# 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 T0384 numbered 1 through 325 Created new target T0384 from T0384.a2m # command:CPU_time= 6.325 sec, elapsed time= 6.388 sec. # command:# reading script from file all-templates.under # Reading fragments from alignment file # Attempting to read fragment alignments from file 1h6dA/T0384-1h6dA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1h6dA expands to /projects/compbio/data/pdb/1h6d.pdb.gz 1h6dA:# T0384 read from 1h6dA/T0384-1h6dA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1h6dA read from 1h6dA/T0384-1h6dA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1h6dA to template set # found chain 1h6dA in template set T0384 2 :LKLGVIGTGAISH 1h6dA 84 :FGYAIVGLGKYAL # choosing archetypes in rotamer library T0384 15 :HFIEAAHTSGEYQLVAIYSRKLETAATFASRYQNI 1h6dA 98 :QILPGFAGCQHSRIEALVSGNAEKAKIVAAEYGVD T0384 50 :QLFDQLEVFFKS 1h6dA 137 :YDYSNFDKIAKD T0384 62 :SFDLVYIASPNSLHFAQAKAALSAGKHVILEKPAVSQPQEWFDLIQTAEKNNCFIFEAARNYHEKAFTTIKNFL 1h6dA 150 :KIDAVYIILPNSLHAEFAIRAFKAGKHVMCEKPMATSVADCQRMIDAAKAANKKLMIGYRCHYDPMNRAAVKLI T0384 137 :DKQVLG 1h6dA 224 :RENQLG T0384 143 :ADFNYAKYSSKM 1h6dA 231 :LGMVTTDNSDVM T0384 158 :LAGQT 1h6dA 243 :DQNDP T0384 163 :PNVFSDRF 1h6dA 250 :QWRLRREL T0384 171 :AGGALMDLGIYPLYAAVRLFG 1h6dA 259 :GGGSLMDIGIYGLNGTRYLLG T0384 192 :KANDATYHAQQLDN 1h6dA 281 :EPIEVRAYTYSDPN T0384 206 :SIDLNGDGILFYPDYQ 1h6dA 300 :EVEDRIIWQMRFRSGA T0384 222 :VHIKAGKNITSNLPCEIYTTDGTLTLNTIEHIRS 1h6dA 317 :SHGASSYSTTTTSRFSVQGDKAVLLMDPATGYYQ T0384 256 :AIFTDHQGNQVQLPIQQAP 1h6dA 353 :ISVQTPGHANQSMMPQFIM T0384 275 :HTMTEEVAAFAHMIQQPD 1h6dA 375 :NQFSAQLDHLAEAVINNK T0384 295 :LYQTWLYDAGSVHELLYTMRQTAGIRFEAE 1h6dA 393 :PVRSPGEEGMQDVRLIQAIYEAARTGRPVN Number of specific fragments extracted= 15 number of extra gaps= 0 total=15 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 1h6dA/T0384-1h6dA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0384 read from 1h6dA/T0384-1h6dA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1h6dA read from 1h6dA/T0384-1h6dA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1h6dA in template set T0384 1 :MLKLGVIGTGAISH 1h6dA 83 :RFGYAIVGLGKYAL T0384 15 :HFIEAAHTSGEYQLVAIYSRKLETAATFASRYQ 1h6dA 98 :QILPGFAGCQHSRIEALVSGNAEKAKIVAAEYG T0384 48 :NIQLFDQL 1h6dA 135 :KIYDYSNF T0384 56 :EVFFKSSFDLVYIASPNSLHFAQAKAALSAGKHVILEKPAVSQPQEWFDLIQTAEKNNCFIFEAARNYHEKAFTTIKNFLADKQ 1h6dA 144 :KIAKDPKIDAVYIILPNSLHAEFAIRAFKAGKHVMCEKPMATSVADCQRMIDAAKAANKKLMIGYRCHYDPMNRAAVKLIRENQ T0384 141 :LG 1h6dA 228 :LG T0384 144 :DFNYAKYSSK 1h6dA 230 :KLGMVTTDNS T0384 155 :PDLLAGQ 1h6dA 240 :DVMDQND T0384 163 :P 1h6dA 247 :P T0384 164 :NVFSDRF 1h6dA 251 :WRLRREL T0384 171 :AGGALMDLGIYPLYAAVRLFG 1h6dA 259 :GGGSLMDIGIYGLNGTRYLLG T0384 192 :KANDATYHAQQLDN 1h6dA 281 :EPIEVRAYTYSDPN T0384 206 :SIDLNGDGILFYPDY 1h6dA 300 :EVEDRIIWQMRFRSG T0384 221 :QVHIKAGKNITSNLPCEIYTTDGTLTLNTI 1h6dA 316 :LSHGASSYSTTTTSRFSVQGDKAVLLMDPA T0384 251 :EHIRSAIFTDHQGNQVQLPIQQAPH 1h6dA 349 :YQNLISVQTPGHANQSMMPQFIMPA T0384 276 :TMTEEVAAFAHMIQQPDLNLY 1h6dA 376 :QFSAQLDHLAEAVINNKPVRS T0384 299 :WLYDAGSVHELLYTMRQTAGIRFEAE 1h6dA 397 :PGEEGMQDVRLIQAIYEAARTGRPVN Number of specific fragments extracted= 16 number of extra gaps= 0 total=31 Will force an alignment to be made, even if fragment is small Number of alignments=2 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1h6dA/T0384-1h6dA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0384 read from 1h6dA/T0384-1h6dA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1h6dA read from 1h6dA/T0384-1h6dA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1h6dA in template set T0384 1 :MLKLGVIGTGAISH 1h6dA 83 :RFGYAIVGLGKYAL T0384 15 :HFIEAAHTSGEYQLVAIYSRKLETAATFASRYQN 1h6dA 98 :QILPGFAGCQHSRIEALVSGNAEKAKIVAAEYGV T0384 49 :IQLFDQLEVFF 1h6dA 136 :IYDYSNFDKIA T0384 60 :KSSFDLVYIASPNSLHFAQAKAALSAGKHVILEKPAVSQPQEWFDLIQTAEKNNCFIFEAARNYHEKAFTTIKNFLADKQVLGADFNYAKYSSKMPDLLAGQTPNVFSDRFAGGALMDLGIYPLYAAVRLFGKANDATYHAQQL 1h6dA 148 :DPKIDAVYIILPNSLHAEFAIRAFKAGKHVMCEKPMATSVADCQRMIDAAKAANKKLMIGYRCHYDPMNRAAVKLIRENQLGKLGMVTTDNSDVMDQNDPAQQWRLRRELAGGGSLMDIGIYGLNGTRYLLGEEPIEVRAYTYS T0384 204 :DNSIDLNGDGILFYPDYQVHIKAGKNIT 1h6dA 298 :FVEVEDRIIWQMRFRSGALSHGASSYST T0384 232 :SNLPCEIYTTDGTLTLNTIEHIRSAIFTDHQ 1h6dA 327 :TTSRFSVQGDKAVLLMDPATGYYQNLISVQT T0384 263 :GNQVQLPIQQAPHTMTEEVAAFAHMIQQPDLNLYQTWLYDAGSVHELLYTMRQTAGIRFEAE 1h6dA 363 :QSMMPQFIMPANNQFSAQLDHLAEAVINNKPVRSPGEEGMQDVRLIQAIYEAARTGRPVNTD Number of specific fragments extracted= 7 number of extra gaps= 0 total=38 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 1ofgA/T0384-1ofgA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1ofgA expands to /projects/compbio/data/pdb/1ofg.pdb.gz 1ofgA:# T0384 read from 1ofgA/T0384-1ofgA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ofgA read from 1ofgA/T0384-1ofgA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1ofgA to template set # found chain 1ofgA in template set T0384 2 :LKLGVIGTGAISH 1ofgA 32 :FGYAIVGLGKYAL T0384 15 :HFIEAAHTSGEYQLVAIYSRKLETAATFASRYQNI 1ofgA 46 :QILPGFAGCQHSRIEALVSGNAEKAKIVAAEYGVD T0384 50 :QLFDQLEVFFKS 1ofgA 85 :YDYSNFDKIAKD T0384 62 :SFDLVYIASPNSLHFAQAKAALSAGKHVILEKPAVSQPQEWFDLIQTAEKNNCFIFEAARNYHEKAFTTIKNFL 1ofgA 98 :KIDAVYIILPNSLHAEFAIRAFKAGKHVMCEKPMATSVADCQRMIDAAKAANKKLMIGYRCHYDPMNRAAVKLI T0384 137 :DKQVLG 1ofgA 172 :RENQLG T0384 143 :ADFNYAKYSSKM 1ofgA 179 :LGMVTTDNSDVM T0384 158 :LAGQT 1ofgA 191 :DQNDP T0384 163 :PNVFSDRF 1ofgA 198 :QWRLRREL T0384 171 :AGGALMDLGIYPLYAAVRLFG 1ofgA 207 :GGGSLMDIGIYGLNGTRYLLG T0384 192 :KANDATYHAQQLDN 1ofgA 229 :EPIEVRAYTYSDPN T0384 206 :SIDLNGDGILFYPDYQ 1ofgA 248 :EVEDRIIWQMRFRSGA T0384 222 :VHIKAGKNITSNLPCEIYTTDGTLTLNTIEHIRS 1ofgA 265 :SHGASSYSTTTTSRFSVQGDKAVLLMDPATGYYQ T0384 256 :AIFTDHQGNQVQLPIQQAP 1ofgA 301 :ISVQTPGHANQSMMPQFIM T0384 275 :HTMTEEVAAFAHMIQQPD 1ofgA 323 :NQFSAQLDHLAEAVINNK T0384 295 :LYQTWLYDAGSVHELLYTMRQTAGIRFEAE 1ofgA 341 :PVRSPGEEGMQDVRLIQAIYEAARTGRPVN Number of specific fragments extracted= 15 number of extra gaps= 0 total=53 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 1ofgA/T0384-1ofgA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0384 read from 1ofgA/T0384-1ofgA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ofgA read from 1ofgA/T0384-1ofgA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1ofgA in template set T0384 1 :MLKLGVIGTGAISH 1ofgA 31 :RFGYAIVGLGKYAL T0384 15 :HFIEAAHTSGEYQLVAIYSRKLETAATFASRYQ 1ofgA 46 :QILPGFAGCQHSRIEALVSGNAEKAKIVAAEYG T0384 48 :NIQLFDQL 1ofgA 83 :KIYDYSNF T0384 56 :EVFFKSSFDLVYIASPNSLHFAQAKAALSAGKHVILEKPAVSQPQEWFDLIQTAEKNNCFIFEAARNYHEKAFTTIKNFLADKQ 1ofgA 92 :KIAKDPKIDAVYIILPNSLHAEFAIRAFKAGKHVMCEKPMATSVADCQRMIDAAKAANKKLMIGYRCHYDPMNRAAVKLIRENQ T0384 141 :LG 1ofgA 176 :LG T0384 144 :DFNYAKYSSK 1ofgA 178 :KLGMVTTDNS T0384 155 :PDLLAGQ 1ofgA 188 :DVMDQND T0384 163 :P 1ofgA 195 :P T0384 164 :NVFSDRF 1ofgA 199 :WRLRREL T0384 171 :AGGALMDLGIYPLYAAVRLFG 1ofgA 207 :GGGSLMDIGIYGLNGTRYLLG T0384 192 :KANDATYHAQQLDN 1ofgA 229 :EPIEVRAYTYSDPN T0384 206 :SIDLNGDGILFYPDY 1ofgA 248 :EVEDRIIWQMRFRSG T0384 221 :QVHIKAGKNITSNLPCEIYTTDGTLTLNTI 1ofgA 264 :LSHGASSYSTTTTSRFSVQGDKAVLLMDPA T0384 251 :EHIRSAIFTDHQGNQVQLPIQQAPH 1ofgA 297 :YQNLISVQTPGHANQSMMPQFIMPA T0384 276 :TMTEEVAAFAHMIQQPDLNLY 1ofgA 324 :QFSAQLDHLAEAVINNKPVRS T0384 299 :WLYDAGSVHELLYTMRQTAGIRFEAE 1ofgA 345 :PGEEGMQDVRLIQAIYEAARTGRPVN Number of specific fragments extracted= 16 number of extra gaps= 0 total=69 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 1ofgA/T0384-1ofgA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0384 read from 1ofgA/T0384-1ofgA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ofgA read from 1ofgA/T0384-1ofgA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1ofgA in template set T0384 1 :MLKLGVIGTGAISH 1ofgA 31 :RFGYAIVGLGKYAL T0384 15 :HFIEAAHTSGEYQLVAIYSRKLETAATFASRYQN 1ofgA 46 :QILPGFAGCQHSRIEALVSGNAEKAKIVAAEYGV T0384 49 :IQLFDQLEVFF 1ofgA 84 :IYDYSNFDKIA T0384 60 :KSSFDLVYIASPNSLHFAQAKAALSAGKHVILEKPAVSQPQEWFDLIQTAEKNNCFIFEAARNYHEKAFTTIKNFLADKQVLGADFNYAKYSSKMPDLLAGQTPNVFSDRFAGGALMDLGIYPLYAAVRLFGKANDATYHAQQL 1ofgA 96 :DPKIDAVYIILPNSLHAEFAIRAFKAGKHVMCEKPMATSVADCQRMIDAAKAANKKLMIGYRCHYDPMNRAAVKLIRENQLGKLGMVTTDNSDVMDQNDPAQQWRLRRELAGGGSLMDIGIYGLNGTRYLLGEEPIEVRAYTYS T0384 204 :DNSIDLNGDGILFYPDYQVHIKAGKNIT 1ofgA 246 :FVEVEDRIIWQMRFRSGALSHGASSYST T0384 232 :SNLPCEIYTTDGTLTLNTIEHIRSAIFTDHQ 1ofgA 275 :TTSRFSVQGDKAVLLMDPATGYYQNLISVQT T0384 263 :GNQVQLPIQQAPHTMTEEVAAFAHMIQQPDLNLYQTWLYDAGSVHELLYTMRQTAGIRFEAE 1ofgA 311 :QSMMPQFIMPANNQFSAQLDHLAEAVINNKPVRSPGEEGMQDVRLIQAIYEAARTGRPVNTD Number of specific fragments extracted= 7 number of extra gaps= 0 total=76 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 1evjA/T0384-1evjA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1evjA expands to /projects/compbio/data/pdb/1evj.pdb.gz 1evjA:# T0384 read from 1evjA/T0384-1evjA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1evjA read from 1evjA/T0384-1evjA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1evjA to template set # found chain 1evjA in template set Warning: unaligning (T0384)D260 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1evjA)M319 Warning: unaligning (T0384)A273 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1evjA)M319 T0384 1 :MLKLGVIGTGAISH 1evjA 31 :RFGYAIVGLGKYAL T0384 15 :HFIEAAHTSGEYQLVAIYSRKLETAATFASRYQNI 1evjA 46 :QILPGFAGCQHSRIEALVDGNAEKAKIVAAEYGVD T0384 50 :QLFDQLEVFFKS 1evjA 85 :YDYSNFDKIAKD T0384 62 :SFDLVYIASPNSLHFAQAKAALSAGKHVILEKPAVSQPQEWFDLIQTAEKNNCFIFEAARNYHEKAFTTIKNFL 1evjA 98 :KIDAVYIILPNSLHAEFAIRAFKAGKHVMCEKPMATSVADCQRMIDAAKAANKKLMIGYRCHYDPMNRAAVKLI T0384 137 :DKQVLG 1evjA 172 :RENQLG T0384 143 :ADFNYAKYSSKMPDLLAGQT 1evjA 179 :LGMVTTDNSDVMDQNDPAQQ T0384 164 :NVFSDRF 1evjA 199 :WRLRREL T0384 171 :AGGALMDLGIYPLYAAVRLFG 1evjA 207 :GGGSLMDIGIYGLNGTRYLLG T0384 192 :KANDATYHAQQLDN 1evjA 229 :EPIEVRAYTYSDPN T0384 206 :SIDLNGDGILFYPDYQ 1evjA 248 :EVEDRIIWQMRFRSGA T0384 222 :VHIKAGKNITSNLPCEIYTTDGTLTLNTIEHIRS 1evjA 265 :SHGASSYSTTTTSRFSVQGDKAVLLMDPATGYYQ T0384 256 :AIFT 1evjA 302 :SVQT T0384 274 :P 1evjA 320 :P T0384 275 :HTMTEEVAAFAHMIQQPD 1evjA 323 :NQFSAQLDHLAEAVINNK T0384 295 :LYQTWLYDAGSVHELLYTMRQTAGIRFEAE 1evjA 341 :PVRSPGEEGMQDVRLIQAIYEAARTGRPVN Number of specific fragments extracted= 15 number of extra gaps= 0 total=91 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 1evjA/T0384-1evjA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0384 read from 1evjA/T0384-1evjA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1evjA read from 1evjA/T0384-1evjA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1evjA in template set Warning: unaligning (T0384)D260 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1evjA)M319 Warning: unaligning (T0384)A273 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1evjA)M319 T0384 1 :MLKLGVIGTGAISH 1evjA 31 :RFGYAIVGLGKYAL T0384 15 :HFIEAAHTSGEYQLVAIYSRKLETAATFASRYQ 1evjA 46 :QILPGFAGCQHSRIEALVDGNAEKAKIVAAEYG T0384 48 :NIQLFDQLEVFFK 1evjA 83 :KIYDYSNFDKIAK T0384 61 :SSFDLVYIASPNSLHFAQAKAALSAGKHVILEKPAVSQPQEWFDLIQTAEKNNCFIFEAARNYHEKAFTTIKNFLADKQ 1evjA 97 :PKIDAVYIILPNSLHAEFAIRAFKAGKHVMCEKPMATSVADCQRMIDAAKAANKKLMIGYRCHYDPMNRAAVKLIRENQ T0384 141 :LG 1evjA 176 :LG T0384 144 :DFNYAKYSSK 1evjA 178 :KLGMVTTDNS T0384 154 :MPDLLAGQ 1evjA 190 :MDQNDPAQ T0384 163 :PNVFSDRF 1evjA 198 :QWRLRREL T0384 171 :AGGALMDLGIYPLYAAVRLFG 1evjA 207 :GGGSLMDIGIYGLNGTRYLLG T0384 192 :KANDATYHAQQLDN 1evjA 229 :EPIEVRAYTYSDPN T0384 206 :SIDLNGDGILFYPDY 1evjA 248 :EVEDRIIWQMRFRSG T0384 221 :QVHIKAGKNITSNLPCEIYTTDGTLTLNTI 1evjA 264 :LSHGASSYSTTTTSRFSVQGDKAVLLMDPA T0384 251 :EHIRSAIFT 1evjA 297 :YQNLISVQT T0384 274 :PH 1evjA 320 :PA T0384 276 :TMTEEVAAFAHMIQQPDLNLY 1evjA 324 :QFSAQLDHLAEAVINNKPVRS T0384 299 :WLYDAGSVHELLYTMRQTAGIRFEAE 1evjA 345 :PGEEGMQDVRLIQAIYEAARTGRPVN Number of specific fragments extracted= 16 number of extra gaps= 0 total=107 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 1evjA/T0384-1evjA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0384 read from 1evjA/T0384-1evjA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1evjA read from 1evjA/T0384-1evjA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1evjA in template set Warning: unaligning (T0384)Q271 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1evjA)M319 T0384 1 :MLKLGVIGTGAISH 1evjA 31 :RFGYAIVGLGKYAL T0384 15 :HFIEAAHTSGEYQLVAIYSRKLETAATFASRYQN 1evjA 46 :QILPGFAGCQHSRIEALVDGNAEKAKIVAAEYGV T0384 49 :IQLFDQLEVFF 1evjA 84 :IYDYSNFDKIA T0384 60 :KSSFDLVYIASPNSLHFAQAKAALSAGKHVILEKPAVSQPQEWFDLIQTAEKNNCFIFEAARNYHEKAFTTIKNFLADKQVLGADFNYAKYSSKMPDLLAGQTPNVFSDRFAGGALMDLGIYPLYAAVRLFGKANDATYHAQQL 1evjA 96 :DPKIDAVYIILPNSLHAEFAIRAFKAGKHVMCEKPMATSVADCQRMIDAAKAANKKLMIGYRCHYDPMNRAAVKLIRENQLGKLGMVTTDNSDVMDQNDPAQQWRLRRELAGGGSLMDIGIYGLNGTRYLLGEEPIEVRAYTYS T0384 204 :DNSIDLNGDGILFYPDYQVHIKAGKNIT 1evjA 246 :FVEVEDRIIWQMRFRSGALSHGASSYST T0384 232 :SNLPCEIYTTDGTLTLNTIEHIRSAIFTDHQ 1evjA 275 :TTSRFSVQGDKAVLLMDPATGYYQNLISVQT T0384 272 :QAPHTMTEEVAAFAHMIQQPDLNLYQTWLYDAGSVHELLYTMRQTAGIRFEAE 1evjA 320 :PANNQFSAQLDHLAEAVINNKPVRSPGEEGMQDVRLIQAIYEAARTGRPVNTD Number of specific fragments extracted= 7 number of extra gaps= 0 total=114 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 1rydA/T0384-1rydA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # Reading fragments from alignment file # Attempting to read fragment alignments from file 1rydA/T0384-1rydA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # Reading fragments from alignment file # Attempting to read fragment alignments from file 1rydA/T0384-1rydA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # Reading fragments from alignment file # Attempting to read fragment alignments from file 1zh8A/T0384-1zh8A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # Reading fragments from alignment file # Attempting to read fragment alignments from file 1zh8A/T0384-1zh8A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # Reading fragments from alignment file # Attempting to read fragment alignments from file 1zh8A/T0384-1zh8A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ydwA/T0384-1ydwA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1ydwA expands to /projects/compbio/data/pdb/1ydw.pdb.gz 1ydwA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0384 read from 1ydwA/T0384-1ydwA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ydwA read from 1ydwA/T0384-1ydwA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1ydwA to template set # found chain 1ydwA in template set Warning: unaligning (T0384)L2 because of BadResidue code BAD_PEPTIDE in next template residue (1ydwA)R8 Warning: unaligning (T0384)K3 because of BadResidue code BAD_PEPTIDE at template residue (1ydwA)R8 Warning: unaligning (T0384)L36 because of BadResidue code BAD_PEPTIDE in next template residue (1ydwA)E42 Warning: unaligning (T0384)E37 because of BadResidue code BAD_PEPTIDE at template residue (1ydwA)E42 Warning: unaligning (T0384)V66 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1ydwA)Y76 Warning: unaligning (T0384)Y67 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1ydwA)Y76 Warning: unaligning (T0384)V89 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1ydwA)L99 Warning: unaligning (T0384)I90 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1ydwA)L99 Warning: unaligning (T0384)R121 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1ydwA)W131 Warning: unaligning (T0384)N122 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1ydwA)W131 Warning: unaligning (T0384)P235 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1ydwA)I251 Warning: unaligning (T0384)C236 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1ydwA)I251 Warning: unaligning (T0384)T240 because of BadResidue code BAD_PEPTIDE in next template residue (1ydwA)T256 Warning: unaligning (T0384)T241 because of BadResidue code BAD_PEPTIDE at template residue (1ydwA)T256 Warning: unaligning (T0384)T249 because of BadResidue code BAD_PEPTIDE in next template residue (1ydwA)F265 Warning: unaligning (T0384)I250 because of BadResidue code BAD_PEPTIDE at template residue (1ydwA)F265 Warning: unaligning (T0384)E251 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1ydwA)I266 Warning: unaligning (T0384)H252 because of BadResidue code BAD_PEPTIDE at template residue (1ydwA)I267 Warning: unaligning (T0384)T298 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ydwA)Y331 T0384 4 :LGVIGTGAISHHFIEAAHTSGEYQLVAIYSRK 1ydwA 9 :IGVMGCADIARKVSRAIHLAPNATISGVASRS T0384 38 :TAATFASRYQNI 1ydwA 43 :KAKAFATANNYP T0384 50 :QLFDQLEVFFKS 1ydwA 58 :KIHGSYESLLED T0384 62 :SFDL 1ydwA 71 :EIDA T0384 68 :IASPNSLHFAQAKAALSAGKH 1ydwA 77 :VPLPTSLHVEWAIKAAEKGKH T0384 91 :LEKPAVSQPQEWFDLIQTAEKNNCFIFEAA 1ydwA 100 :LEKPVAMNVTEFDKIVDACEANGVQIMDGT T0384 123 :YHEKAFTTIKNFLADKQVLG 1ydwA 132 :VHNPRTALLKEFLSDSERFG T0384 143 :ADFNYAKYSSKMPDLLAGQ 1ydwA 153 :LKTVQSCFSFAGDEDFLKN T0384 163 :PNVFSDRFAG 1ydwA 172 :DIRVKPGLDG T0384 173 :GALMDLGIYPLYAAVRLFG 1ydwA 183 :GALGDAGWYAIRATLLANN T0384 192 :KANDATY 1ydwA 204 :LPKTVTA T0384 199 :HAQQLDNSIDLNGDGILFYPDYQ 1ydwA 213 :GAVLNEAGVILSCGASLSWEDGR T0384 222 :VHIKAGKNITSNL 1ydwA 237 :ATIYCSFLANLTM T0384 237 :EIY 1ydwA 252 :TAI T0384 242 :DGTLTLN 1ydwA 257 :KGTLRVH T0384 253 :IRS 1ydwA 268 :PYK T0384 256 :AIFTDHQGNQVQLPIQQ 1ydwA 288 :VTAWVSPPSEHTVKTEL T0384 275 :HTMTEEVAAFAH 1ydwA 305 :PQEACMVREFAR T0384 299 :WLYDAGSVHELLYTMRQTAGIRFE 1ydwA 332 :WPSISRKTQLVVDAVKESVDKNYQ Number of specific fragments extracted= 19 number of extra gaps= 8 total=133 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 1ydwA/T0384-1ydwA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0384 read from 1ydwA/T0384-1ydwA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ydwA read from 1ydwA/T0384-1ydwA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1ydwA in template set Warning: unaligning (T0384)L2 because of BadResidue code BAD_PEPTIDE in next template residue (1ydwA)R8 Warning: unaligning (T0384)K3 because of BadResidue code BAD_PEPTIDE at template residue (1ydwA)R8 Warning: unaligning (T0384)L36 because of BadResidue code BAD_PEPTIDE in next template residue (1ydwA)E42 Warning: unaligning (T0384)E37 because of BadResidue code BAD_PEPTIDE at template residue (1ydwA)E42 Warning: unaligning (T0384)V66 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1ydwA)Y76 Warning: unaligning (T0384)Y67 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1ydwA)Y76 Warning: unaligning (T0384)V89 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1ydwA)L99 Warning: unaligning (T0384)I90 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1ydwA)L99 Warning: unaligning (T0384)R121 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1ydwA)W131 Warning: unaligning (T0384)N122 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1ydwA)W131 Warning: unaligning (T0384)P235 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1ydwA)I251 Warning: unaligning (T0384)C236 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1ydwA)I251 Warning: unaligning (T0384)T240 because of BadResidue code BAD_PEPTIDE in next template residue (1ydwA)T256 Warning: unaligning (T0384)T241 because of BadResidue code BAD_PEPTIDE at template residue (1ydwA)T256 Warning: unaligning (T0384)T249 because of BadResidue code BAD_PEPTIDE in next template residue (1ydwA)F265 Warning: unaligning (T0384)I250 because of BadResidue code BAD_PEPTIDE at template residue (1ydwA)F265 Warning: unaligning (T0384)H261 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1ydwA)W283 Warning: unaligning (T0384)Q262 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1ydwA)W283 Warning: unaligning (T0384)T298 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ydwA)Y331 T0384 4 :LGVIGTGAISHHFIEAAHTSGEYQLVAIYSRK 1ydwA 9 :IGVMGCADIARKVSRAIHLAPNATISGVASRS T0384 38 :TAATFASRYQ 1ydwA 43 :KAKAFATANN T0384 48 :NIQLFDQL 1ydwA 56 :STKIHGSY T0384 56 :EVFFKSSFDL 1ydwA 65 :SLLEDPEIDA T0384 68 :IASPNSLHFAQAKAALSAGKH 1ydwA 77 :VPLPTSLHVEWAIKAAEKGKH T0384 91 :LEKPAVSQPQEWFDLIQTAEKNNCFIFEAA 1ydwA 100 :LEKPVAMNVTEFDKIVDACEANGVQIMDGT T0384 123 :YHEK 1ydwA 132 :VHNP T0384 136 :ADKQ 1ydwA 146 :DSER T0384 141 :LG 1ydwA 150 :FG T0384 144 :DFNYAKYSSKMPDLLA 1ydwA 152 :QLKTVQSCFSFAGDED T0384 163 :PNVFSDRFAG 1ydwA 172 :DIRVKPGLDG T0384 173 :GALMDLGIYPLYAAVRLFG 1ydwA 183 :GALGDAGWYAIRATLLANN T0384 192 :KANDATYH 1ydwA 204 :LPKTVTAF T0384 200 :AQQLDNSIDLNGDGILFYPDY 1ydwA 214 :AVLNEAGVILSCGASLSWEDG T0384 221 :QVHIKAGKNITSNL 1ydwA 236 :TATIYCSFLANLTM T0384 237 :EIY 1ydwA 252 :TAI T0384 242 :DGTLTLN 1ydwA 257 :KGTLRVH T0384 251 :EHIRSAIFTD 1ydwA 272 :TEASFTTSTK T0384 263 :GN 1ydwA 293 :SP T0384 276 :TMTEEVAAFA 1ydwA 306 :QEACMVREFA T0384 299 :WLYDAGSVHELLYTMRQTAGIRFE 1ydwA 332 :WPSISRKTQLVVDAVKESVDKNYQ Number of specific fragments extracted= 21 number of extra gaps= 9 total=154 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 1ydwA/T0384-1ydwA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0384 read from 1ydwA/T0384-1ydwA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ydwA read from 1ydwA/T0384-1ydwA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1ydwA in template set Warning: unaligning (T0384)L2 because of BadResidue code BAD_PEPTIDE in next template residue (1ydwA)R8 Warning: unaligning (T0384)K3 because of BadResidue code BAD_PEPTIDE at template residue (1ydwA)R8 Warning: unaligning (T0384)L36 because of BadResidue code BAD_PEPTIDE in next template residue (1ydwA)E42 Warning: unaligning (T0384)E37 because of BadResidue code BAD_PEPTIDE at template residue (1ydwA)E42 Warning: unaligning (T0384)V66 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1ydwA)Y76 Warning: unaligning (T0384)Y67 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1ydwA)Y76 Warning: unaligning (T0384)V89 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1ydwA)L99 Warning: unaligning (T0384)I90 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1ydwA)L99 Warning: unaligning (T0384)R121 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1ydwA)W131 Warning: unaligning (T0384)N122 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1ydwA)W131 Warning: unaligning (T0384)P235 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1ydwA)I251 Warning: unaligning (T0384)C236 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1ydwA)I251 Warning: unaligning (T0384)T240 because of BadResidue code BAD_PEPTIDE in next template residue (1ydwA)T256 Warning: unaligning (T0384)T241 because of BadResidue code BAD_PEPTIDE at template residue (1ydwA)T256 Warning: unaligning (T0384)T249 because of BadResidue code BAD_PEPTIDE in next template residue (1ydwA)F265 Warning: unaligning (T0384)I250 because of BadResidue code BAD_PEPTIDE at template residue (1ydwA)F265 Warning: unaligning (T0384)E251 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1ydwA)I266 Warning: unaligning (T0384)H252 because of BadResidue code BAD_PEPTIDE at template residue (1ydwA)I267 Warning: unaligning (T0384)Y296 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ydwA)Y331 Warning: unaligning (T0384)E324 because last residue in template chain is (1ydwA)S360 T0384 1 :M 1ydwA 6 :Q T0384 4 :LGVIGTGAISHHFIEAAHTSGEYQLVAIYSRK 1ydwA 9 :IGVMGCADIARKVSRAIHLAPNATISGVASRS T0384 38 :TAATFASRYQN 1ydwA 43 :KAKAFATANNY T0384 49 :IQLFDQLEVFF 1ydwA 57 :TKIHGSYESLL T0384 60 :KSSFDL 1ydwA 69 :DPEIDA T0384 68 :IASPNSLHFAQAKAALSAGKH 1ydwA 77 :VPLPTSLHVEWAIKAAEKGKH T0384 91 :LEKPAVSQPQEWFDLIQTAEKNNCFIFEAA 1ydwA 100 :LEKPVAMNVTEFDKIVDACEANGVQIMDGT T0384 123 :YHEKAFTTIKNFL 1ydwA 132 :VHNPRTALLKEFL T0384 136 :ADKQVLGADFNYAKYSSKMPDLLAGQTPNVFSDRFAGGALMDLGIYPLYAAVRLFGKANDATYHAQQL 1ydwA 146 :DSERFGQLKTVQSCFSFAGDEDFLKNDIRVKPGLDGLGALGDAGWYAIRATLLANNFELPKTVTAFPG T0384 204 :DNSIDLNGDGILFYPDYQVHIKAGKNIT 1ydwA 218 :EAGVILSCGASLSWEDGRTATIYCSFLA T0384 232 :SNL 1ydwA 247 :LTM T0384 237 :EIY 1ydwA 252 :TAI T0384 242 :DGTLTLN 1ydwA 257 :KGTLRVH T0384 253 :IRSAIFTDHQ 1ydwA 268 :PYKETEASFT T0384 263 :GNQVQLPIQQAPHTMTEEVAAF 1ydwA 293 :SPPSEHTVKTELPQEACMVREF T0384 297 :QTWLYDAGSVHELLYTMRQTAG 1ydwA 332 :WPSISRKTQLVVDAVKESVDKN T0384 319 :IRFEA 1ydwA 355 :QQISL Number of specific fragments extracted= 17 number of extra gaps= 8 total=171 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 1tltA/T0384-1tltA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1tltA expands to /projects/compbio/data/pdb/1tlt.pdb.gz 1tltA:# T0384 read from 1tltA/T0384-1tltA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1tltA read from 1tltA/T0384-1tltA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1tltA to template set # found chain 1tltA in template set Warning: unaligning (T0384)K93 because of BadResidue code BAD_PEPTIDE in next template residue (1tltA)P97 Warning: unaligning (T0384)P94 because of BadResidue code BAD_PEPTIDE at template residue (1tltA)P97 Warning: unaligning (T0384)I319 because last residue in template chain is (1tltA)S308 T0384 1 :MLKLGVIGTGAISH 1tltA 5 :KLRIGVVGLGGIAQ T0384 15 :HFIEAAHTSGEYQLVAIYSRKLETAATFASRYQNI 1tltA 20 :AWLPVLAAASDWTLQGAWSPTRAKALPICESWRIP T0384 51 :LFDQLEVFFK 1tltA 55 :YADSLSSLAA T0384 62 :SFDLVYIASPNSLHFAQAKAALSAGKHVILE 1tltA 65 :SCDAVFVHSSTASHFDVVSTLLNAGVHVCVD T0384 95 :AVSQPQEWFDLIQTAEKNNCFIFEAARNYHEKAFTTIKNFL 1tltA 98 :LAENLRDAERLVELAARKKLTLMVGFNRRFAPLYGELKTQL T0384 142 :G 1tltA 139 :A T0384 143 :ADFNYAKYSSKMPDLLAG 1tltA 141 :AASLRMDKHRSNSVGPHD T0384 171 :AGGALMDLGIYPLYAAVRLFG 1tltA 159 :LYFTLLDDYLHVVDTALWLSG T0384 192 :KANDATYHAQQLDNSIDLNGDGILFYPDYQVHIKAGKNITSN 1tltA 181 :KASLDGGTLLTNDAGEMLFAEHHFSAGPLQITTCMHRRAGSQ T0384 234 :LPCEIYTTDGTLTLNTIEH 1tltA 224 :ETVQAVTDGALIDITDMRE T0384 257 :IFTDHQGNQVQLPIQQAP 1tltA 243 :WREERGQGVVHKPIPGWQ T0384 275 :HTMTEEVAAFAHMIQQPD 1tltA 266 :RGFVGCARHFIECVQNQT T0384 295 :LYQTWLYDAGSVHELLYTMRQTAG 1tltA 284 :VPQTAGEQAVLAQRIVDKIWRDAM Number of specific fragments extracted= 13 number of extra gaps= 1 total=184 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 1tltA/T0384-1tltA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0384 read from 1tltA/T0384-1tltA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1tltA read from 1tltA/T0384-1tltA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1tltA in template set Warning: unaligning (T0384)K93 because of BadResidue code BAD_PEPTIDE in next template residue (1tltA)P97 Warning: unaligning (T0384)P94 because of BadResidue code BAD_PEPTIDE at template residue (1tltA)P97 Warning: unaligning (T0384)I319 because last residue in template chain is (1tltA)S308 T0384 1 :MLKLGVIGTGAISH 1tltA 5 :KLRIGVVGLGGIAQ T0384 15 :HFIEAAHTSGEYQLVAIYSRKLETAATFASRYQ 1tltA 20 :AWLPVLAAASDWTLQGAWSPTRAKALPICESWR T0384 49 :IQLFDQLEVFF 1tltA 53 :IPYADSLSSLA T0384 61 :SSFDLVYIASPNSLHFAQAKAALSAGKHVILE 1tltA 64 :ASCDAVFVHSSTASHFDVVSTLLNAGVHVCVD T0384 95 :AVSQPQEWFDLIQTAEKNNCFIFEAARNYHEKAFTTIKN 1tltA 98 :LAENLRDAERLVELAARKKLTLMVGFNRRFAPLYGELKT T0384 140 :VLG 1tltA 137 :QLA T0384 144 :DFNYAKYSSKMPDLLAGQ 1tltA 140 :TAASLRMDKHRSNSVGPH T0384 163 :P 1tltA 158 :D T0384 174 :ALMDLGIYPLYAAVRLFG 1tltA 162 :TLLDDYLHVVDTALWLSG T0384 192 :KANDATYHAQQLDNSIDLNGDGILFYPDYQVHIKAGKNITSN 1tltA 181 :KASLDGGTLLTNDAGEMLFAEHHFSAGPLQITTCMHRRAGSQ T0384 234 :LPCEIYTTDGTLTLNTIE 1tltA 224 :ETVQAVTDGALIDITDMR T0384 256 :AIFTDHQGNQVQLPIQQAPH 1tltA 242 :EWREERGQGVVHKPIPGWQS T0384 276 :TMTEEVAAFAHMIQQPDLNLY 1tltA 267 :GFVGCARHFIECVQNQTVPQT T0384 299 :WLYDAGSVHELLYTMRQTAG 1tltA 288 :AGEQAVLAQRIVDKIWRDAM Number of specific fragments extracted= 14 number of extra gaps= 1 total=198 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 1tltA/T0384-1tltA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0384 read from 1tltA/T0384-1tltA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1tltA read from 1tltA/T0384-1tltA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1tltA in template set Warning: unaligning (T0384)K93 because of BadResidue code BAD_PEPTIDE in next template residue (1tltA)P97 Warning: unaligning (T0384)P94 because of BadResidue code BAD_PEPTIDE at template residue (1tltA)P97 T0384 1 :MLKLGVIGTGAISH 1tltA 5 :KLRIGVVGLGGIAQ T0384 15 :HFIEAAHTSGEYQLVAIYSRKLETAATFASRYQN 1tltA 20 :AWLPVLAAASDWTLQGAWSPTRAKALPICESWRI T0384 50 :QLFDQLEVFF 1tltA 54 :PYADSLSSLA T0384 62 :SFDLVYIASPNSLHFAQAKAALSAGKHVILE 1tltA 65 :SCDAVFVHSSTASHFDVVSTLLNAGVHVCVD T0384 95 :AVSQPQEWFDLIQTAEKNNCFIFEAARNYHEKAFTTIKNF 1tltA 98 :LAENLRDAERLVELAARKKLTLMVGFNRRFAPLYGELKTQ T0384 140 :VLGADFNYAKYSSKMPDLLAGQ 1tltA 138 :LATAASLRMDKHRSNSVGPHDL T0384 172 :GGALMDLGIYPLYAAVRLFGKANDATYHAQQL 1tltA 160 :YFTLLDDYLHVVDTALWLSGGKASLDGGTLLT T0384 204 :DNSIDLNGDGILFYPDYQVHIKAGKNIT 1tltA 193 :DAGEMLFAEHHFSAGPLQITTCMHRRAG T0384 232 :SNLPCEIYTTDGTLTLNTIEHIRSAIFTDHQ 1tltA 222 :QRETVQAVTDGALIDITDMREWREERGQGVV T0384 263 :GNQVQLPIQQAPHTMTEEVAAFAHMIQQPDLNLYQTWLYDAGSVHELLYTMRQT 1tltA 254 :KPIPGWQSTLEQRGFVGCARHFIECVQNQTVPQTAGEQAVLAQRIVDKIWRDAM Number of specific fragments extracted= 10 number of extra gaps= 1 total=208 Will force an alignment to be made, even if fragment is small Number of alignments=15 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1xeaA/T0384-1xeaA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1xeaA expands to /projects/compbio/data/pdb/1xea.pdb.gz 1xeaA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0384 read from 1xeaA/T0384-1xeaA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1xeaA read from 1xeaA/T0384-1xeaA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1xeaA to template set # found chain 1xeaA in template set T0384 2 :LKLGVIGTGAISH 1xeaA 3 :LKIAMIGLGDIAQ T0384 15 :HFIEAAHTSGEYQLV 1xeaA 17 :AYLPVLAQWPDIELV T0384 31 :IYSRKLETAATFASRYQNIQLFDQLEVFFKSSFDLVYIASPNSLHFAQAKAALSAGKHVILEKPAVSQPQEWFDLIQTAEKNNCFIFEAARNYHEKAFTTIKNFL 1xeaA 32 :LCTRNPKVLGTLATRYRVSATCTDYRDVLQYGVDAVMIHAATDVHSTLAAFFLHLGIPTFVDKPLAASAQECENLYELAEKHHQPLYVGFNRRHIPLYNQHLSEL T0384 137 :DKQVLG 1xeaA 137 :AQQECG T0384 143 :ADFNYAKYSSK 1xeaA 144 :LRSLRWEKHRH T0384 156 :DLLAGQT 1xeaA 155 :ALPGDIR T0384 173 :GALMDLGIYPLYAAVRLFG 1xeaA 162 :TFVFDDFIHPLDSVNLSRQ T0384 192 :KANDATYHAQQL 1xeaA 182 :NLDDLHLTYHMS T0384 205 :NSIDLNGDGILFYPDYQVHIKAGKNITSN 1xeaA 194 :EGLLARLDVQWQTGDTLLHASMNRQFGIT T0384 234 :LPCEIYTTDGTLTLNTIEHIR 1xeaA 224 :EHVTASYDNVAYLFDSFTQGK T0384 257 :IFTDHQGNQVQLPIQQAP 1xeaA 245 :MWRDNQESRVALKDWTPM T0384 275 :HTMTEEVAAFAHMIQQPD 1xeaA 266 :KGFDAMVQDWLQVAAAGK T0384 295 :LYQTWLYDAGSVHELLYTMRQTAGI 1xeaA 284 :LPTHIIERNLASHQLAEAICQQITQ Number of specific fragments extracted= 13 number of extra gaps= 0 total=221 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 1xeaA/T0384-1xeaA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0384 read from 1xeaA/T0384-1xeaA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1xeaA read from 1xeaA/T0384-1xeaA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1xeaA in template set T0384 2 :LKLGVIGTGAISH 1xeaA 3 :LKIAMIGLGDIAQ T0384 15 :HFIEAAHTSGEYQLV 1xeaA 17 :AYLPVLAQWPDIELV T0384 31 :IYSRKLETAATFASRYQNIQLFDQLEVFFKSSFDLVYIASPNSLHFAQAKAALSAGKHVILEKPAVSQPQEWFDLIQTAEKNNCFIFEAARNYHEKAFTTIKNFLADKQ 1xeaA 32 :LCTRNPKVLGTLATRYRVSATCTDYRDVLQYGVDAVMIHAATDVHSTLAAFFLHLGIPTFVDKPLAASAQECENLYELAEKHHQPLYVGFNRRHIPLYNQHLSELAQQE T0384 141 :LG 1xeaA 141 :CG T0384 144 :DFNYAKYSSKMPDLLAGQ 1xeaA 143 :ALRSLRWEKHRHALPGDI T0384 174 :ALMDLGIYPLYAAVRLFG 1xeaA 163 :FVFDDFIHPLDSVNLSRQ T0384 192 :KANDATYHAQQLD 1xeaA 182 :NLDDLHLTYHMSE T0384 206 :SIDLNGDGILFYPDYQVHIKAGKNITSN 1xeaA 195 :GLLARLDVQWQTGDTLLHASMNRQFGIT T0384 234 :LPCEIYTTDGTLTLNTI 1xeaA 224 :EHVTASYDNVAYLFDSF T0384 253 :IRSAIFTDHQGNQVQLPIQQAPH 1xeaA 241 :TQGKMWRDNQESRVALKDWTPML T0384 276 :TMTEEVAAFAHMIQQPDLNLY 1xeaA 267 :GFDAMVQDWLQVAAAGKLPTH T0384 299 :WLYDAGSVHELLYTMRQTAG 1xeaA 288 :IIERNLASHQLAEAICQQIT Number of specific fragments extracted= 12 number of extra gaps= 0 total=233 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 1xeaA/T0384-1xeaA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0384 read from 1xeaA/T0384-1xeaA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1xeaA read from 1xeaA/T0384-1xeaA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1xeaA in template set T0384 1 :MLKLGVIGTGAISH 1xeaA 2 :SLKIAMIGLGDIAQ T0384 15 :HFIEAAHTSGEYQLV 1xeaA 17 :AYLPVLAQWPDIELV T0384 31 :IYSRKLETAATFASRYQNIQLFDQLEVFFKSSFDLVYIASPNSLHFAQAKAALSAGKHVILEKPAVSQPQEWFDLIQTAEKNNCFIFEAARNYHEKAFTTIKNFLADKQVLGADFNYAKYSSKMPDL 1xeaA 32 :LCTRNPKVLGTLATRYRVSATCTDYRDVLQYGVDAVMIHAATDVHSTLAAFFLHLGIPTFVDKPLAASAQECENLYELAEKHHQPLYVGFNRRHIPLYNQHLSELAQQECGALRSLRWEKHRHALPG T0384 160 :GQTP 1xeaA 159 :DIRT T0384 174 :ALMDLGIYPLYAAVRLFGKANDATYHAQQLDNSIDLNGDGILFYPDYQVHIKAGKNIT 1xeaA 163 :FVFDDFIHPLDSVNLSRQCNLDDLHLTYHMSEGLLARLDVQWQTGDTLLHASMNRQFG T0384 232 :SNLPCEIYTTDGTLTLNTIEHIRSAI 1xeaA 222 :TTEHVTASYDNVAYLFDSFTQGKMWR T0384 260 :DHQ 1xeaA 248 :DNQ T0384 263 :GNQVQLPIQQAPHTMTEEVAAFAHMIQQPDLNLYQTWLYDAGSVHELLYTMRQ 1xeaA 254 :VALKDWTPMLASKGFDAMVQDWLQVAAAGKLPTHIIERNLASHQLAEAICQQI Number of specific fragments extracted= 8 number of extra gaps= 0 total=241 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 1lc0A/T0384-1lc0A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1lc0A expands to /projects/compbio/data/pdb/1lc0.pdb.gz 1lc0A:# T0384 read from 1lc0A/T0384-1lc0A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1lc0A read from 1lc0A/T0384-1lc0A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1lc0A to template set # found chain 1lc0A in template set Warning: unaligning (T0384)A317 because last residue in template chain is (1lc0A)C291 T0384 2 :LKLGVIGTGAISHHFIEAAHTS 1lc0A 9 :FGVVVVGVGRAGSVRLRDLKDP T0384 24 :GEYQLVAIYSRK 1lc0A 34 :AFLNLIGFVSRR T0384 47 :QNI 1lc0A 46 :ELG T0384 50 :QLF 1lc0A 54 :RQI T0384 54 :QLEVFFKS 1lc0A 57 :SLEDALRS T0384 62 :SFDLVYIASPNSLHFAQAKAALSAGKHVILEKPAVSQPQEWFDLIQTAEKNNCFIFEAARNYHEKAFTTIKNFL 1lc0A 66 :EIDVAYICSESSSHEDYIRQFLQAGKHVLVEYPMTLSFAAAQELWELAAQKGRVLHEEHVELLMEEFEFLRREV T0384 137 :DKQV 1lc0A 140 :LGKE T0384 143 :ADFNYAKYSSKMPDLLAG 1lc0A 144 :LLKGSLRFTASPLEEERF T0384 173 :GALMDLGIYPLYAAVRLFGKANDATYHAQQLDNSIDLNGDGILFYPDYQ 1lc0A 162 :GFPAFSGISRLTWLVSLFGELSLISATLEERKEDQYMKMTVQLETQNKG T0384 222 :VHIKAGKNITSN 1lc0A 212 :LSWIEEKGPGLK T0384 234 :LPCEIYTTDGT 1lc0A 226 :RYVNFQFTSGS T0384 265 :QVQLPI 1lc0A 237 :LEEVPS T0384 271 :QQAPHTMTEEVAAFAHMIQQPDLN 1lc0A 244 :GVNKNIFLKDQDIFVQKLLDQVSA T0384 295 :LYQTWLYDAGSVHELLYTMRQT 1lc0A 269 :DLAAEKKRIMHCLGLASDIQKL Number of specific fragments extracted= 14 number of extra gaps= 0 total=255 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 1lc0A/T0384-1lc0A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0384 read from 1lc0A/T0384-1lc0A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1lc0A read from 1lc0A/T0384-1lc0A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1lc0A in template set Warning: unaligning (T0384)A317 because last residue in template chain is (1lc0A)C291 T0384 2 :LKLGVIGTGAISHHFIEAAHT 1lc0A 9 :FGVVVVGVGRAGSVRLRDLKD T0384 23 :SGEYQLVAIYSRK 1lc0A 33 :AAFLNLIGFVSRR T0384 46 :YQ 1lc0A 47 :LG T0384 48 :NIQL 1lc0A 52 :EVRQ T0384 54 :QL 1lc0A 57 :SL T0384 56 :EVFFKSSFDLVYIASPNSLHFAQAKAALSAGKHVILEKPAVSQPQEWFDLIQTAEKNNCFIFEAARNYHEKAFTTIKNFLA 1lc0A 60 :DALRSQEIDVAYICSESSSHEDYIRQFLQAGKHVLVEYPMTLSFAAAQELWELAAQKGRVLHEEHVELLMEEFEFLRREVL T0384 138 :KQ 1lc0A 141 :GK T0384 144 :DFNYAKYSSKMPDLLAG 1lc0A 143 :ELLKGSLRFTASPLEEE T0384 164 :NV 1lc0A 160 :RF T0384 173 :GALMDLGIYPLYAAVRLFGKANDATYHAQQLDNSIDLNGDGILFYPDY 1lc0A 162 :GFPAFSGISRLTWLVSLFGELSLISATLEERKEDQYMKMTVQLETQNK T0384 221 :QVHIKAGKNITSN 1lc0A 211 :LLSWIEEKGPGLK T0384 234 :LPCEI 1lc0A 226 :RYVNF T0384 259 :TDHQGNQVQLPIQ 1lc0A 231 :QFTSGSLEEVPSV T0384 272 :QAPHTMTEEVAAFAHMIQQPDLNLY 1lc0A 245 :VNKNIFLKDQDIFVQKLLDQVSAED T0384 297 :QTWLYDAGSVHELLYTMRQT 1lc0A 271 :AAEKKRIMHCLGLASDIQKL Number of specific fragments extracted= 15 number of extra gaps= 0 total=270 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 1lc0A/T0384-1lc0A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0384 read from 1lc0A/T0384-1lc0A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1lc0A read from 1lc0A/T0384-1lc0A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1lc0A in template set T0384 2 :LKLGVIGTGAISHHFIEAAHT 1lc0A 9 :FGVVVVGVGRAGSVRLRDLKD T0384 23 :SGEYQLVAIYSRKL 1lc0A 33 :AAFLNLIGFVSRRE T0384 48 :N 1lc0A 47 :L T0384 54 :QLEVFF 1lc0A 57 :SLEDAL T0384 60 :KSSFDLVYIASPNSLHFAQAKAALSAGKHVILEKPAVSQPQEWFDLIQTAEKNNCFIFEAARNYHEKAFTTIKNFLAD 1lc0A 64 :SQEIDVAYICSESSSHEDYIRQFLQAGKHVLVEYPMTLSFAAAQELWELAAQKGRVLHEEHVELLMEEFEFLRREVLG T0384 141 :LGADFNYAKYSSKMPD 1lc0A 142 :KELLKGSLRFTASPLE T0384 162 :TPNVFSDRFAG 1lc0A 158 :EERFGFPAFSG T0384 180 :IYPLYAAVRLFGKANDATYHAQQLDNSIDLNGDGILFYPDYQVHIKAGKNIT 1lc0A 169 :ISRLTWLVSLFGELSLISATLEERKEDQYMKMTVQLETQNKGLLSWIEEKGP T0384 232 :SNLPCEIYTTDGTL 1lc0A 224 :RNRYVNFQFTSGSL T0384 265 :QVQLPIQQAPHTMTEEVAAFAHMIQQP 1lc0A 238 :EEVPSVGVNKNIFLKDQDIFVQKLLDQ T0384 296 :YQTWLYDAGSVHELLYTM 1lc0A 265 :VSAEDLAAEKKRIMHCLG Number of specific fragments extracted= 11 number of extra gaps= 0 total=281 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 1gcuA/T0384-1gcuA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1gcuA expands to /projects/compbio/data/pdb/1gcu.pdb.gz 1gcuA:# T0384 read from 1gcuA/T0384-1gcuA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1gcuA read from 1gcuA/T0384-1gcuA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1gcuA to template set # found chain 1gcuA in template set Warning: unaligning (T0384)G318 because last residue in template chain is (1gcuA)H292 T0384 2 :LKLGVIGTGAISHHFIEAA 1gcuA 9 :FGVVVVGVGRAGSVRLRDL T0384 21 :HT 1gcuA 33 :AA T0384 25 :EYQLVAIYSRK 1gcuA 35 :FLNLIGFVSRR T0384 47 :QNI 1gcuA 46 :ELG T0384 51 :LFDQLEVFFKS 1gcuA 54 :RQISLEDALRS T0384 62 :SFDLVYIASPNSLHFAQAKAALSAGKHVILEKPAVSQPQEWFDLIQTAEKNNCFIFEAARNYHEKAFTTIKNFL 1gcuA 66 :EIDVAYICSESSSHEDYIRQFLQAGKHVLVEYPMTLSFAAAQELWELAAQKGRVLHEEHVELLMEEFEFLRREV T0384 137 :DKQV 1gcuA 140 :LGKE T0384 143 :ADFNYAKYSSKMPDLLAG 1gcuA 144 :LLKGSLRFTASPLEEERF T0384 173 :GALMDLGIYPLYAAVRLFGKANDATYHAQQLDNSIDLNGDGILFYPDYQ 1gcuA 162 :GFPAFSGISRLTWLVSLFGELSLISATLEERKEDQYMKMTVQLETQNKG T0384 222 :VHIKAGKNITSN 1gcuA 212 :LSWIEEKGPGLK T0384 234 :LPCEIYTTDGTL 1gcuA 226 :RYVNFQFTSGSL T0384 265 :QVQLPIQQAPHTMTEEVAAFAHMIQQPD 1gcuA 238 :EEVPSVGVNKNIFLKDQDIFVQKLLDQV T0384 293 :LNLYQTWLYDAGSVHELLYTMRQTA 1gcuA 267 :AEDLAAEKKRIMHCLGLASDIQKLC Number of specific fragments extracted= 13 number of extra gaps= 0 total=294 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 1gcuA/T0384-1gcuA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0384 read from 1gcuA/T0384-1gcuA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1gcuA read from 1gcuA/T0384-1gcuA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1gcuA in template set Warning: unaligning (T0384)G318 because last residue in template chain is (1gcuA)H292 T0384 2 :LKLGVIGTGAISHHFIEAAHT 1gcuA 9 :FGVVVVGVGRAGSVRLRDLKD T0384 23 :SGEYQLVAIYSRKL 1gcuA 33 :AAFLNLIGFVSRRE T0384 46 :YQ 1gcuA 47 :LG T0384 48 :NI 1gcuA 52 :EV T0384 54 :QL 1gcuA 57 :SL T0384 56 :EVFFKSSFDLVYIASPNSLHFAQAKAALSAGKHVILEKPAVSQPQEWFDLIQTAEKNNCFIFEAARNYHEKAFTTIKNFLA 1gcuA 60 :DALRSQEIDVAYICSESSSHEDYIRQFLQAGKHVLVEYPMTLSFAAAQELWELAAQKGRVLHEEHVELLMEEFEFLRREVL T0384 138 :KQ 1gcuA 141 :GK T0384 144 :DFNYAKYSSKMPDLLAG 1gcuA 143 :ELLKGSLRFTASPLEEE T0384 169 :RF 1gcuA 160 :RF T0384 173 :GALMDLGIYPLYAAVRLFGKANDATYHAQQLDNSIDLNGDGILFYPDY 1gcuA 162 :GFPAFSGISRLTWLVSLFGELSLISATLEERKEDQYMKMTVQLETQNK T0384 221 :QVHIKAGKNITSN 1gcuA 211 :LLSWIEEKGPGLK T0384 234 :LPCEIYTTDGTL 1gcuA 226 :RYVNFQFTSGSL T0384 265 :QVQLPIQQAPHTMTEEVAAFAHMIQQP 1gcuA 238 :EEVPSVGVNKNIFLKDQDIFVQKLLDQ T0384 292 :DLNLYQTWLYDAGSVHELLYTMRQTA 1gcuA 266 :SAEDLAAEKKRIMHCLGLASDIQKLC Number of specific fragments extracted= 14 number of extra gaps= 0 total=308 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 1gcuA/T0384-1gcuA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0384 read from 1gcuA/T0384-1gcuA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1gcuA read from 1gcuA/T0384-1gcuA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1gcuA in template set T0384 2 :LKLGVIGTGAISHHFIEAAHT 1gcuA 9 :FGVVVVGVGRAGSVRLRDLKD T0384 23 :SGEYQLVAIYSRKL 1gcuA 33 :AAFLNLIGFVSRRE T0384 46 :Y 1gcuA 47 :L T0384 49 :IQLF 1gcuA 53 :VRQI T0384 54 :QLEVFF 1gcuA 57 :SLEDAL T0384 60 :KSSFDLVYIASPNSLHFAQAKAALSAGKHVILEKPAVSQPQEWFDLIQTAEKNNCFIFEAARNYHEKAFTTIKNFLAD 1gcuA 64 :SQEIDVAYICSESSSHEDYIRQFLQAGKHVLVEYPMTLSFAAAQELWELAAQKGRVLHEEHVELLMEEFEFLRREVLG T0384 141 :LGADFNYAKYSSKMPD 1gcuA 142 :KELLKGSLRFTASPLE T0384 162 :TPNVFSDRFA 1gcuA 158 :EERFGFPAFS T0384 179 :GIYPLYAAVRLFGKANDATYHAQQLDNSIDLNGDGILFYPDYQVHIKAGKNIT 1gcuA 168 :GISRLTWLVSLFGELSLISATLEERKEDQYMKMTVQLETQNKGLLSWIEEKGP T0384 232 :SNLPCEIYTTDGTL 1gcuA 224 :RNRYVNFQFTSGSL T0384 265 :QVQLPIQQAPHTMTEEVAAFAHMIQQP 1gcuA 238 :EEVPSVGVNKNIFLKDQDIFVQKLLDQ T0384 296 :YQTWLYDAGSVHELLYTM 1gcuA 265 :VSAEDLAAEKKRIMHCLG Number of specific fragments extracted= 12 number of extra gaps= 0 total=320 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 2h63A/T0384-2h63A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # Reading fragments from alignment file # Attempting to read fragment alignments from file 2h63A/T0384-2h63A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # Reading fragments from alignment file # Attempting to read fragment alignments from file 2h63A/T0384-2h63A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ff9A/T0384-1ff9A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1ff9A expands to /projects/compbio/data/pdb/1ff9.pdb.gz 1ff9A:# T0384 read from 1ff9A/T0384-1ff9A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ff9A read from 1ff9A/T0384-1ff9A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1ff9A to template set # found chain 1ff9A in template set Warning: unaligning (T0384)P71 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ff9A)F80 Warning: unaligning (T0384)L74 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ff9A)F80 T0384 2 :LKLGVIGTGAISHHFIEAAHTS 1ff9A 4 :KSVLMLGSGFVTRPTLDVLTDS T0384 25 :EYQLV 1ff9A 26 :GIKVT T0384 31 :IYSRKLETAATFAS 1ff9A 31 :VACRTLESAKKLSA T0384 47 :QNI 1ff9A 45 :GVQ T0384 50 :QLFDQLEVFFK 1ff9A 57 :NDDAALDAEVA T0384 62 :SFDLVYIAS 1ff9A 68 :KHDLVISLI T0384 75 :HFAQAKAALSAGKHVIL 1ff9A 81 :HATVIKSAIRQKKHVVT T0384 95 :AVSQPQEWFDLIQTAEKNNCFIF 1ff9A 98 :TSYVSPAMMELDQAAKDAGITVM T0384 118 :EAARNYHEKAF 1ff9A 123 :IGLDPGIDHLY T0384 129 :TTIKNFLADKQ 1ff9A 135 :IKTIEEVHAAG T0384 142 :G 1ff9A 146 :G T0384 143 :ADFNYAKYSS 1ff9A 148 :IKTFLSYCGG T0384 154 :MPDLLAGQTPNVFSDRFAG 1ff9A 158 :LPAPESSDNPLGYKFSWSS T0384 173 :GALMDLG 1ff9A 178 :GVLLALR T0384 194 :ND 1ff9A 185 :NA T0384 200 :AQQLDNS 1ff9A 187 :ASFYKDG T0384 207 :IDLNGDGILF 1ff9A 354 :ERDLVMLQHK T0384 245 :LTLNTIEHIRSAIFT 1ff9A 364 :FEIENKDGSRETRTS T0384 265 :QVQLPIQQAP 1ff9A 379 :SLCEYGAPIG T0384 275 :HTMTEEVAAFAHMIQQPDLNLYQ 1ff9A 397 :KLVGVPCAVAVKFVLDGTISDRG T0384 298 :TWLYDAGSVHELLY 1ff9A 424 :MNSKINDPLMKELK Number of specific fragments extracted= 21 number of extra gaps= 0 total=341 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 1ff9A/T0384-1ff9A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0384 read from 1ff9A/T0384-1ff9A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ff9A read from 1ff9A/T0384-1ff9A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1ff9A in template set Warning: unaligning (T0384)P71 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ff9A)F80 Warning: unaligning (T0384)L74 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ff9A)F80 T0384 1 :MLKLGVIGTGAISHHFIEAAHTS 1ff9A 3 :TKSVLMLGSGFVTRPTLDVLTDS T0384 25 :EYQLV 1ff9A 26 :GIKVT T0384 31 :IYSRKLETAATFASRYQNIQLFD 1ff9A 31 :VACRTLESAKKLSAGVQHSTPIS T0384 55 :L 1ff9A 58 :D T0384 56 :EVFFK 1ff9A 60 :AALDA T0384 61 :SSFDLVYIAS 1ff9A 67 :AKHDLVISLI T0384 75 :HFAQAKAALSAGKHVIL 1ff9A 81 :HATVIKSAIRQKKHVVT T0384 95 :AVSQPQEWFDLIQTAEKNNCFIFEAARNY 1ff9A 98 :TSYVSPAMMELDQAAKDAGITVMNEIGLD T0384 124 :HEKAFTTIKNFLADKQ 1ff9A 131 :HLYAIKTIEEVHAAGG T0384 144 :DFNYAKYSSK 1ff9A 147 :KIKTFLSYCG T0384 154 :MPDLLAGQT 1ff9A 158 :LPAPESSDN T0384 163 :PNVFS 1ff9A 331 :TPRGN T0384 182 :PLYAAVRLFG 1ff9A 336 :ALDTLCATLE T0384 201 :QQLDNSIDLNGDGILF 1ff9A 348 :MQFEEGERDLVMLQHK T0384 245 :LTLNTIEHIRSAIFTD 1ff9A 364 :FEIENKDGSRETRTSS T0384 264 :NQVQLPIQQAPH 1ff9A 380 :LCEYGAPIGSGG T0384 276 :TMTEEVAAFAHMIQQPDLNLY 1ff9A 398 :LVGVPCAVAVKFVLDGTISDR T0384 309 :LLYTMRQTAGIRFEA 1ff9A 428 :INDPLMKELKEKYGI Number of specific fragments extracted= 18 number of extra gaps= 0 total=359 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 1ff9A/T0384-1ff9A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0384 read from 1ff9A/T0384-1ff9A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ff9A read from 1ff9A/T0384-1ff9A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1ff9A in template set Warning: unaligning (T0384)P71 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ff9A)F80 Warning: unaligning (T0384)L74 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ff9A)F80 T0384 2 :LKLGVIGTGAISHHFIEAAHTS 1ff9A 4 :KSVLMLGSGFVTRPTLDVLTDS T0384 25 :EYQLV 1ff9A 26 :GIKVT T0384 31 :IYSRKLETAATFASRYQNIQLFD 1ff9A 31 :VACRTLESAKKLSAGVQHSTPIS T0384 54 :QLEVFF 1ff9A 61 :ALDAEV T0384 62 :SFDLVYIAS 1ff9A 68 :KHDLVISLI T0384 75 :HFAQAKAALSAGKHVILE 1ff9A 81 :HATVIKSAIRQKKHVVTT T0384 96 :VSQPQEWFDLIQTAEKNNCFIFEAARNY 1ff9A 99 :SYVSPAMMELDQAAKDAGITVMNEIGLD T0384 124 :HEKAFTTIKNFLADK 1ff9A 131 :HLYAIKTIEEVHAAG T0384 141 :LGADFNYAKYSSKMPDLLAGQTP 1ff9A 146 :GKIKTFLSYCGGLPAPESSDNPL T0384 165 :V 1ff9A 333 :R T0384 180 :IYPLYAAVRLFGKA 1ff9A 334 :GNALDTLCATLEEK T0384 201 :QQLDNSIDLNGDGILFY 1ff9A 348 :MQFEEGERDLVMLQHKF T0384 218 :PDYQVHIKAGKNIT 1ff9A 369 :KDGSRETRTSSLCE T0384 265 :QVQLPIQQAPHTMTEEVAAFAHMIQQPDLNL 1ff9A 387 :IGSGGYSAMAKLVGVPCAVAVKFVLDGTISD T0384 296 :YQTWLYDAGSVHE 1ff9A 424 :MNSKINDPLMKEL Number of specific fragments extracted= 15 number of extra gaps= 0 total=374 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 1f06A/T0384-1f06A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1f06A expands to /projects/compbio/data/pdb/1f06.pdb.gz 1f06A:# T0384 read from 1f06A/T0384-1f06A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1f06A read from 1f06A/T0384-1f06A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1f06A to template set # found chain 1f06A in template set T0384 2 :LKLGVIGTGAISHHFIEAAHTSGEYQLVAIYSRKLE 1f06A 4 :IRVAIVGYGNLGRSVEKLIAKQPDMDLVGIFSRRAT T0384 46 :YQNI 1f06A 40 :LDTK T0384 50 :QLFD 1f06A 45 :PVFD T0384 55 :LEVF 1f06A 49 :VADV T0384 59 :FKSSFDLVYIASP 1f06A 55 :HADDVDVLFLCMG T0384 72 :NSLHFAQAKAALSA 1f06A 69 :ATDIPEQAPKFAQF T0384 88 :HVILE 1f06A 83 :ACTVD T0384 95 :AVSQPQEW 1f06A 88 :TYDNHRDI T0384 103 :FDLIQTAEKNNCFIF 1f06A 100 :QVMNEAATAAGNVAL T0384 118 :EAARNYHEKAF 1f06A 117 :TGWDPGMFSIN T0384 129 :TTIKNFL 1f06A 129 :VYAAAVL T0384 139 :QV 1f06A 136 :AE T0384 143 :ADFNYAKYSSKMPDLLA 1f06A 138 :HQQHTFWGPGLSQGHSD T0384 188 :RLFG 1f06A 155 :ALRR T0384 192 :KANDATYHAQQLDN 1f06A 161 :GVQKAVQYTLPSED T0384 207 :IDLNGDGILFYPDYQ 1f06A 244 :HGGHVITTGDTGGFN T0384 222 :VHIK 1f06A 260 :TVEY T0384 244 :TLTLN 1f06A 264 :ILKLD T0384 297 :QTWLYDAGSVHELLYTMRQTAGIRFE 1f06A 269 :RNPDFTASSQIAFGRAAHRMKQQGQS Number of specific fragments extracted= 19 number of extra gaps= 0 total=393 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 1f06A/T0384-1f06A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0384 read from 1f06A/T0384-1f06A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1f06A read from 1f06A/T0384-1f06A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1f06A in template set T0384 2 :LKLGVIGTGAISHHFIEAAHTSGEYQLVAIYSRKLE 1f06A 4 :IRVAIVGYGNLGRSVEKLIAKQPDMDLVGIFSRRAT T0384 46 :YQ 1f06A 40 :LD T0384 48 :NIQLFD 1f06A 43 :KTPVFD T0384 54 :QLEVFF 1f06A 51 :DVDKHA T0384 61 :SSFDLVYIASPN 1f06A 57 :DDVDVLFLCMGS T0384 73 :SLHFAQAKAALSA 1f06A 70 :TDIPEQAPKFAQF T0384 88 :HVILE 1f06A 83 :ACTVD T0384 95 :AVSQPQEW 1f06A 88 :TYDNHRDI T0384 103 :FDLIQTAEKNNCFIFEA 1f06A 100 :QVMNEAATAAGNVALVS T0384 174 :ALMDLGI 1f06A 117 :TGWDPGM T0384 183 :LYAAVRLFG 1f06A 124 :FSINRVYAA T0384 192 :KANDATYHAQQL 1f06A 134 :VLAEHQQHTFWG T0384 204 :DNSIDLNGDGILFYPDY 1f06A 239 :HTGMPHGGHVITTGDTG T0384 221 :QVHIKA 1f06A 257 :FNHTVE T0384 243 :GTLTLNT 1f06A 263 :YILKLDR T0384 298 :TWLYDAGSVHELLYTMRQTAGIRFE 1f06A 270 :NPDFTASSQIAFGRAAHRMKQQGQS Number of specific fragments extracted= 16 number of extra gaps= 0 total=409 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 1f06A/T0384-1f06A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0384 read from 1f06A/T0384-1f06A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1f06A read from 1f06A/T0384-1f06A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1f06A in template set T0384 2 :LKLGVIGTGAISHHFIEAAHTSGEYQLVAIYSRKLE 1f06A 4 :IRVAIVGYGNLGRSVEKLIAKQPDMDLVGIFSRRAT T0384 46 :YQN 1f06A 40 :LDT T0384 49 :IQLFD 1f06A 44 :TPVFD T0384 55 :LEVFF 1f06A 49 :VADVD T0384 60 :KSSFDLVYIASPN 1f06A 56 :ADDVDVLFLCMGS T0384 73 :SLHFAQAKAALSA 1f06A 70 :TDIPEQAPKFAQF T0384 88 :HVILEK 1f06A 83 :ACTVDT T0384 96 :VSQ 1f06A 89 :YDN T0384 99 :PQEWFDLIQTAEKNNCFIFEAARNYHEKAFTTIKNFLAD 1f06A 96 :PRHRQVMNEAATAAGNVALVSTGWDPGMFSINRVYAAAV T0384 140 :VLGADFNYAKYSSKMPDL 1f06A 135 :LAEHQQHTFWGPGLSQGH T0384 192 :KANDATYHAQQL 1f06A 161 :GVQKAVQYTLPS T0384 204 :DNSIDLNGDGILFY 1f06A 239 :HTGMPHGGHVITTG T0384 218 :PDYQVHIKAG 1f06A 254 :TGGFNHTVEY T0384 244 :TLTLNTI 1f06A 264 :ILKLDRN T0384 297 :QTWLYDAGSVHELLYTMRQTAGIR 1f06A 271 :PDFTASSQIAFGRAAHRMKQQGQS Number of specific fragments extracted= 15 number of extra gaps= 0 total=424 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 1drw/T0384-1drw-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1drw expands to /projects/compbio/data/pdb/1drw.pdb.gz 1drw:Warning: there is no chain 1drw will retry with 1drwA # T0384 read from 1drw/T0384-1drw-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1drw read from 1drw/T0384-1drw-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1drw to template set # found chain 1drw in template set Warning: unaligning (T0384)I7 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (1drw)G12 Warning: unaligning (T0384)G8 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (1drw)G12 Warning: unaligning (T0384)Y67 because of BadResidue code BAD_PEPTIDE in next template residue (1drw)D78 Warning: unaligning (T0384)I68 because of BadResidue code BAD_PEPTIDE at template residue (1drw)D78 Warning: unaligning (T0384)A69 because of BadResidue code BAD_PEPTIDE in next template residue (1drw)T80 Warning: unaligning (T0384)S70 because of BadResidue code BAD_PEPTIDE at template residue (1drw)T80 Warning: unaligning (T0384)L141 because of BadResidue code BAD_PEPTIDE in next template residue (1drw)D152 Warning: unaligning (T0384)G142 because of BadResidue code BAD_PEPTIDE at template residue (1drw)D152 Warning: unaligning (T0384)K153 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1drw)V164 Warning: unaligning (T0384)M154 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1drw)V164 Warning: unaligning (T0384)Q262 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (1drw)R230 Warning: unaligning (T0384)G263 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (1drw)R230 Warning: unaligning (T0384)L293 because of BadResidue code BAD_PEPTIDE in next template residue (1drw)E258 Warning: unaligning (T0384)N294 because of BadResidue code BAD_PEPTIDE at template residue (1drw)E258 Warning: unaligning (T0384)Y296 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1drw)L261 Warning: unaligning (T0384)Q297 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1drw)L261 T0384 2 :LKLGV 1drw 6 :IRVAI T0384 9 :T 1drw 13 :A T0384 10 :GAISHHFIEAAHTSGEYQLVAIYSRK 1drw 15 :GRMGRQLIQAALALEGVQLGAALERE T0384 47 :QNI 1drw 41 :GSS T0384 50 :QLFDQLEVFFK 1drw 61 :TVQSSLDAVKD T0384 62 :SFDLV 1drw 72 :DFDVF T0384 71 :PNSLHFAQAKAALSAGKHVILEK 1drw 81 :RPEGTLNHLAFCRQHGKGMVIGT T0384 95 :AVSQPQEWFDLIQTAE 1drw 104 :TGFDEAGKQAIRDAAA T0384 113 :NCFIFEA 1drw 120 :DIAIVFA T0384 120 :ARNYHEKAFTTIKNFL 1drw 129 :FSVGVNVMLKLLEKAA T0384 136 :ADKQV 1drw 146 :VMGDY T0384 143 :ADFNYAKYSS 1drw 153 :IEIIEAHHRH T0384 155 :PDLL 1drw 165 :DAPS T0384 173 :GALMDLG 1drw 169 :GTALAMG T0384 184 :YAAVRLFG 1drw 176 :EAIAHALD T0384 192 :K 1drw 185 :D T0384 207 :IDLNGDGILF 1drw 216 :IVGEHTAMFA T0384 259 :TDH 1drw 226 :DIG T0384 264 :NQVQLPIQQAPHTMTEEVAAFA 1drw 231 :LEITHKASSRMTFANGAVRSAL T0384 287 :MIQ 1drw 253 :WLS T0384 292 :D 1drw 256 :G T0384 295 :L 1drw 259 :S T0384 298 :TWLYDAG 1drw 262 :FDMRDVL Number of specific fragments extracted= 23 number of extra gaps= 7 total=447 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 1drw/T0384-1drw-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0384 read from 1drw/T0384-1drw-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1drw read from 1drw/T0384-1drw-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1drw in template set Warning: unaligning (T0384)I7 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (1drw)G12 Warning: unaligning (T0384)G8 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (1drw)G12 Warning: unaligning (T0384)Y67 because of BadResidue code BAD_PEPTIDE in next template residue (1drw)D78 Warning: unaligning (T0384)I68 because of BadResidue code BAD_PEPTIDE at template residue (1drw)D78 Warning: unaligning (T0384)A69 because of BadResidue code BAD_PEPTIDE in next template residue (1drw)T80 Warning: unaligning (T0384)S70 because of BadResidue code BAD_PEPTIDE at template residue (1drw)T80 Warning: unaligning (T0384)A143 because of BadResidue code BAD_PEPTIDE in next template residue (1drw)D152 Warning: unaligning (T0384)Y147 because of BadResidue code BAD_PEPTIDE at template residue (1drw)D152 Warning: unaligning (T0384)L158 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1drw)V164 Warning: unaligning (T0384)A159 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1drw)V164 Warning: unaligning (T0384)Y220 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (1drw)R230 Warning: unaligning (T0384)I253 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (1drw)R230 Warning: unaligning (T0384)L293 because of BadResidue code BAD_PEPTIDE in next template residue (1drw)E258 Warning: unaligning (T0384)N294 because of BadResidue code BAD_PEPTIDE at template residue (1drw)E258 Warning: unaligning (T0384)Y296 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1drw)L261 Warning: unaligning (T0384)Q297 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1drw)L261 T0384 2 :LKLGV 1drw 6 :IRVAI T0384 9 :T 1drw 13 :A T0384 10 :GAISHHFIEAAHTSGEYQLVAIYSRK 1drw 15 :GRMGRQLIQAALALEGVQLGAALERE T0384 47 :Q 1drw 41 :G T0384 48 :NIQLFDQLEVFF 1drw 59 :GVTVQSSLDAVK T0384 61 :SSFDLV 1drw 71 :DDFDVF T0384 71 :PNSLHFAQAKAALSAGKHVILEK 1drw 81 :RPEGTLNHLAFCRQHGKGMVIGT T0384 95 :AVSQPQ 1drw 104 :TGFDEA T0384 102 :WFDLIQTAEK 1drw 110 :GKQAIRDAAA T0384 113 :NCFIFEA 1drw 120 :DIAIVFA T0384 120 :ARNYHEKAFTTIKNFLAD 1drw 129 :FSVGVNVMLKLLEKAAKV T0384 140 :VLG 1drw 147 :MGD T0384 148 :AKYSSKMPDL 1drw 153 :IEIIEAHHRH T0384 160 :GQT 1drw 165 :DAP T0384 181 :YPLYAAVRLFG 1drw 173 :AMGEAIAHALD T0384 192 :K 1drw 185 :D T0384 200 :AQQLDN 1drw 191 :VYSREG T0384 206 :SIDLNGDGILFYPD 1drw 215 :DIVGEHTAMFADIG T0384 254 :RSAIFTDHQG 1drw 231 :LEITHKASSR T0384 278 :TEEVAAFAHMIQQ 1drw 241 :MTFANGAVRSALW T0384 291 :PD 1drw 255 :SG T0384 295 :L 1drw 259 :S T0384 298 :TWLYDAG 1drw 262 :FDMRDVL Number of specific fragments extracted= 23 number of extra gaps= 7 total=470 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 1drw/T0384-1drw-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0384 read from 1drw/T0384-1drw-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1drw read from 1drw/T0384-1drw-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1drw in template set Warning: unaligning (T0384)I7 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (1drw)G12 Warning: unaligning (T0384)G8 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (1drw)G12 Warning: unaligning (T0384)Y67 because of BadResidue code BAD_PEPTIDE in next template residue (1drw)D78 Warning: unaligning (T0384)I68 because of BadResidue code BAD_PEPTIDE at template residue (1drw)D78 Warning: unaligning (T0384)A69 because of BadResidue code BAD_PEPTIDE in next template residue (1drw)T80 Warning: unaligning (T0384)S70 because of BadResidue code BAD_PEPTIDE at template residue (1drw)T80 Warning: unaligning (T0384)L141 because of BadResidue code BAD_PEPTIDE in next template residue (1drw)D152 Warning: unaligning (T0384)G142 because of BadResidue code BAD_PEPTIDE at template residue (1drw)D152 Warning: unaligning (T0384)M154 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1drw)V164 Warning: unaligning (T0384)P155 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1drw)V164 Warning: unaligning (T0384)Q221 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (1drw)R230 Warning: unaligning (T0384)V222 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (1drw)R230 Warning: unaligning (T0384)D292 because of BadResidue code BAD_PEPTIDE in next template residue (1drw)E258 Warning: unaligning (T0384)L293 because of BadResidue code BAD_PEPTIDE at template residue (1drw)E258 Warning: unaligning (T0384)L295 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1drw)L261 T0384 2 :LKLGV 1drw 6 :IRVAI T0384 9 :T 1drw 13 :A T0384 10 :GAISHHFIEAAHTSGEYQLVAIYSRKL 1drw 15 :GRMGRQLIQAALALEGVQLGAALEREG T0384 49 :IQLFDQLEVFF 1drw 60 :VTVQSSLDAVK T0384 62 :SFDLV 1drw 72 :DFDVF T0384 71 :PNSLHFAQAKAALSAGKHVILEK 1drw 81 :RPEGTLNHLAFCRQHGKGMVIGT T0384 95 :AVSQPQEWFDLIQT 1drw 104 :TGFDEAGKQAIRDA T0384 112 :NNCFIFEAARNYH 1drw 119 :ADIAIVFAANFSV T0384 125 :EKAFTTIKNFLAD 1drw 134 :NVMLKLLEKAAKV T0384 139 :QV 1drw 149 :DY T0384 143 :ADFNY 1drw 153 :IEIIE T0384 149 :KYSSK 1drw 158 :AHHRH T0384 156 :DLLAGQ 1drw 165 :DAPSGT T0384 179 :GIYPLYAAVRLFGKANDATYHAQQL 1drw 171 :ALAMGEAIAHALDKDLKDCAVYSRE T0384 204 :DNSIDLNGDGILFYP 1drw 213 :AGDIVGEHTAMFADI T0384 220 :Y 1drw 228 :G T0384 223 :HIKAGKNIT 1drw 231 :LEITHKASS T0384 278 :TEEVAAFAHMIQ 1drw 241 :MTFANGAVRSAL T0384 290 :QP 1drw 255 :SG T0384 294 :N 1drw 259 :S T0384 296 :YQTWLYD 1drw 262 :FDMRDVL Number of specific fragments extracted= 21 number of extra gaps= 7 total=491 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 2czcA/T0384-2czcA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2czcA expands to /projects/compbio/data/pdb/2czc.pdb.gz 2czcA:# T0384 read from 2czcA/T0384-2czcA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2czcA read from 2czcA/T0384-2czcA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2czcA to template set # found chain 2czcA in template set T0384 1 :M 2czcA 1 :M T0384 2 :LKLGVIGTGAISHHFIEAAHTSGEYQLVAIYSRKL 2czcA 3 :VKVGVNGYGTIGKRVAYAVTKQDDMELIGITKTKP T0384 37 :ETAATFAS 2czcA 39 :FEAYRAKE T0384 46 :YQNI 2czcA 47 :LGIP T0384 50 :QLFDQLEVFFK 2czcA 68 :EVAGTLNDLLE T0384 62 :SFDLVYIASPNSLHFAQAKAALSAGKHVILE 2czcA 79 :KVDIIVDATPGGIGAKNKPLYEKAGVKAIFQ T0384 95 :AV 2czcA 129 :AA T0384 112 :NNCFIFEAARNYHEKAFTTIK 2czcA 131 :LGKNYVRVVSCNTTGLVRTLS T0384 134 :FL 2czcA 152 :AI T0384 138 :KQV 2czcA 154 :REY T0384 143 :ADFNYAKYSSK 2czcA 157 :ADYVYAVMIRR T0384 175 :LMDLGIYPLYAAVRLFG 2czcA 299 :ESDVIPENIDAIRAMFE T0384 275 :HTMTEEVAAFAHMI 2czcA 317 :ADKWDSIKKTNKSL Number of specific fragments extracted= 13 number of extra gaps= 0 total=504 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 2czcA/T0384-2czcA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0384 read from 2czcA/T0384-2czcA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2czcA read from 2czcA/T0384-2czcA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2czcA in template set T0384 1 :MLKLGVIGTGAISHHFIEAAHTSGEYQLVAIYSRK 2czcA 2 :KVKVGVNGYGTIGKRVAYAVTKQDDMELIGITKTK T0384 36 :LETAATFASR 2czcA 38 :DFEAYRAKEL T0384 47 :Q 2czcA 48 :G T0384 48 :NIQLFDQL 2czcA 66 :GFEVAGTL T0384 56 :EVF 2czcA 75 :DLL T0384 61 :SSFDLVYIASPNSLHFAQAKAALSAGKHVILE 2czcA 78 :EKVDIIVDATPGGIGAKNKPLYEKAGVKAIFQ T0384 95 :AVSQPQ 2czcA 110 :GGEKAD T0384 115 :FIFEAARN 2czcA 119 :VSFVAQAN T0384 166 :FSDRFAGGALMDLGIYPLYAAVRLFG 2czcA 127 :YEAALGKNYVRVVSCNTTGLVRTLSA T0384 192 :KANDATYHAQQL 2czcA 156 :YADYVYAVMIRR T0384 204 :DNSIDLNGDGILFYPD 2czcA 212 :PTTLMHVHSVMVELKK T0384 283 :AFAHMIQQ 2czcA 233 :DVIDIFEN T0384 291 :PDLNLY 2czcA 249 :KEKGFD T0384 299 :WLYDAGSVHE 2czcA 255 :STAQIIEFAR Number of specific fragments extracted= 14 number of extra gaps= 0 total=518 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 2czcA/T0384-2czcA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0384 read from 2czcA/T0384-2czcA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2czcA read from 2czcA/T0384-2czcA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2czcA in template set T0384 1 :MLKLGVIGTGAISHHFIEAAHTSGEYQLVAIYSRKL 2czcA 2 :KVKVGVNGYGTIGKRVAYAVTKQDDMELIGITKTKP T0384 37 :ETAATFASRY 2czcA 39 :FEAYRAKELG T0384 49 :IQLFDQLEVFF 2czcA 67 :FEVAGTLNDLL T0384 62 :SFDLVYIASPNS 2czcA 79 :KVDIIVDATPGG T0384 101 :EWFDLIQTAEKNNCFIFEAA 2czcA 91 :IGAKNKPLYEKAGVKAIFQG T0384 156 :DL 2czcA 111 :GE T0384 160 :GQT 2czcA 113 :KAD T0384 164 :NVFSDRFAGGALMDLGIYPLYAAVRLFG 2czcA 125 :ANYEAALGKNYVRVVSCNTTGLVRTLSA T0384 194 :NDATYHAQQL 2czcA 158 :DYVYAVMIRR T0384 204 :DNSIDLNGDGILFYPDYQ 2czcA 212 :PTTLMHVHSVMVELKKPL T0384 273 :APH 2czcA 230 :TKD T0384 283 :AFAHMIQQ 2czcA 233 :DVIDIFEN Number of specific fragments extracted= 12 number of extra gaps= 0 total=530 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 1b7gO/T0384-1b7gO-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1b7gO expands to /projects/compbio/data/pdb/1b7g.pdb.gz 1b7gO:# T0384 read from 1b7gO/T0384-1b7gO-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1b7gO read from 1b7gO/T0384-1b7gO-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1b7gO to template set # found chain 1b7gO in template set Warning: unaligning (T0384)F63 because of BadResidue code BAD_PEPTIDE in next template residue (1b7gO)D79 Warning: unaligning (T0384)D64 because of BadResidue code BAD_PEPTIDE at template residue (1b7gO)D79 T0384 1 :MLKLGVIGTGAISHHFIEAAHTSGEYQLVAIYSRKL 1b7gO 1 :MVNVAVNGYGTIGKRVADAIIKQPDMKLVGVAKTSP T0384 37 :ETAATFASR 1b7gO 38 :YEAFIAHRR T0384 47 :QNI 1b7gO 47 :GIR T0384 50 :QLFDQLEVFFK 1b7gO 66 :PVAGTVEDLIK T0384 62 :S 1b7gO 77 :T T0384 65 :LVYIASPNSLHFAQAKAALSAGKHVILE 1b7gO 80 :IVVDTTPNGVGAQYKPIYLQLQRNAIFQ T0384 95 :AVSQPQEW 1b7gO 108 :GGEKAEVA T0384 105 :LIQTAEKNNCFIFEAARNYHEKAFTTIKNF 1b7gO 122 :LCNYNEALGKKYIRVVSCNTTALLRTICTV T0384 138 :KQVLGADFNYAKYSSK 1b7gO 152 :NKVSKVEKVRATIVRR T0384 154 :MPDLLAGQTPNVFSDRFAG 1b7gO 172 :KEVKKGPINSLVPDPATVP T0384 180 :IYPLYAAVRLFGKAN 1b7gO 191 :SHHAKDVNSVIRNLD T0384 196 :ATYHAQQLDNSIDLNGDGILFYPDY 1b7gO 206 :IATMAVIAPTTLMHMHFINITLKDK T0384 222 :VHIKAGKNIT 1b7gO 292 :VMLMYAVHQE T0384 275 :HTMTEEVAAFAHMI 1b7gO 302 :SIVVPENIDAIRAS T0384 295 :LYQTWLYD 1b7gO 316 :MKLMSAED T0384 309 :LLYTMRQTAG 1b7gO 324 :SMRITNESLG Number of specific fragments extracted= 16 number of extra gaps= 1 total=546 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 1b7gO/T0384-1b7gO-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0384 read from 1b7gO/T0384-1b7gO-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1b7gO read from 1b7gO/T0384-1b7gO-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1b7gO in template set Warning: unaligning (T0384)F63 because of BadResidue code BAD_PEPTIDE in next template residue (1b7gO)D79 Warning: unaligning (T0384)D64 because of BadResidue code BAD_PEPTIDE at template residue (1b7gO)D79 T0384 1 :MLKLGVIGTGAISHHFIEAAHTSGEYQLVAIYSRK 1b7gO 1 :MVNVAVNGYGTIGKRVADAIIKQPDMKLVGVAKTS T0384 37 :ETAATFASR 1b7gO 38 :YEAFIAHRR T0384 47 :Q 1b7gO 47 :G T0384 48 :NIQLFDQL 1b7gO 64 :GIPVAGTV T0384 56 :EVFFK 1b7gO 73 :DLIKT T0384 65 :LVYIASPNSLHFAQAKAALSAGKHVIL 1b7gO 80 :IVVDTTPNGVGAQYKPIYLQLQRNAIF T0384 92 :EKPAVSQ 1b7gO 110 :EKAEVAD T0384 102 :WF 1b7gO 125 :YN T0384 110 :EKNNCFIFEAARNYHEKAFTTIKNFLA 1b7gO 127 :EALGKKYIRVVSCNTTALLRTICTVNK T0384 141 :LG 1b7gO 154 :VS T0384 144 :DFNYAKYS 1b7gO 156 :KVEKVRAT T0384 152 :SKMPDLLAGQTP 1b7gO 167 :RAADQKEVKKGP T0384 164 :NVFSDRFAG 1b7gO 182 :LVPDPATVP T0384 180 :IYPLYAAVRLFGKAN 1b7gO 191 :SHHAKDVNSVIRNLD T0384 196 :ATYHAQQLDNSIDLNGDGILFYPD 1b7gO 206 :IATMAVIAPTTLMHMHFINITLKD T0384 257 :IFTDHQGNQV 1b7gO 248 :LISSKYDAEA T0384 281 :VAAFAHMIQQ 1b7gO 258 :TAELVEVARD T0384 291 :PDLNLY 1b7gO 301 :ESIVVP T0384 299 :WLYDAGSVH 1b7gO 307 :ENIDAIRAS T0384 308 :ELLYTMRQTAG 1b7gO 323 :DSMRITNESLG Number of specific fragments extracted= 20 number of extra gaps= 1 total=566 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 1b7gO/T0384-1b7gO-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0384 read from 1b7gO/T0384-1b7gO-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1b7gO read from 1b7gO/T0384-1b7gO-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1b7gO in template set Warning: unaligning (T0384)F63 because of BadResidue code BAD_PEPTIDE in next template residue (1b7gO)D79 Warning: unaligning (T0384)D64 because of BadResidue code BAD_PEPTIDE at template residue (1b7gO)D79 T0384 1 :MLKLGVIGTGAISHHFIEAAHTSGEYQLVAIYSRKL 1b7gO 1 :MVNVAVNGYGTIGKRVADAIIKQPDMKLVGVAKTSP T0384 37 :ETAATFASRY 1b7gO 38 :YEAFIAHRRG T0384 47 :QN 1b7gO 64 :GI T0384 50 :QLFDQLEVFF 1b7gO 66 :PVAGTVEDLI T0384 65 :LVYIASPNSLHFAQAKAALSAGKHVILE 1b7gO 80 :IVVDTTPNGVGAQYKPIYLQLQRNAIFQ T0384 108 :TAEK 1b7gO 124 :NYNE T0384 112 :NNCFIFEAARNYHEKAFTTIK 1b7gO 129 :LGKKYIRVVSCNTTALLRTIC T0384 134 :FLAD 1b7gO 150 :TVNK T0384 140 :VLGADFNYAKYSSKMPDLLAGQTP 1b7gO 154 :VSKVEKVRATIVRRAADQKEVKKG T0384 179 :GIYPLYAAVRLFG 1b7gO 190 :PSHHAKDVNSVIR T0384 193 :ANDATYHAQQLDNSIDLNGDGILFYPDY 1b7gO 203 :NLDIATMAVIAPTTLMHMHFINITLKDK T0384 261 :HQ 1b7gO 231 :VE T0384 263 :GNQVQ 1b7gO 253 :YDAEA T0384 281 :VAAFAHMIQQPDL 1b7gO 258 :TAELVEVARDLKR Number of specific fragments extracted= 14 number of extra gaps= 1 total=580 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 1cf2O/T0384-1cf2O-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1cf2O expands to /projects/compbio/data/pdb/1cf2.pdb.gz 1cf2O:# T0384 read from 1cf2O/T0384-1cf2O-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1cf2O read from 1cf2O/T0384-1cf2O-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1cf2O to template set # found chain 1cf2O in template set T0384 1 :MLKLGVIGTGAISHHFIEAAHTSGEYQLVAIYSRKL 1cf2O 1 :MKAVAINGYGTVGKRVADAIAQQDDMKVIGVSKTRP T0384 37 :ETAATFASR 1cf2O 38 :FEARMALKK T0384 47 :QNI 1cf2O 47 :GYD T0384 50 :QLFDQLEVFFK 1cf2O 67 :EVAGTVDDMLD T0384 62 :SFDLVYIASPNSLHFAQAKAALSAGKHVILE 1cf2O 78 :EADIVIDCTPEGIGAKNLKMYKEKGIKAIFQ T0384 95 :AVSQPQEW 1cf2O 109 :GGEKHEDI T0384 106 :IQTA 1cf2O 126 :YEES T0384 112 :NNCFIFEAARNYHEKAFTTIKNFL 1cf2O 130 :YGKDYTRVVSCNTTGLCRTLKPLH T0384 139 :QVLGADFNYAKYSSK 1cf2O 154 :DSFGIKKVRAVIVRR T0384 176 :MDLGIYPLYAAVRLFG 1cf2O 302 :SDIVPENVDAVRAILE T0384 192 :K 1cf2O 319 :E T0384 275 :HTMTEEVAAFAHMIQ 1cf2O 320 :EDKYKSINKTNKAMN Number of specific fragments extracted= 12 number of extra gaps= 0 total=592 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 1cf2O/T0384-1cf2O-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0384 read from 1cf2O/T0384-1cf2O-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1cf2O read from 1cf2O/T0384-1cf2O-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1cf2O in template set T0384 1 :MLKLGVIGTGAISHHFIEAAHTSGEYQLVAIYSRKL 1cf2O 1 :MKAVAINGYGTVGKRVADAIAQQDDMKVIGVSKTRP T0384 37 :ETAATFASR 1cf2O 38 :FEARMALKK T0384 47 :Q 1cf2O 47 :G T0384 48 :NIQLFDQL 1cf2O 65 :GIEVAGTV T0384 56 :EVF 1cf2O 74 :DML T0384 61 :SSFDLVYIASPNSLHFAQAKAALSAGKHVILE 1cf2O 77 :DEADIVIDCTPEGIGAKNLKMYKEKGIKAIFQ T0384 95 :AVSQPQEW 1cf2O 109 :GGEKHEDI T0384 103 :FDLIQTA 1cf2O 123 :LSNYEES T0384 112 :NNCFIFEAARNYHEKAFTTIKNFLAD 1cf2O 130 :YGKDYTRVVSCNTTGLCRTLKPLHDS T0384 141 :L 1cf2O 156 :F T0384 144 :DFNYAKY 1cf2O 157 :GIKKVRA T0384 151 :SSKMPDLLAGQTP 1cf2O 167 :RRGADPAQVSKGP T0384 164 :NVFSDRFA 1cf2O 184 :IPNPPKLP T0384 180 :IYPLYAAVRLFG 1cf2O 192 :SHHGPDVKTVLD T0384 192 :K 1cf2O 205 :N T0384 196 :ATYHAQQLDNSIDLNGDGILFYPD 1cf2O 206 :IDTMAVIVPTTLMHQHNVMVEVEE T0384 239 :YTTDGTLTLNTI 1cf2O 286 :TVVDNEIYYMQA T0384 276 :TMTEEVAAFAHMIQQPDLNLY 1cf2O 303 :DIVPENVDAVRAILEMEEDKY T0384 308 :ELLYTMRQTAG 1cf2O 324 :KSINKTNKAMN Number of specific fragments extracted= 19 number of extra gaps= 0 total=611 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 1cf2O/T0384-1cf2O-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0384 read from 1cf2O/T0384-1cf2O-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1cf2O read from 1cf2O/T0384-1cf2O-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1cf2O in template set T0384 1 :MLKLGVIGTGAISHHFIEAAHTSGEYQLVAIYSRKL 1cf2O 1 :MKAVAINGYGTVGKRVADAIAQQDDMKVIGVSKTRP T0384 37 :ETAATFASRY 1cf2O 38 :FEARMALKKG T0384 47 :QN 1cf2O 65 :GI T0384 50 :QLFDQLEVFF 1cf2O 67 :EVAGTVDDML T0384 62 :SFDLVYIASPNSLHFAQAKAALSAGKHVILE 1cf2O 78 :EADIVIDCTPEGIGAKNLKMYKEKGIKAIFQ T0384 95 :AVSQPQEW 1cf2O 109 :GGEKHEDI T0384 105 :LIQTAEK 1cf2O 122 :SLSNYEE T0384 112 :NNCFIFEAARNYHEKAFTTIKNFLAD 1cf2O 130 :YGKDYTRVVSCNTTGLCRTLKPLHDS T0384 139 :QVLGADFNYAKYSSKMPDLLAGQTP 1cf2O 157 :GIKKVRAVIVRRGADPAQVSKGPIN T0384 185 :AAVR 1cf2O 197 :DVKT T0384 191 :GKANDATYHAQQLDNSIDLNGDGILFYPD 1cf2O 201 :VLDINIDTMAVIVPTTLMHQHNVMVEVEE T0384 271 :QQAPHTMTEEVAA 1cf2O 230 :TPTVDDIIDVFED T0384 289 :QQPDLNL 1cf2O 251 :AEDGLTS T0384 304 :GSVHELLYTM 1cf2O 258 :TAEIMEYAKE Number of specific fragments extracted= 14 number of extra gaps= 0 total=625 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 1nvmB/T0384-1nvmB-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1nvmB expands to /projects/compbio/data/pdb/1nvm.pdb.gz 1nvmB:Skipped atom 2677, because occupancy 0.5 <= existing 0.500 in 1nvmB Skipped atom 2679, because occupancy 0.500 <= existing 0.500 in 1nvmB Skipped atom 2681, because occupancy 0.500 <= existing 0.500 in 1nvmB Skipped atom 2683, because occupancy 0.500 <= existing 0.500 in 1nvmB Skipped atom 2748, because occupancy 0.500 <= existing 0.500 in 1nvmB Skipped atom 2750, because occupancy 0.500 <= existing 0.500 in 1nvmB Skipped atom 2869, because occupancy 0.500 <= existing 0.500 in 1nvmB Skipped atom 2871, because occupancy 0.500 <= existing 0.500 in 1nvmB Skipped atom 3201, because occupancy 0.500 <= existing 0.500 in 1nvmB Skipped atom 3213, because occupancy 0.500 <= existing 0.500 in 1nvmB Skipped atom 3592, because occupancy 0.500 <= existing 0.500 in 1nvmB Skipped atom 3675, because occupancy 0.500 <= existing 0.500 in 1nvmB Skipped atom 3777, because occupancy 0.500 <= existing 0.500 in 1nvmB Skipped atom 3792, because occupancy 0.500 <= existing 0.500 in 1nvmB Skipped atom 3862, because occupancy 0.500 <= existing 0.500 in 1nvmB Skipped atom 3864, because occupancy 0.500 <= existing 0.500 in 1nvmB Skipped atom 3866, because occupancy 0.500 <= existing 0.500 in 1nvmB Skipped atom 3868, because occupancy 0.500 <= existing 0.500 in 1nvmB Skipped atom 3941, because occupancy 0.500 <= existing 0.500 in 1nvmB Skipped atom 4044, because occupancy 0.500 <= existing 0.500 in 1nvmB Skipped atom 4046, because occupancy 0.500 <= existing 0.500 in 1nvmB Skipped atom 4048, because occupancy 0.500 <= existing 0.500 in 1nvmB Skipped atom 4050, because occupancy 0.500 <= existing 0.500 in 1nvmB Skipped atom 4052, because occupancy 0.500 <= existing 0.500 in 1nvmB Skipped atom 4054, because occupancy 0.500 <= existing 0.500 in 1nvmB Skipped atom 4069, because occupancy 0.500 <= existing 0.500 in 1nvmB Skipped atom 4071, because occupancy 0.500 <= existing 0.500 in 1nvmB Skipped atom 4073, because occupancy 0.500 <= existing 0.500 in 1nvmB # T0384 read from 1nvmB/T0384-1nvmB-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1nvmB read from 1nvmB/T0384-1nvmB-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1nvmB to template set # found chain 1nvmB in template set T0384 1 :MLKLGVIGTGAISHHFIEAAHTS 1nvmB 4 :KLKVAIIGSGNIGTDLMIKVLRN T0384 24 :GEYQLVAIYSRKLET 1nvmB 28 :KYLEMGAMVGIDAAS T0384 39 :AATFASRYQNIQLFDQLEVFFK 1nvmB 44 :GLARAQRMGVTTTYAGVEGLIK T0384 62 :SFDLVYIASPNSLHFAQAKAALSA 1nvmB 71 :DIDFVFDATSASAHVQNEALLRQA T0384 86 :GKHVILEKPAVSQ 1nvmB 97 :GIRLIDLTPAAIG T0384 105 :LIQTAEKNNC 1nvmB 115 :VVNLEEHLGK T0384 115 :FIFEAA 1nvmB 126 :NVNMVT T0384 123 :YHEKAFTTIKNFL 1nvmB 132 :CGGQATIPMVAAV T0384 138 :KQVLGADFNYAKYSSK 1nvmB 145 :SRVAKVHYAEIVASIS T0384 154 :MPDL 1nvmB 165 :GPGT T0384 173 :GALMDLGIYPLYAAVRLFGKANDATYHAQQLDN 1nvmB 169 :RANIDEFTETTSKAIEVIGGAAKGKAIIIMNPA T0384 206 :SIDLNGDGILFYPDY 1nvmB 204 :PLIMRDTVYVLSAAA T0384 225 :KAGKNITSN 1nvmB 248 :QFDVIPESA T0384 234 :LPCEIYTTDGTLTLNTIEHIR 1nvmB 264 :GRFSGLKTSVFLEVEGAAHYL T0384 295 :LYQTWLYD 1nvmB 285 :PAYAGNLD T0384 303 :AGSVHELLYTMRQTAGI 1nvmB 295 :TSAALATAERMAQSMLN Number of specific fragments extracted= 16 number of extra gaps= 0 total=641 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 1nvmB/T0384-1nvmB-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0384 read from 1nvmB/T0384-1nvmB-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1nvmB read from 1nvmB/T0384-1nvmB-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1nvmB in template set Warning: unaligning (T0384)S206 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1nvmB)P203 Warning: unaligning (T0384)I207 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1nvmB)P203 T0384 1 :MLKLGVIGTGAISHHFIEAAHT 1nvmB 4 :KLKVAIIGSGNIGTDLMIKVLR T0384 23 :SGEYQLVAIYSRKLET 1nvmB 27 :AKYLEMGAMVGIDAAS T0384 39 :AATFASRYQNIQLFDQLEVFFK 1nvmB 44 :GLARAQRMGVTTTYAGVEGLIK T0384 61 :SSFDLVYIASPNSLHFAQAKAALSA 1nvmB 70 :ADIDFVFDATSASAHVQNEALLRQA T0384 86 :GKHVILEKPAVSQ 1nvmB 97 :GIRLIDLTPAAIG T0384 112 :NNCFIFEAARNYHEKAFTTIKNFLA 1nvmB 122 :LGKLNVNMVTCGGQATIPMVAAVSR T0384 141 :LG 1nvmB 147 :VA T0384 144 :DFNYAKYSSK 1nvmB 149 :KVHYAEIVAS T0384 154 :MPDLLAG 1nvmB 160 :SSKSAGP T0384 173 :G 1nvmB 167 :G T0384 175 :LMDLGIYPLYAAVRLFGKANDATYHAQQLDN 1nvmB 171 :NIDEFTETTSKAIEVIGGAAKGKAIIIMNPA T0384 208 :DLNGDGILF 1nvmB 204 :PLIMRDTVY T0384 245 :LTLNT 1nvmB 213 :VLSAA T0384 272 :QAPHTMTEEVAAFAHMIQQ 1nvmB 218 :ADQAAVAASVAEMVQAVQA T0384 293 :LNLYQTWLYDAGSVHELLYTMRQTAG 1nvmB 285 :PAYAGNLDIMTSAALATAERMAQSML Number of specific fragments extracted= 15 number of extra gaps= 1 total=656 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 1nvmB/T0384-1nvmB-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0384 read from 1nvmB/T0384-1nvmB-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1nvmB read from 1nvmB/T0384-1nvmB-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1nvmB in template set Warning: unaligning (T0384)D204 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1nvmB)P203 Warning: unaligning (T0384)N205 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1nvmB)P203 T0384 1 :MLKLGVIGTGAISHHFIEAAHT 1nvmB 4 :KLKVAIIGSGNIGTDLMIKVLR T0384 23 :SGEYQLVAIYSRKL 1nvmB 27 :AKYLEMGAMVGIDA T0384 37 :E 1nvmB 43 :D T0384 39 :AATFASRYQNIQLFDQLEVFF 1nvmB 44 :GLARAQRMGVTTTYAGVEGLI T0384 60 :KSSFDLVYIASPNSLHFAQAKAALSA 1nvmB 69 :FADIDFVFDATSASAHVQNEALLRQA T0384 86 :GKHVILEKPAVSQ 1nvmB 97 :GIRLIDLTPAAIG T0384 112 :NNCFIFEAARNYHEKAFT 1nvmB 122 :LGKLNVNMVTCGGQATIP T0384 131 :IKNFLAD 1nvmB 140 :MVAAVSR T0384 140 :VLGADFNYAKYSSKMPDL 1nvmB 147 :VAKVHYAEIVASISSKSA T0384 160 :GQTPNVFSDRF 1nvmB 165 :GPGTRANIDEF T0384 182 :PLYAAVRLFGKANDATYHAQQL 1nvmB 178 :TTSKAIEVIGGAAKGKAIIIMN T0384 206 :SIDLNGDGILFYPD 1nvmB 204 :PLIMRDTVYVLSAA T0384 272 :QAPHTMTEEVAAFAHMIQQ 1nvmB 218 :ADQAAVAASVAEMVQAVQA Number of specific fragments extracted= 13 number of extra gaps= 1 total=669 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 1vpdA/T0384-1vpdA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1vpdA expands to /projects/compbio/data/pdb/1vpd.pdb.gz 1vpdA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 2, because occupancy 0.420 <= existing 0.580 in 1vpdA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 4, because occupancy 0.420 <= existing 0.580 in 1vpdA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 6, because occupancy 0.420 <= existing 0.580 in 1vpdA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 8, because occupancy 0.420 <= existing 0.580 in 1vpdA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 10, because occupancy 0.420 <= existing 0.580 in 1vpdA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 12, because occupancy 0.420 <= existing 0.580 in 1vpdA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 14, because occupancy 0.360 <= existing 0.510 in 1vpdA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 16, because occupancy 0.420 <= existing 0.580 in 1vpdA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 85, because occupancy 0.460 <= existing 0.540 in 1vpdA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 87, because occupancy 0.460 <= existing 0.540 in 1vpdA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 89, because occupancy 0.410 <= existing 0.480 in 1vpdA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 91, because occupancy 0.460 <= existing 0.540 in 1vpdA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 236, because occupancy 0.290 <= existing 0.710 in 1vpdA Skipped atom 238, because occupancy 0.290 <= existing 0.710 in 1vpdA Skipped atom 240, because occupancy 0.290 <= existing 0.710 in 1vpdA Skipped atom 242, because occupancy 0.290 <= existing 0.710 in 1vpdA Skipped atom 244, because occupancy 0.290 <= existing 0.710 in 1vpdA Skipped atom 246, because occupancy 0.290 <= existing 0.710 in 1vpdA Skipped atom 248, because occupancy 0.290 <= existing 0.710 in 1vpdA Skipped atom 296, because occupancy 0.480 <= existing 0.520 in 1vpdA Skipped atom 298, because occupancy 0.480 <= existing 0.520 in 1vpdA Skipped atom 300, because occupancy 0.480 <= existing 0.520 in 1vpdA Skipped atom 302, because occupancy 0.480 <= existing 0.520 in 1vpdA Skipped atom 315, because occupancy 0.330 <= existing 0.670 in 1vpdA Skipped atom 317, because occupancy 0.330 <= existing 0.670 in 1vpdA Skipped atom 319, because occupancy 0.330 <= existing 0.670 in 1vpdA Skipped atom 321, because occupancy 0.330 <= existing 0.670 in 1vpdA Skipped atom 436, because occupancy 0.400 <= existing 0.600 in 1vpdA Skipped atom 438, because occupancy 0.400 <= existing 0.600 in 1vpdA Skipped atom 440, because occupancy 0.400 <= existing 0.600 in 1vpdA Skipped atom 442, because occupancy 0.400 <= existing 0.600 in 1vpdA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 509, because occupancy 0.460 <= existing 0.540 in 1vpdA Skipped atom 511, because occupancy 0.460 <= existing 0.540 in 1vpdA Skipped atom 550, because occupancy 0.470 <= existing 0.530 in 1vpdA Skipped atom 552, because occupancy 0.470 <= existing 0.530 in 1vpdA Skipped atom 554, because occupancy 0.470 <= existing 0.530 in 1vpdA Skipped atom 556, because occupancy 0.470 <= existing 0.530 in 1vpdA Skipped atom 558, because occupancy 0.470 <= existing 0.530 in 1vpdA Skipped atom 588, because occupancy 0.480 <= existing 0.520 in 1vpdA Skipped atom 590, because occupancy 0.480 <= existing 0.520 in 1vpdA Skipped atom 592, because occupancy 0.480 <= existing 0.520 in 1vpdA Skipped atom 594, because occupancy 0.480 <= existing 0.520 in 1vpdA Skipped atom 596, because occupancy 0.480 <= existing 0.520 in 1vpdA Skipped atom 648, because occupancy 0.420 <= existing 0.580 in 1vpdA Skipped atom 650, because occupancy 0.420 <= existing 0.580 in 1vpdA Skipped atom 652, because occupancy 0.420 <= existing 0.580 in 1vpdA Skipped atom 654, because occupancy 0.420 <= existing 0.580 in 1vpdA Skipped atom 656, because occupancy 0.420 <= existing 0.580 in 1vpdA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 770, because occupancy 0.480 <= existing 0.520 in 1vpdA Skipped atom 772, because occupancy 0.480 <= existing 0.520 in 1vpdA Skipped atom 774, because occupancy 0.480 <= existing 0.520 in 1vpdA Skipped atom 776, because occupancy 0.480 <= existing 0.520 in 1vpdA Skipped atom 778, because occupancy 0.480 <= existing 0.520 in 1vpdA Skipped atom 780, because occupancy 0.480 <= existing 0.520 in 1vpdA Skipped atom 782, because occupancy 0.480 <= existing 0.520 in 1vpdA Skipped atom 832, because occupancy 0.490 <= existing 0.510 in 1vpdA Skipped atom 834, because occupancy 0.490 <= existing 0.510 in 1vpdA Skipped atom 836, because occupancy 0.490 <= existing 0.510 in 1vpdA Skipped atom 838, because occupancy 0.490 <= existing 0.510 in 1vpdA Skipped atom 840, because occupancy 0.490 <= existing 0.510 in 1vpdA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 953, because occupancy 0.500 <= existing 0.500 in 1vpdA Skipped atom 955, because occupancy 0.500 <= existing 0.500 in 1vpdA Skipped atom 957, because occupancy 0.500 <= existing 0.500 in 1vpdA Skipped atom 959, because occupancy 0.500 <= existing 0.500 in 1vpdA Skipped atom 961, because occupancy 0.500 <= existing 0.500 in 1vpdA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1044, because occupancy 0.440 <= existing 0.560 in 1vpdA Skipped atom 1046, because occupancy 0.440 <= existing 0.560 in 1vpdA Skipped atom 1048, because occupancy 0.440 <= existing 0.560 in 1vpdA Skipped atom 1054, because occupancy 0.290 <= existing 0.710 in 1vpdA Skipped atom 1056, because occupancy 0.290 <= existing 0.710 in 1vpdA Skipped atom 1058, because occupancy 0.290 <= existing 0.710 in 1vpdA Skipped atom 1060, because occupancy 0.290 <= existing 0.710 in 1vpdA Skipped atom 1062, because occupancy 0.290 <= existing 0.710 in 1vpdA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1346, because occupancy 0.360 <= existing 0.640 in 1vpdA Skipped atom 1348, because occupancy 0.360 <= existing 0.640 in 1vpdA Skipped atom 1350, because occupancy 0.360 <= existing 0.640 in 1vpdA Skipped atom 1352, because occupancy 0.360 <= existing 0.640 in 1vpdA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1420, because occupancy 0.410 <= existing 0.590 in 1vpdA Skipped atom 1422, because occupancy 0.410 <= existing 0.590 in 1vpdA Skipped atom 1424, because occupancy 0.410 <= existing 0.590 in 1vpdA Skipped atom 1490, because occupancy 0.430 <= existing 0.570 in 1vpdA Skipped atom 1492, because occupancy 0.430 <= existing 0.570 in 1vpdA Skipped atom 1494, because occupancy 0.430 <= existing 0.570 in 1vpdA Skipped atom 1496, because occupancy 0.430 <= existing 0.570 in 1vpdA Skipped atom 1529, because occupancy 0.420 <= existing 0.580 in 1vpdA Skipped atom 1531, because occupancy 0.420 <= existing 0.580 in 1vpdA Skipped atom 1533, because occupancy 0.420 <= existing 0.580 in 1vpdA Skipped atom 1535, because occupancy 0.420 <= existing 0.580 in 1vpdA Skipped atom 1537, because occupancy 0.420 <= existing 0.580 in 1vpdA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1757, because occupancy 0.340 <= existing 0.660 in 1vpdA Skipped atom 1759, because occupancy 0.340 <= existing 0.660 in 1vpdA Skipped atom 1761, because occupancy 0.340 <= existing 0.660 in 1vpdA Skipped atom 1763, because occupancy 0.340 <= existing 0.660 in 1vpdA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 2164, because occupancy 0.440 <= existing 0.560 in 1vpdA Skipped atom 2166, because occupancy 0.440 <= existing 0.560 in 1vpdA Skipped atom 2168, because occupancy 0.440 <= existing 0.560 in 1vpdA Skipped atom 2170, because occupancy 0.440 <= existing 0.560 in 1vpdA # T0384 read from 1vpdA/T0384-1vpdA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1vpdA read from 1vpdA/T0384-1vpdA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1vpdA to template set # found chain 1vpdA in template set Warning: unaligning (T0384)L2 because first residue in template chain is (1vpdA)M3 Warning: unaligning (T0384)K3 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1vpdA)K4 Warning: unaligning (T0384)N48 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1vpdA)E47 Warning: unaligning (T0384)I49 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1vpdA)E47 Warning: unaligning (T0384)Y296 because of BadResidue code BAD_PEPTIDE in next template residue (1vpdA)G232 Warning: unaligning (T0384)Q297 because of BadResidue code BAD_PEPTIDE at template residue (1vpdA)G232 T0384 4 :LGVIGTGAISHHFIEAAHTS 1vpdA 5 :VGFIGLGIMGKPMSKNLLKA T0384 25 :EYQLV 1vpdA 25 :GYSLV T0384 31 :IYSRKLETAATFAS 1vpdA 30 :VSDRNPEAIADVIA T0384 46 :YQ 1vpdA 44 :AG T0384 51 :LFDQLEVFFK 1vpdA 48 :TASTAKAIAE T0384 62 :SFDLVYIASPNSLH 1vpdA 58 :QCDVIITMLPNSPH T0384 76 :FAQAKA 1vpdA 73 :KEVALG T0384 82 :ALSA 1vpdA 82 :IIEG T0384 86 :GKHVILE 1vpdA 89 :GTVLIDM T0384 95 :AVSQPQEWFDLIQTAEKNNCFIFEAARNYHEKAFT 1vpdA 96 :SSIAPLASREISDALKAKGVEMLDAPVSGGEPKAI T0384 137 :DKQ 1vpdA 131 :DGT T0384 146 :NYAKYSSK 1vpdA 134 :LSVMVGGD T0384 156 :DLLAG 1vpdA 206 :AIRGG T0384 275 :HTMTEEVAAFAHMIQQPDL 1vpdA 211 :LAGSTVLDAKAPMVMDRNF T0384 295 :L 1vpdA 230 :K T0384 298 :TWLYDAGSVHELLYTMRQTAGIRF 1vpdA 233 :FRIDLHIKDLANALDTSHGVGAQL Number of specific fragments extracted= 16 number of extra gaps= 2 total=685 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 1vpdA/T0384-1vpdA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0384 read from 1vpdA/T0384-1vpdA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1vpdA read from 1vpdA/T0384-1vpdA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1vpdA in template set Warning: unaligning (T0384)L2 because first residue in template chain is (1vpdA)M3 Warning: unaligning (T0384)K3 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1vpdA)K4 Warning: unaligning (T0384)I49 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1vpdA)E47 Warning: unaligning (T0384)Q50 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1vpdA)E47 Warning: unaligning (T0384)V140 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1vpdA)A156 Warning: unaligning (T0384)L141 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1vpdA)A156 T0384 4 :LGVIGTGAISHHFIEAAHTS 1vpdA 5 :VGFIGLGIMGKPMSKNLLKA T0384 25 :EYQLV 1vpdA 25 :GYSLV T0384 31 :IYSRKLETAATFASR 1vpdA 30 :VSDRNPEAIADVIAA T0384 48 :N 1vpdA 45 :G T0384 51 :LFDQL 1vpdA 48 :TASTA T0384 56 :EVFF 1vpdA 54 :AIAE T0384 62 :SFDLVYIASPN 1vpdA 58 :QCDVIITMLPN T0384 73 :SLHFAQAKA 1vpdA 70 :PHVKEVALG T0384 82 :ALSA 1vpdA 82 :IIEG T0384 86 :GKHVILE 1vpdA 89 :GTVLIDM T0384 95 :AVSQPQEWFDLIQTAEKNNCFIFEAARNYHEK 1vpdA 96 :SSIAPLASREISDALKAKGVEMLDAPVSGGEP T0384 127 :AFTTIKNFLAD 1vpdA 144 :IFDKYYDLMKA T0384 142 :G 1vpdA 157 :G T0384 144 :DFNYAK 1vpdA 158 :SVVHTG T0384 163 :P 1vpdA 164 :D T0384 277 :MTEEVAAFAHM 1vpdA 165 :IGAGNVTKLAN T0384 299 :WLYDAGSVHELLYTMRQTAGIRFE 1vpdA 176 :QVIVALNIAAMSEALTLATKAGVN Number of specific fragments extracted= 17 number of extra gaps= 2 total=702 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 1vpdA/T0384-1vpdA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0384 read from 1vpdA/T0384-1vpdA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1vpdA read from 1vpdA/T0384-1vpdA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1vpdA in template set Warning: unaligning (T0384)L2 because first residue in template chain is (1vpdA)M3 Warning: unaligning (T0384)K3 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1vpdA)K4 Warning: unaligning (T0384)I49 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1vpdA)E47 Warning: unaligning (T0384)Q50 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1vpdA)E47 Warning: unaligning (T0384)A193 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1vpdA)A156 Warning: unaligning (T0384)N194 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1vpdA)A156 T0384 4 :LGVIGTGAISHHFIEAAHTS 1vpdA 5 :VGFIGLGIMGKPMSKNLLKA T0384 25 :EYQLV 1vpdA 25 :GYSLV T0384 31 :IYSRKLETAATFASR 1vpdA 30 :VSDRNPEAIADVIAA T0384 51 :LFDQLEVFF 1vpdA 48 :TASTAKAIA T0384 62 :SFDLVYIASPN 1vpdA 58 :QCDVIITMLPN T0384 73 :SLHFAQAK 1vpdA 70 :PHVKEVAL T0384 82 :ALS 1vpdA 82 :IIE T0384 86 :GK 1vpdA 89 :GT T0384 89 :VILEK 1vpdA 91 :VLIDM T0384 95 :AVSQPQEWFDLIQTAEKNNCFIFEAARNYHEKAFTT 1vpdA 96 :SSIAPLASREISDALKAKGVEMLDAPVSGGEPKAID T0384 141 :LGADFNYA 1vpdA 132 :GTLSVMVG T0384 152 :SKMP 1vpdA 140 :GDKA T0384 182 :PLYAAVRLFGK 1vpdA 144 :IFDKYYDLMKA T0384 195 :DATYHA 1vpdA 157 :GSVVHT T0384 271 :QQAPHTMTEEVAAFAHM 1vpdA 163 :GDIGAGNVTKLANQVIV T0384 301 :YDAGSVHELLYTMRQTAGI 1vpdA 180 :ALNIAAMSEALTLATKAGV Number of specific fragments extracted= 16 number of extra gaps= 2 total=718 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 1ys4A/T0384-1ys4A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1ys4A expands to /projects/compbio/data/pdb/1ys4.pdb.gz 1ys4A:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0384 read from 1ys4A/T0384-1ys4A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ys4A read from 1ys4A/T0384-1ys4A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1ys4A to template set # found chain 1ys4A in template set Warning: unaligning (T0384)V96 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1ys4A)I127 T0384 1 :MLKLGVIG 1ys4A 8 :KIKVGVLG T0384 9 :TGAISHHFIEAAHTSGEYQLVAIYS 1ys4A 17 :TGSVGQRFVQLLADHPMFELTALAA T0384 35 :KLET 1ys4A 42 :SERS T0384 39 :AATF 1ys4A 50 :YKDA T0384 46 :YQN 1ys4A 54 :CYW T0384 52 :FDQ 1ys4A 72 :IPT T0384 59 :FK 1ys4A 81 :FE T0384 62 :SFDLVYIASPNSLHFAQAKAALSAGKHVILE 1ys4A 83 :DVDIVFSALPSDLAKKFEPEFAKEGKLIFSN T0384 93 :KPA 1ys4A 123 :VPL T0384 105 :LIQTAEKN 1ys4A 137 :LIEIQREK T0384 113 :NCFIFEAARNYHEKAFTTIKNFL 1ys4A 148 :DGAIITNPNCSTICAVITLKPIM T0384 139 :QVLGADFNYAKYSSKMPDLLAGQT 1ys4A 171 :DKFGLEAVFIATMQAVSGAGYNGV T0384 168 :DRFAGGA 1ys4A 201 :DNLIPFI T0384 176 :MDLGIYPLYAAVRLFG 1ys4A 208 :KNEEEKMQTESLKLLG T0384 202 :QLDNS 1ys4A 224 :TLKDG T0384 207 :IDLNGDGILFY 1ys4A 248 :DGHTESIFVKT T0384 295 :LYQTWLYDAGSVHE 1ys4A 259 :KEGAEPEEIKEVMD Number of specific fragments extracted= 17 number of extra gaps= 1 total=735 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 1ys4A/T0384-1ys4A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0384 read from 1ys4A/T0384-1ys4A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ys4A read from 1ys4A/T0384-1ys4A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1ys4A in template set Warning: unaligning (T0384)V96 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1ys4A)I127 Warning: unaligning (T0384)S97 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1ys4A)I127 T0384 1 :MLKLGVIG 1ys4A 8 :KIKVGVLG T0384 9 :TGAISHHFIEAAHTSGEYQLVAIYSRK 1ys4A 17 :TGSVGQRFVQLLADHPMFELTALAASE T0384 37 :E 1ys4A 44 :R T0384 45 :RYQ 1ys4A 45 :SAG T0384 48 :NIQLFDQL 1ys4A 70 :VVIPTDPK T0384 56 :EVF 1ys4A 79 :EEF T0384 61 :SSFDLVYIASPNSLHFAQAKAALSAGKHVILE 1ys4A 82 :EDVDIVFSALPSDLAKKFEPEFAKEGKLIFSN T0384 93 :KPA 1ys4A 123 :VPL T0384 104 :DLIQTAEKN 1ys4A 136 :ELIEIQREK T0384 113 :NCFIFEAARNYHEKAFTTIKNFLAD 1ys4A 148 :DGAIITNPNCSTICAVITLKPIMDK T0384 141 :LGADFNYAKYSSKMPDLLAGQT 1ys4A 173 :FGLEAVFIATMQAVSGAGYNGV Number of specific fragments extracted= 11 number of extra gaps= 1 total=746 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 1ys4A/T0384-1ys4A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0384 read from 1ys4A/T0384-1ys4A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ys4A read from 1ys4A/T0384-1ys4A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1ys4A in template set Warning: unaligning (T0384)V96 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1ys4A)I127 Warning: unaligning (T0384)S97 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1ys4A)I127 T0384 1 :MLKLGVIGT 1ys4A 8 :KIKVGVLGA T0384 10 :GAISHHFIEAAHTSGEYQLVAIYSRK 1ys4A 18 :GSVGQRFVQLLADHPMFELTALAASE T0384 41 :TFASRY 1ys4A 49 :KYKDAC T0384 49 :IQLFDQ 1ys4A 69 :MVVIPT T0384 55 :LEVF 1ys4A 78 :HEEF T0384 61 :SSFDLVYIASPNSLHFAQAKAALSAGKHVIL 1ys4A 82 :EDVDIVFSALPSDLAKKFEPEFAKEGKLIFS T0384 93 :KPA 1ys4A 123 :VPL T0384 104 :DLIQTAEKN 1ys4A 136 :ELIEIQREK T0384 113 :NCFIFEAARNYHEKAFTTIKNFLAD 1ys4A 148 :DGAIITNPNCSTICAVITLKPIMDK T0384 142 :GADFNYAKYSSKMPDLLAGQTP 1ys4A 174 :GLEAVFIATMQAVSGAGYNGVP T0384 182 :PLYAAVRLFG 1ys4A 214 :MQTESLKLLG T0384 192 :KANDATYHAQQLDNSIDLNGDGILFYPDY 1ys4A 233 :ANFKISASCNRVAVIDGHTESIFVKTKEG Number of specific fragments extracted= 12 number of extra gaps= 1 total=758 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 1gd1O/T0384-1gd1O-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1gd1O expands to /projects/compbio/data/pdb/1gd1.pdb.gz 1gd1O:# T0384 read from 1gd1O/T0384-1gd1O-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1gd1O read from 1gd1O/T0384-1gd1O-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1gd1O to template set # found chain 1gd1O in template set Warning: unaligning (T0384)G24 because of BadResidue code BAD_PEPTIDE in next template residue (1gd1O)D24 Warning: unaligning (T0384)E25 because of BadResidue code BAD_PEPTIDE at template residue (1gd1O)D24 Warning: unaligning (T0384)L51 because of BadResidue code BAD_PEPTIDE in next template residue (1gd1O)E76 Warning: unaligning (T0384)F52 because of BadResidue code BAD_PEPTIDE at template residue (1gd1O)E76 Warning: unaligning (T0384)M154 because of BadResidue code BAD_PEPTIDE at template residue (1gd1O)L218 T0384 2 :LKLGVIGTGAISHHFIEAAHTS 1gd1O 1 :VKVGINGFGRIGRNVFRAALKN T0384 26 :YQLVAIYS 1gd1O 25 :IEVVAVND T0384 34 :RKLE 1gd1O 34 :TDAN T0384 41 :TFASRYQNI 1gd1O 39 :TLAHLLKYD T0384 50 :Q 1gd1O 74 :K T0384 53 :DQLEVF 1gd1O 77 :RDPENL T0384 59 :FKS 1gd1O 84 :WGE T0384 62 :SFDLVYIASPNSLHFAQAKAALSAG 1gd1O 88 :GVDIVVESTGRFTKREDAAKHLEAG T0384 87 :KHVILEKPAV 1gd1O 114 :KKVIISAPAK T0384 97 :SQP 1gd1O 137 :YDP T0384 112 :NNCFIFEAARN 1gd1O 139 :KAHHVISNASC T0384 123 :YHEKAFTTIKNFL 1gd1O 153 :CLAPFAKVLHEQF T0384 142 :GADFNYAKYSSK 1gd1O 166 :GIVRGMMTTVHS T0384 155 :PDLLAG 1gd1O 219 :PELKGK T0384 196 :ATYHAQQLDNSIDLNGDGILFYPDY 1gd1O 225 :LNGMAMRVPTPNVSVVDLVAELEKE T0384 275 :HTMTEEVAAFAHMIQQPDLN 1gd1O 250 :VTVEEVNAALKAAAEGELKG T0384 295 :LYQ 1gd1O 276 :EPL T0384 298 :TWLYDAGSVHELLYTMR 1gd1O 313 :NETGYSHRVVDLAAYIA Number of specific fragments extracted= 18 number of extra gaps= 3 total=776 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 1gd1O/T0384-1gd1O-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0384 read from 1gd1O/T0384-1gd1O-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1gd1O read from 1gd1O/T0384-1gd1O-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1gd1O in template set Warning: unaligning (T0384)G24 because of BadResidue code BAD_PEPTIDE in next template residue (1gd1O)D24 Warning: unaligning (T0384)E25 because of BadResidue code BAD_PEPTIDE at template residue (1gd1O)D24 Warning: unaligning (T0384)L51 because of BadResidue code BAD_PEPTIDE in next template residue (1gd1O)E76 Warning: unaligning (T0384)F52 because of BadResidue code BAD_PEPTIDE at template residue (1gd1O)E76 Warning: unaligning (T0384)F166 because of BadResidue code BAD_PEPTIDE in next template residue (1gd1O)L218 Warning: unaligning (T0384)S167 because of BadResidue code BAD_PEPTIDE at template residue (1gd1O)L218 T0384 2 :LKLGVIGTGAISHHFIEAAHTS 1gd1O 1 :VKVGINGFGRIGRNVFRAALKN T0384 26 :YQLVAIYSRK 1gd1O 25 :IEVVAVNDLT T0384 39 :AATFASRYQ 1gd1O 37 :ANTLAHLLK T0384 48 :NIQ 1gd1O 72 :IVK T0384 53 :DQLEV 1gd1O 77 :RDPEN T0384 58 :FFKSSFDLVYIASPNSLHFAQAKAALSAG 1gd1O 84 :WGEIGVDIVVESTGRFTKREDAAKHLEAG T0384 87 :KHVILEKPAVSQ 1gd1O 114 :KKVIISAPAKNE T0384 111 :KNNCFIFEAARNY 1gd1O 138A:PKAHHVISNASCT T0384 124 :HEKAFTTIKNFL 1gd1O 154 :LAPFAKVLHEQF T0384 144 :DFNYAKYS 1gd1O 166 :GIVRGMMT T0384 153 :KMPDLLAGQT 1gd1O 178 :YTNDQRILDL T0384 163 :PNV 1gd1O 214 :VAL T0384 168 :DRFAG 1gd1O 219 :PELKG T0384 195 :DATYHAQQLDNSIDLNGDGILFYPD 1gd1O 224 :KLNGMAMRVPTPNVSVVDLVAELEK T0384 277 :MTEEVAAFAHMIQQ 1gd1O 252 :VEEVNAALKAAAEG T0384 299 :WLYDAGSVHELLYTMRQ 1gd1O 314 :ETGYSHRVVDLAAYIAS Number of specific fragments extracted= 16 number of extra gaps= 3 total=792 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 1gd1O/T0384-1gd1O-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0384 read from 1gd1O/T0384-1gd1O-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1gd1O read from 1gd1O/T0384-1gd1O-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1gd1O in template set Warning: unaligning (T0384)G24 because of BadResidue code BAD_PEPTIDE in next template residue (1gd1O)D24 Warning: unaligning (T0384)E25 because of BadResidue code BAD_PEPTIDE at template residue (1gd1O)D24 Warning: unaligning (T0384)L51 because of BadResidue code BAD_PEPTIDE in next template residue (1gd1O)E76 Warning: unaligning (T0384)F52 because of BadResidue code BAD_PEPTIDE at template residue (1gd1O)E76 T0384 2 :LKLGVIGTGAISHHFIEAAHTS 1gd1O 1 :VKVGINGFGRIGRNVFRAALKN T0384 26 :YQLVAIYSRKL 1gd1O 25 :IEVVAVNDLTD T0384 39 :AATFASRY 1gd1O 37 :ANTLAHLL T0384 49 :IQ 1gd1O 73 :VK T0384 53 :DQLEVFF 1gd1O 77 :RDPENLA T0384 60 :KSSFDLVYIASPNSLHFAQAKAALSAGK 1gd1O 86 :EIGVDIVVESTGRFTKREDAAKHLEAGA T0384 88 :HVILEKPAVSQ 1gd1O 115 :KVIISAPAKNE T0384 111 :KNNCFIFEAARNYH 1gd1O 138A:PKAHHVISNASCTT T0384 125 :EKAFTTIKNFL 1gd1O 155 :APFAKVLHEQF T0384 142 :GADFNYAKYSSKMPDLLAGQTP 1gd1O 166 :GIVRGMMTTVHSYTNDQRILDL T0384 204 :DNSIDLNGDGILFYPDYQ 1gd1O 233 :PTPNVSVVDLVAELEKEV T0384 276 :TMTEEVAAFAHMIQQP 1gd1O 251 :TVEEVNAALKAAAEGE Number of specific fragments extracted= 12 number of extra gaps= 2 total=804 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 2ahrA/T0384-2ahrA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2ahrA expands to /projects/compbio/data/pdb/2ahr.pdb.gz 2ahrA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0384 read from 2ahrA/T0384-2ahrA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2ahrA read from 2ahrA/T0384-2ahrA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2ahrA to template set # found chain 2ahrA in template set T0384 2 :LKLGVIGTGAISHHFIEAAHTS 2ahrA 1 :MKIGIIGVGKMASAIIKGLKQT T0384 25 :EYQLV 2ahrA 23 :PHELI T0384 31 :IYSRKLETAATFASRYQNI 2ahrA 28 :ISGSSLERSKEIAEQLALP T0384 51 :LFDQLEVFFK 2ahrA 47 :YAMSHQDLID T0384 62 :SFDLVYIASPNSLHFAQA 2ahrA 57 :QVDLVILGIKPQLFETVL T0384 87 :KHVIL 2ahrA 81 :QPIIS T0384 93 :KPAVSQPQEWFDLI 2ahrA 86 :MAAGISLQRLATFV T0384 112 :NNCFIFEA 2ahrA 101 :QDLPLLRI T0384 120 :ARNYHEKAFTTIKNFL 2ahrA 126 :NALVSQELQARVRDLT T0384 139 :QVLG 2ahrA 142 :DSFG T0384 265 :QVQLPIQQAP 2ahrA 147 :TFDISEKDFD T0384 275 :HTMTEEVAAFAHMIQQPD 2ahrA 167 :AYIYLFIEALAKAGVKNG T0384 297 :QTWLYDAGSVHELLYTMRQTA 2ahrA 185 :IPKAKALEIVTQTVLASASNL Number of specific fragments extracted= 13 number of extra gaps= 0 total=817 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 2ahrA/T0384-2ahrA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0384 read from 2ahrA/T0384-2ahrA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2ahrA read from 2ahrA/T0384-2ahrA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2ahrA in template set T0384 2 :LKLGVIGTGAISHHFIEAAHTS 2ahrA 1 :MKIGIIGVGKMASAIIKGLKQT T0384 25 :EYQLV 2ahrA 23 :PHELI T0384 31 :IYSRKLETAATFASRYQ 2ahrA 28 :ISGSSLERSKEIAEQLA T0384 49 :IQLFDQL 2ahrA 45 :LPYAMSH T0384 56 :EVF 2ahrA 53 :DLI T0384 61 :SSFDLVYIASPNSLHFAQA 2ahrA 56 :DQVDLVILGIKPQLFETVL T0384 87 :KHVI 2ahrA 81 :QPII T0384 92 :EKPAVSQPQEWFDLI 2ahrA 85 :SMAAGISLQRLATFV T0384 113 :NCFIFE 2ahrA 102 :DLPLLR T0384 119 :AARNYHEKAFTTIKNFLAD 2ahrA 125 :GNALVSQELQARVRDLTDS T0384 141 :LG 2ahrA 144 :FG T0384 144 :D 2ahrA 146 :S T0384 150 :YSSKMPDL 2ahrA 147 :TFDISEKD T0384 183 :LYA 2ahrA 155 :FDT T0384 276 :TMTEEVAAFAHMIQQPDLNLY 2ahrA 168 :YIYLFIEALAKAGVKNGIPKA T0384 299 :WLYDAG 2ahrA 189 :KALEIV Number of specific fragments extracted= 16 number of extra gaps= 0 total=833 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 2ahrA/T0384-2ahrA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0384 read from 2ahrA/T0384-2ahrA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2ahrA read from 2ahrA/T0384-2ahrA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2ahrA in template set T0384 2 :LKLGVIGTGAISHHFIEAAHTSG 2ahrA 1 :MKIGIIGVGKMASAIIKGLKQTP T0384 26 :YQLV 2ahrA 24 :HELI T0384 31 :IYSRKLETAATFASRYQN 2ahrA 28 :ISGSSLERSKEIAEQLAL T0384 50 :QLFDQLEVFF 2ahrA 46 :PYAMSHQDLI T0384 62 :SFDLVYIASPNSLHFAQA 2ahrA 57 :QVDLVILGIKPQLFETVL T0384 87 :KHVILEKPAVSQPQEWFDLI 2ahrA 80 :KQPIISMAAGISLQRLATFV T0384 112 :NNCFIFE 2ahrA 101 :QDLPLLR T0384 119 :AARNYHEKAFTTIKNFLAD 2ahrA 125 :GNALVSQELQARVRDLTDS T0384 140 :VLGADF 2ahrA 144 :FGSTFD T0384 152 :SKMPD 2ahrA 150 :ISEKD T0384 183 :LYAAVRLFG 2ahrA 155 :FDTFTALAG T0384 272 :QAPHTMTEEVAAFAHMIQQPDLNL 2ahrA 164 :SSPAYIYLFIEALAKAGVKNGIPK T0384 298 :TWLYDAGSVHELLYT 2ahrA 188 :AKALEIVTQTVLASA Number of specific fragments extracted= 13 number of extra gaps= 0 total=846 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 1gadO/T0384-1gadO-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1gadO expands to /projects/compbio/data/pdb/1gad.pdb.gz 1gadO:Skipped atom 1733, because occupancy 0.400 <= existing 0.600 in 1gadO Skipped atom 1735, because occupancy 0.400 <= existing 0.600 in 1gadO Skipped atom 1737, because occupancy 0.400 <= existing 0.600 in 1gadO Skipped atom 1739, because occupancy 0.400 <= existing 0.600 in 1gadO Skipped atom 1741, because occupancy 0.400 <= existing 0.600 in 1gadO Skipped atom 1743, because occupancy 0.400 <= existing 0.600 in 1gadO # T0384 read from 1gadO/T0384-1gadO-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1gadO read from 1gadO/T0384-1gadO-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1gadO to template set # found chain 1gadO in template set T0384 2 :LKLGVIGTGAISHHFIEAAHTSGEYQLVAIYS 1gadO 1 :IKVGINGFGRIGRIVFRAAQKRSDIEIVAIND T0384 34 :RKLE 1gadO 34 :LDAD T0384 41 :TFASRYQNI 1gadO 39 :YMAYMLKYD T0384 50 :QLFDQLEVF 1gadO 74 :TAERDPANL T0384 59 :FKS 1gadO 84 :WDE T0384 62 :SFDLVYIASPNSLHFAQAKAALSAG 1gadO 88 :GVDVVAEATGLFLTDETARKHITAG T0384 87 :KHVILEKPAVSQ 1gadO 114 :KKVVMTGPSKDN T0384 113 :NC 1gadO 138A:GQ T0384 115 :FIFEA 1gadO 143 :IVSNA T0384 122 :NYHEKAFTTIKNFL 1gadO 148 :SCTTNCLAPLAKVI T0384 138 :KQVLGADFNYAKYSSKMPDLLAGQT 1gadO 162 :NDNFGIIEGLMTTVHATTATQKTVD T0384 163 :PNVFSDRFAGGAL 1gadO 192 :DWRGGRGASQNII T0384 176 :MDLG 1gadO 210 :AAKA T0384 186 :AVRLFGKAN 1gadO 214 :VGKVLPELN T0384 195 :DATYHAQQLDNSIDLNGDGILFYPDY 1gadO 224 :KLTGMAFRVPTPNVSVVDLTVRLEKA T0384 275 :HTMTEEVAAFAHMIQQPDLNLY 1gadO 250 :ATYEQIKAAVKAAAEGEMKGVL Number of specific fragments extracted= 16 number of extra gaps= 0 total=862 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 1gadO/T0384-1gadO-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0384 read from 1gadO/T0384-1gadO-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1gadO read from 1gadO/T0384-1gadO-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1gadO in template set T0384 1 :MLKLGVIGTGAISHHFIEAAHTSGEYQLVAIYS 1gadO 0 :TIKVGINGFGRIGRIVFRAAQKRSDIEIVAIND T0384 34 :RKLETAATFASRYQ 1gadO 34 :LDADYMAYMLKYDS T0384 48 :NIQLFDQL 1gadO 72 :RVTAERDP T0384 56 :EV 1gadO 81 :NL T0384 58 :FFKSSFDLVYIASPNSLHFAQAKAALSAG 1gadO 84 :WDEVGVDVVAEATGLFLTDETARKHITAG T0384 87 :KHVILEKPAVSQ 1gadO 114 :KKVVMTGPSKDN T0384 113 :NC 1gadO 138A:GQ T0384 115 :FIFEAARNY 1gadO 143 :IVSNASCTT T0384 124 :HEKAFTTIKNFL 1gadO 154 :LAPLAKVINDNF T0384 144 :DFNYAKYSSK 1gadO 166 :GIIEGLMTTV T0384 154 :MPDLLAGQ 1gadO 179 :TATQKTVD T0384 162 :TPNVFSDRFAGG 1gadO 191 :KDWRGGRGASQN T0384 186 :AVRLFGKAN 1gadO 214 :VGKVLPELN T0384 195 :DATYHAQQLDNSIDLNGDGILFYPD 1gadO 224 :KLTGMAFRVPTPNVSVVDLTVRLEK T0384 277 :MTEEVAAFAHMIQQP 1gadO 252 :YEQIKAAVKAAAEGE Number of specific fragments extracted= 15 number of extra gaps= 0 total=877 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 1gadO/T0384-1gadO-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0384 read from 1gadO/T0384-1gadO-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1gadO read from 1gadO/T0384-1gadO-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1gadO in template set T0384 2 :LKLGVIGTGAISHHFIEAAHTSGEYQLVAIYS 1gadO 1 :IKVGINGFGRIGRIVFRAAQKRSDIEIVAIND T0384 34 :RKLE 1gadO 34 :LDAD T0384 41 :TFASRY 1gadO 39 :YMAYML T0384 49 :IQLFDQLEVFF 1gadO 73 :VTAERDPANLK T0384 60 :KSSFDLVYIASPNSLHFAQAKAALSAGK 1gadO 86 :EVGVDVVAEATGLFLTDETARKHITAGA T0384 88 :HVILEKPAVSQ 1gadO 115 :KVVMTGPSKDN T0384 113 :NCFIFEAARNYHEKAFTTIKNFLAD 1gadO 138A:GQDIVSNASCTTNCLAPLAKVINDN T0384 142 :GADFNYAKYSSKMPDLLAGQTP 1gadO 166 :GIIEGLMTTVHATTATQKTVDG T0384 164 :NVFSDRFA 1gadO 193 :WRGGRGAS T0384 191 :GKANDATYHAQ 1gadO 201 :QNIIPSSTGAA T0384 204 :DNSIDLNGDGILFYPDYQ 1gadO 233 :PTPNVSVVDLTVRLEKAA T0384 276 :TMTEEVAAFAHMIQQP 1gadO 251 :TYEQIKAAVKAAAEGE Number of specific fragments extracted= 12 number of extra gaps= 0 total=889 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 2c82A/T0384-2c82A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2c82A expands to /projects/compbio/data/pdb/2c82.pdb.gz 2c82A:# T0384 read from 2c82A/T0384-2c82A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2c82A read from 2c82A/T0384-2c82A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2c82A to template set # found chain 2c82A in template set T0384 2 :LKLGVIG 2c82A 13 :LRVVVLG T0384 9 :TGAISHHFIEAAHTSGE 2c82A 21 :TGSIGTQALQVIADNPD T0384 26 :YQLVAIYS 2c82A 39 :FEVVGLAA T0384 34 :RKLETAATFASRYQNI 2c82A 49 :AHLDTLLRQRAQTGVT T0384 50 :QLFDQLEVFFKS 2c82A 83 :HGSDAATRLVEQ T0384 62 :SFDLVYIASPNSLHFAQAKAALSAGKHVILE 2c82A 96 :EADVVLNALVGALGLRPTLAALKTGARLALA T0384 95 :AV 2c82A 133 :AG T0384 102 :WFDLIQTA 2c82A 135 :GSLVLRAA T0384 113 :NC 2c82A 145 :GQ T0384 116 :IF 2c82A 147 :IV T0384 123 :YHEKAFTTIKNFL 2c82A 149 :PVDSEHSALAQCL T0384 137 :DKQVLG 2c82A 162 :RGGTPD T0384 143 :ADFNYAKYSSK 2c82A 169 :VAKLVLTASGG T0384 154 :MPDLLAGQTPNVFSDRF 2c82A 193 :TPEQAGAHPTWSMGPMN T0384 171 :AGGALMDLGIYPLY 2c82A 212 :NSASLVNKGLEVIE T0384 186 :AVRLFG 2c82A 226 :THLLFG T0384 192 :KANDATYHAQQL 2c82A 233 :PYDRIDVVVHPQ T0384 209 :LNGDGILFYPDYQVHIKAGKNI 2c82A 245 :SIIHSMVTFIDGSTIAQASPPD T0384 256 :AIFTD 2c82A 286 :AACDF T0384 263 :GNQVQLPIQQAP 2c82A 291 :HTASSWEFEPLD T0384 276 :TMTEEVAAFAHMIQQ 2c82A 343 :GFPAIVGIIADVLHA T0384 291 :PDLNLYQTWLYDAGSVHELL 2c82A 359 :DQWAVEPATVDDVLDAQRWA T0384 311 :YTMRQTAGI 2c82A 380 :ERAQRAVSG Number of specific fragments extracted= 23 number of extra gaps= 0 total=912 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 2c82A/T0384-2c82A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0384 read from 2c82A/T0384-2c82A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2c82A read from 2c82A/T0384-2c82A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2c82A in template set T0384 1 :MLKLGVIG 2c82A 12 :RLRVVVLG T0384 9 :TGAISHHFIEAAHTSGE 2c82A 21 :TGSIGTQALQVIADNPD T0384 26 :YQLVAIYS 2c82A 39 :FEVVGLAA T0384 34 :RKLETAATFASRYQ 2c82A 49 :AHLDTLLRQRAQTG T0384 48 :NIQLFD 2c82A 79 :DIPYHG T0384 54 :QL 2c82A 86 :DA T0384 56 :EVFFKSSFDLVYIASPNSLHFAQAKAALSAGKHVILEK 2c82A 90 :RLVEQTEADVVLNALVGALGLRPTLAALKTGARLALAN T0384 102 :WFDLI 2c82A 128 :KESLV T0384 107 :QTAEKN 2c82A 136 :SLVLRA T0384 113 :NCFIFEAA 2c82A 145 :GQIVPVDS T0384 127 :AFTTIKNFLADKQ 2c82A 153 :EHSALAQCLRGGT T0384 141 :LG 2c82A 166 :PD T0384 144 :DFNYAKYSSKMPDLLAGQT 2c82A 168 :EVAKLVLTASGGPFRGWSA T0384 163 :PNVFSDRFAG 2c82A 200 :HPTWSMGPMN T0384 173 :GALMDLGIYPLY 2c82A 214 :ASLVNKGLEVIE T0384 186 :AVRLFG 2c82A 226 :THLLFG T0384 192 :KANDATYHAQQ 2c82A 233 :PYDRIDVVVHP T0384 208 :DLNGDGILFYPDYQVHIKAGKN 2c82A 244 :QSIIHSMVTFIDGSTIAQASPP T0384 251 :EHIRSAIFTDHQGNQVQLPIQQAPH 2c82A 279 :RRVSGAAAACDFHTASSWEFEPLDT T0384 276 :TMTEEVAAFAHMIQQ 2c82A 343 :GFPAIVGIIADVLHA T0384 291 :PDLNLYQTWLYDAGSVHELL 2c82A 359 :DQWAVEPATVDDVLDAQRWA T0384 311 :YTMRQTAGI 2c82A 380 :ERAQRAVSG Number of specific fragments extracted= 22 number of extra gaps= 0 total=934 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 2c82A/T0384-2c82A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0384 read from 2c82A/T0384-2c82A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2c82A read from 2c82A/T0384-2c82A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2c82A in template set T0384 1 :MLKLGVIGT 2c82A 12 :RLRVVVLGS T0384 10 :GAISHHFIEAAHTSGE 2c82A 22 :GSIGTQALQVIADNPD T0384 26 :YQLVAIYS 2c82A 39 :FEVVGLAA T0384 34 :RKLETAATFASRYQN 2c82A 49 :AHLDTLLRQRAQTGV T0384 49 :IQLFD 2c82A 80 :IPYHG T0384 55 :LEVFF 2c82A 88 :ATRLV T0384 60 :KSSFDLVYIASPNSLHFAQAKAALSAGKHVILEK 2c82A 94 :QTEADVVLNALVGALGLRPTLAALKTGARLALAN T0384 104 :DL 2c82A 129 :ES T0384 106 :IQTAEKN 2c82A 135 :GSLVLRA T0384 113 :NCFIFEA 2c82A 145 :GQIVPVD T0384 126 :KAFTTIKNFLADKQVLGADFNYAKYSSKMPDLLAG 2c82A 152 :SEHSALAQCLRGGTPDEVAKLVLTASGGPFRGWSA T0384 165 :VFSDRFAG 2c82A 205 :MGPMNTLN T0384 173 :GALMDLGIYPLYA 2c82A 214 :ASLVNKGLEVIET T0384 187 :VRLFG 2c82A 227 :HLLFG T0384 192 :KANDATYHAQ 2c82A 233 :PYDRIDVVVH T0384 207 :IDLNGDGILFYPDYQVHIKAGKNIT 2c82A 243 :PQSIIHSMVTFIDGSTIAQASPPDM T0384 248 :NTIEHIRSAIFTDHQ 2c82A 279 :RRVSGAAAACDFHTA T0384 278 :TEEVAAFAHMIQQPD 2c82A 327 :NAANEEAAAAFLAGR Number of specific fragments extracted= 18 number of extra gaps= 0 total=952 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 1ebfA/T0384-1ebfA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1ebfA expands to /projects/compbio/data/pdb/1ebf.pdb.gz 1ebfA:# T0384 read from 1ebfA/T0384-1ebfA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ebfA read from 1ebfA/T0384-1ebfA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1ebfA to template set # found chain 1ebfA in template set T0384 2 :LKLGVIGTGAISHHFIEAAHTSG 1ebfA 6 :VNVAVIGAGVVGSAFLDQLLAMK T0384 25 :EYQLVAIYSR 1ebfA 32 :TYNLVLLAEA T0384 35 :KLET 1ebfA 54 :NVGS T0384 39 :AATFASR 1ebfA 59 :WKAALAA T0384 48 :NIQLFDQLEVFFK 1ebfA 66 :STTKTLPLDDLIA T0384 62 :SFDLVYIASPNSLHFAQAKAALSAGKHVI 1ebfA 85 :KPVILVDNTSSAYIAGFYTKFVENGISIA T0384 91 :LEK 1ebfA 115 :PNK T0384 94 :PAVSQPQEWFDL 1ebfA 119 :AFSSDLATWKAL T0384 113 :NC 1ebfA 136 :TN T0384 115 :FIFEAARNYHEKAFTTIKNFL 1ebfA 140 :VYHEATVGAGLPIISFLREII T0384 137 :DKQ 1ebfA 161 :QTG T0384 142 :G 1ebfA 164 :D T0384 143 :ADFNYAKYSSK 1ebfA 166 :VEKIEGIFSGT T0384 154 :MPDLLAG 1ebfA 208 :EPDPRDD T0384 174 :ALMDLGIYPLYAAVRLFG 1ebfA 215 :LNGLDVARKVTIVGRISG T0384 192 :KAND 1ebfA 234 :EVES T0384 204 :D 1ebfA 239 :T T0384 207 :IDLNGDGILFYPDYQVHIKAGKNITSN 1ebfA 283 :KVLRFIGKVDVATKSVSVGIEKYDYSH T0384 234 :LPCEIY 1ebfA 317 :SDNVIS T0384 245 :LTLNTIEHIRSAIF 1ebfA 323 :IKTKRYTNPVVIQG T0384 295 :LYQTWLYDAGSVHELLYTMRQ 1ebfA 337 :AGAGAAVTAAGVLGDVIKIAQ Number of specific fragments extracted= 21 number of extra gaps= 0 total=973 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 1ebfA/T0384-1ebfA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0384 read from 1ebfA/T0384-1ebfA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ebfA read from 1ebfA/T0384-1ebfA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1ebfA in template set T0384 2 :LKLGVIGTGAISHHFIEAAHTSG 1ebfA 6 :VNVAVIGAGVVGSAFLDQLLAMK T0384 25 :EYQLVAIYSR 1ebfA 32 :TYNLVLLAEA T0384 39 :AATFASRYQ 1ebfA 59 :WKAALAAST T0384 48 :NIQLFDQL 1ebfA 69 :KTLPLDDL T0384 56 :EVFFK 1ebfA 78 :AHLKT T0384 61 :SSFDLVYIASPNSLHFAQAKAALSAGKHVIL 1ebfA 84 :PKPVILVDNTSSAYIAGFYTKFVENGISIAT T0384 92 :EKPAVSQPQEWFDL 1ebfA 117 :KKAFSSDLATWKAL T0384 113 :NC 1ebfA 136 :TN T0384 115 :FIFEAARNYHEKAFTTIKNFLADKQ 1ebfA 140 :VYHEATVGAGLPIISFLREIIQTGD T0384 144 :DFNYAKYSS 1ebfA 165 :EVEKIEGIF T0384 180 :IYPLYAAVRLFGK 1ebfA 174 :SGTLSYIFNEFST T0384 204 :DNSIDLNGDGILFYPDYQVHIKAGKNITSN 1ebfA 280 :TENKVLRFIGKVDVATKSVSVGIEKYDYSH T0384 234 :LPCEIY 1ebfA 317 :SDNVIS T0384 245 :LTLNTIEHIRSAIFTDHQ 1ebfA 323 :IKTKRYTNPVVIQGAGAG T0384 299 :WLYDAGSVHELLYTMRQ 1ebfA 341 :AAVTAAGVLGDVIKIAQ Number of specific fragments extracted= 15 number of extra gaps= 0 total=988 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 1ebfA/T0384-1ebfA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0384 read from 1ebfA/T0384-1ebfA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ebfA read from 1ebfA/T0384-1ebfA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1ebfA in template set T0384 2 :LKLGVIGTGAISHHFIEAAHTSGE 1ebfA 6 :VNVAVIGAGVVGSAFLDQLLAMKS T0384 26 :YQLVAIYSRK 1ebfA 33 :YNLVLLAEAE T0384 39 :AATFASRYQN 1ebfA 59 :WKAALAASTT T0384 50 :QLFD 1ebfA 69 :KTLP T0384 55 :LEVFF 1ebfA 73 :LDDLI T0384 60 :KSSFDLVYIASPNSLHFAQAKAALSAGKHVIL 1ebfA 83 :SPKPVILVDNTSSAYIAGFYTKFVENGISIAT T0384 92 :EKPAVSQPQEWFDL 1ebfA 117 :KKAFSSDLATWKAL T0384 114 :CFIFEAARNYHEKAFTTIKNFLADKQ 1ebfA 139 :FVYHEATVGAGLPIISFLREIIQTGD T0384 142 :GADFNYAKYSS 1ebfA 165 :EVEKIEGIFSG T0384 178 :LGIYPLYAAVRLFGKANDATYHAQQL 1ebfA 219 :DVARKVTIVGRISGVEVESPTSFPVQ T0384 204 :DNSIDLNGDGILFYPDYQVHIKAGKNIT 1ebfA 280 :TENKVLRFIGKVDVATKSVSVGIEKYDY T0384 232 :SNLPCEIY 1ebfA 315 :KGSDNVIS T0384 245 :LTLNTIEHIRSAIFTDHQ 1ebfA 323 :IKTKRYTNPVVIQGAGAG T0384 274 :PHTMTEEVAAFAHMIQ 1ebfA 341 :AAVTAAGVLGDVIKIA Number of specific fragments extracted= 14 number of extra gaps= 0 total=1002 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 2h78A/T0384-2h78A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2h78A expands to /projects/compbio/data/pdb/2h78.pdb.gz 2h78A:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0384 read from 2h78A/T0384-2h78A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2h78A read from 2h78A/T0384-2h78A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2h78A to template set # found chain 2h78A in template set Warning: unaligning (T0384)M1 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2h78A)K2 Warning: unaligning (T0384)L2 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2h78A)K2 Warning: unaligning (T0384)K3 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2h78A)Q3 Warning: unaligning (T0384)L4 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2h78A)A5 Warning: unaligning (T0384)G5 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2h78A)A5 Warning: unaligning (T0384)G10 because of BadResidue code BAD_PEPTIDE in next template residue (2h78A)H11 Warning: unaligning (T0384)A11 because of BadResidue code BAD_PEPTIDE at template residue (2h78A)H11 Warning: unaligning (T0384)L28 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2h78A)N28 Warning: unaligning (T0384)V29 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2h78A)N28 Warning: unaligning (T0384)I31 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2h78A)V29 Warning: unaligning (T0384)D53 because of BadResidue code BAD_PEPTIDE in next template residue (2h78A)S50 Warning: unaligning (T0384)Q54 because of BadResidue code BAD_PEPTIDE at template residue (2h78A)S50 Warning: unaligning (T0384)L55 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2h78A)A51 Warning: unaligning (T0384)F63 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2h78A)D59 Warning: unaligning (T0384)D64 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2h78A)D59 Warning: unaligning (T0384)L65 because of BadResidue code BAD_PEPTIDE at template residue (2h78A)V60 Warning: unaligning (T0384)S73 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2h78A)H70 Warning: unaligning (T0384)L74 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2h78A)H70 Warning: unaligning (T0384)A79 because of BadResidue code BAD_PEPTIDE in next template residue (2h78A)L76 Warning: unaligning (T0384)K80 because of BadResidue code BAD_PEPTIDE at template residue (2h78A)L76 Warning: unaligning (T0384)A81 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2h78A)D78 Warning: unaligning (T0384)K87 because of BadResidue code BAD_PEPTIDE in next template residue (2h78A)L90 Warning: unaligning (T0384)H88 because of BadResidue code BAD_PEPTIDE at template residue (2h78A)L90 Warning: unaligning (T0384)L91 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2h78A)C94 Warning: unaligning (T0384)E92 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2h78A)C94 Warning: unaligning (T0384)F117 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2h78A)D118 Warning: unaligning (T0384)E118 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2h78A)D118 Warning: unaligning (T0384)A120 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2h78A)V137 Warning: unaligning (T0384)R121 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2h78A)V137 Warning: unaligning (T0384)K132 because of BadResidue code BAD_PEPTIDE in next template residue (2h78A)P149 Warning: unaligning (T0384)N133 because of BadResidue code BAD_PEPTIDE at template residue (2h78A)P149 T0384 6 :VIGT 2h78A 6 :FIGL T0384 12 :ISHHFIEAAHTS 2h78A 12 :MGAPMATNLLKA T0384 25 :EYQ 2h78A 24 :GYL T0384 32 :YSRKLETAATFAS 2h78A 30 :FDLVQSAVDGLVA T0384 46 :YQNI 2h78A 43 :AGAS T0384 51 :LF 2h78A 47 :AA T0384 56 :EVFFK 2h78A 52 :RDAVQ T0384 62 :S 2h78A 57 :G T0384 66 :VYIASP 2h78A 61 :VISMLP T0384 72 :N 2h78A 68 :S T0384 75 :HFAQ 2h78A 71 :VEGL T0384 86 :G 2h78A 88 :G T0384 89 :VI 2h78A 91 :VL T0384 95 :AVSQPQEWFDLIQTAEKNNCFI 2h78A 95 :STIAPTSARKIHAAARERGLAM T0384 119 :A 2h78A 119 :A T0384 122 :NYHEKAFTTI 2h78A 138 :GGDAEALEKA T0384 134 :FL 2h78A 150 :LF T0384 137 :DK 2h78A 152 :EA T0384 143 :ADFN 2h78A 155 :GRNI T0384 149 :KYSSK 2h78A 159 :FHAGP T0384 154 :MPDLLAG 2h78A 222 :WPGVMEN T0384 164 :NVFSDRFAGGALMDLGIYPLYAAVRLF 2h78A 229 :APASRDYSGGFMAQLMAKDLGLAQEAA T0384 286 :H 2h78A 256 :Q T0384 295 :LYQTWLYDAGSVHELLYTMRQTA 2h78A 257 :ASASSTPMGSLALSLYRLLLKQG Number of specific fragments extracted= 24 number of extra gaps= 11 total=1026 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 2h78A/T0384-2h78A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0384 read from 2h78A/T0384-2h78A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2h78A read from 2h78A/T0384-2h78A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2h78A in template set Warning: unaligning (T0384)M1 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2h78A)K2 Warning: unaligning (T0384)L2 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2h78A)K2 Warning: unaligning (T0384)K3 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2h78A)Q3 Warning: unaligning (T0384)L4 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2h78A)A5 Warning: unaligning (T0384)G5 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2h78A)A5 Warning: unaligning (T0384)G10 because of BadResidue code BAD_PEPTIDE in next template residue (2h78A)H11 Warning: unaligning (T0384)A11 because of BadResidue code BAD_PEPTIDE at template residue (2h78A)H11 Warning: unaligning (T0384)L28 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2h78A)N28 Warning: unaligning (T0384)V29 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2h78A)N28 Warning: unaligning (T0384)I31 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2h78A)V29 Warning: unaligning (T0384)D53 because of BadResidue code BAD_PEPTIDE in next template residue (2h78A)S50 Warning: unaligning (T0384)Q54 because of BadResidue code BAD_PEPTIDE at template residue (2h78A)S50 Warning: unaligning (T0384)L55 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2h78A)A51 Warning: unaligning (T0384)F63 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2h78A)D59 Warning: unaligning (T0384)D64 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2h78A)D59 Warning: unaligning (T0384)L65 because of BadResidue code BAD_PEPTIDE at template residue (2h78A)V60 Warning: unaligning (T0384)S73 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2h78A)H70 Warning: unaligning (T0384)L74 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2h78A)H70 Warning: unaligning (T0384)A79 because of BadResidue code BAD_PEPTIDE in next template residue (2h78A)L76 Warning: unaligning (T0384)K80 because of BadResidue code BAD_PEPTIDE at template residue (2h78A)L76 Warning: unaligning (T0384)K87 because of BadResidue code BAD_PEPTIDE in next template residue (2h78A)L90 Warning: unaligning (T0384)H88 because of BadResidue code BAD_PEPTIDE at template residue (2h78A)L90 Warning: unaligning (T0384)L91 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2h78A)C94 Warning: unaligning (T0384)E92 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2h78A)C94 Warning: unaligning (T0384)F117 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2h78A)D118 Warning: unaligning (T0384)E118 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2h78A)D118 Warning: unaligning (T0384)A120 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2h78A)V121 Warning: unaligning (T0384)R121 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2h78A)V121 Warning: unaligning (T0384)Y123 because of BadResidue code BAD_PEPTIDE in next template residue (2h78A)G124 Warning: unaligning (T0384)H124 because of BadResidue code BAD_PEPTIDE at template residue (2h78A)G124 Warning: unaligning (T0384)E125 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2h78A)T125 Warning: unaligning (T0384)K132 because of BadResidue code BAD_PEPTIDE in next template residue (2h78A)P149 Warning: unaligning (T0384)N133 because of BadResidue code BAD_PEPTIDE at template residue (2h78A)P149 T0384 6 :VIGT 2h78A 6 :FIGL T0384 12 :ISHHFIEAAHTS 2h78A 12 :MGAPMATNLLKA T0384 25 :EYQ 2h78A 24 :GYL T0384 32 :YSRKLETAATFASR 2h78A 30 :FDLVQSAVDGLVAA T0384 48 :NIQLF 2h78A 44 :GASAA T0384 56 :EVF 2h78A 53 :DAV T0384 61 :SS 2h78A 56 :QG T0384 66 :VYIASPN 2h78A 61 :VISMLPA T0384 75 :HFAQ 2h78A 71 :VEGL T0384 86 :G 2h78A 88 :G T0384 89 :VI 2h78A 91 :VL T0384 95 :AVSQPQEWFDLIQTAEKNNCFI 2h78A 95 :STIAPTSARKIHAAARERGLAM T0384 119 :A 2h78A 119 :A T0384 122 :N 2h78A 122 :S T0384 126 :K 2h78A 126 :A T0384 127 :AFTTI 2h78A 143 :ALEKA T0384 134 :FLAD 2h78A 150 :LFEA T0384 140 :VLG 2h78A 154 :MGR T0384 144 :DFNYAK 2h78A 157 :NIFHAG T0384 153 :K 2h78A 163 :P T0384 274 :PH 2h78A 164 :DG T0384 276 :TMTEEVAAFAHMIQQ 2h78A 181 :LMIGTAEAMALGVAN T0384 291 :PDLN 2h78A 234 :DYSG T0384 297 :QTWLYDAGSVHELLYTMRQTAGIR 2h78A 238 :GFMAQLMAKDLGLAQEAAQASASS Number of specific fragments extracted= 24 number of extra gaps= 12 total=1050 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 2h78A/T0384-2h78A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0384 read from 2h78A/T0384-2h78A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2h78A read from 2h78A/T0384-2h78A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2h78A in template set Warning: unaligning (T0384)M1 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2h78A)K2 Warning: unaligning (T0384)L2 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2h78A)K2 Warning: unaligning (T0384)K3 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2h78A)Q3 Warning: unaligning (T0384)L4 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2h78A)A5 Warning: unaligning (T0384)G5 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2h78A)A5 Warning: unaligning (T0384)G10 because of BadResidue code BAD_PEPTIDE in next template residue (2h78A)H11 Warning: unaligning (T0384)A11 because of BadResidue code BAD_PEPTIDE at template residue (2h78A)H11 Warning: unaligning (T0384)L28 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2h78A)N28 Warning: unaligning (T0384)V29 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2h78A)N28 Warning: unaligning (T0384)I31 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2h78A)V29 Warning: unaligning (T0384)D53 because of BadResidue code BAD_PEPTIDE in next template residue (2h78A)S50 Warning: unaligning (T0384)Q54 because of BadResidue code BAD_PEPTIDE at template residue (2h78A)S50 Warning: unaligning (T0384)L55 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2h78A)A51 Warning: unaligning (T0384)F63 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2h78A)D59 Warning: unaligning (T0384)D64 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2h78A)D59 Warning: unaligning (T0384)L65 because of BadResidue code BAD_PEPTIDE at template residue (2h78A)V60 Warning: unaligning (T0384)L74 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2h78A)H70 Warning: unaligning (T0384)H75 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2h78A)H70 Warning: unaligning (T0384)A79 because of BadResidue code BAD_PEPTIDE in next template residue (2h78A)L76 Warning: unaligning (T0384)K80 because of BadResidue code BAD_PEPTIDE at template residue (2h78A)L76 Warning: unaligning (T0384)K87 because of BadResidue code BAD_PEPTIDE in next template residue (2h78A)L90 Warning: unaligning (T0384)H88 because of BadResidue code BAD_PEPTIDE at template residue (2h78A)L90 Warning: unaligning (T0384)L91 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2h78A)C94 Warning: unaligning (T0384)P94 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2h78A)C94 Warning: unaligning (T0384)F117 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2h78A)D118 Warning: unaligning (T0384)E118 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2h78A)D118 Warning: unaligning (T0384)A120 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2h78A)V121 Warning: unaligning (T0384)R121 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2h78A)V121 Warning: unaligning (T0384)Y123 because of BadResidue code BAD_PEPTIDE in next template residue (2h78A)G124 Warning: unaligning (T0384)H124 because of BadResidue code BAD_PEPTIDE at template residue (2h78A)G124 Warning: unaligning (T0384)E125 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2h78A)T125 Warning: unaligning (T0384)N146 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2h78A)V137 Warning: unaligning (T0384)Y147 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2h78A)V137 Warning: unaligning (T0384)V187 because of BadResidue code BAD_PEPTIDE in next template residue (2h78A)P149 Warning: unaligning (T0384)R188 because of BadResidue code BAD_PEPTIDE at template residue (2h78A)P149 T0384 6 :VIGT 2h78A 6 :FIGL T0384 12 :ISHHFIEAAHTS 2h78A 12 :MGAPMATNLLKA T0384 25 :EYQ 2h78A 24 :GYL T0384 32 :YSRKLETAATFASR 2h78A 30 :FDLVQSAVDGLVAA T0384 49 :IQLF 2h78A 45 :ASAA T0384 56 :EVFF 2h78A 52 :RDAV T0384 62 :S 2h78A 57 :G T0384 66 :VYIASPNS 2h78A 61 :VISMLPAS T0384 76 :FA 2h78A 71 :VE T0384 78 :Q 2h78A 74 :L T0384 86 :G 2h78A 88 :G T0384 89 :VI 2h78A 91 :VL T0384 95 :AVSQPQEWFDLIQTAEKNNCFI 2h78A 95 :STIAPTSARKIHAAARERGLAM T0384 119 :A 2h78A 119 :A T0384 122 :N 2h78A 122 :S T0384 126 :KAFTT 2h78A 126 :AGAAA T0384 141 :LGADF 2h78A 131 :GTLTF T0384 148 :A 2h78A 138 :G T0384 154 :MPD 2h78A 139 :GDA T0384 182 :PLYAA 2h78A 143 :ALEKA T0384 189 :LFGKANDATYHA 2h78A 150 :LFEAMGRNIFHA T0384 271 :QQAPHTMTEEVAAFAH 2h78A 162 :GPDGAGQVAKVCNNQL T0384 300 :LYDAGSVHELLYTMRQTAGIR 2h78A 178 :LAVLMIGTAEAMALGVANGLE Number of specific fragments extracted= 23 number of extra gaps= 13 total=1073 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 1nptO/T0384-1nptO-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1nptO expands to /projects/compbio/data/pdb/1npt.pdb.gz 1nptO:# T0384 read from 1nptO/T0384-1nptO-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1nptO read from 1nptO/T0384-1nptO-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1nptO to template set # found chain 1nptO in template set T0384 2 :LKLGVIGTGAISHHFIEAAHTSGEYQLVAIYS 1nptO 1 :VKVGINGFGRIGRNVFRAALKNPDIEVVAVND T0384 34 :RK 1nptO 34 :TD T0384 39 :AATFASRYQNI 1nptO 37 :ANTLAHLLKYD T0384 50 :QLFDQLEVF 1nptO 74 :KAERDPENL T0384 59 :FKS 1nptO 84 :WGE T0384 62 :SFDLVYIASPNSLHFAQAKAALSAG 1nptO 88 :GVDIVVESTGRFTKREDAAKHLEAG T0384 87 :KHVILEKPAV 1nptO 114 :KKVIISAPAK T0384 97 :SQPQ 1nptO 137 :YDPK T0384 113 :NCFIFEAARN 1nptO 140 :AHHVISNASA T0384 123 :YHEKAFTTIKNFL 1nptO 153 :CLAPFAKVLHEQF T0384 142 :GADFNYAKYSSKMPDLLAGQT 1nptO 166 :GIVRGMMTTVHSYTNDQRILD T0384 163 :PNVFSDRFAGGAL 1nptO 192 :DLRRARAAAESII T0384 180 :IYPLYAAVRLFGKAN 1nptO 208 :TGAAKAVALVLPELK T0384 195 :DATYHAQQLDNSIDLNGDGILFYPDY 1nptO 224 :KLNGMAMRVPTPNVSVVDLVAELEKE T0384 275 :HTMTEEVAAFAHMIQQPDLN 1nptO 250 :VTVEEVNAALKAAAEGELKG T0384 295 :LYQ 1nptO 276 :EPL T0384 298 :TWLYDAGSVHELLYTMRQ 1nptO 313 :NETGYSHRVVDLAAYIAS Number of specific fragments extracted= 17 number of extra gaps= 0 total=1090 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 1nptO/T0384-1nptO-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0384 read from 1nptO/T0384-1nptO-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1nptO read from 1nptO/T0384-1nptO-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1nptO in template set T0384 2 :LKLGVIGTGAISHHFIEAAHTSGEYQLVAIYSRK 1nptO 1 :VKVGINGFGRIGRNVFRAALKNPDIEVVAVNDLT T0384 39 :AATFASRYQ 1nptO 37 :ANTLAHLLK T0384 48 :NIQLFDQL 1nptO 72 :IVKAERDP T0384 56 :EV 1nptO 81 :NL T0384 58 :FFKSSFDLVYIASPNSLHFAQAKAALSAG 1nptO 84 :WGEIGVDIVVESTGRFTKREDAAKHLEAG T0384 87 :KHVILEKPAVSQ 1nptO 114 :KKVIISAPAKNE T0384 111 :KNNCFIFEAARNY 1nptO 138A:PKAHHVISNASAT T0384 124 :HEKAFTTIKNFL 1nptO 154 :LAPFAKVLHEQF T0384 144 :DFNYAKYS 1nptO 166 :GIVRGMMT T0384 152 :SKMPDLLAGQTPNVFSDRFAGGALMDL 1nptO 180 :NDQRILDLPHKDLRRARAAAESIIPTT T0384 180 :IYPLYAAVRLFGKAN 1nptO 208 :TGAAKAVALVLPELK T0384 195 :DATYHAQQLDNSIDLNGDGILFYPD 1nptO 224 :KLNGMAMRVPTPNVSVVDLVAELEK T0384 278 :TEEVAAFAHMIQQ 1nptO 253 :EEVNAALKAAAEG T0384 299 :WLYDAGSVHELLYTMRQT 1nptO 314 :ETGYSHRVVDLAAYIASK Number of specific fragments extracted= 14 number of extra gaps= 0 total=1104 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 1nptO/T0384-1nptO-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0384 read from 1nptO/T0384-1nptO-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1nptO read from 1nptO/T0384-1nptO-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1nptO in template set T0384 2 :LKLGVIGTGAISHHFIEAAHTSGEYQLVAIYSRKL 1nptO 1 :VKVGINGFGRIGRNVFRAALKNPDIEVVAVNDLTD T0384 39 :AATFASRY 1nptO 37 :ANTLAHLL T0384 49 :IQLFDQLEVFF 1nptO 73 :VKAERDPENLA T0384 60 :KSSFDLVYIASPNSLHFAQAKAALSAG 1nptO 86 :EIGVDIVVESTGRFTKREDAAKHLEAG T0384 87 :KHVILEKPAVSQ 1nptO 114 :KKVIISAPAKNE T0384 112 :NNCFIFEAARNYH 1nptO 139 :KAHHVISNASATT T0384 125 :EKAFTTIKNFL 1nptO 155 :APFAKVLHEQF T0384 142 :GADFNYAKYSSKMPDLLAGQTPNVFSDRFAG 1nptO 166 :GIVRGMMTTVHSYTNDQRILDLPHKDLRRAR T0384 180 :IYPLYAAVRLFGKAND 1nptO 208 :TGAAKAVALVLPELKG T0384 196 :ATYHAQQLDNSIDLNGDGILFYPDYQ 1nptO 225 :LNGMAMRVPTPNVSVVDLVAELEKEV T0384 276 :TMTEEVAAFAHMIQQP 1nptO 251 :TVEEVNAALKAAAEGE Number of specific fragments extracted= 11 number of extra gaps= 0 total=1115 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 1nqoA/T0384-1nqoA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1nqoA expands to /projects/compbio/data/pdb/1nqo.pdb.gz 1nqoA:# T0384 read from 1nqoA/T0384-1nqoA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1nqoA read from 1nqoA/T0384-1nqoA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1nqoA to template set # found chain 1nqoA in template set T0384 2 :LKLGVIGTGAISHHFIEAAHTSGEYQLVAIYS 1nqoA 1 :VKVGINGFGRIGRNVFRAALKNPDIEVVAVND T0384 34 :RKLE 1nqoA 34 :TDAN T0384 41 :TFASRYQNI 1nqoA 39 :TLAHLLKYD T0384 50 :QLFDQLEVF 1nqoA 74 :KAERDPENL T0384 59 :FKS 1nqoA 84 :WGE T0384 62 :SFDLVYIASPNSLHFAQAKAALSAG 1nqoA 88 :GVDIVVESTGRFTKREDAAKHLEAG T0384 87 :KHVILEKPAV 1nqoA 114 :KKVIISAPAK T0384 97 :SQPQ 1nqoA 137 :YDPK T0384 113 :NCFIFEAARN 1nqoA 140 :AHHVISNASS T0384 123 :YHEKAFTTIKNFL 1nqoA 153 :CLAPFAKVLHEQF T0384 142 :GADFNYAKYSSK 1nqoA 166 :GIVRGMMTTVHS T0384 186 :AVRLFGKAN 1nqoA 214 :VALVLPELK T0384 195 :DATYHAQQLDNSIDLNGDGILFYPDY 1nqoA 224 :KLNGMAMRVPTPNVSVVDLVAELEKE T0384 275 :HTMTEEVAAFAHMIQQPDLN 1nqoA 250 :VTVEEVNAALKAAAEGELKG T0384 295 :LYQ 1nqoA 276 :EPL T0384 298 :TWLYDAGSVHELLYTMRQ 1nqoA 313 :NETGYSHRVVDLAAYIAS Number of specific fragments extracted= 16 number of extra gaps= 0 total=1131 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 1nqoA/T0384-1nqoA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0384 read from 1nqoA/T0384-1nqoA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1nqoA read from 1nqoA/T0384-1nqoA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1nqoA in template set T0384 2 :LKLGVIGTGAISHHFIEAAHTSGEYQLVAIYS 1nqoA 1 :VKVGINGFGRIGRNVFRAALKNPDIEVVAVND T0384 34 :RK 1nqoA 34 :TD T0384 39 :AATFASRYQ 1nqoA 37 :ANTLAHLLK T0384 48 :NIQLFDQLEV 1nqoA 72 :IVKAERDPEN T0384 58 :FFKSSFDLVYIASPNSLHFAQAKAALSAG 1nqoA 84 :WGEIGVDIVVESTGRFTKREDAAKHLEAG T0384 87 :KHVILEKPAVSQ 1nqoA 114 :KKVIISAPAKNE T0384 111 :KNNCFIFEAARNY 1nqoA 138A:PKAHHVISNASST T0384 124 :HEKAFTTIKNFL 1nqoA 154 :LAPFAKVLHEQF T0384 144 :DFNYAKYS 1nqoA 166 :GIVRGMMT T0384 154 :MPDLLAGQTPNVFSDRFAGGAL 1nqoA 182 :QRILDLPHKDLRRARAAAESII T0384 186 :AVRLFGKAN 1nqoA 214 :VALVLPELK T0384 195 :DATYHAQQLDNSIDLNGDGILFYPD 1nqoA 224 :KLNGMAMRVPTPNVSVVDLVAELEK T0384 277 :MTEEVAAFAHMIQQ 1nqoA 252 :VEEVNAALKAAAEG T0384 299 :WLYDAGSVHELLYTMRQT 1nqoA 314 :ETGYSHRVVDLAAYIASK Number of specific fragments extracted= 14 number of extra gaps= 0 total=1145 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 1nqoA/T0384-1nqoA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0384 read from 1nqoA/T0384-1nqoA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1nqoA read from 1nqoA/T0384-1nqoA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1nqoA in template set T0384 2 :LKLGVIGTGAISHHFIEAAHTSGEYQLVAIYSRKL 1nqoA 1 :VKVGINGFGRIGRNVFRAALKNPDIEVVAVNDLTD T0384 39 :AATFASRY 1nqoA 37 :ANTLAHLL T0384 49 :IQLFDQLEVFF 1nqoA 73 :VKAERDPENLA T0384 60 :KSSFDLVYIASPNSLHFAQAKAALSAGK 1nqoA 86 :EIGVDIVVESTGRFTKREDAAKHLEAGA T0384 88 :HVILEKPAVSQ 1nqoA 115 :KVIISAPAKNE T0384 112 :NNCFIFEAARNYH 1nqoA 139 :KAHHVISNASSTT T0384 125 :EKAFTTIKNFL 1nqoA 155 :APFAKVLHEQF T0384 142 :GADFNYAKYSSKMPDLLAGQTPNVFSDRFAG 1nqoA 166 :GIVRGMMTTVHSYTNDQRILDLPHKDLRRAR T0384 191 :GKANDATYHAQQL 1nqoA 201 :ESIIPTTTGAAKA T0384 204 :DNSIDLNGDGILFYPDYQ 1nqoA 233 :PTPNVSVVDLVAELEKEV T0384 276 :TMTEEVAAFAHMIQQP 1nqoA 251 :TVEEVNAALKAAAEGE Number of specific fragments extracted= 11 number of extra gaps= 0 total=1156 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 1q0qA/T0384-1q0qA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1q0qA expands to /projects/compbio/data/pdb/1q0q.pdb.gz 1q0qA:# T0384 read from 1q0qA/T0384-1q0qA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1q0qA read from 1q0qA/T0384-1q0qA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1q0qA to template set # found chain 1q0qA in template set Warning: unaligning (T0384)L4 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1q0qA)T5 Warning: unaligning (T0384)G5 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1q0qA)T5 Warning: unaligning (T0384)K149 because of BadResidue code BAD_PEPTIDE in next template residue (1q0qA)G185 Warning: unaligning (T0384)Y150 because of BadResidue code BAD_PEPTIDE at template residue (1q0qA)G185 Warning: unaligning (T0384)S151 because of BadResidue code BAD_PEPTIDE at template residue (1q0qA)S186 T0384 1 :MLK 1q0qA 1 :MKQ T0384 6 :VIG 1q0qA 6 :ILG T0384 9 :TGAISHHFIEAAHTS 1q0qA 10 :TGSIGCSTLDVVRHN T0384 24 :GEYQLVAIYSR 1q0qA 26 :EHFRVVALVAG T0384 35 :KLETAATFASRYQNI 1q0qA 38 :NVTRMVEQCLEFSPR T0384 50 :QLFDQ 1q0qA 77 :EVLSG T0384 55 :LEVFFKS 1q0qA 85 :ACDMAAL T0384 62 :SFDLVYIASPNSLHFAQAKAALSAGKHVILE 1q0qA 93 :DVDQVMAAIVGAAGLLPTLAAIRAGKTILLA T0384 103 :FDLIQTAEKNNCFIFEA 1q0qA 133 :RLFMDAVKQSKAQLLPV T0384 125 :EKAFTTIKNF 1q0qA 150 :DSEHNAIFQS T0384 135 :L 1q0qA 164 :I T0384 137 :D 1q0qA 165 :Q T0384 139 :QVL 1q0qA 166 :HNL T0384 142 :GADFNYA 1q0qA 177 :GVVSILL T0384 152 :SK 1q0qA 187 :GG T0384 154 :MPDLLAGQTPNVFSDRF 1q0qA 202 :TPDQACRHPNWSMGRKI T0384 171 :AGGALMDLGIYPLY 1q0qA 221 :DSATMMNKGLEYIE T0384 186 :AVRLFG 1q0qA 235 :ARWLFN T0384 192 :KANDATYHAQQ 1q0qA 242 :SASQMEVLIHP T0384 208 :DLNGDGILFYPDYQVHIKAGKN 1q0qA 253 :QSVIHSMVRYQDGSVLAQLGEP T0384 256 :AIFTDHQGNQVQLPIQQAPHTMTEEVAAFAHMIQQPD 1q0qA 293 :GVKPLDFCKLSALTFAAPDYDRYPCLKLAMEAFEQGQ T0384 301 :YDAGSVHELLYTMRQTAGIR 1q0qA 330 :AATTALNAANEITVAAFLAQ Number of specific fragments extracted= 22 number of extra gaps= 2 total=1178 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 1q0qA/T0384-1q0qA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0384 read from 1q0qA/T0384-1q0qA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1q0qA read from 1q0qA/T0384-1q0qA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1q0qA in template set Warning: unaligning (T0384)L4 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1q0qA)T5 Warning: unaligning (T0384)G5 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1q0qA)T5 Warning: unaligning (T0384)S151 because of BadResidue code BAD_PEPTIDE in next template residue (1q0qA)G185 Warning: unaligning (T0384)S152 because of BadResidue code BAD_PEPTIDE at template residue (1q0qA)G185 Warning: unaligning (T0384)K153 because of BadResidue code BAD_PEPTIDE at template residue (1q0qA)S186 T0384 1 :MLK 1q0qA 1 :MKQ T0384 6 :VIG 1q0qA 6 :ILG T0384 9 :TGAISHHFIEAAHTSGE 1q0qA 10 :TGSIGCSTLDVVRHNPE T0384 26 :YQLVAIYSRK 1q0qA 28 :FRVVALVAGK T0384 36 :LETAATFASRYQ 1q0qA 39 :VTRMVEQCLEFS T0384 48 :NIQLFDQ 1q0qA 75 :RTEVLSG T0384 55 :L 1q0qA 85 :A T0384 56 :EVFFKSSFDLVYIASPNSLHFAQAKAALSAGKHVIL 1q0qA 87 :DMAALEDVDQVMAAIVGAAGLLPTLAAIRAGKTILL T0384 103 :FDLIQTAEKNNCFIFEAA 1q0qA 133 :RLFMDAVKQSKAQLLPVD T0384 126 :KAFTTIKNF 1q0qA 151 :SEHNAIFQS T0384 135 :LADK 1q0qA 164 :IQHN T0384 141 :LG 1q0qA 168 :LG T0384 145 :FNYAKY 1q0qA 178 :VVSILL T0384 154 :MPDLLAGQT 1q0qA 187 :GGPFRETPL T0384 163 :PNVFSDRF 1q0qA 211 :NWSMGRKI T0384 171 :AGGALMDLGIYPL 1q0qA 221 :DSATMMNKGLEYI T0384 185 :AAVRLFG 1q0qA 234 :EARWLFN T0384 192 :KANDATYHAQQ 1q0qA 242 :SASQMEVLIHP T0384 208 :DLNGDGILFYPDYQVHIKA 1q0qA 253 :QSVIHSMVRYQDGSVLAQL T0384 247 :LNTI 1q0qA 272 :GEPD T0384 251 :EHIRSAIFTDHQGNQVQLPIQQAPHTMTEEVAAFAHMIQQ 1q0qA 288 :NRVNSGVKPLDFCKLSALTFAAPDYDRYPCLKLAMEAFEQ T0384 299 :WLYDAGSVHELLYTMRQTAGIRF 1q0qA 328 :GQAATTALNAANEITVAAFLAQQ Number of specific fragments extracted= 22 number of extra gaps= 2 total=1200 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 1q0qA/T0384-1q0qA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0384 read from 1q0qA/T0384-1q0qA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1q0qA read from 1q0qA/T0384-1q0qA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1q0qA in template set Warning: unaligning (T0384)L4 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1q0qA)T5 Warning: unaligning (T0384)G5 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1q0qA)T5 Warning: unaligning (T0384)K149 because of BadResidue code BAD_PEPTIDE in next template residue (1q0qA)G185 Warning: unaligning (T0384)Y150 because of BadResidue code BAD_PEPTIDE at template residue (1q0qA)G185 Warning: unaligning (T0384)S151 because of BadResidue code BAD_PEPTIDE at template residue (1q0qA)S186 T0384 1 :MLK 1q0qA 1 :MKQ T0384 6 :VIGT 1q0qA 6 :ILGS T0384 10 :GAISHHFIEAAHTSGE 1q0qA 11 :GSIGCSTLDVVRHNPE T0384 26 :YQLVAIYSRK 1q0qA 28 :FRVVALVAGK T0384 36 :LETAATFASRY 1q0qA 39 :VTRMVEQCLEF T0384 47 :QN 1q0qA 73 :GS T0384 49 :IQLFDQ 1q0qA 76 :TEVLSG T0384 55 :LEVFF 1q0qA 85 :ACDMA T0384 60 :KSSFDLVYIASPNSLHFAQAKAALSAGKHVIL 1q0qA 91 :LEDVDQVMAAIVGAAGLLPTLAAIRAGKTILL T0384 105 :LIQTAEKNNCFIFEAAR 1q0qA 135 :FMDAVKQSKAQLLPVDS T0384 127 :AFTTIK 1q0qA 152 :EHNAIF T0384 133 :NFLAD 1q0qA 163 :PIQHN T0384 140 :VL 1q0qA 168 :LG T0384 142 :GADFNYA 1q0qA 177 :GVVSILL T0384 152 :SKMPDLLAGQTP 1q0qA 187 :GGPFRETPLRDL T0384 168 :DRFAG 1q0qA 212 :WSMGR T0384 173 :GALMDLGIYPLY 1q0qA 223 :ATMMNKGLEYIE T0384 186 :AVRLFGKANDATYHAQQL 1q0qA 235 :ARWLFNASASQMEVLIHP T0384 208 :DLNGDGILFYPDYQVHIKAGKNIT 1q0qA 253 :QSVIHSMVRYQDGSVLAQLGEPDM T0384 250 :IEHIRSAIFTDH 1q0qA 287 :PNRVNSGVKPLD T0384 263 :GNQVQLPIQQAPHTMTEEVAAFAHMIQQP 1q0qA 300 :CKLSALTFAAPDYDRYPCLKLAMEAFEQG T0384 298 :TWLYDAGSVHELLYTMRQ 1q0qA 329 :QAATTALNAANEITVAAF Number of specific fragments extracted= 22 number of extra gaps= 2 total=1222 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 1oi7A/T0384-1oi7A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1oi7A expands to /projects/compbio/data/pdb/1oi7.pdb.gz 1oi7A:Skipped atom 513, because occupancy 0.500 <= existing 0.500 in 1oi7A Skipped atom 714, because occupancy 0.500 <= existing 0.500 in 1oi7A Skipped atom 716, because occupancy 0.500 <= existing 0.500 in 1oi7A Skipped atom 718, because occupancy 0.500 <= existing 0.500 in 1oi7A Skipped atom 775, because occupancy 0.500 <= existing 0.500 in 1oi7A Skipped atom 777, because occupancy 0.500 <= existing 0.500 in 1oi7A Skipped atom 1770, because occupancy 0.500 <= existing 0.500 in 1oi7A # T0384 read from 1oi7A/T0384-1oi7A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1oi7A read from 1oi7A/T0384-1oi7A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1oi7A to template set # found chain 1oi7A in template set Warning: unaligning (T0384)E118 because of BadResidue code BAD_PEPTIDE in next template residue (1oi7A)G121 Warning: unaligning (T0384)A119 because of BadResidue code BAD_PEPTIDE at template residue (1oi7A)G121 T0384 2 :LKLGVIG 1oi7A 8 :TRVLVQG T0384 9 :TGAISHHFIEAAHTS 1oi7A 16 :TGREGQFHTKQMLTY T0384 25 :EYQLVAIYS 1oi7A 31 :GTKIVAGVT T0384 47 :QNI 1oi7A 40 :PGK T0384 50 :QLFDQLEVFFKS 1oi7A 51 :PVYDTVKEAVAH T0384 62 :SFDLVYIASPNSLHFAQAKAALSAGKHVILEKPAVSQPQEWFDLIQTAEKNNCFIF 1oi7A 64 :EVDASIIFVPAPAAADAALEAAHAGIPLIVLITEGIPTLDMVRAVEEIKALGSRLI T0384 123 :YHEKAFTTIKNFLADKQV 1oi7A 152 :RSGTLTYEAAAALSQAGL T0384 142 :GADFNYAKYSSK 1oi7A 170 :GTTTTVGIGGDP T0384 180 :IYPLYAAVRLFG 1oi7A 185 :TTFKDLLPLFNE T0384 192 :KANDATYHAQQLDN 1oi7A 199 :ETEAVVLIGEIGGS T0384 275 :HTMTEEVAAFAHM 1oi7A 256 :GTPESKLRAFAEA T0384 295 :LYQTWLYDAGSVHE 1oi7A 271 :PVADTIDEIVELVK Number of specific fragments extracted= 12 number of extra gaps= 1 total=1234 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 1oi7A/T0384-1oi7A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0384 read from 1oi7A/T0384-1oi7A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1oi7A read from 1oi7A/T0384-1oi7A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1oi7A in template set Warning: unaligning (T0384)Q271 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1oi7A)V255 T0384 2 :LKLGVIG 1oi7A 8 :TRVLVQG T0384 9 :TGAISHHFIEAAHTS 1oi7A 16 :TGREGQFHTKQMLTY T0384 25 :EYQLVAIYSR 1oi7A 31 :GTKIVAGVTP T0384 47 :Q 1oi7A 41 :G T0384 48 :NIQLFDQL 1oi7A 49 :GVPVYDTV T0384 56 :EVFFKSSFDLVYIASPNSLHFAQAKAALSAGKHVILEKPAVSQPQEWFDLIQTAEKNNCFIF 1oi7A 58 :EAVAHHEVDASIIFVPAPAAADAALEAAHAGIPLIVLITEGIPTLDMVRAVEEIKALGSRLI T0384 118 :EAARNYHEKAFTTIKNFLAD 1oi7A 147 :VGIISRSGTLTYEAAAALSQ T0384 141 :LGADFNYAKYSSKMPDL 1oi7A 167 :AGLGTTTTVGIGGDPVI T0384 179 :GIYPLYAAVRLFG 1oi7A 184 :GTTFKDLLPLFNE T0384 192 :KANDATYHAQQLDN 1oi7A 199 :ETEAVVLIGEIGGS T0384 272 :QAP 1oi7A 256 :GTP T0384 278 :TE 1oi7A 259 :ES T0384 284 :FAHMIQQPDLNLYQ 1oi7A 261 :KLRAFAEAGIPVAD T0384 299 :WLY 1oi7A 275 :TID T0384 308 :ELLYTMRQTA 1oi7A 278 :EIVELVKKAL Number of specific fragments extracted= 15 number of extra gaps= 0 total=1249 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 1oi7A/T0384-1oi7A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0384 read from 1oi7A/T0384-1oi7A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1oi7A read from 1oi7A/T0384-1oi7A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1oi7A in template set Warning: unaligning (T0384)L203 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1oi7A)V255 Warning: unaligning (T0384)Q271 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1oi7A)V255 T0384 2 :LKLGVIGT 1oi7A 8 :TRVLVQGI T0384 10 :GAISHHFIEAAHTS 1oi7A 17 :GREGQFHTKQMLTY T0384 25 :EYQLVAIYSRK 1oi7A 31 :GTKIVAGVTPG T0384 45 :RYQN 1oi7A 42 :KGGM T0384 49 :IQLFDQLEVFF 1oi7A 50 :VPVYDTVKEAV T0384 60 :KSSFDLVYIASPNSLHFAQAKAALSAGKHVILEKPAVSQPQEWFDLIQTAEKNNCFIF 1oi7A 62 :HHEVDASIIFVPAPAAADAALEAAHAGIPLIVLITEGIPTLDMVRAVEEIKALGSRLI T0384 118 :EAARNYHEKAFTTIKNFL 1oi7A 147 :VGIISRSGTLTYEAAAAL T0384 136 :ADKQ 1oi7A 166 :QAGL T0384 142 :GADFNYAKYSSKMPDLLAGQ 1oi7A 170 :GTTTTVGIGGDPVIGTTFKD T0384 164 :NVFSDRFAGGALMDLG 1oi7A 192 :PLFNEDPETEAVVLIG T0384 180 :IYPLYAAVRLFGK 1oi7A 212 :SDEEEAAAWVKDH T0384 193 :ANDATYHAQQ 1oi7A 226 :KKPVVGFIGG T0384 272 :QAPHTMTEEVAAF 1oi7A 256 :GTPESKLRAFAEA T0384 291 :PDLNLYQTWLYDAGSVHE 1oi7A 269 :GIPVADTIDEIVELVKKA Number of specific fragments extracted= 14 number of extra gaps= 0 total=1263 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 3dbvO/T0384-3dbvO-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # Reading fragments from alignment file # Attempting to read fragment alignments from file 3dbvO/T0384-3dbvO-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # Reading fragments from alignment file # Attempting to read fragment alignments from file 3dbvO/T0384-3dbvO-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # Reading fragments from alignment file # Attempting to read fragment alignments from file 2dbvO/T0384-2dbvO-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # Reading fragments from alignment file # Attempting to read fragment alignments from file 2dbvO/T0384-2dbvO-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # Reading fragments from alignment file # Attempting to read fragment alignments from file 2dbvO/T0384-2dbvO-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # Reading fragments from alignment file # Attempting to read fragment alignments from file 1j5pA/T0384-1j5pA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1j5pA expands to /projects/compbio/data/pdb/1j5p.pdb.gz 1j5pA:# T0384 read from 1j5pA/T0384-1j5pA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1j5pA read from 1j5pA/T0384-1j5pA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1j5pA to template set # found chain 1j5pA in template set Warning: unaligning (T0384)A273 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1j5pA)S220 Warning: unaligning (T0384)M277 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1j5pA)S220 T0384 2 :LKLGVIGTGAISHHFIEAA 1j5pA 1 :MTVLIIGMGNIGKKLVELG T0384 25 :EY 1j5pA 20 :NF T0384 27 :QLV 1j5pA 23 :KIY T0384 31 :IYSR 1j5pA 26 :AYDR T0384 49 :I 1j5pA 31 :S T0384 50 :QLFD 1j5pA 44 :QVPS T0384 62 :SFDLVYIASPNSLHFAQAKAALSAGKHVILEK 1j5pA 48 :DVSTVVECASPEAVKEYSLQILKNPVNYIIIS T0384 94 :PAVSQPQEWFDLIQTAEKNNCFIF 1j5pA 81 :SAFADEVFRERFFSELKNSPARVF T0384 120 :ARNYHEKAFTTIKNF 1j5pA 105 :FPSGAIGGLDVLSSI T0384 138 :KQV 1j5pA 120 :KDF T0384 143 :ADFNYAKYSSKMPDLLAGQTPNVFSDR 1j5pA 123 :VKNVRIETIKPPKSLGLDLKGKTVVFE T0384 173 :GALMDLG 1j5pA 150 :GSVEEAS T0384 180 :IYPLYAAVRLFG 1j5pA 163 :INVASTIGLIVG T0384 193 :ANDATYHAQQLDNSIDLNGDGILFY 1j5pA 175 :FEKVKVTIVADPAMDHNIHIVRISS T0384 262 :QGNQVQLPIQQ 1j5pA 200 :AIGNYEFKIEN T0384 278 :TEEVAAFAHMI 1j5pA 221 :MLTVYSILRTL T0384 315 :QTAGIRFEA 1j5pA 232 :RNLESKIIF Number of specific fragments extracted= 17 number of extra gaps= 0 total=1280 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 1j5pA/T0384-1j5pA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0384 read from 1j5pA/T0384-1j5pA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1j5pA read from 1j5pA/T0384-1j5pA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1j5pA in template set Warning: unaligning (T0384)H261 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1j5pA)S220 Warning: unaligning (T0384)I270 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1j5pA)S220 T0384 2 :LKLGVIGTGAISHHFIEAA 1j5pA 1 :MTVLIIGMGNIGKKLVELG T0384 25 :EYQLVAIYSRK 1j5pA 20 :NFEKIYAYDRI T0384 36 :LE 1j5pA 32 :KD T0384 46 :YQNIQLFDQLEVF 1j5pA 34 :IPGVVRLDEFQVP T0384 61 :SSFDLVYIASPNSLHFAQAKAALSAGKHVIL 1j5pA 47 :SDVSTVVECASPEAVKEYSLQILKNPVNYII T0384 92 :EKPAVSQPQEWFDLIQTAEKNNCFI 1j5pA 79 :STSAFADEVFRERFFSELKNSPARV T0384 119 :AARNYHEKAFTTIKNF 1j5pA 104 :FFPSGAIGGLDVLSSI T0384 141 :LG 1j5pA 120 :KD T0384 144 :DFNYAKYSSKMPDLLAGQT 1j5pA 122 :FVKNVRIETIKPPKSLGLD T0384 163 :PNV 1j5pA 160 :PRN T0384 180 :IYPLYAAVRLFG 1j5pA 163 :INVASTIGLIVG T0384 192 :KANDATYHA 1j5pA 176 :EKVKVTIVA T0384 204 :DNSIDLNGD 1j5pA 185 :DPAMDHNIH T0384 244 :TLTLNTIEHIRSAIFTD 1j5pA 194 :IVRISSAIGNYEFKIEN T0384 271 :Q 1j5pA 221 :M T0384 276 :TMTEEVAAFAHMIQQPDLN 1j5pA 222 :LTVYSILRTLRNLESKIIF Number of specific fragments extracted= 16 number of extra gaps= 0 total=1296 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 1j5pA/T0384-1j5pA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0384 read from 1j5pA/T0384-1j5pA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1j5pA read from 1j5pA/T0384-1j5pA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1j5pA in template set Warning: unaligning (T0384)Q265 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1j5pA)S220 Warning: unaligning (T0384)P274 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1j5pA)S220 T0384 2 :LKLGVIGTGAISHHFIEA 1j5pA 1 :MTVLIIGMGNIGKKLVEL T0384 24 :GEYQLVAIYSRKL 1j5pA 19 :GNFEKIYAYDRIS T0384 49 :IQLFDQLEVFF 1j5pA 34 :IPGVVRLDEFQ T0384 60 :KSSFDLVYIASPNSLHFAQAKAALSAGKHVIL 1j5pA 46 :PSDVSTVVECASPEAVKEYSLQILKNPVNYII T0384 94 :PAVSQPQEWFDLIQTA 1j5pA 81 :SAFADEVFRERFFSEL T0384 112 :NNCFIFEAARNYHEKAFTTIKNF 1j5pA 97 :KNSPARVFFPSGAIGGLDVLSSI T0384 140 :VLGADFNYAKYSSKMPDLLAGQTP 1j5pA 120 :KDFVKNVRIETIKPPKSLGLDLKG T0384 168 :DR 1j5pA 161 :RN T0384 180 :IYPLYAAVRLFGKANDATYHAQQLDNSIDLN 1j5pA 163 :INVASTIGLIVGFEKVKVTIVADPAMDHNIH T0384 244 :TLTLNTIEHIRSAIFTD 1j5pA 194 :IVRISSAIGNYEFKIEN T0384 275 :HTMTEEVAAFAHMIQQPDLN 1j5pA 221 :MLTVYSILRTLRNLESKIIF Number of specific fragments extracted= 11 number of extra gaps= 0 total=1307 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 2g5cA/T0384-2g5cA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2g5cA expands to /projects/compbio/data/pdb/2g5c.pdb.gz 2g5cA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0384 read from 2g5cA/T0384-2g5cA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2g5cA read from 2g5cA/T0384-2g5cA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2g5cA to template set # found chain 2g5cA in template set Warning: unaligning (T0384)I270 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2g5cA)A252 Warning: unaligning (T0384)P274 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2g5cA)A252 T0384 2 :LKLGVIGTGAISHHFIEAAHTS 2g5cA 31 :QNVLIVGVGFMGGSFAKSLRRS T0384 25 :EY 2g5cA 53 :GF T0384 27 :QLV 2g5cA 57 :KIY T0384 31 :IYSRKLETAATFASR 2g5cA 60 :GYDINPESISKAVDL T0384 47 :QNI 2g5cA 75 :GII T0384 50 :QLFDQLEVFFKSSFDLVYIASPNSLHFAQAKAA 2g5cA 79 :EGTTSIAKVEDFSPDFVMLSSPVRTFREIAKKL T0384 86 :GKHVILE 2g5cA 118 :DATVTDQ T0384 93 :KPAV 2g5cA 173 :TPTK T0384 97 :SQPQEWFDLIQTAEKNNCFIFEA 2g5cA 178 :TDKKRLKLVKRVWEDVGGVVEYM T0384 120 :ARNYHEKAFTTIK 2g5cA 210 :GVVSHLPHAVAFA T0384 133 :NFL 2g5cA 226 :TLI T0384 156 :DLLAGQTPNVFSDRFAG 2g5cA 229 :HMSTPEVDLFKYPGGGF T0384 269 :P 2g5cA 247 :D T0384 275 :HTMTEEVAAFAHMIQ 2g5cA 253 :KSDPIMWRDIFLENK T0384 304 :GSVHELLYTMRQTAG 2g5cA 268 :ENVMKAIEGFEKSLN Number of specific fragments extracted= 15 number of extra gaps= 0 total=1322 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 2g5cA/T0384-2g5cA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0384 read from 2g5cA/T0384-2g5cA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2g5cA read from 2g5cA/T0384-2g5cA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2g5cA in template set T0384 3 :KLGVIGTGAISHHFIEAAHTSG 2g5cA 32 :NVLIVGVGFMGGSFAKSLRRSG T0384 25 :EYQLV 2g5cA 55 :KGKIY T0384 31 :IYSRKLETAATFASR 2g5cA 60 :GYDINPESISKAVDL T0384 47 :QNI 2g5cA 75 :GII T0384 50 :QLFDQLEVFFKSSFDLVYIASPNSLHFAQAKAALSA 2g5cA 79 :EGTTSIAKVEDFSPDFVMLSSPVRTFREIAKKLSYI T0384 86 :GKHVILE 2g5cA 118 :DATVTDQ T0384 95 :AVSQPQEWFDLIQTAE 2g5cA 125 :GSVKGKLVYDLENILG T0384 112 :NNCFIFEAARNYHEK 2g5cA 166 :EGKKVILTPTKKTDK T0384 127 :AFTTIKNFLAD 2g5cA 182 :RLKLVKRVWED T0384 141 :LG 2g5cA 193 :VG T0384 148 :AKYSS 2g5cA 195 :GVVEY T0384 204 :DNSIDL 2g5cA 232 :TPEVDL T0384 258 :FTDHQGN 2g5cA 238 :FKYPGGG T0384 276 :TMTEEVAAFAHMIQQ 2g5cA 254 :SDPIMWRDIFLENKE T0384 305 :SVHELLYTMR 2g5cA 269 :NVMKAIEGFE Number of specific fragments extracted= 15 number of extra gaps= 0 total=1337 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 2g5cA/T0384-2g5cA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0384 read from 2g5cA/T0384-2g5cA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2g5cA read from 2g5cA/T0384-2g5cA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2g5cA in template set T0384 3 :KLGVIGTGAISHHFIEAAHTSG 2g5cA 32 :NVLIVGVGFMGGSFAKSLRRSG T0384 26 :YQLVA 2g5cA 56 :GKIYG T0384 32 :YSRKLETAATFASR 2g5cA 61 :YDINPESISKAVDL T0384 47 :QN 2g5cA 75 :GI T0384 49 :IQLFDQLEVFFKSSFDLVYIASPNSLHFAQAKAA 2g5cA 78 :DEGTTSIAKVEDFSPDFVMLSSPVRTFREIAKKL T0384 86 :GKHVILEKPAV 2g5cA 118 :DATVTDQGSVK T0384 99 :PQEWFDLIQTAEK 2g5cA 129 :GKLVYDLENILGK T0384 112 :NNCFIFEAARNYHE 2g5cA 166 :EGKKVILTPTKKTD T0384 126 :KAFTTIKNFLAD 2g5cA 181 :KRLKLVKRVWED T0384 140 :VL 2g5cA 193 :VG Number of specific fragments extracted= 10 number of extra gaps= 0 total=1347 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 2cvzA/T0384-2cvzA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2cvzA expands to /projects/compbio/data/pdb/2cvz.pdb.gz 2cvzA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0384 read from 2cvzA/T0384-2cvzA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2cvzA read from 2cvzA/T0384-2cvzA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2cvzA to template set # found chain 2cvzA in template set Warning: unaligning (T0384)L2 because first residue in template chain is (2cvzA)E2 T0384 3 :KLGVIGTGAISHHFIEAAHT 2cvzA 3 :KVAFIGLGAMGYPMAGHLAR T0384 25 :EYQLV 2cvzA 23 :RFPTL T0384 31 :IYSRKLETAATFASRYQNI 2cvzA 28 :VWNRTFEKALRHQEEFGSE T0384 51 :LFD 2cvzA 47 :AVP T0384 59 :FKS 2cvzA 50 :LER T0384 62 :SFDLVYIASP 2cvzA 55 :EARVIFTCLP T0384 72 :NSLHFAQAKAA 2cvzA 66 :TREVYEVAEAL T0384 83 :LSAGKHVILE 2cvzA 80 :LREGTYWVDA T0384 95 :AVSQPQEWFDLIQTAEKNNCFIFEAARNYHEKAFTT 2cvzA 90 :TSGEPEASRRLAERLREKGVTYLDAPVSGGTSGAEA T0384 131 :IKNFL 2cvzA 138 :AVERV T0384 138 :KQVLG 2cvzA 143 :RPFLA T0384 143 :ADFNYA 2cvzA 149 :AKKVVH T0384 151 :SSK 2cvzA 155 :VGP T0384 295 :LYQTWLYDAGSVHELLYTMRQTAGI 2cvzA 224 :PKTFALGLLVKDLGIAMGVLDGEKA Number of specific fragments extracted= 14 number of extra gaps= 0 total=1361 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 2cvzA/T0384-2cvzA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0384 read from 2cvzA/T0384-2cvzA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2cvzA read from 2cvzA/T0384-2cvzA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2cvzA in template set Warning: unaligning (T0384)L2 because first residue in template chain is (2cvzA)E2 T0384 3 :KLGVIGTGAISHHFIEAAHT 2cvzA 3 :KVAFIGLGAMGYPMAGHLAR T0384 25 :EYQLV 2cvzA 23 :RFPTL T0384 31 :IYSRKLETAATFASRYQ 2cvzA 28 :VWNRTFEKALRHQEEFG T0384 49 :IQLFD 2cvzA 45 :SEAVP T0384 55 :LEVF 2cvzA 50 :LERV T0384 61 :SSFDLVYIASPN 2cvzA 54 :AEARVIFTCLPT T0384 73 :SLHFAQAKAA 2cvzA 67 :REVYEVAEAL T0384 83 :LSAGKHVIL 2cvzA 80 :LREGTYWVD T0384 94 :PAVSQPQEWFDLIQTAEKNNCFIFEAARNYHEKAFTT 2cvzA 89 :ATSGEPEASRRLAERLREKGVTYLDAPVSGGTSGAEA T0384 131 :IKNFLAD 2cvzA 138 :AVERVRP T0384 140 :VLG 2cvzA 145 :FLA T0384 144 :DFNYAKYSSKMPD 2cvzA 148 :YAKKVVHVGPVGA T0384 177 :DLGIYPLYAAVRLF 2cvzA 161 :GHAVKAINNALLAV T0384 276 :TMTEEVAAFAHMIQQ 2cvzA 175 :NLWAAGEGLLALVKQ T0384 291 :PDLNLYQTWLYDAGSVHELLYTMRQ 2cvzA 220 :TRAFPKTFALGLLVKDLGIAMGVLD Number of specific fragments extracted= 15 number of extra gaps= 0 total=1376 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 2cvzA/T0384-2cvzA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0384 read from 2cvzA/T0384-2cvzA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2cvzA read from 2cvzA/T0384-2cvzA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2cvzA in template set Warning: unaligning (T0384)L2 because first residue in template chain is (2cvzA)E2 T0384 3 :KLGVIGTGAISHHFIEAAHTSGEY 2cvzA 3 :KVAFIGLGAMGYPMAGHLARRFPT T0384 30 :AIYSRKLETAATFASRYQN 2cvzA 27 :LVWNRTFEKALRHQEEFGS T0384 50 :QLFD 2cvzA 46 :EAVP T0384 55 :LEVFF 2cvzA 50 :LERVA T0384 62 :SFDLVYIASPN 2cvzA 55 :EARVIFTCLPT T0384 73 :SLHFAQAKAA 2cvzA 67 :REVYEVAEAL T0384 85 :AG 2cvzA 82 :EG T0384 89 :VILEKPAVSQPQEWFDLIQTAEKNNCFIFEAARNYHEKAFTT 2cvzA 84 :TYWVDATSGEPEASRRLAERLREKGVTYLDAPVSGGTSGAEA T0384 141 :LGADFNYA 2cvzA 126 :GTLTVMLG T0384 158 :LAGQTPNVFSDRFAG 2cvzA 134 :GPEEAVERVRPFLAY T0384 194 :NDATYHA 2cvzA 150 :KKVVHVG T0384 272 :QAPHTMTEEVAAFAHMI 2cvzA 157 :PVGAGHAVKAINNALLA T0384 302 :DAGSVHELLYTMRQTAGIR 2cvzA 174 :VNLWAAGEGLLALVKQGVS Number of specific fragments extracted= 13 number of extra gaps= 0 total=1389 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 1bg6/T0384-1bg6-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1bg6 expands to /projects/compbio/data/pdb/1bg6.pdb.gz 1bg6:Warning: there is no chain 1bg6 will retry with 1bg6A # T0384 read from 1bg6/T0384-1bg6-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1bg6 read from 1bg6/T0384-1bg6-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1bg6 to template set # found chain 1bg6 in template set T0384 2 :LKLGVIGTGAISHHFIEAAHTS 1bg6 5 :KTYAVLGLGNGGHAFAAYLALK T0384 25 :EYQLV 1bg6 27 :GQSVL T0384 31 :IYSRKLETAATFASR 1bg6 32 :AWDIDAQRIKEIQDR T0384 47 :QNI 1bg6 47 :GAI T0384 50 :QLFDQLEVFFK 1bg6 64 :LLTSDIGLAVK T0384 62 :SFDLVYIASPNSLHFAQAKAA 1bg6 75 :DADVILIVVPAIHHASIAANI T0384 85 :AGKHVILEKPAVS 1bg6 101 :EGQLIILNPGATG T0384 102 :WFDLIQTAEKNNC 1bg6 115 :ALEFRKILRENGA T0384 115 :FIFEAARNYH 1bg6 131 :TIGETSSMLF T0384 142 :G 1bg6 145 :E T0384 143 :ADFNYAKYSSK 1bg6 147 :PGQVTVNAIKG T0384 154 :MPDLLAG 1bg6 276 :GNPAYRG T0384 164 :NVFSDRFAGGAL 1bg6 283 :IAGPINLNTRYF T0384 176 :MDLGIYPLYAAVRLFG 1bg6 298 :VSTGLVPLSELGRAVN T0384 192 :KA 1bg6 315 :PT T0384 275 :HTMTEEVAAFAHMI 1bg6 317 :PLIDAVLDLISSLI T0384 318 :GI 1bg6 331 :DT Number of specific fragments extracted= 17 number of extra gaps= 0 total=1406 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 1bg6/T0384-1bg6-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0384 read from 1bg6/T0384-1bg6-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1bg6 read from 1bg6/T0384-1bg6-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1bg6 in template set T0384 2 :LKLGVIGTGAISHHFIEAAHTS 1bg6 5 :KTYAVLGLGNGGHAFAAYLALK T0384 25 :EYQLV 1bg6 27 :GQSVL T0384 31 :IYSRKLETAATFASR 1bg6 32 :AWDIDAQRIKEIQDR T0384 47 :Q 1bg6 47 :G T0384 48 :NI 1bg6 61 :HP T0384 50 :QLFDQL 1bg6 64 :LLTSDI T0384 56 :EVF 1bg6 71 :LAV T0384 61 :SSFDLVYIASPNSLHFAQAKAA 1bg6 74 :KDADVILIVVPAIHHASIAANI T0384 85 :AGKHVILE 1bg6 101 :EGQLIILN T0384 94 :PAVSQP 1bg6 109 :PGATGG T0384 102 :WFDLIQTAEKNN 1bg6 115 :ALEFRKILRENG T0384 114 :CFIFEAARNY 1bg6 130 :VTIGETSSML T0384 138 :KQ 1bg6 145 :ER T0384 141 :LG 1bg6 147 :PG T0384 143 :ADFNYA 1bg6 150 :VTVNAI T0384 154 :MPDL 1bg6 156 :KGAM Number of specific fragments extracted= 16 number of extra gaps= 0 total=1422 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 1bg6/T0384-1bg6-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0384 read from 1bg6/T0384-1bg6-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1bg6 read from 1bg6/T0384-1bg6-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1bg6 in template set T0384 2 :LKLGVIGTGAISHHFIEAAHT 1bg6 5 :KTYAVLGLGNGGHAFAAYLAL T0384 24 :GEYQLVA 1bg6 26 :KGQSVLA T0384 32 :YSRKLETAATFASRY 1bg6 33 :WDIDAQRIKEIQDRG T0384 49 :IQLFDQLEVFF 1bg6 63 :DLLTSDIGLAV T0384 62 :SFDLVYIASPNSLHFAQAKAA 1bg6 75 :DADVILIVVPAIHHASIAANI T0384 169 :RFAGGALMDLGIYPLYAAVRLF 1bg6 100 :SEGQLIILNPGATGGALEFRKI T0384 191 :GKANDATYHAQ 1bg6 125 :NGAPEVTIGET T0384 234 :LPCEIYTTD 1bg6 138 :MLFTCRSER T0384 243 :GTLTLNTIEHIRSAIFTDHQ 1bg6 148 :GQVTVNAIKGAMDFACLPAA T0384 263 :GNQVQLPIQQAPHTMTEEVAAFAHMIQQPDLNLYQTWL 1bg6 220 :QYYLEGITPSVGSLAEKVDAERIAIAKAFDLNVPSVCE Number of specific fragments extracted= 10 number of extra gaps= 0 total=1432 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 1vknA/T0384-1vknA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1vknA expands to /projects/compbio/data/pdb/1vkn.pdb.gz 1vknA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0384 read from 1vknA/T0384-1vknA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1vknA read from 1vknA/T0384-1vknA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1vknA to template set # found chain 1vknA in template set T0384 1 :MLKLGVIGT 1vknA 1 :MIRAGIIGA T0384 10 :GAISHHFIEAAHTSGEYQLVAIYSRK 1vknA 11 :GYTGLELVRLLKNHPEAKITYLSSRT T0384 36 :LET 1vknA 38 :AGK T0384 39 :AATF 1vknA 42 :LEEI T0384 50 :QLFD 1vknA 54 :ILSE T0384 54 :QLEVFFK 1vknA 59 :DPEKVSK T0384 62 :SFDLVYIASPNSLHFAQA 1vknA 66 :NCDVLFTALPAGASYDLV T0384 86 :GKHVILEKP 1vknA 88 :GVKIIDLGA T0384 98 :QPQEWFD 1vknA 102 :DPGVYRE T0384 106 :IQTAEKNNCFIFEAARNYHEKAFTTIKNFL 1vknA 129 :LHREEIKNAQVVGNPGCYPTSVILALAPAL T0384 137 :DKQVLGADFNYAKYSSKMPDLLAGQT 1vknA 159 :KHNLVDPETILVDAKSGVSGAGRKEK T0384 163 :PNVFSDRF 1vknA 196 :LRPYNVAK T0384 176 :MDLGIYPLYAAVRLFGKANDATYHAQQLDNSIDLNGDGILFYP 1vknA 204 :HRHVPEMEQELGKISGKKVNVVFTPHLVPMTRGILSTIYVKTD T0384 275 :HTMTEEVAAFAHMIQQPD 1vknA 247 :KSLEEIHEAYLEFYKNEP Number of specific fragments extracted= 14 number of extra gaps= 0 total=1446 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 1vknA/T0384-1vknA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0384 read from 1vknA/T0384-1vknA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1vknA read from 1vknA/T0384-1vknA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1vknA in template set T0384 1 :MLKLGVIGT 1vknA 1 :MIRAGIIGA T0384 10 :GAISHHFIEAAHTSGEYQLVAIYSRK 1vknA 11 :GYTGLELVRLLKNHPEAKITYLSSRT T0384 46 :YQ 1vknA 38 :AG T0384 48 :NIQLFD 1vknA 52 :NSILSE T0384 54 :QLEVFFK 1vknA 59 :DPEKVSK T0384 62 :SFDLVYIASPNSLHFAQA 1vknA 66 :NCDVLFTALPAGASYDLV T0384 86 :GKHVILEKP 1vknA 88 :GVKIIDLGA T0384 95 :AVSQPQEWFDLI 1vknA 99 :RFDDPGVYREWY T0384 113 :N 1vknA 116 :G T0384 114 :CFIFEAARNYHEKA 1vknA 120 :IKRVYGLPELHREE T0384 135 :LAD 1vknA 134 :IKN T0384 141 :LG 1vknA 137 :AQ T0384 174 :ALMDLGIYPLYAAVRLF 1vknA 139 :VVGNPGCYPTSVILALA T0384 191 :G 1vknA 161 :N T0384 192 :KANDATYHAQQL 1vknA 164 :DPETILVDAKSG T0384 204 :DNSIDLNGDGILFYPD 1vknA 232 :PMTRGILSTIYVKTDK T0384 228 :KNITSNLPCEIYTT 1vknA 278 :KWCYGSNHVFIGMQ T0384 242 :DGTLTLNTI 1vknA 296 :TNTLILMSA T0384 299 :WLYDAGSVHELL 1vknA 312 :ASGQAVQNMNIM Number of specific fragments extracted= 19 number of extra gaps= 0 total=1465 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 1vknA/T0384-1vknA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0384 read from 1vknA/T0384-1vknA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1vknA read from 1vknA/T0384-1vknA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1vknA in template set T0384 1 :MLKLGVIGT 1vknA 1 :MIRAGIIGA T0384 10 :GAISHHFIEAAHTSGEYQLVAIYSRK 1vknA 11 :GYTGLELVRLLKNHPEAKITYLSSRT T0384 45 :RYQN 1vknA 37 :YAGK T0384 49 :IQLFD 1vknA 53 :SILSE T0384 54 :QLEVFF 1vknA 59 :DPEKVS T0384 62 :SFDLVYIASPNSLHFAQA 1vknA 66 :NCDVLFTALPAGASYDLV T0384 110 :EK 1vknA 84 :RE T0384 112 :NNCFIFEAARNYHEKAFTTIKNFLAD 1vknA 87 :KGVKIIDLGADFRFDDPGVYREWYGK T0384 153 :K 1vknA 113 :E T0384 158 :LAGQTP 1vknA 114 :LSGYEN T0384 164 :NVFSDRFAGGALMDLGIYPLYAAVRLFG 1vknA 129 :LHREEIKNAQVVGNPGCYPTSVILALAP T0384 192 :KANDATYHAQQL 1vknA 164 :DPETILVDAKSG T0384 204 :DNSIDLNGDGILFYPD 1vknA 232 :PMTRGILSTIYVKTDK T0384 276 :TMTEEVAAFAHMIQQ 1vknA 248 :SLEEIHEAYLEFYKN Number of specific fragments extracted= 14 number of extra gaps= 0 total=1479 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 1obfO/T0384-1obfO-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1obfO expands to /projects/compbio/data/pdb/1obf.pdb.gz 1obfO:# T0384 read from 1obfO/T0384-1obfO-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1obfO read from 1obfO/T0384-1obfO-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1obfO to template set # found chain 1obfO in template set Warning: unaligning (T0384)R121 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1obfO)T155 Warning: unaligning (T0384)A148 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1obfO)T178 Warning: unaligning (T0384)K149 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1obfO)T178 Warning: unaligning (T0384)S151 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1obfO)H181 Warning: unaligning (T0384)S152 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1obfO)H181 Warning: unaligning (T0384)G173 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1obfO)M207 Warning: unaligning (T0384)A174 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1obfO)M207 T0384 2 :LKLGVIGTGAISHHFIEAAHTSG 1obfO 2 :IRVAINGYGRIGRNILRAHYEGG T0384 25 :EYQLVAIYS 1obfO 28 :DIEIVAIND T0384 34 :RKLE 1obfO 38 :GDPK T0384 41 :TFASRYQNI 1obfO 42 :TNAHLTRYD T0384 50 :QLFDQLEVF 1obfO 77 :DANRNPAQL T0384 59 :FKS 1obfO 87 :WGA T0384 62 :SFDLVYIASPNSLHFAQAKAALSAG 1obfO 91 :KVDVVLECTGFFTTKEKAGAHIKGG T0384 87 :KHVILEKPAV 1obfO 117 :KKVIISAPGG T0384 97 :SQ 1obfO 142 :LK T0384 112 :NNCFIFEAA 1obfO 144 :STDTVISNA T0384 123 :YHEKAFTTIKNFL 1obfO 158 :CLAPLVKPLNDKL T0384 142 :GADFNY 1obfO 171 :GLQDGL T0384 150 :Y 1obfO 179 :T T0384 153 :K 1obfO 182 :A T0384 155 :PDLLA 1obfO 188 :VLTDV T0384 163 :PNVFSDRFAG 1obfO 196 :DLRRARSATM T0384 175 :L 1obfO 208 :I T0384 180 :IYPLYAAVRLFGKAN 1obfO 212 :TGAAAAVGDVLPELD T0384 195 :DATYHAQQLDNSIDLNGDGILFYPDY 1obfO 228 :KLNGYAIRVPTINVSIVDLSFVAKRN T0384 240 :TTDGTLTLN 1obfO 303 :VSGRLVKVS T0384 298 :TWLYDAGSVHELLYTMR 1obfO 316 :NEWGFSNRMLDTTVALM Number of specific fragments extracted= 21 number of extra gaps= 3 total=1500 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 1obfO/T0384-1obfO-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0384 read from 1obfO/T0384-1obfO-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1obfO read from 1obfO/T0384-1obfO-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1obfO in template set Warning: unaligning (T0384)R121 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1obfO)T155 Warning: unaligning (T0384)Y123 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1obfO)T155 Warning: unaligning (T0384)Y150 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1obfO)T178 Warning: unaligning (T0384)S151 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1obfO)T178 Warning: unaligning (T0384)K153 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1obfO)H181 Warning: unaligning (T0384)G173 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1obfO)M207 Warning: unaligning (T0384)A174 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1obfO)M207 T0384 1 :MLKLGVIGTGAISHHFIEAAHTSG 1obfO 1 :TIRVAINGYGRIGRNILRAHYEGG T0384 25 :EYQLVAIYS 1obfO 28 :DIEIVAIND T0384 34 :RKLE 1obfO 38 :GDPK T0384 41 :TFASRYQ 1obfO 42 :TNAHLTR T0384 48 :NIQLFDQL 1obfO 75 :RVDANRNP T0384 56 :EV 1obfO 84 :QL T0384 58 :FFKSSFDLVYIASPNSLHFAQAKAALSAG 1obfO 87 :WGALKVDVVLECTGFFTTKEKAGAHIKGG T0384 87 :KHVILEKP 1obfO 117 :KKVIISAP T0384 95 :AVSQPQ 1obfO 135 :YGVNHG T0384 112 :NNCFIFEAA 1obfO 144 :STDTVISNA T0384 124 :HEKAFTTIKNF 1obfO 159 :LAPLVKPLNDK T0384 141 :LG 1obfO 170 :LG T0384 145 :FNYAK 1obfO 172 :LQDGL T0384 152 :S 1obfO 179 :T T0384 154 :MPDLLAGQTPNVFSDRFAG 1obfO 187 :QVLTDVYHEDLRRARSATM T0384 175 :LMD 1obfO 208 :IPT T0384 180 :IYPLYAAVRLFGKAN 1obfO 212 :TGAAAAVGDVLPELD T0384 195 :DATYHAQQLDNSIDLNGDGILFYPD 1obfO 228 :KLNGYAIRVPTINVSIVDLSFVAKR T0384 234 :LPCEI 1obfO 292 :ASSTV T0384 239 :YTTDGTLTLNTI 1obfO 302 :KVSGRLVKVSSW T0384 299 :WLYDAGSVHELLYTMRQ 1obfO 317 :EWGFSNRMLDTTVALMS Number of specific fragments extracted= 21 number of extra gaps= 3 total=1521 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 1obfO/T0384-1obfO-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0384 read from 1obfO/T0384-1obfO-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1obfO read from 1obfO/T0384-1obfO-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1obfO in template set Warning: unaligning (T0384)R121 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1obfO)T155 Warning: unaligning (T0384)Y123 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1obfO)T155 Warning: unaligning (T0384)A148 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1obfO)T178 Warning: unaligning (T0384)K149 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1obfO)T178 Warning: unaligning (T0384)S151 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1obfO)H181 Warning: unaligning (T0384)S152 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1obfO)H181 T0384 2 :LKLGVIGTGAISHHFIEAAHTSG 1obfO 2 :IRVAINGYGRIGRNILRAHYEGG T0384 25 :EYQLVAIYS 1obfO 28 :DIEIVAIND T0384 34 :RKLE 1obfO 38 :GDPK T0384 41 :TFASRY 1obfO 42 :TNAHLT T0384 49 :IQLFDQLEVFF 1obfO 76 :VDANRNPAQLP T0384 60 :KSSFDLVYIASPNSLHFAQAKAALSAGK 1obfO 89 :ALKVDVVLECTGFFTTKEKAGAHIKGGA T0384 88 :HVILEKPAV 1obfO 118 :KVIISAPGG T0384 112 :NNCFIFEAA 1obfO 144 :STDTVISNA T0384 124 :HEKAFTTIKNFLAD 1obfO 156 :TNCLAPLVKPLNDK T0384 140 :V 1obfO 170 :L T0384 142 :GADFNY 1obfO 171 :GLQDGL T0384 150 :Y 1obfO 179 :T T0384 153 :KMPDLLAGQTPNVFSDRFAG 1obfO 182 :AYTNNQVLTDVYHEDLRRAR T0384 180 :IYPLYAAVRLF 1obfO 212 :TGAAAAVGDVL T0384 191 :GKANDATYHAQ 1obfO 226 :DGKLNGYAIRV T0384 204 :DNSIDLNGDGILFYPD 1obfO 237 :PTINVSIVDLSFVAKR T0384 271 :QQAPHTMTEEVA 1obfO 253 :NTTVEEVNGILK T0384 286 :HMIQQP 1obfO 265 :AASEGE Number of specific fragments extracted= 18 number of extra gaps= 2 total=1539 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 2gf2A/T0384-2gf2A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # Reading fragments from alignment file # Attempting to read fragment alignments from file 2gf2A/T0384-2gf2A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # Reading fragments from alignment file # Attempting to read fragment alignments from file 2gf2A/T0384-2gf2A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # Reading fragments from alignment file # Attempting to read fragment alignments from file 1s7cA/T0384-1s7cA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # Reading fragments from alignment file # Attempting to read fragment alignments from file 1s7cA/T0384-1s7cA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # Reading fragments from alignment file # Attempting to read fragment alignments from file 1s7cA/T0384-1s7cA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # Reading fragments from alignment file # Attempting to read fragment alignments from file 1yqgA/T0384-1yqgA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1yqgA expands to /projects/compbio/data/pdb/1yqg.pdb.gz 1yqgA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0384 read from 1yqgA/T0384-1yqgA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1yqgA read from 1yqgA/T0384-1yqgA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1yqgA to template set # found chain 1yqgA in template set Warning: unaligning (T0384)L2 because first residue in template chain is (1yqgA)M1 T0384 3 :KLGVIGTGAISHHFIEAAHTSGEYQLV 1yqgA 2 :NVYFLGGGNMAAAVAGGLVKQGGYRIY T0384 31 :IYSRKLETAATFASRYQNI 1yqgA 29 :IANRGAEKRERLEKELGVE T0384 51 :LFDQL 1yqgA 48 :TSATL T0384 62 :SF 1yqgA 54 :EL T0384 64 :DLVYIASPNSLHFAQA 1yqgA 59 :DVLILAVKPQDMEAAC T0384 85 :AGKHVILEK 1yqgA 80 :NGALVLSVA T0384 95 :AVSQPQEWFDL 1yqgA 89 :AGLSVGTLSRY T0384 112 :NNC 1yqgA 101 :GGT T0384 115 :FIFEA 1yqgA 106 :IVRVM T0384 120 :ARNYHEKAFTTIKNFL 1yqgA 127 :EAEVSETDRRIADRIM T0384 139 :QVLG 1yqgA 143 :KSVG T0384 147 :YAKYSSKMPDLL 1yqgA 147 :LTVWLDDEEKMH T0384 173 :GALMDLGI 1yqgA 159 :GITGISGS T0384 274 :P 1yqgA 167 :G T0384 275 :HTMTEEVAAFAHMIQQPD 1yqgA 169 :AYVFYLLDALQNAAIRQG T0384 298 :TWLYDAGSVH 1yqgA 187 :FDMAEARALS Number of specific fragments extracted= 16 number of extra gaps= 0 total=1555 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 1yqgA/T0384-1yqgA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0384 read from 1yqgA/T0384-1yqgA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1yqgA read from 1yqgA/T0384-1yqgA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1yqgA in template set Warning: unaligning (T0384)L2 because first residue in template chain is (1yqgA)M1 T0384 3 :KLGVIGTGAISHHFIEAAHTSGEYQLV 1yqgA 2 :NVYFLGGGNMAAAVAGGLVKQGGYRIY T0384 31 :IYSRKLETAATFASRYQ 1yqgA 29 :IANRGAEKRERLEKELG T0384 49 :IQLFDQL 1yqgA 46 :VETSATL T0384 56 :EVF 1yqgA 54 :ELH T0384 61 :SS 1yqgA 57 :SD T0384 64 :DLVYIASPNSLHFAQA 1yqgA 59 :DVLILAVKPQDMEAAC T0384 85 :AGKHVIL 1yqgA 80 :NGALVLS T0384 93 :KPAVSQPQEWFDL 1yqgA 87 :VAAGLSVGTLSRY T0384 113 :N 1yqgA 102 :G T0384 114 :CFIFEAARNY 1yqgA 105 :RIVRVMPNTP T0384 124 :HEKAFTTIKNFLAD 1yqgA 131 :SETDRRIADRIMKS T0384 141 :LG 1yqgA 145 :VG T0384 149 :KYSS 1yqgA 147 :LTVW Number of specific fragments extracted= 13 number of extra gaps= 0 total=1568 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 1yqgA/T0384-1yqgA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0384 read from 1yqgA/T0384-1yqgA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1yqgA read from 1yqgA/T0384-1yqgA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1yqgA in template set Warning: unaligning (T0384)L2 because first residue in template chain is (1yqgA)M1 T0384 3 :KLGVIGTGAISHHFIEAAHTSGEYQLV 1yqgA 2 :NVYFLGGGNMAAAVAGGLVKQGGYRIY T0384 31 :IYSRKLETAATFASRYQN 1yqgA 29 :IANRGAEKRERLEKELGV T0384 50 :QLFDQLEVF 1yqgA 47 :ETSATLPEL T0384 60 :KSS 1yqgA 56 :HSD T0384 64 :DLVYIASPNSLHFAQA 1yqgA 59 :DVLILAVKPQDMEAAC T0384 85 :AGKHVIL 1yqgA 80 :NGALVLS T0384 93 :KPAVSQPQEWFDL 1yqgA 87 :VAAGLSVGTLSRY T0384 114 :CFIFEAARNY 1yqgA 105 :RIVRVMPNTP T0384 124 :HEKAFTTIKNFLAD 1yqgA 131 :SETDRRIADRIMKS T0384 140 :VLGADF 1yqgA 145 :VGLTVW T0384 151 :SSKMPD 1yqgA 151 :LDDEEK T0384 186 :AVRLFG 1yqgA 157 :MHGITG T0384 269 :PIQQAPHTMTEEVAAFAHMIQQPD 1yqgA 163 :ISGSGPAYVFYLLDALQNAAIRQG T0384 296 :YQTWLYDAGSVHELLYTM 1yqgA 187 :FDMAEARALSLATFKGAV Number of specific fragments extracted= 14 number of extra gaps= 0 total=1582 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 1gaeO/T0384-1gaeO-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1gaeO expands to /projects/compbio/data/pdb/1gae.pdb.gz 1gaeO:# T0384 read from 1gaeO/T0384-1gaeO-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1gaeO read from 1gaeO/T0384-1gaeO-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1gaeO to template set # found chain 1gaeO in template set T0384 2 :LKLGVIGTGAISHHFIEAAHTSGEYQLVAIYS 1gaeO 1 :IKVGINGFGRIGRIVFRAAQKRSDIEIVAIND T0384 34 :RKLE 1gaeO 34 :LDAD T0384 41 :TFASRYQNI 1gaeO 39 :YMAYMLKYD T0384 50 :QLFDQLEVF 1gaeO 74 :TAERDPANL T0384 59 :FKS 1gaeO 84 :WDE T0384 62 :SFDLVYIASPNSLHFAQAKAALSAG 1gaeO 88 :GVDVVAEATGLFLTDETARKHITAG T0384 87 :KHVILEKPAVSQ 1gaeO 114 :KKVVMTGPSKDN T0384 113 :NC 1gaeO 138A:GQ T0384 115 :FIFEA 1gaeO 143 :IVSNA T0384 122 :NYHEKAFTTIKNFL 1gaeO 148 :SCTTNCLAPLAKVI T0384 138 :KQVLGADFNYAKYSSKMPDLLAGQT 1gaeO 162 :NDNFGIIEGLMTTVHATTATQKTVD T0384 163 :PNVFSDRFAGGAL 1gaeO 192 :DWRGGRGASQNII T0384 180 :IYPLYAAVRLFGKAN 1gaeO 208 :TGAAKAVGKVLPELN T0384 195 :DATYHAQQLDNSIDLNGDGILFYPDY 1gaeO 224 :KLTGMAFRVPTPNVSVVDLTVRLEKA T0384 275 :HTMTEEVAAFAHMIQQPDLNLY 1gaeO 250 :ATYEQIKAAVKAAAEGEMKGVL Number of specific fragments extracted= 15 number of extra gaps= 0 total=1597 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 1gaeO/T0384-1gaeO-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0384 read from 1gaeO/T0384-1gaeO-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1gaeO read from 1gaeO/T0384-1gaeO-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1gaeO in template set T0384 1 :MLKLGVIGTGAISHHFIEAAHTSGEYQLVAIYS 1gaeO 0 :TIKVGINGFGRIGRIVFRAAQKRSDIEIVAIND T0384 34 :RK 1gaeO 34 :LD T0384 39 :AATFASRYQ 1gaeO 37 :ADYMAYMLK T0384 48 :NIQLFDQL 1gaeO 72 :RVTAERDP T0384 56 :EV 1gaeO 81 :NL T0384 58 :FFKSSFDLVYIASPNSLHFAQAKAALSAG 1gaeO 84 :WDEVGVDVVAEATGLFLTDETARKHITAG T0384 87 :KHVILEKPAVSQ 1gaeO 114 :KKVVMTGPSKDN T0384 113 :NCFIFEAARNY 1gaeO 138A:GQDIVSNASCT T0384 124 :HEKAFTTIKNFL 1gaeO 154 :LAPLAKVINDNF T0384 144 :DFNYAKYSSK 1gaeO 166 :GIIEGLMTTV T0384 154 :MPDLLAGQTP 1gaeO 179 :TATQKTVDGP T0384 164 :NVFSDRFAGG 1gaeO 193 :WRGGRGASQN T0384 180 :IYPLYAAVRLFGKAN 1gaeO 208 :TGAAKAVGKVLPELN T0384 195 :DATYHAQQLDNSIDLNGDGILFYPDY 1gaeO 224 :KLTGMAFRVPTPNVSVVDLTVRLEKA T0384 276 :TMTEEVAAFAHMIQQ 1gaeO 251 :TYEQIKAAVKAAAEG Number of specific fragments extracted= 15 number of extra gaps= 0 total=1612 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 1gaeO/T0384-1gaeO-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0384 read from 1gaeO/T0384-1gaeO-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1gaeO read from 1gaeO/T0384-1gaeO-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1gaeO in template set T0384 2 :LKLGVIGTGAISHHFIEAAHTSGEYQLVAIYS 1gaeO 1 :IKVGINGFGRIGRIVFRAAQKRSDIEIVAIND T0384 34 :RKLE 1gaeO 34 :LDAD T0384 41 :TFASRY 1gaeO 39 :YMAYML T0384 49 :IQLFDQLEVFF 1gaeO 73 :VTAERDPANLK T0384 60 :KSSFDLVYIASPNSLHFAQAKAALSAGK 1gaeO 86 :EVGVDVVAEATGLFLTDETARKHITAGA T0384 88 :HVILEKPAVSQ 1gaeO 115 :KVVMTGPSKDN T0384 113 :NCFIFEAARNYHEKAFTTIKNFLAD 1gaeO 138A:GQDIVSNASCTTNCLAPLAKVINDN T0384 142 :GADFNYAKYSSKMPDLLAGQTP 1gaeO 166 :GIIEGLMTTVHATTATQKTVDG T0384 164 :NVFSDRFAGG 1gaeO 193 :WRGGRGASQN T0384 180 :IYPLYAAVRLFGKANDATYHAQQL 1gaeO 208 :TGAAKAVGKVLPELNGKLTGMAFR T0384 204 :DNSIDLNGDGILFYPDYQ 1gaeO 233 :PTPNVSVVDLTVRLEKAA T0384 276 :TMTEEVAAFAHMIQQP 1gaeO 251 :TYEQIKAAVKAAAEGE Number of specific fragments extracted= 12 number of extra gaps= 0 total=1624 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 1np3A/T0384-1np3A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1np3A expands to /projects/compbio/data/pdb/1np3.pdb.gz 1np3A:# T0384 read from 1np3A/T0384-1np3A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1np3A read from 1np3A/T0384-1np3A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1np3A to template set # found chain 1np3A in template set T0384 3 :KLGVIGTGAISHHFIEAAHTS 1np3A 18 :KVAIIGYGSQGHAHACNLKDS T0384 25 :EYQLV 1np3A 39 :GVDVT T0384 31 :IYSR 1np3A 44 :VGLR T0384 35 :KLE 1np3A 49 :GSA T0384 39 :AATFASRYQNI 1np3A 52 :TVAKAEAHGLK T0384 52 :FDQLEVFFK 1np3A 63 :VADVKTAVA T0384 62 :SFDLVYIASPNSLHFAQAKA 1np3A 72 :AADVVMILTPDEFQGRLYKE T0384 86 :GKHVILE 1np3A 100 :GATLAFA T0384 93 :KPAV 1np3A 117 :VPRA T0384 113 :NC 1np3A 121 :DL T0384 115 :FIFEAARNYHEKAFTTI 1np3A 124 :VIMIAPKAPGHTVRSEF T0384 136 :ADKQVLG 1np3A 141 :VKGGGIP T0384 146 :NYAKYSSKMPDLLAG 1np3A 148 :DLIAIYQDASGNAKN T0384 181 :YPLYAAVRLFG 1np3A 163 :VALSYACGVGG T0384 192 :K 1np3A 177 :G T0384 275 :HTMTEEVAAFAHMIQQPD 1np3A 201 :GCVELVKAGFETLVEAGY T0384 295 :LYQT 1np3A 219 :APEM Number of specific fragments extracted= 17 number of extra gaps= 0 total=1641 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 1np3A/T0384-1np3A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0384 read from 1np3A/T0384-1np3A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1np3A read from 1np3A/T0384-1np3A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1np3A in template set T0384 3 :KLGVIGTGAISHHFIEAAHTS 1np3A 18 :KVAIIGYGSQGHAHACNLKDS T0384 25 :EYQLVAIYSRKLETAATF 1np3A 39 :GVDVTVGLRSGSATVAKA T0384 44 :SRYQ 1np3A 57 :EAHG T0384 49 :IQL 1np3A 61 :LKV T0384 53 :DQL 1np3A 64 :ADV T0384 56 :EVF 1np3A 68 :TAV T0384 61 :SSFDLVYIASPNSLHFAQAK 1np3A 71 :AAADVVMILTPDEFQGRLYK T0384 85 :AGKHVILE 1np3A 99 :KGATLAFA T0384 112 :NNCFIFEAARNYHEK 1np3A 120 :ADLDVIMIAPKAPGH T0384 130 :TIKNFLADKQVLG 1np3A 135 :TVRSEFVKGGGIP T0384 147 :YAKYSSKMPDLLA 1np3A 149 :LIAIYQDASGNAK T0384 181 :YPLYAAVRLFG 1np3A 163 :VALSYACGVGG T0384 192 :K 1np3A 177 :G T0384 268 :LPIQQAPH 1np3A 178 :IIETTFKD T0384 276 :TMTEEVAAFAHMIQQPDLNLY 1np3A 202 :CVELVKAGFETLVEAGYAPEM T0384 299 :WL 1np3A 223 :AY Number of specific fragments extracted= 16 number of extra gaps= 0 total=1657 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 1np3A/T0384-1np3A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0384 read from 1np3A/T0384-1np3A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1np3A read from 1np3A/T0384-1np3A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1np3A in template set T0384 3 :KLGVIGTGAISHHFIEAAHTS 1np3A 18 :KVAIIGYGSQGHAHACNLKDS T0384 25 :EYQLVAIYSRKLETAATF 1np3A 39 :GVDVTVGLRSGSATVAKA T0384 44 :SRYQN 1np3A 57 :EAHGL T0384 51 :LFDQLEVFF 1np3A 62 :KVADVKTAV T0384 62 :SFDLVYIASPNSLHFAQAK 1np3A 72 :AADVVMILTPDEFQGRLYK T0384 81 :AALSAGK 1np3A 109 :FSIHYNQ T0384 112 :NNCFIFEAARNYHEK 1np3A 120 :ADLDVIMIAPKAPGH T0384 130 :TIKNFLADKQVLGADFNYAKYSSKMPDL 1np3A 135 :TVRSEFVKGGGIPDLIAIYQDASGNAKN T0384 181 :YPLYAAVRLFGKANDATYHA 1np3A 163 :VALSYACGVGGGRTGIIETT T0384 268 :LPIQQAPHTMTEEVAAFAHMIQQPDL 1np3A 194 :EQAVLCGGCVELVKAGFETLVEAGYA Number of specific fragments extracted= 10 number of extra gaps= 0 total=1667 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 1y81A/T0384-1y81A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1y81A expands to /projects/compbio/data/pdb/1y81.pdb.gz 1y81A:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0384 read from 1y81A/T0384-1y81A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1y81A read from 1y81A/T0384-1y81A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1y81A to template set # found chain 1y81A in template set T0384 3 :KLGVIGTG 1y81A 8 :KIALVGAS T0384 11 :AISHHFIEAAHTS 1y81A 20 :KYGNIILKDLLSK T0384 25 :EYQLVAI 1y81A 33 :GFEVLPV T0384 46 :YQNI 1y81A 40 :NPNY T0384 50 :QLFDQLEVF 1y81A 50 :KCYRSVREL T0384 60 :K 1y81A 60 :K T0384 62 :SFDLVYIASPNSLHFAQAKAALSAG 1y81A 61 :DVDVIVFVVPPKVGLQVAKEAVEAG T0384 87 :KHVILE 1y81A 87 :KKLWFQ T0384 95 :AVSQPQEW 1y81A 93 :PGAESEEI T0384 106 :IQTAEKNNCFIF 1y81A 101 :RRFLEKAGVEYS Number of specific fragments extracted= 10 number of extra gaps= 0 total=1677 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 1y81A/T0384-1y81A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0384 read from 1y81A/T0384-1y81A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1y81A read from 1y81A/T0384-1y81A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1y81A in template set T0384 3 :KLGVIGTG 1y81A 8 :KIALVGAS T0384 11 :AISHHFIEAAHTS 1y81A 20 :KYGNIILKDLLSK T0384 25 :EYQLVAI 1y81A 33 :GFEVLPV T0384 33 :SRK 1y81A 40 :NPN T0384 46 :YQ 1y81A 43 :YD T0384 48 :NIQLFDQLEVFF 1y81A 48 :GLKCYRSVRELP T0384 61 :SSFDLVYIASPNSLHFAQAKAALSAG 1y81A 60 :KDVDVIVFVVPPKVGLQVAKEAVEAG T0384 87 :KHVILE 1y81A 87 :KKLWFQ T0384 94 :PAVSQPQ 1y81A 93 :PGAESEE T0384 105 :LIQTAEKNNCFIF 1y81A 100 :IRRFLEKAGVEYS Number of specific fragments extracted= 10 number of extra gaps= 0 total=1687 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 1y81A/T0384-1y81A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0384 read from 1y81A/T0384-1y81A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1y81A read from 1y81A/T0384-1y81A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1y81A in template set T0384 3 :KLGVIGTG 1y81A 8 :KIALVGAS T0384 11 :AISHHFIEAAHT 1y81A 20 :KYGNIILKDLLS T0384 24 :GEYQLVAIY 1y81A 32 :KGFEVLPVN T0384 34 :RK 1y81A 41 :PN T0384 49 :IQLFDQLEVF 1y81A 49 :LKCYRSVREL T0384 60 :KSSFDLVYIASPNSLHFAQAKAALSAGKHVILEKPAVSQPQ 1y81A 59 :PKDVDVIVFVVPPKVGLQVAKEAVEAGFKKLWFQPGAESEE T0384 105 :LIQTAEKNNCFIF 1y81A 100 :IRRFLEKAGVEYS Number of specific fragments extracted= 7 number of extra gaps= 0 total=1694 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 1gpjA/T0384-1gpjA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1gpjA expands to /projects/compbio/data/pdb/1gpj.pdb.gz 1gpjA:Skipped atom 116, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 118, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 120, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 122, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 124, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 126, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 128, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 622, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 624, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 626, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 628, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 630, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 632, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 634, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 636, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 638, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 845, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 847, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 849, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 851, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 853, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 855, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 857, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 859, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 861, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 986, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 988, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 990, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 992, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 994, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 996, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 998, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 1000, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 1002, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 1065, because occupancy 0.300 <= existing 0.700 in 1gpjA Skipped atom 1067, because occupancy 0.300 <= existing 0.700 in 1gpjA Skipped atom 1069, because occupancy 0.300 <= existing 0.700 in 1gpjA Skipped atom 1071, because occupancy 0.300 <= existing 0.700 in 1gpjA Skipped atom 1073, because occupancy 0.300 <= existing 0.700 in 1gpjA Skipped atom 1075, because occupancy 0.300 <= existing 0.700 in 1gpjA Skipped atom 1077, because occupancy 0.300 <= existing 0.700 in 1gpjA Skipped atom 1079, because occupancy 0.300 <= existing 0.700 in 1gpjA Skipped atom 1485, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 1487, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 1489, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 1491, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 1493, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 1495, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 1497, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 1499, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 1501, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 1503, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 1505, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 1763, because occupancy 0.200 <= existing 0.800 in 1gpjA Skipped atom 1765, because occupancy 0.200 <= existing 0.800 in 1gpjA Skipped atom 1767, because occupancy 0.200 <= existing 0.800 in 1gpjA Skipped atom 1769, because occupancy 0.200 <= existing 0.800 in 1gpjA Skipped atom 1771, because occupancy 0.200 <= existing 0.800 in 1gpjA Skipped atom 1773, because occupancy 0.200 <= existing 0.800 in 1gpjA Skipped atom 1775, because occupancy 0.200 <= existing 0.800 in 1gpjA Skipped atom 1777, because occupancy 0.200 <= existing 0.800 in 1gpjA Skipped atom 1999, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 2001, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 2003, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 2005, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 2007, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 2009, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 2011, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 2013, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 2015, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 2036, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 2038, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 2040, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 2042, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 2044, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 2046, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 2048, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 2050, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 2052, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 2054, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 2056, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 2230, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 2232, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 2234, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 2236, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 2238, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 2240, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 2242, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 2244, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 2246, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 2585, because occupancy 0.300 <= existing 0.700 in 1gpjA Skipped atom 2587, because occupancy 0.300 <= existing 0.700 in 1gpjA Skipped atom 2589, because occupancy 0.300 <= existing 0.700 in 1gpjA Skipped atom 2591, because occupancy 0.300 <= existing 0.700 in 1gpjA Skipped atom 2593, because occupancy 0.300 <= existing 0.700 in 1gpjA Skipped atom 2595, because occupancy 0.300 <= existing 0.700 in 1gpjA Skipped atom 2597, because occupancy 0.300 <= existing 0.700 in 1gpjA Skipped atom 2599, because occupancy 0.300 <= existing 0.700 in 1gpjA Skipped atom 2601, because occupancy 0.300 <= existing 0.700 in 1gpjA Skipped atom 2675, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 2677, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 2679, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 2681, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 2683, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 2685, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 2687, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 2689, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 2691, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 2693, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 2695, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 2770, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 2772, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 2774, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 2776, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 2778, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 2780, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 2782, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 2784, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 2786, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 2824, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 2826, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 2828, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 2830, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 2832, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 2834, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 2836, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 2838, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 2840, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 3007, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 3009, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 3011, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 3013, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 3015, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 3017, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 3019, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 3021, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 3023, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 3118, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 3120, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 3122, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 3124, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 3126, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 3128, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 3130, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 3132, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 3202, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 3204, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 3206, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 3208, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 3210, because occupancy 0.500 <= existing 0.500 in 1gpjA Skipped atom 3212, because occupancy 0.500 <= existing 0.500 in 1gpjA # T0384 read from 1gpjA/T0384-1gpjA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1gpjA read from 1gpjA/T0384-1gpjA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1gpjA to template set # found chain 1gpjA in template set Warning: unaligning (T0384)M154 because of BadResidue code BAD_PEPTIDE at template residue (1gpjA)K354 Warning: unaligning (T0384)P155 because of BadResidue code BAD_PEPTIDE at template residue (1gpjA)T355 Warning: unaligning (T0384)Q161 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1gpjA)V361 Warning: unaligning (T0384)P269 because of BadResidue code BAD_PEPTIDE at template residue (1gpjA)L362 Warning: unaligning (T0384)I270 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1gpjA)Q363 Warning: unaligning (T0384)Q271 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1gpjA)D364 Warning: unaligning (T0384)Q289 because of BadResidue code BAD_PEPTIDE in next template residue (1gpjA)E383 Warning: unaligning (T0384)Q290 because of BadResidue code BAD_PEPTIDE at template residue (1gpjA)E383 Warning: unaligning (T0384)P291 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1gpjA)L384 Warning: unaligning (T0384)D292 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1gpjA)P385 Warning: unaligning (T0384)L293 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1gpjA)D386 Warning: unaligning (T0384)N294 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1gpjA)E387 Warning: unaligning (T0384)F321 because last residue in template chain is (1gpjA)G404 T0384 2 :LKLGVIGTGAISHHFIEAAHTS 1gpjA 168 :KTVLVVGAGEMGKTVAKSLVDR T0384 25 :EY 1gpjA 190 :GV T0384 27 :QLV 1gpjA 193 :AVL T0384 31 :IYSRKLETAATFASRYQNI 1gpjA 196 :VANRTYERAVELARDLGGE T0384 50 :QLFDQLEVFFK 1gpjA 216 :VRFDELVDHLA T0384 62 :SFDLVYIASP 1gpjA 227 :RSDVVVSATA T0384 72 :NSLHFAQAKAALSA 1gpjA 240 :PVIHVDDVREALRK T0384 87 :KHVI 1gpjA 258 :SPIL T0384 91 :LE 1gpjA 263 :ID T0384 123 :YHEKAFTTIKNFL 1gpjA 310 :LIEEELSTVEEEL T0384 272 :QAPHTMTEEVAAFAHMI 1gpjA 365 :FAEAYTKRLINVLTSAI T0384 295 :LYQ 1gpjA 388 :YRR T0384 308 :ELLYTMRQTAGIR 1gpjA 391 :AASRALRRASELN Number of specific fragments extracted= 13 number of extra gaps= 2 total=1707 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 1gpjA/T0384-1gpjA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0384 read from 1gpjA/T0384-1gpjA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1gpjA read from 1gpjA/T0384-1gpjA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1gpjA in template set T0384 2 :LKLGVIGTGAISHHFIEAAHTS 1gpjA 168 :KTVLVVGAGEMGKTVAKSLVDR T0384 25 :EYQLVAIYSRKLETAATFASRYQ 1gpjA 190 :GVRAVLVANRTYERAVELARDLG T0384 48 :NIQLFDQL 1gpjA 214 :EAVRFDEL T0384 56 :EVFF 1gpjA 223 :DHLA T0384 62 :SFDLVYIASP 1gpjA 227 :RSDVVVSATA T0384 72 :NSLHFAQAKAALSA 1gpjA 240 :PVIHVDDVREALRK T0384 86 :GKHVI 1gpjA 257 :RSPIL T0384 91 :LE 1gpjA 263 :ID T0384 99 :PQEWFDLIQTAEK 1gpjA 286 :IDDLRVIARENLE T0384 112 :N 1gpjA 303 :E T0384 122 :NYHEKAFTTIKNFLAD 1gpjA 309 :KLIEEELSTVEEELEK Number of specific fragments extracted= 11 number of extra gaps= 0 total=1718 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 1gpjA/T0384-1gpjA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0384 read from 1gpjA/T0384-1gpjA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1gpjA read from 1gpjA/T0384-1gpjA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1gpjA in template set T0384 2 :LKLGVIGTGAISHHFIEAAHTS 1gpjA 168 :KTVLVVGAGEMGKTVAKSLVDR T0384 25 :EYQLVAIYSRKLETAATFASRYQN 1gpjA 190 :GVRAVLVANRTYERAVELARDLGG T0384 50 :QLFD 1gpjA 214 :EAVR T0384 55 :LEVFF 1gpjA 218 :FDELV T0384 62 :SFDLVYIASP 1gpjA 227 :RSDVVVSATA T0384 72 :NSLHFAQAKAALSA 1gpjA 240 :PVIHVDDVREALRK T0384 86 :GKHVIL 1gpjA 257 :RSPILI T0384 96 :VSQPQEWFDLIQTAEK 1gpjA 283 :VRTIDDLRVIARENLE T0384 121 :RNYHEKAFTTIKNFLAD 1gpjA 308 :EKLIEEELSTVEEELEK Number of specific fragments extracted= 9 number of extra gaps= 0 total=1727 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 1vm6A/T0384-1vm6A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1vm6A expands to /projects/compbio/data/pdb/1vm6.pdb.gz 1vm6A:# T0384 read from 1vm6A/T0384-1vm6A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1vm6A read from 1vm6A/T0384-1vm6A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1vm6A to template set # found chain 1vm6A in template set Warning: unaligning (T0384)G304 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1vm6A)F213 T0384 2 :LKLGVIGT 1vm6A 1 :MKYGIVGY T0384 10 :GAISHHFIEAAHTS 1vm6A 10 :GRMGQEIQKVFSEK T0384 25 :EYQLVAIYSR 1vm6A 24 :GHELVLKVDV T0384 47 :QNIQLFD 1vm6A 34 :NGVEELD T0384 62 :SFDLVYIASPNSLHFAQAKAALSAGKHVILEK 1vm6A 41 :SPDVVIDFSSPEALPKTVDLCKKYRAGLVLGT T0384 95 :AVSQPQEWFDLIQTA 1vm6A 73 :TALKEEHLQMLRELS T0384 112 :NNCFIFEA 1vm6A 88 :KEVPVVQA T0384 120 :ARNYHEKAFTTIKNFLADKQVLGADFNYAKYSSKMPDL 1vm6A 98 :FSIGINVLKRFLSELVKVLEDWDVEIVETHHRFKKDAP T0384 180 :IYPLYAAVRLFG 1vm6A 136 :SGTAILLESALG T0384 192 :KAND 1vm6A 149 :SVPI T0384 200 :AQQLDNSIDLNGDGILFYPDYQVHIKAGKNIT 1vm6A 153 :HSLRVGGVPGDHVVVFGNIGETIEIKHRAISR T0384 275 :HTMTEEVAAFAHMIQQPD 1vm6A 185 :TVFAIGALKAAEFLVGKD T0384 295 :LYQTWLYDA 1vm6A 203 :PGMYSFEEV Number of specific fragments extracted= 13 number of extra gaps= 1 total=1740 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 1vm6A/T0384-1vm6A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0384 read from 1vm6A/T0384-1vm6A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1vm6A read from 1vm6A/T0384-1vm6A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1vm6A in template set Warning: unaligning (T0384)G304 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1vm6A)F213 T0384 2 :LKLGVIGT 1vm6A 1 :MKYGIVGY T0384 10 :GAISHHFIEAAHTS 1vm6A 10 :GRMGQEIQKVFSEK T0384 25 :EYQLVAIYSRK 1vm6A 24 :GHELVLKVDVN T0384 48 :NIQ 1vm6A 35 :GVE T0384 59 :FKSSFDLVYIASPNSLHFAQAKAALSAGKHVILEK 1vm6A 38 :ELDSPDVVIDFSSPEALPKTVDLCKKYRAGLVLGT T0384 95 :AVSQPQEWFDLIQ 1vm6A 73 :TALKEEHLQMLRE T0384 109 :AEK 1vm6A 86 :LSK T0384 113 :NCFIFEAAR 1vm6A 89 :EVPVVQAYN T0384 122 :NYHEKAFTTIKNFLA 1vm6A 100 :IGINVLKRFLSELVK T0384 137 :DKQ 1vm6A 117 :EDW T0384 144 :DFNYAKYSSKMPD 1vm6A 120 :DVEIVETHHRFKK T0384 177 :DLGIYPLYAAVRLFG 1vm6A 133 :DAPSGTAILLESALG T0384 192 :KANDA 1vm6A 149 :SVPIH T0384 201 :QQLDNSIDLNGDGILFYPDYQVHIKAGK 1vm6A 154 :SLRVGGVPGDHVVVFGNIGETIEIKHRA T0384 272 :QAPHTMTEEVAAFAHMIQQPDLNLY 1vm6A 182 :ISRTVFAIGALKAAEFLVGKDPGMY T0384 299 :WLYDA 1vm6A 207 :SFEEV Number of specific fragments extracted= 16 number of extra gaps= 1 total=1756 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 1vm6A/T0384-1vm6A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0384 read from 1vm6A/T0384-1vm6A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1vm6A read from 1vm6A/T0384-1vm6A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1vm6A in template set Warning: unaligning (T0384)D302 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1vm6A)F213 T0384 2 :LKLGVIGT 1vm6A 1 :MKYGIVGY T0384 10 :GAISHHFIEAAHT 1vm6A 10 :GRMGQEIQKVFSE T0384 24 :GEYQLVAIYSRK 1vm6A 23 :KGHELVLKVDVN T0384 60 :KSSFDLVYIASPNSLHFAQAKAALSAGKHVILEK 1vm6A 39 :LDSPDVVIDFSSPEALPKTVDLCKKYRAGLVLGT T0384 95 :AVSQPQEWFDLIQT 1vm6A 73 :TALKEEHLQMLREL T0384 112 :NNCFIFEAARNYH 1vm6A 88 :KEVPVVQAYNFSI T0384 125 :EKAFTTIKNFLADKQVLGADFNYAKYSSKMPDL 1vm6A 103 :NVLKRFLSELVKVLEDWDVEIVETHHRFKKDAP T0384 180 :IYPLYAAVRLFGKANDATYHA 1vm6A 136 :SGTAILLESALGKSVPIHSLR T0384 204 :DNSIDLNGDGILFYPDYQVHIKAGKN 1vm6A 157 :VGGVPGDHVVVFGNIGETIEIKHRAI T0384 273 :APHTMTEEVAAFAHMIQQPDLNLYQTWLY 1vm6A 183 :SRTVFAIGALKAAEFLVGKDPGMYSFEEV Number of specific fragments extracted= 10 number of extra gaps= 1 total=1766 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 1obbA/T0384-1obbA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1obbA expands to /projects/compbio/data/pdb/1obb.pdb.gz 1obbA:Skipped atom 3514, because occupancy 0.500 <= existing 0.500 in 1obbA Skipped atom 3516, because occupancy 0.500 <= existing 0.500 in 1obbA Skipped atom 3518, because occupancy 0.500 <= existing 0.500 in 1obbA Skipped atom 3520, because occupancy 0.500 <= existing 0.500 in 1obbA Skipped atom 3522, because occupancy 0.500 <= existing 0.500 in 1obbA Skipped atom 3524, because occupancy 0.500 <= existing 0.500 in 1obbA Skipped atom 3526, because occupancy 0.500 <= existing 0.500 in 1obbA Skipped atom 3528, because occupancy 0.500 <= existing 0.500 in 1obbA Skipped atom 3530, because occupancy 0.500 <= existing 0.500 in 1obbA Skipped atom 3532, because occupancy 0.500 <= existing 0.500 in 1obbA Skipped atom 3534, because occupancy 0.500 <= existing 0.500 in 1obbA # T0384 read from 1obbA/T0384-1obbA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1obbA read from 1obbA/T0384-1obbA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1obbA to template set # found chain 1obbA in template set Warning: unaligning (T0384)A119 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1obbA)H175 Warning: unaligning (T0384)Y123 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1obbA)H175 T0384 1 :M 1obbA 2 :P T0384 2 :LKLGVIGTG 1obbA 4 :VKIGIIGAG T0384 11 :AISHHFIEAAHTSG 1obbA 15 :VFSLRLVSDLCKTP T0384 25 :EYQLV 1obbA 32 :GSTVT T0384 31 :IYSRKLET 1obbA 37 :LMDIDEER T0384 39 :AATFASRYQNI 1obbA 52 :AKKYVEEVGAD T0384 50 :QLFDQLEVFFK 1obbA 66 :EKTMNLDDVII T0384 62 :SFDLVYIASPNSLH 1obbA 77 :DADFVINTAMVGGH T0384 76 :FAQAKAALSA 1obbA 133 :VDIARKIEKL T0384 86 :GKHVIL 1obbA 145 :KAWYLQ T0384 95 :AVSQPQEWFDLI 1obbA 151 :AANPIFEGTTLV T0384 109 :AEKNNCFIFE 1obbA 163 :TRTVPIKAVG T0384 124 :HEKAFTTIKNFL 1obbA 176 :GHYGVMEIVEKL T0384 136 :ADKQVL 1obbA 189 :LEEEKV T0384 142 :GADFNYAKYSSK 1obbA 204 :GIWLNRFRYNGG T0384 154 :MPDLLAG 1obbA 347 :DPERKSG T0384 180 :IYPLYAAVRLFGKANDATYHAQQLDN 1obbA 354 :EQHIPFIDALLNDNKARFVVNIPNKG T0384 206 :SIDLNGDGILFY 1obbA 383 :GIDDDVVVEVPA T0384 257 :IFTDHQGNQVQLPIQQAP 1obbA 395 :LVDKNGIHPEKIEPPLPD T0384 275 :HTMTEEVAAFAHMIQQPD 1obbA 420 :RPRIMRMEMALEAFLTGD T0384 300 :LYDAGSVHE 1obbA 438 :IRIIKELLY T0384 309 :LLYTMRQTA 1obbA 456 :QVEKVIEEI Number of specific fragments extracted= 22 number of extra gaps= 0 total=1788 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 1obbA/T0384-1obbA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0384 read from 1obbA/T0384-1obbA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1obbA read from 1obbA/T0384-1obbA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1obbA in template set Warning: unaligning (T0384)Y150 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1obbA)H175 Warning: unaligning (T0384)S152 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1obbA)H175 T0384 2 :LKLGVIGTGAISH 1obbA 4 :VKIGIIGAGSAVF T0384 15 :HFIEAAHTSG 1obbA 19 :RLVSDLCKTP T0384 25 :EYQLV 1obbA 32 :GSTVT T0384 31 :IYSRKLET 1obbA 37 :LMDIDEER T0384 39 :AATFASRYQ 1obbA 52 :AKKYVEEVG T0384 48 :NIQLFDQL 1obbA 64 :KFEKTMNL T0384 56 :EVF 1obbA 73 :DVI T0384 61 :SSFDLVYIASPN 1obbA 76 :IDADFVINTAMV T0384 73 :SLHFAQAKAALSAGK 1obbA 91 :TYLEKVRQIGEKYGY T0384 93 :KPAVSQPQE 1obbA 120 :YYTFSNYNQ T0384 102 :WFDLIQTAEK 1obbA 132 :FVDIARKIEK T0384 112 :NNCFIFEAARNYHEKAFTTIKN 1obbA 144 :PKAWYLQAANPIFEGTTLVTRT T0384 141 :L 1obbA 166 :V T0384 144 :DFNYAK 1obbA 167 :PIKAVG T0384 179 :GIYPLYAAVRLFG 1obbA 176 :GHYGVMEIVEKLG T0384 192 :KANDATYHAQQL 1obbA 190 :EEEKVDWQVAGV T0384 206 :SIDLNGDGILFYPDY 1obbA 366 :DNKARFVVNIPNKGI T0384 228 :KNITSNLPCEIY 1obbA 382 :HGIDDDVVVEVP T0384 245 :LTLNT 1obbA 394 :ALVDK T0384 261 :HQGNQVQLPIQQAPH 1obbA 399 :NGIHPEKIEPPLPDR T0384 276 :TMTEEVAAFAHMIQQP 1obbA 421 :PRIMRMEMALEAFLTG T0384 299 :WLYDAGSVH 1obbA 437 :DIRIIKELL T0384 308 :ELLYTMR 1obbA 459 :KVIEEIL Number of specific fragments extracted= 23 number of extra gaps= 0 total=1811 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 1obbA/T0384-1obbA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0384 read from 1obbA/T0384-1obbA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1obbA read from 1obbA/T0384-1obbA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1obbA in template set Warning: unaligning (T0384)H199 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1obbA)H175 Warning: unaligning (T0384)Q201 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1obbA)H175 T0384 2 :LKLGVIGTGAISH 1obbA 4 :VKIGIIGAGSAVF T0384 15 :HFIEAAHTSGE 1obbA 19 :RLVSDLCKTPG T0384 26 :YQLV 1obbA 33 :STVT T0384 31 :IYSRKLETAATFA 1obbA 37 :LMDIDEERLDAIL T0384 44 :SRYQN 1obbA 57 :EEVGA T0384 49 :IQLFDQLEVFF 1obbA 65 :FEKTMNLDDVI T0384 62 :SFDLVYIASPNSL 1obbA 77 :DADFVINTAMVGG T0384 99 :PQEWFDLIQTAEKNNCFIFEAARNYH 1obbA 90 :HTYLEKVRQIGEKYGYYRGIDAQEFN T0384 126 :KAFTTIKNFLAD 1obbA 130 :KYFVDIARKIEK T0384 168 :DRFAGGALMDLGIYPLYAAVRLFGKANDATY 1obbA 142 :LSPKAWYLQAANPIFEGTTLVTRTVPIKAVG T0384 202 :QL 1obbA 176 :GH T0384 204 :DNSIDLNGDGIL 1obbA 190 :EEEKVDWQVAGV T0384 234 :LPCEIYTTDGT 1obbA 206 :WLNRFRYNGGN T0384 263 :GNQVQLPIQQAPHTMTEEVAAFAHMIQQP 1obbA 408 :PPLPDRVVKYYLRPRIMRMEMALEAFLTG Number of specific fragments extracted= 14 number of extra gaps= 0 total=1825 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 1jvsA/T0384-1jvsA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1jvsA expands to /projects/compbio/data/pdb/1jvs.pdb.gz 1jvsA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0384 read from 1jvsA/T0384-1jvsA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1jvsA read from 1jvsA/T0384-1jvsA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1jvsA to template set # found chain 1jvsA in template set T0384 2 :LKLGVIG 1jvsA 1 :KQLTILG T0384 9 :TGAISHHFIEAAHTS 1jvsA 9 :TGSIGCSTLDVVRHN T0384 24 :GEYQLVAIYSR 1jvsA 25 :EHFRVVALVAG T0384 35 :KLETAATFASRYQNI 1jvsA 37 :NVTRMVEQCLEFSPR T0384 50 :QLFDQLEVFFK 1jvsA 76 :EVLSGQQAACD T0384 61 :SSFDLVYIASPNSLHFAQAKAALSAGKHVILE 1jvsA 91 :EDVDQVMAAIVGAAGLLPTLAAIRAGKTILLA T0384 96 :V 1jvsA 123 :N T0384 99 :PQEWFDLIQTAEKNNCFIFEA 1jvsA 128 :VTCGRLFMDAVKQSKAQLLPV T0384 125 :EKAFTTIKNF 1jvsA 149 :DSEHNAIFQS T0384 135 :L 1jvsA 163 :I T0384 138 :KQVL 1jvsA 164 :QHNL T0384 142 :GADFNYAKYSSK 1jvsA 176 :GVVSILLTGSGG T0384 154 :MPDLLAGQTPNVFSDRF 1jvsA 201 :TPDQACRHPNWSMGRKI T0384 171 :AGGALMDLGIYPLY 1jvsA 220 :DSATMMNKGLEYIE T0384 186 :AVRLFG 1jvsA 234 :ARWLFN T0384 192 :KANDATYHAQQL 1jvsA 241 :SASQMEVLIHPQ T0384 209 :LNGDGILFYPDYQVHIKAGKN 1jvsA 253 :SVIHSMVRYQDGSVLAQLGEP T0384 273 :AP 1jvsA 274 :DM T0384 275 :HTMTEEVAAFAHMIQQPDL 1jvsA 332 :TALNAANEITVAAFLAQQI Number of specific fragments extracted= 19 number of extra gaps= 0 total=1844 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 1jvsA/T0384-1jvsA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0384 read from 1jvsA/T0384-1jvsA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1jvsA read from 1jvsA/T0384-1jvsA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1jvsA in template set T0384 2 :LKLGVIG 1jvsA 1 :KQLTILG T0384 9 :TGAISHHFIEAAHTSGE 1jvsA 9 :TGSIGCSTLDVVRHNPE T0384 26 :YQLVAIYSR 1jvsA 27 :FRVVALVAG T0384 36 :LETAATFASRYQ 1jvsA 38 :VTRMVEQCLEFS T0384 48 :NIQLFDQ 1jvsA 74 :RTEVLSG T0384 55 :L 1jvsA 84 :A T0384 56 :EVFFKSSFDLVYIASPNSLHFAQAKAALSAGKHVIL 1jvsA 86 :DMAALEDVDQVMAAIVGAAGLLPTLAAIRAGKTILL T0384 101 :EWFDLIQTAEKNNCFIFEAA 1jvsA 130 :CGRLFMDAVKQSKAQLLPVD T0384 126 :KAFTTIK 1jvsA 150 :SEHNAIF T0384 133 :NFLAD 1jvsA 162 :PIQHN T0384 141 :LG 1jvsA 167 :LG T0384 143 :ADFNYAKYSSKMPDLLAGQT 1jvsA 175 :NGVVSILLTGSGGPFRETPL T0384 163 :PNVFSDRF 1jvsA 210 :NWSMGRKI T0384 171 :AGGALMDLGIYPL 1jvsA 220 :DSATMMNKGLEYI T0384 185 :AAVRLFG 1jvsA 233 :EARWLFN T0384 192 :KANDATYHAQQ 1jvsA 241 :SASQMEVLIHP T0384 208 :DLNGDGILFYPDYQVHIKAG 1jvsA 252 :QSVIHSMVRYQDGSVLAQLG T0384 248 :NTI 1jvsA 272 :EPD T0384 251 :EHIRSAIFTDHQGNQVQLPIQQAPHTMTEEVAAFAHMIQQ 1jvsA 287 :NRVNSGVKPLDFCKLSALTFAAPDYDRYPCLKLAMEAFEQ T0384 299 :WLYDAGSVHELLYTMRQTAGIRF 1jvsA 327 :GQAATTALNAANEITVAAFLAQQ Number of specific fragments extracted= 20 number of extra gaps= 0 total=1864 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 1jvsA/T0384-1jvsA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0384 read from 1jvsA/T0384-1jvsA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1jvsA read from 1jvsA/T0384-1jvsA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1jvsA in template set T0384 2 :LKLGVIGT 1jvsA 1 :KQLTILGS T0384 10 :GAISHHFIEAAHTSGE 1jvsA 10 :GSIGCSTLDVVRHNPE T0384 26 :YQLVAIYS 1jvsA 27 :FRVVALVA T0384 35 :KLETAATFASRY 1jvsA 57 :DEASAKLLKTML T0384 47 :Q 1jvsA 72 :G T0384 49 :IQLFDQLEVFF 1jvsA 75 :TEVLSGQQAAC T0384 60 :KSSFDLVYIASPNSLHFAQAKAALSAGKHVIL 1jvsA 90 :LEDVDQVMAAIVGAAGLLPTLAAIRAGKTILL T0384 102 :WFDLIQTAEKNNCFIFEAAR 1jvsA 131 :GRLFMDAVKQSKAQLLPVDS T0384 127 :AFTTIK 1jvsA 151 :EHNAIF T0384 133 :NFLAD 1jvsA 162 :PIQHN T0384 140 :VL 1jvsA 167 :LG T0384 142 :GADFNYAKYSSKMPDLLAGQTP 1jvsA 176 :GVVSILLTGSGGPFRETPLRDL T0384 164 :NVFSDRFAGGALMDLGIYPLY 1jvsA 213 :MGRKISVDSATMMNKGLEYIE T0384 186 :AVRLFGKANDATYHAQQL 1jvsA 234 :ARWLFNASASQMEVLIHP T0384 208 :DLNGDGILFYPDYQVHIKAGKNIT 1jvsA 252 :QSVIHSMVRYQDGSVLAQLGEPDM T0384 250 :IEHIRSAIFTDH 1jvsA 286 :PNRVNSGVKPLD T0384 263 :GNQVQLPIQQAPHTMTEEVAAFAHMIQQP 1jvsA 299 :CKLSALTFAAPDYDRYPCLKLAMEAFEQG T0384 301 :YDAGSVHELLYTMRQT 1jvsA 328 :QAATTALNAANEITVA Number of specific fragments extracted= 18 number of extra gaps= 0 total=1882 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 2gd1O/T0384-2gd1O-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2gd1O expands to /projects/compbio/data/pdb/2gd1.pdb.gz 2gd1O:# T0384 read from 2gd1O/T0384-2gd1O-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2gd1O read from 2gd1O/T0384-2gd1O-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2gd1O to template set # found chain 2gd1O in template set Warning: unaligning (T0384)K3 because of BadResidue code BAD_PEPTIDE in next template residue (2gd1O)V3 Warning: unaligning (T0384)L4 because of BadResidue code BAD_PEPTIDE at template residue (2gd1O)V3 Warning: unaligning (T0384)I116 because of BadResidue code BAD_PEPTIDE in next template residue (2gd1O)I144 Warning: unaligning (T0384)F117 because of BadResidue code BAD_PEPTIDE at template residue (2gd1O)I144 Warning: unaligning (T0384)M277 because of BadResidue code BAD_PEPTIDE in next template residue (2gd1O)E253 Warning: unaligning (T0384)T278 because of BadResidue code BAD_PEPTIDE at template residue (2gd1O)E253 T0384 2 :L 2gd1O 1 :V T0384 5 :GVIGTGAISHHFIEAAHTSGEYQLVAIYS 2gd1O 4 :GINGFGRIGRNVFRAALKNPDIEVVAVND T0384 34 :RKLE 2gd1O 34 :TDAN T0384 41 :TFASRYQNI 2gd1O 39 :TLAHLLKYD T0384 50 :QLFDQLEVF 2gd1O 74 :KAERDPENL T0384 59 :FKS 2gd1O 84 :WGE T0384 62 :SFDLVYIASPNSLHFAQAKAALSAG 2gd1O 88 :GVDIVVESTGRFTKREDAAKHLEAG T0384 87 :KHVILEKPAV 2gd1O 114 :KKVIISAPAK T0384 97 :SQP 2gd1O 137 :YDP T0384 112 :NNCF 2gd1O 139 :KAHH T0384 118 :EAARN 2gd1O 145 :SNASC T0384 123 :YHEKAFTTIKNFL 2gd1O 153 :CLAPFAKVLHEQF T0384 142 :GADFNYAKYSSK 2gd1O 166 :GIVRGMMTTVHS T0384 154 :MPDLLAG 2gd1O 218 :LPELKGK T0384 196 :ATYHAQQLDNSIDLNGDGILFYPDY 2gd1O 225 :LNGMAMRVPTPNVSVVDLVAELEKE T0384 275 :HT 2gd1O 250 :VT T0384 279 :EEVAAFAHMIQQPDLN 2gd1O 254 :EVNAALKAAAEGELKG Number of specific fragments extracted= 17 number of extra gaps= 3 total=1899 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 2gd1O/T0384-2gd1O-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0384 read from 2gd1O/T0384-2gd1O-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2gd1O read from 2gd1O/T0384-2gd1O-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2gd1O in template set Warning: unaligning (T0384)K3 because of BadResidue code BAD_PEPTIDE in next template residue (2gd1O)V3 Warning: unaligning (T0384)L4 because of BadResidue code BAD_PEPTIDE at template residue (2gd1O)V3 Warning: unaligning (T0384)I116 because of BadResidue code BAD_PEPTIDE in next template residue (2gd1O)I144 Warning: unaligning (T0384)F117 because of BadResidue code BAD_PEPTIDE at template residue (2gd1O)I144 Warning: unaligning (T0384)M277 because of BadResidue code BAD_PEPTIDE in next template residue (2gd1O)E253 Warning: unaligning (T0384)T278 because of BadResidue code BAD_PEPTIDE at template residue (2gd1O)E253 T0384 2 :L 2gd1O 1 :V T0384 5 :GVIGTGAISHHFIEAAHTSGEYQLVAIYS 2gd1O 4 :GINGFGRIGRNVFRAALKNPDIEVVAVND T0384 34 :RKLE 2gd1O 34 :TDAN T0384 41 :TFASRYQ 2gd1O 39 :TLAHLLK T0384 48 :NIQLFDQLEVF 2gd1O 72 :IVKAERDPENL T0384 59 :FKSSFDLVYIASPNSLHFAQAKAALSAG 2gd1O 85 :GEIGVDIVVESTGRFTKREDAAKHLEAG T0384 87 :KHVILEKP 2gd1O 114 :KKVIISAP T0384 95 :AVSQPQ 2gd1O 130 :MGVNQD T0384 111 :KNNCF 2gd1O 138A:PKAHH T0384 118 :EAARNY 2gd1O 145 :SNASCT T0384 124 :HEKAFTTIKNFL 2gd1O 154 :LAPFAKVLHEQF T0384 144 :DFNYAKYS 2gd1O 166 :GIVRGMMT T0384 153 :KMPDLLAGQTPNVFSDRFAGGALMD 2gd1O 181 :DQRILDLPHKDLRRARAAAESIIPT T0384 179 :GIYPLYAAVRLFGKAN 2gd1O 207 :TTGAAKAVALVLPELK T0384 195 :DATYHAQQLDNSIDLNGDGILFYPDY 2gd1O 224 :KLNGMAMRVPTPNVSVVDLVAELEKE T0384 276 :T 2gd1O 251 :T T0384 279 :EEVAAFAHMIQQ 2gd1O 254 :EVNAALKAAAEG T0384 299 :WLYDAGSVHELLYTMRQ 2gd1O 314 :ETGYSHRVVDLAAYIAS Number of specific fragments extracted= 18 number of extra gaps= 3 total=1917 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 2gd1O/T0384-2gd1O-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0384 read from 2gd1O/T0384-2gd1O-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2gd1O read from 2gd1O/T0384-2gd1O-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2gd1O in template set Warning: unaligning (T0384)K3 because of BadResidue code BAD_PEPTIDE in next template residue (2gd1O)V3 Warning: unaligning (T0384)L4 because of BadResidue code BAD_PEPTIDE at template residue (2gd1O)V3 Warning: unaligning (T0384)I116 because of BadResidue code BAD_PEPTIDE in next template residue (2gd1O)I144 Warning: unaligning (T0384)F117 because of BadResidue code BAD_PEPTIDE at template residue (2gd1O)I144 Warning: unaligning (T0384)M277 because of BadResidue code BAD_PEPTIDE in next template residue (2gd1O)E253 Warning: unaligning (T0384)T278 because of BadResidue code BAD_PEPTIDE at template residue (2gd1O)E253 T0384 2 :L 2gd1O 1 :V T0384 5 :GVIGTGAISHHFIEAAHTSGEYQLVAIYS 2gd1O 4 :GINGFGRIGRNVFRAALKNPDIEVVAVND T0384 34 :RKLE 2gd1O 34 :TDAN T0384 41 :TFASRY 2gd1O 39 :TLAHLL T0384 49 :IQLFDQLEVFF 2gd1O 73 :VKAERDPENLA T0384 60 :KSSFDLVYIASPNSLHFAQAKAALSAGK 2gd1O 86 :EIGVDIVVESTGRFTKREDAAKHLEAGA T0384 88 :HVILEKPAVS 2gd1O 115 :KVIISAPAKN T0384 111 :KNNCF 2gd1O 138A:PKAHH T0384 118 :EAARNYH 2gd1O 145 :SNASCTT T0384 125 :EKAFTTIKNFL 2gd1O 155 :APFAKVLHEQF T0384 142 :GADFNYAKYSSKMPDLLAGQTP 2gd1O 166 :GIVRGMMTTVHSYTNDQRILDL T0384 164 :NVFSDRFAG 2gd1O 215 :ALVLPELKG T0384 196 :ATYHAQQLDNSIDLNGDGILFYPDYQ 2gd1O 225 :LNGMAMRVPTPNVSVVDLVAELEKEV T0384 276 :T 2gd1O 251 :T T0384 279 :EEVAAFAHMIQQP 2gd1O 254 :EVNAALKAAAEGE Number of specific fragments extracted= 15 number of extra gaps= 3 total=1932 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 1r0kA/T0384-1r0kA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1r0kA expands to /projects/compbio/data/pdb/1r0k.pdb.gz 1r0kA:# T0384 read from 1r0kA/T0384-1r0kA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1r0kA read from 1r0kA/T0384-1r0kA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1r0kA to template set # found chain 1r0kA in template set Warning: unaligning (T0384)G160 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1r0kA)G205 Warning: unaligning (T0384)S167 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1r0kA)G205 T0384 1 :MLKLGVIGT 1r0kA 4 :PRTVTVLGA T0384 10 :GAISHHFIEAAHTS 1r0kA 14 :GSIGHSTLDLIERN T0384 24 :GEYQLVAIYS 1r0kA 29 :DRYQVIALTA T0384 34 :RKLETAATFASRYQNI 1r0kA 40 :RNVKDLADAAKRTNAK T0384 50 :QLFDQLEVFFK 1r0kA 63 :SLYNDLKEALA T0384 61 :S 1r0kA 91 :M T0384 62 :SFDLVYIASPNSLHFAQAKAALSAGKHVILE 1r0kA 93 :GADWTMAAIIGCAGLKATLAAIRKGKTVALA T0384 95 :AV 1r0kA 130 :SA T0384 102 :WFDLIQTAEKNNCFIFEA 1r0kA 132 :GGLMIDAVREHGTTLLPV T0384 125 :EKAFTTIKNFL 1r0kA 150 :DSEHNAIFQCF T0384 137 :DKQVLG 1r0kA 161 :PHHNRD T0384 143 :ADFNYAKYSSK 1r0kA 168 :VRRIIITASGG T0384 154 :MPDLLA 1r0kA 192 :TPERAV T0384 168 :DRF 1r0kA 206 :AKI T0384 171 :AGGALMDLGIYPLY 1r0kA 211 :DSATMMNKGLELIE T0384 186 :AVRLFG 1r0kA 225 :AFHLFQ T0384 192 :KANDATYHAQQLD 1r0kA 232 :PLEKFEILVHPQS T0384 210 :NGDGILFYPDYQVHIKAGKN 1r0kA 245 :VIHSMVEYLDGSILAQIGSP T0384 253 :IRS 1r0kA 265 :DMR T0384 265 :QVQLPIQQAP 1r0kA 279 :RMETPAESLD T0384 275 :HTMTEEVAAFAHMIQQPDLN 1r0kA 323 :AVMNAANEIAVAAFLDKKIG Number of specific fragments extracted= 21 number of extra gaps= 0 total=1953 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 1r0kA/T0384-1r0kA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0384 read from 1r0kA/T0384-1r0kA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1r0kA read from 1r0kA/T0384-1r0kA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1r0kA in template set T0384 1 :MLKLGVIGT 1r0kA 4 :PRTVTVLGA T0384 10 :GAISHHFIEAAHT 1r0kA 14 :GSIGHSTLDLIER T0384 23 :SGEYQLVAIYS 1r0kA 28 :LDRYQVIALTA T0384 34 :RKLETAATFASRYQ 1r0kA 40 :RNVKDLADAAKRTN T0384 48 :NIQLFDQLEVFFK 1r0kA 76 :SVEAAAGADALVE T0384 61 :SSFDLVYIASPNSLHFAQAKAALSAGKHVIL 1r0kA 92 :MGADWTMAAIIGCAGLKATLAAIRKGKTVAL T0384 95 :AV 1r0kA 130 :SA T0384 102 :WFDLIQTAEKNNCFIFEAA 1r0kA 132 :GGLMIDAVREHGTTLLPVD T0384 126 :KAFTTIKNFLADKQ 1r0kA 151 :SEHNAIFQCFPHHN T0384 141 :LG 1r0kA 165 :RD T0384 144 :DFNYAKYSSKMPDLLAGQT 1r0kA 167 :YVRRIIITASGGPFRTTSL T0384 173 :GALMDLGIYPLY 1r0kA 213 :ATMMNKGLELIE T0384 186 :AVRLFG 1r0kA 225 :AFHLFQ T0384 192 :KANDATYHAQQL 1r0kA 232 :PLEKFEILVHPQ T0384 209 :LNGDGILFYPDYQVHIKAGKN 1r0kA 244 :SVIHSMVEYLDGSILAQIGSP T0384 264 :NQVQLPIQQAPH 1r0kA 278 :KRMETPAESLDF T0384 276 :TMTEEVAAFAHMIQ 1r0kA 342 :GFLDIAKIVEKTLD Number of specific fragments extracted= 17 number of extra gaps= 0 total=1970 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 1r0kA/T0384-1r0kA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0384 read from 1r0kA/T0384-1r0kA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1r0kA read from 1r0kA/T0384-1r0kA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1r0kA in template set Warning: unaligning (T0384)V165 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1r0kA)G205 T0384 1 :MLKLGVIGT 1r0kA 4 :PRTVTVLGA T0384 10 :GAISHHFIEAAHTS 1r0kA 14 :GSIGHSTLDLIERN T0384 24 :GEYQLVAIYS 1r0kA 29 :DRYQVIALTA T0384 34 :RKLETAATFASRYQN 1r0kA 40 :RNVKDLADAAKRTNA T0384 49 :IQLFDQLEVFF 1r0kA 77 :VEAAAGADALV T0384 60 :KSSFDLVYIASPNSLHFAQAKAALSAGKHVILEK 1r0kA 91 :MMGADWTMAAIIGCAGLKATLAAIRKGKTVALAN T0384 102 :WFDLIQTAEKNNCFIFEA 1r0kA 132 :GGLMIDAVREHGTTLLPV T0384 125 :EKAFTTIKNFLADKQVLGADFNYAKYSSKMPDLLA 1r0kA 150 :DSEHNAIFQCFPHHNRDYVRRIIITASGGPFRTTS T0384 166 :FSDRFAGGALMDLGIYPLYA 1r0kA 206 :AKISIDSATMMNKGLELIEA T0384 187 :VRLFGKANDATYHAQQL 1r0kA 226 :FHLFQIPLEKFEILVHP T0384 208 :DLNGDGILFYPDYQVHIKAGKNIT 1r0kA 243 :QSVIHSMVEYLDGSILAQIGSPDM T0384 251 :EHIRSAIFT 1r0kA 277 :PKRMETPAE T0384 263 :GNQVQLPIQQAPHT 1r0kA 292 :LRQMDFEAPDYERF T0384 279 :EEVAAFAHMIQQPD 1r0kA 306 :PALTLAMESIKSGG T0384 298 :TWLYDAGSVHELLYTMRQTA 1r0kA 320 :ARPAVMNAANEIAVAAFLDK Number of specific fragments extracted= 15 number of extra gaps= 0 total=1985 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 2b4rO/T0384-2b4rO-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2b4rO expands to /projects/compbio/data/pdb/2b4r.pdb.gz 2b4rO:# T0384 read from 2b4rO/T0384-2b4rO-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2b4rO read from 2b4rO/T0384-2b4rO-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2b4rO to template set # found chain 2b4rO in template set Warning: unaligning (T0384)G173 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2b4rO)I209 Warning: unaligning (T0384)A174 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2b4rO)I209 T0384 2 :LKLGVIGTGAISHHFIEAAHTSGEYQLVAIYSR 2b4rO 4 :TKLGINGFGRIGRLVFRAAFGRKDIEVVAINDP T0384 35 :KLETAATFAS 2b4rO 39 :DLNHLCYLLK T0384 48 :NI 2b4rO 49 :YD T0384 50 :QLFDQLEVF 2b4rO 77 :FAEKDPSQI T0384 59 :FKS 2b4rO 87 :WGK T0384 62 :SFDLVYIASPNSLHFAQAKAALSAG 2b4rO 91 :QVDVVCESTGVFLTKELASSHLKGG T0384 87 :KHVILEKPAV 2b4rO 117 :KKVIMSAPPK T0384 97 :SQ 2b4rO 141 :YD T0384 112 :NNCFIFEAAR 2b4rO 143 :TKQLIVSNAS T0384 123 :YHEKAFTTIKNFL 2b4rO 153 :CTTNCLAPLAKVI T0384 138 :KQVLGADFNYAKYSSK 2b4rO 166 :NDRFGIVEGLMTTVHA T0384 154 :MPDLLAGQTPNVFSDRFAG 2b4rO 189 :VDGPSKGGKDWRAGRCALS T0384 175 :L 2b4rO 210 :I T0384 180 :IYPLYAAVRLFGKAN 2b4rO 214 :TGAAKAVGKVLPELN T0384 195 :DATYHAQQLDNSIDLNGDGILFYPDY 2b4rO 230 :KLTGVAFRVPIGTVSVVDLVCRLQKP T0384 275 :HTMTEEVAAFAHMIQQPDLNLYQT 2b4rO 256 :AKYEEVALEIKKAAEGPLKGILGY Number of specific fragments extracted= 16 number of extra gaps= 1 total=2001 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 2b4rO/T0384-2b4rO-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0384 read from 2b4rO/T0384-2b4rO-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2b4rO read from 2b4rO/T0384-2b4rO-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2b4rO in template set Warning: unaligning (T0384)G173 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2b4rO)I209 T0384 2 :LKLGVIGTGAISHHFIEAAHTSGEYQLVAIYSR 2b4rO 4 :TKLGINGFGRIGRLVFRAAFGRKDIEVVAINDP T0384 35 :KLETAATFASRYQ 2b4rO 39 :DLNHLCYLLKYDS T0384 48 :NIQLFDQLEVF 2b4rO 75 :SVFAEKDPSQI T0384 61 :S 2b4rO 86 :P T0384 62 :SFDLVYIASPNSLHFAQAKAALSAG 2b4rO 91 :QVDVVCESTGVFLTKELASSHLKGG T0384 87 :KHVILEKPAVSQ 2b4rO 117 :KKVIMSAPPKDD T0384 112 :NNCFIFEAARNYHEKAFTTIKNFLAD 2b4rO 143 :TKQLIVSNASCTTNCLAPLAKVINDR T0384 141 :L 2b4rO 169 :F T0384 144 :DFNYAKYS 2b4rO 170 :GIVEGLMT T0384 152 :SKMPDLLAGQ 2b4rO 188 :VVDGPSKGGK T0384 163 :PNVFSDRFAG 2b4rO 198 :DWRAGRCALS T0384 180 :IYPLYAAVRLFGKAN 2b4rO 214 :TGAAKAVGKVLPELN T0384 195 :DATYHAQQLDNSIDLNGDGILFYPD 2b4rO 230 :KLTGVAFRVPIGTVSVVDLVCRLQK T0384 220 :Y 2b4rO 295 :S T0384 221 :QVHIKAGKNITSN 2b4rO 297 :IFDMKAGLALNDN T0384 234 :LPCEIYTT 2b4rO 311 :FKLVSWYD T0384 299 :WLYDAGSVHELLYTMR 2b4rO 320 :EWGYSNRVLDLAVHIT Number of specific fragments extracted= 17 number of extra gaps= 1 total=2018 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 2b4rO/T0384-2b4rO-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0384 read from 2b4rO/T0384-2b4rO-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2b4rO read from 2b4rO/T0384-2b4rO-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2b4rO in template set Warning: unaligning (T0384)G172 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2b4rO)I209 T0384 2 :LKLGVIGTGAISHHFIEAAHTSGEYQLVAIYS 2b4rO 4 :TKLGINGFGRIGRLVFRAAFGRKDIEVVAIND T0384 34 :RKLETA 2b4rO 38 :MDLNHL T0384 43 :ASRY 2b4rO 44 :CYLL T0384 49 :IQLFDQLEVFF 2b4rO 76 :VFAEKDPSQIP T0384 62 :SFDLVYIASPNSLHFAQAKAALSAG 2b4rO 91 :QVDVVCESTGVFLTKELASSHLKGG T0384 87 :KHVILEKPAVSQ 2b4rO 117 :KKVIMSAPPKDD T0384 112 :NNCFIFEAARNYHEKAFTTIKNFLAD 2b4rO 143 :TKQLIVSNASCTTNCLAPLAKVINDR T0384 142 :GADFNYAKYSSKMPDLLAGQTP 2b4rO 170 :GIVEGLMTTVHASTANQLVVDG T0384 164 :NVFSDRFA 2b4rO 200 :RAGRCALS T0384 180 :IYPLYAAVRLFGKAND 2b4rO 214 :TGAAKAVGKVLPELNG T0384 196 :ATYHAQQLDNSIDLNGDGILFYPDYQ 2b4rO 231 :LTGVAFRVPIGTVSVVDLVCRLQKPA T0384 276 :TMTEEVAAFAHMIQQP 2b4rO 257 :KYEEVALEIKKAAEGP Number of specific fragments extracted= 12 number of extra gaps= 1 total=2030 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 1nytA/T0384-1nytA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1nytA expands to /projects/compbio/data/pdb/1nyt.pdb.gz 1nytA:Skipped atom 15, because occupancy 0.400 <= existing 0.600 in 1nytA Skipped atom 17, because occupancy 0.400 <= existing 0.600 in 1nytA Skipped atom 19, because occupancy 0.400 <= existing 0.600 in 1nytA Skipped atom 21, because occupancy 0.400 <= existing 0.600 in 1nytA Skipped atom 212, because occupancy 0.450 <= existing 0.550 in 1nytA Skipped atom 214, because occupancy 0.450 <= existing 0.550 in 1nytA Skipped atom 216, because occupancy 0.450 <= existing 0.550 in 1nytA Skipped atom 218, because occupancy 0.450 <= existing 0.550 in 1nytA Skipped atom 489, because occupancy 0.400 <= existing 0.600 in 1nytA Skipped atom 491, because occupancy 0.400 <= existing 0.600 in 1nytA Skipped atom 835, because occupancy 0.450 <= existing 0.550 in 1nytA Skipped atom 1636, because occupancy 0.400 <= existing 0.600 in 1nytA Skipped atom 1638, because occupancy 0.400 <= existing 0.600 in 1nytA Skipped atom 1640, because occupancy 0.400 <= existing 0.600 in 1nytA Skipped atom 1642, because occupancy 0.400 <= existing 0.600 in 1nytA Skipped atom 1644, because occupancy 0.400 <= existing 0.600 in 1nytA Skipped atom 1646, because occupancy 0.400 <= existing 0.600 in 1nytA Skipped atom 1648, because occupancy 0.400 <= existing 0.600 in 1nytA Skipped atom 1828, because occupancy 0.500 <= existing 0.500 in 1nytA Skipped atom 1830, because occupancy 0.500 <= existing 0.500 in 1nytA Skipped atom 1832, because occupancy 0.500 <= existing 0.500 in 1nytA # T0384 read from 1nytA/T0384-1nytA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1nytA read from 1nytA/T0384-1nytA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1nytA to template set # found chain 1nytA in template set T0384 2 :LKLGVIGTGAISHHFIEAAHTS 1nytA 120 :LRILLIGAGGASRGVLLPLLSL T0384 25 :EYQLV 1nytA 142 :DCAVT T0384 31 :IYSRKLETAATFASRYQNI 1nytA 147 :ITNRTVSRAEELAKLFAHT T0384 50 :QLFDQLEVF 1nytA 168 :IQALSMDEL T0384 60 :KS 1nytA 177 :EG T0384 62 :SFDLVYIASPNSLH 1nytA 180 :EFDLIINATSSGIS T0384 86 :GKHVIL 1nytA 207 :GIYCYD T0384 95 :AVSQ 1nytA 213 :MFYQ T0384 104 :DLIQTAEKNNC 1nytA 221 :PFLAWCEQRGS T0384 115 :FIFEAA 1nytA 233 :RNADGL T0384 173 :GALMDLGIYPLYAAV 1nytA 239 :GMLVAQAAHAFLLWH T0384 191 :G 1nytA 254 :G T0384 192 :K 1nytA 256 :L T0384 275 :HTMTEEVAAFAH 1nytA 257 :PDVEPVIKQLQE Number of specific fragments extracted= 14 number of extra gaps= 0 total=2044 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 1nytA/T0384-1nytA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0384 read from 1nytA/T0384-1nytA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1nytA read from 1nytA/T0384-1nytA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1nytA in template set T0384 2 :LKLGVIGTGAISHHFIEAAHTS 1nytA 120 :LRILLIGAGGASRGVLLPLLSL T0384 25 :EYQLV 1nytA 142 :DCAVT T0384 31 :IYSRKLETAATFASRYQ 1nytA 147 :ITNRTVSRAEELAKLFA T0384 48 :NIQLFDQLEVFFKSSFDLVYIASPNSL 1nytA 166 :GSIQALSMDELEGHEFDLIINATSSGI T0384 86 :GKHVIL 1nytA 207 :GIYCYD T0384 95 :AVSQ 1nytA 213 :MFYQ T0384 104 :DLIQTAEKNNC 1nytA 221 :PFLAWCEQRGS T0384 115 :FIFEAARNY 1nytA 233 :RNADGLGML T0384 125 :EKAFTTIK 1nytA 242 :VAQAAHAF Number of specific fragments extracted= 9 number of extra gaps= 0 total=2053 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 1nytA/T0384-1nytA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0384 read from 1nytA/T0384-1nytA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1nytA read from 1nytA/T0384-1nytA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1nytA in template set T0384 2 :LKLGVIGTGAISHHFIEAAHTS 1nytA 120 :LRILLIGAGGASRGVLLPLLSL T0384 25 :EYQLV 1nytA 142 :DCAVT T0384 31 :IYSRKLETAATFASRY 1nytA 147 :ITNRTVSRAEELAKLF T0384 47 :QNIQL 1nytA 166 :GSIQA T0384 53 :DQLEVFFKSSFDLVYIASPNSL 1nytA 171 :LSMDELEGHEFDLIINATSSGI T0384 86 :GKHVIL 1nytA 207 :GIYCYD T0384 104 :DLIQTAEKNNCFIFEA 1nytA 221 :PFLAWCEQRGSKRNAD Number of specific fragments extracted= 7 number of extra gaps= 0 total=2060 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 1ldnA/T0384-1ldnA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1ldnA expands to /projects/compbio/data/pdb/1ldn.pdb.gz 1ldnA:# T0384 read from 1ldnA/T0384-1ldnA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ldnA read from 1ldnA/T0384-1ldnA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1ldnA to template set # found chain 1ldnA in template set Warning: unaligning (T0384)K80 because of BadResidue code BAD_PEPTIDE in next template residue (1ldnA)K112 Warning: unaligning (T0384)A81 because of BadResidue code BAD_PEPTIDE at template residue (1ldnA)K112 Warning: unaligning (T0384)Y181 because of BadResidue code BAD_PEPTIDE in next template residue (1ldnA)D166 Warning: unaligning (T0384)P182 because of BadResidue code BAD_PEPTIDE at template residue (1ldnA)D166 Warning: unaligning (T0384)H275 because of BadResidue code BAD_PEPTIDE at template residue (1ldnA)N312 T0384 2 :LKLGVIGTGAISHHFIEAAHTS 1ldnA 21 :ARVVVIGAGFVGASYVFALMNQ T0384 25 :EY 1ldnA 43 :GI T0384 27 :QLV 1ldnA 47 :EIV T0384 31 :IYSRKLETAATFASRYQNI 1ldnA 50 :LIDANESKAIGDAMDFNHG T0384 50 :QLFDQLEVF 1ldnA 78 :IWHGDYDDC T0384 62 :SFDLVYIASP 1ldnA 88 :DADLVVICAG T0384 72 :NSLHFAQA 1ldnA 103 :GETRLDLV T0384 82 :A 1ldnA 113 :N T0384 99 :PQEWFDLIQTAEKNNC 1ldnA 114 :IAIFRSIVESVMASGF T0384 115 :FIFEAAR 1ldnA 132 :LFLVATN T0384 123 :YHEKAFTTIKNFL 1ldnA 139 :PVDILTYATWKFS T0384 139 :Q 1ldnA 152 :G T0384 154 :MPDLL 1ldnA 153 :LPHER T0384 174 :ALMDLGI 1ldnA 158 :VIGSGTI T0384 183 :LYAAVRLFG 1ldnA 167 :TARFRFLLG T0384 192 :KANDATYHAQQLDNS 1ldnA 181 :APQNVHAYIIGEHGD T0384 207 :IDLNGDGILFYPDY 1ldnA 266 :ENAILTVSAYLDGL T0384 254 :RS 1ldnA 283 :RD T0384 256 :AIFTDHQGNQVQLPIQQAP 1ldnA 290 :PAVINRNGIREVIEIELND T0384 276 :TMTEEVAAFAHMIQ 1ldnA 313 :RFHHSAATLKSVLA Number of specific fragments extracted= 20 number of extra gaps= 3 total=2080 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 1ldnA/T0384-1ldnA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0384 read from 1ldnA/T0384-1ldnA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ldnA read from 1ldnA/T0384-1ldnA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1ldnA in template set Warning: unaligning (T0384)N72 because of BadResidue code BAD_PEPTIDE in next template residue (1ldnA)N99 Warning: unaligning (T0384)K80 because of BadResidue code BAD_PEPTIDE in next template residue (1ldnA)K112 Warning: unaligning (T0384)A81 because of BadResidue code BAD_PEPTIDE at template residue (1ldnA)K112 Warning: unaligning (T0384)Y181 because of BadResidue code BAD_PEPTIDE in next template residue (1ldnA)D166 Warning: unaligning (T0384)P182 because of BadResidue code BAD_PEPTIDE at template residue (1ldnA)D166 T0384 2 :LKLGVIGTGAISHHFIEAAHTSG 1ldnA 21 :ARVVVIGAGFVGASYVFALMNQG T0384 26 :YQLVAIYSRKLETAATFASRYQ 1ldnA 45 :ADEIVLIDANESKAIGDAMDFN T0384 48 :NIQL 1ldnA 75 :PVDI T0384 52 :FDQLEVF 1ldnA 80 :HGDYDDC T0384 61 :SSFDLVYIASP 1ldnA 87 :RDADLVVICAG T0384 73 :SLHFAQA 1ldnA 104 :ETRLDLV T0384 82 :ALSA 1ldnA 113 :NIAI T0384 102 :WFDLIQTAEKNNC 1ldnA 117 :FRSIVESVMASGF T0384 115 :FIFEAARNYHEKAFTTIKNFLA 1ldnA 131 :GLFLVATNPVDILTYATWKFSG T0384 141 :LG 1ldnA 153 :LP T0384 163 :PNV 1ldnA 155 :HER T0384 174 :ALMDLGI 1ldnA 158 :VIGSGTI T0384 183 :LYAAVRLFG 1ldnA 167 :TARFRFLLG T0384 192 :KANDATYHAQQL 1ldnA 181 :APQNVHAYIIGE T0384 205 :N 1ldnA 265 :N T0384 206 :SIDLNGDGIL 1ldnA 267 :NAILTVSAYL T0384 218 :PD 1ldnA 277 :DG T0384 254 :RSAIFTDHQGNQVQLPIQQAPH 1ldnA 287 :IGVPAVINRNGIREVIEIELND T0384 276 :TMTEEVAAFAHMIQ 1ldnA 313 :RFHHSAATLKSVLA Number of specific fragments extracted= 19 number of extra gaps= 3 total=2099 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 1ldnA/T0384-1ldnA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0384 read from 1ldnA/T0384-1ldnA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ldnA read from 1ldnA/T0384-1ldnA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1ldnA in template set Warning: unaligning (T0384)N72 because of BadResidue code BAD_PEPTIDE in next template residue (1ldnA)N99 Warning: unaligning (T0384)K80 because of BadResidue code BAD_PEPTIDE in next template residue (1ldnA)K112 Warning: unaligning (T0384)A81 because of BadResidue code BAD_PEPTIDE at template residue (1ldnA)K112 Warning: unaligning (T0384)Y181 because of BadResidue code BAD_PEPTIDE in next template residue (1ldnA)D166 Warning: unaligning (T0384)P182 because of BadResidue code BAD_PEPTIDE at template residue (1ldnA)D166 Warning: unaligning (T0384)F216 because of BadResidue code BAD_PEPTIDE in next template residue (1ldnA)I206 Warning: unaligning (T0384)Y217 because of BadResidue code BAD_PEPTIDE at template residue (1ldnA)I206 Warning: unaligning (T0384)Q271 because of BadResidue code BAD_PEPTIDE in next template residue (1ldnA)E221 Warning: unaligning (T0384)Q272 because of BadResidue code BAD_PEPTIDE at template residue (1ldnA)E221 T0384 2 :LKLGVIGTGAISHHFIEAAHTSGEYQLVAIYSRKLETAATFASRY 1ldnA 21 :ARVVVIGAGFVGASYVFALMNQGIADEIVLIDANESKAIGDAMDF T0384 47 :QNIQLFDQLEVF 1ldnA 75 :PVDIWHGDYDDC T0384 61 :SSFDLVYIASP 1ldnA 87 :RDADLVVICAG T0384 73 :SLHFAQA 1ldnA 104 :ETRLDLV T0384 82 :ALS 1ldnA 113 :NIA T0384 101 :EWFDLIQTAEKNN 1ldnA 116 :IFRSIVESVMASG T0384 114 :C 1ldnA 131 :G T0384 116 :IFEAARNYHEKAFTTIKNFLA 1ldnA 132 :LFLVATNPVDILTYATWKFSG T0384 154 :MPDL 1ldnA 153 :LPHE T0384 173 :GALMDLGI 1ldnA 157 :RVIGSGTI T0384 183 :LYAAVRLFG 1ldnA 167 :TARFRFLLG T0384 192 :KANDATYHAQQLDNSIDLNGDGIL 1ldnA 181 :APQNVHAYIIGEHGDTELPVWSQA T0384 218 :PD 1ldnA 207 :GV T0384 263 :GNQVQLPI 1ldnA 212 :RKLVESKG T0384 273 :APHTMTEEVAAFAHMIQQ 1ldnA 222 :AQKDLERIFVNVRDAAYQ T0384 294 :NLYQTWLYDAGSVHELLYT 1ldnA 245 :GATYYGIAMGLARVTRAIL Number of specific fragments extracted= 16 number of extra gaps= 5 total=2115 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 1arzC/T0384-1arzC-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1arzC expands to /projects/compbio/data/pdb/1arz.pdb.gz 1arzC:# T0384 read from 1arzC/T0384-1arzC-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1arzC read from 1arzC/T0384-1arzC-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1arzC to template set # found chain 1arzC in template set T0384 2 :LKLGVIGT 1arzC 6 :IRVAIAGA T0384 10 :GAISHHFIEAAHTSGEYQLVAIYSR 1arzC 15 :GRMGRQLIQAALALEGVQLGAALER T0384 41 :TFASRYQNI 1arzC 48 :DAGELAGAG T0384 50 :QLFDQLEVFFK 1arzC 61 :TVQSSLDAVKD T0384 62 :SFDLVYIASPNSLHFAQAKAALSAGKHVILEK 1arzC 72 :DFDVFIDFTRPEGTLNHLAFCRQHGKGMVIGT T0384 95 :AVSQPQEWFDLIQTA 1arzC 104 :TGFDEAGKQAIRDAA T0384 112 :NNCFIFEA 1arzC 119 :ADIAIVFA T0384 120 :ARNYHEKAFTTIKNFL 1arzC 129 :FSVGVNVMLKLLEKAA T0384 136 :ADKQVLGADFNYAKYSSKMPDLL 1arzC 146 :VMGDYTDIEIIEAHHRHKVDAPS T0384 173 :GALMDLG 1arzC 169 :GTALAMG T0384 184 :YAAVRLFG 1arzC 176 :EAIAHALD T0384 192 :K 1arzC 185 :D T0384 207 :IDLNGDGILFYPDYQVHIKAGK 1arzC 216 :IVGEHTAMFADIGERLEITHKA T0384 275 :HTMTEEVAAFAHMIQQ 1arzC 238 :SSRMTFANGAVRSALW T0384 291 :PDLNLYQTWLYDAG 1arzC 255 :SGKESGLFDMRDVL Number of specific fragments extracted= 15 number of extra gaps= 0 total=2130 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 1arzC/T0384-1arzC-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0384 read from 1arzC/T0384-1arzC-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1arzC read from 1arzC/T0384-1arzC-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1arzC in template set T0384 2 :LKLGVIGT 1arzC 6 :IRVAIAGA T0384 10 :GAISHHFIEAAHTSGEYQLVAIYSRK 1arzC 15 :GRMGRQLIQAALALEGVQLGAALERE T0384 42 :FASRYQ 1arzC 49 :AGELAG T0384 48 :NIQLFDQLEVFF 1arzC 59 :GVTVQSSLDAVK T0384 61 :SSFDLVYIASPNSLHFAQAKAALSAGKHVILEK 1arzC 71 :DDFDVFIDFTRPEGTLNHLAFCRQHGKGMVIGT T0384 95 :AVSQPQEWFDLIQT 1arzC 104 :TGFDEAGKQAIRDA T0384 112 :NNCFIFEA 1arzC 119 :ADIAIVFA T0384 120 :ARNYHEKAFTTIKNFLAD 1arzC 129 :FSVGVNVMLKLLEKAAKV T0384 138 :K 1arzC 149 :D T0384 143 :ADFNYAKYSSKMPDL 1arzC 151 :TDIEIIEAHHRHKVD T0384 174 :ALMDLGIYPLYAAVRLFG 1arzC 166 :APSGTALAMGEAIAHALD T0384 192 :K 1arzC 185 :D T0384 200 :AQQLDN 1arzC 191 :VYSREG T0384 206 :SIDLNGDGILFYPDYQVHIKA 1arzC 215 :DIVGEHTAMFADIGERLEITH T0384 259 :TDH 1arzC 236 :KAS T0384 276 :TMTEEVAAFAHMIQQ 1arzC 239 :SRMTFANGAVRSALW T0384 291 :PDLNLYQTWLYDAG 1arzC 255 :SGKESGLFDMRDVL Number of specific fragments extracted= 17 number of extra gaps= 0 total=2147 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 1arzC/T0384-1arzC-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0384 read from 1arzC/T0384-1arzC-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1arzC read from 1arzC/T0384-1arzC-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1arzC in template set T0384 2 :LKLGVIGT 1arzC 6 :IRVAIAGA T0384 10 :GAISHHFIEAAHTSGEYQLVAIYSRK 1arzC 15 :GRMGRQLIQAALALEGVQLGAALERE T0384 41 :TFASRYQN 1arzC 48 :DAGELAGA T0384 49 :IQLFDQLEVF 1arzC 60 :VTVQSSLDAV T0384 60 :KSSFDLVYIASPNSLHFAQAKAALSAGKHVILEK 1arzC 70 :KDDFDVFIDFTRPEGTLNHLAFCRQHGKGMVIGT T0384 95 :AVSQPQEWFDLIQT 1arzC 104 :TGFDEAGKQAIRDA T0384 112 :NNCFIFEAARNY 1arzC 119 :ADIAIVFAANFS T0384 124 :HEKAFTTIKNFLAD 1arzC 133 :VNVMLKLLEKAAKV T0384 138 :KQV 1arzC 149 :DYT T0384 145 :FNYAKYSSKMPDL 1arzC 152 :DIEIIEAHHRHKV T0384 173 :GALMDLGIYPLYAAVRLFGKANDATYHAQQL 1arzC 165 :DAPSGTALAMGEAIAHALDKDLKDCAVYSRE T0384 204 :DNSIDLNGDGILFYPDYQVHIKAG 1arzC 213 :AGDIVGEHTAMFADIGERLEITHK T0384 229 :NIT 1arzC 237 :ASS T0384 276 :TMTEEVAAFAHMIQQPDLNLYQTWLYD 1arzC 242 :TFANGAVRSALWLSGKESGLFDMRDVL Number of specific fragments extracted= 14 number of extra gaps= 0 total=2161 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 1a5z/T0384-1a5z-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1a5z expands to /projects/compbio/data/pdb/1a5z.pdb.gz 1a5z:Warning: there is no chain 1a5z will retry with 1a5zA # T0384 read from 1a5z/T0384-1a5z-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1a5z read from 1a5z/T0384-1a5z-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1a5z to template set # found chain 1a5z in template set Warning: unaligning (T0384)L2 because first residue in template chain is (1a5z)M22 Warning: unaligning (T0384)N48 because of BadResidue code BAD_PEPTIDE in next template residue (1a5z)P71 Warning: unaligning (T0384)I49 because of BadResidue code BAD_PEPTIDE at template residue (1a5z)P71 T0384 3 :KLGVIGTGAISHHFIEAAHTS 1a5z 23 :KIGIVGLGRVGSSTAFALLMK T0384 25 :EY 1a5z 44 :GF T0384 27 :QLV 1a5z 48 :EMV T0384 31 :IYSRKLETAATFASRY 1a5z 51 :LIDVDKKRAEGDALDL T0384 47 :Q 1a5z 69 :G T0384 50 :QLFDQLEVF 1a5z 78 :IYAGDYADL T0384 60 :K 1a5z 89 :K T0384 62 :SFDLVYIASPNSLH 1a5z 90 :GSDVVIVAAGVPQK T0384 76 :FAQAKAALSA 1a5z 110 :LQLLGRNARV T0384 102 :WFDLIQTAEK 1a5z 120 :MKEIARNVSK T0384 112 :NNCFIFEAARNYHEKAFTTIKNF 1a5z 132A:PDSIVIVVTNPVDVLTYFFLKES T0384 156 :DLLAG 1a5z 154 :GMDPR T0384 173 :GALMDLGIYPLYAAVRL 1a5z 159 :KVFGSGTVLDTARLRTL T0384 190 :FG 1a5z 180 :CG T0384 192 :KANDATYHAQQLDNS 1a5z 183 :SPRSVHVYVIGEHGD T0384 207 :IDLNGDGILFYPDY 1a5z 265 :EKRVLTLSVYLEDY T0384 251 :EHIRSAIFTDHQGNQVQLP 1a5z 283 :DLCISVPVTLGKHGVERIL T0384 295 :LYQTWLYDAGSVHELLYTMRQTAG 1a5z 304 :ELNLNEEELEAFRKSASILKNAIN Number of specific fragments extracted= 18 number of extra gaps= 1 total=2179 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 1a5z/T0384-1a5z-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0384 read from 1a5z/T0384-1a5z-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1a5z read from 1a5z/T0384-1a5z-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1a5z in template set Warning: unaligning (T0384)L2 because first residue in template chain is (1a5z)M22 Warning: unaligning (T0384)Q47 because of BadResidue code BAD_PEPTIDE at template residue (1a5z)P71 T0384 3 :KLGVIGTGAISHHFIEAAHTSG 1a5z 23 :KIGIVGLGRVGSSTAFALLMKG T0384 27 :QLV 1a5z 48 :EMV T0384 31 :IYSRKLETAATFASRY 1a5z 51 :LIDVDKKRAEGDALDL T0384 48 :NIQLFDQL 1a5z 75 :RANIYAGD T0384 56 :EVF 1a5z 86 :ADL T0384 61 :SSFDLVYIASPN 1a5z 89 :KGSDVVIVAAGV T0384 74 :LHFAQAKAALSA 1a5z 108 :TRLQLLGRNARV T0384 102 :WFDLIQTAEKN 1a5z 120 :MKEIARNVSKY T0384 113 :NCFIFEAARNYHEKAFTTIKN 1a5z 132B:DSIVIVVTNPVDVLTYFFLKE T0384 141 :LG 1a5z 153 :SG T0384 166 :FSDRF 1a5z 155 :MDPRK T0384 174 :ALMDLGIYPLYAAVRLF 1a5z 160 :VFGSGTVLDTARLRTLI T0384 191 :G 1a5z 181 :G T0384 192 :KANDATYHAQQL 1a5z 183 :SPRSVHVYVIGE T0384 206 :SIDLNGDGILFYPD 1a5z 264 :DEKRVLTLSVYLED T0384 251 :EHIRSAIFTDHQGNQVQLPIQQAPH 1a5z 283 :DLCISVPVTLGKHGVERILELNLNE T0384 276 :TMTEEVAAFAHMIQQ 1a5z 314 :AFRKSASILKNAINE Number of specific fragments extracted= 17 number of extra gaps= 1 total=2196 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 1a5z/T0384-1a5z-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0384 read from 1a5z/T0384-1a5z-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1a5z read from 1a5z/T0384-1a5z-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1a5z in template set Warning: unaligning (T0384)L2 because first residue in template chain is (1a5z)M22 T0384 3 :KLGVIGTGAISHHFIEAAHTSGEYQLVAIYSRKLETAATFASRY 1a5z 23 :KIGIVGLGRVGSSTAFALLMKGFAREMVLIDVDKKRAEGDALDL T0384 47 :QNIQLFDQLEVF 1a5z 75 :RANIYAGDYADL T0384 61 :SSFDLVYIASPN 1a5z 89 :KGSDVVIVAAGV T0384 76 :FAQAKAALS 1a5z 110 :LQLLGRNAR T0384 101 :EWFDLIQTAEK 1a5z 119 :VMKEIARNVSK T0384 112 :NNCFIFEAARNYHEKAFTTIKNF 1a5z 132A:PDSIVIVVTNPVDVLTYFFLKES T0384 153 :KMPDL 1a5z 154 :GMDPR T0384 173 :GALMDLGIYPLYAAVRLFG 1a5z 159 :KVFGSGTVLDTARLRTLIA T0384 192 :KANDATYHAQQL 1a5z 183 :SPRSVHVYVIGE T0384 204 :DNSIDLNGDGILFYPD 1a5z 262 :FFDEKRVLTLSVYLED T0384 220 :YQVHIKAGKNIT 1a5z 283 :DLCISVPVTLGK T0384 252 :HIR 1a5z 297 :GVE T0384 263 :GNQVQLPIQQAPHTMTEEVAAFAHMIQQ 1a5z 301 :RILELNLNEEELEAFRKSASILKNAINE Number of specific fragments extracted= 13 number of extra gaps= 0 total=2209 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 1dih/T0384-1dih-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1dih expands to /projects/compbio/data/pdb/1dih.pdb.gz 1dih:Warning: there is no chain 1dih will retry with 1dihA # T0384 read from 1dih/T0384-1dih-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1dih read from 1dih/T0384-1dih-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1dih to template set # found chain 1dih in template set Warning: unaligning (T0384)A69 because of BadResidue code BAD_PEPTIDE in next template residue (1dih)T80 Warning: unaligning (T0384)S70 because of BadResidue code BAD_PEPTIDE at template residue (1dih)T80 Warning: unaligning (T0384)V140 because of BadResidue code BAD_PEPTIDE in next template residue (1dih)T151 Warning: unaligning (T0384)L141 because of BadResidue code BAD_PEPTIDE at template residue (1dih)T151 Warning: unaligning (T0384)Y296 because of BadResidue code BAD_PEPTIDE in next template residue (1dih)L261 Warning: unaligning (T0384)Q297 because of BadResidue code BAD_PEPTIDE at template residue (1dih)L261 T0384 2 :LKLGVIGT 1dih 6 :IRVAIAGA T0384 10 :GAISHHFIEAAHTSGEYQLVAIYSR 1dih 15 :GRMGRQLIQAALALEGVQLGAALER T0384 48 :NI 1dih 41 :GS T0384 50 :QLFDQLEVFFK 1dih 61 :TVQSSLDAVKD T0384 62 :SFDLVYI 1dih 72 :DFDVFID T0384 71 :PNSLHFAQAKAALSAGKHVILEK 1dih 81 :RPEGTLNHLAFCRQHGKGMVIGT T0384 95 :AVSQPQEWFDLIQTA 1dih 104 :TGFDEAGKQAIRDAA T0384 112 :NNCFIFEA 1dih 119 :ADIAIVFA T0384 120 :ARNYHEKAFTTIKNFL 1dih 129 :FSVGVNVMLKLLEKAA T0384 137 :D 1dih 145 :K T0384 138 :KQ 1dih 148 :GD T0384 142 :GADFNYAKYSSKMPDLL 1dih 152 :DIEIIEAHHRHKVDAPS T0384 173 :GALMDLG 1dih 169 :GTALAMG T0384 184 :YAAVRLFG 1dih 176 :EAIAHALD T0384 192 :KANDATYHAQQLDNS 1dih 185 :DLKDCAVYSREGHTG T0384 207 :IDLNGDGI 1dih 216 :IVGEHTAM T0384 257 :IFTDHQGNQVQLPIQQAPHTMTEEVAAFA 1dih 224 :FADIGERLEITHKASSRMTFANGAVRSAL T0384 287 :MI 1dih 253 :WL T0384 291 :PDLNL 1dih 255 :SGKES T0384 298 :TWLYDA 1dih 262 :FDMRDV Number of specific fragments extracted= 20 number of extra gaps= 3 total=2229 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 1dih/T0384-1dih-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0384 read from 1dih/T0384-1dih-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1dih read from 1dih/T0384-1dih-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1dih in template set Warning: unaligning (T0384)A69 because of BadResidue code BAD_PEPTIDE in next template residue (1dih)T80 Warning: unaligning (T0384)S70 because of BadResidue code BAD_PEPTIDE at template residue (1dih)T80 Warning: unaligning (T0384)Q139 because of BadResidue code BAD_PEPTIDE in next template residue (1dih)T151 Warning: unaligning (T0384)L141 because of BadResidue code BAD_PEPTIDE at template residue (1dih)T151 T0384 2 :LKLGVIGT 1dih 6 :IRVAIAGA T0384 10 :GAISHHFIEAAHTSGEYQLVAIYSRK 1dih 15 :GRMGRQLIQAALALEGVQLGAALERE T0384 47 :Q 1dih 41 :G T0384 48 :NIQLFDQLEVFF 1dih 59 :GVTVQSSLDAVK T0384 61 :SSFDLVYI 1dih 71 :DDFDVFID T0384 71 :PNSLHFAQAKAALSAGKHVILEK 1dih 81 :RPEGTLNHLAFCRQHGKGMVIGT T0384 95 :AVSQPQEWFDLIQT 1dih 104 :TGFDEAGKQAIRDA T0384 112 :NNCFIFEA 1dih 119 :ADIAIVFA T0384 120 :ARNYHEKAFTTIKNFLAD 1dih 129 :FSVGVNVMLKLLEKAAKV T0384 138 :K 1dih 149 :D T0384 147 :YAKYSSKMPDLLAGQTP 1dih 152 :DIEIIEAHHRHKVDAPS T0384 180 :IYPLYAAVRLFG 1dih 172 :LAMGEAIAHALD T0384 192 :KANDATY 1dih 185 :DLKDCAV T0384 201 :QQLDN 1dih 192 :YSREG T0384 206 :SIDLNGDGILFYPD 1dih 215 :DIVGEHTAMFADIG T0384 252 :HIRSAIFTDHQG 1dih 229 :ERLEITHKASSR T0384 278 :TEEVAAFAHMIQ 1dih 241 :MTFANGAVRSAL T0384 312 :TM 1dih 253 :WL Number of specific fragments extracted= 18 number of extra gaps= 2 total=2247 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 1dih/T0384-1dih-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0384 read from 1dih/T0384-1dih-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1dih read from 1dih/T0384-1dih-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1dih in template set Warning: unaligning (T0384)A69 because of BadResidue code BAD_PEPTIDE in next template residue (1dih)T80 Warning: unaligning (T0384)S70 because of BadResidue code BAD_PEPTIDE at template residue (1dih)T80 Warning: unaligning (T0384)Q139 because of BadResidue code BAD_PEPTIDE in next template residue (1dih)T151 Warning: unaligning (T0384)V140 because of BadResidue code BAD_PEPTIDE at template residue (1dih)T151 Warning: unaligning (T0384)N294 because of BadResidue code BAD_PEPTIDE in next template residue (1dih)L261 Warning: unaligning (T0384)L295 because of BadResidue code BAD_PEPTIDE at template residue (1dih)L261 T0384 2 :LKLGVIGT 1dih 6 :IRVAIAGA T0384 10 :GAISHHFIEAAHTSGEYQLVAIYSRK 1dih 15 :GRMGRQLIQAALALEGVQLGAALERE T0384 49 :IQLFDQLEVFF 1dih 60 :VTVQSSLDAVK T0384 62 :SFDLVYI 1dih 72 :DFDVFID T0384 71 :PNSLHFAQAKAALSAGKHVILEK 1dih 81 :RPEGTLNHLAFCRQHGKGMVIGT T0384 95 :AVSQPQEWFDLIQTA 1dih 104 :TGFDEAGKQAIRDAA T0384 112 :NNCFIFEAARNYH 1dih 119 :ADIAIVFAANFSV T0384 125 :EKAFTTIKNFLAD 1dih 134 :NVMLKLLEKAAKV T0384 138 :K 1dih 149 :D T0384 141 :L 1dih 152 :D T0384 146 :NYAKYSSKMPDL 1dih 153 :IEIIEAHHRHKV T0384 160 :GQTPNV 1dih 165 :DAPSGT T0384 179 :GIYPLYAAVRLFGKANDATYHAQQL 1dih 171 :ALAMGEAIAHALDKDLKDCAVYSRE T0384 204 :DNSIDLNGDGILFYPD 1dih 213 :AGDIVGEHTAMFADIG T0384 221 :QVHIKAGKNIT 1dih 229 :ERLEITHKASS T0384 275 :HTMTEEVAAFAHMIQQPDL 1dih 241 :MTFANGAVRSALWLSGKES T0384 296 :YQTWLY 1dih 262 :FDMRDV Number of specific fragments extracted= 17 number of extra gaps= 3 total=2264 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 3dapA/T0384-3dapA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 3dapA expands to /projects/compbio/data/pdb/3dap.pdb.gz 3dapA:# T0384 read from 3dapA/T0384-3dapA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3dapA read from 3dapA/T0384-3dapA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3dapA to template set # found chain 3dapA in template set Warning: unaligning (T0384)R121 because of BadResidue code BAD_PEPTIDE in next template residue (3dapA)P121 Warning: unaligning (T0384)N122 because of BadResidue code BAD_PEPTIDE at template residue (3dapA)P121 T0384 1 :M 3dapA 1 :M T0384 2 :LKLGVIGTGAISHHFIEAAHTSGEYQLVAIYSRKLE 3dapA 4 :IRVAIVGYGNLGRSVEKLIAKQPDMDLVGIFSRRAT T0384 46 :YQNI 3dapA 40 :LDTK T0384 50 :QLFDQLEVFFK 3dapA 47 :FDVADVDKHAD T0384 62 :SFDLVYIASP 3dapA 58 :DVDVLFLCMG T0384 72 :NSLHFAQAKAALSA 3dapA 69 :ATDIPEQAPKFAQF T0384 88 :HVILE 3dapA 83 :ACTVD T0384 95 :AVSQPQEW 3dapA 88 :TYDNHRDI T0384 103 :FDLIQTAEKNNCFIF 3dapA 100 :QVMNEAATAAGNVAL T0384 118 :EAA 3dapA 117 :TGW T0384 123 :YHEKAF 3dapA 122 :GMFSIN T0384 129 :TTIKNFL 3dapA 129 :VYAAAVL T0384 138 :KQ 3dapA 136 :AE T0384 143 :ADFNYAKYSSKMPDLLAG 3dapA 138 :HQQHTFWGPGLSQGHSDA T0384 189 :LFG 3dapA 156 :LRR T0384 192 :KANDATYHAQQLDN 3dapA 161 :GVQKAVQYTLPSED T0384 207 :IDLNGDGILFY 3dapA 242 :MPHGGHVITTG T0384 218 :PDYQ 3dapA 254 :TGGF T0384 222 :VHIKA 3dapA 259 :HTVEY T0384 244 :TLTLN 3dapA 264 :ILKLD T0384 297 :QTWLYDAGSVHELLYTMRQTAGIRF 3dapA 269 :RNPDFTASSQIAFGRAAHRMKQQGQ Number of specific fragments extracted= 21 number of extra gaps= 1 total=2285 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 3dapA/T0384-3dapA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0384 read from 3dapA/T0384-3dapA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3dapA read from 3dapA/T0384-3dapA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3dapA in template set Warning: unaligning (T0384)E125 because of BadResidue code BAD_PEPTIDE in next template residue (3dapA)P121 Warning: unaligning (T0384)K126 because of BadResidue code BAD_PEPTIDE at template residue (3dapA)P121 T0384 2 :LKLGVIGTGAISHHFIEAAHTSGEYQLVAIYSRKLE 3dapA 4 :IRVAIVGYGNLGRSVEKLIAKQPDMDLVGIFSRRAT T0384 46 :YQ 3dapA 40 :LD T0384 48 :NIQLFD 3dapA 43 :KTPVFD T0384 54 :QLEVFF 3dapA 51 :DVDKHA T0384 61 :SSFDLVYIASPN 3dapA 57 :DDVDVLFLCMGS T0384 73 :SLHFAQAKAALSA 3dapA 70 :TDIPEQAPKFAQF T0384 88 :HVILE 3dapA 83 :ACTVD T0384 95 :AVSQPQEW 3dapA 88 :TYDNHRDI T0384 103 :FDLIQTAEKNNCFIFEAA 3dapA 100 :QVMNEAATAAGNVALVST T0384 123 :YH 3dapA 118 :GW T0384 127 :AFTTIKNFLAD 3dapA 124 :FSINRVYAAAV T0384 141 :LG 3dapA 135 :LA T0384 144 :DFNYAKYSSKMP 3dapA 137 :EHQQHTFWGPGL T0384 167 :SDR 3dapA 149 :SQG T0384 185 :AAVRLFG 3dapA 152 :HSDALRR T0384 192 :KANDATYHAQQL 3dapA 161 :GVQKAVQYTLPS T0384 204 :DNSIDLNGDGILFYPDY 3dapA 239 :HTGMPHGGHVITTGDTG T0384 221 :QVHIKA 3dapA 257 :FNHTVE T0384 243 :GTLTLNT 3dapA 263 :YILKLDR T0384 298 :TWLYDAGSVHELLYTMRQTAGIRF 3dapA 270 :NPDFTASSQIAFGRAAHRMKQQGQ Number of specific fragments extracted= 20 number of extra gaps= 1 total=2305 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 3dapA/T0384-3dapA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0384 read from 3dapA/T0384-3dapA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3dapA read from 3dapA/T0384-3dapA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3dapA in template set Warning: unaligning (T0384)Y123 because of BadResidue code BAD_PEPTIDE in next template residue (3dapA)P121 Warning: unaligning (T0384)H124 because of BadResidue code BAD_PEPTIDE at template residue (3dapA)P121 T0384 2 :LKLGVIGTGAISHHFIEAAHTSGEYQLVAIYSRKLE 3dapA 4 :IRVAIVGYGNLGRSVEKLIAKQPDMDLVGIFSRRAT T0384 46 :YQN 3dapA 40 :LDT T0384 49 :IQLFD 3dapA 44 :TPVFD T0384 55 :LEVFF 3dapA 49 :VADVD T0384 60 :KSSFDLVYIASPN 3dapA 56 :ADDVDVLFLCMGS T0384 73 :SLHFAQAKAALSA 3dapA 70 :TDIPEQAPKFAQF T0384 88 :HVILEK 3dapA 83 :ACTVDT T0384 96 :VS 3dapA 89 :YD T0384 99 :PQEWFDLIQTAEKNNCFIFEAARN 3dapA 96 :PRHRQVMNEAATAAGNVALVSTGW T0384 125 :EKAFTTIKNFLAD 3dapA 122 :GMFSINRVYAAAV T0384 140 :VLGADFNYAKYSSKMPDL 3dapA 135 :LAEHQQHTFWGPGLSQGH T0384 184 :YAAVRLFGKANDATYHAQQL 3dapA 153 :SDALRRIPGVQKAVQYTLPS T0384 204 :DNSIDLNGDGILFY 3dapA 239 :HTGMPHGGHVITTG T0384 218 :PDYQVHIKAG 3dapA 254 :TGGFNHTVEY T0384 244 :TLTLNTI 3dapA 264 :ILKLDRN T0384 297 :QTWLYDAGSVHELLYTMRQTAGI 3dapA 271 :PDFTASSQIAFGRAAHRMKQQGQ Number of specific fragments extracted= 16 number of extra gaps= 1 total=2321 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 1dapA/T0384-1dapA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1dapA expands to /projects/compbio/data/pdb/1dap.pdb.gz 1dapA:# T0384 read from 1dapA/T0384-1dapA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1dapA read from 1dapA/T0384-1dapA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1dapA to template set # found chain 1dapA in template set Warning: unaligning (T0384)Y150 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (1dapA)P146 Warning: unaligning (T0384)S151 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (1dapA)P146 T0384 1 :M 1dapA 1 :M T0384 2 :LKLGVIGTGAISHHFIEAAHTSGEYQLVAIYSRKLE 1dapA 4 :IRVAIVGYGNLGRSVEKLIAKQPDMDLVGIFSRRAT T0384 46 :YQNI 1dapA 40 :LDTK T0384 50 :QLFD 1dapA 45 :PVFD T0384 55 :LEVF 1dapA 49 :VADV T0384 59 :FKSSFDLVYIASP 1dapA 55 :HADDVDVLFLCMG T0384 72 :NSLHFAQAKAALSA 1dapA 69 :ATDIPEQAPKFAQF T0384 88 :HVILE 1dapA 83 :ACTVD T0384 95 :AVSQPQEW 1dapA 88 :TYDNHRDI T0384 103 :FDLIQTAEKNNCFIFEA 1dapA 100 :QVMNEAATAAGNVALVS T0384 120 :ARNYHEKAF 1dapA 119 :WDPGMFSIN T0384 129 :TTIKNFL 1dapA 129 :VYAAAVL T0384 138 :KQ 1dapA 136 :AE T0384 143 :ADFNYAK 1dapA 138 :HQQHTFW T0384 152 :SKMPDLLAG 1dapA 147 :GLSQGHSDA T0384 189 :LFG 1dapA 156 :LRR T0384 192 :KANDATYHAQQLDN 1dapA 161 :GVQKAVQYTLPSED T0384 207 :IDLNGDGILFY 1dapA 242 :MPHGGHVITTG T0384 218 :PDYQ 1dapA 255 :GGFN T0384 222 :VHIK 1dapA 260 :TVEY T0384 244 :TLTLN 1dapA 264 :ILKLD T0384 297 :QTWLYDAGSVHELLYTMRQTAGIRF 1dapA 269 :RNPDFTASSQIAFGRAAHRMKQQGQ Number of specific fragments extracted= 22 number of extra gaps= 1 total=2343 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 1dapA/T0384-1dapA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0384 read from 1dapA/T0384-1dapA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1dapA read from 1dapA/T0384-1dapA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1dapA in template set Warning: unaligning (T0384)S152 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (1dapA)P146 Warning: unaligning (T0384)K153 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (1dapA)P146 T0384 2 :LKLGVIGTGAISHHFIEAAHTSGEYQLVAIYSRKLE 1dapA 4 :IRVAIVGYGNLGRSVEKLIAKQPDMDLVGIFSRRAT T0384 46 :YQ 1dapA 40 :LD T0384 48 :NIQLFD 1dapA 43 :KTPVFD T0384 54 :QLEVFF 1dapA 51 :DVDKHA T0384 61 :SSFDLVYIASPN 1dapA 57 :DDVDVLFLCMGS T0384 73 :SLHFAQAKAALSA 1dapA 70 :TDIPEQAPKFAQF T0384 88 :HVILE 1dapA 83 :ACTVD T0384 95 :AVSQPQEW 1dapA 88 :TYDNHRDI T0384 103 :FDLIQTAEKNNCFIFEAARNYHEKAFTTIKNFLAD 1dapA 100 :QVMNEAATAAGNVALVSTGWDPGMFSINRVYAAAV T0384 141 :LG 1dapA 135 :LA T0384 144 :DFNYAKYS 1dapA 137 :EHQQHTFW T0384 154 :MPDL 1dapA 147 :GLSQ T0384 169 :R 1dapA 151 :G T0384 185 :AAVRLFG 1dapA 152 :HSDALRR T0384 192 :KANDATYHAQQL 1dapA 161 :GVQKAVQYTLPS T0384 204 :DNSIDLNGDGILFYPDY 1dapA 239 :HTGMPHGGHVITTGDTG T0384 221 :QVHIKA 1dapA 257 :FNHTVE T0384 243 :GTLTLNT 1dapA 263 :YILKLDR T0384 298 :TWLYDAGSVHELLYTMRQTAGIRF 1dapA 270 :NPDFTASSQIAFGRAAHRMKQQGQ Number of specific fragments extracted= 19 number of extra gaps= 1 total=2362 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 1dapA/T0384-1dapA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0384 read from 1dapA/T0384-1dapA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1dapA read from 1dapA/T0384-1dapA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1dapA in template set Warning: unaligning (T0384)R121 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (1dapA)P146 T0384 1 :MLKLGVIGTGAISHHFIEAAHTSGEYQLVAIYSRKLE 1dapA 3 :NIRVAIVGYGNLGRSVEKLIAKQPDMDLVGIFSRRAT T0384 46 :YQN 1dapA 40 :LDT T0384 49 :IQLFD 1dapA 44 :TPVFD T0384 55 :LEVFF 1dapA 49 :VADVD T0384 60 :KSSFDLVYIASPN 1dapA 56 :ADDVDVLFLCMGS T0384 73 :SLHFAQAKAALSA 1dapA 70 :TDIPEQAPKFAQF T0384 88 :HVILEK 1dapA 83 :ACTVDT T0384 96 :VSQ 1dapA 89 :YDN T0384 99 :PQEWFDLIQTAEKNNCFIFE 1dapA 96 :PRHRQVMNEAATAAGNVALV T0384 122 :NYHEKAFTTIK 1dapA 147 :GLSQGHSDALR T0384 133 :NFLADKQVLGA 1dapA 177 :EKARRGEAGDL T0384 144 :DFNYAKYSSKMPDL 1dapA 193 :HKRQCFVVADAADH T0384 164 :NVFSDRFAG 1dapA 213 :IRTMPDYFV T0384 191 :GK 1dapA 222 :GY T0384 195 :DATYHAQQ 1dapA 224 :EVEVNFID T0384 204 :DNSIDLNGDGILFY 1dapA 239 :HTGMPHGGHVITTG T0384 218 :PDYQVHIKAG 1dapA 254 :TGGFNHTVEY T0384 244 :TLTLNTI 1dapA 264 :ILKLDRN T0384 297 :QTWLYDAGSVHELLYTMRQTAGI 1dapA 271 :PDFTASSQIAFGRAAHRMKQQGQ Number of specific fragments extracted= 19 number of extra gaps= 1 total=2381 Will force an alignment to be made, even if fragment is small Number of alignments=153 # command:CPU_time= 56.211 sec, elapsed time= 60.368 sec. # command:Using radius: 8.000 NUMB_ALIGNS: 153 Adding 52650 constraints to all_contacts Done adding distance constraints # command:CPU_time= 56.503 sec, elapsed time= 60.689 sec. # command:Reading probabilities from T0384.t06.CB8-sep9.rdb Reading constraints from ConstraintSet all_contacts maxweight: 40.502 Optimizing... Probability sum: -571.045, CN propb: -571.045 weights: 0.256 constraints: 1165 # command:CPU_time= 1376.586 sec, elapsed time= 1383.030 sec. # command:Found ConstraintSet # PrintContacts log_align.constraints Number of constraints in align 1165 # command:Found ConstraintSet # PrintContacts log_align_bonus.constraints Number of constraints in align.bonus 1165 # command:Found ConstraintSet # PrintContacts log_rejected.constraints Number of constraints in rejected 7179 # command:Found ConstraintSet # PrintContacts log_rejected_bonus.constraints Number of constraints in rejected.bonus 7179 # command:Found ConstraintSet # PrintContacts log_noncontact.constraints Number of constraints in noncontact 41742 # command:Found ConstraintSet # PrintContacts log_noncontact_bonus.constraints Number of constraints in noncontact.bonus 41742 # command:CPU_time= 1377.495 sec, elapsed time= 1384.568 sec. # command: