 :TQVPH 1nhp 246 :PNTAW T0334 288 :M 1nhp 251 :L T0334 317 :HLDPETQPLNRIRFRVGR 1nhp 252 :KGTLELHPNGLIKTDEYM T0334 337 :RAWVGNCVSIGTSS 1nhp 270 :RTSEPDVFAVGDAT T0334 361 :IYFVYAALYQLVKHFPDKS 1nhp 299 :ATNARKQGRFAVKNLEEPV Number of specific fragments extracted= 11 number of extra gaps= 0 total=3489 Will force an alignment to be made, even if fragment is small Number of alignments=153 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ebdA/T0334-1ebdA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1ebdA expands to /projects/compbio/data/pdb/1ebd.pdb.gz 1ebdA:# T0334 read from 1ebdA/T0334-1ebdA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ebdA read from 1ebdA/T0334-1ebdA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1ebdA to template set # found chain 1ebdA in template set T0334 5 :ID 1ebdA 8 :IE T0334 7 :KILIVGGGTAGWMAASYLGK 1ebdA 11 :ETLVVGAGPGGYVAAIRAAQ T0334 29 :QGT 1ebdA 31 :LGQ T0334 33 :DITLLQAPDIPTLGVGEATIPN 1ebdA 34 :KVTIVEKGNLGGVCLNVGCIPS T0334 57 :TAF 1ebdA 56 :KAL T0334 82 :IKFINWRTAGEGTS 1ebdA 59 :ISASHRYEQAKHSE T0334 96 :EARELDG 1ebdA 151 :PIELPNF T0334 103 :GPDHFYHSFGLL 1ebdA 159 :FSNRILDSTGAL T0334 115 :KYHEQIPLSHYWFDRSYRG 1ebdA 174 :EVPKSLVVIGGGYIGIELG T0334 139 :FDYACYKEPVILD 1ebdA 193 :TAYANFGTKVTIL T0334 152 :ANRSPRRL 1ebdA 207 :GAGEILSG T0334 172 :DAHLVADFLRRFA 1ebdA 215 :FEKQMAAIIKKRL T0334 186 :EKLGVRHVED 1ebdA 228 :KKKGVEVVTN T0334 196 :RVEHVQRDANG 1ebdA 239 :LAKGAEEREDG T0334 209 :ESVRTA 1ebdA 250 :VTVTYE T0334 215 :TGR 1ebdA 257 :NGE T0334 218 :VFDADLFVDCSGFRG 1ebdA 262 :TIDADYVLVTVGRRP T0334 233 :LLINKAMEEPFLD 1ebdA 280 :ELGLEQIGIKMTN T0334 247 :SDHLLNDSAVATQVPHDDDANGV 1ebdA 293 :RGLIEVDQQCRTSVPNIFAIGDI T0334 280 :SGWTWKIPM 1ebdA 395 :DGFLKLVVR T0334 289 :LGRFGTGYVY 1ebdA 405 :EDGVIIGAQI T0334 346 :IGTS 1ebdA 415 :IGPN T0334 364 :VYAALYQLVKHFPDKSLNPVLTA 1ebdA 419 :ASDMIAELGLAIEAGMTAEDIAL Number of specific fragments extracted= 23 number of extra gaps= 0 total=3512 Will force an alignment to be made, even if fragment is small Number of alignments=154 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ebdA/T0334-1ebdA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0334 read from 1ebdA/T0334-1ebdA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ebdA read from 1ebdA/T0334-1ebdA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1ebdA in template set T0334 4 :KIDKILIVGGGTAGWMAASYLGKA 1ebdA 8 :IETETLVVGAGPGGYVAAIRAAQL T0334 31 :TADITLLQAPDIPTLGVGEATIPN 1ebdA 32 :GQKVTIVEKGNLGGVCLNVGCIPS T0334 57 :TAF 1ebdA 56 :KAL T0334 66 :PE 1ebdA 84 :DF T0334 75 :NASYKVAIKFINWRTAGE 1ebdA 86 :AKVQEWKASVVKKLTGGV T0334 96 :EARELDGGP 1ebdA 104 :EGLLKGNKV T0334 105 :DHFYHSFGLL 1ebdA 125 :NTVRVVNGDS T0334 129 :RSYR 1ebdA 147 :TGSR T0334 136 :VEPFDYACYKEPVILD 1ebdA 151 :PIELPNFKFSNRILDS T0334 152 :ANRSPRRLDGSKVTNYAW 1ebdA 169 :ALNLGEVPKSLVVIGGGY T0334 170 :HFD 1ebdA 214 :GFE T0334 174 :HLVADFLRRFA 1ebdA 217 :KQMAAIIKKRL T0334 186 :EKLGVRHVED 1ebdA 228 :KKKGVEVVTN T0334 196 :RVEHVQRDANG 1ebdA 239 :LAKGAEEREDG T0334 209 :ESVRTA 1ebdA 250 :VTVTYE T0334 215 :TG 1ebdA 257 :NG T0334 217 :RVFDADLFVDCSGFRGLL 1ebdA 261 :KTIDADYVLVTVGRRPNT T0334 235 :IN 1ebdA 281 :LG T0334 237 :KAMEEPFLD 1ebdA 284 :EQIGIKMTN T0334 247 :SDHLLNDSAVATQV 1ebdA 293 :RGLIEVDQQCRTSV T0334 264 :DD 1ebdA 307 :PN T0334 266 :ANGVEPFTSAIAMKS 1ebdA 370 :DEGIDVIAAKFPFAA T0334 281 :GWTWKIPMLGRFGTGYVY 1ebdA 397 :FLKLVVRKEDGVIIGAQI T0334 299 :SSRFA 1ebdA 416 :GPNAS T0334 307 :EAVREFCEMW 1ebdA 421 :DMIAELGLAI T0334 317 :HL 1ebdA 433 :GM T0334 380 :L 1ebdA 435 :T Number of specific fragments extracted= 27 number of extra gaps= 0 total=3539 Will force an alignment to be made, even if fragment is small Number of alignments=155 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ebdA/T0334-1ebdA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0334 read from 1ebdA/T0334-1ebdA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ebdA read from 1ebdA/T0334-1ebdA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1ebdA in template set T0334 5 :IDKILIVGGGTAGWMAASYLGK 1ebdA 176 :PKSLVVIGGGYIGIELGTAYAN T0334 30 :GTADITLLQAPDI 1ebdA 198 :FGTKVTILEGAGE T0334 45 :LG 1ebdA 211 :IL T0334 63 :LGIP 1ebdA 213 :SGFE T0334 174 :HLVADFLRRFATEKLGVRHVEDRVEHVQRDANGNIESVRTATGR 1ebdA 217 :KQMAAIIKKRLKKKGVEVVTNALAKGAEEREDGVTVTYEANGET T0334 218 :VFDADLFVDCSGF 1ebdA 262 :TIDADYVLVTVGR T0334 260 :VPHDDDAN 1ebdA 275 :RPNTDELG T0334 316 :WHLDP 1ebdA 283 :LEQIG T0334 321 :ETQPLNRIRFRVGRN 1ebdA 289 :KMTNRGLIEVDQQCR T0334 338 :AWVGNCVSIGTSSCFV 1ebdA 304 :TSVPNIFAIGDIVPGP T0334 361 :IYFVYAALYQLVKHFPDKS 1ebdA 322 :AHKASYEGKVAAEAIAGHP Number of specific fragments extracted= 11 number of extra gaps= 0 total=3550 Will force an alignment to be made, even if fragment is small Number of alignments=156 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1lvl/T0334-1lvl-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1lvl expands to /projects/compbio/data/pdb/1lvl.pdb.gz 1lvl:Warning: there is no chain 1lvl will retry with 1lvlA # T0334 read from 1lvl/T0334-1lvl-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1lvl read from 1lvl/T0334-1lvl-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1lvl to template set # found chain 1lvl in template set Warning: unaligning (T0334)D105 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1lvl)P157 Warning: unaligning (T0334)H106 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1lvl)P157 Warning: unaligning (T0334)T215 because of BadResidue code BAD_PEPTIDE in next template residue (1lvl)G248 Warning: unaligning (T0334)G216 because of BadResidue code BAD_PEPTIDE at template residue (1lvl)G248 T0334 3 :GKID 1lvl 2 :QTIQ T0334 7 :KILIVGGGTAGWMAASYLGK 1lvl 7 :TLLIIGGGPGGYVAAIRAGQ T0334 29 :QGT 1lvl 27 :LGI T0334 33 :DITLLQAPDIPTL 1lvl 30 :PTVLVEGQALGGT T0334 52 :IP 1lvl 76 :SV T0334 61 :DFLGIPEDEWMRECNASYKVAIKFINWRTAGEGTS 1lvl 78 :ASPRLDIGQSVAWKDGIVDRLTTGVAALLKKHGVK T0334 96 :EARELDG 1lvl 148 :ELPMLPL T0334 104 :P 1lvl 155 :G T0334 107 :FYHSFGLL 1lvl 158 :VISSTEAL T0334 115 :KYHEQIPLSHYWFDRSYRG 1lvl 169 :ALPQHLVVVGGGYIGLELG T0334 139 :FDYACYKEPVILD 1lvl 188 :IAYRKLGAQVSVV T0334 152 :ANRSPRRL 1lvl 202 :ARERILPT T0334 172 :DAHLVADFLRRFA 1lvl 210 :YDSELTAPVAESL T0334 186 :EKLGVRHVED 1lvl 223 :KKLGIALHLG T0334 196 :RVEHV 1lvl 234 :SVEGY T0334 203 :DANG 1lvl 239 :ENGC T0334 211 :VRTA 1lvl 243 :LLAN T0334 217 :R 1lvl 249 :K T0334 218 :VFDADLFVDCSGFRG 1lvl 254 :RLEADRVLVAVGRRP T0334 233 :LLINKAMEEPFL 1lvl 272 :GFNLECLDLKMN T0334 247 :SDHLLNDSAVATQVPHDDDANGV 1lvl 284 :GAAIAIDERCQTSMHNVWAIGDV Number of specific fragments extracted= 21 number of extra gaps= 2 total=3571 Will force an alignment to be made, even if fragment is small Number of alignments=157 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1lvl/T0334-1lvl-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0334 read from 1lvl/T0334-1lvl-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1lvl read from 1lvl/T0334-1lvl-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1lvl in template set Warning: unaligning (T0334)N166 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1lvl)P157 Warning: unaligning (T0334)Y167 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1lvl)P157 Warning: unaligning (T0334)T213 because of BadResidue code BAD_PEPTIDE in next template residue (1lvl)G248 Warning: unaligning (T0334)A214 because of BadResidue code BAD_PEPTIDE at template residue (1lvl)G248 Warning: unaligning (T0334)R217 because of BadResidue code BAD_PEPTIDE at template residue (1lvl)L253 Warning: unaligning (T0334)K279 because of BadResidue code BAD_PEPTIDE in next template residue (1lvl)A375 Warning: unaligning (T0334)S280 because of BadResidue code BAD_PEPTIDE at template residue (1lvl)A375 T0334 2 :SGKIDKILIVGGGTAGWMAASYLGKA 1lvl 2 :QTIQTTLLIIGGGPGGYVAAIRAGQL T0334 31 :TADITLLQAPDIPTLGVGEATIPN 1lvl 28 :GIPTVLVEGQALGGTCLNIGCIPS T0334 57 :TAF 1lvl 52 :KAL T0334 64 :GI 1lvl 81 :RL T0334 73 :ECNASYKVAIKFINWRTAGE 1lvl 83 :DIGQSVAWKDGIVDRLTTGV T0334 123 :SHYWFDRSYR 1lvl 103 :AALLKKHGVK T0334 142 :ACYKEPVILD 1lvl 113 :VVHGWAKVLD T0334 152 :ANRSPRRLDGSKVT 1lvl 142 :TGSSSVELPMLPLG T0334 168 :AW 1lvl 158 :VI T0334 170 :HFDAHLVADFLRRFA 1lvl 208 :PTYDSELTAPVAESL T0334 186 :EKLGVRHVED 1lvl 223 :KKLGIALHLG T0334 196 :RVEHV 1lvl 234 :SVEGY T0334 204 :ANG 1lvl 239 :ENG T0334 208 :IESVR 1lvl 242 :CLLAN T0334 215 :TG 1lvl 249 :KG T0334 218 :VFDADLFVDCSGFRGLL 1lvl 254 :RLEADRVLVAVGRRPRT T0334 239 :MEEPFLDMSDHLLN 1lvl 328 :AGKARRFEPAAIAA T0334 253 :DSAVAT 1lvl 347 :PEVVVV T0334 260 :VPHDDDA 1lvl 353 :GKTPEQA T0334 267 :NGVEPFTSAIAM 1lvl 362 :QGLDCIVAQFPF T0334 281 :GWTWKIPMLGR 1lvl 387 :GFVRVVARRDN T0334 292 :FGTGYVY 1lvl 399 :LILGWQA T0334 299 :SSRFA 1lvl 407 :GVAVS T0334 307 :EAVREFCEMW 1lvl 412 :ELSTAFAQSL T0334 317 :HLD 1lvl 432 :GTI Number of specific fragments extracted= 25 number of extra gaps= 4 total=3596 Will force an alignment to be made, even if fragment is small Number of alignments=158 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1lvl/T0334-1lvl-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0334 read from 1lvl/T0334-1lvl-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1lvl read from 1lvl/T0334-1lvl-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1lvl in template set Warning: unaligning (T0334)T213 because of BadResidue code BAD_PEPTIDE in next template residue (1lvl)G248 Warning: unaligning (T0334)A214 because of BadResidue code BAD_PEPTIDE at template residue (1lvl)G248 Warning: unaligning (T0334)C351 because of BadResidue code BAD_PEPTIDE in next template residue (1lvl)E309 Warning: unaligning (T0334)E354 because of BadResidue code BAD_PEPTIDE at template residue (1lvl)E309 Warning: unaligning (T0334)P355 because of BadResidue code BAD_PEPTIDE at template residue (1lvl)P310 T0334 5 :IDKILIVGGGTAGWMAASYLGK 1lvl 171 :PQHLVVVGGGYIGLELGIAYRK T0334 30 :GTADITLLQAPDI 1lvl 193 :LGAQVSVVEARER T0334 51 :TI 1lvl 206 :IL T0334 63 :LGIPE 1lvl 208 :PTYDS T0334 175 :LVADFLRRFATEKLGVRHVEDRVEHVQ 1lvl 213 :ELTAPVAESLKKLGIALHLGHSVEGYE T0334 205 :NG 1lvl 240 :NG T0334 208 :IESVR 1lvl 242 :CLLAN T0334 215 :TGR 1lvl 249 :KGG T0334 218 :VFDADLFVDCSGF 1lvl 254 :RLEADRVLVAVGR T0334 258 :TQV 1lvl 267 :RPR T0334 264 :DDANGVE 1lvl 270 :TKGFNLE T0334 322 :TQPLNRIRF 1lvl 277 :CLDLKMNGA T0334 331 :RVGRNRRAWVGNCVSIGTSS 1lvl 288 :AIDERCQTSMHNVWAIGDVA T0334 356 :LE 1lvl 311 :ML T0334 361 :IYFVYAALYQLVKHFPDKSLN 1lvl 313 :AHRAMAQGEMVAEIIAGKARR Number of specific fragments extracted= 15 number of extra gaps= 2 total=3611 Will force an alignment to be made, even if fragment is small Number of alignments=159 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1m64A/T0334-1m64A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1m64A expands to /projects/compbio/data/pdb/1m64.pdb.gz 1m64A:# T0334 read from 1m64A/T0334-1m64A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1m64A read from 1m64A/T0334-1m64A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1m64A to template set # found chain 1m64A in template set Warning: unaligning (T0334)P66 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1m64A)W176 Warning: unaligning (T0334)E67 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1m64A)W176 T0334 3 :GKID 1m64A 122 :APHD T0334 7 :KILIVGGGTAGWMAASYLGK 1m64A 128 :DVVVVGSGGAGFSAAISATD T0334 29 :QGT 1m64A 148 :SGA T0334 33 :DITLLQAPD 1m64A 151 :KVILIEKEP T0334 42 :IPTL 1m64A 161 :IGGN T0334 57 :TAFFDFLGI 1m64A 166 :KLAAGGMNA T0334 68 :DEWMRECNASYKVAIKFINWRTAGEGTS 1m64A 177 :TDQQKAKKITDSPELMFEDTMKGGQNIN T0334 96 :EARELDGGPDHFYHSFGLL 1m64A 222 :WMTAMGADLTDVGMMGGAS T0334 115 :KYHE 1m64A 246 :RPTG T0334 152 :AN 1m64A 251 :AG T0334 172 :DAHLVADFLRRFA 1m64A 253 :VGAHVVQVLYDNA T0334 186 :EKLGVRHVED 1m64A 266 :VKRNIDLRMN T0334 196 :RVEHVQRDANGNIESVRTA 1m64A 277 :RGIEVLKDDKGTVKGILVK T0334 215 :T 1m64A 297 :M T0334 216 :GR 1m64A 299 :KG T0334 218 :VFDADLFVDCSGF 1m64A 303 :WVKADAVILATGG T0334 231 :RGLLINKAMEEPFLD 1m64A 344 :DGLDVAENAGGALKD T0334 280 :SGWTWKIPM 1m64A 359 :MQYIFAHPT T0334 289 :LGR 1m64A 371 :KGG T0334 292 :FGTGYVYSSRFATE 1m64A 383 :NGAILVNREGKRFV T0334 306 :DEAVREFCEM 1m64A 462 :TETVARYNSL T0334 316 :WHLDPETQPLNRIRF 1m64A 473 :SSGKDTDFERPNLPR T0334 331 :RVGRNR 1m64A 503 :VHHTMG T0334 337 :RAWVGNCVSIGTSSCFVEP 1m64A 523 :KQVIPGLYGAGEVTGGVHG T0334 356 :LESTGIYFVYAALYQLVKHF 1m64A 545 :LGGNAISDIITFGRLAGEEA Number of specific fragments extracted= 25 number of extra gaps= 1 total=3636 Will force an alignment to be made, even if fragment is small Number of alignments=160 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1m64A/T0334-1m64A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0334 read from 1m64A/T0334-1m64A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1m64A read from 1m64A/T0334-1m64A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1m64A in template set T0334 4 :KIDKILIVGGGTAGWMAASYLGK 1m64A 125 :DTVDVVVVGSGGAGFSAAISATD T0334 30 :GTADITLLQAPDIPTLGVGEATI 1m64A 148 :SGAKVILIEKEPVIGGNAKLAAG T0334 57 :TAF 1m64A 178 :DQQ T0334 61 :DFLGI 1m64A 181 :KAKKI T0334 66 :PEDEWMREC 1m64A 188 :SPELMFEDT T0334 75 :NASYKVAIKFINWR 1m64A 206 :PALVKVLSSHSKDS T0334 123 :SHYWFDRSYR 1m64A 220 :VDWMTAMGAD T0334 144 :YKEPVI 1m64A 230 :LTDVGM T0334 152 :ANRSPRRL 1m64A 236 :MGGASVNR T0334 162 :SKVTNYAW 1m64A 244 :AHRPTGGA T0334 171 :FDAHLVADFLRRFAT 1m64A 252 :GVGAHVVQVLYDNAV T0334 187 :KLGVRHVED 1m64A 267 :KRNIDLRMN T0334 196 :RVEHVQRDANGNIESVRTA 1m64A 277 :RGIEVLKDDKGTVKGILVK T0334 215 :TG 1m64A 299 :KG T0334 217 :RVFDADLFVDCSGFR 1m64A 302 :YWVKADAVILATGGF T0334 232 :GLL 1m64A 321 :ERV T0334 236 :NKAM 1m64A 324 :AKLD T0334 244 :LDMSDHLLNDS 1m64A 328 :PSLKGFISTNQ T0334 267 :NGVE 1m64A 339 :PGAV T0334 271 :PFTSAIAMKSGWTWKIPM 1m64A 350 :ENAGGALKDMQYIFAHPT T0334 289 :LGRFGT 1m64A 371 :KGGVMV T0334 295 :GYVYSSRFATE 1m64A 384 :GAILVNREGKR T0334 306 :DEAVREFCEMW 1m64A 462 :TETVARYNSLV T0334 317 :HLDPETQ 1m64A 475 :GKDTDFE T0334 324 :PLNRIRFRVG 1m64A 493 :NYYAIEVTPG T0334 334 :RNRRAWVGNCVSIG 1m64A 520 :NAKKQVIPGLYGAG T0334 348 :TSSCFVEPLESTGIYFVYAALYQLVKHF 1m64A 537 :GGVHGANRLGGNAISDIITFGRLAGEEA Number of specific fragments extracted= 27 number of extra gaps= 0 total=3663 Will force an alignment to be made, even if fragment is small Number of alignments=161 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1m64A/T0334-1m64A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0334 read from 1m64A/T0334-1m64A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1m64A read from 1m64A/T0334-1m64A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1m64A in template set T0334 4 :KIDKILIVGGGTAGWMAASYLGK 1m64A 125 :DTVDVVVVGSGGAGFSAAISATD T0334 30 :GTADITLLQAPDI 1m64A 148 :SGAKVILIEKEPV T0334 45 :LGVGEATI 1m64A 161 :IGGNAKLA T0334 53 :P 1m64A 178 :D T0334 58 :AF 1m64A 179 :QQ T0334 61 :DFLGI 1m64A 181 :KAKKI T0334 66 :PEDEWMR 1m64A 188 :SPELMFE T0334 113 :LLKYHEQIPLSHYWFDRSY 1m64A 195 :DTMKGGQNINDPALVKVLS T0334 137 :EPFDYACYKEPVILDANRSPRRLDGSKVTN 1m64A 214 :SHSKDSVDWMTAMGADLTDVGMMGGASVNR T0334 169 :WHF 1m64A 244 :AHR T0334 172 :DAHLVADFLRRFATEKLGVRHVEDRVEHVQRDANGNIESVRT 1m64A 253 :VGAHVVQVLYDNAVKRNIDLRMNTRGIEVLKDDKGTVKGILV T0334 214 :ATGR 1m64A 297 :MYKG T0334 218 :VFDADLFVDCSGFRG 1m64A 303 :WVKADAVILATGGFA T0334 233 :LLINK 1m64A 322 :RVAKL T0334 243 :FLDMSDHLLND 1m64A 327 :DPSLKGFISTN T0334 307 :EAVREFCEMWHLDP 1m64A 463 :ETVARYNSLVSSGK T0334 322 :TQ 1m64A 477 :DT T0334 324 :PLNRIRFRVGRNRRA 1m64A 493 :NYYAIEVTPGVHHTM T0334 339 :WVGNCVSIGTSSCFVEP 1m64A 525 :VIPGLYGAGEVTGGVHG T0334 356 :LESTGIYFVYAALYQLVKHFPD 1m64A 545 :LGGNAISDIITFGRLAGEEAAK Number of specific fragments extracted= 20 number of extra gaps= 0 total=3683 Will force an alignment to be made, even if fragment is small Number of alignments=162 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1lj1A/T0334-1lj1A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1lj1A expands to /projects/compbio/data/pdb/1lj1.pdb.gz 1lj1A:# T0334 read from 1lj1A/T0334-1lj1A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1lj1A read from 1lj1A/T0334-1lj1A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1lj1A to template set # found chain 1lj1A in template set Warning: unaligning (T0334)P66 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1lj1A)W176 Warning: unaligning (T0334)E67 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1lj1A)W176 T0334 3 :GKID 1lj1A 122 :APHD T0334 7 :KILIVGGGTAGWMAASYLGK 1lj1A 128 :DVVVVGSGGAGFSAAISATD T0334 29 :QGT 1lj1A 148 :SGA T0334 33 :DITLLQAPD 1lj1A 151 :KVILIEKEP T0334 42 :IPTL 1lj1A 161 :IGGN T0334 59 :FFDFLGI 1lj1A 168 :AAGGMNA T0334 68 :DEWMRECNASYKVAIKFINWRTAGEGTS 1lj1A 177 :TDQQKAKKITDSPELMFEDTMKGGQNIN T0334 96 :EARELDGGPDHFYHSFGLL 1lj1A 222 :WMTAMGADLTDVGMMGGAS T0334 115 :KYHE 1lj1A 246 :RPTG T0334 152 :AN 1lj1A 251 :AG T0334 172 :DAHLVADFLRRFA 1lj1A 253 :VGAHVVQVLYDNA T0334 186 :EKLGVRHVED 1lj1A 266 :VKRNIDLRMN T0334 196 :RVEHVQRDANGNIESVRTA 1lj1A 277 :RGIEVLKDDKGTVKGILVK T0334 215 :T 1lj1A 297 :M T0334 216 :GR 1lj1A 299 :KG T0334 218 :VFDADLFVDCSGFRG 1lj1A 303 :WVKADAVILATGGFA T0334 233 :LLINKAM 1lj1A 321 :ERVAKLD T0334 264 :DDANGVEPFTSAIAMK 1lj1A 328 :PSLKGFISTNQPGAVG T0334 280 :SGWTWKIPM 1lj1A 359 :MQYIFAHPT T0334 289 :LGR 1lj1A 371 :KGG T0334 292 :FGTGYVYSSRFATE 1lj1A 383 :NGAILVNREGKRFV T0334 306 :DEAVREFCEM 1lj1A 462 :TETVARYNSL T0334 316 :WHLDPETQPLNRIRF 1lj1A 473 :SSGKDTDFERPNLPR T0334 334 :RNR 1lj1A 503 :VHH T0334 337 :RAWVGNCVSIGTSSCFVEP 1lj1A 523 :KQVIPGLYGAGEVTGGVHG T0334 356 :LESTGIYFVYAALYQLVKHFP 1lj1A 545 :LGGNAISDIITFGRLAGEEAA Number of specific fragments extracted= 26 number of extra gaps= 1 total=3709 Will force an alignment to be made, even if fragment is small Number of alignments=163 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1lj1A/T0334-1lj1A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0334 read from 1lj1A/T0334-1lj1A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1lj1A read from 1lj1A/T0334-1lj1A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1lj1A in template set T0334 4 :KIDKILIVGGGTAGWMAASYLGK 1lj1A 125 :DTVDVVVVGSGGAGFSAAISATD T0334 30 :GTADITLLQAPDIPTLGVGEATI 1lj1A 148 :SGAKVILIEKEPVIGGNAKLAAG T0334 57 :TAF 1lj1A 178 :DQQ T0334 61 :DFLGI 1lj1A 181 :KAKKI T0334 66 :PEDEWMRECNA 1lj1A 188 :SPELMFEDTMK T0334 77 :SYKVAIK 1lj1A 208 :LVKVLSS T0334 84 :FINW 1lj1A 216 :SKDS T0334 123 :SHYWFDRSYR 1lj1A 220 :VDWMTAMGAD T0334 144 :YKEPVI 1lj1A 230 :LTDVGM T0334 152 :ANRSPRRL 1lj1A 236 :MGGASVNR T0334 162 :SKVTNYAW 1lj1A 244 :AHRPTGGA T0334 171 :FDAHLVADFLRRFAT 1lj1A 252 :GVGAHVVQVLYDNAV T0334 187 :KLGVRHVED 1lj1A 267 :KRNIDLRMN T0334 196 :RVEHVQRDANGNIESVRTA 1lj1A 277 :RGIEVLKDDKGTVKGILVK T0334 215 :TG 1lj1A 299 :KG T0334 217 :RVFDADLFVDCSGFRGL 1lj1A 302 :YWVKADAVILATGGFAK T0334 234 :L 1lj1A 323 :V T0334 236 :NKAM 1lj1A 324 :AKLD T0334 244 :LDMSDHLLNDS 1lj1A 328 :PSLKGFISTNQ T0334 267 :NGVE 1lj1A 339 :PGAV T0334 271 :PFTSAIAMKSGWTWKIPM 1lj1A 350 :ENAGGALKDMQYIFAHPT T0334 289 :LGRFGT 1lj1A 371 :KGGVMV T0334 295 :GYVYSSRFATE 1lj1A 384 :GAILVNREGKR T0334 306 :DEAVREFCEMW 1lj1A 459 :KALTETVARYN T0334 317 :HLDPETQ 1lj1A 475 :GKDTDFE T0334 324 :PLNRIRFRVG 1lj1A 493 :NYYAIEVTPG T0334 334 :RNRRAWVGNCVSIG 1lj1A 520 :NAKKQVIPGLYGAG T0334 348 :TSSCFVEPLESTGIYFVYAALYQLVKHF 1lj1A 537 :GGVHGANRLGGNAISDIITFGRLAGEEA Number of specific fragments extracted= 28 number of extra gaps= 0 total=3737 Will force an alignment to be made, even if fragment is small Number of alignments=164 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1lj1A/T0334-1lj1A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0334 read from 1lj1A/T0334-1lj1A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1lj1A read from 1lj1A/T0334-1lj1A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1lj1A in template set T0334 5 :IDKILIVGGGTAGWMAASYLGK 1lj1A 126 :TVDVVVVGSGGAGFSAAISATD T0334 30 :GTADITLLQAPD 1lj1A 148 :SGAKVILIEKEP T0334 44 :TLGVGEATI 1lj1A 160 :VIGGNAKLA T0334 57 :TAF 1lj1A 178 :DQQ T0334 61 :DFLGI 1lj1A 181 :KAKKI T0334 66 :PED 1lj1A 188 :SPE T0334 109 :HSFGLLKYHEQIPLSHYWFDRSY 1lj1A 191 :LMFEDTMKGGQNINDPALVKVLS T0334 137 :EPFDYACYKEPVILDANRSPRRLDGSKVTN 1lj1A 214 :SHSKDSVDWMTAMGADLTDVGMMGGASVNR T0334 169 :WHF 1lj1A 244 :AHR T0334 172 :DAHLVADFLRRFATEKLGVRHVEDRVEHVQRDANGNIESVRT 1lj1A 253 :VGAHVVQVLYDNAVKRNIDLRMNTRGIEVLKDDKGTVKGILV T0334 214 :ATGR 1lj1A 297 :MYKG T0334 218 :VFDADLFVDCSGFRG 1lj1A 303 :WVKADAVILATGGFA T0334 233 :LLINK 1lj1A 322 :RVAKL T0334 243 :FLDMSDHLLND 1lj1A 327 :DPSLKGFISTN T0334 307 :EAVREFCEMWHLDP 1lj1A 463 :ETVARYNSLVSSGK T0334 322 :TQ 1lj1A 477 :DT T0334 324 :PLNRIRFRVGRNRRA 1lj1A 493 :NYYAIEVTPGVHHTM T0334 339 :WVGNCVSIGTSSCFVEP 1lj1A 525 :VIPGLYGAGEVTGGVHG T0334 356 :LESTGIYFVYAALYQLVKHFPD 1lj1A 545 :LGGNAISDIITFGRLAGEEAAK Number of specific fragments extracted= 19 number of extra gaps= 0 total=3756 Will force an alignment to be made, even if fragment is small Number of alignments=165 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1l9fA/T0334-1l9fA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1l9fA expands to /projects/compbio/data/pdb/1l9f.pdb.gz 1l9fA:# T0334 read from 1l9fA/T0334-1l9fA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1l9fA read from 1l9fA/T0334-1l9fA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1l9fA to template set # found chain 1l9fA in template set Warning: unaligning (T0334)K4 because first residue in template chain is (1l9fA)S1 T0334 5 :ID 1l9fA 2 :TH T0334 7 :KILIVGGGTAGWMAASYLGK 1l9fA 5 :DVIVVGAGSMGMAAGYQLAK T0334 29 :QGT 1l9fA 25 :QGV T0334 33 :DITLLQAPD 1l9fA 28 :KTLLVDAFD T0334 42 :IPTL 1l9fA 38 :PHTN T0334 46 :GVGEATIPNLQTAF 1l9fA 52 :RHAYGEGREYVPLA T0334 67 :ED 1l9fA 66 :LR T0334 69 :EWMRECNAS 1l9fA 70 :ELWYELEKE T0334 103 :GPDHFYHSFGLL 1l9fA 79 :THHKIFTKTGVL T0334 115 :KYHEQIPLSHYW 1l9fA 94 :PKGESAFVAETM T0334 139 :FDYACYKEPVILDANRSPRRLDGSKVTNYAWHF 1l9fA 106 :EAAKEHSLTVDLLEGDEINKRWPGITVPENYNA T0334 172 :DAHLVADFLRRFA 1l9fA 148 :FSENCIRAYRELA T0334 186 :EKLGVRHVED 1l9fA 161 :EARGAKVLTH T0334 196 :RVEHVQRDAN 1l9fA 172 :RVEDFDISPD T0334 207 :NIE 1l9fA 182 :SVK T0334 211 :VRTATG 1l9fA 185 :IETANG T0334 218 :VFDADLFVDCSGFRGLLINKAMEEPFLDM 1l9fA 191 :SYTADKLIVSMGAWNSKLLSKLNLDIPLQ T0334 252 :NDSAVATQVPHDDDANGV 1l9fA 222 :RQVVGFFESDESKYSNDI T0334 271 :PFTS 1l9fA 240 :DFPG T0334 275 :AIAMKSGWTWKIPM 1l9fA 245 :MVEVPNGIYYGFPS T0334 289 :LGR 1l9fA 260 :GGC T0334 292 :FGTGYVYSSRFATE 1l9fA 264 :LKLGYHTFGQKIDP T0334 306 :DEAVREFCEMWHLDPETQPLNRIRFRVGRNR 1l9fA 288 :PEDESNLRAFLEEYMPGANGELKRGAVCMYT T0334 338 :AWVGNCVSIG 1l9fA 319 :KTLDEHFIID T0334 348 :TSSCFVEPLESTGIYFVYAALYQLVKHFPDKS 1l9fA 334 :SNVVIAAGFSGHGFKFSSGVGEVLSQLALTGK T0334 482 :PDAPSPRLAHM 1l9fA 366 :TEHDISIFSIN Number of specific fragments extracted= 26 number of extra gaps= 0 total=3782 Will force an alignment to be made, even if fragment is small Number of alignments=166 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1l9fA/T0334-1l9fA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0334 read from 1l9fA/T0334-1l9fA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1l9fA read from 1l9fA/T0334-1l9fA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1l9fA in template set Warning: unaligning (T0334)G3 because first residue in template chain is (1l9fA)S1 T0334 4 :KIDKILIVGGGTAGWMAASYLGK 1l9fA 2 :THFDVIVVGAGSMGMAAGYQLAK T0334 30 :GTADITLLQAPDI 1l9fA 25 :QGVKTLLVDAFDP T0334 43 :PTLGVGEATIPNLQTAF 1l9fA 46 :GDTRIIRHAYGEGREYV T0334 79 :KVAIKFINWRTAGE 1l9fA 63 :PLALRSQELWYELE T0334 96 :EARELDGGP 1l9fA 77 :KETHHKIFT T0334 105 :DHFYHSFGLLKYHEQIPLSHYWFDRSYR 1l9fA 87 :TGVLVFGPKGESAFVAETMEAAKEHSLT T0334 136 :VEPFDYACYKEPVI 1l9fA 115 :VDLLEGDEINKRWP T0334 152 :ANRSPRRLDGSKVTNYAW 1l9fA 129 :GITVPENYNAIFEPNSGV T0334 171 :FDAHLVADFLRRFA 1l9fA 147 :LFSENCIRAYRELA T0334 186 :EKLGVRHVED 1l9fA 161 :EARGAKVLTH T0334 196 :RVEHVQRDANG 1l9fA 172 :RVEDFDISPDS T0334 209 :ESVRTATG 1l9fA 183 :VKIETANG T0334 218 :VFDADLFVDCSGFRGLLINKAMEEPFLDMSDH 1l9fA 191 :SYTADKLIVSMGAWNSKLLSKLNLDIPLQPYR T0334 253 :DSAVATQVP 1l9fA 223 :QVVGFFESD T0334 264 :DDAN 1l9fA 237 :NDID T0334 271 :PFTSAIAMKSGWTWKIPMLGRFGTGYVY 1l9fA 241 :FPGFMVEVPNGIYYGFPSFGGCGLKLGY T0334 299 :SSRFATE 1l9fA 276 :DPDTINR T0334 306 :DEAVREFCEMW 1l9fA 288 :PEDESNLRAFL T0334 317 :HLDPETQ 1l9fA 300 :EYMPGAN T0334 325 :LNRIRFRVGRNR 1l9fA 307 :GELKRGAVCMYT T0334 338 :AWVGNCVSIG 1l9fA 319 :KTLDEHFIID T0334 348 :TSSCFVEPLESTGIYFVYAALYQLVKHFPDKSL 1l9fA 334 :SNVVIAAGFSGHGFKFSSGVGEVLSQLALTGKT Number of specific fragments extracted= 22 number of extra gaps= 0 total=3804 Will force an alignment to be made, even if fragment is small Number of alignments=167 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1l9fA/T0334-1l9fA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0334 read from 1l9fA/T0334-1l9fA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1l9fA read from 1l9fA/T0334-1l9fA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1l9fA in template set Warning: unaligning (T0334)G3 because first residue in template chain is (1l9fA)S1 T0334 4 :KIDKILIVGGGTAGWMAASYLGK 1l9fA 2 :THFDVIVVGAGSMGMAAGYQLAK T0334 30 :GTADITLLQAPDIPT 1l9fA 25 :QGVKTLLVDAFDPPH T0334 45 :LGVGEA 1l9fA 53 :HAYGEG T0334 51 :TIPNLQTAF 1l9fA 61 :YVPLALRSQ T0334 61 :DFL 1l9fA 70 :ELW T0334 68 :DEWMRECNASYKVAIKFINWRTAGEGTS 1l9fA 73 :YELEKETHHKIFTKTGVLVFGPKGESAF T0334 110 :SFGLLKYHEQIPLSHYWFD 1l9fA 101 :VAETMEAAKEHSLTVDLLE T0334 146 :EPVILDANRSPRRLDGSK 1l9fA 120 :GDEINKRWPGITVPENYN T0334 167 :Y 1l9fA 138 :A T0334 168 :AWHFDAHLVADFLRRFATEKLGVRHVEDRVEHVQRDANG 1l9fA 144 :SGVLFSENCIRAYRELAEARGAKVLTHTRVEDFDISPDS T0334 209 :ESVRTAT 1l9fA 183 :VKIETAN T0334 217 :RVFDADLFVDCSGFRGL 1l9fA 190 :GSYTADKLIVSMGAWNS T0334 237 :KAM 1l9fA 207 :KLL T0334 245 :DMSDH 1l9fA 210 :SKLNL T0334 250 :LLNDSAVATQVPHDDD 1l9fA 218 :LQPYRQVVGFFESDES T0334 266 :ANGVEPFTSAIAMKSGWTWKIPMLGRFGTGYVYSS 1l9fA 236 :SNDIDFPGFMVEVPNGIYYGFPSFGGCGLKLGYHT T0334 307 :EAVREFCEMWHLDPETQPLNRIRFRVGRNRRAW 1l9fA 289 :EDESNLRAFLEEYMPGANGELKRGAVCMYTKTL T0334 340 :VGNCVSIGTSSCFVEPLESTGIYFVYAALY 1l9fA 333 :HSNVVIAAGFSGHGFKFSSGVGEVLSQLAL T0334 377 :DKS 1l9fA 363 :TGK T0334 410 :SPRTDTPFWRANKEL 1l9fA 366 :TEHDISIFSINRPAL Number of specific fragments extracted= 20 number of extra gaps= 0 total=3824 Will force an alignment to be made, even if fragment is small Number of alignments=168 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1b3mA/T0334-1b3mA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1b3mA expands to /projects/compbio/data/pdb/1b3m.pdb.gz 1b3mA:# T0334 read from 1b3mA/T0334-1b3mA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1b3mA read from 1b3mA/T0334-1b3mA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1b3mA to template set # found chain 1b3mA in template set Warning: unaligning (T0334)K4 because first residue in template chain is (1b3mA)S1 Warning: unaligning (T0334)H249 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1b3mA)P220 Warning: unaligning (T0334)L250 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1b3mA)P220 Warning: unaligning (T0334)V297 because of BadResidue code BAD_PEPTIDE in next template residue (1b3mA)T270 Warning: unaligning (T0334)Y298 because of BadResidue code BAD_PEPTIDE at template residue (1b3mA)T270 T0334 5 :ID 1b3mA 2 :TH T0334 7 :KILIVGGGTAGWMAASYLGK 1b3mA 5 :DVIVVGAGSMGMAAGYQLAK T0334 29 :QGT 1b3mA 25 :QGV T0334 33 :DITLLQAPD 1b3mA 28 :KTLLVDAFD T0334 42 :IPTL 1b3mA 38 :PHTN T0334 46 :GVGEATIPNLQTAF 1b3mA 49 :RIIRHAYGEGREYV T0334 67 :E 1b3mA 63 :P T0334 69 :EWMRECNAS 1b3mA 70 :ELWYELEKE T0334 103 :GPDHFYHSFGLL 1b3mA 79 :THHKIFTKTGVL T0334 115 :KYHEQIPLSHYW 1b3mA 94 :PKGESAFVAETM T0334 139 :FDYACYKEPVILDANRSPRRLDGSKVTNYAWHF 1b3mA 106 :EAAKEHSLTVDLLEGDEINKRWPGITVPENYNA T0334 172 :DAHLVADFLRRFA 1b3mA 148 :FSENCIRAYRELA T0334 186 :EKLGVRHVED 1b3mA 161 :EARGAKVLTH T0334 196 :RVEHVQRDANG 1b3mA 172 :RVEDFDISPDS T0334 209 :ESVRTATG 1b3mA 183 :VKIETANG T0334 218 :VFDADLFVDCSGFRGLLINKAMEEPF 1b3mA 191 :SYTADKLIVSMGAWNSKLLSKLNLDI T0334 247 :SD 1b3mA 217 :PQ T0334 251 :LNDSAVATQVPHDDDANGVEPFTSAIAMKSGWTWKIPM 1b3mA 221 :YRQVVGFFESDESKYSNDIDFPGFMVEVPNGIYYGFPS T0334 289 :LGR 1b3mA 260 :GGC T0334 292 :FGTGY 1b3mA 264 :LKLGY T0334 299 :SSRFATE 1b3mA 271 :FGQKIDP T0334 306 :DEAVREFCEMWHLDPETQPLNRIRFRVGRNR 1b3mA 288 :PEDESNLRAFLEEYMPGANGELKRGAVCMYT T0334 338 :AWVGNCVSIG 1b3mA 319 :KTLDEHFIID T0334 348 :TSSCFVEPLESTGIYFVYAALYQLVKHFPDKS 1b3mA 334 :SNVVIAAGFSGHGFKFSSGVGEVLSQLALTGK T0334 482 :PDAPSPRLAH 1b3mA 366 :TEHDISIFSI Number of specific fragments extracted= 25 number of extra gaps= 2 total=3849 Will force an alignment to be made, even if fragment is small Number of alignments=169 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1b3mA/T0334-1b3mA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0334 read from 1b3mA/T0334-1b3mA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1b3mA read from 1b3mA/T0334-1b3mA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1b3mA in template set Warning: unaligning (T0334)G3 because first residue in template chain is (1b3mA)S1 Warning: unaligning (T0334)M246 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1b3mA)P220 Warning: unaligning (T0334)S247 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1b3mA)P220 T0334 4 :KIDKILIVGGGTAGWMAASYLGK 1b3mA 2 :THFDVIVVGAGSMGMAAGYQLAK T0334 30 :GTADITLLQAPDI 1b3mA 25 :QGVKTLLVDAFDP T0334 44 :TLGVGEATIPNLQTAF 1b3mA 47 :DTRIIRHAYGEGREYV T0334 79 :KVAIKFINWRTAGE 1b3mA 63 :PLALRSQELWYELE T0334 96 :EARELDGGP 1b3mA 77 :KETHHKIFT T0334 105 :DHFYHSFGLLKYHEQIPLSHYWFDRSYR 1b3mA 87 :TGVLVFGPKGESAFVAETMEAAKEHSLT T0334 136 :VEPFDYACYKEPVI 1b3mA 115 :VDLLEGDEINKRWP T0334 152 :ANRSPRRLDGSKVTNYAW 1b3mA 129 :GITVPENYNAIFEPNSGV T0334 171 :FDAHLVADFLRRFA 1b3mA 147 :LFSENCIRAYRELA T0334 186 :EKLGVRHVED 1b3mA 161 :EARGAKVLTH T0334 196 :RVEHVQRDANG 1b3mA 172 :RVEDFDISPDS T0334 209 :ESVRTATG 1b3mA 183 :VKIETANG T0334 218 :VFDADLFVDCSGFRGLLINKAMEEPFLD 1b3mA 191 :SYTADKLIVSMGAWNSKLLSKLNLDIPQ T0334 248 :DH 1b3mA 221 :YR T0334 253 :DSAVATQVPHDDDANGVEPFTSAIAMKSGWTWKIPMLGRFGTGYVY 1b3mA 223 :QVVGFFESDESKYSNDIDFPGFMVEVPNGIYYGFPSFGGCGLKLGY T0334 299 :SSRFATE 1b3mA 276 :DPDTINR T0334 306 :DEAVREFCEMW 1b3mA 288 :PEDESNLRAFL T0334 317 :HLDPET 1b3mA 300 :EYMPGA T0334 324 :PLNRIRFRVGRNR 1b3mA 306 :NGELKRGAVCMYT T0334 338 :AWVGNCVSIG 1b3mA 319 :KTLDEHFIID T0334 348 :TSSCFVEPLESTGIYFVYAALYQLVKHFPDKSL 1b3mA 334 :SNVVIAAGFSGHGFKFSSGVGEVLSQLALTGKT Number of specific fragments extracted= 21 number of extra gaps= 1 total=3870 Will force an alignment to be made, even if fragment is small Number of alignments=170 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1b3mA/T0334-1b3mA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0334 read from 1b3mA/T0334-1b3mA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1b3mA read from 1b3mA/T0334-1b3mA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1b3mA in template set Warning: unaligning (T0334)G3 because first residue in template chain is (1b3mA)S1 Warning: unaligning (T0334)L250 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1b3mA)P220 Warning: unaligning (T0334)L251 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1b3mA)P220 Warning: unaligning (T0334)S299 because of BadResidue code BAD_PEPTIDE in next template residue (1b3mA)T270 Warning: unaligning (T0334)S300 because of BadResidue code BAD_PEPTIDE at template residue (1b3mA)T270 T0334 4 :KIDKILIVGGGTAGWMAASYLGK 1b3mA 2 :THFDVIVVGAGSMGMAAGYQLAK T0334 30 :GTADITLLQAPDIPT 1b3mA 25 :QGVKTLLVDAFDPPH T0334 45 :LGVGEA 1b3mA 53 :HAYGEG T0334 51 :TIPNLQTAF 1b3mA 61 :YVPLALRSQ T0334 61 :DFL 1b3mA 70 :ELW T0334 68 :DEWMRECNASYKVAIKFINWRTAGEGTS 1b3mA 73 :YELEKETHHKIFTKTGVLVFGPKGESAF T0334 110 :SFGLLKYHEQIPLSHYWFDR 1b3mA 101 :VAETMEAAKEHSLTVDLLEG T0334 147 :PVILDANRSPRRLDGSK 1b3mA 121 :DEINKRWPGITVPENYN T0334 167 :Y 1b3mA 138 :A T0334 168 :AWHFDAHLVADFLRRFATEKLGVRHVEDRVEHVQRDANG 1b3mA 144 :SGVLFSENCIRAYRELAEARGAKVLTHTRVEDFDISPDS T0334 209 :ESVRTAT 1b3mA 183 :VKIETAN T0334 217 :RVFDADLFVDCSGFRG 1b3mA 190 :GSYTADKLIVSMGAWN T0334 233 :LLI 1b3mA 207 :KLL T0334 245 :DMSD 1b3mA 210 :SKLN T0334 252 :NDSAVATQ 1b3mA 221 :YRQVVGFF T0334 260 :VPHDDDANGVEPFTSAIAMKSGWTWKIPMLGRFGTGYVY 1b3mA 230 :SDESKYSNDIDFPGFMVEVPNGIYYGFPSFGGCGLKLGY T0334 307 :EAVREFCEMWHLDPETQPLNRIRFRVGRNRRAW 1b3mA 289 :EDESNLRAFLEEYMPGANGELKRGAVCMYTKTL T0334 340 :VGNCVSIGTSSCFVEPLESTGIYFVYAALY 1b3mA 333 :HSNVVIAAGFSGHGFKFSSGVGEVLSQLAL Number of specific fragments extracted= 18 number of extra gaps= 2 total=3888 Will force an alignment to be made, even if fragment is small Number of alignments=171 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1dxlA/T0334-1dxlA-t06-local-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1dxlA expands to /projects/compbio/data/pdb/1dxl.pdb.gz 1dxlA:Skipped atom 1337, because occupancy 0.500 <= existing 0.500 in 1dxlA Skipped atom 1339, because occupancy 0.500 <= existing 0.500 in 1dxlA Skipped atom 1341, because occupancy 0.500 <= existing 0.500 in 1dxlA Skipped atom 1343, because occupancy 0.500 <= existing 0.500 in 1dxlA Skipped atom 1345, because occupancy 0.500 <= existing 0.500 in 1dxlA Skipped atom 1347, because occupancy 0.500 <= existing 0.500 in 1dxlA Skipped atom 1349, because occupancy 0.500 <= existing 0.500 in 1dxlA Skipped atom 1351, because occupancy 0.500 <= existing 0.500 in 1dxlA Skipped atom 1353, because occupancy 0.500 <= existing 0.500 in 1dxlA Skipped atom 1355, because occupancy 0.500 <= existing 0.500 in 1dxlA Skipped atom 1357, because occupancy 0.500 <= existing 0.500 in 1dxlA Skipped atom 1359, because occupancy 0.500 <= existing 0.500 in 1dxlA # T0334 read from 1dxlA/T0334-1dxlA-t06-local-adpstyle5.a2m # 1dxlA read from 1dxlA/T0334-1dxlA-t06-local-adpstyle5.a2m # adding 1dxlA to template set # found chain 1dxlA in template set Warning: unaligning (T0334)S299 because of BadResidue code BAD_PEPTIDE in next template residue (1dxlA)P359 Warning: unaligning (T0334)S300 because of BadResidue code BAD_PEPTIDE at template residue (1dxlA)P359 Warning: unaligning (T0334)D319 because of BadResidue code BAD_PEPTIDE in next template residue (1dxlA)P384 Warning: unaligning (T0334)P320 because of BadResidue code BAD_PEPTIDE at template residue (1dxlA)P384 T0334 6 :D 1dxlA 5 :D T0334 7 :KILIVGGGTAGWMAASYLGK 1dxlA 8 :DVVIIGGGPGGYVAAIKAAQ T0334 29 :QGT 1dxlA 28 :LGF T0334 33 :DITLLQAPD 1dxlA 31 :KTTCIEKRG T0334 42 :IPTLGVGEATIPN 1dxlA 41 :LGGTCLNVGCIPS T0334 57 :TAFFDFLGIPED 1dxlA 54 :KALLHSSHMYHE T0334 69 :EWMRECNASYKVAIKFINWRTAGEGTS 1dxlA 68 :HSFANHGVKVSNVEIDLAAMMGQKDKA T0334 104 :PDHFYHSFGLL 1dxlA 161 :EKKIVSSTGAL T0334 131 :YRGKTV 1dxlA 175 :EIPKKL T0334 139 :FDYACYK 1dxlA 194 :SVWGRIG T0334 146 :EPVI 1dxlA 203 :VTVV T0334 172 :DAHLVADFLRRFA 1dxlA 216 :MDAEIRKQFQRSL T0334 186 :EKLGVRHVED 1dxlA 229 :EKQGMKFKLK T0334 196 :RVEHVQRDANG 1dxlA 240 :KVVGVDTSGDG T0334 209 :ESVRTAT 1dxlA 251 :VKLTVEP T0334 216 :GR 1dxlA 261 :GE T0334 218 :VFDADLFVDCSGFRG 1dxlA 265 :IIEADVVLVSAGRTP T0334 233 :LLINKAMEEPFLD 1dxlA 283 :GLNLDKIGVETDK T0334 247 :SDHLLNDSAVATQVPHDDDANGVEPFTS 1dxlA 296 :LGRILVNERFSTNVSGVYAIGDVIPGPM T0334 275 :AIAMKSGWTWKIPMLGR 1dxlA 326 :HKAEEDGVACVEYLAGK T0334 292 :FGTGYVY 1dxlA 351 :VPGVVYT T0334 301 :RFATE 1dxlA 360 :EVASV T0334 306 :DEAVREFCEM 1dxlA 369 :EQVKETGVEY T0334 316 :WHL 1dxlA 380 :VGK T0334 321 :ETQPLNRIRFRVGRNR 1dxlA 387 :ANSRAKAIDNAEGLVK T0334 342 :NCVSI 1dxlA 414 :GVHIM T0334 364 :VYAALYQLVKHFP 1dxlA 419 :APNAGELIHEAAI Number of specific fragments extracted= 27 number of extra gaps= 2 total=3915 Will force an alignment to be made, even if fragment is small Number of alignments=172 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1zy8A/T0334-1zy8A-t06-local-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1zy8A expands to /projects/compbio/data/pdb/1zy8.pdb.gz 1zy8A:Skipped atom 346, because occupancy 0.200 <= existing 0.300 in 1zy8A # T0334 read from 1zy8A/T0334-1zy8A-t06-local-adpstyle5.a2m # 1zy8A read from 1zy8A/T0334-1zy8A-t06-local-adpstyle5.a2m # adding 1zy8A to template set # found chain 1zy8A in template set Warning: unaligning (T0334)P53 because of BadResidue code BAD_PEPTIDE in next template residue (1zy8A)S53 Warning: unaligning (T0334)N54 because of BadResidue code BAD_PEPTIDE at template residue (1zy8A)S53 Warning: unaligning (T0334)F243 because of BadResidue code BAD_PEPTIDE in next template residue (1zy8A)D297 Warning: unaligning (T0334)L244 because of BadResidue code BAD_PEPTIDE at template residue (1zy8A)D297 T0334 3 :GKID 1zy8A 3 :QPID T0334 7 :KILIVGGGTAGWMAASYLGK 1zy8A 8 :DVTVIGSGPGGYVAAIKAAQ T0334 29 :QGT 1zy8A 28 :LGF T0334 33 :DITLLQAPD 1zy8A 31 :KTVCIEKNE T0334 42 :IPTLGVGEATI 1zy8A 41 :LGGTCLNVGCI T0334 57 :TAFFDFLGIPED 1zy8A 54 :KALLNNSHYYHM T0334 69 :EWMRECNASYKVAIKFINWRTAGEGTS 1zy8A 69 :KDFASRGIEMSEVRLNLDKMMEQKSTA T0334 104 :PDHFYHSFGLL 1zy8A 162 :EDTIVSSTGAL T0334 131 :YRGKTV 1zy8A 176 :KVPEKM T0334 139 :FDYACYK 1zy8A 195 :SVWQRLG T0334 146 :EPVI 1zy8A 204 :VTAV T0334 172 :DAHLVADFLRRFA 1zy8A 218 :IDMEISKNFQRIL T0334 186 :EKLGVRHVED 1zy8A 231 :QKQGFKFKLN T0334 196 :RVEHVQRDANGNI 1zy8A 242 :KVTGATKKSDGKI T0334 209 :ESVRTAT 1zy8A 256 :VSIEAAS T0334 216 :GR 1zy8A 264 :GK T0334 218 :VFDADLFVDCSGFRG 1zy8A 268 :VITCDVLLVCIGRRP T0334 233 :LLINKAMEEP 1zy8A 286 :NLGLEELGIE T0334 245 :D 1zy8A 298 :P T0334 247 :SDHLLNDSAVATQVPHDDDANGVEPFTS 1zy8A 299 :RGRIPVNTRFQTKIPNIYAIGDVVAGPM T0334 275 :AIAMKSGWTWKIPM 1zy8A 329 :HKAEDEGIICVEGM T0334 289 :LGR 1zy8A 344 :GGA T0334 292 :FGTGYVYSSRFATE 1zy8A 354 :VPSVIYTHPEVAWV T0334 306 :DEAVREFCEM 1zy8A 372 :EQLKEEGIEY T0334 316 :WHLDP 1zy8A 383 :VGKFP T0334 321 :ETQPLNRIRFRVGRNR 1zy8A 390 :ANSRAKTNADTDGMVK T0334 337 :RAWVGNCV 1zy8A 409 :QKSTDRVL T0334 349 :SSCFVEPLESTGIYFVYAA 1zy8A 417 :GAHILGPGAGEMVNEAALA Number of specific fragments extracted= 28 number of extra gaps= 2 total=3943 Will force an alignment to be made, even if fragment is small Number of alignments=173 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1y56B/T0334-1y56B-t06-local-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1y56B expands to /projects/compbio/data/pdb/1y56.pdb.gz 1y56B:# T0334 read from 1y56B/T0334-1y56B-t06-local-adpstyle5.a2m # 1y56B read from 1y56B/T0334-1y56B-t06-local-adpstyle5.a2m # adding 1y56B to template set # found chain 1y56B in template set Warning: unaligning (T0334)A58 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1y56B)I51 Warning: unaligning (T0334)F59 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1y56B)I51 Warning: unaligning (T0334)P147 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1y56B)I125 Warning: unaligning (T0334)V148 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1y56B)I125 Warning: unaligning (T0334)E194 because of BadResidue code BAD_PEPTIDE in next template residue (1y56B)Y169 Warning: unaligning (T0334)D195 because of BadResidue code BAD_PEPTIDE at template residue (1y56B)Y169 Warning: unaligning (T0334)S228 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1y56B)N202 Warning: unaligning (T0334)G229 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1y56B)N202 Warning: unaligning (T0334)S280 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1y56B)G248 Warning: unaligning (T0334)G281 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1y56B)G248 Warning: unaligning (T0334)S300 because of BadResidue code BAD_PEPTIDE in next template residue (1y56B)G269 Warning: unaligning (T0334)R301 because of BadResidue code BAD_PEPTIDE at template residue (1y56B)G269 Warning: unaligning (T0334)R334 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1y56B)Y308 Warning: unaligning (T0334)N335 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1y56B)Y308 Warning: unaligning (T0334)T348 because of BadResidue code BAD_PEPTIDE in next template residue (1y56B)D326 Warning: unaligning (T0334)S349 because of BadResidue code BAD_PEPTIDE at template residue (1y56B)D326 Warning: unaligning (T0334)F375 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1y56B)T353 Warning: unaligning (T0334)P376 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1y56B)T353 T0334 4 :KID 1y56B 3 :PEK T0334 7 :KILIVGGGTAGWMAASYLGK 1y56B 7 :EIVVIGGGIVGVTIAHELAK T0334 29 :QGT 1y56B 27 :RGE T0334 33 :DITLLQAP 1y56B 30 :EVTVIEKR T0334 46 :GVGEATIPNLQT 1y56B 38 :FIGSGSTFRCGT T0334 61 :DFLGIPED 1y56B 52 :RQQFNDEA T0334 69 :EWMRECNASYKVAIKFIN 1y56B 61 :VRVMKRSVELWKKYSEEY T0334 104 :PDHFYHSFGL 1y56B 88 :LFLLYDDEEV T0334 131 :YRGKTV 1y56B 99 :TFKRNI T0334 139 :FDYACYK 1y56B 105 :EIQNKFG T0334 146 :E 1y56B 123 :K T0334 149 :I 1y56B 126 :V T0334 172 :DAHLVADFLRRFA 1y56B 147 :DPFEATTAFAVKA T0334 186 :EKLGVRHV 1y56B 160 :KEYGAKLL T0334 196 :RVEHVQRDAN 1y56B 171 :EVKGFLIENN T0334 207 :NIESVRTATG 1y56B 181 :EIKGVKTNKG T0334 218 :VFDADLFVDC 1y56B 191 :IIKTGIVVNA T0334 230 :FRGLLINKAMEEPFLDM 1y56B 203 :AWANLINAMAGIKTKIP T0334 254 :SAVATQVPHDDDANGVEPFTSAIAMK 1y56B 221 :EPYKHQAVITQPIKRGTINPMVISFK T0334 282 :WTWKIPM 1y56B 249 :HAYLTQT T0334 289 :LGRFGTGYVYS 1y56B 257 :HGGIIGGIGYE T0334 302 :FATE 1y56B 270 :PTYD T0334 306 :DEAVREFCEM 1y56B 278 :YEFLREVSYY T0334 316 :WHLDPETQPLNRIRFRVG 1y56B 289 :TKIIPALKNLLILRTWAG T0334 336 :R 1y56B 309 :A T0334 338 :AWVGNCVSIG 1y56B 310 :KTPDSNPAIG T0334 350 :SCFVEPLESTGIYFVYAALYQLVKH 1y56B 327 :YYIAAGFSGHGFMMAPAVGEMVAEL T0334 377 :DKSLNPVLTARFNREIETM 1y56B 356 :KTKLPVEWYDPYRFERGEL Number of specific fragments extracted= 28 number of extra gaps= 9 total=3971 Will force an alignment to be made, even if fragment is small Number of alignments=174 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1lpfA/T0334-1lpfA-t06-local-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1lpfA expands to /projects/compbio/data/pdb/1lpf.pdb.gz 1lpfA:# T0334 read from 1lpfA/T0334-1lpfA-t06-local-adpstyle5.a2m # 1lpfA read from 1lpfA/T0334-1lpfA-t06-local-adpstyle5.a2m # adding 1lpfA to template set # found chain 1lpfA in template set Warning: unaligning (T0334)L233 because of BadResidue code BAD_PEPTIDE at template residue (1lpfA)D284 T0334 5 :ID 1lpfA 2 :QK T0334 7 :KILIVGGGTAGWMAASYLGK 1lpfA 5 :DVVVIGAGPGGYVAAIRAAQ T0334 29 :QGT 1lpfA 25 :LGL T0334 33 :DITLLQ 1lpfA 28 :KTACIE T0334 39 :APDIPTLGVGEATIPN 1lpfA 41 :KVALGGTCLNVGCIPS T0334 57 :TAFFDFLGIPED 1lpfA 57 :KALLDSSYKYHE T0334 69 :EWMRECNASYKVAIKFINWRTAGEGTS 1lpfA 71 :EAFKVHGIEAKGVTIDVPAMVARKANI T0334 104 :PDHFYHSFGLL 1lpfA 164 :DDIIVDSTGAL T0334 131 :YRGKTV 1lpfA 178 :AVPKKL T0334 139 :FDYACYK 1lpfA 197 :SVWARLG T0334 146 :EPVI 1lpfA 206 :VTVL T0334 172 :DAHLVADFLRRFA 1lpfA 219 :ADEQIAKEALKVL T0334 186 :EKLGVRHVED 1lpfA 232 :TKQGLNIRLG T0334 196 :RVEHVQRDANG 1lpfA 243 :RVTASEVKKKQ T0334 209 :ESVRTAT 1lpfA 254 :VTVTFTD T0334 216 :GR 1lpfA 263 :GE T0334 218 :VFDADLFVDCSGFRG 1lpfA 266 :KETFDKLIVAVGRRP T0334 234 :LINKAMEEPFLD 1lpfA 285 :LLAADSGVTLDE T0334 247 :SDHLLNDSAVATQVPHDDDANGVEPFTS 1lpfA 297 :RGFIYVDDHCKTSVPGVFAIGDVVRGAM T0334 275 :AIAMKSGWTWKIPM 1lpfA 327 :HKASEEGVMVAERI T0334 289 :LGR 1lpfA 342 :GHK T0334 292 :FGTGYVYSSRFATE 1lpfA 352 :IPSVIYTHPEIAWV T0334 306 :DEAVREFCEM 1lpfA 370 :QTLKAEGVEV T0334 316 :WHLDP 1lpfA 381 :VGTFP T0334 321 :ETQPLNRIRFRVGRNR 1lpfA 388 :ASGRAMAANDTTGLVK T0334 338 :AWVG 1lpfA 404 :VIAD T0334 342 :NCVSIGTSSCFVEPLESTGIY 1lpfA 415 :GVHVIGPSAAELVQQGAIGME Number of specific fragments extracted= 27 number of extra gaps= 1 total=3998 Will force an alignment to be made, even if fragment is small Number of alignments=175 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1aogA/T0334-1aogA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1aogA expands to /projects/compbio/data/pdb/1aog.pdb.gz 1aogA:# T0334 read from 1aogA/T0334-1aogA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1aogA read from 1aogA/T0334-1aogA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1aogA to template set # found chain 1aogA in template set Warning: unaligning (T0334)K4 because first residue in template chain is (1aogA)S3 Warning: unaligning (T0334)I5 because of BadResidue code BAD_PEPTIDE in next template residue (1aogA)I5 Warning: unaligning (T0334)D6 because of BadResidue code BAD_PEPTIDE at template residue (1aogA)I5 Warning: unaligning (T0334)Y144 because of BadResidue code BAD_PEPTIDE in next template residue (1aogA)D215 Warning: unaligning (T0334)K145 because of BadResidue code BAD_PEPTIDE at template residue (1aogA)D215 Warning: unaligning (T0334)E146 because of BadResidue code BAD_PEPTIDE at template residue (1aogA)G216 T0334 7 :KILIVGGGTAGWMAASYLGK 1aogA 7 :DLVVIGAGSGGLEAAWNAAT T0334 28 :LQGT 1aogA 27 :LYKK T0334 33 :DITLLQAPD 1aogA 31 :RVAVIDVQM T0334 42 :IPTL 1aogA 41 :HGPP T0334 48 :GEATIPN 1aogA 79 :GFGWEFD T0334 60 :FDFLGIPEDEWMRECNASYKVAIKFINWRTAGEGTS 1aogA 86 :RTTLRAEWKNLIAVKDEAVLNINKSYDEMFRDTEGL T0334 96 :EARELDG 1aogA 164 :WPHMPNI T0334 103 :GPDHFYHSFGLL 1aogA 172 :GIEHCISSNEAF T0334 115 :KYHEQIPLSHYWFDRSYRGKTV 1aogA 187 :EPPRRVLTVGGGFISVEFAGIF T0334 139 :FDYAC 1aogA 209 :NAYKP T0334 147 :PVILD 1aogA 217 :QVTLC T0334 152 :ANRSPRRL 1aogA 223 :RGEMILRG T0334 172 :DAHLVADFLRRFA 1aogA 231 :FDHTLREELTKQL T0334 186 :EKLGVRHVED 1aogA 244 :TANGIQILTK T0334 196 :RVEHVQRDANGN 1aogA 255 :NPAKVELNADGS T0334 209 :ESVRTATGRVFDADLFVDCSGFRG 1aogA 267 :KSVTFESGKKMDFDLVMMAIGRSP T0334 233 :LLINKAMEEPFL 1aogA 294 :DLQLQNAGVMIK T0334 247 :SDHLLNDSAVATQVPHDDDANGV 1aogA 306 :NGGVQVDEYSRTNVSNIYAIGDV T0334 333 :GRNR 1aogA 367 :FSIP T0334 337 :RAWVG 1aogA 417 :TNHSD T0334 342 :NCVSIGTSS 1aogA 426 :GVHLLGDNA T0334 427 :ADGMQEKIDMYRAG 1aogA 435 :PEIIQGIGICLKLN T0334 441 :MAINAPASDDAQLYYGNFEE 1aogA 454 :FYNTIGVHPTSAEELCSMRT Number of specific fragments extracted= 23 number of extra gaps= 1 total=4021 Will force an alignment to be made, even if fragment is small Number of alignments=176 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1aogA/T0334-1aogA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0334 read from 1aogA/T0334-1aogA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1aogA read from 1aogA/T0334-1aogA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1aogA in template set Warning: unaligning (T0334)G3 because first residue in template chain is (1aogA)S3 Warning: unaligning (T0334)K4 because of BadResidue code BAD_PEPTIDE in next template residue (1aogA)I5 Warning: unaligning (T0334)I5 because of BadResidue code BAD_PEPTIDE at template residue (1aogA)I5 T0334 6 :DKILIVGGGTAGWMAASYLGKA 1aogA 6 :FDLVVIGAGSGGLEAAWNAATL T0334 30 :GTADITLLQAP 1aogA 28 :YKKRVAVIDVQ T0334 41 :DI 1aogA 40 :VH T0334 43 :PTLGVGEATIPNLQTAF 1aogA 43 :PPFFSALGGTCVNVGCV T0334 73 :ECNASYKVAIKFINWRTA 1aogA 60 :PKKLMVTGAQYMEHLRES T0334 96 :EARELDGGPDHFYHSFGLL 1aogA 78 :AGFGWEFDRTTLRAEWKNL T0334 115 :KYHEQI 1aogA 103 :AVLNIN T0334 121 :PLSHYWFDRS 1aogA 110 :SYDEMFRDTE T0334 141 :YACYKE 1aogA 120 :GLEFFL T0334 166 :NYAW 1aogA 126 :GWGS T0334 170 :HFD 1aogA 230 :GFD T0334 174 :HLVADFLRRFA 1aogA 233 :HTLREELTKQL T0334 186 :EKLGVRHVED 1aogA 244 :TANGIQILTK T0334 196 :RVEHVQRDANGN 1aogA 255 :NPAKVELNADGS T0334 209 :ESVRTATGRVFDADLFVDCSGFRGLL 1aogA 267 :KSVTFESGKKMDFDLVMMAIGRSPRT T0334 236 :NKA 1aogA 293 :KDL T0334 239 :MEEPFL 1aogA 350 :FGTTPR T0334 281 :GWTWKIPMLGR 1aogA 412 :VAKIITNHSDG T0334 292 :FGTGYVYSSRFA 1aogA 424 :VLGVHLLGDNAP T0334 307 :EAVREFCEMW 1aogA 436 :EIIQGIGICL T0334 320 :PETQPLNRIRFRVGRNRRAWVG 1aogA 459 :GVHPTSAEELCSMRTPSYYYVK Number of specific fragments extracted= 21 number of extra gaps= 0 total=4042 Will force an alignment to be made, even if fragment is small Number of alignments=177 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1aogA/T0334-1aogA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0334 read from 1aogA/T0334-1aogA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1aogA read from 1aogA/T0334-1aogA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1aogA in template set Warning: unaligning (T0334)G30 because of BadResidue code BAD_PEPTIDE in next template residue (1aogA)D215 Warning: unaligning (T0334)T31 because of BadResidue code BAD_PEPTIDE at template residue (1aogA)D215 Warning: unaligning (T0334)A32 because of BadResidue code BAD_PEPTIDE at template residue (1aogA)G216 T0334 3 :GKIDKILIVGGGTAGWMAASYLGKALQ 1aogA 187 :EPPRRVLTVGGGFISVEFAGIFNAYKP T0334 33 :DITLLQAPDI 1aogA 217 :QVTLCYRGEM T0334 51 :TI 1aogA 227 :IL T0334 63 :LGIPE 1aogA 229 :RGFDH T0334 175 :LVADFLRRFATEKLGVRHVEDRVEHVQRDANGN 1aogA 234 :TLREELTKQLTANGIQILTKENPAKVELNADGS T0334 209 :ESVRTATGRVFDADLFVDCSGFR 1aogA 267 :KSVTFESGKKMDFDLVMMAIGRS T0334 244 :LDMSDH 1aogA 290 :PRTKDL T0334 287 :PMLGR 1aogA 296 :QLQNA T0334 292 :FGTGYVYSSRFA 1aogA 304 :IKNGGVQVDEYS T0334 337 :RAWVGNCVSIGTSSCFVEPL 1aogA 316 :RTNVSNIYAIGDVTNRVMLT T0334 362 :YFVYAALYQLVKHFPDKS 1aogA 336 :PVAINEAAALVDTVFGTT Number of specific fragments extracted= 11 number of extra gaps= 1 total=4053 Will force an alignment to be made, even if fragment is small Number of alignments=178 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1x31B/T0334-1x31B-t06-local-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1x31B expands to /projects/compbio/data/pdb/1x31.pdb.gz 1x31B:# T0334 read from 1x31B/T0334-1x31B-t06-local-adpstyle5.a2m # 1x31B read from 1x31B/T0334-1x31B-t06-local-adpstyle5.a2m # adding 1x31B to template set # found chain 1x31B in template set T0334 2 :SGKID 1x31B 15 :PEPKK T0334 7 :KILIVGGGTAGWMAASYLGK 1x31B 22 :DVVIVGGGGHGLATAYYLAK T0334 29 :QGTADITLLQAP 1x31B 43 :HGITNVAVLEKG T0334 46 :GVGEATIPNLQTAF 1x31B 55 :WLAGGNMARNTTII T0334 61 :DFLGIPED 1x31B 69 :RSNYLWDE T0334 69 :EWMRECNAS 1x31B 78 :AGIYEKSLK T0334 104 :PDHFYHSFGLL 1x31B 97 :YDFLFSQRGVL T0334 131 :YRGKTV 1x31B 111 :HTLGDV T0334 137 :EP 1x31B 130 :GV T0334 139 :FDYACYK 1x31B 134 :EWLTPEQ T0334 146 :EPVI 1x31B 145 :CPII T0334 172 :DAHLVADFLRRFA 1x31B 171 :KHDHVAWAFARKA T0334 186 :EKLGVRHVED 1x31B 184 :NEMGVDIIQN T0334 196 :RVEHVQRDAN 1x31B 195 :EVTGFLKDGE T0334 207 :NIESVRTATG 1x31B 205 :KVTGVKTTRG T0334 218 :VFDADLFVDCSGFRGLLINKAMEEPFLDM 1x31B 215 :TILAGKVALAGAGHSSVLAELAGFELPIQ T0334 247 :SDHLLNDSAV 1x31B 246 :PLQALVSELF T0334 271 :PFTS 1x31B 256 :EPVH T0334 275 :AIAMKSGWTWKIPM 1x31B 262 :VVMSNHIHVYVSQA T0334 289 :LGRFGTGYVYSSRFATE 1x31B 277 :KGELVMGAGIDSYNGYG T0334 306 :DEAVREFCEMWHLDPETQPLNRIRFRVGRNR 1x31B 299 :HVIEEQMAAAVELFPIFARAHVLRTWGGIVD T0334 338 :AWVGNCVSIG 1x31B 330 :TTMDASPIIS T0334 348 :TSSCFVEPLESTGIYFVYAALYQLVKHFP 1x31B 344 :QNLYVNCGWGTGGFKGTPGAGYTLAHTIA T0334 378 :KSLNPVLTARFNREIETMFDDT 1x31B 373 :HDEPHKLNAPFALERFETGHLI Number of specific fragments extracted= 24 number of extra gaps= 0 total=4077 Will force an alignment to be made, even if fragment is small Number of alignments=179 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1gv4A/T0334-1gv4A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1gv4A expands to /projects/compbio/data/pdb/1gv4.pdb.gz 1gv4A:# T0334 read from 1gv4A/T0334-1gv4A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1gv4A read from 1gv4A/T0334-1gv4A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1gv4A to template set # found chain 1gv4A in template set T0334 3 :GKID 1gv4A 127 :APSH T0334 7 :KILIVGGGTAGWMAASYLGK 1gv4A 132 :PFLLIGGGTAAFAAARSIRA T0334 28 :L 1gv4A 152 :R T0334 29 :QGT 1gv4A 154 :PGA T0334 33 :DITLLQAPD 1gv4A 157 :RVLIVSEDP T0334 42 :IPTLGVG 1gv4A 167 :LPYMRPP T0334 57 :TAF 1gv4A 174 :LSK T0334 61 :DFLGIPEDEWMRECNAS 1gv4A 177 :ELWFSDDPNVTKTLQFR T0334 78 :YKVAIKFINWRTAGEGTS 1gv4A 195 :WNGKERSIYFQPPSFYVS T0334 96 :EARELDG 1gv4A 215 :DLPNIEN T0334 123 :SHYWFDRSYRGKTVEP 1gv4A 222 :GGVAVLTGKKVVHLDV T0334 139 :FDYACYKEPVILD 1gv4A 320 :RKSQASGIEVIQL T0334 152 :ANRSPRRLD 1gv4A 334 :PEKGNMGKI T0334 172 :DAHLVADFLRRFA 1gv4A 343 :LPQYLSNWTMEKV T0334 186 :EKLGVRHVED 1gv4A 356 :KREGVKVMPN T0334 196 :RVEHVQRDAN 1gv4A 367 :IVQSVGVSGG T0334 207 :NIE 1gv4A 377 :RLL T0334 211 :VRTATGRVFDADLFVDCSGFRG 1gv4A 380 :IKLKDGRKVETDHIVTAVGLEP T0334 233 :LLINKAMEEPFLDMSDHLLNDSAV 1gv4A 403 :VELAKTGGLEIDSDFGGFRVNAEL T0334 338 :AWVGNCVSIGTSSCF 1gv4A 427 :QARSNIWVAGDAACF T0334 363 :FVYAALYQLVKHFPDKSLN 1gv4A 456 :HAVVSGRLAGENMTGAAKP Number of specific fragments extracted= 21 number of extra gaps= 0 total=4098 Will force an alignment to be made, even if fragment is small Number of alignments=180 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1gv4A/T0334-1gv4A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0334 read from 1gv4A/T0334-1gv4A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1gv4A read from 1gv4A/T0334-1gv4A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1gv4A in template set T0334 2 :SGKIDKILIVGGGTAGWMAASYLGK 1gv4A 127 :APSHVPFLLIGGGTAAFAAARSIRA T0334 28 :LQGTADITLLQAPDIPTLGVGEATI 1gv4A 152 :RDPGARVLIVSEDPELPYMRPPLSK T0334 61 :DFLGIPEDEW 1gv4A 177 :ELWFSDDPNV T0334 127 :FDR 1gv4A 187 :TKT T0334 136 :VE 1gv4A 190 :LQ T0334 141 :YACYKEPVILDANRSPRR 1gv4A 192 :FRQWNGKERSIYFQPPSF T0334 159 :LDGSKVTNYAW 1gv4A 213 :AQDLPNIENGG T0334 170 :HFD 1gv4A 342 :ILP T0334 174 :HLVADFLRRFA 1gv4A 345 :QYLSNWTMEKV T0334 186 :EKLGVRHVED 1gv4A 356 :KREGVKVMPN T0334 196 :RVEHVQRDANG 1gv4A 367 :IVQSVGVSGGR T0334 209 :ESVRTATGRVFDADLFVDCSGFRGLL 1gv4A 378 :LLIKLKDGRKVETDHIVTAVGLEPNV T0334 235 :INKAMEEPFLDMSDH 1gv4A 405 :LAKTGGLEIDSDFGG T0334 250 :LLNDSAVAT 1gv4A 426 :LQARSNIWV T0334 266 :ANGVE 1gv4A 472 :AKPYW T0334 271 :PFTSAIA 1gv4A 478 :QSMFWSD T0334 278 :MKSGWTWKIPM 1gv4A 486 :GPDVGYEAIGL T0334 289 :LGR 1gv4A 499 :SSL T0334 292 :FGTGYVYSSRFATEDEAVREF 1gv4A 503 :TVGVFAKATAQDNPKSATEQS T0334 313 :CEMW 1gv4A 529 :SESE T0334 317 :HLDPETQPLNRIRFRVGRNRRAWV 1gv4A 550 :PQVPVEGEDYGKGVIFYLRDKVVV T0334 342 :NCVSIG 1gv4A 574 :GIVLWN T0334 361 :IYFVYAALYQ 1gv4A 584 :MPIARKIIKD Number of specific fragments extracted= 23 number of extra gaps= 0 total=4121 Will force an alignment to be made, even if fragment is small Number of alignments=181 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1gv4A/T0334-1gv4A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0334 read from 1gv4A/T0334-1gv4A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1gv4A read from 1gv4A/T0334-1gv4A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1gv4A in template set T0334 4 :KIDKILIVGGGTAGWMAASYLGKAL 1gv4A 298 :EVKSITVIGGGFLGSELACALGRKS T0334 29 :QGTADITLLQAPDI 1gv4A 324 :ASGIEVIQLFPEKG T0334 46 :GVGEATIPNLQTAF 1gv4A 338 :NMGKILPQYLSNWT T0334 181 :RRFATEKLGVRHVEDRVEHVQRDANG 1gv4A 352 :MEKVKREGVKVMPNAIVQSVGVSGGR T0334 209 :ESVRTATGRVFDADLFVDCSGF 1gv4A 378 :LLIKLKDGRKVETDHIVTAVGL T0334 235 :INKAMEEPFLDMSDHLL 1gv4A 405 :LAKTGGLEIDSDFGGFR T0334 260 :V 1gv4A 422 :V T0334 300 :SRFA 1gv4A 423 :NAEL T0334 338 :AWVGNCVSIGTSSCFVE 1gv4A 427 :QARSNIWVAGDAACFYD T0334 358 :STGIYFVYAALYQLVKHFPDKSL 1gv4A 451 :VEHHDHAVVSGRLAGENMTGAAK Number of specific fragments extracted= 10 number of extra gaps= 0 total=4131 Will force an alignment to be made, even if fragment is small Number of alignments=182 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1v59A/T0334-1v59A-t06-local-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1v59A expands to /projects/compbio/data/pdb/1v59.pdb.gz 1v59A:# T0334 read from 1v59A/T0334-1v59A-t06-local-adpstyle5.a2m # 1v59A read from 1v59A/T0334-1v59A-t06-local-adpstyle5.a2m # adding 1v59A to template set # found chain 1v59A in template set T0334 5 :ID 1v59A 3 :NK T0334 7 :KILIVGGGTAGWMAASYLGK 1v59A 7 :DVVIIGGGPAGYVAAIKAAQ T0334 29 :QGT 1v59A 27 :LGF T0334 33 :DITLLQAPD 1v59A 30 :NTACVEKRG T0334 42 :IPTLGVGEATIPN 1v59A 40 :LGGTCLNVGCIPS T0334 57 :TAFFDFLGIPED 1v59A 53 :KALLNNSHLFHQ T0334 69 :EWMRECNASYKVAIKFINWRTAGEGTS 1v59A 67 :TEAQKRGIDVNGDIKINVANFQKAKDD T0334 104 :PDHFYHSFGLL 1v59A 167 :EEKIVSSTGAL T0334 131 :YRGKTV 1v59A 181 :EIPKRL T0334 139 :FDYACYK 1v59A 200 :SVYSRLG T0334 146 :EPVI 1v59A 209 :VTVV T0334 172 :DAHLVADFLRRFA 1v59A 222 :MDGEVAKATQKFL T0334 186 :EKLGVRHVED 1v59A 235 :KKQGLDFKLS T0334 196 :RVEHVQRDANGNIESVRTAT 1v59A 246 :KVISAKRNDDKNVVEIVVED T0334 216 :GRVFDADLFVDCSGFRG 1v59A 271 :QENLEAEVLLVAVGRRP T0334 233 :LLINKAMEEPFLD 1v59A 291 :GLGAEKIGLEVDK T0334 247 :SDHLLNDSAVATQVPHDDDANGVEPFTS 1v59A 304 :RGRLVIDDQFNSKFPHIKVVGDVTFGPM T0334 275 :AIAMKSGWTWKIPM 1v59A 334 :HKAEEEGIAAVEML T0334 289 :LGR 1v59A 349 :TGH T0334 292 :FGTGYVYSSRFATE 1v59A 359 :IPSVMYSHPEVAWV T0334 306 :DEAVREFCEM 1v59A 377 :EQLKEAGIDY T0334 316 :WHLDP 1v59A 388 :IGKFP T0334 321 :ETQPLNRIRFRVGRNR 1v59A 395 :ANSRAKTNQDTEGFVK T0334 338 :AWVG 1v59A 411 :ILID T0334 342 :NCVSIGTSSCFV 1v59A 422 :GAHIIGPNAGEM T0334 358 :STGIYFVYAALYQLV 1v59A 434 :IAEAGLALEYGASAE Number of specific fragments extracted= 26 number of extra gaps= 0 total=4157 Will force an alignment to be made, even if fragment is small Number of alignments=183 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ojt/T0334-1ojt-t06-local-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1ojt expands to /projects/compbio/data/pdb/1ojt.pdb.gz 1ojt:Warning: there is no chain 1ojt will retry with 1ojtA # T0334 read from 1ojt/T0334-1ojt-t06-local-adpstyle5.a2m # 1ojt read from 1ojt/T0334-1ojt-t06-local-adpstyle5.a2m # adding 1ojt to template set # found chain 1ojt in template set Warning: unaligning (T0334)K7 because of BadResidue code BAD_PEPTIDE at template residue (1ojt)D124 Warning: unaligning (T0334)T15 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1ojt)G133 Warning: unaligning (T0334)A16 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1ojt)G133 Warning: unaligning (T0334)G17 because of BadResidue code BAD_PEPTIDE in next template residue (1ojt)Y135 Warning: unaligning (T0334)W18 because of BadResidue code BAD_PEPTIDE at template residue (1ojt)Y135 Warning: unaligning (T0334)P40 because of BadResidue code BAD_PEPTIDE in next template residue (1ojt)K155 Warning: unaligning (T0334)D41 because of BadResidue code BAD_PEPTIDE at template residue (1ojt)K155 Warning: unaligning (T0334)V47 because of BadResidue code BAD_PEPTIDE in next template residue (1ojt)N163 Warning: unaligning (T0334)G48 because of BadResidue code BAD_PEPTIDE at template residue (1ojt)N163 Warning: unaligning (T0334)E49 because of BadResidue code BAD_PEPTIDE at template residue (1ojt)V164 Warning: unaligning (T0334)V197 because of BadResidue code BAD_PEPTIDE in next template residue (1ojt)V366 Warning: unaligning (T0334)E198 because of BadResidue code BAD_PEPTIDE at template residue (1ojt)V366 Warning: unaligning (T0334)A277 because of BadResidue code BAD_PEPTIDE in next template residue (1ojt)V452 Warning: unaligning (T0334)M278 because of BadResidue code BAD_PEPTIDE at template residue (1ojt)V452 Warning: unaligning (T0334)W339 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1ojt)F528 Warning: unaligning (T0334)V340 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1ojt)F528 Warning: unaligning (T0334)P355 because of BadResidue code BAD_PEPTIDE in next template residue (1ojt)D547 Warning: unaligning (T0334)L356 because of BadResidue code BAD_PEPTIDE at template residue (1ojt)D547 Warning: unaligning (T0334)T359 because of BadResidue code BAD_PEPTIDE in next template residue (1ojt)E551 Warning: unaligning (T0334)G360 because of BadResidue code BAD_PEPTIDE at template residue (1ojt)E551 Warning: unaligning (T0334)I361 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1ojt)C553 Warning: unaligning (T0334)Y362 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1ojt)C553 Warning: unaligning (T0334)F363 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1ojt)L554 T0334 5 :ID 1ojt 121 :AE T0334 8 :ILIVGGG 1ojt 125 :VVVLGGG T0334 19 :MAASYLGK 1ojt 136 :SAAFAAAD T0334 29 :QGT 1ojt 144 :EGL T0334 33 :DITLLQA 1ojt 147 :KVAIVER T0334 42 :IPTLG 1ojt 157 :LGGVC T0334 50 :ATIPN 1ojt 165 :GCIPS T0334 57 :TAFFDFLGIPED 1ojt 170 :KALLHNAAVIDE T0334 69 :EWMRECNASYKVAIKFINWRTAGEGTS 1ojt 183 :RHLAANGIKYPEPELDIDMLRAYKDGV T0334 104 :PDHFYHSFGLL 1ojt 285 :DPRIIDSSGAL T0334 131 :YRGKTV 1ojt 299 :EVPGKL T0334 139 :FDYACYK 1ojt 318 :TVYSTLG T0334 146 :EPVI 1ojt 327 :LDVV T0334 172 :DAHLVADFLRRFA 1ojt 340 :ADRDLVKVWQKQN T0334 186 :EKLGVRHVED 1ojt 353 :EYRFDNIMVN T0334 196 :R 1ojt 364 :K T0334 199 :HVQRDANG 1ojt 367 :AVEPKEDG T0334 209 :ESVRTAT 1ojt 375 :VYVTFEG T0334 216 :GRVFDADLFVDCSGFRG 1ojt 386 :KEPQRYDAVLVAAGRAP T0334 233 :LLINKAMEEPFLD 1ojt 406 :LISAEKAGVAVTD T0334 247 :SDHLLNDSAVATQVPHDDDANGVEPFTS 1ojt 419 :RGFIEVDKQMRTNVPHIYAIGDIVGQPM T0334 275 :AI 1ojt 449 :HK T0334 279 :KSGWTWKIPM 1ojt 453 :HEGHVAAENC T0334 289 :LGR 1ojt 464 :GHK T0334 292 :FGTGYVYSSRFATE 1ojt 474 :IPGVAYTSPEVAWV T0334 306 :DEAVREFCEM 1ojt 492 :LSAKASARKI T0334 316 :WHLDP 1ojt 503 :KANFP T0334 321 :ETQPLNRIRFRVGRNRRA 1ojt 509 :AASGRAIANGCDKPFTKL T0334 341 :G 1ojt 529 :D T0334 342 :NCVSIGTSSCFVE 1ojt 533 :GRIIGGGIVGPNG T0334 357 :ES 1ojt 548 :MI T0334 364 :VYAALYQLVKH 1ojt 555 :AIEMGCDAADI Number of specific fragments extracted= 32 number of extra gaps= 9 total=4189 Will force an alignment to be made, even if fragment is small Number of alignments=184 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1bhy/T0334-1bhy-t06-local-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1bhy expands to /projects/compbio/data/pdb/1bhy.pdb.gz 1bhy:Warning: there is no chain 1bhy will retry with 1bhyA # T0334 read from 1bhy/T0334-1bhy-t06-local-adpstyle5.a2m # 1bhy read from 1bhy/T0334-1bhy-t06-local-adpstyle5.a2m # adding 1bhy to template set # found chain 1bhy in template set Warning: unaligning (T0334)K7 because of BadResidue code BAD_PEPTIDE at template residue (1bhy)D124 Warning: unaligning (T0334)T15 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1bhy)G133 Warning: unaligning (T0334)A16 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1bhy)G133 Warning: unaligning (T0334)G17 because of BadResidue code BAD_PEPTIDE in next template residue (1bhy)Y135 Warning: unaligning (T0334)W18 because of BadResidue code BAD_PEPTIDE at template residue (1bhy)Y135 Warning: unaligning (T0334)P40 because of BadResidue code BAD_PEPTIDE in next template residue (1bhy)K155 Warning: unaligning (T0334)D41 because of BadResidue code BAD_PEPTIDE at template residue (1bhy)K155 Warning: unaligning (T0334)V47 because of BadResidue code BAD_PEPTIDE in next template residue (1bhy)N163 Warning: unaligning (T0334)G48 because of BadResidue code BAD_PEPTIDE at template residue (1bhy)N163 Warning: unaligning (T0334)E49 because of BadResidue code BAD_PEPTIDE at template residue (1bhy)V164 Warning: unaligning (T0334)V197 because of BadResidue code BAD_PEPTIDE in next template residue (1bhy)V366 Warning: unaligning (T0334)E198 because of BadResidue code BAD_PEPTIDE at template residue (1bhy)V366 Warning: unaligning (T0334)G232 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1bhy)N403 Warning: unaligning (T0334)A277 because of BadResidue code BAD_PEPTIDE in next template residue (1bhy)V452 Warning: unaligning (T0334)M278 because of BadResidue code BAD_PEPTIDE at template residue (1bhy)V452 Warning: unaligning (T0334)W339 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1bhy)F528 Warning: unaligning (T0334)V340 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1bhy)F528 Warning: unaligning (T0334)P355 because of BadResidue code BAD_PEPTIDE in next template residue (1bhy)D547 Warning: unaligning (T0334)L356 because of BadResidue code BAD_PEPTIDE at template residue (1bhy)D547 Warning: unaligning (T0334)T359 because of BadResidue code BAD_PEPTIDE in next template residue (1bhy)E551 Warning: unaligning (T0334)G360 because of BadResidue code BAD_PEPTIDE at template residue (1bhy)E551 T0334 5 :ID 1bhy 121 :AE T0334 8 :ILIVGGG 1bhy 125 :VVVLGGG T0334 19 :MAASYLGK 1bhy 136 :SAAFAAAD T0334 29 :QGT 1bhy 144 :EGL T0334 33 :DITLLQA 1bhy 147 :KVAIVER T0334 42 :IPTLG 1bhy 157 :LGGVC T0334 50 :ATIPN 1bhy 165 :GCIPS T0334 57 :TAFFDFLGIPED 1bhy 170 :KALLHNAAVIDE T0334 69 :EWMRECNASYKVAIKFINWRTAGEGTS 1bhy 183 :RHLAANGIKYPEPELDIDMLRAYKDGV T0334 104 :PDHFYHSFGLL 1bhy 285 :DPRIIDSSGAL T0334 131 :YRGKTV 1bhy 299 :EVPGKL T0334 139 :FDYACYK 1bhy 318 :TVYSTLG T0334 146 :EPVI 1bhy 327 :LDVV T0334 172 :DAHLVADFLRRFA 1bhy 340 :ADRDLVKVWQKQN T0334 186 :EKLGVRHVED 1bhy 353 :EYRFDNIMVN T0334 196 :R 1bhy 364 :K T0334 199 :HVQRDANG 1bhy 367 :AVEPKEDG T0334 209 :ESVRTAT 1bhy 375 :VYVTFEG T0334 216 :GRVFDADLFVDCSGFR 1bhy 386 :KEPQRYDAVLVAAGRA T0334 233 :LLINKAMEEPFLD 1bhy 406 :LISAEKAGVAVTD T0334 247 :SDHLLNDSAVATQVPHDDDANGVEPFTS 1bhy 419 :RGFIEVDKQMRTNVPHIYAIGDIVGQPM T0334 275 :AI 1bhy 449 :HK T0334 279 :KSGWTWKIPM 1bhy 453 :HEGHVAAENC T0334 289 :LGR 1bhy 464 :GHK T0334 292 :FGTGYVYSSRFATE 1bhy 474 :IPGVAYTSPEVAWV T0334 306 :DEAVREFCEM 1bhy 492 :LSAKASARKI T0334 316 :WHLDP 1bhy 503 :KANFP T0334 321 :ETQPLNRIRFRVGRNRRA 1bhy 509 :AASGRAIANGCDKPFTKL T0334 341 :G 1bhy 529 :D T0334 342 :NCVSIGTSSCFVE 1bhy 533 :GRIIGGGIVGPNG T0334 357 :ES 1bhy 548 :MI T0334 361 :IYFVYAALYQLVKH 1bhy 552 :VYLAIEMGCDAADI Number of specific fragments extracted= 32 number of extra gaps= 10 total=4221 Will force an alignment to be made, even if fragment is small Number of alignments=185 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2a8xA/T0334-2a8xA-t06-local-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2a8xA expands to /projects/compbio/data/pdb/2a8x.pdb.gz 2a8xA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0334 read from 2a8xA/T0334-2a8xA-t06-local-adpstyle5.a2m # 2a8xA read from 2a8xA/T0334-2a8xA-t06-local-adpstyle5.a2m # adding 2a8xA to template set # found chain 2a8xA in template set Warning: unaligning (T0334)K4 because first residue in template chain is (2a8xA)M1 T0334 5 :ID 2a8xA 2 :TH T0334 7 :KILIVGGGTAGWMAASYLGK 2a8xA 5 :DVVVLGAGPGGYVAAIRAAQ T0334 29 :QGT 2a8xA 25 :LGL T0334 33 :DITLLQAPDIPTLGVGEATIPN 2a8xA 28 :STAIVEPKYWGGVCLNVGCIPS T0334 57 :TAFFDFLGIPED 2a8xA 50 :KALLRNAELVHI T0334 69 :EWMRECNAS 2a8xA 64 :KDAKAFGIS T0334 78 :YKVAIKFINWRTAGEGTS 2a8xA 74 :EVTFDYGIAYDRSRKVAE T0334 104 :PDHFYHSFGLL 2a8xA 155 :SANVVTYEEQI T0334 131 :YRGKTV 2a8xA 169 :ELPKSI T0334 139 :FDYACYK 2a8xA 188 :YVLKNYG T0334 146 :EPVI 2a8xA 197 :VTIV T0334 172 :DAHLVADFLRRFA 2a8xA 210 :EDADVSKEIEKQF T0334 186 :EKLGVRHVED 2a8xA 223 :KKLGVTILTA T0334 196 :RVEHVQRDAN 2a8xA 234 :KVESIADGGS T0334 207 :N 2a8xA 244 :Q T0334 209 :ESVRTA 2a8xA 245 :VTVTVT T0334 215 :TGR 2a8xA 252 :DGV T0334 218 :VFDADLFVDCSGFRG 2a8xA 257 :ELKAEKVLQAIGFAP T0334 233 :LLINKAMEEPFLD 2a8xA 275 :GYGLDKAGVALTD T0334 247 :SDHLLNDSAVATQVPHDDDANGVEPFTS 2a8xA 288 :RKAIGVDDYMRTNVGHIYAIGDVNGLLQ T0334 275 :AIAMKSGWTWKIPM 2a8xA 318 :HVAEAQGVVAAETI T0334 290 :GR 2a8xA 333 :GA T0334 292 :FGTGYVYSSRFATE 2a8xA 345 :LPRATFCQPNVASF T0334 306 :DEAVREFCEM 2a8xA 363 :QQARNEGYDV T0334 316 :WHLDP 2a8xA 374 :VAKFP T0334 321 :ETQPLNRIRFRVGRNR 2a8xA 381 :ANAKAHGVGDPSGFVK T0334 338 :AWVG 2a8xA 397 :LVAD T0334 342 :NCVSIG 2a8xA 408 :GGHLVG T0334 370 :QLVKHFP 2a8xA 415 :DVAELLP T0334 378 :KSLNPV 2a8xA 422 :ELTLAQ Number of specific fragments extracted= 30 number of extra gaps= 0 total=4251 Will force an alignment to be made, even if fragment is small Number of alignments=186 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1qjdA/T0334-1qjdA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1qjdA expands to /projects/compbio/data/pdb/1qjd.pdb.gz 1qjdA:# T0334 read from 1qjdA/T0334-1qjdA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1qjdA read from 1qjdA/T0334-1qjdA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1qjdA to template set # found chain 1qjdA in template set Warning: unaligning (T0334)F62 because of BadResidue code BAD_PEPTIDE in next template residue (1qjdA)M172 Warning: unaligning (T0334)L63 because of BadResidue code BAD_PEPTIDE at template residue (1qjdA)M172 Warning: unaligning (T0334)P66 because of BadResidue code BAD_PEPTIDE in next template residue (1qjdA)W176 Warning: unaligning (T0334)E67 because of BadResidue code BAD_PEPTIDE at template residue (1qjdA)W176 Warning: unaligning (T0334)N207 because of BadResidue code BAD_PEPTIDE in next template residue (1qjdA)V289 Warning: unaligning (T0334)I208 because of BadResidue code BAD_PEPTIDE at template residue (1qjdA)V289 Warning: unaligning (T0334)V211 because of BadResidue code BAD_PEPTIDE in next template residue (1qjdA)L293 Warning: unaligning (T0334)R212 because of BadResidue code BAD_PEPTIDE at template residue (1qjdA)L293 T0334 3 :GKID 1qjdA 122 :APHD T0334 7 :KILIVGGGTAGWMAASYLGK 1qjdA 128 :DVVVVGSGGAGFSAAISATD T0334 29 :QGT 1qjdA 148 :SGA T0334 33 :DITLLQAPD 1qjdA 151 :KVILIEKEP T0334 42 :IPTL 1qjdA 161 :IGGN T0334 57 :TAFFD 1qjdA 166 :KLAAG T0334 64 :GI 1qjdA 173 :NA T0334 68 :DEWMRECNASYKVAIKFINWRTAGEGTS 1qjdA 177 :TDQQKAKKITDSPELMFEDTMKGGQNIN T0334 96 :EARELDGGPDHFYHSFGLL 1qjdA 222 :WMTAMGADLTDVGMMGGAS T0334 115 :KYHE 1qjdA 246 :RPTG T0334 152 :AN 1qjdA 251 :AG T0334 172 :DAHLVADFLRRFA 1qjdA 253 :VGAHVVQVLYDNA T0334 186 :EKLGVRHVED 1qjdA 266 :VKRNIDLRMN T0334 196 :RVEHVQRDANG 1qjdA 277 :RGIEVLKDDKG T0334 209 :ES 1qjdA 290 :KG T0334 213 :TA 1qjdA 294 :VK T0334 215 :T 1qjdA 297 :M T0334 216 :GR 1qjdA 299 :KG T0334 218 :VFDADLFVDCSGFRG 1qjdA 303 :WVKADAVILATGGFA T0334 233 :LLINKAM 1qjdA 321 :ERVAKLD T0334 264 :DDANGVEPFTSAIAMK 1qjdA 328 :PSLKGFISTNQPGAVG T0334 280 :SGWTWKIPM 1qjdA 359 :MQYIQAHPT T0334 289 :LGR 1qjdA 371 :KGG T0334 292 :FGTGYVYSSRFATE 1qjdA 383 :NGAILVNREGKRFV T0334 306 :DEAVREFCEM 1qjdA 462 :TETVARYNSL T0334 316 :WHLD 1qjdA 473 :SSGK T0334 321 :ETQPLNRIRF 1qjdA 478 :TDFERPNLPR T0334 331 :RVGRNR 1qjdA 503 :VHHTMG T0334 337 :RAWVGNCVSIGTSSCFVEP 1qjdA 523 :KQVIPGLYGAGEVTGGVHG T0334 356 :LESTGIYFVYAALYQLVKHFP 1qjdA 545 :LGGNAISDIITFGRLAGEEAA Number of specific fragments extracted= 30 number of extra gaps= 4 total=4281 Will force an alignment to be made, even if fragment is small Number of alignments=187 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1qjdA/T0334-1qjdA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0334 read from 1qjdA/T0334-1qjdA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1qjdA read from 1qjdA/T0334-1qjdA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1qjdA in template set Warning: unaligning (T0334)N207 because of BadResidue code BAD_PEPTIDE in next template residue (1qjdA)V289 Warning: unaligning (T0334)I208 because of BadResidue code BAD_PEPTIDE at template residue (1qjdA)V289 Warning: unaligning (T0334)V211 because of BadResidue code BAD_PEPTIDE in next template residue (1qjdA)L293 Warning: unaligning (T0334)R212 because of BadResidue code BAD_PEPTIDE at template residue (1qjdA)L293 T0334 4 :KIDKILIVGGGTAGWMAASYLGK 1qjdA 125 :DTVDVVVVGSGGAGFSAAISATD T0334 30 :GTADITLLQAPDIPTLGVGEATI 1qjdA 148 :SGAKVILIEKEPVIGGNAKLAAG T0334 57 :TAF 1qjdA 178 :DQQ T0334 61 :DFLGI 1qjdA 181 :KAKKI T0334 66 :PEDEWMREC 1qjdA 188 :SPELMFEDT T0334 75 :NASYKVAIKFINWR 1qjdA 206 :PALVKVLSSHSKDS T0334 123 :SHYWFDRSYR 1qjdA 220 :VDWMTAMGAD T0334 144 :YKEPVI 1qjdA 230 :LTDVGM T0334 152 :ANRSPRRL 1qjdA 236 :MGGASVNR T0334 162 :SKVTNYAW 1qjdA 244 :AHRPTGGA T0334 171 :FDAHLVADFLRRFAT 1qjdA 252 :GVGAHVVQVLYDNAV T0334 187 :KLGVRHVED 1qjdA 267 :KRNIDLRMN T0334 196 :RVEHVQRDANG 1qjdA 277 :RGIEVLKDDKG T0334 209 :ES 1qjdA 290 :KG T0334 213 :TA 1qjdA 294 :VK T0334 215 :TG 1qjdA 299 :KG T0334 217 :RVFDADLFVDCSGFRGL 1qjdA 302 :YWVKADAVILATGGFAK T0334 234 :L 1qjdA 323 :V T0334 236 :NKAM 1qjdA 324 :AKLD T0334 244 :LDMSDHLLNDS 1qjdA 328 :PSLKGFISTNQ T0334 267 :NGVE 1qjdA 339 :PGAV T0334 272 :FTSAIAMKSGWTWKIPM 1qjdA 351 :NAGGALKDMQYIQAHPT T0334 289 :LGRFGT 1qjdA 371 :KGGVMV T0334 295 :GYVYSSRFATE 1qjdA 384 :GAILVNREGKR T0334 306 :DEAVREFCEMW 1qjdA 459 :KALTETVARYN T0334 317 :HLDPETQ 1qjdA 475 :GKDTDFE T0334 324 :PLNRIRFRVG 1qjdA 493 :NYYAIEVTPG T0334 334 :RNRRAWVGNCVSIG 1qjdA 520 :NAKKQVIPGLYGAG T0334 348 :TSSCFVEPLESTGIYFVYAALYQLVKHF 1qjdA 537 :GGVHGANRLGGNAISDIITFGRLAGEEA Number of specific fragments extracted= 29 number of extra gaps= 2 total=4310 Will force an alignment to be made, even if fragment is small Number of alignments=188 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1qjdA/T0334-1qjdA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0334 read from 1qjdA/T0334-1qjdA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1qjdA read from 1qjdA/T0334-1qjdA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1qjdA in template set Warning: unaligning (T0334)N207 because of BadResidue code BAD_PEPTIDE in next template residue (1qjdA)V289 Warning: unaligning (T0334)I208 because of BadResidue code BAD_PEPTIDE at template residue (1qjdA)V289 Warning: unaligning (T0334)V211 because of BadResidue code BAD_PEPTIDE in next template residue (1qjdA)L293 Warning: unaligning (T0334)R212 because of BadResidue code BAD_PEPTIDE at template residue (1qjdA)L293 T0334 4 :KIDKILIVGGGTAGWMAASYLGK 1qjdA 125 :DTVDVVVVGSGGAGFSAAISATD T0334 30 :GTADITLLQAPD 1qjdA 148 :SGAKVILIEKEP T0334 44 :TLGVGEATI 1qjdA 160 :VIGGNAKLA T0334 57 :TAF 1qjdA 178 :DQQ T0334 61 :DFLGIPE 1qjdA 181 :KAKKITD T0334 68 :D 1qjdA 189 :P T0334 108 :YHSFGLLKYHEQIPLSHYWFDRSY 1qjdA 190 :ELMFEDTMKGGQNINDPALVKVLS T0334 137 :EPFDYACYKEPVILDANRSPRRLDGSKVTN 1qjdA 214 :SHSKDSVDWMTAMGADLTDVGMMGGASVNR T0334 169 :WHF 1qjdA 244 :AHR T0334 172 :DAHLVADFLRRFATEKLGVRHVEDRVEHVQRDANG 1qjdA 253 :VGAHVVQVLYDNAVKRNIDLRMNTRGIEVLKDDKG T0334 209 :ES 1qjdA 290 :KG T0334 213 :T 1qjdA 294 :V T0334 214 :ATGR 1qjdA 297 :MYKG T0334 218 :VFDADLFVDCSGFRG 1qjdA 303 :WVKADAVILATGGFA T0334 233 :LLINK 1qjdA 322 :RVAKL T0334 243 :FLDMSDHLLND 1qjdA 327 :DPSLKGFISTN T0334 307 :EAVREFCEMWHLDP 1qjdA 463 :ETVARYNSLVSSGK T0334 322 :TQ 1qjdA 477 :DT T0334 324 :PLNRIRFRVGRNRRA 1qjdA 493 :NYYAIEVTPGVHHTM T0334 339 :WVGNCVSIGTSSCFVEP 1qjdA 525 :VIPGLYGAGEVTGGVHG T0334 356 :LESTGIYFVYAALYQLVKHFPD 1qjdA 545 :LGGNAISDIITFGRLAGEEAAK Number of specific fragments extracted= 21 number of extra gaps= 2 total=4331 Will force an alignment to be made, even if fragment is small Number of alignments=189 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1l9cA/T0334-1l9cA-t06-local-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1l9cA expands to /projects/compbio/data/pdb/1l9c.pdb.gz 1l9cA:Skipped atom 1482, because occupancy 0.500 <= existing 0.500 in 1l9cA Skipped atom 1484, because occupancy 0.500 <= existing 0.500 in 1l9cA Skipped atom 1486, because occupancy 0.500 <= existing 0.500 in 1l9cA Skipped atom 1488, because occupancy 0.500 <= existing 0.500 in 1l9cA Skipped atom 1490, because occupancy 0.500 <= existing 0.500 in 1l9cA Skipped atom 1492, because occupancy 0.500 <= existing 0.500 in 1l9cA Skipped atom 2797, because occupancy 0.500 <= existing 0.500 in 1l9cA Skipped atom 2799, because occupancy 0.500 <= existing 0.500 in 1l9cA Skipped atom 2801, because occupancy 0.500 <= existing 0.500 in 1l9cA Skipped atom 2803, because occupancy 0.500 <= existing 0.500 in 1l9cA Skipped atom 2805, because occupancy 0.500 <= existing 0.500 in 1l9cA Skipped atom 2807, because occupancy 0.500 <= existing 0.500 in 1l9cA # T0334 read from 1l9cA/T0334-1l9cA-t06-local-adpstyle5.a2m # 1l9cA read from 1l9cA/T0334-1l9cA-t06-local-adpstyle5.a2m # adding 1l9cA to template set # found chain 1l9cA in template set T0334 5 :ID 1l9cA 2 :TH T0334 7 :KILIVGGGTAGWMAASYLGK 1l9cA 5 :DVIVVGAGSMGMAAGYQLAK T0334 29 :QGT 1l9cA 25 :QGV T0334 33 :DITLLQAPD 1l9cA 28 :KTLLVDAFD T0334 42 :IPTL 1l9cA 38 :PHTN T0334 46 :GVGEATIPNLQTAF 1l9cA 49 :RIIRHAYGEGREYV T0334 62 :FLGIPEDEW 1l9cA 63 :PLALRSQEL T0334 104 :PDHFYHSFGLL 1l9cA 80 :HHKIFTKTGVL T0334 131 :YRGKTV 1l9cA 94 :PKGESA T0334 139 :FDYACYK 1l9cA 106 :EAAKEHS T0334 146 :EPVI 1l9cA 115 :VDLL T0334 172 :DAHLVADFLRRFA 1l9cA 148 :FSENCIRAYRELA T0334 186 :EKLGVRHVED 1l9cA 161 :EARGAKVLTH T0334 196 :RVEHVQRDANG 1l9cA 172 :RVEDFDISPDS T0334 209 :ESVRTATG 1l9cA 183 :VKIETANG T0334 218 :VFDADLFVDCSGFRGLLINKAMEEPFLDM 1l9cA 191 :SYTADKLIVSMGAWNSKLLSKLNLDIPLQ T0334 249 :HLLNDSAVATQV 1l9cA 222 :RQVVGFFESDES T0334 264 :DDANGV 1l9cA 234 :KYSNDI T0334 271 :PFTS 1l9cA 240 :DFPG T0334 275 :AIAMKSGWTWKIPM 1l9cA 245 :MVEVPNGIYYGFPS T0334 289 :LGR 1l9cA 260 :GGC T0334 292 :FGTGYVYSSRFATE 1l9cA 264 :LKLGYNTFGQKIDP T0334 306 :DEAVREFCEMWHLDPETQPLNRIRFRVGRNR 1l9cA 288 :PEDESNLRAFLEEYMPGANGELKRGAVCMYT T0334 338 :AWVGNCVSIG 1l9cA 319 :KTLDEHFIID T0334 348 :TSSCFVEPLESTGIYFVYAALYQLVKHFP 1l9cA 334 :SNVVIAAGFSGHGFKFSSGVGEVLSQLAL T0334 378 :KSLNPVLTARFNREIE 1l9cA 363 :TGKTEHDISIFSINRP Number of specific fragments extracted= 26 number of extra gaps= 0 total=4357 Will force an alignment to be made, even if fragment is small Number of alignments=190 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1cj2A/T0334-1cj2A-t06-local-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1cj2A expands to /projects/compbio/data/pdb/1cj2.pdb.gz 1cj2A:# T0334 read from 1cj2A/T0334-1cj2A-t06-local-adpstyle5.a2m # 1cj2A read from 1cj2A/T0334-1cj2A-t06-local-adpstyle5.a2m # adding 1cj2A to template set # found chain 1cj2A in template set Warning: unaligning (T0334)I5 because first residue in template chain is (1cj2A)M1 T0334 6 :D 1cj2A 2 :K T0334 7 :KILIVGGGTAGWMAASYLGK 1cj2A 4 :QVAIIGAGPSGLLLGQLLHK T0334 29 :QGT 1cj2A 24 :AGI T0334 33 :DITLLQAP 1cj2A 27 :DNVILERR T0334 46 :GVGEATIPNLQTAFFDFLGIPED 1cj2A 35 :TPDYVLGRIRAGVLEQGMVDLLR T0334 104 :PDHFYHSFGLL 1cj2A 66 :ARDGLVHEGVE T0334 131 :YRGK 1cj2A 78 :AFAG T0334 172 :DAHLVADFLRRFA 1cj2A 101 :GQTEVTRDLMEAR T0334 186 :EKLGVRHVED 1cj2A 114 :EASGATTVYQ T0334 196 :RVEHVQRDANGNIE 1cj2A 125 :AEVRLHDLQGERPY T0334 211 :VRTA 1cj2A 139 :VTFE T0334 215 :TGR 1cj2A 144 :DGE T0334 218 :VFDADLFVDCSGFRG 1cj2A 149 :RLDCDYIAGCDGFHG T0334 233 :LLINKAMEEPFL 1cj2A 166 :RQSIPAERLKVF T0334 247 :SDHLLNDSAVATQVP 1cj2A 178 :ERVYPFGWLGLLADT T0334 262 :HD 1cj2A 194 :PV T0334 271 :PFTS 1cj2A 196 :SHEL T0334 275 :AIAMKSGWTWKIPM 1cj2A 201 :YANHPRGFALCSQR T0334 289 :LGR 1cj2A 216 :ATR T0334 292 :FGTGYVYSSRFATEDEAVREFCEMWHLDP 1cj2A 223 :VQVPLTEKVEDWSDERFWTELKARLPAEV T0334 321 :ETQPLNRIRFRVGRNRRAWVGNCVSIGTSSCFVEPLESTGIYFVYAALYQLVKHFP 1cj2A 259 :PSLEKSIAPLRSFVVEPMQHGRLFLAGDAAHIVPPTGAKGLNLAASDVSTLYRLLL T0334 377 :DKSLNPVLTARFNREIETMFDDTRDFIQAHFYFSPRTDTP 1cj2A 317 :YREGRGELLERYSAICLRRIWKAERFSWWMTSVLHRFPDT T0334 417 :FWRANKELRLA 1cj2A 359 :FSQRIQQTELE Number of specific fragments extracted= 23 number of extra gaps= 0 total=4380 Will force an alignment to be made, even if fragment is small Number of alignments=191 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1dob/T0334-1dob-t06-local-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1dob expands to /projects/compbio/data/pdb/1dob.pdb.gz 1dob:Warning: there is no chain 1dob will retry with 1dobA # T0334 read from 1dob/T0334-1dob-t06-local-adpstyle5.a2m # 1dob read from 1dob/T0334-1dob-t06-local-adpstyle5.a2m # adding 1dob to template set # found chain 1dob in template set Warning: unaligning (T0334)I5 because first residue in template chain is (1dob)M1 T0334 6 :D 1dob 2 :K T0334 7 :KILIVGGGTAGWMAASYLGK 1dob 4 :QVAIIGAGPSGLLLGQLLHK T0334 29 :QGT 1dob 24 :AGI T0334 33 :DITLLQAP 1dob 27 :DNVILERQ T0334 46 :GVGEATIPNLQTAFFDFLGIPED 1dob 35 :TPDYVLGRIRAGVLEQGMVDLLR T0334 104 :PDHFYHSFGLL 1dob 66 :ARDGLVHEGVE T0334 131 :YRGK 1dob 78 :AFAG T0334 172 :DAHLVADFLRRFA 1dob 101 :GQTEVTRDLMEAR T0334 186 :EKLGVRHVED 1dob 114 :EACGATTVYQ T0334 196 :RVEHVQRDANGNIE 1dob 125 :AEVRLHDLQGERPY T0334 211 :VRTA 1dob 139 :VTFE T0334 215 :TGR 1dob 144 :DGE T0334 218 :VFDADLFVDCSGFRG 1dob 149 :RLDCDYIAGCDGFHG T0334 233 :LLINKAMEEPFL 1dob 166 :RQSIPAERLKVF T0334 247 :SDHLLNDSAVATQVP 1dob 178 :ERVYPFGWLGLLADT T0334 262 :HD 1dob 194 :PV T0334 271 :PFTS 1dob 196 :SHEL T0334 275 :AIAMKSGWTWKIPM 1dob 201 :YANHPRGFALCSQR T0334 289 :LGR 1dob 216 :ATR T0334 292 :FGTGYVYSSRFATEDEAVREFCEMWHLDP 1dob 223 :VQVPLSEKVEDWSDERFWTELKARLPSEV T0334 321 :ETQPLNRIRFRVGRNRRAWVGNCVSIGTSSCFVEPLESTGIYFVYAALYQLVKHFP 1dob 259 :PSLEKSIAPLRSFVVEPMQHGRLFLAGDAAHIVPPTGAKGLNLAASDVSTLYRLLL T0334 377 :DKSLNPVLTARFNREIETMFDDTRDFIQAHFYFSPRTDTP 1dob 317 :YREGRGELLERYSAICLRRIWKAERFSWWMTSVLHRFPDT T0334 417 :FWRANKELRLAD 1dob 359 :FSQRIQQTELEY Number of specific fragments extracted= 23 number of extra gaps= 0 total=4403 Will force an alignment to be made, even if fragment is small Number of alignments=192 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1pxc/T0334-1pxc-t06-local-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1pxc expands to /projects/compbio/data/pdb/1pxc.pdb.gz 1pxc:Warning: there is no chain 1pxc will retry with 1pxcA Skipped atom 1529, because occupancy 0.500 <= existing 0.500 in 1pxc Skipped atom 1531, because occupancy 0.500 <= existing 0.500 in 1pxc Skipped atom 1533, because occupancy 0.500 <= existing 0.500 in 1pxc Skipped atom 1535, because occupancy 0.500 <= existing 0.500 in 1pxc Skipped atom 1537, because occupancy 0.500 <= existing 0.500 in 1pxc # T0334 read from 1pxc/T0334-1pxc-t06-local-adpstyle5.a2m # 1pxc read from 1pxc/T0334-1pxc-t06-local-adpstyle5.a2m # adding 1pxc to template set # found chain 1pxc in template set Warning: unaligning (T0334)I5 because first residue in template chain is (1pxc)M1 Warning: unaligning (T0334)T413 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1pxc)P354 Warning: unaligning (T0334)D414 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1pxc)P354 Warning: unaligning (T0334)T415 because of BadResidue code BAD_PEPTIDE in next template residue (1pxc)T356 Warning: unaligning (T0334)P416 because of BadResidue code BAD_PEPTIDE at template residue (1pxc)T356 T0334 6 :D 1pxc 2 :K T0334 7 :KILIVGGGTAGWMAASYLGK 1pxc 4 :QVAIIGAGPSGLLLGQLLHK T0334 29 :QGT 1pxc 24 :AGI T0334 33 :DITLLQAP 1pxc 27 :DNVILERQ T0334 46 :GVGEATIPNLQTAFFDFLGIPED 1pxc 35 :TPDYVLGRIRAGVLEQGMVDLLR T0334 104 :PDHFYHSFGLL 1pxc 66 :ARDGLVHEGVE T0334 131 :YRGK 1pxc 78 :AFAG T0334 172 :DAHLVADFLRRFA 1pxc 101 :GQTEVTRDLMEAR T0334 186 :EKLGVRHVED 1pxc 114 :EACGATTVYQ T0334 196 :RVEHVQRDANGNIE 1pxc 125 :AEVRLHDLQGERPY T0334 211 :VRTA 1pxc 139 :VTFE T0334 215 :TGR 1pxc 144 :DGE T0334 218 :VFDADLFVDCSGFRG 1pxc 149 :RLDCDYIAGCDGFHG T0334 233 :LLINKAMEEPFL 1pxc 166 :RQSIPAERLKVF T0334 247 :SDHLLNDSAVATQVP 1pxc 178 :ERVYPFGWLGLLADT T0334 262 :HD 1pxc 194 :PV T0334 271 :PFTS 1pxc 196 :SHEL T0334 275 :AIAMKSGWTWKIPM 1pxc 201 :YANHPRGFALCSQR T0334 289 :LGR 1pxc 216 :ATR T0334 292 :FGTGYVYSSRFATEDEAVREFCEMWHLDP 1pxc 223 :VQVPLSEKVEDWSDERFWTELKARLPSEV T0334 321 :ETQPLNRIRFRVGRNRRAWVGNCVSIGTSSCFVEPLESTGIYFVYAALYQLVKHFP 1pxc 259 :PSLEKSIAPLRSFVVEPMQHGRLFLAGDAAHIVPPTGAKGLNLAASDVSTLYRLLL T0334 377 :DKSLNPVLTARFNREIETMFDDTRDFIQAHFYFSPR 1pxc 317 :YREGRGELLERYSAICLRRIWKAERFSWWMTSVLHR T0334 417 :FWRANKELRLA 1pxc 359 :FSQRIQQTELE Number of specific fragments extracted= 23 number of extra gaps= 1 total=4426 Will force an alignment to be made, even if fragment is small Number of alignments=193 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1iut/T0334-1iut-t06-local-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1iut expands to /projects/compbio/data/pdb/1iut.pdb.gz 1iut:Warning: there is no chain 1iut will retry with 1iutA # T0334 read from 1iut/T0334-1iut-t06-local-adpstyle5.a2m # 1iut read from 1iut/T0334-1iut-t06-local-adpstyle5.a2m # adding 1iut to template set # found chain 1iut in template set Warning: unaligning (T0334)I5 because first residue in template chain is (1iut)M1 T0334 6 :D 1iut 2 :K T0334 7 :KILIVGGGTAGWMAASYLGK 1iut 4 :QVAIIGAGPSGLLLGQLLHK T0334 29 :QGT 1iut 24 :AGI T0334 33 :DITLLQAP 1iut 27 :DNVILERQ T0334 46 :GVGEATIPNLQTAFFDFLGIPED 1iut 35 :TPDYVLGRIRAGVLEQGMVDLLR T0334 104 :PDHFYHSFGLL 1iut 66 :ARDGLVHEGVE T0334 131 :YRGK 1iut 78 :AFAG T0334 172 :DAHLVADFLRRFA 1iut 101 :GQTEVTRDLMEAR T0334 186 :EKLGVRHVED 1iut 114 :EACGATTVYQ T0334 196 :RVEHVQRDANGNIE 1iut 125 :AEVRLHDLQGERPY T0334 211 :VRTA 1iut 139 :VTFE T0334 215 :TGR 1iut 144 :DGE T0334 218 :VFDADLFVDCSGFRG 1iut 149 :RLDCDYIAGCDGFHG T0334 233 :LLINKAMEEPFL 1iut 166 :RQSIPAERLKVF T0334 247 :SDHLLNDSAVATQVP 1iut 178 :ERVYPFGWLGLLADT T0334 262 :HD 1iut 194 :PV T0334 271 :PFTS 1iut 196 :SHEL T0334 275 :AIAMKSGWTWKIPM 1iut 201 :YANHPRGFALCSQR T0334 289 :LGR 1iut 216 :ATR T0334 292 :FGTGYVYSSRFATEDEAVREFCEMWHLDP 1iut 223 :VQVPLSEKVEDWSDERFWTELKARLPSEV T0334 321 :ETQPLNRIRFRVGRNRRAWVGNCVSIGTSSCFVEPLESTGIYFVYAALYQLVKHFP 1iut 259 :PSLEKSIAPLRSFVVEPMQHGRLFLAGDAAHIVPPTGAKGLNLAASDVSTLYRLLL T0334 377 :DKSLNPVLTARFNREIETMFDDTRDFIQAHFYFSPRTDTP 1iut 317 :YREGRGELLERYSAICLRRIWKAERFSWWMTSVLHRFPDT T0334 417 :FWRANKELRLAD 1iut 359 :FSQRIQQTELEY Number of specific fragments extracted= 23 number of extra gaps= 0 total=4449 Will force an alignment to be made, even if fragment is small Number of alignments=194 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1pxb/T0334-1pxb-t06-local-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1pxb expands to /projects/compbio/data/pdb/1pxb.pdb.gz 1pxb:Warning: there is no chain 1pxb will retry with 1pxbA # T0334 read from 1pxb/T0334-1pxb-t06-local-adpstyle5.a2m # 1pxb read from 1pxb/T0334-1pxb-t06-local-adpstyle5.a2m # adding 1pxb to template set # found chain 1pxb in template set Warning: unaligning (T0334)I5 because first residue in template chain is (1pxb)M1 Warning: unaligning (T0334)T413 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1pxb)P354 Warning: unaligning (T0334)D414 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1pxb)P354 T0334 6 :D 1pxb 2 :K T0334 7 :KILIVGGGTAGWMAASYLGK 1pxb 4 :QVAIIGAGPSGLLLGQLLHK T0334 29 :QGT 1pxb 24 :AGI T0334 33 :DITLLQAP 1pxb 27 :DNVILERQ T0334 46 :GVGEATIPNLQTAFFDFLGIPED 1pxb 35 :TPDYVLGRIRAGVLEQGMVDLLR T0334 104 :PDHFYHSFGLL 1pxb 66 :ARDGLVHEGVE T0334 131 :YRGK 1pxb 78 :AFAG T0334 172 :DAHLVADFLRRFA 1pxb 101 :GQTEVTRDLMEAR T0334 186 :EKLGVRHVED 1pxb 114 :EACGATTVYQ T0334 196 :RVEHVQRDANGNIE 1pxb 125 :AEVRLHDLQGERPY T0334 211 :VRTA 1pxb 139 :VTFE T0334 215 :TGR 1pxb 144 :DGE T0334 218 :VFDADLFVDCSGFRG 1pxb 149 :RLDCDYIAGCDGFHG T0334 233 :LLINKAMEEPFL 1pxb 166 :RQSIPAERLKVF T0334 247 :SDHLLNDSAVATQVP 1pxb 178 :ERVYPFGWLGLLADT T0334 262 :HD 1pxb 194 :PV T0334 271 :PFTS 1pxb 196 :SHEL T0334 275 :AIAMKSGWTWKIPM 1pxb 201 :FANHPRGFALCSQR T0334 289 :LGR 1pxb 216 :ATR T0334 292 :FGTGYVYSSRFATEDEAVREFCEMWHLDP 1pxb 223 :VQVPLSEKVEDWSDERFWTELKARLPSEV T0334 321 :ETQPLNRIRFRVGRNRRAWVGNCVSIGTSSCFVEPLESTGIYFVYAALYQLVKHFP 1pxb 259 :PSLEKSIAPLRSFVVEPMQHGRLFLAGDAAHIVPPTGAKGLNLAASDVSTLYRLLL T0334 377 :DKSLNPVLTARFNREIETMFDDTRDFIQAHFYFSPR 1pxb 317 :YREGRGELLERYSAICLRRIWKAERFSWWMTSVLHR T0334 415 :TP 1pxb 355 :DT T0334 417 :FWRANKELRLAD 1pxb 359 :FSQRIQQTELEY Number of specific fragments extracted= 24 number of extra gaps= 1 total=4473 Will force an alignment to be made, even if fragment is small Number of alignments=195 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1cc4A/T0334-1cc4A-t06-local-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1cc4A expands to /projects/compbio/data/pdb/1cc4.pdb.gz 1cc4A:# T0334 read from 1cc4A/T0334-1cc4A-t06-local-adpstyle5.a2m # 1cc4A read from 1cc4A/T0334-1cc4A-t06-local-adpstyle5.a2m # adding 1cc4A to template set # found chain 1cc4A in template set Warning: unaligning (T0334)I5 because first residue in template chain is (1cc4A)M1 T0334 6 :D 1cc4A 2 :K T0334 7 :KILIVGGGTAGWMAASYLGK 1cc4A 4 :QVAIIGAGPSGLLLGQLLHK T0334 29 :QGT 1cc4A 24 :AGI T0334 33 :DITLLQAP 1cc4A 27 :DNVILERQ T0334 46 :GVGEATIPNLQTAFFDFLGIPED 1cc4A 35 :TPDYVLGRIRAGVLEQGMVDLLR T0334 104 :PDHFYHSFGLL 1cc4A 66 :ARDGLVHEGVE T0334 131 :YRGK 1cc4A 78 :AFAG T0334 172 :DAHLVADFLRRFA 1cc4A 101 :GQTEVTRDLMEAR T0334 186 :EKLGVRHVED 1cc4A 114 :EASGATTVYQ T0334 196 :RVEHVQRDANGNIE 1cc4A 125 :AEVRLHDLQGERPY T0334 211 :VRTA 1cc4A 139 :VTFE T0334 215 :TGR 1cc4A 144 :DGE T0334 218 :VFDADLFVDCSGFRG 1cc4A 149 :RLDCDYIAGCDGAHG T0334 233 :LLINKAMEEPFL 1cc4A 166 :RQSIPAERLKVF T0334 247 :SDHLLNDSAVATQVP 1cc4A 178 :ERVYPFGWLGLLADT T0334 262 :HD 1cc4A 194 :PV T0334 271 :PFTS 1cc4A 196 :SHEL T0334 275 :AIAMKSGWTWKIPM 1cc4A 201 :YANHPRGFALCSQR T0334 289 :LGR 1cc4A 216 :ATR T0334 292 :FGTGYVYSSRFATEDEAVREFCEMWHLDP 1cc4A 223 :VQVPLTEKVEDWSDERFWTELKARLPAEV T0334 321 :ETQPLNRIRFRVGRNRRAWVGNCVSIGTSSCFVEPLESTGIYFVYAALYQLVKHFP 1cc4A 259 :PSLEKSIAPLRSFVVEPMQHGRLFLAGDAAHIVPPTGAKGLNLAASDVSTLYRLLL T0334 377 :DKSLNPVLTARFNREIETMFDDTRDFIQAHFYFSPRTDTP 1cc4A 317 :YREGRGELLERYSAICLRRIWKAERFSWWMTSVLHRFPDT T0334 417 :FWRANKELRLAD 1cc4A 359 :FSQRIQQTELEY Number of specific fragments extracted= 23 number of extra gaps= 0 total=4496 Will force an alignment to be made, even if fragment is small Number of alignments=196 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1zovA/T0334-1zovA-t06-local-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1zovA expands to /projects/compbio/data/pdb/1zov.pdb.gz 1zovA:# T0334 read from 1zovA/T0334-1zovA-t06-local-adpstyle5.a2m # 1zovA read from 1zovA/T0334-1zovA-t06-local-adpstyle5.a2m # adding 1zovA to template set # found chain 1zovA in template set Warning: unaligning (T0334)R202 because of BadResidue code BAD_PEPTIDE in next template residue (1zovA)T179 Warning: unaligning (T0334)D203 because of BadResidue code BAD_PEPTIDE at template residue (1zovA)T179 T0334 5 :ID 1zovA 2 :TH T0334 7 :KILIVGGGTAGWMAASYLGK 1zovA 5 :DVIVVGAGSMGMAAGYYLAK T0334 29 :QGT 1zovA 25 :QGV T0334 33 :DITLLQAPD 1zovA 28 :KTLLVDSFD T0334 42 :IPTL 1zovA 38 :PHTN T0334 46 :GVGEATIPNLQTAFFDFLGIPED 1zovA 49 :RIIRHAYGEGREYVPFALRAQEL T0334 104 :PDHFYHSFGLL 1zovA 80 :HHKIFTQTGVL T0334 131 :YRGKTV 1zovA 94 :PKGGSA T0334 172 :DAHLVADFLRRFA 1zovA 148 :FSENCIQAYRELA T0334 186 :EKLGVRHVED 1zovA 161 :EAHGATVLTY T0334 196 :RVEHVQ 1zovA 172 :PVEDFE T0334 204 :ANG 1zovA 180 :EDL T0334 209 :ESVRTATG 1zovA 183 :VTIKTAKG T0334 218 :VFDADLFVDCSGFRGLLINKAMEEPFLDM 1zovA 191 :SYTANKLVVSMGAWNSKLLSKLDVEIPLQ T0334 247 :SDHLLNDSAVATQV 1zovA 225 :VGFFECDEAKYSNN T0334 271 :PFTS 1zovA 239 :AHYP T0334 275 :AIAMKSGWTWKIPM 1zovA 245 :MVEVENGIYYGFPS T0334 289 :LGR 1zovA 260 :GGS T0334 292 :FGTGYVYSSRFATE 1zovA 264 :LKIGYHSYGQQIDP T0334 306 :DEAVREFCEMWHLDPETQPLNRIRFRVGRNR 1zovA 288 :PEDEANLRKFLEQYMPGANGELKKGAVCMYT T0334 338 :AWVGNCVSIG 1zovA 319 :KTPDEHFVID T0334 348 :TSSCFVEPLESTGIYFVYAALYQLVKHFP 1zovA 334 :SNVAIAAGFSGHGFKFSSVVGETLAQLAT T0334 379 :SLNPVLTARFNR 1zovA 364 :GKTEHDISIFSL Number of specific fragments extracted= 23 number of extra gaps= 1 total=4519 Will force an alignment to be made, even if fragment is small Number of alignments=197 # command:CPU_time= 79.232 sec, elapsed time= 99.565 sec. # command:Using radius: 8.000 NUMB_ALIGNS: 197 Adding 18629 constraints to all_contacts Done adding distance constraints # command:CPU_time= 79.719 sec, elapsed time= 100.099 sec. # command:Reading probabilities from T0334.t06.CB8-sep9.rdb Reading constraints from ConstraintSet all_contacts maxweight: 27.208 Optimizing... Probability sum: -1002.211, CN propb: -1002.211 weights: 0.176 constraints: 1677 # command:CPU_time= 87.954 sec, elapsed time= 108.365 sec. # command:Found ConstraintSet # PrintContacts log_align.constraints Number of constraints in align 1677 # command:Found ConstraintSet # PrintContacts log_align_bonus.constraints Number of constraints in align.bonus 1677 # command:Found ConstraintSet # PrintContacts log_rejected.constraints Number of constraints in rejected 16952 # command:Found ConstraintSet # PrintContacts log_rejected_bonus.constraints Number of constraints in rejected.bonus 16952 # command:Found ConstraintSet # PrintContacts log_noncontact.constraints Number of constraints in noncontact 0 # command:Found ConstraintSet # PrintContacts log_noncontact_bonus.constraints Number of constraints in noncontact.bonus 0 # command:CPU_time= 88.234 sec, elapsed time= 108.736 sec. # command: