# 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 T0298 numbered 1 through 336 Created new target T0298 from T0298.a2m # command:CPU_time= 6.356 sec, elapsed time= 6.424 sec. # command:# reading script from file all-templates.under # Reading fragments from alignment file # Attempting to read fragment alignments from file 1t4bA/T0298-1t4bA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1t4bA expands to /projects/compbio/data/pdb/1t4b.pdb.gz 1t4bA:# T0298 read from 1t4bA/T0298-1t4bA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1t4bA read from 1t4bA/T0298-1t4bA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1t4bA to template set # found chain 1t4bA in template set T0298 5 :LNVAVVGATGSVGEALVGLLDERD 1t4bA 2 :QNVGFIGWRGMVGSVLMQRMVEER # choosing archetypes in rotamer library T0298 29 :FPLHRLHLL 1t4bA 27 :FDAIRPVFF T0298 39 :SAESAGQRM 1t4bA 36 :STSQLGQAA T0298 48 :GFAESSLRVGDVDSFD 1t4bA 46 :SFGGTTGTLQDAFDLE T0298 64 :FSSVGLAFFAAAAEVSRAHAERARAAGC 1t4bA 63 :LKALDIIVTCQGGDYTNEIYPKLRESGW T0298 92 :SVIDLSGALEPS 1t4bA 93 :YWIDAASSLRMK T0298 104 :VAPPVMVSVNAERLA 1t4bA 106 :DAIIILDPVNQDVIT T0298 119 :SQAAPFLLSSPCAVAA 1t4bA 124 :NNGIRTFVGGNCTVSL T0298 136 :LCEVLAPLLATLDCRQLNLTACLSVSSLGREGVKEL 1t4bA 140 :MLMSLGGLFANDLVDWVSVATYQAASGGGARHMREL T0298 172 :ARQTAELLNARPLEPRL 1t4bA 183 :YGHVADELATPSSAILD T0298 189 :FDRQIAFNLLAQVGAVDAEGHSAIERRIFAEVQALLG 1t4bA 218 :FGVPLAGSLIPWIDKQLDNGQSREEWKGQAETNKILN T0298 226 :ERIGPLNVTCIQAPVFFGDSLSVTLQCAEPVDLAAVTRVLDAT 1t4bA 256 :SSVIPVDGLCVRVGALRCHSQAFTIKLKKDVSIPTVEELLAAH T0298 269 :KGIEWVGE 1t4bA 300 :PWAKVVPN T0298 284 :GDALGQDETYVGRVRAGQADPCQVNLWIVSDNVRKGAALNAVLLGELL 1t4bA 319 :AAVTGTLTTPVGRLRKLNMGPEFLSAFTVGDQLLWGAAEPLRRMLRQL Number of specific fragments extracted= 14 number of extra gaps= 0 total=14 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 1t4bA/T0298-1t4bA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0298 read from 1t4bA/T0298-1t4bA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1t4bA read from 1t4bA/T0298-1t4bA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1t4bA in template set Warning: unaligning (T0298)P4 because first residue in template chain is (1t4bA)M1 T0298 5 :LNVAVVGATGSVGEALVGLLDERD 1t4bA 2 :QNVGFIGWRGMVGSVLMQRMVEER T0298 29 :FPLHRLHLLASAESAGQRMGFAESSLRVGDVDSFD 1t4bA 27 :FDAIRPVFFSTSQLGQAAPSFGGTTGTLQDAFDLE T0298 64 :FSSVGLAFFAAAAEVSRAHAERARAAGC 1t4bA 63 :LKALDIIVTCQGGDYTNEIYPKLRESGW T0298 92 :SVIDLSGALEP 1t4bA 93 :YWIDAASSLRM T0298 103 :SVAPPVMVSVNAERLA 1t4bA 105 :DDAIIILDPVNQDVIT T0298 119 :SQ 1t4bA 125 :NG T0298 122 :APFLLSSPCAVAA 1t4bA 127 :IRTFVGGNCTVSL T0298 136 :LCEVLAPLLATLDCRQLNLTACLSVSSLGREGVKELARQTAEL 1t4bA 140 :MLMSLGGLFANDLVDWVSVATYQAASGGGARHMRELLTQMGHL T0298 179 :LNARPL 1t4bA 190 :LATPSS T0298 185 :EPRLFDRQIAFNLLAQVGAVDAEGHSAIERRIFAEVQALLG 1t4bA 214 :PVDNFGVPLAGSLIPWIDKQLDNGQSREEWKGQAETNKILN T0298 226 :ERIGPLNVTCIQAPVFFGDSLSVTLQCAEPVDLAAVTRVLDAT 1t4bA 256 :SSVIPVDGLCVRVGALRCHSQAFTIKLKKDVSIPTVEELLAAH T0298 269 :KGIEWVGE 1t4bA 300 :PWAKVVPN T0298 283 :VGDALGQDETYVGRVRAGQADPCQVNLWIVSDNVRKGAALNAVLLGELL 1t4bA 318 :PAAVTGTLTTPVGRLRKLNMGPEFLSAFTVGDQLLWGAAEPLRRMLRQL Number of specific fragments extracted= 13 number of extra gaps= 0 total=27 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 1t4bA/T0298-1t4bA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0298 read from 1t4bA/T0298-1t4bA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1t4bA read from 1t4bA/T0298-1t4bA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1t4bA in template set T0298 5 :LNVAVVGATGSVGEALVGLLDERDFPLH 1t4bA 2 :QNVGFIGWRGMVGSVLMQRMVEERDFDA T0298 33 :RLHLLASAESAGQRMGFAESSLRVGDV 1t4bA 31 :RPVFFSTSQLGQAAPSFGGTTGTLQDA T0298 60 :DSFDFSSVGLAFFAAAAEVSRAHAERARAAGC 1t4bA 59 :DLEALKALDIIVTCQGGDYTNEIYPKLRESGW T0298 92 :SVIDLSGALEPS 1t4bA 93 :YWIDAASSLRMK T0298 104 :VAPPVMVSVNAERLASQ 1t4bA 106 :DAIIILDPVNQDVITDG T0298 121 :AAPFLLSSPCAVAAELCEVLAPLLATLDCRQLNLTACLSVSSLGREGVKELARQTAEL 1t4bA 125 :NGIRTFVGGNCTVSLMLMSLGGLFANDLVDWVSVATYQAASGGGARHMRELLTQMGHL T0298 179 :LNARPLEPRLFDRQIAFNLLAQVGAVDAEGHSAIERRIFAEVQALLG 1t4bA 208 :TRSGELPVDNFGVPLAGSLIPWIDKQLDNGQSREEWKGQAETNKILN T0298 226 :ERIGPLNVTCIQAPVFFGDSLSVTLQCAEPVDLAAVTRVLDATKGIEWVGEG 1t4bA 256 :SSVIPVDGLCVRVGALRCHSQAFTIKLKKDVSIPTVEELLAAHNPWAKVVPN T0298 281 :TVVGDALGQDETYVGRVRAGQADPCQVNLWIVSDNVRKGAALNAVLLGELL 1t4bA 316 :LTPAAVTGTLTTPVGRLRKLNMGPEFLSAFTVGDQLLWGAAEPLRRMLRQL Number of specific fragments extracted= 9 number of extra gaps= 0 total=36 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 1vknA/T0298-1vknA-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 # T0298 read from 1vknA/T0298-1vknA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1vknA read from 1vknA/T0298-1vknA-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 Warning: unaligning (T0298)Q3 because first residue in template chain is (1vknA)H0 T0298 4 :PLNVAVVGATGSVGEALVGLLD 1vknA 1 :MIRAGIIGATGYTGLELVRLLK T0298 28 :DFPLHRLHLLASAESAGQRMGFAESSLR 1vknA 23 :NHPEAKITYLSSRTYAGKKLEEIFPSTL T0298 56 :VG 1vknA 55 :LS T0298 63 :DFS 1vknA 57 :EFD T0298 66 :SVGLAFFAAAAEVSRAHA 1vknA 66 :NCDVLFTALPAGASYDLV T0298 90 :GCSVIDLSGALEPSV 1vknA 88 :GVKIIDLGADFRFDD T0298 105 :APPVMVSVNAERLA 1vknA 122 :RVYGLPELHREEIK T0298 122 :APFLLSSP 1vknA 136 :NAQVVGNP T0298 130 :CAVAA 1vknA 145 :CYPTS T0298 136 :LCEVLAPLLAT 1vknA 150 :VILALAPALKH T0298 147 :LDCRQLNLTACLSVSSLGRE 1vknA 163 :VDPETILVDAKSGVSGAGRK T0298 167 :GVKELARQTAELLNARPL 1vknA 184 :KVDYLFSEVNESLRPYNV T0298 205 :DAEGHSAIERRIFAE 1vknA 202 :AKHRHVPEMEQELGK T0298 224 :LGERIGPLNVTCIQAPVFFGDSLSVTLQCAE 1vknA 217 :ISGKKVNVVFTPHLVPMTRGILSTIYVKTDK T0298 257 :DLAAVTRVLDAT 1vknA 248 :SLEEIHEAYLEF T0298 269 :KGIEWVGEGDYPTVVG 1vknA 264 :PFVHVLPMGIYPSTKW T0298 286 :ALGQDETYVG 1vknA 280 :CYGSNHVFIG T0298 297 :VRAG 1vknA 290 :MQME T0298 302 :ADPCQVNLWIVSDNVRKGAALNAVLLGELLIKHYL 1vknA 294 :ERTNTLILMSAIDNLVKGASGQAVQNMNIMFGLDE Number of specific fragments extracted= 19 number of extra gaps= 0 total=55 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 1vknA/T0298-1vknA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0298 read from 1vknA/T0298-1vknA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1vknA read from 1vknA/T0298-1vknA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1vknA in template set Warning: unaligning (T0298)Q3 because first residue in template chain is (1vknA)H0 T0298 4 :PLNVAVVGATGSVGEALVGLLD 1vknA 1 :MIRAGIIGATGYTGLELVRLLK T0298 28 :DFPLHRLHLLASAESAGQRMGFAESSLRVGD 1vknA 23 :NHPEAKITYLSSRTYAGKKLEEIFPSTLENS T0298 62 :FDFS 1vknA 56 :SEFD T0298 66 :SVGLAFFAAAAEVSRAHA 1vknA 66 :NCDVLFTALPAGASYDLV T0298 89 :A 1vknA 84 :R T0298 90 :GCSVIDLSGALEPSV 1vknA 88 :GVKIIDLGADFRFDD T0298 105 :APPVMVSVNAERLA 1vknA 122 :RVYGLPELHREEIK T0298 122 :APFLLSSP 1vknA 136 :NAQVVGNP T0298 130 :CAVAA 1vknA 145 :CYPTS T0298 136 :LCEVLAPLLAT 1vknA 150 :VILALAPALKH T0298 147 :LDCRQLNLTACLSVSSLGREG 1vknA 163 :VDPETILVDAKSGVSGAGRKE T0298 176 :AELLNARPLEPRLFDRQI 1vknA 184 :KVDYLFSEVNESLRPYNV T0298 205 :DAEGHSAIERRIFAEVQA 1vknA 202 :AKHRHVPEMEQELGKISG T0298 227 :RIGPLNVTCIQAPVFFGDSLSVTLQCAE 1vknA 220 :KKVNVVFTPHLVPMTRGILSTIYVKTDK T0298 257 :DLAAVTRVLDAT 1vknA 248 :SLEEIHEAYLEF T0298 269 :KGIEWVGEGDYPTVV 1vknA 264 :PFVHVLPMGIYPSTK T0298 285 :DALGQDETYVGR 1vknA 279 :WCYGSNHVFIGM T0298 299 :AGQADPCQVNLWIVSDNVRKGAALNAVLLGELLIK 1vknA 291 :QMEERTNTLILMSAIDNLVKGASGQAVQNMNIMFG Number of specific fragments extracted= 18 number of extra gaps= 0 total=73 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 1vknA/T0298-1vknA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0298 read from 1vknA/T0298-1vknA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1vknA read from 1vknA/T0298-1vknA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1vknA in template set Warning: unaligning (T0298)Q3 because first residue in template chain is (1vknA)H0 T0298 4 :PLNVAVVGATGSVGEALVGLLDERD 1vknA 1 :MIRAGIIGATGYTGLELVRLLKNHP T0298 31 :LHRLHLLASAESAGQR 1vknA 26 :EAKITYLSSRTYAGKK T0298 49 :FAES 1vknA 46 :FPST T0298 53 :SLRVGDVDSFDFS 1vknA 52 :NSILSEFDPEKVS T0298 66 :SVGLAFFAAAAEVSRAHA 1vknA 66 :NCDVLFTALPAGASYDLV T0298 90 :GCSVIDLSGALEPSV 1vknA 88 :GVKIIDLGADFRFDD T0298 109 :MVSVNAERLASQAAPFLLSSPCAVAAELCEVLAPLL 1vknA 123 :VYGLPELHREEIKNAQVVGNPGCYPTSVILALAPAL T0298 145 :ATLDCRQLNLTACLSVSSLGRE 1vknA 161 :NLVDPETILVDAKSGVSGAGRK T0298 184 :LEPRLFDRQI 1vknA 183 :EKVDYLFSEV T0298 202 :GAVDAEGHSAIERRIFAEVQALLGERIGPLNVTCIQAPVFFGDSLSVTLQC 1vknA 195 :SLRPYNVAKHRHVPEMEQELGKISGKKVNVVFTPHLVPMTRGILSTIYVKT T0298 255 :PVDLAAVTRVLDAT 1vknA 246 :DKSLEEIHEAYLEF T0298 270 :G 1vknA 261 :K T0298 271 :IEWVGEGDYPTVVGDALGQDETYVGR 1vknA 265 :FVHVLPMGIYPSTKWCYGSNHVFIGM T0298 299 :AGQADPCQVNLWIVSDNVRKGAALNAVLLGELLI 1vknA 291 :QMEERTNTLILMSAIDNLVKGASGQAVQNMNIMF Number of specific fragments extracted= 14 number of extra gaps= 0 total=87 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 1gadO/T0298-1gadO-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 0.4 <= 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 # T0298 read from 1gadO/T0298-1gadO-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1gadO read from 1gadO/T0298-1gadO-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 Warning: unaligning (T0298)P4 because first residue in template chain is (1gadO)T0 T0298 5 :LNVAVVGA 1gadO 1 :IKVGINGF T0298 14 :GSVGEALVGLLD 1gadO 9 :GRIGRIVFRAAQ T0298 28 :DFPLHRLHLLASAESAGQRMGFAE 1gadO 21 :KRSDIEIVAINDLLDADYMAYMLK T0298 52 :SSLRVGDVDSFDFS 1gadO 72 :RVTAERDPANLKWD T0298 66 :SVGLAFFAAAAEVSRAHAERARAAGCSVIDLSGAL 1gadO 88 :GVDVVAEATGLFLTDETARKHITAGAKKVVMTGPS T0298 103 :S 1gadO 122A:K T0298 104 :VAPPVMVSVNAERLA 1gadO 124 :NTPMFVKGANFDKYA T0298 122 :APFLLSSP 1gadO 138A:GQDIVSNA T0298 130 :CAVAA 1gadO 149 :CTTNC T0298 136 :LCEVLAPLLATLDCRQLNLTACLSVSS 1gadO 154 :LAPLAKVINDNFGIIEGLMTTVHATTA T0298 175 :TAELLNARPLEPRLFDRQIAFNLLA 1gadO 181 :TQKTVDGPSHKDWRGGRGASQNIIP T0298 205 :DAEG 1gadO 206 :SSTG T0298 213 :ERRIFAEV 1gadO 210 :AAKAVGKV T0298 224 :LGERIGPLNVTCIQAPVFFGDSLSVTLQCAEPVDLAAVTRVLDAT 1gadO 218 :LPELNGKLTGMAFRVPTPNVSVVDLTVRLEKAATYEQIKAAVKAA T0298 269 :KGIEWVGEGDYPTVVGDALGQDETYVGRVRAGQ 1gadO 266 :EMKGVLGYTEDDVVSTDFNGEVCTSVFDAKAGI T0298 302 :ADPCQVNLWIVSDN 1gadO 300 :LNDNFVKLVSWYDN T0298 317 :RKGAALNAVLLGEL 1gadO 314 :ETGYSNKVLDLIAH Number of specific fragments extracted= 17 number of extra gaps= 0 total=104 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 1gadO/T0298-1gadO-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0298 read from 1gadO/T0298-1gadO-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1gadO read from 1gadO/T0298-1gadO-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1gadO in template set Warning: unaligning (T0298)P4 because first residue in template chain is (1gadO)T0 T0298 5 :LNVAVVG 1gadO 1 :IKVGING T0298 13 :TGSVGEALVGLLDER 1gadO 8 :FGRIGRIVFRAAQKR T0298 28 :DFPLHRLHLLASAESAGQRMGFA 1gadO 24 :DIEIVAINDLLDADYMAYMLKYD T0298 51 :ESSLRVGDVDSFDFS 1gadO 71 :IRVTAERDPANLKWD T0298 66 :SVGLAFFAAAAEVSRAHAERARAAGCSVI 1gadO 88 :GVDVVAEATGLFLTDETARKHITAGAKKV T0298 96 :LSGALEPSVAPPVMVSVNAERLA 1gadO 117 :VMTGPSKDNTPMFVKGANFDKYA T0298 122 :APFLLSSP 1gadO 138A:GQDIVSNA T0298 130 :CAVAA 1gadO 149 :CTTNC T0298 136 :LCEVLAPLLATLDCRQLNLTACLSVSSL 1gadO 154 :LAPLAKVINDNFGIIEGLMTTVHATTAT T0298 176 :AELLNARPLEPRLFDRQIAFNLLA 1gadO 182 :QKTVDGPSHKDWRGGRGASQNIIP T0298 205 :DAEGHSAIERRIFAEVQA 1gadO 206 :SSTGAAKAVGKVLPELNG T0298 230 :PLNVTCIQAPVFFGDSLSVTLQCAEPVDLAAVTRVLDAT 1gadO 224 :KLTGMAFRVPTPNVSVVDLTVRLEKAATYEQIKAAVKAA T0298 269 :KGIEWVGEGDYPTVVGDALGQDETYVGRVRAGQAD 1gadO 266 :EMKGVLGYTEDDVVSTDFNGEVCTSVFDAKAGIAL T0298 304 :PCQVNLWIVSDN 1gadO 302 :DNFVKLVSWYDN T0298 317 :RKGAALNAVLLGELL 1gadO 314 :ETGYSNKVLDLIAHI Number of specific fragments extracted= 15 number of extra gaps= 0 total=119 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 1gadO/T0298-1gadO-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0298 read from 1gadO/T0298-1gadO-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1gadO read from 1gadO/T0298-1gadO-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1gadO in template set Warning: unaligning (T0298)P4 because first residue in template chain is (1gadO)T0 T0298 5 :LNVAVVGA 1gadO 1 :IKVGINGF T0298 14 :GSVGEALVGLLDERDFPLHRLHLLASAESA 1gadO 9 :GRIGRIVFRAAQKRSDIEIVAINDLLDADY T0298 45 :QRMGFAES 1gadO 55 :GTVEVKDG T0298 53 :SLRVGDVDSFDFS 1gadO 70 :KIRVTAERDPANL T0298 66 :SVGLAFFAAA 1gadO 88 :GVDVVAEATG T0298 76 :AEVSR 1gadO 102 :DETAR T0298 85 :RARAAGCSVIDLSGALE 1gadO 107 :KHITAGAKKVVMTGPSK T0298 103 :SVAPPVMVSV 1gadO 123 :DNTPMFVKGA T0298 116 :RLASQAAPFLLSSPCAVAAELCEVLAPLLATLDCRQLNLTACLSVSSLGRE 1gadO 133 :NFDKYAGQDIVSNASCTTNCLAPLAKVINDNFGIIEGLMTTVHATTATQKT T0298 180 :NARPLEPRLFDRQIAFNLLAQVGAVDAE 1gadO 186 :DGPSHKDWRGGRGASQNIIPSSTGAAKA T0298 220 :VQALLGERIGPLNVTCIQAPVFFGDSLSVTLQCAEPVDLAAVTRVLDAT 1gadO 214 :VGKVLPELNGKLTGMAFRVPTPNVSVVDLTVRLEKAATYEQIKAAVKAA T0298 269 :KGIEWVGEGD 1gadO 268 :KGVLGYTEDD T0298 281 :TVVGDALGQDETYVGR 1gadO 278 :VVSTDFNGEVCTSVFD T0298 297 :VR 1gadO 297 :GI T0298 301 :QADPCQVNLWIVSDNVR 1gadO 299 :ALNDNFVKLVSWYDNET T0298 319 :GAALNAVLLGEL 1gadO 316 :GYSNKVLDLIAH Number of specific fragments extracted= 16 number of extra gaps= 0 total=135 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 1gd1O/T0298-1gd1O-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:# T0298 read from 1gd1O/T0298-1gd1O-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1gd1O read from 1gd1O/T0298-1gd1O-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 (T0298)P4 because first residue in template chain is (1gd1O)A0 Warning: unaligning (T0298)P30 because of BadResidue code BAD_PEPTIDE in next template residue (1gd1O)D24 Warning: unaligning (T0298)L31 because of BadResidue code BAD_PEPTIDE at template residue (1gd1O)D24 Warning: unaligning (T0298)R55 because of BadResidue code BAD_PEPTIDE in next template residue (1gd1O)E76 Warning: unaligning (T0298)V56 because of BadResidue code BAD_PEPTIDE at template residue (1gd1O)E76 Warning: unaligning (T0298)V110 because of BadResidue code BAD_PEPTIDE in next template residue (1gd1O)G131 Warning: unaligning (T0298)S111 because of BadResidue code BAD_PEPTIDE at template residue (1gd1O)G131 Warning: unaligning (T0298)N196 because of BadResidue code BAD_PEPTIDE in next template residue (1gd1O)I203 Warning: unaligning (T0298)L197 because of BadResidue code BAD_PEPTIDE at template residue (1gd1O)I203 Warning: unaligning (T0298)L223 because of BadResidue code BAD_PEPTIDE in next template residue (1gd1O)L218 Warning: unaligning (T0298)L224 because of BadResidue code BAD_PEPTIDE at template residue (1gd1O)L218 T0298 5 :LNVAVVGA 1gd1O 1 :VKVGINGF T0298 14 :GSVGEALVGLLD 1gd1O 9 :GRIGRNVFRAAL T0298 28 :DF 1gd1O 21 :KN T0298 32 :HRLHLLASAESAGQRMGFAE 1gd1O 25 :IEVVAVNDLTDANTLAHLLK T0298 52 :SSL 1gd1O 72 :IVK T0298 57 :GDVDSFDFS 1gd1O 77 :RDPENLAWG T0298 66 :SVGLAFFAAAAEVSRAHAERARAAGCSVIDLSGALEPSV 1gd1O 88 :GVDIVVESTGRFTKREDAAKHLEAGAKKVIISAPAKNED T0298 106 :PPVM 1gd1O 126 :ITIV T0298 112 :VNAERLASQ 1gd1O 132 :VNQDKYDPK T0298 122 :APFLLSSP 1gd1O 140 :AHHVISNA T0298 130 :CAVAA 1gd1O 149 :CTTNC T0298 136 :LCEVLAPLLATLDCRQLNLTACLSVSS 1gd1O 154 :LAPFAKVLHEQFGIVRGMMTTVHSYTN T0298 177 :ELL 1gd1O 181 :DQR T0298 180 :NARPLEPRL 1gd1O 186 :DLPHKDLRR T0298 190 :DRQIAF 1gd1O 196 :ARAAAE T0298 198 :LAQVGAVDAE 1gd1O 204 :IPTTTGAAKA T0298 220 :VQA 1gd1O 214 :VAL T0298 225 :GERIGPLNVTCIQAPVFFGDSLSVTLQCAEPVDLAAVTRVLDAT 1gd1O 219 :PELKGKLNGMAMRVPTPNVSVVDLVAELEKEVTVEEVNAALKAA T0298 269 :KGIEWVGEGDYPTVVGDALGQDETYVGRVRAGQ 1gd1O 266 :ELKGILAYSEEPLVSRDYNGSTVSSTIDALSTM T0298 302 :ADPCQVNLWIVSDN 1gd1O 300 :IDGKMVKVVSWYDN T0298 317 :RKGAALNAVLLGELLIKHYL 1gd1O 314 :ETGYSHRVVDLAAYIASKGL Number of specific fragments extracted= 21 number of extra gaps= 5 total=156 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 1gd1O/T0298-1gd1O-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0298 read from 1gd1O/T0298-1gd1O-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1gd1O read from 1gd1O/T0298-1gd1O-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1gd1O in template set Warning: unaligning (T0298)P4 because first residue in template chain is (1gd1O)A0 Warning: unaligning (T0298)P30 because of BadResidue code BAD_PEPTIDE in next template residue (1gd1O)D24 Warning: unaligning (T0298)L31 because of BadResidue code BAD_PEPTIDE at template residue (1gd1O)D24 Warning: unaligning (T0298)R55 because of BadResidue code BAD_PEPTIDE in next template residue (1gd1O)E76 Warning: unaligning (T0298)V56 because of BadResidue code BAD_PEPTIDE at template residue (1gd1O)E76 Warning: unaligning (T0298)V110 because of BadResidue code BAD_PEPTIDE in next template residue (1gd1O)G131 Warning: unaligning (T0298)S111 because of BadResidue code BAD_PEPTIDE at template residue (1gd1O)G131 Warning: unaligning (T0298)N196 because of BadResidue code BAD_PEPTIDE in next template residue (1gd1O)I203 Warning: unaligning (T0298)L197 because of BadResidue code BAD_PEPTIDE at template residue (1gd1O)I203 Warning: unaligning (T0298)I216 because of BadResidue code BAD_PEPTIDE in next template residue (1gd1O)L218 Warning: unaligning (T0298)F217 because of BadResidue code BAD_PEPTIDE at template residue (1gd1O)L218 T0298 5 :LNVAVVG 1gd1O 1 :VKVGING T0298 13 :TGSVGEALVGLLD 1gd1O 8 :FGRIGRNVFRAAL T0298 28 :DF 1gd1O 21 :KN T0298 32 :HRLHLL 1gd1O 25 :IEVVAV T0298 38 :ASAESAGQRMGFA 1gd1O 34 :TDANTLAHLLKYD T0298 51 :ESSL 1gd1O 71 :IIVK T0298 57 :GDVDSFDFS 1gd1O 77 :RDPENLAWG T0298 66 :SVGLAFFAAAAEVSRAHAERARAAGCSVI 1gd1O 88 :GVDIVVESTGRFTKREDAAKHLEAGAKKV T0298 96 :LSGALEPSVAPPVM 1gd1O 117 :IISAPAKNEDITIV T0298 112 :VNAERLASQ 1gd1O 132 :VNQDKYDPK T0298 122 :APFLLSSP 1gd1O 140 :AHHVISNA T0298 130 :CAVAA 1gd1O 149 :CTTNC T0298 136 :LCEVLAPLLATLDCRQLNLTACLSVSSL 1gd1O 154 :LAPFAKVLHEQFGIVRGMMTTVHSYTND T0298 176 :AELLNARP 1gd1O 182 :QRILDLPH T0298 185 :EPRLFDRQIAF 1gd1O 191 :KDLRRARAAAE T0298 198 :LA 1gd1O 204 :IP T0298 205 :DAEGHSAIERR 1gd1O 206 :TTTGAAKAVAL T0298 218 :AEVQA 1gd1O 219 :PELKG T0298 230 :PLNVTCIQAPVFFGDSLSVTLQCAEPVDLAAVTRVLDAT 1gd1O 224 :KLNGMAMRVPTPNVSVVDLVAELEKEVTVEEVNAALKAA T0298 269 :KGIEWVGEGDYPTVVGDALGQDETYVGRVRAGQAD 1gd1O 266 :ELKGILAYSEEPLVSRDYNGSTVSSTIDALSTMVI T0298 304 :PCQVNLWIVSDN 1gd1O 302 :GKMVKVVSWYDN T0298 317 :RKGAALNAVLLGELLIKHYL 1gd1O 314 :ETGYSHRVVDLAAYIASKGL Number of specific fragments extracted= 22 number of extra gaps= 5 total=178 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 1gd1O/T0298-1gd1O-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0298 read from 1gd1O/T0298-1gd1O-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1gd1O read from 1gd1O/T0298-1gd1O-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1gd1O in template set Warning: unaligning (T0298)P4 because first residue in template chain is (1gd1O)A0 Warning: unaligning (T0298)D28 because of BadResidue code BAD_PEPTIDE in next template residue (1gd1O)D24 Warning: unaligning (T0298)F29 because of BadResidue code BAD_PEPTIDE at template residue (1gd1O)D24 Warning: unaligning (T0298)D58 because of BadResidue code BAD_PEPTIDE in next template residue (1gd1O)E76 Warning: unaligning (T0298)V59 because of BadResidue code BAD_PEPTIDE at template residue (1gd1O)E76 Warning: unaligning (T0298)V110 because of BadResidue code BAD_PEPTIDE in next template residue (1gd1O)G131 Warning: unaligning (T0298)S111 because of BadResidue code BAD_PEPTIDE at template residue (1gd1O)G131 Warning: unaligning (T0298)R187 because of BadResidue code BAD_PEPTIDE in next template residue (1gd1O)I203 Warning: unaligning (T0298)L188 because of BadResidue code BAD_PEPTIDE at template residue (1gd1O)I203 Warning: unaligning (T0298)V201 because of BadResidue code BAD_PEPTIDE in next template residue (1gd1O)L218 Warning: unaligning (T0298)G202 because of BadResidue code BAD_PEPTIDE at template residue (1gd1O)L218 T0298 5 :LNVAVVGA 1gd1O 1 :VKVGINGF T0298 14 :GSVGEALVGLLDER 1gd1O 9 :GRIGRNVFRAALKN T0298 30 :PLHRLHLLASAESA 1gd1O 25 :IEVVAVNDLTDANT T0298 44 :GQRMGFAES 1gd1O 54 :DAEVSVNGN T0298 53 :SLRVG 1gd1O 70 :EIIVK T0298 60 :D 1gd1O 77 :R T0298 61 :SFD 1gd1O 79 :PEN T0298 64 :FS 1gd1O 84 :WG T0298 66 :SVGLAFFAAA 1gd1O 88 :GVDIVVESTG T0298 76 :AEVSR 1gd1O 102 :REDAA T0298 85 :RARAAGCSVIDLSGALEPSV 1gd1O 107 :KHLEAGAKKVIISAPAKNED T0298 106 :PPVM 1gd1O 126 :ITIV T0298 112 :VNAERLAS 1gd1O 132 :VNQDKYDP T0298 121 :AAPFLLSSPCAVAAELCEVLAPLLATLDCRQLNLTACLSVSSLGRE 1gd1O 139 :KAHHVISNASCTTNCLAPFAKVLHEQFGIVRGMMTTVHSYTNDQRI T0298 179 :LNARPLEP 1gd1O 194 :RRARAAAE T0298 189 :FDRQI 1gd1O 204 :IPTTT T0298 194 :AFNLLAQ 1gd1O 210 :AAKAVAL T0298 203 :AVDAEG 1gd1O 219 :PELKGK T0298 231 :LNVTCIQAPVFFGDSLSVTLQCAEPVDLAAVTRVLDAT 1gd1O 225 :LNGMAMRVPTPNVSVVDLVAELEKEVTVEEVNAALKAA T0298 269 :KGIEWVGE 1gd1O 269 :GILAYSEE T0298 280 :PTVVGDALGQDETYVGRVRAGQADPC 1gd1O 277 :PLVSRDYNGSTVSSTIDALSTMVIDG T0298 306 :QVNLWIVSDNV 1gd1O 304 :MVKVVSWYDNE T0298 318 :KGAALNAVLLGELLIKHYL 1gd1O 315 :TGYSHRVVDLAAYIASKGL Number of specific fragments extracted= 23 number of extra gaps= 5 total=201 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 1obfO/T0298-1obfO-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:# T0298 read from 1obfO/T0298-1obfO-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1obfO read from 1obfO/T0298-1obfO-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 (T0298)P4 because first residue in template chain is (1obfO)T1 Warning: unaligning (T0298)V108 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1obfO)V134 Warning: unaligning (T0298)M109 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1obfO)V134 Warning: unaligning (T0298)A131 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1obfO)T155 Warning: unaligning (T0298)L154 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1obfO)T178 Warning: unaligning (T0298)T155 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1obfO)T178 Warning: unaligning (T0298)C157 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1obfO)H181 Warning: unaligning (T0298)L158 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1obfO)H181 Warning: unaligning (T0298)N196 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1obfO)M207 Warning: unaligning (T0298)L197 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1obfO)M207 T0298 5 :LNVAVVGA 1obfO 2 :IRVAINGY T0298 14 :GSVGEALVGLLDERDFP 1obfO 10 :GRIGRNILRAHYEGGKS T0298 31 :LHRLHLLASAESAGQRMGFAE 1obfO 28 :DIEIVAINDLGDPKTNAHLTR T0298 52 :SSLRVGDVDSFDFS 1obfO 75 :RVDANRNPAQLPWG T0298 66 :SVGLAFFAAAAEVSRAHAERARAAGCSVIDLSGALEPS 1obfO 91 :KVDVVLECTGFFTTKEKAGAHIKGGAKKVIISAPGGAD T0298 104 :V 1obfO 130 :D T0298 106 :PP 1obfO 131 :AT T0298 110 :VSVNAERLAS 1obfO 135 :YGVNHGTLKS T0298 122 :APFLLSSP 1obfO 145 :TDTVISNA T0298 132 :VAA 1obfO 156 :TNC T0298 136 :LCEVLAPLLATLDCRQLN 1obfO 159 :LAPLVKPLNDKLGLQDGL T0298 156 :A 1obfO 179 :T T0298 159 :SVSS 1obfO 182 :AYTN T0298 177 :ELL 1obfO 186 :NQV T0298 180 :NARPLEPRL 1obfO 191 :DVYHEDLRR T0298 190 :DRQIAF 1obfO 200 :ARSATM T0298 198 :LA 1obfO 208 :IP T0298 205 :DAEG 1obfO 210 :TKTG T0298 213 :ERRIFAEV 1obfO 214 :AAAAVGDV T0298 224 :LGERIGPLNVTCIQAPVFFGDSLSVTLQCAEPVDLAAVTRVLDAT 1obfO 222 :LPELDGKLNGYAIRVPTINVSIVDLSFVAKRNTTVEEVNGILKAA T0298 269 :KGIEWVGEGDYPTVVGDALGQDETYVGRVRAGQADPCQVNLWIVSDN 1obfO 270 :ELKGILDYNTEPLVSVDYNHDPASSTVDASLTKVSGRLVKVSSWYDN T0298 317 :RKGAALNAVLLGELLIK 1obfO 317 :EWGFSNRMLDTTVALMS Number of specific fragments extracted= 22 number of extra gaps= 4 total=223 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 1obfO/T0298-1obfO-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0298 read from 1obfO/T0298-1obfO-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1obfO read from 1obfO/T0298-1obfO-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1obfO in template set Warning: unaligning (T0298)P4 because first residue in template chain is (1obfO)T1 Warning: unaligning (T0298)V108 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1obfO)V134 Warning: unaligning (T0298)M109 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1obfO)V134 Warning: unaligning (T0298)A131 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1obfO)T155 Warning: unaligning (T0298)L154 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1obfO)T178 Warning: unaligning (T0298)T155 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1obfO)T178 Warning: unaligning (T0298)C157 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1obfO)H181 Warning: unaligning (T0298)L158 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1obfO)H181 Warning: unaligning (T0298)N196 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1obfO)M207 Warning: unaligning (T0298)L197 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1obfO)M207 T0298 5 :LNVAVVG 1obfO 2 :IRVAING T0298 13 :TGSVGEALVGLLDER 1obfO 9 :YGRIGRNILRAHYEG T0298 28 :DFPLHRLHLLASAESAGQRMGFA 1obfO 28 :DIEIVAINDLGDPKTNAHLTRYD T0298 51 :ESSLRVGDVDSFDFS 1obfO 74 :IRVDANRNPAQLPWG T0298 66 :SVGLAFFAAAAEVSRAHAERARAAGCSVI 1obfO 91 :KVDVVLECTGFFTTKEKAGAHIKGGAKKV T0298 96 :LSGALEPSVA 1obfO 120 :IISAPGGADV T0298 106 :PP 1obfO 131 :AT T0298 110 :VSVNAERLAS 1obfO 135 :YGVNHGTLKS T0298 122 :APFLLSSP 1obfO 145 :TDTVISNA T0298 132 :VAA 1obfO 156 :TNC T0298 136 :LCEVLAPLLATLDCRQLN 1obfO 159 :LAPLVKPLNDKLGLQDGL T0298 156 :A 1obfO 179 :T T0298 159 :SVSSL 1obfO 182 :AYTNN T0298 176 :AELLNARP 1obfO 187 :QVLTDVYH T0298 185 :EPRLFDRQIAF 1obfO 195 :EDLRRARSATM T0298 198 :LA 1obfO 208 :IP T0298 205 :DAEGHSAIERRIFAEVQA 1obfO 210 :TKTGAAAAVGDVLPELDG T0298 230 :PLNVTCIQAPVFFGDSLSVTLQCAEPVDLAAVTRVLDAT 1obfO 228 :KLNGYAIRVPTINVSIVDLSFVAKRNTTVEEVNGILKAA T0298 269 :KGIEWVGEGDYPTVVGDALGQDETYVGRVRAGQADPCQVNLWIVSDN 1obfO 270 :ELKGILDYNTEPLVSVDYNHDPASSTVDASLTKVSGRLVKVSSWYDN T0298 317 :RKGAALNAVLLGELLIK 1obfO 317 :EWGFSNRMLDTTVALMS Number of specific fragments extracted= 20 number of extra gaps= 4 total=243 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 1obfO/T0298-1obfO-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0298 read from 1obfO/T0298-1obfO-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1obfO read from 1obfO/T0298-1obfO-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1obfO in template set Warning: unaligning (T0298)P4 because first residue in template chain is (1obfO)T1 Warning: unaligning (T0298)V108 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1obfO)V134 Warning: unaligning (T0298)M109 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1obfO)V134 Warning: unaligning (T0298)C130 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1obfO)T155 Warning: unaligning (T0298)V132 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1obfO)T155 Warning: unaligning (T0298)L154 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1obfO)T178 Warning: unaligning (T0298)T155 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1obfO)T178 Warning: unaligning (T0298)C157 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1obfO)H181 Warning: unaligning (T0298)L158 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1obfO)H181 Warning: unaligning (T0298)N196 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1obfO)M207 Warning: unaligning (T0298)L197 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1obfO)M207 T0298 5 :LNVAVVGA 1obfO 2 :IRVAINGY T0298 14 :GSVGEALVGLLDERDFPLHRLHLLA 1obfO 10 :GRIGRNILRAHYEGGKSHDIEIVAI T0298 39 :SAESA 1obfO 36 :DLGDP T0298 44 :GQRMGFAES 1obfO 57 :PGTVSVNGS T0298 53 :SLRVGDVDSFDFS 1obfO 73 :KIRVDANRNPAQL T0298 67 :VGLAFFAAA 1obfO 92 :VDVVLECTG T0298 80 :RAHAERARAAGCSVIDLSGALEPSVAPP 1obfO 105 :KEKAGAHIKGGAKKVIISAPGGADVDAT T0298 110 :VSVNAERLA 1obfO 135 :YGVNHGTLK T0298 121 :AAPFLLSSP 1obfO 144 :STDTVISNA T0298 133 :AAELCEVLAPLLATLDCRQLN 1obfO 156 :TNCLAPLVKPLNDKLGLQDGL T0298 156 :A 1obfO 179 :T T0298 159 :SVSSLGRE 1obfO 182 :AYTNNQVL T0298 180 :NARPLEPRLFDRQIAF 1obfO 190 :TDVYHEDLRRARSATM T0298 198 :LAQVGA 1obfO 208 :IPTKTG T0298 216 :IFAEVQALLGERIGPLNVTCIQAPVFFGDSLSVTLQCAEPVDLAAVTRVLDAT 1obfO 214 :AAAAVGDVLPELDGKLNGYAIRVPTINVSIVDLSFVAKRNTTVEEVNGILKAA T0298 269 :KGIEWVGEG 1obfO 272 :KGILDYNTE T0298 280 :PTVVGDALGQDETYVGRVRAGQADPCQVNLWIVSDNV 1obfO 281 :PLVSVDYNHDPASSTVDASLTKVSGRLVKVSSWYDNE T0298 318 :KGAALNAVLLGELLIK 1obfO 318 :WGFSNRMLDTTVALMS Number of specific fragments extracted= 18 number of extra gaps= 4 total=261 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 1mb4A/T0298-1mb4A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1mb4A expands to /projects/compbio/data/pdb/1mb4.pdb.gz 1mb4A:# T0298 read from 1mb4A/T0298-1mb4A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1mb4A read from 1mb4A/T0298-1mb4A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1mb4A to template set # found chain 1mb4A in template set Warning: unaligning (T0298)L5 because first residue in template chain is (1mb4A)M1 T0298 6 :NVAVVGATGSVGEALVGLLDERD 1mb4A 2 :RVGLVGWRGMVGSVLMQRMVEER T0298 29 :FPLHRLHLL 1mb4A 26 :FDLIEPVFF T0298 39 :SAESAGQRMGFAESSLR 1mb4A 35 :STSQIGVPAPNFGKDAG T0298 56 :VGDVDSFD 1mb4A 53 :LHDAFDIE T0298 64 :FSSVGLAFFAAAAEVSRAHAERARAAGCS 1mb4A 62 :LKQLDAVITCQGGSYTEKVYPALRQAGWK T0298 93 :VIDLSGALEPS 1mb4A 93 :WIDAASTLRMD T0298 104 :VAPPVMVSVNAERLAS 1mb4A 105 :EAIITLDPVNLKQILH T0298 120 :QAAPFLLSSPCAVAA 1mb4A 124 :HGTKTFVGGNCTVSL T0298 136 :LCEVLAPLLATLDCRQLNLTACLSVSSLGREGVKEL 1mb4A 139 :MLMALGGLYERGLVEWMSAMTYQAASGAGAQNMREL T0298 172 :ARQTAELLN 1mb4A 178 :MGVINDAVS T0298 181 :ARPLEPRL 1mb4A 191 :NPASSILD T0298 189 :FDRQIAFNLLAQVGAVDAEGHSAIERRIFAEVQALLG 1mb4A 217 :FGVPLAGSLIPWIDVKRDNGQSKEEWKAGVEANKILG T0298 226 :ERIGPLNVTCIQAPVFFGDSLSVTLQCAEPVDLAAVTRVLDAT 1mb4A 256 :DSPVPIDGTCVRIGAMRCHSQALTIKLKQNIPLDEIEEMIATH T0298 269 :KGIEWVGE 1mb4A 300 :DWVKVIPN T0298 285 :DALGQDETYVGRVRAGQADPCQVNLWIVSDNVRKGAALNAVLLGELLIK 1mb4A 320 :KVTGTLSVPVGRLRKMAMGDDFLNAFTVGDQLLWGAAEPLRRTLRIILA Number of specific fragments extracted= 15 number of extra gaps= 0 total=276 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 1mb4A/T0298-1mb4A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0298 read from 1mb4A/T0298-1mb4A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1mb4A read from 1mb4A/T0298-1mb4A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1mb4A in template set Warning: unaligning (T0298)L5 because first residue in template chain is (1mb4A)M1 T0298 6 :NVAVVGATGSVGEALVGLLDERD 1mb4A 2 :RVGLVGWRGMVGSVLMQRMVEER T0298 29 :FPLHRLHLLASAESAGQRMGFAESSLRVGDVDSFD 1mb4A 26 :FDLIEPVFFSTSQIGVPAPNFGKDAGMLHDAFDIE T0298 64 :FSSVGLAFFAAAAEVSRAHAERARAAGCS 1mb4A 62 :LKQLDAVITCQGGSYTEKVYPALRQAGWK T0298 93 :VIDLSGALEPS 1mb4A 93 :WIDAASTLRMD T0298 104 :VAPPVMVSVNAERLA 1mb4A 105 :EAIITLDPVNLKQIL T0298 119 :SQAAPFLLSSPCAVAA 1mb4A 123 :HHGTKTFVGGNCTVSL T0298 136 :LCEVLAPLLATLDCRQLNLTACLSVSSLGREGVKELARQTAELLNARPL 1mb4A 139 :MLMALGGLYERGLVEWMSAMTYQAASGAGAQNMRELISQMGVINDAVSS T0298 185 :EPRLFDRQIAFNLLAQVGAVDAEGHSAIERRIFAEVQALLG 1mb4A 213 :PTDNFGVPLAGSLIPWIDVKRDNGQSKEEWKAGVEANKILG T0298 226 :ERIGPLNVTCIQAPVFFGDSLSVTLQCAEPVDLAAVTRVLDAT 1mb4A 256 :DSPVPIDGTCVRIGAMRCHSQALTIKLKQNIPLDEIEEMIATH T0298 269 :KGIEWVGE 1mb4A 300 :DWVKVIPN T0298 284 :GDALGQDETYVGRVRAGQADPCQVNLWIVSDNVRKGAALNAVLLGELLIK 1mb4A 319 :AKVTGTLSVPVGRLRKMAMGDDFLNAFTVGDQLLWGAAEPLRRTLRIILA Number of specific fragments extracted= 11 number of extra gaps= 0 total=287 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 1mb4A/T0298-1mb4A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0298 read from 1mb4A/T0298-1mb4A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1mb4A read from 1mb4A/T0298-1mb4A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1mb4A in template set Warning: unaligning (T0298)L5 because first residue in template chain is (1mb4A)M1 T0298 6 :NVAVVGATGSVGEALVGLLDERDFPLHRLHLLASAESAGQRMGFAES 1mb4A 2 :RVGLVGWRGMVGSVLMQRMVEERDFDLIEPVFFSTSQIGVPAPNFGK T0298 53 :SLRVGDVDSFDFSSVGLAFFAAAAEVSRAHAERARAAGC 1mb4A 51 :GMLHDAFDIESLKQLDAVITCQGGSYTEKVYPALRQAGW T0298 92 :SVIDLSGALEPS 1mb4A 92 :YWIDAASTLRMD T0298 104 :VAPPVMVSVNAERLASQ 1mb4A 105 :EAIITLDPVNLKQILHG T0298 121 :AAPFLLSSPCAVAAELCEVLAPLLATLDCRQLNLTACLSVSSLGREGVKELARQTAEL 1mb4A 124 :HGTKTFVGGNCTVSLMLMALGGLYERGLVEWMSAMTYQAASGAGAQNMRELISQMGVI T0298 179 :LNARPLEPRLFDRQIAFNLLAQVGAVDAEGHSAIERRIFAEVQALLG 1mb4A 207 :MRSGSFPTDNFGVPLAGSLIPWIDVKRDNGQSKEEWKAGVEANKILG T0298 226 :ERIGPLNVTCIQAPVFFGDSLSVTLQCAEPVDLAAVTRVLDATKGIEWVGEG 1mb4A 256 :DSPVPIDGTCVRIGAMRCHSQALTIKLKQNIPLDEIEEMIATHNDWVKVIPN T0298 281 :TVVGDALGQDETYVGRVRAGQADPCQVNLWIVSDNVRKGAALNAVLLGELLIK 1mb4A 316 :LTPAKVTGTLSVPVGRLRKMAMGDDFLNAFTVGDQLLWGAAEPLRRTLRIILA Number of specific fragments extracted= 8 number of extra gaps= 0 total=295 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 1brmA/T0298-1brmA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1brmA expands to /projects/compbio/data/pdb/1brm.pdb.gz 1brmA:# T0298 read from 1brmA/T0298-1brmA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1brmA read from 1brmA/T0298-1brmA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1brmA to template set # found chain 1brmA in template set Warning: unaligning (T0298)G202 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1brmA)W243 Warning: unaligning (T0298)R214 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1brmA)W243 T0298 1 :M 1brmA 1 :M T0298 5 :LNVAVVGATGSVGEALVGLLDERD 1brmA 2 :KNVGFIGWRGMVGSVLMQRMVEER T0298 29 :FPLHRLHLL 1brmA 27 :FDAIRPVFF T0298 39 :SAESAGQRMGFAESS 1brmA 36 :STSQLGQAAPSFGGT T0298 54 :LRVGDVDSFD 1brmA 52 :GTLQDAFDLE T0298 64 :FSSVGLAFFAAAAEVSRAHAERARAAGC 1brmA 63 :LKALDIIVTCQGGDYTNEIYPKLRESGW T0298 92 :SVIDLSGALEPS 1brmA 93 :YWIDAASSLRMK T0298 104 :VAPPVMVSVNAERLASQA 1brmA 106 :DAIIILDPVNQDVITDGL T0298 122 :A 1brmA 126 :G T0298 123 :PFLLSSPCAVAA 1brmA 128 :RTFVGGNCTVSL T0298 136 :LCEVLAPLLATLDCRQLNLTACLSVSSLGREGVKEL 1brmA 140 :MLMSLGGLFANDLVDWVSVATYQAASGGGARHMREL T0298 172 :ARQTAELLNARPLEPRL 1brmA 183 :YGHVADELATPSSAILD T0298 189 :FDRQIAFNLLAQV 1brmA 218 :FGVPLAGSLIPWI T0298 215 :RIFAEVQALLG 1brmA 244 :KGQAETNKILN T0298 226 :ERIGPLNVTCIQAPVFFGDSLSVTLQCAEPVDLAAVTRVLDAT 1brmA 256 :SSVIPVDGLCVRVGALRCHSQAFTIKLKKDVSIPTVEELLAAH T0298 269 :KGIEWVGE 1brmA 300 :PWAKVVPN T0298 284 :GDALGQDETYVGRVRAGQADPCQVNLWIVSDNVRKGAALNAVLLGELL 1brmA 319 :AAVTGTLTTPVGRLRKLNMGPEFLSAFTVGDQLLWGAAEPLRRMLRQL Number of specific fragments extracted= 17 number of extra gaps= 0 total=312 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 1brmA/T0298-1brmA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0298 read from 1brmA/T0298-1brmA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1brmA read from 1brmA/T0298-1brmA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1brmA in template set Warning: unaligning (T0298)P4 because first residue in template chain is (1brmA)M1 Warning: unaligning (T0298)G202 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1brmA)W243 Warning: unaligning (T0298)R214 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1brmA)W243 T0298 5 :LNVAVVGATGSVGEALVGLLDERD 1brmA 2 :KNVGFIGWRGMVGSVLMQRMVEER T0298 29 :FPLHRLHLLASAESAGQRMGFAESSLRVGDVDSFD 1brmA 27 :FDAIRPVFFSTSQLGQAAPSFGGTTGTLQDAFDLE T0298 64 :FSSVGLAFFAAAAEVSRAHAERARAAGC 1brmA 63 :LKALDIIVTCQGGDYTNEIYPKLRESGW T0298 92 :SVIDLSGALEP 1brmA 93 :YWIDAASSLRM T0298 103 :SVAPPVMVSVNAERLA 1brmA 105 :DDAIIILDPVNQDVIT T0298 119 :SQ 1brmA 125 :NG T0298 122 :APFLLSSPCAVAA 1brmA 127 :IRTFVGGNCTVSL T0298 136 :LCEVLAPLLATLDCRQLNLTACLSVSSLGREGVKELARQTAEL 1brmA 140 :MLMSLGGLFANDLVDWVSVATYQAASGGGARHMRELLTQMGHL T0298 179 :LNARPL 1brmA 190 :LATPSS T0298 185 :EPRLFDRQIAFNLLAQV 1brmA 214 :PVDNFGVPLAGSLIPWI T0298 215 :RIFAEVQALLG 1brmA 244 :KGQAETNKILN T0298 226 :ERIGPLNVTCIQAPVFFGDSLSVTLQCAEPVDLAAVTRVLDAT 1brmA 256 :SSVIPVDGLCVRVGALRCHSQAFTIKLKKDVSIPTVEELLAAH T0298 269 :KGIEWVGE 1brmA 300 :PWAKVVPN T0298 283 :VGDALGQDETYVGRVRAGQADPCQVNLWIVSDNVRKGAALNAVLLGELL 1brmA 318 :PAAVTGTLTTPVGRLRKLNMGPEFLSAFTVGDQLLWGAAEPLRRMLRQL Number of specific fragments extracted= 14 number of extra gaps= 0 total=326 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 1brmA/T0298-1brmA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0298 read from 1brmA/T0298-1brmA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1brmA read from 1brmA/T0298-1brmA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1brmA in template set Warning: unaligning (T0298)G202 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1brmA)W243 Warning: unaligning (T0298)R214 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1brmA)W243 T0298 5 :LNVAVVGATGSVGEALVGLLDERDFPLHRLHLLASAESAGQRM 1brmA 2 :KNVGFIGWRGMVGSVLMQRMVEERDFDAIRPVFFSTSQLGQAA T0298 48 :GFAESSLRVGDV 1brmA 46 :SFGGTTGTLQDA T0298 60 :DSFDFSSVGLAFFAAAAEVSRAHAERARAAGC 1brmA 59 :DLEALKALDIIVTCQGGDYTNEIYPKLRESGW T0298 92 :SVIDLSGALEPS 1brmA 93 :YWIDAASSLRMK T0298 104 :VAPPVMVSVNAERLASQ 1brmA 106 :DAIIILDPVNQDVITDG T0298 121 :AAPFLLSSPCAVAAELCEVLAPLLATLDCRQLNLTACLSVSSLGREGVKELARQTAEL 1brmA 125 :NGIRTFVGGNCTVSLMLMSLGGLFANDLVDWVSVATYQAASGGGARHMRELLTQMGHL T0298 179 :LNARPLEPRLFDRQIAFNLLAQV 1brmA 208 :TRSGELPVDNFGVPLAGSLIPWI T0298 215 :RIFAEVQALLG 1brmA 244 :KGQAETNKILN T0298 226 :ERIGPLNVTCIQAPVFFGDSLSVTLQCAEPVDLAAVTRVLDATKGIEWVGEG 1brmA 256 :SSVIPVDGLCVRVGALRCHSQAFTIKLKKDVSIPTVEELLAAHNPWAKVVPN T0298 281 :TVVGDALGQDETYVGRVRAGQADPCQVNLWIVSDNVRKGAALNAVLLGELL 1brmA 316 :LTPAAVTGTLTTPVGRLRKLNMGPEFLSAFTVGDQLLWGAAEPLRRMLRQL Number of specific fragments extracted= 10 number of extra gaps= 0 total=336 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 1ys4A/T0298-1ys4A-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 # T0298 read from 1ys4A/T0298-1ys4A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ys4A read from 1ys4A/T0298-1ys4A-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 (T0298)V108 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1ys4A)I127 Warning: unaligning (T0298)M109 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1ys4A)I127 T0298 1 :M 1ys4A 7 :M T0298 4 :PLNVAVVGATGSVGEALVGLLD 1ys4A 8 :KIKVGVLGATGSVGQRFVQLLA T0298 28 :DFPLHRLHLL 1ys4A 30 :DHPMFELTAL T0298 38 :ASAESAGQRMGFAE 1ys4A 41 :ASERSAGKKYKDAC T0298 52 :SSLRVGDVDSFDFSSVGLAFFAAAAEVSRAHAERARAAGCSVIDLSGALEPS 1ys4A 69 :MVVIPTDPKHEEFEDVDIVFSALPSDLAKKFEPEFAKEGKLIFSNASAYRME T0298 104 :VAPP 1ys4A 122 :DVPL T0298 110 :VSVNAERLA 1ys4A 128 :PEVNADHLE T0298 119 :S 1ys4A 143 :E T0298 120 :QAAPFLLSSP 1ys4A 146 :GWDGAIITNP T0298 130 :CAVAA 1ys4A 157 :CSTIC T0298 136 :LCEVLAPLLATLDCRQLNLTACLSVSSLGREG 1ys4A 162 :AVITLKPIMDKFGLEAVFIATMQAVSGAGYNG T0298 168 :VKELARQ 1ys4A 196 :SMAILDN T0298 178 :LLN 1ys4A 203 :LIP T0298 205 :DAEGH 1ys4A 206 :FIKNE T0298 213 :ERRIFAEVQALLGER 1ys4A 211 :EEKMQTESLKLLGTL T0298 228 :IGPLNVTCIQAPVFFGDSLSVTLQCAEPVDLAAVTRVLDAT 1ys4A 234 :NFKISASCNRVAVIDGHTESIFVKTKEGAEPEEIKEVMDKF T0298 269 :KGIEWVGEGDYPTVVGDAL 1ys4A 287 :KPIVIREEIDRPQPRLDRN T0298 288 :GQDETYVGRVRAGQADP 1ys4A 308 :NGMSIVVGRIRKDPIFD T0298 307 :VNLWIVSDNVRKGAALNAVLLGELLIKHY 1ys4A 325 :VKYTALEHNTIRGAAGASVLNAEYFVKKY Number of specific fragments extracted= 19 number of extra gaps= 1 total=355 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 1ys4A/T0298-1ys4A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0298 read from 1ys4A/T0298-1ys4A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ys4A read from 1ys4A/T0298-1ys4A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1ys4A in template set Warning: unaligning (T0298)Q3 because first residue in template chain is (1ys4A)M7 Warning: unaligning (T0298)V108 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1ys4A)I127 Warning: unaligning (T0298)M109 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1ys4A)I127 T0298 4 :PLNVAVVGATGSVGEALVGLLD 1ys4A 8 :KIKVGVLGATGSVGQRFVQLLA T0298 28 :DFPLHRLHLL 1ys4A 30 :DHPMFELTAL T0298 38 :ASAESAGQRMGFA 1ys4A 41 :ASERSAGKKYKDA T0298 51 :ESSLRVGDVDSFDFSSVGLAFFAAAAEVSRAHAERARAAGCSVIDLSGALEPS 1ys4A 68 :DMVVIPTDPKHEEFEDVDIVFSALPSDLAKKFEPEFAKEGKLIFSNASAYRME T0298 104 :VAPP 1ys4A 122 :DVPL T0298 110 :VSVNAERLA 1ys4A 128 :PEVNADHLE T0298 120 :QAAPFLLSSP 1ys4A 146 :GWDGAIITNP T0298 130 :CAVAA 1ys4A 157 :CSTIC T0298 136 :LCEVLAPLLATLDCRQLNLTACLSVSSLGREG 1ys4A 162 :AVITLKPIMDKFGLEAVFIATMQAVSGAGYNG T0298 181 :ARP 1ys4A 194 :VPS T0298 187 :RLFDRQ 1ys4A 197 :MAILDN T0298 205 :DAEGHSAIERRIFAEVQALLG 1ys4A 203 :LIPFIKNEEEKMQTESLKLLG T0298 226 :ER 1ys4A 227 :DG T0298 228 :IGPLNVTCIQAPVFFGDSLSVTLQCAEPVDLAAVTRVLDAT 1ys4A 234 :NFKISASCNRVAVIDGHTESIFVKTKEGAEPEEIKEVMDKF T0298 269 :KGIEWVGEGDYPTVV 1ys4A 287 :KPIVIREEIDRPQPR T0298 284 :GDALGQDETYVGRVRAGQADP 1ys4A 304 :RNEGNGMSIVVGRIRKDPIFD T0298 307 :VNLWIVSDNVRKGAALNAVLLGELLIKHYL 1ys4A 325 :VKYTALEHNTIRGAAGASVLNAEYFVKKYI Number of specific fragments extracted= 17 number of extra gaps= 1 total=372 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 1ys4A/T0298-1ys4A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0298 read from 1ys4A/T0298-1ys4A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ys4A read from 1ys4A/T0298-1ys4A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1ys4A in template set Warning: unaligning (T0298)Q3 because first residue in template chain is (1ys4A)M7 Warning: unaligning (T0298)V108 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1ys4A)I127 Warning: unaligning (T0298)M109 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1ys4A)I127 T0298 4 :PLNVAVVGATGSVGEALVGLLDERDFPLHRLHL 1ys4A 8 :KIKVGVLGATGSVGQRFVQLLADHPMFELTALA T0298 38 :ASAESAGQR 1ys4A 41 :ASERSAGKK T0298 47 :MGFAES 1ys4A 56 :WFQDRD T0298 53 :SLRVGDVD 1ys4A 68 :DMVVIPTD T0298 61 :SFDFSSVGLAFFAAAAEVSRAHAERARAAGCSVIDLSGALEPS 1ys4A 78 :HEEFEDVDIVFSALPSDLAKKFEPEFAKEGKLIFSNASAYRME T0298 104 :VAPP 1ys4A 122 :DVPL T0298 110 :VSVNAERLASQ 1ys4A 128 :PEVNADHLELI T0298 121 :AAPFLLSSPCAVAAELCEVLAPLLATLDCRQLNLTACLSVSSLGREG 1ys4A 147 :WDGAIITNPNCSTICAVITLKPIMDKFGLEAVFIATMQAVSGAGYNG T0298 184 :LEPRLFD 1ys4A 194 :VPSMAIL T0298 195 :FNLLAQV 1ys4A 201 :DNLIPFI T0298 210 :SAIERRIFAEVQALLG 1ys4A 208 :KNEEEKMQTESLKLLG T0298 226 :ER 1ys4A 227 :DG T0298 228 :IGPLNVTCIQAPVFFGDSLSVTLQCAEPVDLAAVTRVLDATKG 1ys4A 234 :NFKISASCNRVAVIDGHTESIFVKTKEGAEPEEIKEVMDKFDP T0298 271 :IEWVGEGDYPTVV 1ys4A 289 :IVIREEIDRPQPR T0298 284 :GDALGQDETYVGRVRAGQ 1ys4A 304 :RNEGNGMSIVVGRIRKDP T0298 304 :PCQVNLWIVSDNVRKGAALNAVLLGELLIKHYL 1ys4A 322 :IFDVKYTALEHNTIRGAAGASVLNAEYFVKKYI Number of specific fragments extracted= 16 number of extra gaps= 1 total=388 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 1xygD/T0298-1xygD-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1xygD expands to /projects/compbio/data/pdb/1xyg.pdb.gz 1xygD:# T0298 read from 1xygD/T0298-1xygD-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1xygD read from 1xygD/T0298-1xygD-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1xygD to template set # found chain 1xygD in template set Warning: unaligning (T0298)Q3 because first residue in template chain is (1xygD)K15 T0298 4 :PLNVAVVGATGSVGEALVGLLD 1xygD 16 :DIRIGLLGASGYTGAEIVRLLA T0298 28 :DFPLHRLHLLASAESAGQRMGFAESSLR 1xygD 38 :NHPHFQVTLMTADRKAGQSMESVFPHLR T0298 56 :VGDVDSFDFSSVGLAFFAAAAEVSRAHAE 1xygD 72 :LVSVKDADFSTVDAVFCCLPHGTTQEIIK T0298 89 :AGCSVIDLSGALEPSV 1xygD 104 :TALKIVDLSADFRLRN T0298 105 :APPVMVSVNAERLA 1xygD 140 :VVYGLTEILREDIK T0298 122 :APFLLSSP 1xygD 154 :KARLVANP T0298 130 :CAVAA 1xygD 163 :CYPTT T0298 136 :LCEVLAPLLATLDCR 1xygD 168 :IQLPLVPLLKANLIK T0298 151 :QLNLTACLSVSSLG 1xygD 185 :NIIIDAKSGVSGAG T0298 165 :REG 1xygD 203 :EAN T0298 168 :VKELAR 1xygD 207 :YSEIAE T0298 178 :LLNARPL 1xygD 213 :GISSYGV T0298 205 :DAEGHSAIERRIFAEV 1xygD 220 :TRHRHVPEIEQGLSDV T0298 225 :GERIGPLNVTCIQAPVFFGDSLSVTLQCAEPVDLAAVTRVLDAT 1xygD 236 :AQSKVTVSFTPHLMPMIRGMQSTIYVEMAPGVRTEDLHQQLKTS T0298 269 :KGIEWVGEGDYPTVV 1xygD 284 :EFVKVLDEGVVPRTH T0298 285 :DALGQDETYVG 1xygD 299 :NVRGSNYCHMS T0298 297 :VRAGQ 1xygD 310 :VFPDR T0298 303 :DPCQVNLWIVSDNVRKGAALNAVLLGELLIKHYL 1xygD 315 :IPGRAIIISVIDNLVKGASGQALQNLNIMLGYPE Number of specific fragments extracted= 18 number of extra gaps= 0 total=406 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 1xygD/T0298-1xygD-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0298 read from 1xygD/T0298-1xygD-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1xygD read from 1xygD/T0298-1xygD-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1xygD in template set Warning: unaligning (T0298)Q3 because first residue in template chain is (1xygD)K15 T0298 4 :PLNVAVVGATGSVGEALVGLLD 1xygD 16 :DIRIGLLGASGYTGAEIVRLLA T0298 28 :DFPLHRLHLLASAESAGQRMGFAESSLR 1xygD 38 :NHPHFQVTLMTADRKAGQSMESVFPHLR T0298 56 :VGDVDSFDFSSVGLAFFAAAAEVSRAHAE 1xygD 72 :LVSVKDADFSTVDAVFCCLPHGTTQEIIK T0298 89 :AGCSVIDLSGALEPSV 1xygD 104 :TALKIVDLSADFRLRN T0298 105 :APPVMVSVNAERLA 1xygD 140 :VVYGLTEILREDIK T0298 122 :APFLLSSP 1xygD 154 :KARLVANP T0298 130 :CAVAA 1xygD 163 :CYPTT T0298 136 :LCEVLAPLLATLDCR 1xygD 168 :IQLPLVPLLKANLIK T0298 151 :QLNLTACLSVSSLGR 1xygD 185 :NIIIDAKSGVSGAGR T0298 181 :ARP 1xygD 200 :GAK T0298 186 :PRLFDRQIA 1xygD 203 :EANLYSEIA T0298 202 :GAVDAEGHSAIERRIFAEVQA 1xygD 217 :YGVTRHRHVPEIEQGLSDVAQ T0298 227 :RIGPLNVTCIQAPVFFGDSLSVTLQCAEPVDLAAVTRVLDAT 1xygD 238 :SKVTVSFTPHLMPMIRGMQSTIYVEMAPGVRTEDLHQQLKTS T0298 269 :KGIEWVGEGDYPTVV 1xygD 284 :EFVKVLDEGVVPRTH T0298 285 :DALGQDETYVGRVR 1xygD 299 :NVRGSNYCHMSVFP T0298 301 :QADPCQVNLWIVSDNVRKGAALNAVLLGELLIK 1xygD 313 :DRIPGRAIIISVIDNLVKGASGQALQNLNIMLG Number of specific fragments extracted= 16 number of extra gaps= 0 total=422 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 1xygD/T0298-1xygD-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0298 read from 1xygD/T0298-1xygD-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1xygD read from 1xygD/T0298-1xygD-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1xygD in template set Warning: unaligning (T0298)Q3 because first residue in template chain is (1xygD)K15 T0298 4 :PLNVAVVGATGSVGEALVGLLDERDFPLHRLHLLASAESA 1xygD 16 :DIRIGLLGASGYTGAEIVRLLANHPHFQVTLMTADRKAGQ T0298 46 :R 1xygD 56 :S T0298 47 :MGFAESS 1xygD 62 :PHLRAQK T0298 54 :LRVGDVDSFDFSSVGLAFFAAAAEVSRAHAE 1xygD 70 :PTLVSVKDADFSTVDAVFCCLPHGTTQEIIK T0298 89 :AGCSVIDLSGALEPS 1xygD 104 :TALKIVDLSADFRLR T0298 109 :MVSVNAERLASQAAPFLLSSPCAVAAELCEVLAPLLA 1xygD 141 :VYGLTEILREDIKKARLVANPGCYPTTIQLPLVPLLK T0298 146 :TLDCRQLNLTACLSVSSLGRE 1xygD 180 :LIKHENIIIDAKSGVSGAGRG T0298 184 :LEPRLFDRQIA 1xygD 201 :AKEANLYSEIA T0298 202 :GAVDAEGHSAIERRIFAEVQALLGERIGPLNVTCIQAPVFFGDSLSVTLQCAEPVDLAAVTRVLDAT 1xygD 213 :GISSYGVTRHRHVPEIEQGLSDVAQSKVTVSFTPHLMPMIRGMQSTIYVEMAPGVRTEDLHQQLKTS T0298 269 :KG 1xygD 281 :ED T0298 271 :IEWVGEGDYPTVVGDALGQDETYVGR 1xygD 285 :FVKVLDEGVVPRTHNVRGSNYCHMSV T0298 299 :AGQADPCQVNLWIVSDNVRKGAALNAVLLGELLI 1xygD 311 :FPDRIPGRAIIISVIDNLVKGASGQALQNLNIML Number of specific fragments extracted= 12 number of extra gaps= 0 total=434 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 1u8fO/T0298-1u8fO-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1u8fO expands to /projects/compbio/data/pdb/1u8f.pdb.gz 1u8fO:Skipped atom 702, because occupancy 0.500 <= existing 0.500 in 1u8fO Skipped atom 704, because occupancy 0.500 <= existing 0.500 in 1u8fO Skipped atom 706, because occupancy 0.500 <= existing 0.500 in 1u8fO Skipped atom 708, because occupancy 0.500 <= existing 0.500 in 1u8fO Skipped atom 710, because occupancy 0.500 <= existing 0.500 in 1u8fO Skipped atom 712, because occupancy 0.500 <= existing 0.500 in 1u8fO Skipped atom 714, because occupancy 0.500 <= existing 0.500 in 1u8fO Skipped atom 716, because occupancy 0.500 <= existing 0.500 in 1u8fO Skipped atom 718, because occupancy 0.500 <= existing 0.500 in 1u8fO # T0298 read from 1u8fO/T0298-1u8fO-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1u8fO read from 1u8fO/T0298-1u8fO-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1u8fO to template set # found chain 1u8fO in template set Warning: unaligning (T0298)P4 because first residue in template chain is (1u8fO)K3 Warning: unaligning (T0298)Y335 because last residue in template chain is (1u8fO)E335 T0298 5 :LNVAVVGA 1u8fO 4 :VKVGVNGF T0298 14 :GSVGEALVGLLDERD 1u8fO 12 :GRIGRLVTRAAFNSG T0298 31 :LHRLHLLASAE 1u8fO 27 :KVDIVAINDPF T0298 42 :SAGQRMGFAE 1u8fO 39 :DLNYMVYMFQ T0298 52 :SSLRVGDVDSFDFS 1u8fO 75 :TIFQERDPSKIKWG T0298 66 :SVGLAFFAAAAEVSRAHAERARAAGCSVIDLSGA 1u8fO 91 :GAEYVVESTGVFTTMEKAGAHLQGGAKRVIISAP T0298 102 :PSVAPPVMVSVNAERLAS 1u8fO 125 :SADAPMFVMGVNHEKYDN T0298 122 :APFLLSSP 1u8fO 143 :SLKIISNA T0298 130 :CAVAA 1u8fO 152 :CTTNC T0298 136 :LCEVLAPLLATLDCRQLNLTACLSVSS 1u8fO 157 :LAPLAKVIHDNFGIVEGLMTTVHAITA T0298 175 :TAELLNARPLEPRLFDRQIAFNLLA 1u8fO 184 :TQKTVDGPSGKLWRDGRGALQNIIP T0298 205 :DAEG 1u8fO 209 :ASTG T0298 213 :ERRIFAEV 1u8fO 213 :AAKAVGKV T0298 224 :LGERIGPLNVTCIQAPVFFGDSLSVTLQCAEPVDLAAVTRVLDAT 1u8fO 221 :IPELNGKLTGMAFRVPTANVSVVDLTCRLEKPAKYDDIKKVVKQA T0298 269 :KGIEWVGEGDYPTVVGDALGQDETYVGRVRAGQ 1u8fO 269 :PLKGILGYTEHQVVSSDFNSDTHSSTFDAGAGI T0298 302 :ADPCQVNLWIVSDN 1u8fO 303 :LNDHFVKLISWYDN T0298 317 :RKGAALNAVLLGELLIKH 1u8fO 317 :EFGYSNRVVDLMAHMASK Number of specific fragments extracted= 17 number of extra gaps= 0 total=451 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 1u8fO/T0298-1u8fO-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0298 read from 1u8fO/T0298-1u8fO-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1u8fO read from 1u8fO/T0298-1u8fO-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1u8fO in template set Warning: unaligning (T0298)P4 because first residue in template chain is (1u8fO)K3 T0298 5 :LNVAVVG 1u8fO 4 :VKVGVNG T0298 13 :TGSVGEALVGLLDER 1u8fO 11 :FGRIGRLVTRAAFNS T0298 28 :DFPLHRLHL 1u8fO 27 :KVDIVAIND T0298 37 :LASAESAGQRMGFA 1u8fO 37 :FIDLNYMVYMFQYD T0298 51 :ESSLRVGDVDSFDFS 1u8fO 74 :ITIFQERDPSKIKWG T0298 66 :SVGLAFFAAAAEVSRAHAERARAAGCSVI 1u8fO 91 :GAEYVVESTGVFTTMEKAGAHLQGGAKRV T0298 96 :LSGALE 1u8fO 120 :IISAPS T0298 103 :SVAPPVMVSVNAERLAS 1u8fO 126 :ADAPMFVMGVNHEKYDN T0298 122 :APFLLSSP 1u8fO 143 :SLKIISNA T0298 130 :CAVAA 1u8fO 152 :CTTNC T0298 136 :LCEVLAPLLATLDCRQLNLTACLSVSSL 1u8fO 157 :LAPLAKVIHDNFGIVEGLMTTVHAITAT T0298 176 :AELLNARPLEPRLFDRQIAFNLLA 1u8fO 185 :QKTVDGPSGKLWRDGRGALQNIIP T0298 205 :DAEGHSAIERRIFAEVQA 1u8fO 209 :ASTGAAKAVGKVIPELNG T0298 230 :PLNVTCIQAPVFFGDSLSVTLQCAEPVDLAAVTRVLDAT 1u8fO 227 :KLTGMAFRVPTANVSVVDLTCRLEKPAKYDDIKKVVKQA T0298 269 :KGIEWVGEGDYPTVVGDALGQDETYVGRVRAGQAD 1u8fO 269 :PLKGILGYTEHQVVSSDFNSDTHSSTFDAGAGIAL T0298 304 :PCQVNLWIVSDN 1u8fO 305 :DHFVKLISWYDN T0298 317 :RKGAALNAVLLGELLIKH 1u8fO 317 :EFGYSNRVVDLMAHMASK Number of specific fragments extracted= 17 number of extra gaps= 0 total=468 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 1u8fO/T0298-1u8fO-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0298 read from 1u8fO/T0298-1u8fO-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1u8fO read from 1u8fO/T0298-1u8fO-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1u8fO in template set Warning: unaligning (T0298)P4 because first residue in template chain is (1u8fO)K3 T0298 5 :LNVAVVGA 1u8fO 4 :VKVGVNGF T0298 14 :GSVGEALVGLLDERDFPLHRLHLLASAESA 1u8fO 12 :GRIGRLVTRAAFNSGKVDIVAINDPFIDLN T0298 44 :GQRMGFAES 1u8fO 57 :HGTVKAENG T0298 53 :SLRVGDVDSFD 1u8fO 73 :PITIFQERDPS T0298 66 :S 1u8fO 84 :K T0298 67 :VGLAFFAAA 1u8fO 92 :AEYVVESTG T0298 76 :AEVSR 1u8fO 105 :MEKAG T0298 85 :RARAAGCSVIDLSGAL 1u8fO 110 :AHLQGGAKRVIISAPS T0298 103 :SVAPPVMVSVNAER 1u8fO 126 :ADAPMFVMGVNHEK T0298 120 :Q 1u8fO 140 :Y T0298 121 :AAPFLLSSPCAVAAELCEVLAPLLATLDCRQLNLTACLSVSSLGRE 1u8fO 142 :NSLKIISNASCTTNCLAPLAKVIHDNFGIVEGLMTTVHAITATQKT T0298 180 :NARPLEPRLFDRQIAFNLLAQVGAVDAE 1u8fO 189 :DGPSGKLWRDGRGALQNIIPASTGAAKA T0298 220 :VQALLGERIGPLNVTCIQAPVFFGDSLSVTLQCAEPVDLAAVTRVLDAT 1u8fO 217 :VGKVIPELNGKLTGMAFRVPTANVSVVDLTCRLEKPAKYDDIKKVVKQA T0298 269 :KGIEWVGEG 1u8fO 271 :KGILGYTEH T0298 281 :TVVGDALGQDETYVGR 1u8fO 280 :QVVSSDFNSDTHSSTF T0298 297 :V 1u8fO 300 :G T0298 300 :GQADPCQVNLWIVSDNV 1u8fO 301 :IALNDHFVKLISWYDNE T0298 318 :KGAALNAVLLGELLIKH 1u8fO 318 :FGYSNRVVDLMAHMASK Number of specific fragments extracted= 18 number of extra gaps= 0 total=486 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 1rm4A/T0298-1rm4A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1rm4A expands to /projects/compbio/data/pdb/1rm4.pdb.gz 1rm4A:Skipped atom 3025, because occupancy 0.500 <= existing 0.500 in 1rm4A Skipped atom 3027, because occupancy 0.500 <= existing 0.500 in 1rm4A Skipped atom 3029, because occupancy 0.500 <= existing 0.500 in 1rm4A Skipped atom 3031, because occupancy 0.500 <= existing 0.500 in 1rm4A Skipped atom 3182, because occupancy 0.500 <= existing 0.500 in 1rm4A Skipped atom 3184, because occupancy 0.500 <= existing 0.500 in 1rm4A Skipped atom 3186, because occupancy 0.500 <= existing 0.500 in 1rm4A Skipped atom 3188, because occupancy 0.500 <= existing 0.500 in 1rm4A Skipped atom 3190, because occupancy 0.500 <= existing 0.500 in 1rm4A Skipped atom 3192, because occupancy 0.500 <= existing 0.500 in 1rm4A Skipped atom 3194, because occupancy 0.500 <= existing 0.500 in 1rm4A Skipped atom 4114, because occupancy 0.500 <= existing 0.500 in 1rm4A Skipped atom 4116, because occupancy 0.500 <= existing 0.500 in 1rm4A Skipped atom 4745, because occupancy 0.500 <= existing 0.500 in 1rm4A Skipped atom 4747, because occupancy 0.500 <= existing 0.500 in 1rm4A # T0298 read from 1rm4A/T0298-1rm4A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1rm4A read from 1rm4A/T0298-1rm4A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1rm4A to template set # found chain 1rm4A in template set Warning: unaligning (T0298)P4 because first residue in template chain is (1rm4A)K0 T0298 5 :LNVAVVGA 1rm4A 1 :LKVAINGF T0298 14 :GSVGEALVGLLDERDFPLHRLHLLASAESAGQRMGFAE 1rm4A 9 :GRIGRNFLRCWHGRKDSPLDVVVINDTGGVKQASHLLK T0298 52 :SSLRVGDVDSFDFS 1rm4A 72 :KVVSDRNPVNLPWG T0298 66 :SVGLAFFAAAAEVSRAHAERARAAGCSVIDLSGALE 1rm4A 88 :GIDLVIEGTGVFVDRDGAGKHLQAGAKKVLITAPGK T0298 103 :SVAPPVMVSVNAERLAS 1rm4A 123 :GDIPTYVVGVNEEGYTH T0298 122 :APFLLSSP 1rm4A 140 :ADTIISNA T0298 130 :CAVAA 1rm4A 149 :CTTNC T0298 136 :LCEVLAPLLATLDCRQLNLTACLSVSSL 1rm4A 154 :LAPFVKVLDQKFGIIKGTMTTTHSYTGD T0298 176 :AELLNARPLEPRL 1rm4A 182 :QRLLDASHRDLRR T0298 190 :DRQIAFNLLA 1rm4A 196 :ARAACLNIVP T0298 205 :DAEG 1rm4A 206 :TSTG T0298 213 :ERRIFAEV 1rm4A 210 :AAKAVALV T0298 224 :LGERIGPLNVTCIQAPVFFGDSLSVTLQCAEPVDLAAVTRVLDAT 1rm4A 218 :LPNLKGKLNGIALRVPTPNVSVVDLVVQVSKKTFAEEVNAAFRES T0298 269 :KGIEWVGEGDYPTVVGDALGQDETYVGRVRAGQ 1rm4A 266 :ELKGILSVCDEPLVSIDFRCTDVSSTIDSSLTM T0298 302 :ADPCQVNLWIVSDN 1rm4A 300 :MGDDMVKVIAWYDN T0298 317 :RKGAALNAVLLGELLIKHY 1rm4A 314 :EWGYSQRVVDLADIVANKW Number of specific fragments extracted= 16 number of extra gaps= 0 total=502 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 1rm4A/T0298-1rm4A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0298 read from 1rm4A/T0298-1rm4A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1rm4A read from 1rm4A/T0298-1rm4A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1rm4A in template set Warning: unaligning (T0298)P4 because first residue in template chain is (1rm4A)K0 T0298 5 :LNVAVVG 1rm4A 1 :LKVAING T0298 13 :TGSVGEALVGLLDERD 1rm4A 8 :FGRIGRNFLRCWHGRK T0298 29 :FPLHRLHLLASAESAGQRMGFA 1rm4A 25 :LDVVVINDTGGVKQASHLLKYD T0298 51 :ESSLRVGDVDSFDFS 1rm4A 71 :IKVVSDRNPVNLPWG T0298 66 :SVGLAFFAAAAEVSRAHAERARAAGCSVI 1rm4A 88 :GIDLVIEGTGVFVDRDGAGKHLQAGAKKV T0298 96 :LSGALEPSVAPPVMVSVNAERLAS 1rm4A 117 :LITAPGKGDIPTYVVGVNEEGYTH T0298 122 :APFLLSSP 1rm4A 140 :ADTIISNA T0298 130 :CAVAA 1rm4A 149 :CTTNC T0298 136 :LCEVLAPLLATLDCRQLNLTACLSVSSL 1rm4A 154 :LAPFVKVLDQKFGIIKGTMTTTHSYTGD T0298 176 :AELLNARP 1rm4A 182 :QRLLDASH T0298 185 :EPRLFDRQIAFNLLA 1rm4A 191 :RDLRRARAACLNIVP T0298 205 :DAEGHSAIERRIFAEVQA 1rm4A 206 :TSTGAAKAVALVLPNLKG T0298 230 :PLNVTCIQAPVFFGDSLSVTLQCAEPVDLAAVTRVLDAT 1rm4A 224 :KLNGIALRVPTPNVSVVDLVVQVSKKTFAEEVNAAFRES T0298 269 :KGIEWVGEGDYPTVVGDALGQDETYVGRVRAGQAD 1rm4A 266 :ELKGILSVCDEPLVSIDFRCTDVSSTIDSSLTMVM T0298 304 :PCQVNLWIVSDN 1rm4A 302 :DDMVKVIAWYDN T0298 317 :RKGAALNAVLLGELLIKHYL 1rm4A 314 :EWGYSQRVVDLADIVANKWQ Number of specific fragments extracted= 16 number of extra gaps= 0 total=518 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 1rm4A/T0298-1rm4A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0298 read from 1rm4A/T0298-1rm4A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1rm4A read from 1rm4A/T0298-1rm4A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1rm4A in template set Warning: unaligning (T0298)P4 because first residue in template chain is (1rm4A)K0 T0298 5 :LNVAVVGA 1rm4A 1 :LKVAINGF T0298 14 :GSVGEALVGLLDERDFPLHRLHLLASAESA 1rm4A 9 :GRIGRNFLRCWHGRKDSPLDVVVINDTGGV T0298 44 :GQRMGFAESSLRVGDVDSFDFSS 1rm4A 61 :DSAISVDGKVIKVVSDRNPVNLP T0298 67 :VGLAFFAAA 1rm4A 89 :IDLVIEGTG T0298 80 :RAHAERARAAGCSVIDLSGALE 1rm4A 102 :RDGAGKHLQAGAKKVLITAPGK T0298 104 :VAPPVMVSVNAERLA 1rm4A 124 :DIPTYVVGVNEEGYT T0298 121 :AAPFLLSSPCAVAAELCEVLAPLLATLDCRQLNLTACLSVSSL 1rm4A 139 :HADTIISNASCTTNCLAPFVKVLDQKFGIIKGTMTTTHSYTGD T0298 181 :ARPLEPRLFDRQIA 1rm4A 182 :QRLLDASHRDLRRA T0298 195 :FNLLAQVGA 1rm4A 201 :LNIVPTSTG T0298 216 :IFAEVQALLGERIGPLNVTCIQAPVFFGDSLSVTLQCAEPVDLAAVTRVLDATKG 1rm4A 210 :AAKAVALVLPNLKGKLNGIALRVPTPNVSVVDLVVQVSKKTFAEEVNAAFRESAD T0298 271 :IEWVGE 1rm4A 271 :LSVCDE T0298 280 :PTVVGDALGQDETYVGRVRAGQ 1rm4A 277 :PLVSIDFRCTDVSSTIDSSLTM T0298 302 :ADPCQVNLWIVSDNV 1rm4A 300 :MGDDMVKVIAWYDNE T0298 318 :KGAALNAVLLGELLIKHY 1rm4A 315 :WGYSQRVVDLADIVANKW Number of specific fragments extracted= 14 number of extra gaps= 0 total=532 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 2b4rO/T0298-2b4rO-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:# T0298 read from 2b4rO/T0298-2b4rO-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2b4rO read from 2b4rO/T0298-2b4rO-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 (T0298)P4 because first residue in template chain is (2b4rO)A3 Warning: unaligning (T0298)N196 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2b4rO)I209 Warning: unaligning (T0298)L197 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2b4rO)I209 T0298 5 :LNVAVVGA 2b4rO 4 :TKLGINGF T0298 14 :GSVGEALVGLLD 2b4rO 12 :GRIGRLVFRAAF T0298 28 :DFPLHRLHLLASAE 2b4rO 24 :GRKDIEVVAINDPF T0298 42 :SAGQRMGFAE 2b4rO 39 :DLNHLCYLLK T0298 52 :SSLRVGDVDSFDFS 2b4rO 75 :SVFAEKDPSQIPWG T0298 66 :SVGLAFFAAAAEVSRAHAERARAAGCSVIDLSGALE 2b4rO 91 :QVDVVCESTGVFLTKELASSHLKGGAKKVIMSAPPK T0298 103 :SVAPPVMVSVNAERLAS 2b4rO 127 :DDTPIYVMGINHHQYDT T0298 122 :APFLLSSP 2b4rO 144 :KQLIVSNA T0298 130 :CAVAA 2b4rO 153 :CTTNC T0298 136 :LCEVLAPLLATLDCRQLNLTACLSVSS 2b4rO 158 :LAPLAKVINDRFGIVEGLMTTVHASTA T0298 177 :ELL 2b4rO 185 :NQL T0298 180 :NARPLEPRLFDRQIAF 2b4rO 192 :PSKGGKDWRAGRCALS T0298 198 :LA 2b4rO 210 :IP T0298 205 :DAEG 2b4rO 212 :ASTG T0298 213 :ERRIFAEV 2b4rO 216 :AAKAVGKV T0298 224 :LGERIGPLNVTCIQAPVFFGDSLSVTLQCAEPVDLAAVTRVLDAT 2b4rO 224 :LPELNGKLTGVAFRVPIGTVSVVDLVCRLQKPAKYEEVALEIKKA T0298 269 :KGIEWVGEGDYPTVVGDALGQDETYVGRVRAGQ 2b4rO 272 :PLKGILGYTEDEVVSQDFVHDNRSSIFDMKAGL T0298 302 :ADPCQVNLWIVSDN 2b4rO 306 :LNDNFFKLVSWYDN T0298 317 :RKGAALNAVLLGELLI 2b4rO 320 :EWGYSNRVLDLAVHIT Number of specific fragments extracted= 19 number of extra gaps= 1 total=551 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 2b4rO/T0298-2b4rO-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0298 read from 2b4rO/T0298-2b4rO-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2b4rO read from 2b4rO/T0298-2b4rO-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2b4rO in template set Warning: unaligning (T0298)P4 because first residue in template chain is (2b4rO)A3 Warning: unaligning (T0298)N196 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2b4rO)I209 Warning: unaligning (T0298)L197 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2b4rO)I209 T0298 5 :LNVAVVG 2b4rO 4 :TKLGING T0298 13 :TGSVGEALVGLLDER 2b4rO 11 :FGRIGRLVFRAAFGR T0298 28 :DFPLHRLHL 2b4rO 27 :DIEVVAIND T0298 38 :ASAESAGQRMGFA 2b4rO 38 :MDLNHLCYLLKYD T0298 51 :ESSLRVGDVDSFDFS 2b4rO 74 :VSVFAEKDPSQIPWG T0298 66 :SVGLAFFAAAAEVSRAHAERARAAGCSVI 2b4rO 91 :QVDVVCESTGVFLTKELASSHLKGGAKKV T0298 96 :LSGALEPSVAPPVMVSVNAERLAS 2b4rO 120 :IMSAPPKDDTPIYVMGINHHQYDT T0298 122 :APFLLSSP 2b4rO 144 :KQLIVSNA T0298 130 :CAVAA 2b4rO 153 :CTTNC T0298 136 :LCEVLAPLLATLDCRQLNLTACLSVSSL 2b4rO 158 :LAPLAKVINDRFGIVEGLMTTVHASTAN T0298 176 :AELLNARPL 2b4rO 186 :QLVVDGPSK T0298 185 :EPRLFDRQIAF 2b4rO 197 :KDWRAGRCALS T0298 198 :LA 2b4rO 210 :IP T0298 205 :DAEGHSAIERRIFAEVQA 2b4rO 212 :ASTGAAKAVGKVLPELNG T0298 230 :PLNVTCIQAPVFFGDSLSVTLQCAEPVDLAAVTRVLDAT 2b4rO 230 :KLTGVAFRVPIGTVSVVDLVCRLQKPAKYEEVALEIKKA T0298 269 :KGIEWVGEGDYPTVVGDALGQDETYVGRVRAGQAD 2b4rO 272 :PLKGILGYTEDEVVSQDFVHDNRSSIFDMKAGLAL T0298 304 :PCQVNLWIVSDN 2b4rO 308 :DNFFKLVSWYDN T0298 317 :RKGAALNAVLLGELLI 2b4rO 320 :EWGYSNRVLDLAVHIT Number of specific fragments extracted= 18 number of extra gaps= 1 total=569 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 2b4rO/T0298-2b4rO-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0298 read from 2b4rO/T0298-2b4rO-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2b4rO read from 2b4rO/T0298-2b4rO-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2b4rO in template set Warning: unaligning (T0298)P4 because first residue in template chain is (2b4rO)A3 Warning: unaligning (T0298)N196 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2b4rO)I209 Warning: unaligning (T0298)L197 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2b4rO)I209 T0298 5 :LNVAVVGA 2b4rO 4 :TKLGINGF T0298 14 :GSVGEALVGLLDERDF 2b4rO 12 :GRIGRLVFRAAFGRKD T0298 32 :HRLHLLASAESA 2b4rO 28 :IEVVAINDPFMD T0298 44 :GQRMGFAES 2b4rO 57 :PCEVTHADG T0298 53 :SLRVGDVDSFDFSS 2b4rO 71 :EKKVSVFAEKDPSQ T0298 67 :VGLAFFAAA 2b4rO 92 :VDVVCESTG T0298 80 :RAHAERARAAGCSVIDLSGALE 2b4rO 105 :KELASSHLKGGAKKVIMSAPPK T0298 103 :SVAPPVMVSVNAERLA 2b4rO 127 :DDTPIYVMGINHHQYD T0298 121 :AAPFLLSSPCAVAAELCEVLAPLLATLDCRQLNLTACLSVSSLGRE 2b4rO 143 :TKQLIVSNASCTTNCLAPLAKVINDRFGIVEGLMTTVHASTANQLV T0298 182 :RPLEPRLFDRQIAF 2b4rO 189 :VDGPSKGGKDWRAG T0298 198 :LAQVGA 2b4rO 210 :IPASTG T0298 216 :IFAEVQALLGERIGPLNVTCIQAPVFFGDSLSVTLQCAEPVDLAAVTRVLDAT 2b4rO 216 :AAKAVGKVLPELNGKLTGVAFRVPIGTVSVVDLVCRLQKPAKYEEVALEIKKA T0298 269 :KGIEWVGEG 2b4rO 274 :KGILGYTED T0298 280 :PTVVGDALGQDETYVGRVRAGQ 2b4rO 283 :EVVSQDFVHDNRSSIFDMKAGL T0298 302 :ADPCQVNLWIVSDNV 2b4rO 306 :LNDNFFKLVSWYDNE T0298 318 :KGAALNAVLLGELLI 2b4rO 321 :WGYSNRVLDLAVHIT Number of specific fragments extracted= 16 number of extra gaps= 1 total=585 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 1dssG/T0298-1dssG-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1dssG expands to /projects/compbio/data/pdb/1dss.pdb.gz 1dssG:Bad short name: OZ1 for alphabet: pdb_atoms Bad short name: OZ2 for alphabet: pdb_atoms # T0298 read from 1dssG/T0298-1dssG-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1dssG read from 1dssG/T0298-1dssG-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1dssG to template set # found chain 1dssG in template set Warning: unaligning (T0298)L5 because first residue in template chain is (1dssG)S1 Warning: unaligning (T0298)A131 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1dssG)T150 Warning: unaligning (T0298)C157 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1dssG)H176 Warning: unaligning (T0298)L158 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1dssG)H176 Warning: unaligning (T0298)F195 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1dssG)N202 Warning: unaligning (T0298)N196 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1dssG)N202 Warning: unaligning (T0298)L197 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1dssG)I203 Warning: unaligning (T0298)C235 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1dssG)F230 Warning: unaligning (T0298)I236 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1dssG)F230 Warning: unaligning (T0298)R317 because of BadResidue code BAD_PEPTIDE in next template residue (1dssG)F315 Warning: unaligning (T0298)K318 because of BadResidue code BAD_PEPTIDE at template residue (1dssG)F315 Warning: unaligning (T0298)Y335 because of BadResidue code BAD_PEPTIDE in next template residue (1dssG)S333 T0298 6 :NVAVVGA 1dssG 2 :KIGINGF T0298 14 :GSVGEALVGLLDERDFP 1dssG 9 :GRIGRLVLRAALEMGAQ T0298 34 :LHLLASAE 1dssG 27 :VVAVNDPF T0298 42 :SAGQRMGFAE 1dssG 36 :ALEYMVYMFK T0298 52 :SSLRVGDVDSFDFS 1dssG 72 :TVFNEMKPENIPWS T0298 66 :SVGLAFFAAAAEVSRAHAERARAAGCSVIDLSGA 1dssG 88 :GAEYIVESTGVFTTIEKASAHFKGGAKKVIISAP T0298 102 :PSVAPPVMVSVNAERLAS 1dssG 122 :SADAPMFVCGVNLEKYSK T0298 122 :APFLLSSP 1dssG 140 :DMKVVSNA T0298 132 :VAA 1dssG 151 :TNC T0298 136 :LCEVLAPLLATLDCRQLNLTA 1dssG 154 :LAPVAKVLHENFEIVEGLMTT T0298 159 :SVSS 1dssG 177 :AVTA T0298 175 :TAELLNARPLEPRLFDRQIA 1dssG 181 :TQKTVDGPSAKDWRGGRGAA T0298 198 :LA 1dssG 204 :IP T0298 205 :DAEG 1dssG 206 :SSTG T0298 213 :ERRIFAEV 1dssG 210 :AAKAVGKV T0298 224 :LGERIGPLNVT 1dssG 218 :IPELDGKLTGM T0298 237 :QAPVFFGDSLSVTLQCAEPVDLAAVTRVLDAT 1dssG 231 :RVPTPNVSVVDLTVRLGKECSYDDIKAAMKAA T0298 269 :KGIEWVGEGDYPTVVGDALGQDETYVGRVRAGQ 1dssG 266 :PLQGVLGYTEDDVVSCDFTGDNRSSIFDAKAGI T0298 302 :ADPCQVNLWIVSDN 1dssG 300 :LSKTFVKVVSWYDN T0298 319 :GAALNAVLLGELLIKH 1dssG 316 :GYSQRVIDLIKHMQKV Number of specific fragments extracted= 20 number of extra gaps= 5 total=605 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 1dssG/T0298-1dssG-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0298 read from 1dssG/T0298-1dssG-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1dssG read from 1dssG/T0298-1dssG-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1dssG in template set Warning: unaligning (T0298)L5 because first residue in template chain is (1dssG)S1 Warning: unaligning (T0298)A131 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1dssG)T150 Warning: unaligning (T0298)C157 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1dssG)H176 Warning: unaligning (T0298)L158 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1dssG)H176 Warning: unaligning (T0298)F195 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1dssG)N202 Warning: unaligning (T0298)N196 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1dssG)N202 Warning: unaligning (T0298)L197 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1dssG)I203 Warning: unaligning (T0298)C235 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1dssG)F230 Warning: unaligning (T0298)I236 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1dssG)F230 Warning: unaligning (T0298)R317 because of BadResidue code BAD_PEPTIDE in next template residue (1dssG)F315 Warning: unaligning (T0298)K318 because of BadResidue code BAD_PEPTIDE at template residue (1dssG)F315 T0298 6 :NVAVVG 1dssG 2 :KIGING T0298 13 :TGSVGEALVGLLDERDFPLHRLHL 1dssG 8 :FGRIGRLVLRAALEMGAQVVAVND T0298 37 :LASAESAGQRMGFA 1dssG 34 :FIALEYMVYMFKYD T0298 51 :ESSLRVGDVDSFDFS 1dssG 71 :ITVFNEMKPENIPWS T0298 66 :SVGLAFFAAAAEVSRAHAERARAAGCSVI 1dssG 88 :GAEYIVESTGVFTTIEKASAHFKGGAKKV T0298 96 :LSGALE 1dssG 117 :IISAPS T0298 103 :SVAPPVMVSVNAERLAS 1dssG 123 :ADAPMFVCGVNLEKYSK T0298 122 :APFLLSSP 1dssG 140 :DMKVVSNA T0298 132 :VAA 1dssG 151 :TNC T0298 136 :LCEVLAPLLATLDCRQLNLTA 1dssG 154 :LAPVAKVLHENFEIVEGLMTT T0298 159 :SVSSL 1dssG 177 :AVTAT T0298 176 :AELLNARPLEPRLFDRQIA 1dssG 182 :QKTVDGPSAKDWRGGRGAA T0298 198 :LA 1dssG 204 :IP T0298 205 :DAEGHSAIERRIFAEVQA 1dssG 206 :SSTGAAKAVGKVIPELDG T0298 230 :PLNVT 1dssG 224 :KLTGM T0298 237 :QAPVFFGDSLSVTLQCAEPVDLAAVTRVLDAT 1dssG 231 :RVPTPNVSVVDLTVRLGKECSYDDIKAAMKAA T0298 269 :KGIEWVGEGDYPTVVGDALGQDETYVGRVRAGQAD 1dssG 266 :PLQGVLGYTEDDVVSCDFTGDNRSSIFDAKAGIQL T0298 304 :PCQVNLWIVSDN 1dssG 302 :KTFVKVVSWYDN T0298 319 :GAALNAVLLGELLIKH 1dssG 316 :GYSQRVIDLIKHMQKV Number of specific fragments extracted= 19 number of extra gaps= 4 total=624 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 1dssG/T0298-1dssG-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0298 read from 1dssG/T0298-1dssG-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1dssG read from 1dssG/T0298-1dssG-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1dssG in template set Warning: unaligning (T0298)L5 because first residue in template chain is (1dssG)S1 Warning: unaligning (T0298)C130 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1dssG)T150 Warning: unaligning (T0298)V132 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1dssG)T150 Warning: unaligning (T0298)C157 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1dssG)H176 Warning: unaligning (T0298)L158 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1dssG)H176 Warning: unaligning (T0298)F195 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1dssG)N202 Warning: unaligning (T0298)N196 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1dssG)N202 Warning: unaligning (T0298)L197 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1dssG)I203 Warning: unaligning (T0298)C235 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1dssG)F230 Warning: unaligning (T0298)I236 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1dssG)F230 Warning: unaligning (T0298)V316 because of BadResidue code BAD_PEPTIDE in next template residue (1dssG)F315 Warning: unaligning (T0298)K318 because of BadResidue code BAD_PEPTIDE at template residue (1dssG)F315 T0298 6 :NVAVVGA 1dssG 2 :KIGINGF T0298 14 :GSVGEALVGLLDERDFPLHRLHL 1dssG 9 :GRIGRLVLRAALEMGAQVVAVND T0298 40 :AESA 1dssG 33 :PFIA T0298 44 :GQRMGFAES 1dssG 54 :KGEVKAEDG T0298 53 :SLRVGDVDSFDFSS 1dssG 68 :GKKITVFNEMKPEN T0298 67 :VGLAFFAAA 1dssG 89 :AEYIVESTG T0298 76 :AEVS 1dssG 102 :IEKA T0298 87 :RAAGCSVIDLSGAL 1dssG 109 :FKGGAKKVIISAPS T0298 103 :SVAPPVMVSVNAER 1dssG 123 :ADAPMFVCGVNLEK T0298 120 :Q 1dssG 137 :Y T0298 121 :AAPFLLSSP 1dssG 139 :KDMKVVSNA T0298 133 :AAELCEVLAPLLATLDCRQLNLTA 1dssG 151 :TNCLAPVAKVLHENFEIVEGLMTT T0298 159 :SVSSLGRE 1dssG 177 :AVTATQKT T0298 180 :NARPLEPRLFDRQIA 1dssG 186 :DGPSAKDWRGGRGAA T0298 198 :LAQVGA 1dssG 204 :IPSSTG T0298 216 :IFAEVQALLGERIGPLNVT 1dssG 210 :AAKAVGKVIPELDGKLTGM T0298 237 :QAPVFFGDSLSVTLQCAEPVDLAAVTRVLDAT 1dssG 231 :RVPTPNVSVVDLTVRLGKECSYDDIKAAMKAA T0298 269 :KGIEWVGEGD 1dssG 268 :QGVLGYTEDD T0298 281 :TVVGDALGQDETYVGR 1dssG 278 :VVSCDFTGDNRSSIFD T0298 297 :V 1dssG 297 :G T0298 300 :GQADPCQVNLWIVSDN 1dssG 298 :IQLSKTFVKVVSWYDN T0298 319 :GAALNAVLLGELLIKH 1dssG 316 :GYSQRVIDLIKHMQKV Number of specific fragments extracted= 22 number of extra gaps= 4 total=646 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 1gypA/T0298-1gypA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1gypA expands to /projects/compbio/data/pdb/1gyp.pdb.gz 1gypA:# T0298 read from 1gypA/T0298-1gypA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1gypA read from 1gypA/T0298-1gypA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1gypA to template set # found chain 1gypA in template set Warning: unaligning (T0298)Q3 because first residue in template chain is (1gypA)A1 Warning: unaligning (T0298)F242 because of BadResidue code BAD_PEPTIDE in next template residue (1gypA)V255 Warning: unaligning (T0298)G243 because of BadResidue code BAD_PEPTIDE at template residue (1gypA)V255 Warning: unaligning (T0298)G300 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1gypA)P321 Warning: unaligning (T0298)Q301 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1gypA)P321 T0298 4 :PLNVAVVGA 1gypA 2 :PIKVGINGF T0298 14 :GSVGEALVGLLDERDF 1gypA 11 :GRIGRMVFQAICDQGL T0298 30 :PLHRLHLLASAE 1gypA 29 :TEIDVVAVVDMS T0298 42 :SAGQRMGFAE 1gypA 42 :NAEYFAYQMK T0298 52 :SSLR 1gypA 86 :KCVK T0298 56 :VGDVDSFDFS 1gypA 91 :QRNPADLPWG T0298 66 :SVGLAFFAAAAEVSRAHAERARAAGCSVIDLSGALE 1gypA 103 :GVDYVIESTGLFTDKLKAEGHIKGGAKKVVISAPAS T0298 103 :SVAPPVMVSVNAERLASQ 1gypA 139 :GGAKTIVMGVNQHEYSPA T0298 122 :APFLLSSP 1gypA 157 :SHHVVSNA T0298 130 :CAVAA 1gypA 166 :CTTNC T0298 136 :LCEVLAPLLA 1gypA 171 :LAPIVHVLTK T0298 146 :TLDCRQLNLTACLSVSS 1gypA 182 :NFGIETGLMTTIHSYTA T0298 175 :TAELLNARPLEPRLFDRQIAFNLLA 1gypA 199 :TQKTVDGVSLKDWRGGRAAAVNIIP T0298 205 :DAEG 1gypA 224 :STTG T0298 213 :ERRIFAEV 1gypA 228 :AAKAVGMV T0298 224 :LGERIGPLNVTCIQAPVF 1gypA 236 :IPSTKGKLTGMSFRVPTP T0298 244 :DSLSVTLQCAEPVDLAAVTRVLDAT 1gypA 256 :SVVDLTFRATRDTSIQEIDKAIKKA T0298 269 :KGIEWVGEGDYPTVVGDALGQDETYVGR 1gypA 284 :YMKGILGFTDEELVSADFINDNRSSVYD T0298 298 :RA 1gypA 318 :NN T0298 302 :ADPCQVNLWIVSDN 1gypA 322 :GEKRFFKVVSWYDN T0298 317 :RKGAALNAVLLGELLIKHY 1gypA 336 :EWAYSHRVVDLVRYMAAKD Number of specific fragments extracted= 21 number of extra gaps= 2 total=667 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 1gypA/T0298-1gypA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0298 read from 1gypA/T0298-1gypA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1gypA read from 1gypA/T0298-1gypA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1gypA in template set Warning: unaligning (T0298)Q3 because first residue in template chain is (1gypA)A1 Warning: unaligning (T0298)F242 because of BadResidue code BAD_PEPTIDE in next template residue (1gypA)V255 Warning: unaligning (T0298)G243 because of BadResidue code BAD_PEPTIDE at template residue (1gypA)V255 Warning: unaligning (T0298)G300 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1gypA)P321 Warning: unaligning (T0298)Q301 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1gypA)P321 T0298 4 :PLNVAVVG 1gypA 2 :PIKVGING T0298 13 :TGSVGEALVGLLDERDF 1gypA 10 :FGRIGRMVFQAICDQGL T0298 30 :PLHRLHL 1gypA 32 :DVVAVVD T0298 37 :LASAESAGQRMGFA 1gypA 40 :STNAEYFAYQMKHD T0298 51 :ESSLR 1gypA 82 :GHRIK T0298 56 :VGDVDSFDFS 1gypA 91 :QRNPADLPWG T0298 66 :SVGLAFFAAAAEVSRAHAERARAAGCSVI 1gypA 103 :GVDYVIESTGLFTDKLKAEGHIKGGAKKV T0298 96 :LSGALEPSVAPPVMVSVNAERLASQ 1gypA 132 :VISAPASGGAKTIVMGVNQHEYSPA T0298 122 :APFLLSSP 1gypA 157 :SHHVVSNA T0298 130 :CAVAA 1gypA 166 :CTTNC T0298 136 :LCEVLAPLLAT 1gypA 171 :LAPIVHVLTKE T0298 147 :LDCRQLNLTACLSVSSL 1gypA 183 :FGIETGLMTTIHSYTAT T0298 176 :AELLNARPLEPRLFDRQIAFNLLA 1gypA 200 :QKTVDGVSLKDWRGGRAAAVNIIP T0298 205 :DAEGHSAIERRIFAEVQA 1gypA 224 :STTGAAKAVGMVIPSTKG T0298 230 :PLNVTCIQAPVF 1gypA 242 :KLTGMSFRVPTP T0298 244 :DSLSVTLQCAEPVDLAAVTRVLDAT 1gypA 256 :SVVDLTFRATRDTSIQEIDKAIKKA T0298 269 :KGIEWVGEGDYPTVVGDALGQDETYVGR 1gypA 284 :YMKGILGFTDEELVSADFINDNRSSVYD T0298 298 :RA 1gypA 318 :NN T0298 302 :ADPCQVNLWIVSDN 1gypA 322 :GEKRFFKVVSWYDN T0298 317 :RKGAALNAVLLGELLIKH 1gypA 336 :EWAYSHRVVDLVRYMAAK Number of specific fragments extracted= 20 number of extra gaps= 2 total=687 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 1gypA/T0298-1gypA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0298 read from 1gypA/T0298-1gypA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1gypA read from 1gypA/T0298-1gypA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1gypA in template set Warning: unaligning (T0298)Q3 because first residue in template chain is (1gypA)A1 Warning: unaligning (T0298)F242 because of BadResidue code BAD_PEPTIDE in next template residue (1gypA)V255 Warning: unaligning (T0298)G243 because of BadResidue code BAD_PEPTIDE at template residue (1gypA)V255 Warning: unaligning (T0298)G300 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1gypA)P321 Warning: unaligning (T0298)Q301 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1gypA)P321 T0298 4 :PLNVAVVGA 1gypA 2 :PIKVGINGF T0298 14 :GSVGEALVGLL 1gypA 11 :GRIGRMVFQAI T0298 27 :RDFPLHRLHLLASAESAGQR 1gypA 56 :HGRPKYTVEAVKSSPSVETA T0298 47 :MGFAESSLRVGDVDSFDFS 1gypA 78 :LVVNGHRIKCVKAQRNPAD T0298 66 :SVGLAFFAAA 1gypA 103 :GVDYVIESTG T0298 80 :RAHAERARAAGCSVIDLSGALE 1gypA 117 :KLKAEGHIKGGAKKVVISAPAS T0298 104 :VAPPVMVSVNAERLAS 1gypA 140 :GAKTIVMGVNQHEYSP T0298 121 :AAPFLLSSPCAVAAELCEVLAPLLA 1gypA 156 :ASHHVVSNASCTTNCLAPIVHVLTK T0298 146 :TLDCRQLNLTACLSVSSLGRE 1gypA 182 :NFGIETGLMTTIHSYTATQKT T0298 180 :NARPLEPRLFDRQIAFNLLAQVGA 1gypA 204 :DGVSLKDWRGGRAAAVNIIPSTTG T0298 217 :FAEVQALLGER 1gypA 228 :AAKAVGMVIPS T0298 228 :IGPLNVTCIQAPVF 1gypA 240 :KGKLTGMSFRVPTP T0298 244 :DSLSVTLQCAEPVDLAAVTRVLDAT 1gypA 256 :SVVDLTFRATRDTSIQEIDKAIKKA T0298 269 :KGIEWVG 1gypA 287 :GILGFTD T0298 279 :YPTVVGDALGQDETYVG 1gypA 294 :EELVSADFINDNRSSVY T0298 299 :A 1gypA 319 :N T0298 302 :ADPCQVNLWIVSDNVRK 1gypA 322 :GEKRFFKVVSWYDNEWA T0298 320 :AALNAVLLGELLIKH 1gypA 339 :YSHRVVDLVRYMAAK Number of specific fragments extracted= 18 number of extra gaps= 2 total=705 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 1k3tA/T0298-1k3tA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1k3tA expands to /projects/compbio/data/pdb/1k3t.pdb.gz 1k3tA:# T0298 read from 1k3tA/T0298-1k3tA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1k3tA read from 1k3tA/T0298-1k3tA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1k3tA to template set # found chain 1k3tA in template set Warning: unaligning (T0298)S97 because of BadResidue code BAD_PEPTIDE in next template residue (1k3tA)A135 Warning: unaligning (T0298)G98 because of BadResidue code BAD_PEPTIDE at template residue (1k3tA)A135 T0298 4 :PLNVAVVGA 1k3tA 2 :PIKVGINGF T0298 14 :GSVGEALVGLLDERDF 1k3tA 11 :GRIGRMVFQALCEDGL T0298 30 :PLHRLHLLASAE 1k3tA 29 :TEIDVVAVVDMN T0298 42 :SAGQRMGFAE 1k3tA 42 :DAEYFAYQMR T0298 56 :VGDVDSFDFS 1k3tA 91 :QRNPADLPWG T0298 66 :SVGLAFFAAAAEVSRAHAERARAAGCSVIDL 1k3tA 103 :GVEYVIESTGLFTAKAAAEGHLRGGARKVVI T0298 99 :ALE 1k3tA 136 :PAS T0298 103 :SVAPPVMVSVNAERLASQ 1k3tA 139 :GGAKTLVMGVNHHEYNPS T0298 122 :APFLLSSP 1k3tA 157 :EHHVVSNA T0298 130 :CAVAA 1k3tA 166 :CTTNC T0298 136 :LCEVLAPLLA 1k3tA 171 :LAPIVHVLVK T0298 146 :TLDCRQLNLTACLSVSS 1k3tA 182 :GFGVQTGLMTTIHSYTA T0298 175 :TAELLNARPLEPRLFDRQIAFNLLA 1k3tA 199 :TQKTVDGVSVKDWRGGRAAAVNIIP T0298 205 :DAEG 1k3tA 224 :STTG T0298 213 :ERRIFAEV 1k3tA 228 :AAKAVGMV T0298 224 :LGERIGPLNVTCIQAPVFFGDSLSVTLQCAEPVDLAAVTRVLDAT 1k3tA 236 :IPSTQGKLTGMSFRVPTPDVSVVDLTFTAARDTSIQEIDAALKRA T0298 269 :KGIEWVGEGDYPTVVGDALGQDETYVGR 1k3tA 284 :YMKGILGYTDEELVSADFINDNRSSIYD T0298 298 :RAGQADPCQVNLWIVSDN 1k3tA 318 :NNLPKERRFFKIVSWYDN T0298 317 :RKGAALNAVLLGELLIKHY 1k3tA 336 :EWGYSHRVVDLVRHMASKD Number of specific fragments extracted= 19 number of extra gaps= 1 total=724 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 1k3tA/T0298-1k3tA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0298 read from 1k3tA/T0298-1k3tA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1k3tA read from 1k3tA/T0298-1k3tA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1k3tA in template set Warning: unaligning (T0298)Q3 because first residue in template chain is (1k3tA)M1 Warning: unaligning (T0298)E51 because of BadResidue code BAD_PEPTIDE at template residue (1k3tA)G82 Warning: unaligning (T0298)G98 because of BadResidue code BAD_PEPTIDE in next template residue (1k3tA)A135 Warning: unaligning (T0298)A99 because of BadResidue code BAD_PEPTIDE at template residue (1k3tA)A135 T0298 4 :PLNVAVVG 1k3tA 2 :PIKVGING T0298 13 :TGSVGEALVGLLDERDF 1k3tA 10 :FGRIGRMVFQALCEDGL T0298 30 :PLHRLHL 1k3tA 32 :DVVAVVD T0298 37 :LASAESAGQRMGFA 1k3tA 40 :NTDAEYFAYQMRYD T0298 52 :SSLR 1k3tA 83 :HRIL T0298 56 :VGDVDSFDFS 1k3tA 91 :QRNPADLPWG T0298 66 :SVGLAFFAAAAEVSRAHAERARAAGCSVI 1k3tA 103 :GVEYVIESTGLFTAKAAAEGHLRGGARKV T0298 96 :LS 1k3tA 132 :VI T0298 100 :LEPSVAPPVMVSVNAERLASQ 1k3tA 136 :PASGGAKTLVMGVNHHEYNPS T0298 122 :APFLLSSP 1k3tA 157 :EHHVVSNA T0298 130 :CAVAA 1k3tA 166 :CTTNC T0298 136 :LCEVLAPLLAT 1k3tA 171 :LAPIVHVLVKE T0298 147 :LDCRQLNLTACLSVSSL 1k3tA 183 :FGVQTGLMTTIHSYTAT T0298 176 :AELLNARPLEPRLFDRQIAFNLLA 1k3tA 200 :QKTVDGVSVKDWRGGRAAAVNIIP T0298 205 :DAEGHSAIERRIFAEVQA 1k3tA 224 :STTGAAKAVGMVIPSTQG T0298 230 :PLNVTCIQAPVFFGDSLSVTLQCAEPVDLAAVTRVLDAT 1k3tA 242 :KLTGMSFRVPTPDVSVVDLTFTAARDTSIQEIDAALKRA T0298 269 :KGIEWVGEGDYPTVVGDALGQDETYVGR 1k3tA 284 :YMKGILGYTDEELVSADFINDNRSSIYD T0298 298 :RAGQADPCQVNLWIVSDN 1k3tA 318 :NNLPKERRFFKIVSWYDN T0298 317 :RKGAALNAVLLGELLIKH 1k3tA 336 :EWGYSHRVVDLVRHMASK Number of specific fragments extracted= 19 number of extra gaps= 2 total=743 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 1k3tA/T0298-1k3tA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0298 read from 1k3tA/T0298-1k3tA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1k3tA read from 1k3tA/T0298-1k3tA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1k3tA in template set Warning: unaligning (T0298)Q3 because first residue in template chain is (1k3tA)M1 Warning: unaligning (T0298)P30 because of BadResidue code BAD_PEPTIDE in next template residue (1k3tA)G28 Warning: unaligning (T0298)L31 because of BadResidue code BAD_PEPTIDE at template residue (1k3tA)G28 Warning: unaligning (T0298)A50 because of BadResidue code BAD_PEPTIDE in next template residue (1k3tA)G82 Warning: unaligning (T0298)E51 because of BadResidue code BAD_PEPTIDE at template residue (1k3tA)G82 Warning: unaligning (T0298)S97 because of BadResidue code BAD_PEPTIDE in next template residue (1k3tA)A135 Warning: unaligning (T0298)G98 because of BadResidue code BAD_PEPTIDE at template residue (1k3tA)A135 T0298 4 :PLNVAVVGA 1k3tA 2 :PIKVGINGF T0298 14 :GSVGEALVGLLDERDF 1k3tA 11 :GRIGRMVFQALCEDGL T0298 32 :HRLHLL 1k3tA 29 :TEIDVV T0298 38 :ASAESAGQR 1k3tA 68 :SSPSVAKDD T0298 47 :MGF 1k3tA 78 :LVV T0298 52 :SSLRVGDVDSFDFS 1k3tA 83 :HRILCVKAQRNPAD T0298 66 :SVGLAFFAAA 1k3tA 103 :GVEYVIESTG T0298 76 :AEVSR 1k3tA 117 :KAAAE T0298 85 :RARAAGCSVIDL 1k3tA 122 :GHLRGGARKVVI T0298 99 :ALE 1k3tA 136 :PAS T0298 104 :VAPPVMVSVNAERLA 1k3tA 140 :GAKTLVMGVNHHEYN T0298 121 :AAPFLLSSPCAVAAELCEVLAPLLA 1k3tA 156 :SEHHVVSNASCTTNCLAPIVHVLVK T0298 146 :TLDCRQLNLTACLSVSSLGRE 1k3tA 182 :GFGVQTGLMTTIHSYTATQKT T0298 179 :LNARPLEPRLFDRQIAFNLLAQVGA 1k3tA 203 :VDGVSVKDWRGGRAAAVNIIPSTTG T0298 216 :IFAEVQALLGERIGPLNVTCIQAPVFFGDSLSVTLQCAEPVDLAAVTRVLDAT 1k3tA 228 :AAKAVGMVIPSTQGKLTGMSFRVPTPDVSVVDLTFTAARDTSIQEIDAALKRA T0298 269 :KGIEWVGEG 1k3tA 286 :KGILGYTDE T0298 280 :PTVVGDALGQDETYVGR 1k3tA 295 :ELVSADFINDNRSSIYD T0298 299 :AGQADPCQVNLWIVSDNV 1k3tA 319 :NLPKERRFFKIVSWYDNE T0298 318 :KGAALNAVLLGELLIKH 1k3tA 337 :WGYSHRVVDLVRHMASK Number of specific fragments extracted= 19 number of extra gaps= 3 total=762 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 1nvmB/T0298-1nvmB-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 0.500 <= 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 # T0298 read from 1nvmB/T0298-1nvmB-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1nvmB read from 1nvmB/T0298-1nvmB-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 Warning: unaligning (T0298)P239 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1nvmB)P203 Warning: unaligning (T0298)V240 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1nvmB)P203 T0298 1 :MSQPLNVAVVGA 1nvmB 1 :MNQKLKVAIIGS T0298 14 :GSVGEALVGLLD 1nvmB 13 :GNIGTDLMIKVL T0298 27 :RDFPLHRLHLL 1nvmB 25 :RNAKYLEMGAM T0298 38 :ASAESAGQRMGFAESSLRVGD 1nvmB 38 :IDAASDGLARAQRMGVTTTYA T0298 59 :VDS 1nvmB 66 :LPE T0298 64 :FSSVGLAFFAAAAEVSRAHAERARAA 1nvmB 69 :FADIDFVFDATSASAHVQNEALLRQA T0298 90 :GCSVIDLSGALE 1nvmB 97 :GIRLIDLTPAAI T0298 105 :APPVMVSVNAERLAS 1nvmB 109 :GPYCVPVVNLEEHLG T0298 122 :APFLLSSPCAVAA 1nvmB 124 :KLNVNMVTCGGQA T0298 136 :LCEVLAPLLATLDCRQLNLTACLSVSSLG 1nvmB 137 :TIPMVAAVSRVAKVHYAEIVASISSKSAG T0298 165 :REGVKELARQ 1nvmB 169 :RANIDEFTET T0298 213 :ERRIFAEV 1nvmB 179 :TSKAIEVI T0298 224 :LGERIGPLNVTCIQA 1nvmB 187 :GGAAKGKAIIIMNPA T0298 241 :FFGDSLSVTLQCA 1nvmB 204 :PLIMRDTVYVLSA T0298 255 :PVDLAAVTRVLDAT 1nvmB 217 :AADQAAVAASVAEM T0298 269 :KGIEWV 1nvmB 239 :PGYRLK T0298 280 :PTVVGDALGQDETYVG 1nvmB 245 :QQVQFDVIPESAPLNI T0298 300 :GQADP 1nvmB 261 :PGLGR T0298 305 :CQVNLWIVSD 1nvmB 267 :SGLKTSVFLE T0298 315 :NVRKGAALNAVLLGELLIKH 1nvmB 289 :GNLDIMTSAALATAERMAQS Number of specific fragments extracted= 20 number of extra gaps= 1 total=782 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 1nvmB/T0298-1nvmB-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0298 read from 1nvmB/T0298-1nvmB-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1nvmB read from 1nvmB/T0298-1nvmB-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1nvmB in template set Warning: unaligning (T0298)P239 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1nvmB)P203 Warning: unaligning (T0298)V240 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1nvmB)P203 T0298 1 :MSQPLNVAVVG 1nvmB 1 :MNQKLKVAIIG T0298 13 :TGSVGEALVGLLDE 1nvmB 12 :SGNIGTDLMIKVLR T0298 28 :DFPLHRLHLL 1nvmB 26 :NAKYLEMGAM T0298 38 :ASAES 1nvmB 38 :IDAAS T0298 43 :AGQRMGFAESSLR 1nvmB 44 :GLARAQRMGVTTT T0298 59 :V 1nvmB 66 :L T0298 62 :FDFSSVGLAFFAAAAEVSRAHAERARAA 1nvmB 67 :PEFADIDFVFDATSASAHVQNEALLRQA T0298 90 :GCSVIDLSGALE 1nvmB 97 :GIRLIDLTPAAI T0298 105 :APPVMVSV 1nvmB 109 :GPYCVPVV T0298 116 :RLASQAAPFLLSSP 1nvmB 117 :NLEEHLGKLNVNMV T0298 130 :CAVAA 1nvmB 132 :CGGQA T0298 136 :LCEVLAPLLATLDCRQLNLTACLSVSSLGREG 1nvmB 137 :TIPMVAAVSRVAKVHYAEIVASISSKSAGPGT T0298 207 :EGHSAIERRIFAEV 1nvmB 169 :RANIDEFTETTSKA T0298 221 :QALLGERIGPLNVTCIQA 1nvmB 184 :EVIGGAAKGKAIIIMNPA T0298 241 :FFGDSLSVTLQCA 1nvmB 204 :PLIMRDTVYVLSA T0298 255 :PVDLAAVTRVLDAT 1nvmB 217 :AADQAAVAASVAEM T0298 269 :KGIEWVGE 1nvmB 239 :PGYRLKQQ T0298 277 :GDYPT 1nvmB 254 :ESAPL T0298 285 :DALGQDETYVGRVRA 1nvmB 259 :NIPGLGRFSGLKTSV T0298 306 :QVNL 1nvmB 274 :FLEV T0298 315 :N 1nvmB 290 :N T0298 317 :RKGAALNAVLLGELLIKHY 1nvmB 291 :LDIMTSAALATAERMAQSM Number of specific fragments extracted= 22 number of extra gaps= 1 total=804 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 1nvmB/T0298-1nvmB-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0298 read from 1nvmB/T0298-1nvmB-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1nvmB read from 1nvmB/T0298-1nvmB-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1nvmB in template set T0298 1 :MSQPLNVAVVGATGSVGEALVGLLDERDFPLHRLHLLASAESA 1nvmB 1 :MNQKLKVAIIGSGNIGTDLMIKVLRNAKYLEMGAMVGIDAASD T0298 44 :GQRMGFAE 1nvmB 52 :GVTTTYAG T0298 60 :DSFDFSSVGLAFFAAAAEVSRAHAERARAA 1nvmB 65 :KLPEFADIDFVFDATSASAHVQNEALLRQA T0298 90 :GCSVIDLSGALE 1nvmB 97 :GIRLIDLTPAAI T0298 105 :APPVMVS 1nvmB 109 :GPYCVPV T0298 115 :ERLASQAAPFLLSSPCAVAAELCEVLAPLLATLDCRQLNLTACLS 1nvmB 116 :VNLEEHLGKLNVNMVTCGGQATIPMVAAVSRVAKVHYAEIVASIS T0298 161 :SSLGREGVKELARQTAELL 1nvmB 161 :SKSAGPGTRANIDEFTETT T0298 217 :FAEVQALLGERIGPLNVTCI 1nvmB 180 :SKAIEVIGGAAKGKAIIIMN T0298 244 :DSLSVTLQCA 1nvmB 207 :MRDTVYVLSA T0298 255 :PVDLAAVTRVLDA 1nvmB 217 :AADQAAVAASVAE T0298 268 :TKG 1nvmB 238 :VPG T0298 271 :IEW 1nvmB 247 :VQF T0298 274 :VGEGDYPTVVGDALGQDETYVGRVRAGQADPC 1nvmB 251 :VIPESAPLNIPGLGRFSGLKTSVFLEVEGAAH T0298 313 :SDNVRK 1nvmB 288 :AGNLDI T0298 320 :AALNAVLLGELLIKH 1nvmB 294 :MTSAALATAERMAQS Number of specific fragments extracted= 15 number of extra gaps= 0 total=819 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 1cf2O/T0298-1cf2O-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:# T0298 read from 1cf2O/T0298-1cf2O-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1cf2O read from 1cf2O/T0298-1cf2O-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 T0298 1 :M 1cf2O 1 :M T0298 5 :LNVAVVGA 1cf2O 2 :KAVAINGY T0298 14 :GSVGEALVGLLD 1cf2O 10 :GTVGKRVADAIA T0298 28 :DFPLHRLHLLASAE 1cf2O 22 :QQDDMKVIGVSKTR T0298 42 :SAGQRMGFAESS 1cf2O 37 :DFEARMALKKGY T0298 54 :LRVGDVDS 1cf2O 50 :LYVAIPER T0298 62 :FDFS 1cf2O 66 :IEVA T0298 66 :SVGLAFFAAAAEVSRAHAERARAAGCSVI 1cf2O 78 :EADIVIDCTPEGIGAKNLKMYKEKGIKAI T0298 96 :LSGALEPSV 1cf2O 107 :FQGGEKHED T0298 105 :APPVMVSVNAERLA 1cf2O 117 :GLSFNSLSNYEESY T0298 122 :APFLLSSP 1cf2O 131 :GKDYTRVV T0298 130 :CAVAA 1cf2O 140 :CNTTG T0298 136 :LCEVLAPLLATLDCRQLNLTACLSVSSLGRE 1cf2O 145 :LCRTLKPLHDSFGIKKVRAVIVRRGADPAQV T0298 173 :RQTAELLNARPL 1cf2O 178 :GPINAIIPNPPK T0298 205 :DAEGHSAI 1cf2O 190 :LPSHHGPD T0298 217 :FAEV 1cf2O 198 :VKTV T0298 227 :RIGPLNVTCIQAPVFFGDSLSVTLQCAEPVDLAAVTRVLDATKGIEWVGEGDY 1cf2O 202 :LDINIDTMAVIVPTTLMHQHNVMVEVEETPTVDDIIDVFEDTPRVILISAEDG T0298 285 :DALGQDETYVGRVRAG 1cf2O 269 :GRSRNDLFEIPVWRES T0298 302 :ADPCQVNLWIVSDN 1cf2O 287 :VVDNEIYYMQAVHQ T0298 317 :RKGAALNAVLLGELLIKHYL 1cf2O 301 :ESDIVPENVDAVRAILEMEE Number of specific fragments extracted= 20 number of extra gaps= 0 total=839 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 1cf2O/T0298-1cf2O-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0298 read from 1cf2O/T0298-1cf2O-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1cf2O read from 1cf2O/T0298-1cf2O-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1cf2O in template set Warning: unaligning (T0298)P4 because first residue in template chain is (1cf2O)M1 T0298 5 :LNVAVVG 1cf2O 2 :KAVAING T0298 13 :TGSVGEALVGLLDE 1cf2O 9 :YGTVGKRVADAIAQ T0298 27 :RDFPLHRLHLLASAESAGQRMGFAESSLRVGDVD 1cf2O 24 :DDMKVIGVSKTRPDFEARMALKKGYDLYVAIPER T0298 61 :SFDFS 1cf2O 65 :GIEVA T0298 66 :SVGLAFFAAAAEVSRAHAERARAAGCSVI 1cf2O 78 :EADIVIDCTPEGIGAKNLKMYKEKGIKAI T0298 96 :LSGALE 1cf2O 107 :FQGGEK T0298 114 :AERLA 1cf2O 113 :HEDIG T0298 119 :SQAAPFLLSSP 1cf2O 128 :ESYGKDYTRVV T0298 130 :CAVAA 1cf2O 140 :CNTTG T0298 136 :LCEVLAPLLATLDCRQLNLTACLS 1cf2O 145 :LCRTLKPLHDSFGIKKVRAVIVRR T0298 176 :AELLNARPLEPRLFDRQI 1cf2O 169 :GADPAQVSKGPINAIIPN T0298 205 :DAEGHS 1cf2O 187 :PPKLPS T0298 215 :RIFAEVQALLG 1cf2O 193 :HHGPDVKTVLD T0298 229 :GPLNVTCIQAPVFFGDSLSVTLQCAEPVDLAAVTRVLDATKGIEWVGEGDY 1cf2O 204 :INIDTMAVIVPTTLMHQHNVMVEVEETPTVDDIIDVFEDTPRVILISAEDG T0298 285 :DALGQDETYVGRVR 1cf2O 269 :GRSRNDLFEIPVWR T0298 299 :AGQADPCQVNLWIVSDN 1cf2O 284 :SITVVDNEIYYMQAVHQ T0298 317 :RKGAALNAVLLGELLIK 1cf2O 301 :ESDIVPENVDAVRAILE Number of specific fragments extracted= 17 number of extra gaps= 0 total=856 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 1cf2O/T0298-1cf2O-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0298 read from 1cf2O/T0298-1cf2O-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1cf2O read from 1cf2O/T0298-1cf2O-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1cf2O in template set T0298 5 :LNVAVVG 1cf2O 2 :KAVAING T0298 13 :TGSVGEALVGLLDERDFPLHRLHLLASAESA 1cf2O 9 :YGTVGKRVADAIAQQDDMKVIGVSKTRPDFE T0298 44 :GQRMGFAES 1cf2O 47 :GYDLYVAIP T0298 53 :SLRVGDVDSFDFSSVGLAFFAAAAEVSRAHAERARAAGCSVIDLSG 1cf2O 65 :GIEVAGTVDDMLDEADIVIDCTPEGIGAKNLKMYKEKGIKAIFQGG T0298 100 :LEPSVAPPVMVS 1cf2O 111 :EKHEDIGLSFNS T0298 116 :RLASQAAPFLLSSPCAVAAELCEVLAPLLATLDCRQLNLTACLS 1cf2O 125 :NYEESYGKDYTRVVSCNTTGLCRTLKPLHDSFGIKKVRAVIVRR T0298 162 :SL 1cf2O 169 :GA T0298 182 :RPLEPRLFDRQ 1cf2O 171 :DPAQVSKGPIN T0298 201 :VGAVDAEGHSAI 1cf2O 183 :IIPNPPKLPSHH T0298 218 :AEVQALL 1cf2O 195 :GPDVKTV T0298 227 :RIGPLNVTCIQAPVFFGDSLSVTLQCAEPVDLAAVTRVLDATKGIEWVGEGDYPTVV 1cf2O 202 :LDINIDTMAVIVPTTLMHQHNVMVEVEETPTVDDIIDVFEDTPRVILISAEDGLTST T0298 284 :GDALGQDETYVGRVRA 1cf2O 268 :LGRSRNDLFEIPVWRE T0298 300 :GQADPCQVNLWIVSDNVRK 1cf2O 285 :ITVVDNEIYYMQAVHQESD T0298 320 :AALNAVLLGELLIK 1cf2O 304 :IVPENVDAVRAILE Number of specific fragments extracted= 14 number of extra gaps= 0 total=870 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 1crwG/T0298-1crwG-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1crwG expands to /projects/compbio/data/pdb/1crw.pdb.gz 1crwG:# T0298 read from 1crwG/T0298-1crwG-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1crwG read from 1crwG/T0298-1crwG-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1crwG to template set # found chain 1crwG in template set Warning: unaligning (T0298)L5 because first residue in template chain is (1crwG)S1 Warning: unaligning (T0298)F195 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1crwG)N202 Warning: unaligning (T0298)N196 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1crwG)N202 Warning: unaligning (T0298)L197 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1crwG)I203 T0298 6 :NVAVVGA 1crwG 2 :KIGINGF T0298 14 :GSVGEALVGLLDERDFP 1crwG 9 :GRIGRLVLRAALEMGAQ T0298 34 :LHLLASAE 1crwG 27 :VVAVNDPF T0298 42 :SAGQRMGFAE 1crwG 36 :ALEYMVYMFK T0298 52 :SSLRVGDVDSFDFS 1crwG 72 :TVFNEMKPENIPWS T0298 66 :SVGLAFFAAAAEVSRAHAERARAAGCSVIDLSGA 1crwG 88 :GAEYIVESTGVFTTIEKASAHFKGGAKKVIISAP T0298 102 :PSVAPPVMVSVNAERLAS 1crwG 122 :SADAPMFVCGVNLEKYSK T0298 122 :APFLLSSP 1crwG 140 :DMKVVSNA T0298 130 :CAVAA 1crwG 149 :CTTNC T0298 136 :LCEVLAPLLATLDCRQLNLTACLSVSS 1crwG 154 :LAPVAKVLHENFEIVEGLMTTVHAVTA T0298 175 :TAELLNARPLEPRLFDRQIA 1crwG 181 :TQKTVDGPSAKDWRGGRGAA T0298 198 :LA 1crwG 204 :IP T0298 205 :DAEG 1crwG 206 :SSTG T0298 213 :ERRIFAEV 1crwG 210 :AAKAVGKV T0298 224 :LGERIGPLNVTCIQAPVFFGDSLSVTLQCAEPVDLAAVTRVLDAT 1crwG 218 :IPELDGKLTGMAFRVPTPNVSVVDLTVRLGKECSYDDIKAAMKAA T0298 269 :KGIEWVGEGDYPTVVGDALGQDETYVGRVRAGQ 1crwG 266 :PLQGVLGYTEDDVVSCDFTGDNRSSIFDAKAGI T0298 302 :ADPCQVNLWIVSDN 1crwG 300 :LSKTFVKVVSWYDN T0298 317 :RKGAALNAVLLGELLIKHY 1crwG 314 :EFGYSQRVIDLIKHMQKVD Number of specific fragments extracted= 18 number of extra gaps= 1 total=888 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 1crwG/T0298-1crwG-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0298 read from 1crwG/T0298-1crwG-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1crwG read from 1crwG/T0298-1crwG-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1crwG in template set Warning: unaligning (T0298)L5 because first residue in template chain is (1crwG)S1 Warning: unaligning (T0298)F195 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1crwG)N202 Warning: unaligning (T0298)N196 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1crwG)N202 Warning: unaligning (T0298)L197 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1crwG)I203 T0298 6 :NVAVVG 1crwG 2 :KIGING T0298 13 :TGSVGEALVGLLDERDFPLHRLHL 1crwG 8 :FGRIGRLVLRAALEMGAQVVAVND T0298 37 :LASAESAGQRMGFA 1crwG 34 :FIALEYMVYMFKYD T0298 51 :ESSLRVGDVDSFDFS 1crwG 71 :ITVFNEMKPENIPWS T0298 66 :SVGLAFFAAAAEVSRAHAERARAAGCSVI 1crwG 88 :GAEYIVESTGVFTTIEKASAHFKGGAKKV T0298 96 :LSGALE 1crwG 117 :IISAPS T0298 103 :SVAPPVMVSVNAERLAS 1crwG 123 :ADAPMFVCGVNLEKYSK T0298 122 :APFLLSSP 1crwG 140 :DMKVVSNA T0298 130 :CAVAA 1crwG 149 :CTTNC T0298 136 :LCEVLAPLLATLDCRQLNLTACLSVSSL 1crwG 154 :LAPVAKVLHENFEIVEGLMTTVHAVTAT T0298 176 :AELLNARPLEPRLFDRQIA 1crwG 182 :QKTVDGPSAKDWRGGRGAA T0298 198 :LA 1crwG 204 :IP T0298 205 :DAEGHSAIERRIFAEVQA 1crwG 206 :SSTGAAKAVGKVIPELDG T0298 230 :PLNVTCIQAPVFFGDSLSVTLQCAEPVDLAAVTRVLDAT 1crwG 224 :KLTGMAFRVPTPNVSVVDLTVRLGKECSYDDIKAAMKAA T0298 269 :KGIEWVGEGDYPTVVGDALGQDETYVGRVRAGQAD 1crwG 266 :PLQGVLGYTEDDVVSCDFTGDNRSSIFDAKAGIQL T0298 304 :PCQVNLWIVSDN 1crwG 302 :KTFVKVVSWYDN T0298 317 :RKGAALNAVLLGELLIKH 1crwG 314 :EFGYSQRVIDLIKHMQKV Number of specific fragments extracted= 17 number of extra gaps= 1 total=905 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 1crwG/T0298-1crwG-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0298 read from 1crwG/T0298-1crwG-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1crwG read from 1crwG/T0298-1crwG-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1crwG in template set Warning: unaligning (T0298)L5 because first residue in template chain is (1crwG)S1 Warning: unaligning (T0298)F195 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1crwG)N202 Warning: unaligning (T0298)N196 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1crwG)N202 Warning: unaligning (T0298)L197 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1crwG)I203 T0298 6 :NVAVVGA 1crwG 2 :KIGINGF T0298 14 :GSVGEALVGLLDERDFPLHRLHLLASAESA 1crwG 9 :GRIGRLVLRAALEMGAQVVAVNDPFIALEY T0298 44 :GQRMGFAES 1crwG 54 :KGEVKAEDG T0298 53 :SLRVGDVD 1crwG 70 :KITVFNEM T0298 61 :SFDFSSVGLAFFAAA 1crwG 83 :PWSKAGAEYIVESTG T0298 76 :AEVSR 1crwG 102 :IEKAS T0298 87 :RAAGCSVIDLSGAL 1crwG 109 :FKGGAKKVIISAPS T0298 103 :SVAPPVMVSVNAERL 1crwG 123 :ADAPMFVCGVNLEKY T0298 121 :AAPFLLSSPCAVAAELCEVLAPLLATLDCRQLNLTACLSVSSLGRE 1crwG 139 :KDMKVVSNASCTTNCLAPVAKVLHENFEIVEGLMTTVHAVTATQKT T0298 180 :NARPLEPRLFDRQIA 1crwG 186 :DGPSAKDWRGGRGAA T0298 198 :LAQVGA 1crwG 204 :IPSSTG T0298 216 :IFAEVQALLGERIGPLNVTCIQAPVFFGDSLSVTLQCAEPVDLAAVTRVLDAT 1crwG 210 :AAKAVGKVIPELDGKLTGMAFRVPTPNVSVVDLTVRLGKECSYDDIKAAMKAA T0298 269 :KGIEWVGEGD 1crwG 268 :QGVLGYTEDD T0298 281 :TVVGDALGQDETYVGR 1crwG 278 :VVSCDFTGDNRSSIFD T0298 299 :AGQADPCQVNLWIVSDNV 1crwG 297 :GIQLSKTFVKVVSWYDNE T0298 318 :KGAALNAVLLGELLIKH 1crwG 315 :FGYSQRVIDLIKHMQKV Number of specific fragments extracted= 16 number of extra gaps= 1 total=921 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 2czcA/T0298-2czcA-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:# T0298 read from 2czcA/T0298-2czcA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2czcA read from 2czcA/T0298-2czcA-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 T0298 1 :M 2czcA 1 :M T0298 4 :PLNVAVVGA 2czcA 2 :KVKVGVNGY T0298 14 :GSVGEALVGLLD 2czcA 11 :GTIGKRVAYAVT T0298 28 :DFPLHRLHLLASAE 2czcA 23 :KQDDMELIGITKTK T0298 42 :SAGQRMGFAESSLRVGDVD 2czcA 40 :EAYRAKELGIPVYAASEEF T0298 61 :SFDFS 2czcA 66 :GFEVA T0298 66 :SVGLAFFAAAAEVSRAHAERARAAGCSVI 2czcA 79 :KVDIIVDATPGGIGAKNKPLYEKAGVKAI T0298 96 :LSGALEPS 2czcA 108 :FQGGEKAD T0298 104 :VAPPVMVSVNAERLA 2czcA 117 :AEVSFVAQANYEAAL T0298 122 :APFLLSSP 2czcA 132 :GKNYVRVV T0298 130 :CAVAA 2czcA 141 :CNTTG T0298 136 :LCEVLAPLLAT 2czcA 146 :LVRTLSAIREY T0298 149 :CRQLNLTACLSVSSLG 2czcA 157 :ADYVYAVMIRRAADPN T0298 177 :ELLNARPLEP 2czcA 173 :DTKRGPINAI T0298 198 :LAQVGAVDAEG 2czcA 183 :KPTVEVPSHHG T0298 218 :AEVQALL 2czcA 194 :PDVQTVI T0298 228 :IGPLNVTCIQAPVFFGDSLSVTLQCAEPVDLAAVTRVLDATKGIEWVGEGD 2czcA 201 :PINIETMAFVVPTTLMHVHSVMVELKKPLTKDDVIDIFENTTRVLLFEKEK T0298 279 :Y 2czcA 253 :F T0298 284 :GDALGQDETYVG 2czcA 266 :LHREWNNLYEIA T0298 297 :VRAGQ 2czcA 278 :VWKES T0298 302 :ADPCQVNLWIVSDN 2czcA 285 :IKGNRLFYIQAVHQ T0298 317 :RKGAALNAVLLGELLIK 2czcA 299 :ESDVIPENIDAIRAMFE Number of specific fragments extracted= 22 number of extra gaps= 0 total=943 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 2czcA/T0298-2czcA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0298 read from 2czcA/T0298-2czcA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2czcA read from 2czcA/T0298-2czcA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2czcA in template set Warning: unaligning (T0298)Q3 because first residue in template chain is (2czcA)M1 T0298 4 :PLNVAVVG 2czcA 2 :KVKVGVNG T0298 13 :TGSVGEALVGLLDE 2czcA 10 :YGTIGKRVAYAVTK T0298 27 :RDFPLHRLHLLASAESAGQRMGFAESSLRVGDVD 2czcA 25 :DDMELIGITKTKPDFEAYRAKELGIPVYAASEEF T0298 61 :SFDFS 2czcA 66 :GFEVA T0298 66 :SVGLAFFAAAAEVSRAHAERARAAGCSVI 2czcA 79 :KVDIIVDATPGGIGAKNKPLYEKAGVKAI T0298 96 :LSGALEPS 2czcA 108 :FQGGEKAD T0298 104 :VAPPVMVSVNAERLA 2czcA 117 :AEVSFVAQANYEAAL T0298 122 :APFLLSSP 2czcA 132 :GKNYVRVV T0298 130 :CAVAA 2czcA 141 :CNTTG T0298 136 :LCEVLAPLLAT 2czcA 146 :LVRTLSAIREY T0298 149 :CRQLNLTACLSVSSL 2czcA 157 :ADYVYAVMIRRAADP T0298 180 :NARPLEPRLFDRQI 2czcA 172 :NDTKRGPINAIKPT T0298 205 :DAEGH 2czcA 186 :VEVPS T0298 215 :RIFAEVQAL 2czcA 191 :HHGPDVQTV T0298 227 :RIGPLNVTCIQAPVFFGDSLSVTLQCAEPVDLAAVTRVLDATKGIEWVGEG 2czcA 200 :IPINIETMAFVVPTTLMHVHSVMVELKKPLTKDDVIDIFENTTRVLLFEKE T0298 278 :DY 2czcA 252 :GF T0298 284 :GDALGQDETYVGRV 2czcA 266 :LHREWNNLYEIAVW T0298 298 :RAGQADPCQVNLWIVSDN 2czcA 281 :ESINIKGNRLFYIQAVHQ T0298 317 :RKGAALNAVLLGELLIK 2czcA 299 :ESDVIPENIDAIRAMFE Number of specific fragments extracted= 19 number of extra gaps= 0 total=962 Will force an alignment to be made, even if fragment is small Number of alignments=56 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2czcA/T0298-2czcA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0298 read from 2czcA/T0298-2czcA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2czcA read from 2czcA/T0298-2czcA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2czcA in template set Warning: unaligning (T0298)Q3 because first residue in template chain is (2czcA)M1 T0298 4 :PLNVAVVG 2czcA 2 :KVKVGVNG T0298 13 :TGSVGEALVGLLDERDFPLHRLHLLASAESA 2czcA 10 :YGTIGKRVAYAVTKQDDMELIGITKTKPDFE T0298 44 :GQRMGFAES 2czcA 48 :GIPVYAASE T0298 53 :SLRVGDVDSFDFSSVGLAFFAAAAEVSRAHAERARAAGCSVIDL 2czcA 66 :GFEVAGTLNDLLEKVDIIVDATPGGIGAKNKPLYEKAGVKAIFQ T0298 98 :GALEPSVAPPVM 2czcA 110 :GGEKADVAEVSF T0298 112 :VNAERLASQAAPFLLSSPCAVAAELCEVLAPLLAT 2czcA 122 :VAQANYEAALGKNYVRVVSCNTTGLVRTLSAIREY T0298 149 :CRQLNLTACLSVSSL 2czcA 157 :ADYVYAVMIRRAADP T0298 180 :NARPLEPRLFD 2czcA 172 :NDTKRGPINAI T0298 202 :GAVDAEGH 2czcA 183 :KPTVEVPS T0298 219 :EVQALLG 2czcA 191 :HHGPDVQ T0298 226 :ERIGPLNVTCIQAPVFFGDSLSVTLQCAEPVDLAAVTRVLDATKGIEWVGEG 2czcA 199 :VIPINIETMAFVVPTTLMHVHSVMVELKKPLTKDDVIDIFENTTRVLLFEKE T0298 278 :DYPT 2czcA 252 :GFDS T0298 284 :GDALGQDETYVGRVR 2czcA 266 :LHREWNNLYEIAVWK T0298 299 :AGQADPCQVNLWIVSDNVRK 2czcA 282 :SINIKGNRLFYIQAVHQESD T0298 320 :AALNAVLLGELLI 2czcA 302 :VIPENIDAIRAMF Number of specific fragments extracted= 15 number of extra gaps= 0 total=977 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 1b7gO/T0298-1b7gO-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:# T0298 read from 1b7gO/T0298-1b7gO-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1b7gO read from 1b7gO/T0298-1b7gO-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 (T0298)P4 because first residue in template chain is (1b7gO)M1 Warning: unaligning (T0298)V67 because of BadResidue code BAD_PEPTIDE in next template residue (1b7gO)D79 Warning: unaligning (T0298)G68 because of BadResidue code BAD_PEPTIDE at template residue (1b7gO)D79 T0298 5 :LNVAVVGA 1b7gO 2 :VNVAVNGY T0298 14 :GSVGEALVGLLD 1b7gO 10 :GTIGKRVADAII T0298 28 :DFPLHRLHLLASAE 1b7gO 22 :KQPDMKLVGVAKTS T0298 42 :SAGQRMGFAESSLRVGDVDS 1b7gO 37 :NYEAFIAHRRGIRIYVPQQS T0298 62 :FDFSS 1b7gO 65 :IPVAG T0298 69 :LAFFAAAAEVSRAHAERARAAGCSVI 1b7gO 80 :IVVDTTPNGVGAQYKPIYLQLQRNAI T0298 96 :LSGALEPSVA 1b7gO 106 :FQGGEKAEVA T0298 106 :PPVMVSVNAERLA 1b7gO 117 :ISFSALCNYNEAL T0298 122 :APFLLSSP 1b7gO 130 :GKKYIRVV T0298 130 :CAVAA 1b7gO 139 :CNTTA T0298 136 :LCEVLAPLLATLDCRQLNLTACLSVSSLG 1b7gO 144 :LLRTICTVNKVSKVEKVRATIVRRAADQK T0298 166 :E 1b7gO 175 :K T0298 173 :RQTAELLNARPL 1b7gO 177 :GPINSLVPDPAT T0298 205 :DAEG 1b7gO 189 :VPSH T0298 213 :ERRIFAEV 1b7gO 193 :HAKDVNSV T0298 224 :LGE 1b7gO 201 :IRN T0298 229 :GPLNVTCIQAPVFFGDSLSVTLQCAEPVDLAAVTRVLDATKGIEWVGEGDY 1b7gO 204 :LDIATMAVIAPTTLMHMHFINITLKDKVEKKDILSVLENTPRIVLISSKYD T0298 283 :VGDALGQDETYVG 1b7gO 269 :KRDRNDIPEVMIF T0298 297 :VRAGQADPCQVNLWIVSDN 1b7gO 282 :SDSIYVKDDEVMLMYAVHQ T0298 317 :RKGAALNAVLLGELLIK 1b7gO 301 :ESIVVPENIDAIRASMK Number of specific fragments extracted= 20 number of extra gaps= 1 total=997 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 1b7gO/T0298-1b7gO-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0298 read from 1b7gO/T0298-1b7gO-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1b7gO read from 1b7gO/T0298-1b7gO-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1b7gO in template set Warning: unaligning (T0298)P4 because first residue in template chain is (1b7gO)M1 Warning: unaligning (T0298)V67 because of BadResidue code BAD_PEPTIDE in next template residue (1b7gO)D79 Warning: unaligning (T0298)G68 because of BadResidue code BAD_PEPTIDE at template residue (1b7gO)D79 T0298 5 :LNVAVVG 1b7gO 2 :VNVAVNG T0298 13 :TGSVGEALVGLLDE 1b7gO 9 :YGTIGKRVADAIIK T0298 27 :RDFPLHRLHLLASAESAGQRMGFAESSLRVGDV 1b7gO 24 :PDMKLVGVAKTSPNYEAFIAHRRGIRIYVPQQS T0298 60 :DSFDFSS 1b7gO 63 :SGIPVAG T0298 69 :LAFFAAAAEVSRAHAERARAAGCSVI 1b7gO 80 :IVVDTTPNGVGAQYKPIYLQLQRNAI T0298 96 :LSGALEPSVAPPVMV 1b7gO 106 :FQGGEKAEVADISFS T0298 111 :SVN 1b7gO 122 :LCN T0298 117 :LASQAAPFLLSSP 1b7gO 125 :YNEALGKKYIRVV T0298 130 :CAVAA 1b7gO 139 :CNTTA T0298 136 :LCEVLAPLLATLDCRQLNLTACLSVSSL 1b7gO 144 :LLRTICTVNKVSKVEKVRATIVRRAADQ T0298 180 :NARPLEPRLFDRQI 1b7gO 172 :KEVKKGPINSLVPD T0298 205 :DAEGHSAI 1b7gO 186 :PATVPSHH T0298 217 :FAEVQALL 1b7gO 194 :AKDVNSVI T0298 227 :RIGPLNVTCIQAPVFFGDSLSVTLQCAEPVDLAAVTRVLDATKGIEWVGEGDYP 1b7gO 202 :RNLDIATMAVIAPTTLMHMHFINITLKDKVEKKDILSVLENTPRIVLISSKYDA T0298 283 :VGDALGQDETYVG 1b7gO 269 :KRDRNDIPEVMIF T0298 297 :VRAGQADPCQVNLWIVSDN 1b7gO 282 :SDSIYVKDDEVMLMYAVHQ T0298 317 :RKGAALNAVLLGELLIK 1b7gO 301 :ESIVVPENIDAIRASMK Number of specific fragments extracted= 17 number of extra gaps= 1 total=1014 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 1b7gO/T0298-1b7gO-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0298 read from 1b7gO/T0298-1b7gO-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1b7gO read from 1b7gO/T0298-1b7gO-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1b7gO in template set Warning: unaligning (T0298)P4 because first residue in template chain is (1b7gO)M1 Warning: unaligning (T0298)V67 because of BadResidue code BAD_PEPTIDE in next template residue (1b7gO)D79 Warning: unaligning (T0298)G68 because of BadResidue code BAD_PEPTIDE at template residue (1b7gO)D79 T0298 5 :LNVAVVGA 1b7gO 2 :VNVAVNGY T0298 14 :GSVGEALVGLLDERDFPLHRLHLLASAESA 1b7gO 10 :GTIGKRVADAIIKQPDMKLVGVAKTSPNYE T0298 44 :GQRMGFAES 1b7gO 47 :GIRIYVPQQ T0298 53 :SLRVGDVDSFDFSS 1b7gO 64 :GIPVAGTVEDLIKT T0298 69 :LAFFAAAAEVSRAHAERARAAGCSVID 1b7gO 80 :IVVDTTPNGVGAQYKPIYLQLQRNAIF T0298 97 :SGALEPSVAPPVMV 1b7gO 107 :QGGEKAEVADISFS T0298 116 :RLASQAAPFLLSSPCAVAAELCEVLAPLLATLDCRQLNLTACLSVSSL 1b7gO 124 :NYNEALGKKYIRVVSCNTTALLRTICTVNKVSKVEKVRATIVRRAADQ T0298 180 :NARPLEPRLFDRQ 1b7gO 172 :KEVKKGPINSLVP T0298 204 :VDAEGHSA 1b7gO 185 :DPATVPSH T0298 220 :VQALLG 1b7gO 193 :HAKDVN T0298 226 :ERIGPLNVTCIQAPVFFGDSLSVTLQCAEPVDLAAVTRVLDATKGIEWVGEGDYPT 1b7gO 201 :IRNLDIATMAVIAPTTLMHMHFINITLKDKVEKKDILSVLENTPRIVLISSKYDAE T0298 284 :GDALGQ 1b7gO 268 :LKRDRN T0298 291 :ETYVGRVRA 1b7gO 274 :DIPEVMIFS T0298 300 :GQADPCQVNLWIVSDNVRK 1b7gO 285 :IYVKDDEVMLMYAVHQESI T0298 320 :AALNAVLLGEL 1b7gO 304 :VVPENIDAIRA Number of specific fragments extracted= 15 number of extra gaps= 1 total=1029 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 1f06A/T0298-1f06A-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:# T0298 read from 1f06A/T0298-1f06A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1f06A read from 1f06A/T0298-1f06A-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 T0298 1 :MSQ 1f06A 1 :MTN T0298 5 :LNVAVVGA 1f06A 4 :IRVAIVGY T0298 14 :GSVGEALVGLLD 1f06A 12 :GNLGRSVEKLIA T0298 28 :DFPLHRLHLL 1f06A 24 :KQPDMDLVGI T0298 38 :ASAESAGQ 1f06A 35 :SRRATLDT T0298 50 :AESSLRVGDVDSF 1f06A 43 :KTPVFDVADVDKH T0298 64 :FSSVGLAFFAAA 1f06A 56 :ADDVDVLFLCMG T0298 76 :AEVSRAHAERA 1f06A 69 :ATDIPEQAPKF T0298 90 :GCSVIDLSGA 1f06A 82 :FACTVDTYDN T0298 102 :PSV 1f06A 92 :HRD T0298 114 :AERLASQAAPFLLSSPCAVAA 1f06A 103 :NEAATAAGNVALVSTGWDPGM T0298 136 :LCEVLAP 1f06A 124 :FSINRVY T0298 143 :LLATLDCRQLNLTACLS 1f06A 156 :LRRIPGVQKAVQYTLPS T0298 165 :REGVKELARQ 1f06A 173 :EDALEKARRG T0298 180 :NARPLEPRL 1f06A 183 :EAGDLTGKQ T0298 201 :V 1f06A 201 :A T0298 205 :DAEG 1f06A 202 :DAAD T0298 213 :ERRIFAEVQA 1f06A 206 :HERIENDIRT T0298 224 :LGER 1f06A 216 :MPDY T0298 228 :IGPLNV 1f06A 224 :EVEVNF T0298 256 :VDLAAVTR 1f06A 230 :IDEATFDS T0298 285 :DALGQDETYVGRVRAGQ 1f06A 238 :EHTGMPHGGHVITTGDT T0298 302 :ADPCQVNLWIVSDNVRKGAALNAVLLGELLIK 1f06A 256 :GFNHTVEYILKLDRNPDFTASSQIAFGRAAHR Number of specific fragments extracted= 23 number of extra gaps= 0 total=1052 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 1f06A/T0298-1f06A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0298 read from 1f06A/T0298-1f06A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1f06A read from 1f06A/T0298-1f06A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1f06A in template set T0298 1 :MS 1f06A 1 :MT T0298 4 :PLNVAVVG 1f06A 3 :NIRVAIVG T0298 13 :TGSVGEALVGLLD 1f06A 11 :YGNLGRSVEKLIA T0298 28 :DFPLHRLHL 1f06A 24 :KQPDMDLVG T0298 37 :LASAE 1f06A 34 :FSRRA T0298 46 :RMGFAESSLRVGDVDSF 1f06A 39 :TLDTKTPVFDVADVDKH T0298 64 :FSSVGLAFFAAAAEVS 1f06A 56 :ADDVDVLFLCMGSATD T0298 80 :RAHAERA 1f06A 73 :PEQAPKF T0298 90 :GCSV 1f06A 82 :FACT T0298 96 :LSGALEPSV 1f06A 86 :VDTYDNHRD T0298 114 :AERLASQ 1f06A 103 :NEAATAA T0298 123 :PFLLSSPCAVAA 1f06A 110 :GNVALVSTGWDP T0298 136 :LCEVLAPLLATLDCRQLNLTACLS 1f06A 122 :GMFSINRVYAAAVLAEHQQHTFWG T0298 160 :VS 1f06A 148 :LS T0298 165 :REGVKELARQ 1f06A 150 :QGHSDALRRI T0298 182 :RPLE 1f06A 160 :PGVQ T0298 192 :QIAFNLLA 1f06A 164 :KAVQYTLP T0298 205 :D 1f06A 172 :S T0298 214 :RRIFAEVQA 1f06A 173 :EDALEKARR T0298 224 :LGERIGP 1f06A 182 :GEAGDLT T0298 244 :DSLSVTLQCAEP 1f06A 193 :HKRQCFVVADAA T0298 258 :LAAVTRVLDAT 1f06A 206 :HERIENDIRTM T0298 269 :KGIEWVGE 1f06A 221 :VGYEVEVN T0298 277 :GDYPT 1f06A 240 :TGMPH T0298 291 :ETYVGRVRAGQADPCQVNLWIVSDNVRKGAALNAVLLGELLIK 1f06A 245 :GGHVITTGDTGGFNHTVEYILKLDRNPDFTASSQIAFGRAAHR Number of specific fragments extracted= 25 number of extra gaps= 0 total=1077 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 1f06A/T0298-1f06A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0298 read from 1f06A/T0298-1f06A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1f06A read from 1f06A/T0298-1f06A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1f06A in template set T0298 3 :QPLNVAVVG 1f06A 2 :TNIRVAIVG T0298 13 :TGSVGEALVGLLDERDFPLHRLHLLASAE 1f06A 11 :YGNLGRSVEKLIAKQPDMDLVGIFSRRAT T0298 50 :AESSLRVGDVDSFD 1f06A 40 :LDTKTPVFDVADVD T0298 64 :FSSVGLAFFAAAA 1f06A 56 :ADDVDVLFLCMGS T0298 77 :EVSRAHAERA 1f06A 70 :TDIPEQAPKF T0298 89 :AGCSVIDLSGALEPS 1f06A 81 :QFACTVDTYDNHRDI T0298 114 :AERLASQAAPFLLSS 1f06A 103 :NEAATAAGNVALVST T0298 129 :PCAVAAELCEV 1f06A 121 :PGMFSINRVYA T0298 142 :PLLATLDCRQLNLTACLS 1f06A 155 :ALRRIPGVQKAVQYTLPS T0298 165 :REGVKELARQ 1f06A 173 :EDALEKARRG T0298 204 :VDAEGHSAIE 1f06A 183 :EAGDLTGKQT T0298 244 :DSLSVTLQCAEP 1f06A 193 :HKRQCFVVADAA T0298 258 :LAAVTRVLDATKG 1f06A 206 :HERIENDIRTMPD T0298 271 :IEWVGEG 1f06A 225 :VEVNFID T0298 286 :ALGQDETYVGRVRAGQADPCQVNLWIV 1f06A 239 :HTGMPHGGHVITTGDTGGFNHTVEYIL T0298 313 :SDNVRKGAALNAVLLGELLIK 1f06A 267 :LDRNPDFTASSQIAFGRAAHR Number of specific fragments extracted= 16 number of extra gaps= 0 total=1093 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 1drw/T0298-1drw-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 # T0298 read from 1drw/T0298-1drw-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1drw read from 1drw/T0298-1drw-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 (T0298)V10 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (1drw)G12 Warning: unaligning (T0298)G11 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (1drw)G12 Warning: unaligning (T0298)G48 because of BadResidue code BAD_PEPTIDE in next template residue (1drw)D48 Warning: unaligning (T0298)F49 because of BadResidue code BAD_PEPTIDE at template residue (1drw)D48 Warning: unaligning (T0298)F71 because of BadResidue code BAD_PEPTIDE in next template residue (1drw)D78 Warning: unaligning (T0298)F72 because of BadResidue code BAD_PEPTIDE at template residue (1drw)D78 Warning: unaligning (T0298)A73 because of BadResidue code BAD_PEPTIDE in next template residue (1drw)T80 Warning: unaligning (T0298)A74 because of BadResidue code BAD_PEPTIDE at template residue (1drw)T80 Warning: unaligning (T0298)R150 because of BadResidue code BAD_PEPTIDE in next template residue (1drw)D152 Warning: unaligning (T0298)Q151 because of BadResidue code BAD_PEPTIDE at template residue (1drw)D152 Warning: unaligning (T0298)E291 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (1drw)R230 Warning: unaligning (T0298)T292 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (1drw)R230 T0298 4 :PLNVAV 1drw 5 :NIRVAI T0298 12 :ATGSVGEALVGLLD 1drw 13 :AGGRMGRQLIQAAL T0298 28 :DFPLHRLHLLASAESAGQRM 1drw 27 :ALEGVQLGAALEREGSSLLG T0298 50 :AE 1drw 49 :AG T0298 52 :SSLRVGDVDSF 1drw 59 :GVTVQSSLDAV T0298 64 :FSSVGLA 1drw 70 :KDDFDVF T0298 75 :AAEVSRAHAERARAAGCSVIDLSGALE 1drw 81 :RPEGTLNHLAFCRQHGKGMVIGTTGFD T0298 113 :NAERLASQAAPFLLSSPCAVAAELCEVLAPLLA 1drw 110 :GKQAIRDAAADIAIVFAANFSVGVNVMLKLLEK T0298 146 :TLDC 1drw 147 :MGDY T0298 152 :LNLTACL 1drw 153 :IEIIEAH T0298 159 :SVSSLGREGVKELARQ 1drw 166 :APSGTALAMGEAIAHA T0298 182 :RPLEPRL 1drw 182 :LDKDLKD T0298 196 :NLLAQVGAVDAEG 1drw 189 :CAVYSREGHTGER T0298 224 :L 1drw 202 :V T0298 228 :IGPLNVTCIQ 1drw 203 :PGTIGFATVR T0298 243 :GDSLSVTLQ 1drw 217 :VGEHTAMFA T0298 288 :GQD 1drw 226 :DIG T0298 293 :YVGRVRAGQ 1drw 231 :LEITHKASS T0298 317 :RKGAALNAVLLGELLIK 1drw 240 :RMTFANGAVRSALWLSG Number of specific fragments extracted= 19 number of extra gaps= 5 total=1112 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 1drw/T0298-1drw-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0298 read from 1drw/T0298-1drw-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1drw read from 1drw/T0298-1drw-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1drw in template set Warning: unaligning (T0298)V10 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (1drw)G12 Warning: unaligning (T0298)G11 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (1drw)G12 Warning: unaligning (T0298)Q45 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1drw)L52 Warning: unaligning (T0298)R46 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1drw)L52 Warning: unaligning (T0298)F71 because of BadResidue code BAD_PEPTIDE in next template residue (1drw)D78 Warning: unaligning (T0298)F72 because of BadResidue code BAD_PEPTIDE at template residue (1drw)D78 Warning: unaligning (T0298)A73 because of BadResidue code BAD_PEPTIDE in next template residue (1drw)T80 Warning: unaligning (T0298)A74 because of BadResidue code BAD_PEPTIDE at template residue (1drw)T80 Warning: unaligning (T0298)R150 because of BadResidue code BAD_PEPTIDE in next template residue (1drw)D152 Warning: unaligning (T0298)Q151 because of BadResidue code BAD_PEPTIDE at template residue (1drw)D152 Warning: unaligning (T0298)D278 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (1drw)R230 Warning: unaligning (T0298)T292 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (1drw)R230 T0298 3 :QPLNVAV 1drw 4 :ANIRVAI T0298 12 :ATGSVGEALVGLLD 1drw 13 :AGGRMGRQLIQAAL T0298 28 :DFPLHRLHLLASAES 1drw 27 :ALEGVQLGAALEREG T0298 43 :AG 1drw 49 :AG T0298 47 :MGFAESSLRVGD 1drw 53 :AGAGKTGVTVQS T0298 64 :FSSVGLA 1drw 70 :KDDFDVF T0298 75 :AAEVSRAHAERARAAGCSVIDLSGALE 1drw 81 :RPEGTLNHLAFCRQHGKGMVIGTTGFD T0298 114 :AERLASQAAPFLLSSPCAVAAELCEVLAPLLATL 1drw 111 :KQAIRDAAADIAIVFAANFSVGVNVMLKLLEKAA T0298 148 :DC 1drw 149 :DY T0298 152 :LNLTACL 1drw 153 :IEIIEAH T0298 159 :SVSSLGREGVKELARQT 1drw 166 :APSGTALAMGEAIAHAL T0298 177 :E 1drw 188 :D T0298 178 :LLNARPLE 1drw 190 :AVYSREGH T0298 205 :DAEGH 1drw 198 :TGERV T0298 227 :RI 1drw 203 :PG T0298 230 :PLNVTCIQ 1drw 205 :TIGFATVR T0298 243 :GDSLSVTLQ 1drw 217 :VGEHTAMFA T0298 275 :GEG 1drw 226 :DIG T0298 293 :YVGRVRAGQ 1drw 231 :LEITHKASS T0298 317 :RKGAALNAVLLGELLIK 1drw 240 :RMTFANGAVRSALWLSG Number of specific fragments extracted= 20 number of extra gaps= 5 total=1132 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 1drw/T0298-1drw-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0298 read from 1drw/T0298-1drw-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1drw read from 1drw/T0298-1drw-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1drw in template set Warning: unaligning (T0298)S2 because of BadResidue code TOO_FEW_ATOMS+BAD_PEPTIDE at template residue (1drw)D3 Warning: unaligning (T0298)V10 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (1drw)G12 Warning: unaligning (T0298)G11 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (1drw)G12 Warning: unaligning (T0298)Q45 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1drw)L52 Warning: unaligning (T0298)R46 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1drw)L52 Warning: unaligning (T0298)F71 because of BadResidue code BAD_PEPTIDE in next template residue (1drw)D78 Warning: unaligning (T0298)F72 because of BadResidue code BAD_PEPTIDE at template residue (1drw)D78 Warning: unaligning (T0298)A73 because of BadResidue code BAD_PEPTIDE in next template residue (1drw)T80 Warning: unaligning (T0298)A74 because of BadResidue code BAD_PEPTIDE at template residue (1drw)T80 Warning: unaligning (T0298)R150 because of BadResidue code BAD_PEPTIDE in next template residue (1drw)D152 Warning: unaligning (T0298)Q151 because of BadResidue code BAD_PEPTIDE at template residue (1drw)D152 Warning: unaligning (T0298)Y279 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (1drw)R230 Warning: unaligning (T0298)P280 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (1drw)R230 T0298 3 :QPLNVAV 1drw 4 :ANIRVAI T0298 12 :ATGSVGEALVGLLDERDFPLHRLHLLASAESA 1drw 13 :AGGRMGRQLIQAALALEGVQLGAALEREGSSL T0298 44 :G 1drw 50 :G T0298 47 :MGFAESSLRVGDVDSFDFSSVGLA 1drw 53 :AGAGKTGVTVQSSLDAVKDDFDVF T0298 75 :AAEVSRAHAERARAAGCSVIDLSGALE 1drw 81 :RPEGTLNHLAFCRQHGKGMVIGTTGFD T0298 113 :NAERLASQAAPFLLSSPCAVAAELCEVLAPLLA 1drw 110 :GKQAIRDAAADIAIVFAANFSVGVNVMLKLLEK T0298 146 :TLDC 1drw 147 :MGDY T0298 152 :LNLTACL 1drw 153 :IEIIEAH T0298 162 :SLGREGVKELARQTAEL 1drw 165 :DAPSGTALAMGEAIAHA T0298 179 :LNARPLEPRLF 1drw 192 :YSREGHTGERV T0298 228 :IGPLNVTCIQ 1drw 203 :PGTIGFATVR T0298 244 :DSLSVTLQ 1drw 218 :GEHTAMFA T0298 276 :EGD 1drw 226 :DIG T0298 281 :TV 1drw 231 :LE T0298 295 :GRV 1drw 233 :ITH T0298 299 :AGQA 1drw 236 :KASS T0298 317 :RKGAALNAVLLGELL 1drw 240 :RMTFANGAVRSALWL Number of specific fragments extracted= 17 number of extra gaps= 6 total=1149 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 2gd1O/T0298-2gd1O-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:# T0298 read from 2gd1O/T0298-2gd1O-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2gd1O read from 2gd1O/T0298-2gd1O-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 (T0298)P4 because first residue in template chain is (2gd1O)A0 Warning: unaligning (T0298)N6 because of BadResidue code BAD_PEPTIDE in next template residue (2gd1O)V3 Warning: unaligning (T0298)V7 because of BadResidue code BAD_PEPTIDE at template residue (2gd1O)V3 Warning: unaligning (T0298)V108 because of BadResidue code BAD_PEPTIDE in next template residue (2gd1O)V129 Warning: unaligning (T0298)M109 because of BadResidue code BAD_PEPTIDE at template residue (2gd1O)V129 Warning: unaligning (T0298)L125 because of BadResidue code BAD_PEPTIDE in next template residue (2gd1O)I144 Warning: unaligning (T0298)L126 because of BadResidue code BAD_PEPTIDE at template residue (2gd1O)I144 Warning: unaligning (T0298)L258 because of BadResidue code BAD_PEPTIDE in next template residue (2gd1O)E253 Warning: unaligning (T0298)A259 because of BadResidue code BAD_PEPTIDE at template residue (2gd1O)E253 Warning: unaligning (T0298)V307 because of BadResidue code BAD_PEPTIDE in next template residue (2gd1O)K306 Warning: unaligning (T0298)N308 because of BadResidue code BAD_PEPTIDE at template residue (2gd1O)K306 T0298 5 :L 2gd1O 1 :V T0298 8 :AVVGA 2gd1O 4 :GINGF T0298 14 :GSVGEALVGLLD 2gd1O 9 :GRIGRNVFRAAL T0298 28 :DFPLHRLHLLASAESAGQRMGFAE 2gd1O 21 :KNPDIEVVAVNDLTDANTLAHLLK T0298 53 :SLR 2gd1O 70 :EII T0298 56 :VGDVDSFDFS 2gd1O 76 :ERDPENLAWG T0298 66 :SVGLAFFAAAAEVSRAHAERARAAGCSVIDLSGALEPSV 2gd1O 88 :GVDIVVESTGRFTKREDAAKHLEAGAKKVIISAPAKNED T0298 106 :PP 2gd1O 126 :IT T0298 110 :VSVNAERLASQ 2gd1O 130 :MGVNQDKYDPK T0298 122 :APF 2gd1O 140 :AHH T0298 127 :SSP 2gd1O 145 :SNA T0298 130 :CAVAA 2gd1O 149 :CTTNC T0298 136 :LCEVLAPLLATLDCRQLNLTACLSVSS 2gd1O 154 :LAPFAKVLHEQFGIVRGMMTTVHSYTN T0298 173 :RQ 2gd1O 181 :DQ T0298 177 :ELLNARPLEPRL 2gd1O 183 :RILDLPHKDLRR T0298 190 :DRQIAFNLLA 2gd1O 196 :ARAAAESIIP T0298 205 :DAEG 2gd1O 206 :TTTG T0298 213 :ERRIFAEV 2gd1O 210 :AAKAVALV T0298 224 :LGERIGPLNVTCIQAPVFFGDSLSVTLQCAEPVD 2gd1O 218 :LPELKGKLNGMAMRVPTPNVSVVDLVAELEKEVT T0298 260 :AVTRVLDAT 2gd1O 254 :EVNAALKAA T0298 269 :KGIEWVGEGDYPTVVGDALGQDETYVGRVRAGQ 2gd1O 266 :ELKGILAYSEEPLVSRDYNGSTVSSTIDALSTM T0298 302 :ADPCQ 2gd1O 300 :IDGKM T0298 309 :LWIVSDN 2gd1O 307 :VVSWYDN T0298 317 :RKGAALNAVLLGELLIKHYL 2gd1O 314 :ETGYSHRVVDLAAYIASKGL Number of specific fragments extracted= 24 number of extra gaps= 5 total=1173 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 2gd1O/T0298-2gd1O-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0298 read from 2gd1O/T0298-2gd1O-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2gd1O read from 2gd1O/T0298-2gd1O-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2gd1O in template set Warning: unaligning (T0298)P4 because first residue in template chain is (2gd1O)A0 Warning: unaligning (T0298)N6 because of BadResidue code BAD_PEPTIDE in next template residue (2gd1O)V3 Warning: unaligning (T0298)V7 because of BadResidue code BAD_PEPTIDE at template residue (2gd1O)V3 Warning: unaligning (T0298)V108 because of BadResidue code BAD_PEPTIDE in next template residue (2gd1O)V129 Warning: unaligning (T0298)M109 because of BadResidue code BAD_PEPTIDE at template residue (2gd1O)V129 Warning: unaligning (T0298)L125 because of BadResidue code BAD_PEPTIDE in next template residue (2gd1O)I144 Warning: unaligning (T0298)L126 because of BadResidue code BAD_PEPTIDE at template residue (2gd1O)I144 Warning: unaligning (T0298)L258 because of BadResidue code BAD_PEPTIDE in next template residue (2gd1O)E253 Warning: unaligning (T0298)A259 because of BadResidue code BAD_PEPTIDE at template residue (2gd1O)E253 Warning: unaligning (T0298)V307 because of BadResidue code BAD_PEPTIDE in next template residue (2gd1O)K306 Warning: unaligning (T0298)N308 because of BadResidue code BAD_PEPTIDE at template residue (2gd1O)K306 T0298 5 :L 2gd1O 1 :V T0298 8 :AVVG 2gd1O 4 :GING T0298 13 :TGSVGEALVGLLDE 2gd1O 8 :FGRIGRNVFRAALK T0298 27 :RDFPLHRLHLLASAESAGQRMGFA 2gd1O 23 :PDIEVVAVNDLTDANTLAHLLKYD T0298 51 :ESSLR 2gd1O 68 :GKEII T0298 56 :VGDVDSFDFS 2gd1O 76 :ERDPENLAWG T0298 66 :SVGLAFFAAAAEVSRAHAERARAAGCSVI 2gd1O 88 :GVDIVVESTGRFTKREDAAKHLEAGAKKV T0298 96 :LSGALEPSVAPP 2gd1O 117 :IISAPAKNEDIT T0298 110 :VSVNAERLASQ 2gd1O 130 :MGVNQDKYDPK T0298 122 :APF 2gd1O 140 :AHH T0298 127 :SSP 2gd1O 145 :SNA T0298 130 :CAVAA 2gd1O 149 :CTTNC T0298 136 :LCEVLAPLLATLDCRQLNLTACLSVSSL 2gd1O 154 :LAPFAKVLHEQFGIVRGMMTTVHSYTND T0298 176 :AELLNARP 2gd1O 182 :QRILDLPH T0298 185 :EPRLFDRQIAFNLLA 2gd1O 191 :KDLRRARAAAESIIP T0298 205 :DAEGHSAIERRIFAEVQA 2gd1O 206 :TTTGAAKAVALVLPELKG T0298 230 :PLNVTCIQAPVFFGDSLSVTLQCAEPVD 2gd1O 224 :KLNGMAMRVPTPNVSVVDLVAELEKEVT T0298 260 :AVTRVLDAT 2gd1O 254 :EVNAALKAA T0298 269 :KGIEWVGEGDYPTVVGDALGQDETYVGRVRAGQAD 2gd1O 266 :ELKGILAYSEEPLVSRDYNGSTVSSTIDALSTMVI T0298 304 :PCQ 2gd1O 302 :GKM T0298 309 :LWIVSDN 2gd1O 307 :VVSWYDN T0298 317 :RKGAALNAVLLGELLIKHYL 2gd1O 314 :ETGYSHRVVDLAAYIASKGL Number of specific fragments extracted= 22 number of extra gaps= 5 total=1195 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 2gd1O/T0298-2gd1O-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0298 read from 2gd1O/T0298-2gd1O-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2gd1O read from 2gd1O/T0298-2gd1O-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2gd1O in template set Warning: unaligning (T0298)P4 because first residue in template chain is (2gd1O)A0 Warning: unaligning (T0298)N6 because of BadResidue code BAD_PEPTIDE in next template residue (2gd1O)V3 Warning: unaligning (T0298)V7 because of BadResidue code BAD_PEPTIDE at template residue (2gd1O)V3 Warning: unaligning (T0298)V108 because of BadResidue code BAD_PEPTIDE in next template residue (2gd1O)V129 Warning: unaligning (T0298)M109 because of BadResidue code BAD_PEPTIDE at template residue (2gd1O)V129 Warning: unaligning (T0298)L125 because of BadResidue code BAD_PEPTIDE in next template residue (2gd1O)I144 Warning: unaligning (T0298)L126 because of BadResidue code BAD_PEPTIDE at template residue (2gd1O)I144 Warning: unaligning (T0298)L258 because of BadResidue code BAD_PEPTIDE in next template residue (2gd1O)E253 Warning: unaligning (T0298)A259 because of BadResidue code BAD_PEPTIDE at template residue (2gd1O)E253 Warning: unaligning (T0298)V307 because of BadResidue code BAD_PEPTIDE in next template residue (2gd1O)K306 Warning: unaligning (T0298)N308 because of BadResidue code BAD_PEPTIDE at template residue (2gd1O)K306 T0298 5 :L 2gd1O 1 :V T0298 8 :AVVGA 2gd1O 4 :GINGF T0298 14 :GSVGEALVGLLDERDFPLHRLHLLASAESA 2gd1O 9 :GRIGRNVFRAALKNPDIEVVAVNDLTDANT T0298 44 :GQRMGFAESSLRVGDV 2gd1O 61 :GNNLVVNGKEIIVKAE T0298 60 :DSFDFS 2gd1O 78 :DPENLA T0298 66 :SVGLAFFAAA 2gd1O 88 :GVDIVVESTG T0298 76 :AEVSR 2gd1O 102 :REDAA T0298 85 :RARAAGCSVIDLSGALEPSV 2gd1O 107 :KHLEAGAKKVIISAPAKNED T0298 106 :PP 2gd1O 126 :IT T0298 110 :VSVNAERLAS 2gd1O 130 :MGVNQDKYDP T0298 121 :AAPF 2gd1O 139 :KAHH T0298 127 :SSPCAVAAELCEVLAPLLATLDCRQLNLTACLSVSSLGRE 2gd1O 145 :SNASCTTNCLAPFAKVLHEQFGIVRGMMTTVHSYTNDQRI T0298 180 :NARPLEPRLFDRQIAFNLLAQVGA 2gd1O 185 :LDLPHKDLRRARAAAESIIPTTTG T0298 220 :VQALLG 2gd1O 210 :AAKAVA T0298 226 :ERIGPLNVTCIQAPVFFGDSLSVTLQCAEPVD 2gd1O 220 :ELKGKLNGMAMRVPTPNVSVVDLVAELEKEVT T0298 260 :AVTRVLDAT 2gd1O 254 :EVNAALKAA T0298 271 :IEWVGE 2gd1O 271 :LAYSEE T0298 280 :PTVVGDALGQDETYVGRVRAGQA 2gd1O 277 :PLVSRDYNGSTVSSTIDALSTMV T0298 303 :DPCQ 2gd1O 301 :DGKM T0298 309 :LWIVSDNV 2gd1O 307 :VVSWYDNE T0298 318 :KGAALNAVLLGELLIKHYL 2gd1O 315 :TGYSHRVVDLAAYIASKGL Number of specific fragments extracted= 21 number of extra gaps= 5 total=1216 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 1znqO/T0298-1znqO-t06-local-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1znqO expands to /projects/compbio/data/pdb/1znq.pdb.gz 1znqO:# T0298 read from 1znqO/T0298-1znqO-t06-local-adpstyle5.a2m # 1znqO read from 1znqO/T0298-1znqO-t06-local-adpstyle5.a2m # adding 1znqO to template set # found chain 1znqO in template set Warning: unaligning (T0298)Q3 because first residue in template chain is (1znqO)K3 T0298 5 :LNVAVVGA 1znqO 4 :VKVGVNGF T0298 14 :GSVGEALVGLLD 1znqO 12 :GRIGRLVTRAAF T0298 28 :DFPLHRLHLLASAE 1znqO 24 :NSGKVDIVAINDPF T0298 42 :SAGQRMGFAE 1znqO 39 :DLNYMVYMFQ T0298 52 :SSLRVGDVDSFDFS 1znqO 75 :TIFQERDPSKIKWG T0298 66 :SVGLAFFAAAAEVSRAHAERARAAGCSVIDLSGA 1znqO 91 :GAEYVVESTGVFTTMEKAGAHLQGGAKRVIISAP T0298 102 :PSVAPPVMVSVNAERLAS 1znqO 125 :SADAPMFVMGVNHEKYDN T0298 122 :APFLLSSP 1znqO 143 :SLKIISNA T0298 130 :CAVAA 1znqO 152 :CTTNC T0298 136 :LCEVLAPLLATLDCRQLNLTACLSVSS 1znqO 157 :LAPLAKVIHDNFGIVEGLMTTVHAITA T0298 175 :TAELLNARPLEPRLFDRQIAFNLLA 1znqO 184 :TQKTVDGPSGKLWRDGRGALQNIIP T0298 205 :DAEG 1znqO 209 :ASTG T0298 213 :ERRIFAEV 1znqO 213 :AAKAVGKV T0298 224 :LGERIGPLNVTCIQAPVFFGDSLSVTLQCAEPVDLAAVTRVLDAT 1znqO 221 :IPELNGKLTGMAFRVPTANVSVVDLTCRLEKPAKYDDIKKVVKQA T0298 269 :KGIEWVGEGDYPTVVGDALGQDETYVGRVRAGQ 1znqO 269 :PLKGILGYTEHQVVSSDFNSDTHSSTFDAGAGI T0298 302 :ADPCQVNLWIVSDN 1znqO 303 :LNDHFVKLISWYDN T0298 317 :RKGAALNAVLLGELLIKH 1znqO 317 :EFGYSNRVVDLMAHMASK Number of specific fragments extracted= 17 number of extra gaps= 0 total=1233 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 1j0xO/T0298-1j0xO-t06-local-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1j0xO expands to /projects/compbio/data/pdb/1j0x.pdb.gz 1j0xO:Bad short name: OD for alphabet: pdb_atoms # T0298 read from 1j0xO/T0298-1j0xO-t06-local-adpstyle5.a2m # 1j0xO read from 1j0xO/T0298-1j0xO-t06-local-adpstyle5.a2m # adding 1j0xO to template set # found chain 1j0xO in template set Warning: unaligning (T0298)L5 because first residue in template chain is (1j0xO)V1 Warning: unaligning (T0298)A131 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1j0xO)T150 T0298 6 :NVAVVGA 1j0xO 2 :KVGVNGF T0298 14 :GSVGEALVGLLD 1j0xO 9 :GRIGRLVTRAAF T0298 28 :DFPLHRLHLLASAE 1j0xO 21 :NSGKVDVVAINDPF T0298 42 :SAGQRMGFAE 1j0xO 36 :DLHYMVYMFQ T0298 52 :SSLRVGDVDSFDFS 1j0xO 72 :TIFQERDPANIKWG T0298 66 :SVGLAFFAAAAEVSRAHAERARAAGCSVIDLSGA 1j0xO 88 :GAEYVVESTGVFTTMEKAGAHLKGGAKRVIISAP T0298 102 :PSVAPPVMVSVNAERLAS 1j0xO 122 :SADAPMFVMGVNHEKYDN T0298 122 :APFLLSSP 1j0xO 140 :SLKIVSNA T0298 132 :VAA 1j0xO 151 :TNC T0298 136 :LCEVLAPLLATLDCRQLNLTACLSVSS 1j0xO 154 :LAPLAKVIHDHFGIVEGLMTTVHAITA T0298 175 :TAELLNARPLEPRLFDRQIAFNLLA 1j0xO 181 :TQKTVDGPSGKLWRDGRGAAQNIIP T0298 205 :DAEG 1j0xO 206 :ASTG T0298 213 :ERRIFAEV 1j0xO 210 :AAKAVGKV T0298 224 :LGERIGPLNVTCIQAPVFFGDSLSVTLQCAEPVDLAAVTRVLDAT 1j0xO 218 :IPELNGKLTGMAFRVPTPNVSVVDLTCRLEKAAKYDDIKKVVKQA T0298 269 :KGIEWVGEGDYPTVVGDALGQDETYVGRVRAGQ 1j0xO 266 :PLKGILGYTEDQVVSCDFNSDTHSSTFDAGAGI T0298 302 :ADPCQVNLWIVSDN 1j0xO 300 :LNDHFVKLISWYDN T0298 317 :RKGAALNAVLLGELLIKH 1j0xO 314 :EFGYSNRVVDLMVHMASK Number of specific fragments extracted= 17 number of extra gaps= 0 total=1250 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 2bkaA/T0298-2bkaA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2bkaA expands to /projects/compbio/data/pdb/2bka.pdb.gz 2bkaA:# T0298 read from 2bkaA/T0298-2bkaA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2bkaA read from 2bkaA/T0298-2bkaA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2bkaA to template set # found chain 2bkaA in template set T0298 4 :PLNVAVVGATGSVGEALVGLLDERDF 2bkaA 18 :NKSVFILGASGETGRVLLKEILEQGL T0298 30 :PLHRLHL 2bkaA 45 :SKVTLIG T0298 39 :SAE 2bkaA 52 :RRK T0298 42 :SAGQRMGFAESSLRVGDVDSFD 2bkaA 58 :DEEAYKNVNQEVVDFEKLDDYA T0298 64 :FSSVGLAFFAAAAEVS 2bkaA 82 :FQGHDVGFCCLGTTRG T0298 80 :RAHAERARAAGCSVIDLSGALEPS 2bkaA 113 :LKSAELAKAGGCKHFNLLSSKGAD T0298 104 :V 2bkaA 138 :S T0298 135 :ELCEVLAPLLATLDCRQLNLTA 2bkaA 145 :QVKGEVEAKVEELKFDRYSVFR T0298 175 :TAELLNAR 2bkaA 167 :PGVLLCDR T0298 205 :DAEG 2bkaA 175 :QESR T0298 211 :AIERRIFAEVQA 2bkaA 179 :PGEWLVRKFFGS T0298 224 :LGER 2bkaA 191 :LPDS T0298 228 :IGPLN 2bkaA 198 :GHSVP T0298 258 :LAAVTRVLDAT 2bkaA 203 :VVTVVRAMLNN T0298 269 :KGIEWVG 2bkaA 220 :KQMELLE Number of specific fragments extracted= 15 number of extra gaps= 0 total=1265 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 2bkaA/T0298-2bkaA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0298 read from 2bkaA/T0298-2bkaA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2bkaA read from 2bkaA/T0298-2bkaA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2bkaA in template set T0298 4 :PLNVAVVGATGSVGEALVGLLDERD 2bkaA 18 :NKSVFILGASGETGRVLLKEILEQG T0298 29 :FPLHRLHL 2bkaA 44 :FSKVTLIG T0298 46 :RMGFA 2bkaA 54 :KLTFD T0298 51 :ESSLRVGDVDSFD 2bkaA 64 :NVNQEVVDFEKLD T0298 64 :FSSVGLAFFAAAAE 2bkaA 82 :FQGHDVGFCCLGTT T0298 78 :VSRAHAERARAAGCSVIDLSGALE 2bkaA 111 :YVLKSAELAKAGGCKHFNLLSSKG T0298 118 :ASQAAP 2bkaA 136 :DKSSNF T0298 134 :AELCEVLAPLLATLDCRQLNLTA 2bkaA 144 :LQVKGEVEAKVEELKFDRYSVFR T0298 175 :TAELLNARPL 2bkaA 167 :PGVLLCDRQE T0298 185 :EPRLFDRQI 2bkaA 193 :DSWASGHSV T0298 199 :A 2bkaA 202 :P T0298 213 :ERRIFAEV 2bkaA 203 :VVTVVRAM T0298 221 :QALLGERIGPLNVT 2bkaA 212 :NNVVRPRDKQMELL T0298 257 :DLAAVTRV 2bkaA 226 :ENKAIHDL Number of specific fragments extracted= 14 number of extra gaps= 0 total=1279 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 2bkaA/T0298-2bkaA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0298 read from 2bkaA/T0298-2bkaA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2bkaA read from 2bkaA/T0298-2bkaA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2bkaA in template set T0298 4 :PLNVAVVGATGSVGEALVGLLDERDFPLHRLHLLAS 2bkaA 18 :NKSVFILGASGETGRVLLKEILEQGLFSKVTLIGRR T0298 46 :RMGFAES 2bkaA 54 :KLTFDEE T0298 53 :SLRVGDVDSFDFSS 2bkaA 64 :NVNQEVVDFEKLDD T0298 67 :VGLAFFAAA 2bkaA 85 :HDVGFCCLG T0298 76 :AEVSRAHAERARAAGCSVIDLSGALEPS 2bkaA 109 :RDYVLKSAELAKAGGCKHFNLLSSKGAD T0298 104 :VAPP 2bkaA 138 :SSNF T0298 115 :ERLA 2bkaA 142 :LYLQ T0298 135 :ELCEVLAPLLA 2bkaA 146 :VKGEVEAKVEE T0298 147 :LDCRQLNLTAC 2bkaA 157 :LKFDRYSVFRP T0298 163 :LGREG 2bkaA 176 :ESRPG T0298 171 :LARQTAEL 2bkaA 181 :EWLVRKFF T0298 182 :RPLEPRLFD 2bkaA 189 :GSLPDSWAS T0298 191 :RQIA 2bkaA 199 :HSVP T0298 213 :ERRIFAEVQALLG 2bkaA 203 :VVTVVRAMLNNVV T0298 226 :ERIGPLNVT 2bkaA 217 :PRDKQMELL T0298 257 :DLAAVTRV 2bkaA 226 :ENKAIHDL Number of specific fragments extracted= 16 number of extra gaps= 0 total=1295 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 3gpdG/T0298-3gpdG-t06-local-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 3gpdG expands to /projects/compbio/data/pdb/3gpd.pdb.gz 3gpdG:# T0298 read from 3gpdG/T0298-3gpdG-t06-local-adpstyle5.a2m # 3gpdG read from 3gpdG/T0298-3gpdG-t06-local-adpstyle5.a2m # adding 3gpdG to template set # found chain 3gpdG in template set Warning: unaligning (T0298)P4 because of BadResidue code BAD_PEPTIDE at template residue (3gpdG)K2 Warning: unaligning (T0298)V7 because of BadResidue code BAD_PEPTIDE in next template residue (3gpdG)G6 Warning: unaligning (T0298)A8 because of BadResidue code BAD_PEPTIDE at template residue (3gpdG)G6 Warning: unaligning (T0298)F29 because of BadResidue code BAD_PEPTIDE in next template residue (3gpdG)G25 Warning: unaligning (T0298)P30 because of BadResidue code BAD_PEPTIDE at template residue (3gpdG)G25 Warning: unaligning (T0298)L31 because of BadResidue code BAD_PEPTIDE at template residue (3gpdG)K26 Warning: unaligning (T0298)H32 because of BadResidue code BAD_PEPTIDE in next template residue (3gpdG)D28 Warning: unaligning (T0298)R33 because of BadResidue code BAD_PEPTIDE at template residue (3gpdG)D28 Warning: unaligning (T0298)E41 because of BadResidue code BAD_PEPTIDE in next template residue (3gpdG)I37 Warning: unaligning (T0298)G48 because of BadResidue code BAD_PEPTIDE in next template residue (3gpdG)M45 Warning: unaligning (T0298)F49 because of BadResidue code BAD_PEPTIDE at template residue (3gpdG)M45 Warning: unaligning (T0298)V56 because of BadResidue code BAD_PEPTIDE in next template residue (3gpdG)R79 Warning: unaligning (T0298)G57 because of BadResidue code BAD_PEPTIDE at template residue (3gpdG)R79 Warning: unaligning (T0298)D58 because of BadResidue code BAD_PEPTIDE at template residue (3gpdG)D80 Warning: unaligning (T0298)S61 because of BadResidue code BAD_PEPTIDE in next template residue (3gpdG)I84 Warning: unaligning (T0298)F62 because of BadResidue code BAD_PEPTIDE at template residue (3gpdG)I84 Warning: unaligning (T0298)D63 because of BadResidue code BAD_PEPTIDE in next template residue (3gpdG)W86 Warning: unaligning (T0298)F64 because of BadResidue code BAD_PEPTIDE at template residue (3gpdG)W86 Warning: unaligning (T0298)A70 because of BadResidue code BAD_PEPTIDE in next template residue (3gpdG)V95 Warning: unaligning (T0298)F71 because of BadResidue code BAD_PEPTIDE at template residue (3gpdG)V95 Warning: unaligning (T0298)S103 because of BadResidue code BAD_PEPTIDE in next template residue (3gpdG)D126 Warning: unaligning (T0298)V104 because of BadResidue code BAD_PEPTIDE at template residue (3gpdG)D126 Warning: unaligning (T0298)V108 because of BadResidue code BAD_PEPTIDE in next template residue (3gpdG)V131 Warning: unaligning (T0298)M109 because of BadResidue code BAD_PEPTIDE at template residue (3gpdG)V131 Warning: unaligning (T0298)A118 because of BadResidue code BAD_PEPTIDE in next template residue (3gpdG)N141 Warning: unaligning (T0298)S119 because of BadResidue code BAD_PEPTIDE at template residue (3gpdG)N141 Warning: unaligning (T0298)A122 because of BadResidue code BAD_PEPTIDE at template residue (3gpdG)S142 Warning: unaligning (T0298)A131 because of BadResidue code BAD_PEPTIDE in next template residue (3gpdG)T153 Warning: unaligning (T0298)V132 because of BadResidue code BAD_PEPTIDE at template residue (3gpdG)T153 Warning: unaligning (T0298)L144 because of BadResidue code BAD_PEPTIDE in next template residue (3gpdG)D165 Warning: unaligning (T0298)A145 because of BadResidue code BAD_PEPTIDE at template residue (3gpdG)D165 Warning: unaligning (T0298)C149 because of BadResidue code BAD_PEPTIDE in next template residue (3gpdG)V170 Warning: unaligning (T0298)R150 because of BadResidue code BAD_PEPTIDE at template residue (3gpdG)V170 Warning: unaligning (T0298)Q151 because of BadResidue code BAD_PEPTIDE in next template residue (3gpdG)G172 Warning: unaligning (T0298)L152 because of BadResidue code BAD_PEPTIDE at template residue (3gpdG)G172 Warning: unaligning (T0298)N153 because of BadResidue code BAD_PEPTIDE at template residue (3gpdG)L173 Warning: unaligning (T0298)C157 because of BadResidue code BAD_PEPTIDE in next template residue (3gpdG)H178 Warning: unaligning (T0298)L158 because of BadResidue code BAD_PEPTIDE at template residue (3gpdG)H178 Warning: unaligning (T0298)V160 because of BadResidue code BAD_PEPTIDE in next template residue (3gpdG)T181 Warning: unaligning (T0298)S161 because of BadResidue code BAD_PEPTIDE at template residue (3gpdG)T181 Warning: unaligning (T0298)S162 because of BadResidue code BAD_PEPTIDE in next template residue (3gpdG)T183 Warning: unaligning (T0298)T175 because of BadResidue code BAD_PEPTIDE at template residue (3gpdG)T183 Warning: unaligning (T0298)A176 because of BadResidue code BAD_PEPTIDE in next template residue (3gpdG)K185 Warning: unaligning (T0298)E177 because of BadResidue code BAD_PEPTIDE at template residue (3gpdG)K185 Warning: unaligning (T0298)L178 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (3gpdG)T186 Warning: unaligning (T0298)L179 because of BadResidue code BAD_PEPTIDE at template residue (3gpdG)V187 Warning: unaligning (T0298)N180 because of BadResidue code BAD_PEPTIDE in next template residue (3gpdG)S189 Warning: unaligning (T0298)A181 because of BadResidue code BAD_PEPTIDE at template residue (3gpdG)S189 Warning: unaligning (T0298)P183 because of BadResidue code BAD_PEPTIDE in next template residue (3gpdG)G192 Warning: unaligning (T0298)L184 because of BadResidue code BAD_PEPTIDE at template residue (3gpdG)G192 Warning: unaligning (T0298)E185 because of BadResidue code BAD_PEPTIDE at template residue (3gpdG)K193 Warning: unaligning (T0298)P186 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (3gpdG)L194 Warning: unaligning (T0298)R187 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (3gpdG)W195 Warning: unaligning (T0298)L188 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (3gpdG)R196 Warning: unaligning (T0298)F189 because of BadResidue code BAD_PEPTIDE at template residue (3gpdG)G197 Warning: unaligning (T0298)D190 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (3gpdG)G198 Warning: unaligning (T0298)R191 because of BadResidue code BAD_PEPTIDE at template residue (3gpdG)R199 Warning: unaligning (T0298)I193 because of BadResidue code BAD_PEPTIDE in next template residue (3gpdG)A202 Warning: unaligning (T0298)A194 because of BadResidue code BAD_PEPTIDE at template residue (3gpdG)A202 Warning: unaligning (T0298)F195 because of BadResidue code BAD_PEPTIDE at template residue (3gpdG)Q203 Warning: unaligning (T0298)N196 because of BadResidue code BAD_PEPTIDE in next template residue (3gpdG)L205 Warning: unaligning (T0298)L197 because of BadResidue code BAD_PEPTIDE at template residue (3gpdG)L205 Warning: unaligning (T0298)A206 because of BadResidue code BAD_PEPTIDE in next template residue (3gpdG)T210 Warning: unaligning (T0298)E207 because of BadResidue code BAD_PEPTIDE at template residue (3gpdG)T210 Warning: unaligning (T0298)E213 because of BadResidue code BAD_PEPTIDE in next template residue (3gpdG)A213 Warning: unaligning (T0298)R214 because of BadResidue code BAD_PEPTIDE at template residue (3gpdG)A213 Warning: unaligning (T0298)R215 because of BadResidue code BAD_PEPTIDE in next template residue (3gpdG)A215 Warning: unaligning (T0298)I216 because of BadResidue code BAD_PEPTIDE at template residue (3gpdG)A215 Warning: unaligning (T0298)E219 because of BadResidue code BAD_PEPTIDE in next template residue (3gpdG)V219 Warning: unaligning (T0298)V220 because of BadResidue code BAD_PEPTIDE at template residue (3gpdG)V219 Warning: unaligning (T0298)E226 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (3gpdG)L223 Warning: unaligning (T0298)R227 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (3gpdG)L223 Warning: unaligning (T0298)I228 because of BadResidue code BAD_PEPTIDE at template residue (3gpdG)D224 Warning: unaligning (T0298)V233 because of BadResidue code BAD_PEPTIDE in next template residue (3gpdG)M230 Warning: unaligning (T0298)T234 because of BadResidue code BAD_PEPTIDE at template residue (3gpdG)M230 Warning: unaligning (T0298)F242 because of BadResidue code BAD_PEPTIDE in next template residue (3gpdG)V239 Warning: unaligning (T0298)G243 because of BadResidue code BAD_PEPTIDE at template residue (3gpdG)V239 Warning: unaligning (T0298)Q251 because of BadResidue code BAD_PEPTIDE in next template residue (3gpdG)L248 Warning: unaligning (T0298)C252 because of BadResidue code BAD_PEPTIDE at template residue (3gpdG)L248 Warning: unaligning (T0298)A253 because of BadResidue code BAD_PEPTIDE at template residue (3gpdG)E249 Warning: unaligning (T0298)I271 because of BadResidue code BAD_PEPTIDE in next template residue (3gpdG)G271 Warning: unaligning (T0298)E272 because of BadResidue code BAD_PEPTIDE at template residue (3gpdG)G271 Warning: unaligning (T0298)E276 because of BadResidue code BAD_PEPTIDE in next template residue (3gpdG)T276 Warning: unaligning (T0298)G277 because of BadResidue code BAD_PEPTIDE at template residue (3gpdG)T276 Warning: unaligning (T0298)D278 because of BadResidue code BAD_PEPTIDE in next template residue (3gpdG)D278 Warning: unaligning (T0298)Y279 because of BadResidue code BAD_PEPTIDE at template residue (3gpdG)D278 Warning: unaligning (T0298)P280 because of BadResidue code BAD_PEPTIDE at template residue (3gpdG)E279 Warning: unaligning (T0298)T281 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (3gpdG)V280 Warning: unaligning (T0298)V282 because of BadResidue code BAD_PEPTIDE at template residue (3gpdG)V281 Warning: unaligning (T0298)V283 because of BadResidue code BAD_PEPTIDE at template residue (3gpdG)S282 Warning: unaligning (T0298)D290 because of BadResidue code BAD_PEPTIDE in next template residue (3gpdG)H290 Warning: unaligning (T0298)E291 because of BadResidue code BAD_PEPTIDE at template residue (3gpdG)H290 Warning: unaligning (T0298)V294 because of BadResidue code BAD_PEPTIDE in next template residue (3gpdG)F294 Warning: unaligning (T0298)G295 because of BadResidue code BAD_PEPTIDE at template residue (3gpdG)F294 Warning: unaligning (T0298)P304 because of BadResidue code BAD_PEPTIDE in next template residue (3gpdG)T305 Warning: unaligning (T0298)C305 because of BadResidue code BAD_PEPTIDE at template residue (3gpdG)T305 Warning: unaligning (T0298)W310 because of BadResidue code BAD_PEPTIDE in next template residue (3gpdG)S311 Warning: unaligning (T0298)I311 because of BadResidue code BAD_PEPTIDE at template residue (3gpdG)S311 Warning: unaligning (T0298)V312 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (3gpdG)Y313 Warning: unaligning (T0298)S313 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (3gpdG)Y313 Warning: unaligning (T0298)D314 because of BadResidue code BAD_PEPTIDE at template residue (3gpdG)D314 Warning: unaligning (T0298)N315 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (3gpdG)N315 Warning: unaligning (T0298)H334 because of BadResidue code BAD_PEPTIDE in next template residue (3gpdG)E334 T0298 5 :LN 3gpdG 3 :VK T0298 9 :VVGA 3gpdG 7 :VDGF T0298 14 :GSVGEALVGLLD 3gpdG 11 :GRIGRLVTRAAF T0298 28 :D 3gpdG 23 :N T0298 34 :LHLLASA 3gpdG 29 :IVAINDP T0298 42 :SAGQRM 3gpdG 38 :DLHYMV T0298 50 :AE 3gpdG 46 :FQ T0298 52 :SSLR 3gpdG 74 :TIFQ T0298 59 :VD 3gpdG 81 :PE T0298 65 :S 3gpdG 87 :G T0298 66 :SVGL 3gpdG 90 :GTAY T0298 72 :FAAAAEVSRAHAERARAAGCSVIDLSGA 3gpdG 96 :ESTGVFTTMEKAGAHLKGGAKRIVISAP T0298 102 :P 3gpdG 124 :S T0298 105 :APP 3gpdG 127 :APM T0298 110 :VSVNAERL 3gpdG 132 :MGVNHFKY T0298 123 :PFLLSSP 3gpdG 143 :LKIISNA T0298 130 :C 3gpdG 151 :C T0298 133 :AA 3gpdG 154 :NC T0298 136 :LCEVLAPL 3gpdG 156 :LAPLAKVI T0298 146 :TLD 3gpdG 166 :HFG T0298 154 :LTA 3gpdG 174 :MTT T0298 159 :S 3gpdG 179 :A T0298 182 :R 3gpdG 190 :P T0298 192 :Q 3gpdG 200 :G T0298 198 :LA 3gpdG 206 :IP T0298 205 :D 3gpdG 208 :A T0298 208 :G 3gpdG 211 :G T0298 217 :FA 3gpdG 216 :VG T0298 224 :LG 3gpdG 220 :IP T0298 229 :GPLN 3gpdG 225 :GKLT T0298 235 :CIQAPVF 3gpdG 231 :AFRVPTA T0298 244 :DSLSVTL 3gpdG 240 :SVLDLTC T0298 254 :EPVDLAAVTRVLDAT 3gpdG 250 :KPAKYDDIKKVVKEA T0298 269 :KG 3gpdG 268 :PL T0298 273 :WVG 3gpdG 272 :ILG T0298 284 :GDALGQ 3gpdG 283 :DDFNGS T0298 292 :TY 3gpdG 291 :SS T0298 296 :RVRAGQ 3gpdG 295 :DAGAGI T0298 302 :AD 3gpdG 302 :LN T0298 306 :QVNL 3gpdG 306 :FVKL T0298 317 :RKGAALNAVLLGELLIK 3gpdG 316 :EFGYSERVVDLMAHMAS Number of specific fragments extracted= 41 number of extra gaps= 32 total=1336 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 1ihxA/T0298-1ihxA-t06-local-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1ihxA expands to /projects/compbio/data/pdb/1ihx.pdb.gz 1ihxA:# T0298 read from 1ihxA/T0298-1ihxA-t06-local-adpstyle5.a2m # 1ihxA read from 1ihxA/T0298-1ihxA-t06-local-adpstyle5.a2m # adding 1ihxA to template set # found chain 1ihxA in template set T0298 6 :NVAVVGA 1ihxA 2 :KIGINGF T0298 14 :GSVGEALVGLLDERD 1ihxA 9 :GRIGRLVLRTALEMG T0298 32 :HRLHLLASAE 1ihxA 25 :AQVVAVNDPF T0298 42 :SAGQRMGFAE 1ihxA 36 :ALEYMVYMFK T0298 52 :SSLRVGDVDSFDFS 1ihxA 72 :TVFNEMKPENIPWS T0298 66 :SVGLAFFAAAAEVSRAHAERARAAGCSVIDLSGA 1ihxA 88 :GAEYIVESTGVFTTIEKASAHFKGGAKKVIISAP T0298 102 :PSVAPPVMVSVNAERLAS 1ihxA 122 :SADAPMFVCGVNLEKYSK T0298 122 :APFLLSSP 1ihxA 140 :DMKVVSNA T0298 130 :CAVAA 1ihxA 149 :CTTNC T0298 136 :LCEVLAPLLATLDCRQLNLTACLSVSS 1ihxA 154 :LAPVAKVLHENFEIVEGLMTTVHAVTA T0298 175 :TAELLNARPLEPRLFDRQIAFNLLA 1ihxA 181 :TQKTVDGPSAKDWRGGRGAAQNIIP T0298 205 :DAEG 1ihxA 206 :SSTG T0298 213 :ERRIFAEV 1ihxA 210 :AAKAVGKV T0298 224 :LGERIGPLNVTCIQAPVFFGDSLSVTLQCAEPVDLAAVTRVLDAT 1ihxA 218 :IPELDGKLTGMAFRVPTPNVSVVDLTVRLGKECSYDDIKAAMKTA T0298 269 :KGIEWVGEGDYPTVVGDALGQDETYVGRVRAGQ 1ihxA 266 :PLQGVLGYTEDDVVSCDFTGDNRSSIFDAKAGI T0298 302 :ADPCQVNLWIVSDN 1ihxA 300 :LSKTFVKVVSWYDN T0298 317 :RKGAALNAVLLGELLIKH 1ihxA 314 :EFGYSQRVIDLIKHMQKV Number of specific fragments extracted= 17 number of extra gaps= 0 total=1353 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 1hdgO/T0298-1hdgO-t06-local-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1hdgO expands to /projects/compbio/data/pdb/1hdg.pdb.gz 1hdgO:# T0298 read from 1hdgO/T0298-1hdgO-t06-local-adpstyle5.a2m # 1hdgO read from 1hdgO/T0298-1hdgO-t06-local-adpstyle5.a2m # adding 1hdgO to template set # found chain 1hdgO in template set T0298 6 :NVAVVGA 1hdgO 2 :RVAINGF T0298 14 :GSVGEALVGLLDERDFPLHRLHLLASAESAGQRMGFAE 1hdgO 9 :GRIGRLVYRIIYERKNPDIEVVAINDLTDTKTLAHLLK T0298 52 :SSLRVGDVDSFDFS 1hdgO 72 :KVFAEPDPSKLPWK T0298 66 :SVGLAFFAAAAEVSRAHAERARAAGCSVIDLSGALEPSV 1hdgO 88 :GVDFVIESTGVFRNREKAELHLQAGAKKVIITAPAKGED T0298 106 :PPVMVSVNAERLAS 1hdgO 126 :ITVVIGCNEDQLKP T0298 122 :APFLLSSP 1hdgO 140 :EHTIISCA T0298 130 :CAVAA 1hdgO 149 :CTTNS T0298 136 :LCEVLAPLLATLDCRQLNLTACLSVSS 1hdgO 154 :IAPIVKVLHEKFGIVSGMLTTVHSYTN T0298 173 :RQ 1hdgO 181 :DQ T0298 177 :ELLNARPLEPRL 1hdgO 183 :RVLDLPHKDLRR T0298 190 :DRQIAFNLLA 1hdgO 196 :ARAAAVNIIP T0298 205 :DAEG 1hdgO 206 :TTTG T0298 213 :ERRIFAEV 1hdgO 210 :AAKAVALV T0298 224 :LGERIGPLNVTCIQAPVFFGDSLSVTLQCAEPVDLAAVTRVLDAT 1hdgO 218 :VPEVKGKLDGMAIRVPTPDGSITDLTVLVEKETTVEEVNAVMKEA T0298 269 :KGIEWVGEGDYPTVVGDALGQDETYVGRVRAGQ 1hdgO 266 :RLKGIIGYNDEPIVSSDIIGTTFSGIFDATITN T0298 302 :ADPCQVNLWIVSDN 1hdgO 300 :IGGKLVKVASWYDN T0298 317 :RKGAALNAVLLGELLIK 1hdgO 314 :EYGYSNRVVDTLELLLK Number of specific fragments extracted= 17 number of extra gaps= 0 total=1370 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 1s7cA/T0298-1s7cA-t06-local-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1s7cA expands to /projects/compbio/data/pdb/1s7c.pdb.gz 1s7cA:# T0298 read from 1s7cA/T0298-1s7cA-t06-local-adpstyle5.a2m # 1s7cA read from 1s7cA/T0298-1s7cA-t06-local-adpstyle5.a2m # adding 1s7cA to template set # found chain 1s7cA in template set Warning: unaligning (T0298)S2 because first residue in template chain is (1s7cA)T2 Warning: unaligning (T0298)E207 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1s7cA)G210 Warning: unaligning (T0298)G208 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1s7cA)G210 T0298 5 :LNVAVVGA 1s7cA 3 :IKVGINGF T0298 14 :GSVGEALVGLLD 1s7cA 11 :GRIGRIVFRAAQ T0298 28 :DFPLHRLHLLASAESAGQRMGFAE 1s7cA 23 :KRSDIEIVAINDLLDADYMAYMLK T0298 52 :SSLRVGDVDSFDFS 1s7cA 73 :RVTAERDPANLKWD T0298 66 :SVGLAFFAAAAEVSRAHAERARAAGCSVIDLSGA 1s7cA 89 :GVDVVAEATGLFLTDETARKHITAGAKKVVMTGP T0298 102 :PS 1s7cA 123 :SK T0298 104 :VAPPVMVSVNAERLA 1s7cA 126 :NTPMFVKGANFDKYA T0298 122 :APFLLSSP 1s7cA 141 :GQDIVSNA T0298 130 :CAVAA 1s7cA 150 :CTTNC T0298 136 :LCEVLAPLLATLDCRQLNLTACLSVSS 1s7cA 155 :LAPLAKVINDNFGIIEGLMTTVHATTA T0298 175 :TAELLNARPLEPRLFDRQIAFNLLA 1s7cA 182 :TQKTVDGPSHKDWRGGRGASQNIIP T0298 205 :DA 1s7cA 207 :SS T0298 213 :ERRIFAEV 1s7cA 211 :AAKAVGKV T0298 224 :LGERIGPLNVTCIQAPVFFGDSLSVTLQCAEPVDLAAVTRVLDAT 1s7cA 219 :LPELNGKLTGMAFRVPTPNVSVVDLTVRLEKAATYEQIKAAVKAA T0298 269 :KGIEWVGEGDYPTVVGDALGQDETYVGRVRAGQ 1s7cA 267 :EMKGVLGYTEDDVVSTDFNGEVCTSVFDAKAGI T0298 302 :ADPCQVNLWIVSDN 1s7cA 301 :LNDNFVKLVSWYDN T0298 317 :RKGAALNAVLLGELL 1s7cA 315 :ETGYSNKVLDLIAHI Number of specific fragments extracted= 17 number of extra gaps= 1 total=1387 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 2dbvO/T0298-2dbvO-t06-local-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2dbvO expands to /projects/compbio/data/pdb/2dbv.pdb.gz 2dbvO:# T0298 read from 2dbvO/T0298-2dbvO-t06-local-adpstyle5.a2m # 2dbvO read from 2dbvO/T0298-2dbvO-t06-local-adpstyle5.a2m # adding 2dbvO to template set # found chain 2dbvO in template set Warning: unaligning (T0298)E138 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (2dbvO)F157 Warning: unaligning (T0298)V139 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (2dbvO)F157 T0298 5 :LNVAVVGA 2dbvO 1 :VKVGINGF T0298 14 :GSVGEALVGLLD 2dbvO 9 :GRIGRNVFRAAL T0298 28 :DFPLHRLHLLASAESAGQRMGFAE 2dbvO 21 :KNPDIEVVAVNGLTDANTLAHLLK T0298 52 :S 2dbvO 72 :I T0298 56 :VGDVDSFDFS 2dbvO 76 :ERDPENLAWG T0298 66 :SVGLAFFAAAAEVSRAHAERARAAGCSVIDLSGALEPSV 2dbvO 88 :GVDIVVESTGRFTKREDAAKHLEAGAKKVIISAPAKNED T0298 106 :PPVMVSVNAERLASQ 2dbvO 126 :ITIVMGVNQDKYDPK T0298 122 :APFLLSSP 2dbvO 140 :AHHVISNA T0298 130 :CAVAA 2dbvO 149 :CTTNC T0298 136 :LC 2dbvO 154 :LA T0298 140 :LAPLLATLDCRQLNLTACLSVSS 2dbvO 158 :AKVLHEQFGIVRGMMTTVHSYTN T0298 173 :RQ 2dbvO 181 :DQ T0298 177 :ELLNARPLEPRL 2dbvO 183 :RILDASHKDLRR T0298 190 :DRQIAFNLLA 2dbvO 196 :ARAAAESIIP T0298 205 :DAEG 2dbvO 206 :TTTG T0298 213 :ERRIFAEV 2dbvO 210 :AAKAVALV T0298 224 :LGERIGPLNVTCIQAPVFFGDSLSVTLQCAEPVDLAAVTRVLDAT 2dbvO 218 :LPELKGKLNGMAMRVPTPNVSVVDLVAELEKEVTVEEVNAALKAA T0298 269 :KGIEWVGEGDYPTVVGDALGQDETYVGRVRAGQ 2dbvO 266 :ELKGILAYSEEPLVSRDYNGSTVSSTIDALSTM T0298 302 :ADPCQVNLWIVSDN 2dbvO 300 :IDGKMVKVVSWYDN T0298 317 :RKGAALNAVLLGELLIKH 2dbvO 314 :ETGYSHRVVDLAAYIASK Number of specific fragments extracted= 20 number of extra gaps= 1 total=1407 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 1gpdG/T0298-1gpdG-t06-local-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1gpdG expands to /projects/compbio/data/pdb/1gpd.pdb.gz 1gpdG:# T0298 read from 1gpdG/T0298-1gpdG-t06-local-adpstyle5.a2m # 1gpdG read from 1gpdG/T0298-1gpdG-t06-local-adpstyle5.a2m # adding 1gpdG to template set # found chain 1gpdG in template set Warning: unaligning (T0298)L5 because first residue in template chain is (1gpdG)S1 T0298 6 :NVAVVGA 1gpdG 2 :KIGINGF T0298 14 :GSVGEALVGLLDERD 1gpdG 9 :GRIGRLVLRAALSCG T0298 32 :HRLHLLASAE 1gpdG 25 :AQVVAVNDPF T0298 42 :SAGQRMGFAE 1gpdG 36 :ALEYMVYMFK T0298 52 :SSLRVGDVDSFDFS 1gpdG 72 :TVFNEMKPENIPWS T0298 66 :SVGLAFFAAAAEVSRAHAERARAAGCSVIDLSGA 1gpdG 88 :GAEYIVESTGVFTTIEKASAHFKGGAKKVVISAP T0298 102 :PSVAPPVMVSVNAERLAS 1gpdG 122 :SADAPMFVCGVNLEKYSK T0298 122 :APFLLSSP 1gpdG 140 :DMTVVSNA T0298 130 :CAVAA 1gpdG 149 :CTTNC T0298 136 :LCEVLAPLLATLDCRQLNLTACLSVSS 1gpdG 154 :LAPVAKVLHENFEIVEGLMTTVHAVTA T0298 175 :TAELLNARPLEPRLFDRQIAFNLLA 1gpdG 181 :TQKTVDGPSAKDWRGGRGAAQNIIP T0298 205 :DAEG 1gpdG 206 :SSTG T0298 213 :ERRIFAEV 1gpdG 210 :AAKAVGKV T0298 224 :LGERIGPLNVTCIQAPVFFGDSLSVTLQCAEPVDLAAVTRVLDAT 1gpdG 218 :IPELDGKLTGMAFRVPTPDVSVVDLTVRLGKECSYDDIKAAMKTA T0298 269 :KGIEWVGEGDYPTVVGDALGQDETYVGRVRAGQ 1gpdG 266 :PLQGFLGYTEDDVVSSDFIGDNRSSIFDAKAGI T0298 302 :ADPCQVNLWIVSDN 1gpdG 300 :LSKTFVKVVSWYDN T0298 317 :RKGAALNAVLLGELLIKH 1gpdG 314 :EFGYSQRVIDLLKHMQKV Number of specific fragments extracted= 17 number of extra gaps= 0 total=1424 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 4gpd1/T0298-4gpd1-t06-local-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 4gpd1 expands to /projects/compbio/data/pdb/4gpd.pdb.gz 4gpd1:# T0298 read from 4gpd1/T0298-4gpd1-t06-local-adpstyle5.a2m # 4gpd1 read from 4gpd1/T0298-4gpd1-t06-local-adpstyle5.a2m # adding 4gpd1 to template set # found chain 4gpd1 in template set Warning: unaligning (T0298)L34 because of BadResidue code BAD_PEPTIDE in next template residue (4gpd1)V27 Warning: unaligning (T0298)H35 because of BadResidue code BAD_PEPTIDE at template residue (4gpd1)V27 Warning: unaligning (T0298)L36 because of BadResidue code BAD_PEPTIDE at template residue (4gpd1)A28 Warning: unaligning (T0298)Q45 because of BadResidue code BAD_PEPTIDE in next template residue (4gpd1)M39 Warning: unaligning (T0298)R46 because of BadResidue code BAD_PEPTIDE at template residue (4gpd1)M39 Warning: unaligning (T0298)R55 because of BadResidue code BAD_PEPTIDE in next template residue (4gpd1)E75 Warning: unaligning (T0298)V56 because of BadResidue code BAD_PEPTIDE at template residue (4gpd1)E75 Warning: unaligning (T0298)A70 because of BadResidue code BAD_PEPTIDE in next template residue (4gpd1)V92 Warning: unaligning (T0298)F71 because of BadResidue code BAD_PEPTIDE at template residue (4gpd1)V92 Warning: unaligning (T0298)I94 because of BadResidue code BAD_PEPTIDE in next template residue (4gpd1)V116 Warning: unaligning (T0298)D95 because of BadResidue code BAD_PEPTIDE at template residue (4gpd1)V116 Warning: unaligning (T0298)V108 because of BadResidue code BAD_PEPTIDE in next template residue (4gpd1)V128 Warning: unaligning (T0298)M109 because of BadResidue code BAD_PEPTIDE at template residue (4gpd1)V128 Warning: unaligning (T0298)N113 because of BadResidue code BAD_PEPTIDE in next template residue (4gpd1)L133 Warning: unaligning (T0298)A114 because of BadResidue code BAD_PEPTIDE at template residue (4gpd1)L133 Warning: unaligning (T0298)P129 because of BadResidue code BAD_PEPTIDE in next template residue (4gpd1)S147 Warning: unaligning (T0298)C130 because of BadResidue code BAD_PEPTIDE at template residue (4gpd1)C148 Warning: unaligning (T0298)L143 because of BadResidue code BAD_PEPTIDE in next template residue (4gpd1)H161 Warning: unaligning (T0298)L144 because of BadResidue code BAD_PEPTIDE at template residue (4gpd1)H161 Warning: unaligning (T0298)V160 because of BadResidue code BAD_PEPTIDE in next template residue (4gpd1)T178 Warning: unaligning (T0298)S161 because of BadResidue code BAD_PEPTIDE at template residue (4gpd1)T178 Warning: unaligning (T0298)P186 because of BadResidue code BAD_PEPTIDE in next template residue (4gpd1)W192 Warning: unaligning (T0298)R187 because of BadResidue code BAD_PEPTIDE at template residue (4gpd1)W192 Warning: unaligning (T0298)D190 because of BadResidue code BAD_PEPTIDE in next template residue (4gpd1)R196 Warning: unaligning (T0298)R191 because of BadResidue code BAD_PEPTIDE at template residue (4gpd1)R196 Warning: unaligning (T0298)F195 because of BadResidue code BAD_PEPTIDE in next template residue (4gpd1)N201 Warning: unaligning (T0298)N196 because of BadResidue code BAD_PEPTIDE at template residue (4gpd1)N201 Warning: unaligning (T0298)L197 because of BadResidue code BAD_PEPTIDE at template residue (4gpd1)I202 Warning: unaligning (T0298)L224 because of BadResidue code BAD_PEPTIDE in next template residue (4gpd1)P218 Warning: unaligning (T0298)G225 because of BadResidue code BAD_PEPTIDE at template residue (4gpd1)P218 Warning: unaligning (T0298)P230 because of BadResidue code BAD_PEPTIDE in next template residue (4gpd1)L224 Warning: unaligning (T0298)L231 because of BadResidue code BAD_PEPTIDE at template residue (4gpd1)L224 Warning: unaligning (T0298)C235 because of BadResidue code BAD_PEPTIDE in next template residue (4gpd1)F229 Warning: unaligning (T0298)I236 because of BadResidue code BAD_PEPTIDE at template residue (4gpd1)F229 Warning: unaligning (T0298)Q237 because of BadResidue code BAD_PEPTIDE in next template residue (4gpd1)V231 Warning: unaligning (T0298)A238 because of BadResidue code BAD_PEPTIDE at template residue (4gpd1)V231 Warning: unaligning (T0298)F242 because of BadResidue code BAD_PEPTIDE in next template residue (4gpd1)V236 Warning: unaligning (T0298)G243 because of BadResidue code BAD_PEPTIDE at template residue (4gpd1)V236 Warning: unaligning (T0298)V248 because of BadResidue code BAD_PEPTIDE in next template residue (4gpd1)T242 Warning: unaligning (T0298)T249 because of BadResidue code BAD_PEPTIDE at template residue (4gpd1)T242 Warning: unaligning (T0298)A259 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (4gpd1)D253 Warning: unaligning (T0298)A260 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (4gpd1)D253 Warning: unaligning (T0298)V274 because of BadResidue code BAD_PEPTIDE in next template residue (4gpd1)G271 Warning: unaligning (T0298)G275 because of BadResidue code BAD_PEPTIDE at template residue (4gpd1)G271 Warning: unaligning (T0298)Y279 because of BadResidue code BAD_PEPTIDE in next template residue (4gpd1)D276 Warning: unaligning (T0298)P280 because of BadResidue code BAD_PEPTIDE at template residue (4gpd1)D276 Warning: unaligning (T0298)V283 because of BadResidue code BAD_PEPTIDE in next template residue (4gpd1)S280 Warning: unaligning (T0298)G284 because of BadResidue code BAD_PEPTIDE at template residue (4gpd1)S280 Warning: unaligning (T0298)D285 because of BadResidue code BAD_PEPTIDE in next template residue (4gpd1)F282 Warning: unaligning (T0298)A286 because of BadResidue code BAD_PEPTIDE at template residue (4gpd1)F282 Warning: unaligning (T0298)G288 because of BadResidue code BAD_PEPTIDE in next template residue (4gpd1)D285 Warning: unaligning (T0298)Q289 because of BadResidue code BAD_PEPTIDE at template residue (4gpd1)D285 Warning: unaligning (T0298)T292 because of BadResidue code BAD_PEPTIDE in next template residue (4gpd1)S289 Warning: unaligning (T0298)Y293 because of BadResidue code BAD_PEPTIDE at template residue (4gpd1)S289 Warning: unaligning (T0298)A302 because of BadResidue code BAD_PEPTIDE in next template residue (4gpd1)S300 Warning: unaligning (T0298)D303 because of BadResidue code BAD_PEPTIDE at template residue (4gpd1)S300 Warning: unaligning (T0298)P304 because of BadResidue code BAD_PEPTIDE at template residue (4gpd1)K301 Warning: unaligning (T0298)V312 because of BadResidue code BAD_PEPTIDE in next template residue (4gpd1)Y310 Warning: unaligning (T0298)S313 because of BadResidue code BAD_PEPTIDE at template residue (4gpd1)Y310 Warning: unaligning (T0298)D314 because of BadResidue code BAD_PEPTIDE at template residue (4gpd1)D311 Warning: unaligning (T0298)R317 because of BadResidue code BAD_PEPTIDE in next template residue (4gpd1)F314 Warning: unaligning (T0298)K318 because of BadResidue code BAD_PEPTIDE at template residue (4gpd1)F314 T0298 6 :NVAVVGA 4gpd1 2 :KIGINGF T0298 14 :GSVGEALVGLLDERD 4gpd1 9 :GRIGRLVLRAALSCG T0298 32 :HR 4gpd1 24 :AQ T0298 37 :LASAE 4gpd1 29 :VNDPF T0298 42 :SAG 4gpd1 35 :ALE T0298 47 :MGFAE 4gpd1 40 :VYMFK T0298 52 :SSL 4gpd1 71 :TVF T0298 57 :GDVDSFDFS 4gpd1 76 :MKPENIPWS T0298 66 :SVGL 4gpd1 87 :GAEY T0298 72 :FAAAAEVSRAHAERARAAGCSV 4gpd1 93 :ESTGVFTTIEKASAHFKGGAKK T0298 96 :LSGA 4gpd1 117 :ISAP T0298 102 :PSVAPP 4gpd1 121 :SADAPM T0298 110 :VSV 4gpd1 129 :CGV T0298 115 :ERLAS 4gpd1 134 :EKYSK T0298 122 :APFLLSS 4gpd1 139 :DMTVVSN T0298 131 :AVAA 4gpd1 149 :TTNC T0298 136 :LCEVLAP 4gpd1 153 :LAPVAKV T0298 145 :ATLDCRQLNLTACLS 4gpd1 162 :ENFEIVEGLMTTVHA T0298 162 :S 4gpd1 179 :A T0298 175 :TAELLNARPLE 4gpd1 180 :TQKTVDGPSAK T0298 188 :LF 4gpd1 193 :RG T0298 192 :QIA 4gpd1 197 :GAA T0298 198 :LA 4gpd1 203 :IP T0298 205 :DAEG 4gpd1 205 :SSTG T0298 213 :ERRIFAEV 4gpd1 209 :AAKAVGKV T0298 226 :ERIG 4gpd1 219 :ELDG T0298 232 :NVT 4gpd1 225 :TGM T0298 239 :PVF 4gpd1 232 :PTP T0298 244 :DSLS 4gpd1 237 :SVVD T0298 250 :LQCAEPVDL 4gpd1 243 :VRLGKECSY T0298 261 :VTRVLDAT 4gpd1 254 :IKAAMKTA T0298 269 :KGIEW 4gpd1 265 :PLQGF T0298 276 :EGD 4gpd1 272 :YTE T0298 281 :TV 4gpd1 277 :VV T0298 287 :L 4gpd1 283 :I T0298 290 :DE 4gpd1 286 :NR T0298 294 :VGRVRAGQ 4gpd1 290 :IFDAKAGI T0298 305 :CQVNLWI 4gpd1 302 :TFVKVVS T0298 315 :N 4gpd1 312 :N T0298 319 :GAALNAVLLGELLIKH 4gpd1 315 :GYSQRVIDLLKHMQKV Number of specific fragments extracted= 40 number of extra gaps= 28 total=1464 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/T0298-3dbvO-t06-local-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 3dbvO expands to /projects/compbio/data/pdb/3dbv.pdb.gz 3dbvO:# T0298 read from 3dbvO/T0298-3dbvO-t06-local-adpstyle5.a2m # 3dbvO read from 3dbvO/T0298-3dbvO-t06-local-adpstyle5.a2m # adding 3dbvO to template set # found chain 3dbvO in template set Warning: unaligning (T0298)D58 because of BadResidue code BAD_PEPTIDE in next template residue (3dbvO)P79 Warning: unaligning (T0298)V59 because of BadResidue code BAD_PEPTIDE at template residue (3dbvO)P79 Warning: unaligning (T0298)E138 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (3dbvO)F157 Warning: unaligning (T0298)V139 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (3dbvO)F157 T0298 5 :LNVAVVGA 3dbvO 1 :VKVGINGF T0298 14 :GSVGEALVGLLD 3dbvO 9 :GRIGRNVFRAAL T0298 28 :DFPLHRLHLLASAESAGQRMGFAE 3dbvO 21 :KNPDIEVVAVNDTGGANTLAHLLK T0298 52 :S 3dbvO 72 :I T0298 56 :VG 3dbvO 76 :ER T0298 60 :DSFDFS 3dbvO 80 :ENLAWG T0298 66 :SVGLAFFAAAAEVSRAHAERARAAGCSVIDLSGALEPSV 3dbvO 88 :GVDIVVESTGRFTKREDAAKHLEAGAKKVIISAPAKNED T0298 106 :PPVMVSVNAERLASQ 3dbvO 126 :ITIVMGVNQDKYDPK T0298 122 :APFLLSSP 3dbvO 140 :AHHVISNA T0298 130 :CAVAA 3dbvO 149 :CTTNC T0298 136 :LC 3dbvO 154 :LA T0298 140 :LAPLLATLDCRQLNLTACLSVSS 3dbvO 158 :AKVLHEQFGIVRGMMTTVHSYTN T0298 173 :RQ 3dbvO 181 :DQ T0298 177 :ELLNARPLEPRL 3dbvO 183 :RILDASHKDLRR T0298 190 :DRQIAFNLLA 3dbvO 196 :ARAAAESIIP T0298 205 :DAEG 3dbvO 206 :TTTG T0298 213 :ERRIFAEV 3dbvO 210 :AAKAVALV T0298 224 :LGERIGPLNVTCIQAPVFFGDSLSVTLQCAEPVDLAAVTRVLDAT 3dbvO 218 :LPELKGKLNGMAMRVPTPNVSVVDLVAELEKEVTVEEVNAALKAA T0298 269 :KGIEWVGEGDYPTVVGDALGQDETYVGRVRAGQ 3dbvO 266 :ELKGILAYSEEPLVSRDYNGSTVSSTIDALSTM T0298 302 :ADPCQVNLWIVSDN 3dbvO 300 :IDGKMVKVVSWYDN T0298 317 :RKGAALNAVLLGELLIKH 3dbvO 314 :ETGYSHRVVDLAAYIASK Number of specific fragments extracted= 21 number of extra gaps= 2 total=1485 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 1nptO/T0298-1nptO-t06-local-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1nptO expands to /projects/compbio/data/pdb/1npt.pdb.gz 1nptO:# T0298 read from 1nptO/T0298-1nptO-t06-local-adpstyle5.a2m # 1nptO read from 1nptO/T0298-1nptO-t06-local-adpstyle5.a2m # adding 1nptO to template set # found chain 1nptO in template set T0298 5 :LNVAVVGA 1nptO 1 :VKVGINGF T0298 14 :GSVGEALVGLLD 1nptO 9 :GRIGRNVFRAAL T0298 28 :DFPLHRLHLLASAESAGQRMGFAE 1nptO 21 :KNPDIEVVAVNDLTDANTLAHLLK T0298 52 :S 1nptO 72 :I T0298 56 :VGDVDSFDFS 1nptO 76 :ERDPENLAWG T0298 66 :SVGLAFFAAAAEVSRAHAERARAAGCSVIDLSGALEPSV 1nptO 88 :GVDIVVESTGRFTKREDAAKHLEAGAKKVIISAPAKNED T0298 106 :PPVMVSVNAERLASQ 1nptO 126 :ITIVMGVNQDKYDPK T0298 122 :APFLLSSP 1nptO 140 :AHHVISNA T0298 130 :CAVAA 1nptO 149 :ATTNC T0298 136 :LCEVLAPLLATLDCRQLNLTACLSVSS 1nptO 154 :LAPFAKVLHEQFGIVRGMMTTVHSYTN T0298 173 :RQ 1nptO 181 :DQ T0298 177 :ELLNARPLEPRL 1nptO 183 :RILDLPHKDLRR T0298 190 :DRQIAFNLLA 1nptO 196 :ARAAAESIIP T0298 205 :DAEG 1nptO 206 :TTTG T0298 213 :ERRIFAEV 1nptO 210 :AAKAVALV T0298 224 :LGERIGPLNVTCIQAPVFFGDSLSVTLQCAEPVDLAAVTRVLDAT 1nptO 218 :LPELKGKLNGMAMRVPTPNVSVVDLVAELEKEVTVEEVNAALKAA T0298 269 :KGIEWVGEGDYPTVVGDALGQDETYVGRVRAGQ 1nptO 266 :ELKGILAYSEEPLVSRDYNGSTVSSTIDALSTM T0298 302 :ADPCQVNLWIVSDN 1nptO 300 :IDGKMVKVVSWYDN T0298 317 :RKGAALNAVLLGELLIKH 1nptO 314 :ETGYSHRVVDLAAYIASK Number of specific fragments extracted= 19 number of extra gaps= 0 total=1504 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 1gaeO/T0298-1gaeO-t06-local-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1gaeO expands to /projects/compbio/data/pdb/1gae.pdb.gz 1gaeO:# T0298 read from 1gaeO/T0298-1gaeO-t06-local-adpstyle5.a2m # 1gaeO read from 1gaeO/T0298-1gaeO-t06-local-adpstyle5.a2m # adding 1gaeO to template set # found chain 1gaeO in template set T0298 5 :LNVAVVGA 1gaeO 1 :IKVGINGF T0298 14 :GSVGEALVGLLD 1gaeO 9 :GRIGRIVFRAAQ T0298 28 :DFPLHRLHLLASAESAGQRMGFAE 1gaeO 21 :KRSDIEIVAINDLLDADYMAYMLK T0298 52 :SSLRVGDVDSFDFS 1gaeO 72 :RVTAERDPANLKWD T0298 66 :SVGLAFFAAAAEVSRAHAERARAAGCSVIDLSGA 1gaeO 88 :GVDVVAEATGLFLTDETARKHITAGAKKVVMTGP T0298 102 :PS 1gaeO 122 :SK T0298 104 :VAPPVMVSVNAERLA 1gaeO 124 :NTPMFVKGANFDKYA T0298 122 :APFLLSSP 1gaeO 138A:GQDIVSNA T0298 130 :CAVAA 1gaeO 149 :CTTNC T0298 136 :LCEVLAPLLATLDCRQLNLTACLSVSS 1gaeO 154 :LAPLAKVINDNFGIIEGLMTTVHATTA T0298 175 :TAELLNARPLEPRLFDRQIAFNLLA 1gaeO 181 :TQKTVDGPSHKDWRGGRGASQNIIP T0298 205 :DAEG 1gaeO 206 :SSTG T0298 213 :ERRIFAEV 1gaeO 210 :AAKAVGKV T0298 224 :LGERIGPLNVTCIQAPVFFGDSLSVTLQCAEPVDLAAVTRVLDAT 1gaeO 218 :LPELNGKLTGMAFRVPTPNVSVVDLTVRLEKAATYEQIKAAVKAA T0298 269 :KGIEWVGEGDYPTVVGDALGQDETYVGRVRAGQ 1gaeO 266 :EMKGVLGYTEDDVVSTDFNGEVCTSVFDAKAGI T0298 302 :ADPCQVNLWIVSDN 1gaeO 300 :LNDNFVKLVSWYDT T0298 317 :RKGAALNAVLLGELL 1gaeO 314 :ETGYSNKVLDLIAHI Number of specific fragments extracted= 17 number of extra gaps= 0 total=1521 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 1nqoA/T0298-1nqoA-t06-local-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1nqoA expands to /projects/compbio/data/pdb/1nqo.pdb.gz 1nqoA:# T0298 read from 1nqoA/T0298-1nqoA-t06-local-adpstyle5.a2m # 1nqoA read from 1nqoA/T0298-1nqoA-t06-local-adpstyle5.a2m # adding 1nqoA to template set # found chain 1nqoA in template set T0298 5 :LNVAVVGA 1nqoA 1 :VKVGINGF T0298 14 :GSVGEALVGLLD 1nqoA 9 :GRIGRNVFRAAL T0298 28 :DFPLHRLHLLASAESAGQRMGFAE 1nqoA 21 :KNPDIEVVAVNDLTDANTLAHLLK T0298 52 :S 1nqoA 72 :I T0298 56 :VGDVDSFDFS 1nqoA 76 :ERDPENLAWG T0298 66 :SVGLAFFAAAAEVSRAHAERARAAGCSVIDLSGALEPSV 1nqoA 88 :GVDIVVESTGRFTKREDAAKHLEAGAKKVIISAPAKNED T0298 106 :PPVMVSVNAERLASQ 1nqoA 126 :ITIVMGVNQDKYDPK T0298 122 :APFLLSSP 1nqoA 140 :AHHVISNA T0298 130 :CAVAA 1nqoA 149 :STTNC T0298 136 :LCEVLAPLLATLDCRQLNLTACLSVSS 1nqoA 154 :LAPFAKVLHEQFGIVRGMMTTVHSYTN T0298 173 :RQ 1nqoA 181 :DQ T0298 177 :ELLNARPLEPRL 1nqoA 183 :RILDLPHKDLRR T0298 190 :DRQIAFNLLA 1nqoA 196 :ARAAAESIIP T0298 205 :DAEG 1nqoA 206 :TTTG T0298 213 :ERRIFAEV 1nqoA 210 :AAKAVALV T0298 224 :LGERIGPLNVTCIQAPVFFGDSLSVTLQCAEPVDLAAVTRVLDAT 1nqoA 218 :LPELKGKLNGMAMRVPTPNVSVVDLVAELEKEVTVEEVNAALKAA T0298 269 :KGIEWVGEGDYPTVVGDALGQDETYVGRVRAGQ 1nqoA 266 :ELKGILAYSEEPLVSRDYNGSTVSSTIDALSTM T0298 302 :ADPCQVNLWIVSDN 1nqoA 300 :IDGKMVKVVSWYDN T0298 317 :RKGAALNAVLLGELLIKH 1nqoA 314 :ETGYSHRVVDLAAYIASK Number of specific fragments extracted= 19 number of extra gaps= 0 total=1540 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 1vc2A/T0298-1vc2A-t06-local-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1vc2A expands to /projects/compbio/data/pdb/1vc2.pdb.gz 1vc2A:# T0298 read from 1vc2A/T0298-1vc2A-t06-local-adpstyle5.a2m # 1vc2A read from 1vc2A/T0298-1vc2A-t06-local-adpstyle5.a2m # adding 1vc2A to template set # found chain 1vc2A in template set Warning: unaligning (T0298)L5 because first residue in template chain is (1vc2A)M1 Warning: unaligning (T0298)N196 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1vc2A)I202 Warning: unaligning (T0298)L197 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1vc2A)I202 T0298 6 :NVAVVGA 1vc2A 2 :KVGINGF T0298 14 :GSVGEALVGLLDERD 1vc2A 9 :GRIGRQVFRILHERG T0298 32 :HRLHLLASAESAGQRMGFAE 1vc2A 24 :VEVALINDLTDNKTLAHLLK T0298 52 :SSLRVGDVDSFDFS 1vc2A 70 :RATAIKDPREIPWK T0298 66 :SVGLAFFAAAAEVSRAHAERARAAGCSVIDLSGALEPSV 1vc2A 86 :GVGVVVESTGVFTDGEKARAHLEAGAKKVIITAPAKNED T0298 106 :PPVMVSVNAERLASQ 1vc2A 125 :ITVVLGVNHEQYDPA T0298 122 :APFLLSSP 1vc2A 140 :KHHILSNA T0298 130 :CAVAA 1vc2A 149 :CTTNS T0298 136 :LCEVLAPLLATLDCRQLNLTACLSVSS 1vc2A 154 :LAPVMKVLEKAFGVEKALMTTVHSYTN T0298 173 :RQ 1vc2A 181 :DQ T0298 177 :ELLNARPLEPRL 1vc2A 183 :RLLDLPHKDLRR T0298 190 :DRQIAF 1vc2A 195 :ARAAAL T0298 198 :LA 1vc2A 203 :IP T0298 205 :DAEG 1vc2A 205 :TTTG T0298 213 :ERRIFAEV 1vc2A 209 :AAKATALV T0298 224 :LGERIGPLNVTCIQAPVFFGDSLSVTLQCAEPVDLAAVTRVLDAT 1vc2A 217 :LPSLKGRFDGMALRVPTPTGSISDITALLKREVTAEEVNAALKAA T0298 269 :KGIEWVGEGDYPTVVGDALGQDETYVGRVRAGQADPCQVNLWIVSDN 1vc2A 265 :PLKGILAYTEDEIVLRDIVMDPHSSIVDGKLTKAIGNLVKVFAWYDN T0298 317 :RKGAALNAVLLGELLIKH 1vc2A 312 :EWGYANRVADLVELVLKK Number of specific fragments extracted= 18 number of extra gaps= 1 total=1558 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 1cerA/T0298-1cerA-t06-local-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1cerA expands to /projects/compbio/data/pdb/1cer.pdb.gz 1cerA:# T0298 read from 1cerA/T0298-1cerA-t06-local-adpstyle5.a2m # 1cerA read from 1cerA/T0298-1cerA-t06-local-adpstyle5.a2m # adding 1cerA to template set # found chain 1cerA in template set Warning: unaligning (T0298)L5 because first residue in template chain is (1cerA)M1 Warning: unaligning (T0298)F62 because of BadResidue code BAD_PEPTIDE in next template residue (1cerA)P83 Warning: unaligning (T0298)D63 because of BadResidue code BAD_PEPTIDE at template residue (1cerA)P83 Warning: unaligning (T0298)I193 because of BadResidue code BAD_PEPTIDE in next template residue (1cerA)A200 Warning: unaligning (T0298)A194 because of BadResidue code BAD_PEPTIDE at template residue (1cerA)A200 T0298 6 :NVAVVGA 1cerA 2 :KVGINGF T0298 14 :GSVGEALVGLLDERD 1cerA 9 :GRIGRQVFRILHSRG T0298 32 :HRLHLLASAESAGQRMGFAE 1cerA 25 :VEVALINDLTDNKTLAHLLK T0298 52 :SSLRVGDVDS 1cerA 72 :RATAVKDPKE T0298 64 :FS 1cerA 84 :WA T0298 66 :SVGLAFFAAAAEVSRAHAERARAAGCSVIDLSGALEPSV 1cerA 88 :GVGVVIESTGVFTDADKAKAHLEGGAKKVIITAPAKGED T0298 106 :PPVMVSVNAERLASQ 1cerA 126 :ITIVMGVNHEAYDPS T0298 122 :APFLLSSP 1cerA 140 :RHHIISNA T0298 130 :CAVAA 1cerA 149 :CTTNS T0298 136 :LCEVLAPLLATLDCRQLNLTACLSVSS 1cerA 154 :LAPVMKVLEEAFGVEKALMTTVHSYTN T0298 173 :RQ 1cerA 181 :DQ T0298 177 :ELLNARPLEPRL 1cerA 183 :RLLDLPHKDLRR T0298 190 :DRQ 1cerA 196 :ARA T0298 195 :FNLLA 1cerA 201 :INIIP T0298 205 :DAEG 1cerA 206 :TTTG T0298 213 :ERRIFAEV 1cerA 210 :AAKATALV T0298 224 :LGERIGPLNVTCIQAPVFFGDSLSVTLQCAEPVDLAAVTRVLDAT 1cerA 218 :LPSLKGRFDGMALRVPTATGSISDITALLKREVTAEEVNAALKAA T0298 269 :KGIEWVGEGDYPTVVGDALGQDETYVGRVRAGQADPCQVNLWIVSDN 1cerA 266 :PLKGILAYTEDEIVLQDIVMDPHSSIVDAKLTKALGNMVKVFAWYDN T0298 317 :RKGAALNAVLLGELLIKH 1cerA 314 :EWGYANRVADLVELVLRK Number of specific fragments extracted= 19 number of extra gaps= 2 total=1577 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 1hyeA/T0298-1hyeA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1hyeA expands to /projects/compbio/data/pdb/1hye.pdb.gz 1hyeA:# T0298 read from 1hyeA/T0298-1hyeA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1hyeA read from 1hyeA/T0298-1hyeA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1hyeA to template set # found chain 1hyeA in template set Warning: unaligning (T0298)L5 because first residue in template chain is (1hyeA)M1 Warning: unaligning (T0298)N180 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1hyeA)F230 Warning: unaligning (T0298)E207 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1hyeA)F230 T0298 6 :NVAVVGATGSVGEALVGLLD 1hyeA 2 :KVTIIGASGRVGSATALLLA T0298 28 :DFPLH 1hyeA 22 :KEPFM T0298 33 :RLHLLASAESAGQRMGFAE 1hyeA 28 :DLVLIGREHSINKLEGLRE T0298 52 :SSLRVGDVDSFD 1hyeA 59 :ANIYVESDENLR T0298 64 :FSSVGLAFFAAAAEVS 1hyeA 72 :IDESDVVIITSGVPRK T0298 80 :RAHAERARAA 1hyeA 104 :GKYAKKIAEI T0298 90 :GCSVIDLSGA 1hyeA 115 :DTKIFVITNP T0298 121 :AAPFLLSSPCAVAA 1hyeA 138 :FERNQVFGLGTHLD T0298 136 :LCEVLAPLLATLDCR 1hyeA 152 :SLRFKVAIAKFFGVH T0298 151 :QLNLTACLSVSSL 1hyeA 169 :EVRTRIIGEHGDS T0298 164 :G 1hyeA 193 :G T0298 166 :E 1hyeA 203 :K T0298 168 :VKELARQTA 1hyeA 207 :IDEIIEDVK T0298 177 :ELL 1hyeA 220 :QII T0298 208 :GHSAIERRIF 1hyeA 231 :GPAAAILNVV T0298 221 :QALLGERIGPLNVTCIQ 1hyeA 241 :RCIVNNEKRLLTLSAYV T0298 238 :APVFF 1hyeA 261 :FDGIR T0298 243 :GDSLSVTLQ 1hyeA 268 :CIGVPVKIG T0298 252 :CAE 1hyeA 280 :IEE T0298 255 :PVDLAA 1hyeA 287 :ELDKDE T0298 261 :VTRVLDATKG 1hyeA 303 :IKKYCEEVKN Number of specific fragments extracted= 21 number of extra gaps= 0 total=1598 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 1hyeA/T0298-1hyeA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0298 read from 1hyeA/T0298-1hyeA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1hyeA read from 1hyeA/T0298-1hyeA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1hyeA in template set Warning: unaligning (T0298)L5 because first residue in template chain is (1hyeA)M1 Warning: unaligning (T0298)F189 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1hyeA)F230 Warning: unaligning (T0298)E207 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1hyeA)F230 T0298 6 :NVAVVGATGSVGEALVGLLD 1hyeA 2 :KVTIIGASGRVGSATALLLA T0298 28 :DFPLH 1hyeA 22 :KEPFM T0298 33 :RLHLLASAESAGQRMGFA 1hyeA 28 :DLVLIGREHSINKLEGLR T0298 51 :ESSLRVGDVDSFD 1hyeA 58 :DANIYVESDENLR T0298 64 :FSSVGLAFFAAAA 1hyeA 72 :IDESDVVIITSGV T0298 77 :EVSRAHAERARAA 1hyeA 94 :DLAKTNAKIVGKY T0298 114 :AERLASQAAPFLLSS 1hyeA 107 :AKKIAEICDTKIFVI T0298 132 :VAA 1hyeA 122 :TNP T0298 136 :LCEVLAPLLATLDCRQLNLTACLSVSS 1hyeA 125 :VDVMTYKALVDSKFERNQVFGLGTHLD T0298 168 :VKELARQTAELLNA 1hyeA 152 :SLRFKVAIAKFFGV T0298 183 :PL 1hyeA 166 :HI T0298 185 :EPRL 1hyeA 219 :EQII T0298 208 :GHSAIERRIFAE 1hyeA 231 :GPAAAILNVVRC T0298 223 :LLGERIGPLNVTC 1hyeA 243 :IVNNEKRLLTLSA T0298 237 :QA 1hyeA 256 :YV T0298 241 :FFGDSLSVTLQCAE 1hyeA 264 :IRDVCIGVPVKIGR T0298 255 :PVDLAA 1hyeA 287 :ELDKDE T0298 261 :VTRVLDATKG 1hyeA 303 :IKKYCEEVKN Number of specific fragments extracted= 18 number of extra gaps= 0 total=1616 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 1hyeA/T0298-1hyeA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0298 read from 1hyeA/T0298-1hyeA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1hyeA read from 1hyeA/T0298-1hyeA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1hyeA in template set Warning: unaligning (T0298)L5 because first residue in template chain is (1hyeA)M1 Warning: unaligning (T0298)P183 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1hyeA)F230 Warning: unaligning (T0298)S210 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1hyeA)F230 T0298 6 :NVAVVGATGSVGEALVGLLDERDFPLHRLHLLASAESA 1hyeA 2 :KVTIIGASGRVGSATALLLAKEPFMKDLVLIGREHSIN T0298 44 :GQRM 1hyeA 54 :GTRS T0298 51 :ESSLRVGDV 1hyeA 58 :DANIYVESD T0298 60 :DSFDFSSVGLAFFAAA 1hyeA 68 :NLRIIDESDVVIITSG T0298 76 :AEVSRAHAERARAA 1hyeA 93 :MDLAKTNAKIVGKY T0298 115 :ERLASQAAPFLLSSPCAVAAELCEVLAP 1hyeA 108 :KKIAEICDTKIFVITNPVDVMTYKALVD T0298 147 :LDCRQLNLTACLS 1hyeA 136 :SKFERNQVFGLGT T0298 165 :REGVKELARQTAEL 1hyeA 149 :HLDSLRFKVAIAKF T0298 179 :LNAR 1hyeA 219 :EQII T0298 211 :AIERRIFAEVQALLGERIGPLNVTCIQ 1hyeA 231 :GPAAAILNVVRCIVNNEKRLLTLSAYV T0298 241 :FFGDSLSVTLQCAEP 1hyeA 264 :IRDVCIGVPVKIGRD T0298 256 :VD 1hyeA 288 :LD T0298 258 :LAAVTRVLDATKG 1hyeA 300 :AEIIKKYCEEVKN Number of specific fragments extracted= 13 number of extra gaps= 0 total=1629 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 1ywgO/T0298-1ywgO-t06-local-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1ywgO expands to /projects/compbio/data/pdb/1ywg.pdb.gz 1ywgO:# T0298 read from 1ywgO/T0298-1ywgO-t06-local-adpstyle5.a2m # 1ywgO read from 1ywgO/T0298-1ywgO-t06-local-adpstyle5.a2m # adding 1ywgO to template set # found chain 1ywgO in template set T0298 5 :LNVAVVGA 1ywgO 4 :TKLGINGF T0298 14 :GSVGEALVGLLD 1ywgO 12 :GRIGRLVFRAAF T0298 28 :DFPLHRLHLLASAE 1ywgO 24 :GRKDIEVVAINDPF T0298 42 :SAGQRMGFAE 1ywgO 39 :DLNHLCYLLK T0298 52 :SSLRVGDVDSFDFS 1ywgO 75 :SVFAEKDPSQIPWG T0298 66 :SVGLAFFAAAAEVSRAHAERARAAGCSVIDLSGAL 1ywgO 91 :QVDVVCESTGVFLTKELASSHLKGGAKKVIMSAPP T0298 103 :S 1ywgO 126 :K T0298 104 :VAPPVMVSVNAERLAS 1ywgO 128 :DTPIYVMGINHHQYDT T0298 122 :APFLLSSP 1ywgO 144 :KQLIVSNA T0298 130 :CAVAA 1ywgO 153 :CTTNC T0298 136 :LCEVLAPLLATLDCRQLNLTACLSVSS 1ywgO 158 :LAPLAKVINDRFGIVEGLMTTVHASTA T0298 175 :TAELLNAR 1ywgO 185 :NQLVVDGP T0298 183 :PLEPRLFDRQIAFNLLA 1ywgO 195 :GGKDWRAGRCALSNIIP T0298 205 :DAEG 1ywgO 212 :ASTG T0298 213 :ERRIFAEV 1ywgO 216 :AAKAVGKV T0298 224 :LGERIGPLNVTCIQAPVFFGDSLSVTLQCAEPVDLAAVTRVLDAT 1ywgO 224 :LPELNGKLTGVAFRVPIGTVSVVDLVCRLQKPAKYEEVALEIKKA T0298 269 :KGIEWVGEGDYPTVVGDALGQDETYVGRVRAGQ 1ywgO 272 :PLKGILGYTEDEVVSQDFVHDNRSSIFDMKAGL T0298 302 :ADPCQVNLWIVSDN 1ywgO 306 :LNDNFFKLVSWYDN T0298 317 :RKGAALNAVLLGELL 1ywgO 320 :EWGYSNRVLDLAVHI Number of specific fragments extracted= 19 number of extra gaps= 0 total=1648 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 1nwcA/T0298-1nwcA-t06-local-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1nwcA expands to /projects/compbio/data/pdb/1nwc.pdb.gz 1nwcA:# T0298 read from 1nwcA/T0298-1nwcA-t06-local-adpstyle5.a2m # 1nwcA read from 1nwcA/T0298-1nwcA-t06-local-adpstyle5.a2m # adding 1nwcA to template set # found chain 1nwcA in template set Warning: unaligning (T0298)S42 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1nwcA)L55 Warning: unaligning (T0298)V56 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1nwcA)L55 T0298 1 :M 1nwcA 1 :M T0298 5 :LNVAVVGATGSVGEALV 1nwcA 2 :KNVGFIGWRGMVGSVLM T0298 22 :GLLDERDFPLHRLHLL 1nwcA 20 :RMSQENDFENLNPVFF T0298 39 :SAE 1nwcA 36 :TTS T0298 57 :GDVDSFD 1nwcA 56 :KSAFDIE T0298 64 :FSSVGLAFFAAAAEVSRAHAERARAAGC 1nwcA 64 :LKKLDIIVTCQGGDYTNEVYPKLKATGW T0298 92 :SVIDLSGALEPS 1nwcA 94 :YWVDAASALRMK T0298 104 :VAPPVMVSVNAERLASQAAPF 1nwcA 107 :DAIIVLDPVNQHVISEGLKKG T0298 125 :LLSSPCAVAA 1nwcA 131 :FVGGNCTVSL T0298 136 :LCEVLAPLLATLDCRQLNLTACLSVSSLGREGVKELARQTAELLNARPLEPRL 1nwcA 141 :MLMAIGGLFEKDLVEWISVATYQAASGAGAKNMRELLSQMGLLEQAVSSELKD T0298 189 :FDRQIAFNLLAQVGA 1nwcA 219 :FGAALGGSLIPWIDK T0298 204 :VDAEGHSAIERRIFAEVQALLG 1nwcA 235 :LPETGQTKEEWKGYAETNKILG T0298 226 :ERIGPLNVTCIQAPVFFGDSLSVTLQCAEPVDLAAVTRVLDAT 1nwcA 259 :DNPIPVDGLCVRIGALRCHSQAFTIKLKKDLPLEEIEQIIASH T0298 269 :KGIEWVGEGDY 1nwcA 303 :EWVKVIPNDKE T0298 280 :PTVVGDALGQDETYVGRVRAGQADPCQVNLWIVSDNVRKGAALNAVLLGELL 1nwcA 318 :ELTPAKVTGTLSVPVGRLRKLAMGPEYLAAFTVGDQLLWGAAEPVRRILKQL Number of specific fragments extracted= 15 number of extra gaps= 0 total=1663 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 1pr3A/T0298-1pr3A-t06-local-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1pr3A expands to /projects/compbio/data/pdb/1pr3.pdb.gz 1pr3A:# T0298 read from 1pr3A/T0298-1pr3A-t06-local-adpstyle5.a2m # 1pr3A read from 1pr3A/T0298-1pr3A-t06-local-adpstyle5.a2m # adding 1pr3A to template set # found chain 1pr3A in template set Warning: unaligning (T0298)A43 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1pr3A)L55 Warning: unaligning (T0298)V56 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1pr3A)L55 T0298 1 :M 1pr3A 1 :M T0298 5 :LNVAVVGATGSVGEALV 1pr3A 2 :KNVGFIGWRGMVGSVLM T0298 22 :GLLDERDFPLHRLHLL 1pr3A 20 :RMSQENDFENLNPVFF T0298 39 :SAES 1pr3A 36 :TTSQ T0298 57 :GDVDSFD 1pr3A 56 :KSAFDIE T0298 64 :FSSVGLAFFAAAAEVSRAHAERARAAGC 1pr3A 64 :LKKLDIIVTCQGGDYTNEVYPKLKATGW T0298 92 :SVIDLSGALEPS 1pr3A 94 :YWVDAASALKMK T0298 104 :VAPPVMVSVNAERLASQAAPF 1pr3A 107 :DAIIVLDPVNQHVISEGLKKG T0298 125 :LLSSPCAVAA 1pr3A 131 :FVGGNCTVSL T0298 136 :LCEVLAPLLATLDCRQLNLTACLSVSSLGREGVKELARQTAELLNARPLEPRL 1pr3A 141 :MLMAIGGLFEKDLVEWISVATYQAASGAGAKNMRELLSQMGLLEQAVSSELKD T0298 189 :FDRQIAFNLLAQVGA 1pr3A 219 :FGAALGGSLIPWIDK T0298 204 :VDAEGHSAIERRIFAEVQALLG 1pr3A 235 :LPETGQTKEEWKGYAETNKILG T0298 226 :ERIGPLNVTCIQAPVFFGDSLSVTLQCAEPVDLAAVTRVLDAT 1pr3A 259 :DNPIPVDGLCVRIGALRCHSQAFTIKLKKDLPLEEIEQIIASH T0298 269 :KGIEWVGEGDY 1pr3A 303 :EWVKVIPNDKE T0298 280 :PTVVGDALGQDETYVGRVRAGQADPCQVNLWIVSDNVRKGAALNAVLLGELL 1pr3A 318 :ELTPAKVTGTLSVPVGRLRKLAMGPEYLAAFTVGDQLLWGAAEPVRRILKQL Number of specific fragments extracted= 15 number of extra gaps= 0 total=1678 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 1ozaA/T0298-1ozaA-t06-local-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1ozaA expands to /projects/compbio/data/pdb/1oza.pdb.gz 1ozaA:# T0298 read from 1ozaA/T0298-1ozaA-t06-local-adpstyle5.a2m # 1ozaA read from 1ozaA/T0298-1ozaA-t06-local-adpstyle5.a2m # adding 1ozaA to template set # found chain 1ozaA in template set Warning: unaligning (T0298)A43 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ozaA)L55 Warning: unaligning (T0298)V56 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ozaA)L55 T0298 1 :M 1ozaA 1 :M T0298 5 :LNVAVVGATGSVGEALV 1ozaA 2 :KNVGFIGWRGMVGSVLM T0298 22 :GLLDERDFPLHRLHLL 1ozaA 20 :RMSQENDFENLNPVFF T0298 39 :SAES 1ozaA 36 :TTSQ T0298 57 :GDVDSFD 1ozaA 56 :KSAFDIE T0298 64 :FSSVGLAFFAAAAEVSRAHAERARAAGC 1ozaA 64 :LKKLDIIVTCQGGDYTNEVYPKLKATGW T0298 92 :SVIDLSGALEPS 1ozaA 94 :YWVDAASALLMK T0298 104 :VAPPVMVSVNAERLASQAAPF 1ozaA 107 :DAIIVLDPVNQHVISEGLKKG T0298 125 :LLSSPCAVAA 1ozaA 131 :FVGGNCTVSL T0298 136 :LCEVLAPLLATLDCRQLNLTACLSVSSLGREGVKELARQTAELLNARPLEPRL 1ozaA 141 :MLMAIGGLFEKDLVEWISVATYQAASGAGAKNMRELLSQMGLLEQAVSSELKD T0298 189 :FDRQIAFNLLAQVGA 1ozaA 219 :FGAALGGSLIPWIDK T0298 204 :VDAEGHSAIERRIFAEVQALLG 1ozaA 235 :LPETGQTKEEWKGYAETNKILG T0298 226 :ERIGPLNVTCIQAPVFFGDSLSVTLQCAEPVDLAAVTRVLDAT 1ozaA 259 :DNPIPVDGLCVRIGALRCHSQAFTIKLKKDLPLEEIEQIIASH T0298 269 :KGIEWVGEGDY 1ozaA 303 :EWVKVIPNDKE T0298 280 :PTVVGDALGQDETYVGRVRAGQADPCQVNLWIVSDNVRKGAALNAVLLGELL 1ozaA 318 :ELTPAKVTGTLSVPVGRLRKLAMGPEYLAAFTVGDQLLWGAAEPVRRILKQL Number of specific fragments extracted= 15 number of extra gaps= 0 total=1693 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 1ps8A/T0298-1ps8A-t06-local-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1ps8A expands to /projects/compbio/data/pdb/1ps8.pdb.gz 1ps8A:# T0298 read from 1ps8A/T0298-1ps8A-t06-local-adpstyle5.a2m # 1ps8A read from 1ps8A/T0298-1ps8A-t06-local-adpstyle5.a2m # adding 1ps8A to template set # found chain 1ps8A in template set Warning: unaligning (T0298)A43 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ps8A)L55 Warning: unaligning (T0298)V56 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ps8A)L55 T0298 1 :M 1ps8A 1 :M T0298 5 :LNVAVVGATGSVGEALV 1ps8A 2 :KNVGFIGWRGMVGSVLM T0298 22 :GLLDERDFPLHRLHLL 1ps8A 20 :RMSQENDFENLNPVFF T0298 39 :SAES 1ps8A 36 :TTSQ T0298 57 :GDVDSFD 1ps8A 56 :KSAFDIE T0298 64 :FSSVGLAFFAAAAEVSRAHAERARAAGC 1ps8A 64 :LKKLDIIVTCQGGDYTNEVYPKLKATGW T0298 92 :SVIDLSGALEPS 1ps8A 94 :YWVDAASALRMK T0298 104 :VAPPVMVSVNAERLASQAAPF 1ps8A 107 :DAIIVLDPVNQHVISEGLKKG T0298 125 :LLSSPCAVAA 1ps8A 131 :FVGGNCTVSL T0298 136 :LCEVLAPLLATLDCRQLNLTACLSVSSLGREGVKELARQTAELLNARPLEPRL 1ps8A 141 :MLMAIGGLFEKDLVEWISVATYQAASGAGAKNMRELLSQMGLLEQAVSSELKD T0298 189 :FDRQIAFNLLAQVGA 1ps8A 219 :FGAALGGSLIPWIDK T0298 204 :VDAEGHSAIERRIFAEVQALLG 1ps8A 235 :LPETGQTKEEWKGYAETNKILG T0298 226 :ERIGPLNVTCIQAPVFFGDSLSVTLQCAEPVDLAAVTRVLDAT 1ps8A 259 :DNPIPVDGLCVKIGALRCHSQAFTIKLKKDLPLEEIEQIIASH T0298 269 :KGIEWVGEGDY 1ps8A 303 :EWVKVIPNDKE T0298 280 :PTVVGDALGQDETYVGRVRAGQADPCQVNLWIVSDNVRKGAALNAVLLGELL 1ps8A 318 :ELTPAKVTGTLSVPVGRLRKLAMGPEYLAAFTVGDQLLWGAAEPVRRILKQL Number of specific fragments extracted= 15 number of extra gaps= 0 total=1708 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 1pquA/T0298-1pquA-t06-local-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1pquA expands to /projects/compbio/data/pdb/1pqu.pdb.gz 1pquA:# T0298 read from 1pquA/T0298-1pquA-t06-local-adpstyle5.a2m # 1pquA read from 1pquA/T0298-1pquA-t06-local-adpstyle5.a2m # adding 1pquA to template set # found chain 1pquA in template set T0298 1 :M 1pquA 1 :M T0298 5 :LNVAVVGATGSVGEALV 1pquA 2 :KNVGFIGWRGMVGSVLM T0298 22 :GLLDERDFPLHRLHLL 1pquA 20 :RMSQENDFENLNPVFF T0298 39 :SAESAGQRMGFAESSLR 1pquA 36 :TTSQAGQKAPVFGGKDA T0298 56 :VGDVDSFD 1pquA 55 :LKSAFDIE T0298 64 :FSSVGLAFFAAAAEVSRAHAERARAAGC 1pquA 64 :LKKLDIIVTCQGGDYTNEVYPKLKATGW T0298 92 :SVIDLSGALEPS 1pquA 94 :YWVDAASALRMK T0298 104 :VAPPVMVSVNAERLASQAAPF 1pquA 107 :DAIIVLDPVNQHVISEGLKKG T0298 125 :LLSSPCAVAA 1pquA 131 :FVGGNCTVSL T0298 136 :LCEVLAPLLATLDCRQLNLTACLSVSSLGREGVKELARQTAELLNARPLEPRL 1pquA 141 :MLMAIGGLFEKDLVEWISVATYQAASGAGAKNMRELLSQMGLLEQAVSSELKD T0298 189 :FDRQIAFNLLAQVGA 1pquA 219 :FGAALGGSLIPWIDK T0298 204 :VDAEGHSAIERRIFAEVQALLG 1pquA 235 :LPETGQTKEEWKGYAETNKILG T0298 226 :ERIGPLNVTCIQAPVFFGDSLSVTLQCAEPVDLAAVTRVLDAT 1pquA 259 :DNPIPVDGLCVRIGALRCNSQAFTIKLKKDLPLEEIEQIIASH T0298 269 :KGIEWVGEGDY 1pquA 303 :EWVKVIPNDKE T0298 280 :PTVVGDALGQDETYVGRVRAGQADPCQVNLWIVSDNVRKGAALNAVLLGELL 1pquA 318 :ELTPAKVTGTLSVPVGRLRKLAMGPEYLAAFTVGDQLLWGAAEPVRRILKQL Number of specific fragments extracted= 15 number of extra gaps= 0 total=1723 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 1nwhA/T0298-1nwhA-t06-local-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1nwhA expands to /projects/compbio/data/pdb/1nwh.pdb.gz 1nwhA:Bad short name: S for alphabet: pdb_atoms Bad short name: CAH for alphabet: pdb_atoms Bad short name: OAI for alphabet: pdb_atoms Bad short name: CAJ for alphabet: pdb_atoms Bad short name: CAK for alphabet: pdb_atoms Bad short name: NAL for alphabet: pdb_atoms Bad short name: CAM for alphabet: pdb_atoms Bad short name: OAN for alphabet: pdb_atoms Bad short name: OAO for alphabet: pdb_atoms # T0298 read from 1nwhA/T0298-1nwhA-t06-local-adpstyle5.a2m # 1nwhA read from 1nwhA/T0298-1nwhA-t06-local-adpstyle5.a2m # adding 1nwhA to template set # found chain 1nwhA in template set Warning: unaligning (T0298)S42 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1nwhA)L55 Warning: unaligning (T0298)V56 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1nwhA)L55 Warning: unaligning (T0298)P129 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1nwhA)T137 Warning: unaligning (T0298)A131 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1nwhA)T137 T0298 1 :M 1nwhA 1 :M T0298 5 :LNVAVVGATGSVGEALV 1nwhA 2 :KNVGFIGWRGMVGSVLM T0298 22 :GLLDERDFPLHRLHLL 1nwhA 20 :RMSQENDFENLNPVFF T0298 39 :SAE 1nwhA 36 :TTS T0298 57 :GDVDSFD 1nwhA 56 :KSAFDIE T0298 64 :FSSVGLAFFAAAAEVSRAHAERARAAGC 1nwhA 64 :LKKLDIIVTCQGGDYTNEVYPKLKATGW T0298 92 :SVIDLSGALEPS 1nwhA 94 :YWVDAASALRMK T0298 104 :VAPPVMVSVNAERLASQAAPF 1nwhA 107 :DAIIVLDPVNQHVISEGLKKG T0298 125 :LLSS 1nwhA 131 :FVGG T0298 132 :VAA 1nwhA 138 :VSL T0298 136 :LCEVLAPLLATLDCRQLNLTACLSVSSLGREGVKELARQTAELLNARPLEPRL 1nwhA 141 :MLMAIGGLFEKDLVEWISVATYQAASGAGAKNMRELLSQMGLLEQAVSSELKD T0298 189 :FDRQIAFNLLAQVGA 1nwhA 219 :FGAALGGSLIPWIDK T0298 204 :VDAEGHSAIERRIFAEVQALLG 1nwhA 235 :LPETGQTKEEWKGYAETNKILG T0298 226 :ERIGPLNVTCIQAPVFFGDSLSVTLQCAEPVDLAAVTRVLDAT 1nwhA 259 :DNPIPVDGLCVRIGALRCHSQAFTIKLKKDLPLEEIEQIIASH T0298 269 :KGIEWVGEGDY 1nwhA 303 :EWVKVIPNDKE T0298 280 :PTVVGDALGQDETYVGRVRAGQADPCQVNLWIVSDNVRKGAALNAVLLGELL 1nwhA 318 :ELTPAKVTGTLSVPVGRLRKLAMGPEYLAAFTVGDQLLWGAAEPVRRILKQL Number of specific fragments extracted= 16 number of extra gaps= 0 total=1739 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 1rm3A/T0298-1rm3A-t06-local-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1rm3A expands to /projects/compbio/data/pdb/1rm3.pdb.gz 1rm3A:Skipped atom 3012, because occupancy 0.500 <= existing 0.500 in 1rm3A Skipped atom 3014, because occupancy 0.500 <= existing 0.500 in 1rm3A Skipped atom 3016, because occupancy 0.500 <= existing 0.500 in 1rm3A Skipped atom 3018, because occupancy 0.500 <= existing 0.500 in 1rm3A Skipped atom 4094, because occupancy 0.400 <= existing 0.600 in 1rm3A Skipped atom 4096, because occupancy 0.400 <= existing 0.600 in 1rm3A Skipped atom 4147, because occupancy 0.500 <= existing 0.500 in 1rm3A Skipped atom 4149, because occupancy 0.500 <= existing 0.500 in 1rm3A Skipped atom 4278, because occupancy 0.500 <= existing 0.500 in 1rm3A Skipped atom 4280, because occupancy 0.500 <= existing 0.500 in 1rm3A Skipped atom 4282, because occupancy 0.500 <= existing 0.500 in 1rm3A Skipped atom 4284, because occupancy 0.500 <= existing 0.500 in 1rm3A Skipped atom 4435, because occupancy 0.500 <= existing 0.500 in 1rm3A Skipped atom 4437, because occupancy 0.500 <= existing 0.500 in 1rm3A Skipped atom 4443, because occupancy 0.500 <= existing 0.500 in 1rm3A Skipped atom 4445, because occupancy 0.500 <= existing 0.500 in 1rm3A Skipped atom 4447, because occupancy 0.500 <= existing 0.500 in 1rm3A Skipped atom 4449, because occupancy 0.500 <= existing 0.500 in 1rm3A Skipped atom 4451, because occupancy 0.500 <= existing 0.500 in 1rm3A Skipped atom 4843, because occupancy 0.500 <= existing 0.500 in 1rm3A Skipped atom 4845, because occupancy 0.500 <= existing 0.500 in 1rm3A Skipped atom 4847, because occupancy 0.500 <= existing 0.500 in 1rm3A Skipped atom 4849, because occupancy 0.500 <= existing 0.500 in 1rm3A # T0298 read from 1rm3A/T0298-1rm3A-t06-local-adpstyle5.a2m # 1rm3A read from 1rm3A/T0298-1rm3A-t06-local-adpstyle5.a2m # adding 1rm3A to template set # found chain 1rm3A in template set T0298 5 :LNVAVVGA 1rm3A 1 :LKVAINGF T0298 14 :GSVGEALVGLLDERDFPLHRLHLLASAESAGQRMGFAE 1rm3A 9 :GRIGRNFLRCWHGRKDSPLDVVVINDAGGVKQASHLLK T0298 52 :SSLRVGDVDSFDFS 1rm3A 72 :KVVSDRNPVNLPWG T0298 66 :SVGLAFFAAAAEVSRAHAERARAAGCSVIDLSGA 1rm3A 88 :GIDLVIEGTGVFVDRDGAGKHLQAGAKKVLITAP T0298 102 :PS 1rm3A 122 :GK T0298 104 :VAPPVMVSVNAERLAS 1rm3A 124 :DIPTYVVGVNEEGYTH T0298 122 :APFLLSSP 1rm3A 140 :ADTIISNA T0298 130 :CAVAA 1rm3A 149 :CTTNC T0298 136 :LCEVLAPLLATLDCRQLNLTACLSVSS 1rm3A 154 :LAPFVKVLDQKFGIIKGTMTTTHSYTG T0298 173 :RQ 1rm3A 181 :DQ T0298 177 :ELLNARPLEPRL 1rm3A 183 :RLLDASHRDLRR T0298 190 :DRQIAFNLLA 1rm3A 196 :ARAACLNIVP T0298 205 :DAEG 1rm3A 206 :TSTG T0298 213 :ERRIFAEV 1rm3A 210 :AAKAVALV T0298 224 :LGERIGPLNVTCIQAPVFFGDSLSVTLQCAEPVDLAAVTRVLDAT 1rm3A 218 :LPNLKGKLNGIALRVPTPNVSVVDLVVQVSKKTFAEEVNAAFRES T0298 269 :KGIEWVGEGDYPTVVGDALGQDETYVGRVRAGQ 1rm3A 266 :ELKGILSVCDEPLVSIDFRCTDVSSTIDSSLTM T0298 302 :ADPCQVNLWIVSDN 1rm3A 300 :MGDDMVKVIAWYDN T0298 317 :RKGAALNAVLLGELLIKH 1rm3A 314 :EWGYSQRVVDLADIVANK Number of specific fragments extracted= 18 number of extra gaps= 0 total=1757 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 1pqpA/T0298-1pqpA-t06-local-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1pqpA expands to /projects/compbio/data/pdb/1pqp.pdb.gz 1pqpA:# T0298 read from 1pqpA/T0298-1pqpA-t06-local-adpstyle5.a2m # 1pqpA read from 1pqpA/T0298-1pqpA-t06-local-adpstyle5.a2m # adding 1pqpA to template set # found chain 1pqpA in template set Warning: unaligning (T0298)A43 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1pqpA)L55 Warning: unaligning (T0298)V56 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1pqpA)L55 T0298 1 :M 1pqpA 1 :M T0298 5 :LNVAVVGATGSVGEALV 1pqpA 2 :KNVGFIGWRGMVGSVLM T0298 22 :GLLDERDFPLHRLHLL 1pqpA 20 :RMSQENDFENLNPVFF T0298 39 :SAES 1pqpA 36 :TTSQ T0298 57 :GDVDSFD 1pqpA 56 :KSAFDIE T0298 64 :FSSVGLAFFAAAAEVSRAHAERARAAGC 1pqpA 64 :LKKLDIIVTCQGGDYTNEVYPKLKATGW T0298 92 :SVIDLSGALEPS 1pqpA 94 :YWVDAASALRMK T0298 104 :VAPPVMVSVNAERLASQAAPF 1pqpA 107 :DAIIVLDPVNQHVISEGLKKG T0298 125 :LLSSPCAVAA 1pqpA 131 :FVGGNSTVSL T0298 136 :LCEVLAPLLATLDCRQLNLTACLSVSSLGREGVKELARQTAELLNARPLEPRL 1pqpA 141 :MLMAIGGLFEKDLVEWISVATYQAASGAGAKNMRELLSQMGLLEQAVSSELKD T0298 189 :FDRQIAFNLLAQVGA 1pqpA 219 :FGAALGGSLIPWIDK T0298 204 :VDAEGHSAIERRIFAEVQALLG 1pqpA 235 :LPETGQTKEEWKGYAETNKILG T0298 226 :ERIGPLNVTCIQAPVFFGDSLSVTLQCAEPVDLAAVTRVLDAT 1pqpA 259 :DNPIPVDGLCVRIGALRCHSQAFTIKLKKDLPLEEIEQIIASH T0298 269 :KGIEWVGEGDY 1pqpA 303 :EWVKVIPNDKE T0298 280 :PTVVGDALGQDETYVGRVRAGQADPCQVNLWIVSDNVRKGAALNAVLLGELL 1pqpA 318 :ELTPAKVTGTLSVPVGRLRKLAMGPEYLAAFTVGDQLLWGAAEPVRRILKQL Number of specific fragments extracted= 15 number of extra gaps= 0 total=1772 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 1rm5A/T0298-1rm5A-t06-local-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1rm5A expands to /projects/compbio/data/pdb/1rm5.pdb.gz 1rm5A:Skipped atom 3027, because occupancy 0.500 <= existing 0.500 in 1rm5A Skipped atom 3029, because occupancy 0.500 <= existing 0.500 in 1rm5A Skipped atom 3031, because occupancy 0.500 <= existing 0.500 in 1rm5A Skipped atom 3033, because occupancy 0.500 <= existing 0.500 in 1rm5A Skipped atom 4108, because occupancy 0.500 <= existing 0.500 in 1rm5A Skipped atom 4110, because occupancy 0.500 <= existing 0.500 in 1rm5A Skipped atom 4290, because occupancy 0.500 <= existing 0.500 in 1rm5A Skipped atom 4292, because occupancy 0.500 <= existing 0.500 in 1rm5A Skipped atom 4294, because occupancy 0.500 <= existing 0.500 in 1rm5A Skipped atom 4296, because occupancy 0.500 <= existing 0.500 in 1rm5A Skipped atom 4848, because occupancy 0.500 <= existing 0.500 in 1rm5A Skipped atom 4850, because occupancy 0.500 <= existing 0.500 in 1rm5A Skipped atom 4852, because occupancy 0.500 <= existing 0.500 in 1rm5A Skipped atom 4854, because occupancy 0.500 <= existing 0.500 in 1rm5A # T0298 read from 1rm5A/T0298-1rm5A-t06-local-adpstyle5.a2m # 1rm5A read from 1rm5A/T0298-1rm5A-t06-local-adpstyle5.a2m # adding 1rm5A to template set # found chain 1rm5A in template set T0298 5 :LNVAVVGA 1rm5A 1 :LKVAINGF T0298 14 :GSVGEALVGLLDERDFPLHRLHLLASAESAGQRMGFAE 1rm5A 9 :GRIGRNFLRCWHGRKDSPLDVVVINDTGGVKQASHLLK T0298 52 :SSLRVGDVDSFDFS 1rm5A 72 :KVVSDRNPVNLPWG T0298 66 :SVGLAFFAAAAEVSRAHAERARAAGCSVIDLSGA 1rm5A 88 :GIDLVIEGTGVFVDRDGAGKHLQAGAKKVLITAP T0298 102 :PS 1rm5A 122 :GK T0298 104 :VAPPVMVSVNAERLAS 1rm5A 124 :DIPTYVVGVNEEGYTH T0298 122 :APFLLSSP 1rm5A 140 :ADTIISNA T0298 130 :CAVAA 1rm5A 149 :CTTNC T0298 136 :LCEVLAPLLATLDCRQLNLTACLSVSS 1rm5A 154 :LAPFVKVLDQKFGIIKGTMTTTHSYTG T0298 173 :RQ 1rm5A 181 :DQ T0298 177 :ELLNARPLEPRL 1rm5A 183 :RLLDAAHRDLRR T0298 190 :DRQIAFNLLA 1rm5A 196 :ARAACLNIVP T0298 205 :DAEG 1rm5A 206 :TSTG T0298 213 :ERRIFAEV 1rm5A 210 :AAKAVALV T0298 224 :LGERIGPLNVTCIQAPVFFGDSLSVTLQCAEPVDLAAVTRVLDAT 1rm5A 218 :LPNLKGKLNGIALRVPTPNVSVVDLVVQVSKKTFAEEVNAAFRES T0298 269 :KGIEWVGEGDYPTVVGDALGQDETYVGRVRAGQ 1rm5A 266 :ELKGILSVCDEPLVSIDFRCTDVSSTIDSSLTM T0298 302 :ADPCQVNLWIVSDN 1rm5A 300 :MGDDMVKVIAWYDN T0298 317 :RKGAALNAVLLGELLIKH 1rm5A 314 :EWGYSQRVVDLADIVANK Number of specific fragments extracted= 18 number of extra gaps= 0 total=1790 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 1pu2A/T0298-1pu2A-t06-local-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1pu2A expands to /projects/compbio/data/pdb/1pu2.pdb.gz 1pu2A:Bad short name: S for alphabet: pdb_atoms Bad short name: CAH for alphabet: pdb_atoms Bad short name: OAI for alphabet: pdb_atoms Bad short name: CAJ for alphabet: pdb_atoms Bad short name: CAK for alphabet: pdb_atoms Bad short name: NAL for alphabet: pdb_atoms Bad short name: CAM for alphabet: pdb_atoms Bad short name: OAN for alphabet: pdb_atoms Bad short name: OAO for alphabet: pdb_atoms # T0298 read from 1pu2A/T0298-1pu2A-t06-local-adpstyle5.a2m # 1pu2A read from 1pu2A/T0298-1pu2A-t06-local-adpstyle5.a2m # adding 1pu2A to template set # found chain 1pu2A in template set Warning: unaligning (T0298)A43 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1pu2A)L55 Warning: unaligning (T0298)V56 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1pu2A)L55 Warning: unaligning (T0298)P129 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1pu2A)T137 Warning: unaligning (T0298)A131 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1pu2A)T137 T0298 1 :M 1pu2A 1 :M T0298 5 :LNVAVVGATGSVGEALV 1pu2A 2 :KNVGFIGWRGMVGSVLM T0298 22 :GLLDERDFPLHRLHLL 1pu2A 20 :RMSQENDFENLNPVFF T0298 39 :SAES 1pu2A 36 :TTSQ T0298 57 :GDVDSFD 1pu2A 56 :KSAFDIE T0298 64 :FSSVGLAFFAAAAEVSRAHAERARAAGC 1pu2A 64 :LKKLDIIVTCQGGDYTNEVYPKLKATGW T0298 92 :SVIDLSGALEPS 1pu2A 94 :YWVDAASALRMK T0298 104 :VAPPVMVSVNAERLASQAAPF 1pu2A 107 :DAIIVLDPVNQHVISEGLKKG T0298 125 :LLSS 1pu2A 131 :FVGG T0298 132 :VAA 1pu2A 138 :VSL T0298 136 :LCEVLAPLLATLDCRQLNLTACLSVSSLGREGVKELARQTAELLNARPLEPRL 1pu2A 141 :MLMAIGGLFEKDLVEWISVATYQAASGAGAKNMRELLSQMGLLEQAVSSELKD T0298 189 :FDRQIAFNLLAQVGA 1pu2A 219 :FGAALGGSLIPWIDK T0298 204 :VDAEGHSAIERRIFAEVQALLG 1pu2A 235 :LPETGQTKEEWRGYAETNKILG T0298 226 :ERIGPLNVTCIQAPVFFGDSLSVTLQCAEPVDLAAVTRVLDAT 1pu2A 259 :DNPIPVDGLCVRIGALRCHSQAFTIKLKKDLPLEEIEQIIASH T0298 269 :KGIEWVGEGDY 1pu2A 303 :EWVKVIPNDKE T0298 280 :PTVVGDALGQDETYVGRVRAGQADPCQVNLWIVSDNVRKGAALNAVLLGELL 1pu2A 318 :ELTPAKVTGTLSVPVGRLRKLAMGPEYLAAFTVGDQLLWGAAEPVRRILKQL Number of specific fragments extracted= 16 number of extra gaps= 0 total=1806 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 1q2xA/T0298-1q2xA-t06-local-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1q2xA expands to /projects/compbio/data/pdb/1q2x.pdb.gz 1q2xA:Bad short name: S for alphabet: pdb_atoms Bad short name: CAH for alphabet: pdb_atoms Bad short name: OAI for alphabet: pdb_atoms Bad short name: CAJ for alphabet: pdb_atoms Bad short name: CAK for alphabet: pdb_atoms Bad short name: NAL for alphabet: pdb_atoms Bad short name: CAM for alphabet: pdb_atoms Bad short name: OAN for alphabet: pdb_atoms Bad short name: OAO for alphabet: pdb_atoms # T0298 read from 1q2xA/T0298-1q2xA-t06-local-adpstyle5.a2m # 1q2xA read from 1q2xA/T0298-1q2xA-t06-local-adpstyle5.a2m # adding 1q2xA to template set # found chain 1q2xA in template set Warning: unaligning (T0298)A43 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1q2xA)L55 Warning: unaligning (T0298)V56 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1q2xA)L55 Warning: unaligning (T0298)P129 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1q2xA)T137 Warning: unaligning (T0298)A131 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1q2xA)T137 T0298 1 :M 1q2xA 1 :M T0298 5 :LNVAVVGATGSVGEALV 1q2xA 2 :KNVGFIGWRGMVGSVLM T0298 22 :GLLDERDFPLHRLHLL 1q2xA 20 :RMSQENDFENLNPVFF T0298 39 :SAES 1q2xA 36 :TTSQ T0298 57 :GDVDSFD 1q2xA 56 :KSAFDIE T0298 64 :FSSVGLAFFAAAAEVSRAHAERARAAGC 1q2xA 64 :LKKLDIIVTCQGGDYTNEVYPKLKATGW T0298 92 :SVIDLSGALEPS 1q2xA 94 :YWVDAASALRMK T0298 104 :VAPPVMVSVNAERLASQAAPF 1q2xA 107 :DAIIVLDPVNQHVISEGLKKG T0298 125 :LLSS 1q2xA 131 :FVGG T0298 132 :VAA 1q2xA 138 :VSL T0298 136 :LCEVLAPLLATLDCRQLNLTACLSVSSLGREGVKELARQTAELLNARPLEPRL 1q2xA 141 :MLMAIGGLFEKDLVEWISVATYQAASGAGAKNMRELLSQMGLLEQAVSSELKD T0298 189 :FDRQIAFNLLAQVGA 1q2xA 219 :FGAALGGSLIPWIDK T0298 204 :VDAEGHSAIERRIFAEVQALLG 1q2xA 235 :LPETGQTKDEWKGYAETNKILG T0298 226 :ERIGPLNVTCIQAPVFFGDSLSVTLQCAEPVDLAAVTRVLDAT 1q2xA 259 :DNPIPVDGLCVRIGALRCHSQAFTIKLKKDLPLEEIEQIIASH T0298 269 :KGIEWVGEGDY 1q2xA 303 :EWVKVIPNDKE T0298 280 :PTVVGDALGQDETYVGRVRAGQADPCQVNLWIVSDNVRKGAALNAVLLGELL 1q2xA 318 :ELTPAKVTGTLSVPVGRLRKLAMGPEYLAAFTVGDQLLWGAAEPVRRILKQL Number of specific fragments extracted= 16 number of extra gaps= 0 total=1822 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 1jn0A/T0298-1jn0A-t06-local-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1jn0A expands to /projects/compbio/data/pdb/1jn0.pdb.gz 1jn0A:# T0298 read from 1jn0A/T0298-1jn0A-t06-local-adpstyle5.a2m # 1jn0A read from 1jn0A/T0298-1jn0A-t06-local-adpstyle5.a2m # adding 1jn0A to template set # found chain 1jn0A in template set Warning: unaligning (T0298)F62 because of BadResidue code BAD_PEPTIDE in next template residue (1jn0A)P83 Warning: unaligning (T0298)D63 because of BadResidue code BAD_PEPTIDE at template residue (1jn0A)P83 Warning: unaligning (T0298)L331 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1jn0A)A329 Warning: unaligning (T0298)I332 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1jn0A)A329 T0298 5 :LNVAVVGA 1jn0A 1 :LKVAINGF T0298 14 :GSVGEALVGLLDERDFP 1jn0A 9 :GRIGRNFLRCWHGKDSP T0298 32 :HRLHLLASAESAGQRMGFAE 1jn0A 25 :LDVVVINDTGGVKQASHLLK T0298 52 :SSLRVGDVDS 1jn0A 72 :KVVSDRNPVN T0298 64 :FS 1jn0A 84 :WG T0298 66 :SVGLAFFAAAAEVSRAHAERARAAGCSVIDLSGA 1jn0A 88 :GIDLVIEGTGVFVDRDGAGKHLQAGAKKVLITAP T0298 102 :PS 1jn0A 122 :GK T0298 104 :VAPPVMVSVNAERLAS 1jn0A 124 :DIPTYVVGVNEEGYTH T0298 122 :APFLLSSP 1jn0A 140 :ADTIISNA T0298 130 :CAVAA 1jn0A 149 :CTTNC T0298 136 :LCEVLAPLLATLDCRQLNLTACLSVSS 1jn0A 154 :LAPFVKVLDQKFGIIKGTMTTTHSYTG T0298 173 :RQ 1jn0A 181 :DQ T0298 177 :ELLNARPLEPRL 1jn0A 183 :RLLDASHRDLRR T0298 190 :DRQIAFNLLA 1jn0A 196 :ARAACLNIVP T0298 205 :DAEG 1jn0A 206 :TSTG T0298 213 :ERRIFAEV 1jn0A 210 :AAKAVALV T0298 224 :LGERIGPLNVTCIQAPVFFGDSLSVTLQCAEPVDLAAVTRVLDAT 1jn0A 218 :LPQLKGKLNGIALRVPTPNVSVVDLVVQVSKKTFAEEVNAAFRES T0298 269 :KGIEWVGEGDYPTVVGDALGQDETYVGRVRAGQ 1jn0A 266 :ELKGILSVCDEPLVSIDFRCTDVSSTIDSSLTM T0298 302 :ADPCQVNLWIVSDN 1jn0A 300 :MGDDMVKVIAWYDN T0298 317 :RKGAALNAVLLGEL 1jn0A 314 :EWGYSQRVVDLADI T0298 333 :KH 1jn0A 330 :NK Number of specific fragments extracted= 21 number of extra gaps= 2 total=1843 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 1xygA/T0298-1xygA-t06-local-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1xygA expands to /projects/compbio/data/pdb/1xyg.pdb.gz 1xygA:# T0298 read from 1xygA/T0298-1xygA-t06-local-adpstyle5.a2m # 1xygA read from 1xygA/T0298-1xygA-t06-local-adpstyle5.a2m # adding 1xygA to template set # found chain 1xygA in template set Warning: unaligning (T0298)Q3 because first residue in template chain is (1xygA)K15 T0298 4 :PLNVAVVGATGSVGEALVGLLD 1xygA 16 :DIRIGLLGASGYTGAEIVRLLA T0298 28 :DFPLHRLHLLASAESAGQRMGFAESSLR 1xygA 38 :NHPHFQVTLMTADRKAGQSMESVFPHLR T0298 56 :VGDVDSFDFSSVGLAFFAAAAEVSRAHAERARAA 1xygA 72 :LVSVKDADFSTVDAVFCCLPHGTTQEIIKELPTA T0298 91 :CSVIDLSGALEPSV 1xygA 106 :LKIVDLSADFRLRN T0298 105 :APPVMVSVNAERLA 1xygA 140 :VVYGLTEILREDIK T0298 122 :APFLLSSP 1xygA 154 :KARLVANP T0298 130 :CAVAA 1xygA 163 :CYPTT T0298 136 :LCEVLAPLLATLDCR 1xygA 168 :IQLPLVPLLKANLIK T0298 151 :QLNLTACLSVSSLGREGVK 1xygA 185 :NIIIDAKSGVSGAGRGAKE T0298 170 :ELARQTAELLNARPL 1xygA 205 :NLYSEIAEGISSYGV T0298 205 :DAEGHSAIERRIFAE 1xygA 220 :TRHRHVPEIEQGLSD T0298 224 :LGERIGPLNVTCIQAPVFFGDSLSVTLQCAEPVDLAAVTRVLDAT 1xygA 235 :VAQSKVTVSFTPHLMPMIRGMQSTIYVEMAPGVRTEDLHQQLKTS T0298 269 :KGIEWVGEGDYPTVV 1xygA 284 :EFVKVLDEGVVPRTH T0298 285 :DALGQDETYVG 1xygA 299 :NVRGSNYCHMS T0298 297 :VRAGQADPCQV 1xygA 310 :VFPDRIPGRAI T0298 309 :LWIVSDNVRKGAALNAVLLGELLIKH 1xygA 321 :IISVIDNLVKGASGQALQNLNIMLGY Number of specific fragments extracted= 16 number of extra gaps= 0 total=1859 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 1i32A/T0298-1i32A-t06-local-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1i32A expands to /projects/compbio/data/pdb/1i32.pdb.gz 1i32A:# T0298 read from 1i32A/T0298-1i32A-t06-local-adpstyle5.a2m # 1i32A read from 1i32A/T0298-1i32A-t06-local-adpstyle5.a2m # adding 1i32A to template set # found chain 1i32A in template set T0298 4 :PLNVAVVGA 1i32A 2 :PIKVGINGF T0298 14 :GSVGEALVGLLDERDF 1i32A 11 :GRIGRMVFQAICDQGL T0298 30 :PLHRLHLLASAE 1i32A 29 :TEIDVVAVVDMS T0298 42 :SAGQRMGFAE 1i32A 42 :NAEYFAYQMK T0298 52 :SSLRVGDVDSFDFS 1i32A 87 :CVKAQRNPADLPWG T0298 66 :SVGLAFFAAAAEVSRAHAERARAAGCSVIDLSGAL 1i32A 103 :GVDYVIESTGLFTDKLKAEGHIKGGAKKVVISAPA T0298 103 :S 1i32A 138 :S T0298 104 :VAPPVMVSVNAERLASQ 1i32A 140 :GAKTIVMGVNQHEYSPA T0298 122 :APFLLSSP 1i32A 157 :SHHVVSNA T0298 130 :CAVAA 1i32A 166 :CTTNC T0298 136 :LCEVLAPLLA 1i32A 171 :LAPIVHVLTK T0298 146 :TLDCRQLNLTACLSVSS 1i32A 182 :NFGIETGLMTTIHSYTA T0298 175 :TAELLNARPLEPRLFDRQIAFNLLA 1i32A 199 :TQKTVDGVSLKDWRGGRAAAVNIIP T0298 205 :DAEG 1i32A 224 :STTG T0298 213 :ERRIFAEV 1i32A 228 :AAKAVGMV T0298 224 :LGERIGPLNVTCIQAPVFFGDSLSVTLQCAEPVDLAAVTRVLDAT 1i32A 236 :IPSTKGKLTGMSFRVPTPDVSVVDLTFRATRDTSIQEIDKAIKKA T0298 269 :KGIEWVGEGDYPTVVGDALGQDETYVGRVRAGQADP 1i32A 284 :YMKGILGFTDEELVSADFINDNRSSVYDSKATLQNN T0298 305 :CQVNLWIVSDN 1i32A 325 :RFFKVVSWYDN T0298 317 :RKGAALNAVLLGELLIKH 1i32A 336 :EWAYSHRVVDLVRYMAAK Number of specific fragments extracted= 19 number of extra gaps= 0 total=1878 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 1ggaA/T0298-1ggaA-t06-local-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1ggaA expands to /projects/compbio/data/pdb/1gga.pdb.gz 1ggaA:# T0298 read from 1ggaA/T0298-1ggaA-t06-local-adpstyle5.a2m # 1ggaA read from 1ggaA/T0298-1ggaA-t06-local-adpstyle5.a2m # adding 1ggaA to template set # found chain 1ggaA in template set Warning: unaligning (T0298)L5 because of BadResidue code BAD_PEPTIDE in next template residue (1ggaA)K3 Warning: unaligning (T0298)N6 because of BadResidue code BAD_PEPTIDE at template residue (1ggaA)K3 Warning: unaligning (T0298)C157 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1ggaA)H193 Warning: unaligning (T0298)L158 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1ggaA)H193 Warning: unaligning (T0298)F242 because of BadResidue code BAD_PEPTIDE in next template residue (1ggaA)V254 Warning: unaligning (T0298)G243 because of BadResidue code BAD_PEPTIDE at template residue (1ggaA)V254 T0298 7 :VAVVGA 1ggaA 4 :VGINGF T0298 14 :GSVGEALVGLLDERDF 1ggaA 10 :GRIGRMVFQALCDDGL T0298 30 :PLHRLHLLASAE 1ggaA 28 :NEIDVVAVVDMN T0298 42 :SAGQRMGFAE 1ggaA 41 :DARYFAYQMK T0298 52 :SSLRVGDVDSFDFS 1ggaA 86 :CVKAQRNPADLPWG T0298 66 :SVGLAFFAAAAEVSRAHAERARAAGCSVIDLSGAL 1ggaA 102 :GVEYVIESTGLFTVKSAAEGHLRGGARKVVISAPA T0298 103 :S 1ggaA 137 :S T0298 104 :VAPPVMVSVNAERLASQ 1ggaA 139 :GAKTFVMGVNHNNYNPR T0298 122 :APFLLSSP 1ggaA 156 :EQHVVSNA T0298 130 :CAVAA 1ggaA 165 :CTTNC T0298 136 :LCEVLAPLLA 1ggaA 170 :LAPLVHVLVK T0298 146 :TLDCRQLNLTA 1ggaA 181 :GFGISTGLMTT T0298 159 :SVSS 1ggaA 194 :SYTA T0298 175 :TAELLNARPLEPRLFDRQIAFNLLA 1ggaA 198 :TQKTVDGVSVKDWRGGRAAALNIIP T0298 205 :DAEG 1ggaA 223 :STTG T0298 213 :ERRIFAEV 1ggaA 227 :AAKAVGMV T0298 224 :LGERIGPLNVTCIQAPVF 1ggaA 235 :IPSTQGKLTGMAFRVPTA T0298 244 :DSLSVTLQCAEPVDLAAVTRVLDAT 1ggaA 255 :SVVDLTFIATRDTSIKEIDAALKRA T0298 269 :KGIEWVGEGDYPTVVGDALGQDETYVGRVRAGQADP 1ggaA 283 :YMKNILGYTDEELVSADFISDSRSSIYDSKATLQNN T0298 305 :CQVNLWIVSDN 1ggaA 324 :RFFKIVSWYDN T0298 317 :RKGAALNAVLLGELLIKH 1ggaA 335 :EWGYSHRVVDLVRHMAAR Number of specific fragments extracted= 21 number of extra gaps= 3 total=1899 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 2cvoA/T0298-2cvoA-t06-local-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2cvoA expands to /projects/compbio/data/pdb/2cvo.pdb.gz 2cvoA:Bad short name: OD for alphabet: pdb_atoms # T0298 read from 2cvoA/T0298-2cvoA-t06-local-adpstyle5.a2m # 2cvoA read from 2cvoA/T0298-2cvoA-t06-local-adpstyle5.a2m # adding 2cvoA to template set # found chain 2cvoA in template set Warning: unaligning (T0298)F72 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2cvoA)L146 Warning: unaligning (T0298)A74 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2cvoA)L146 T0298 4 :PLNVAVVGATGSVGEALVGLLD 2cvoA 72 :EVRIAVLGASGYTGAEIVRLLA T0298 28 :DFPLHRLHLLASAESAGQRMGFAESSLRVGDVDSFD 2cvoA 94 :NHPQFRIKVMTADRKAGEQFGSVFPHLITQDLPNLV T0298 64 :FSSVGLAF 2cvoA 136 :FSNVDAVF T0298 75 :AAEVSRAHAERA 2cvoA 147 :PHGTTQEIIKGL T0298 88 :AAGCSVIDLSGALEPSV 2cvoA 159 :PQELKIVDLSADFRLRD T0298 105 :APPVMVSVNAERLA 2cvoA 196 :AVYGLTEVLRNEIR T0298 122 :APFLLSSP 2cvoA 210 :NARLVANP T0298 130 :CAVAA 2cvoA 219 :CYPTS T0298 136 :LCEVLAPLLATLDCR 2cvoA 224 :IQLPLVPLIKAKLIK T0298 151 :QLNLTACLSVSSLGREGVK 2cvoA 241 :NIIIDAKSGVSGAGRGAKE T0298 170 :ELARQTAELLNARPL 2cvoA 261 :NLYTEIAEGIHAYGI T0298 205 :DAEGHSAIERRIFAE 2cvoA 276 :KGHRHVPEIEQGLSE T0298 224 :LGERIGPLNVTCIQAPVFFGDSLSVTLQCAEPVDLAAVTRVLDAT 2cvoA 291 :AAESKVTISFTPNLICMKRGMQSTMFVEMAPGVTANDLYQHLKST T0298 269 :KGIEWVGEGDYPTVV 2cvoA 340 :EFVKLLNGSSVPHTR T0298 285 :DALGQDETYVG 2cvoA 355 :HVVGSNYCFMN T0298 297 :VRAGQADPCQV 2cvoA 366 :VFEDRIPGRAI T0298 309 :LWIVSDNVRKGAALNAVLLGELLIKH 2cvoA 377 :IISVIDNLVKGASGQAVQNLNLMMGL Number of specific fragments extracted= 17 number of extra gaps= 0 total=1916 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 2g17A/T0298-2g17A-t06-local-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2g17A expands to /projects/compbio/data/pdb/2g17.pdb.gz 2g17A:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 664, because occupancy 0.500 <= existing 0.500 in 2g17A Skipped atom 666, because occupancy 0.500 <= existing 0.500 in 2g17A Skipped atom 668, because occupancy 0.500 <= existing 0.500 in 2g17A Skipped atom 670, because occupancy 0.500 <= existing 0.500 in 2g17A Skipped atom 672, because occupancy 0.500 <= existing 0.500 in 2g17A Skipped atom 674, because occupancy 0.500 <= existing 0.500 in 2g17A Skipped atom 676, because occupancy 0.500 <= existing 0.500 in 2g17A Skipped atom 678, because occupancy 0.500 <= existing 0.500 in 2g17A Skipped atom 1019, because occupancy 0.500 <= existing 0.500 in 2g17A Skipped atom 1021, because occupancy 0.500 <= existing 0.500 in 2g17A Skipped atom 1023, because occupancy 0.500 <= existing 0.500 in 2g17A Skipped atom 1025, because occupancy 0.500 <= existing 0.500 in 2g17A Skipped atom 1027, because occupancy 0.500 <= existing 0.500 in 2g17A Skipped atom 1029, because occupancy 0.500 <= existing 0.500 in 2g17A Skipped atom 1031, because occupancy 0.500 <= existing 0.500 in 2g17A Skipped atom 1033, because occupancy 0.500 <= existing 0.500 in 2g17A Skipped atom 1035, because occupancy 0.500 <= existing 0.500 in 2g17A Skipped atom 1377, because occupancy 0.500 <= existing 0.500 in 2g17A Skipped atom 1379, because occupancy 0.500 <= existing 0.500 in 2g17A Skipped atom 1381, because occupancy 0.500 <= existing 0.500 in 2g17A Skipped atom 1383, because occupancy 0.500 <= existing 0.500 in 2g17A Skipped atom 1385, because occupancy 0.500 <= existing 0.500 in 2g17A Skipped atom 1387, because occupancy 0.500 <= existing 0.500 in 2g17A Skipped atom 1389, because occupancy 0.500 <= existing 0.500 in 2g17A Skipped atom 1391, because occupancy 0.500 <= existing 0.500 in 2g17A Skipped atom 1393, because occupancy 0.500 <= existing 0.500 in 2g17A Skipped atom 1918, because occupancy 0.500 <= existing 0.500 in 2g17A Skipped atom 1922, because occupancy 0.500 <= existing 0.500 in 2g17A Skipped atom 1924, because occupancy 0.500 <= existing 0.500 in 2g17A Skipped atom 1926, because occupancy 0.500 <= existing 0.500 in 2g17A Skipped atom 1928, because occupancy 0.500 <= existing 0.500 in 2g17A Skipped atom 1930, because occupancy 0.500 <= existing 0.500 in 2g17A Skipped atom 1932, because occupancy 0.500 <= existing 0.500 in 2g17A Skipped atom 1934, because occupancy 0.500 <= existing 0.500 in 2g17A # T0298 read from 2g17A/T0298-2g17A-t06-local-adpstyle5.a2m # 2g17A read from 2g17A/T0298-2g17A-t06-local-adpstyle5.a2m # adding 2g17A to template set # found chain 2g17A in template set Warning: unaligning (T0298)M109 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2g17A)A136 Warning: unaligning (T0298)V110 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2g17A)A136 Warning: unaligning (T0298)E291 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2g17A)C289 Warning: unaligning (T0298)T292 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2g17A)C289 T0298 1 :M 2g17A 1 :M T0298 5 :LNVAVVGATGSVGEALVGLLD 2g17A 2 :LNTLIVGASGYAGAELVSYVN T0298 28 :DFPLHRLHLL 2g17A 23 :RHPHMTITAL T0298 38 :ASAESAGQRMGFAESSLR 2g17A 36 :AQSNDAGKLISDLHPQLK T0298 56 :VGDVDSFD 2g17A 60 :LQPMSDVR T0298 64 :FS 2g17A 69 :FS T0298 66 :SVGLAFFAAAAEVSRAHAERARAAGCSVIDLSGALEPSV 2g17A 72 :DVDVVFLATAHEVSHDLAPQFLQAGCVVFDLSGAFRVND T0298 105 :APPV 2g17A 131 :AVYG T0298 111 :SVNAERLA 2g17A 137 :EWNVDKLN T0298 122 :APFLLSSP 2g17A 145 :TANLIAVP T0298 130 :CAVAA 2g17A 154 :CYPTA T0298 136 :LCEVLAPLLATLDCR 2g17A 159 :AQLSLKPLIDGGLLD T0298 151 :QLNLTACLSVSSLGREG 2g17A 177 :WPVINATSGVSGAGRKA T0298 168 :VKELARQ 2g17A 195 :ISNSFCE T0298 177 :ELLNARPL 2g17A 202 :VSLQPYGV T0298 205 :DAEGHSAIERRIF 2g17A 210 :FTHRHQPEIAVHL T0298 228 :IGPLNVTCIQAPVFFGDSLSVTLQCAEPVDLAAVTRVLDAT 2g17A 223 :GAEVIFTPHLGNFPRGILETITCRLKAGVTHAQVADVLQKA T0298 269 :KGIEWVGEGDYPT 2g17A 268 :PLVRLYDKGVPAL T0298 284 :GDALGQD 2g17A 281 :KNVVGLP T0298 293 :YVG 2g17A 290 :DIG T0298 300 :GQADPCQVNLWIVSDNVRKGAALNAVLLGELLIKH 2g17A 293 :FAVQGEHLIVVATEDNLLKGAAAQAVQCANIRFGF Number of specific fragments extracted= 21 number of extra gaps= 2 total=1937 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 1vm6A/T0298-1vm6A-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:# T0298 read from 1vm6A/T0298-1vm6A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1vm6A read from 1vm6A/T0298-1vm6A-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 (T0298)P4 because first residue in template chain is (1vm6A)H0 T0298 5 :LNVAVVGATGSVGEALVGLLDERDF 1vm6A 1 :MKYGIVGYSGRMGQEIQKVFSEKGH T0298 33 :RLHLLASAESA 1vm6A 26 :ELVLKVDVNGV T0298 55 :RV 1vm6A 37 :EE T0298 64 :FSSVGLAFFAAAAEVSRAHAERARAAGCSVIDLSGALE 1vm6A 39 :LDSPDVVIDFSSPEALPKTVDLCKKYRAGLVLGTTALK T0298 113 :NAERLASQAAPFLLSSPCAVAAELCEVLAPLLATL 1vm6A 79 :HLQMLRELSKEVPVVQAYNFSIGINVLKRFLSELV T0298 148 :DCR 1vm6A 118 :DWD T0298 151 :QLNLTAC 1vm6A 122 :EIVETHH T0298 159 :SVSS 1vm6A 134 :APSG T0298 213 :ERRIFAEV 1vm6A 138 :TAILLESA T0298 224 :LGE 1vm6A 146 :LGK T0298 255 :PV 1vm6A 149 :SV T0298 270 :GIEWVGEGDYP 1vm6A 151 :PIHSLRVGGVP T0298 282 :VVGDALGQDETYVGRVRAGQ 1vm6A 164 :HVVVFGNIGETIEIKHRAIS T0298 317 :RKGAALNAVLLGELLIKHY 1vm6A 184 :RTVFAIGALKAAEFLVGKD Number of specific fragments extracted= 14 number of extra gaps= 0 total=1951 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 1vm6A/T0298-1vm6A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0298 read from 1vm6A/T0298-1vm6A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1vm6A read from 1vm6A/T0298-1vm6A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1vm6A in template set Warning: unaligning (T0298)P4 because first residue in template chain is (1vm6A)H0 T0298 5 :LNVAVVGATGSVGEALVGLLDERDFPLHR 1vm6A 1 :MKYGIVGYSGRMGQEIQKVFSEKGHELVL T0298 48 :GFAESSLRVGD 1vm6A 30 :KVDVNGVEELD T0298 66 :SVGLAFFAAAAEVSRAHAERARAAGCSVIDLSGALE 1vm6A 41 :SPDVVIDFSSPEALPKTVDLCKKYRAGLVLGTTALK T0298 103 :S 1vm6A 77 :E T0298 113 :NAERLASQAAPFLLSSP 1vm6A 79 :HLQMLRELSKEVPVVQA T0298 130 :CAVAA 1vm6A 97 :NFSIG T0298 136 :LCEVLAPLLATL 1vm6A 102 :INVLKRFLSELV T0298 149 :CR 1vm6A 119 :WD T0298 151 :QLNLTA 1vm6A 122 :EIVETH T0298 181 :ARPLEPRLFD 1vm6A 128 :HRFKKDAPSG T0298 216 :IFAEVQALLG 1vm6A 138 :TAILLESALG T0298 254 :EPV 1vm6A 148 :KSV T0298 270 :GIEWVGEGDYP 1vm6A 151 :PIHSLRVGGVP T0298 283 :VGDALGQDETYVGRVRAGQ 1vm6A 165 :VVVFGNIGETIEIKHRAIS T0298 317 :RKGAALNAVLLGELLIK 1vm6A 184 :RTVFAIGALKAAEFLVG Number of specific fragments extracted= 15 number of extra gaps= 0 total=1966 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 1vm6A/T0298-1vm6A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0298 read from 1vm6A/T0298-1vm6A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1vm6A read from 1vm6A/T0298-1vm6A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1vm6A in template set Warning: unaligning (T0298)P4 because first residue in template chain is (1vm6A)H0 T0298 5 :LNVAVVGATGSVGEALVGLLDERDFPLHRLHL 1vm6A 1 :MKYGIVGYSGRMGQEIQKVFSEKGHELVLKVD T0298 51 :ESSLRVGD 1vm6A 33 :VNGVEELD T0298 66 :SVGLAFFAAAAEVSRAHAERARAAGCSVID 1vm6A 41 :SPDVVIDFSSPEALPKTVDLCKKYRAGLVL T0298 108 :VMVSVNAERLAS 1vm6A 71 :GTTALKEEHLQM T0298 140 :LAPLLATL 1vm6A 83 :LRELSKEV T0298 153 :NLTACLSVS 1vm6A 91 :PVVQAYNFS T0298 169 :KELARQTAEL 1vm6A 100 :IGINVLKRFL T0298 218 :AEVQALLGERIGPLNVTCI 1vm6A 110 :SELVKVLEDWDVEIVETHH T0298 261 :VTRVLDATKGIEWVGEGDYPTVVGDALGQDETYVGRVRAGQA 1vm6A 142 :LESALGKSVPIHSLRVGGVPGDHVVVFGNIGETIEIKHRAIS T0298 317 :RKGAALNAVLLGELLI 1vm6A 184 :RTVFAIGALKAAEFLV Number of specific fragments extracted= 10 number of extra gaps= 0 total=1976 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 1arzC/T0298-1arzC-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:# T0298 read from 1arzC/T0298-1arzC-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1arzC read from 1arzC/T0298-1arzC-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 Warning: unaligning (T0298)S2 because first residue in template chain is (1arzC)D3 T0298 3 :QPLNVAVVGATGSVGEALVGLLD 1arzC 4 :ANIRVAIAGAGGRMGRQLIQAAL T0298 28 :DFPLHRLHLLASAE 1arzC 27 :ALEGVQLGAALERE T0298 42 :SAGQRMGFAESSLR 1arzC 44 :LLGSDAGELAGAGK T0298 56 :VGDVDSFD 1arzC 63 :QSSLDAVK T0298 65 :SSVGLAFFAAAAEVSRAHAERARAAGCSVIDLSGALE 1arzC 71 :DDFDVFIDFTRPEGTLNHLAFCRQHGKGMVIGTTGFD T0298 113 :NAERLASQAAPFLLSSPCAVAAELCEVLAPLLA 1arzC 110 :GKQAIRDAAADIAIVFAANFSVGVNVMLKLLEK T0298 146 :TLDCR 1arzC 148 :GDYTD T0298 151 :QLNLTA 1arzC 154 :EIIEAH T0298 159 :SVSSLGREGVKELARQT 1arzC 166 :APSGTALAMGEAIAHAL T0298 183 :PLEPRL 1arzC 183 :DKDLKD T0298 196 :NLLAQVGAVDAEG 1arzC 189 :CAVYSREGHTGER T0298 224 :LGE 1arzC 202 :VPG T0298 230 :PLNVTCIQ 1arzC 205 :TIGFATVR T0298 277 :G 1arzC 214 :G T0298 290 :DETYVGRVRAGQ 1arzC 215 :DIVGEHTAMFAD T0298 303 :DPCQVNLWIVSDN 1arzC 227 :IGERLEITHKASS T0298 317 :RKGAALNAVLLGELL 1arzC 240 :RMTFANGAVRSALWL Number of specific fragments extracted= 17 number of extra gaps= 0 total=1993 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 1arzC/T0298-1arzC-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0298 read from 1arzC/T0298-1arzC-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1arzC read from 1arzC/T0298-1arzC-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1arzC in template set Warning: unaligning (T0298)S2 because first residue in template chain is (1arzC)D3 T0298 3 :QPLNVAVVGATGSVGEALVGLLD 1arzC 4 :ANIRVAIAGAGGRMGRQLIQAAL T0298 28 :DFPLHRLHLLA 1arzC 27 :ALEGVQLGAAL T0298 39 :SAES 1arzC 41 :GSSL T0298 43 :AGQRMGFAESSLRVGD 1arzC 49 :AGELAGAGKTGVTVQS T0298 64 :FSSVGLAFFAAAAEVSRAHAERARAAGCSVIDLSGALE 1arzC 70 :KDDFDVFIDFTRPEGTLNHLAFCRQHGKGMVIGTTGFD T0298 114 :AERLASQAAPFLLSSPCAVAAELCEVLAPLLATL 1arzC 111 :KQAIRDAAADIAIVFAANFSVGVNVMLKLLEKAA T0298 148 :DCR 1arzC 150 :YTD T0298 151 :QLNLTAC 1arzC 154 :EIIEAHH T0298 158 :LSVSSLGREGVKELARQTAE 1arzC 165 :DAPSGTALAMGEAIAHALDK T0298 178 :LLNARPLEPRLF 1arzC 190 :AVYSREGHTGER T0298 205 :DA 1arzC 202 :VP T0298 228 :I 1arzC 204 :G T0298 230 :PLNVTCIQ 1arzC 205 :TIGFATVR T0298 241 :FF 1arzC 216 :IV T0298 246 :LSVTLQCAE 1arzC 218 :GEHTAMFAD T0298 289 :QDETYVGRVRAGQ 1arzC 227 :IGERLEITHKASS T0298 317 :RKGAALNAVLLGELL 1arzC 240 :RMTFANGAVRSALWL Number of specific fragments extracted= 17 number of extra gaps= 0 total=2010 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 1arzC/T0298-1arzC-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0298 read from 1arzC/T0298-1arzC-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1arzC read from 1arzC/T0298-1arzC-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1arzC in template set Warning: unaligning (T0298)S2 because first residue in template chain is (1arzC)D3 T0298 3 :QPLNVAVVGATGSVGEALVGLLDERDFPLHRLHLLASAESA 1arzC 4 :ANIRVAIAGAGGRMGRQLIQAALALEGVQLGAALEREGSSL T0298 44 :GQR 1arzC 46 :GSD T0298 47 :MGFAESSLRVGDVDSFDFSSVGLAFFAAAAEVSRAHAERARAAGCSVIDL 1arzC 53 :AGAGKTGVTVQSSLDAVKDDFDVFIDFTRPEGTLNHLAFCRQHGKGMVIG T0298 109 :MVSVNAERLASQ 1arzC 103 :TTGFDEAGKQAI T0298 121 :AAPFLLSSPCAV 1arzC 119 :ADIAIVFAANFS T0298 134 :AELCEVLAPLLA 1arzC 131 :VGVNVMLKLLEK T0298 146 :TLDCRQLNLTACL 1arzC 147 :MGDYTDIEIIEAH T0298 159 :SV 1arzC 166 :AP T0298 165 :REGVKELARQTAELLNAR 1arzC 168 :SGTALAMGEAIAHALDKD T0298 183 :PLEPRLFDRQ 1arzC 196 :GHTGERVPGT T0298 231 :LNVTCIQ 1arzC 206 :IGFATVR T0298 244 :DSLSVTLQCA 1arzC 216 :IVGEHTAMFA T0298 288 :GQDETYVGRVRAGQ 1arzC 226 :DIGERLEITHKASS T0298 317 :RKGAALNAVLLGEL 1arzC 240 :RMTFANGAVRSALW Number of specific fragments extracted= 14 number of extra gaps= 0 total=2024 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 1dih/T0298-1dih-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 # T0298 read from 1dih/T0298-1dih-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1dih read from 1dih/T0298-1dih-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 (T0298)A50 because of BadResidue code BAD_PEPTIDE in next template residue (1dih)G46 Warning: unaligning (T0298)E51 because of BadResidue code BAD_PEPTIDE at template residue (1dih)G46 Warning: unaligning (T0298)A73 because of BadResidue code BAD_PEPTIDE in next template residue (1dih)T80 Warning: unaligning (T0298)A74 because of BadResidue code BAD_PEPTIDE at template residue (1dih)T80 Warning: unaligning (T0298)D148 because of BadResidue code BAD_PEPTIDE in next template residue (1dih)T151 Warning: unaligning (T0298)C149 because of BadResidue code BAD_PEPTIDE at template residue (1dih)T151 Warning: unaligning (T0298)P230 because of BadResidue code BAD_PEPTIDE in next template residue (1dih)I206 Warning: unaligning (T0298)L231 because of BadResidue code BAD_PEPTIDE at template residue (1dih)I206 T0298 3 :QPLNVAVVGATGSVGEALVGLLD 1dih 4 :ANIRVAIAGAGGRMGRQLIQAAL T0298 28 :DFPLHRL 1dih 27 :ALEGVQL T0298 35 :HLLASAE 1dih 35 :AALEREG T0298 42 :S 1dih 43 :S T0298 49 :F 1dih 44 :L T0298 52 :SSLRVGDVDSFD 1dih 59 :GVTVQSSLDAVK T0298 65 :SSVGLAFF 1dih 71 :DDFDVFID T0298 75 :AAEVSRAHAERARAAGCSVIDLSGALE 1dih 81 :RPEGTLNHLAFCRQHGKGMVIGTTGFD T0298 113 :NAERLASQA 1dih 110 :GKQAIRDAA T0298 122 :APFLLSSPC 1dih 120 :DIAIVFAAN T0298 132 :VAAELCEVLAPLLATL 1dih 129 :FSVGVNVMLKLLEKAA T0298 150 :R 1dih 152 :D T0298 152 :LNLTACL 1dih 153 :IEIIEAH T0298 159 :SVSSLGREGVKELARQ 1dih 166 :APSGTALAMGEAIAHA T0298 182 :RPLEPRL 1dih 182 :LDKDLKD T0298 196 :NLLAQVGAVDAEG 1dih 189 :CAVYSREGHTGER T0298 224 :LGE 1dih 202 :VPG T0298 232 :NVTCIQ 1dih 207 :GFATVR T0298 243 :GDSLSVTLQ 1dih 217 :VGEHTAMFA T0298 288 :GQDETYVGRVRAGQ 1dih 226 :DIGERLEITHKASS T0298 317 :RKGAALNAVLLGELLI 1dih 240 :RMTFANGAVRSALWLS Number of specific fragments extracted= 21 number of extra gaps= 4 total=2045 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 1dih/T0298-1dih-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0298 read from 1dih/T0298-1dih-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1dih read from 1dih/T0298-1dih-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1dih in template set Warning: unaligning (T0298)S2 because of BadResidue code TOO_FEW_ATOMS+BAD_PEPTIDE at template residue (1dih)D3 Warning: unaligning (T0298)A43 because of BadResidue code BAD_PEPTIDE at template residue (1dih)A49 Warning: unaligning (T0298)Q45 because of BadResidue code BAD_PEPTIDE in next template residue (1dih)L52 Warning: unaligning (T0298)R46 because of BadResidue code BAD_PEPTIDE at template residue (1dih)L52 Warning: unaligning (T0298)A73 because of BadResidue code BAD_PEPTIDE in next template residue (1dih)T80 Warning: unaligning (T0298)A74 because of BadResidue code BAD_PEPTIDE at template residue (1dih)T80 Warning: unaligning (T0298)D148 because of BadResidue code BAD_PEPTIDE in next template residue (1dih)T151 Warning: unaligning (T0298)C149 because of BadResidue code BAD_PEPTIDE at template residue (1dih)T151 Warning: unaligning (T0298)P230 because of BadResidue code BAD_PEPTIDE in next template residue (1dih)I206 Warning: unaligning (T0298)L231 because of BadResidue code BAD_PEPTIDE at template residue (1dih)I206 T0298 3 :QPLNVAVVGATGSVGEALVGLLD 1dih 4 :ANIRVAIAGAGGRMGRQLIQAAL T0298 28 :DFPLHRLHL 1dih 27 :ALEGVQLGA T0298 37 :LASAES 1dih 37 :LEREGS T0298 44 :G 1dih 50 :G T0298 47 :MGFAESSLR 1dih 53 :AGAGKTGVT T0298 56 :VGDVDSF 1dih 63 :QSSLDAV T0298 64 :FSSVGLAFF 1dih 70 :KDDFDVFID T0298 75 :AAEVSRAHAERARAAGCSVIDLSGALE 1dih 81 :RPEGTLNHLAFCRQHGKGMVIGTTGFD T0298 114 :AERLASQAAPFLLSSP 1dih 111 :KQAIRDAAADIAIVFA T0298 130 :CAVAA 1dih 128 :NFSVG T0298 136 :LCEVLAPLLATL 1dih 133 :VNVMLKLLEKAA T0298 151 :QLNLTACL 1dih 152 :DIEIIEAH T0298 159 :SVSSLGREGVKELARQTA 1dih 166 :APSGTALAMGEAIAHALD T0298 182 :RPLEPRLFD 1dih 184 :KDLKDCAVY T0298 205 :DAEGHSAI 1dih 193 :SREGHTGE T0298 226 :ERIG 1dih 201 :RVPG T0298 232 :NVTCIQ 1dih 207 :GFATVR T0298 245 :SLSVTLQCA 1dih 217 :VGEHTAMFA T0298 275 :GEGD 1dih 226 :DIGE T0298 292 :TYVGRVRAGQ 1dih 230 :RLEITHKASS T0298 317 :RKGAALNAVLLGELLIK 1dih 240 :RMTFANGAVRSALWLSG Number of specific fragments extracted= 21 number of extra gaps= 6 total=2066 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 1dih/T0298-1dih-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0298 read from 1dih/T0298-1dih-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1dih read from 1dih/T0298-1dih-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1dih in template set Warning: unaligning (T0298)S2 because of BadResidue code TOO_FEW_ATOMS+BAD_PEPTIDE at template residue (1dih)D3 Warning: unaligning (T0298)G44 because of BadResidue code BAD_PEPTIDE in next template residue (1dih)G46 Warning: unaligning (T0298)Q45 because of BadResidue code BAD_PEPTIDE at template residue (1dih)G46 Warning: unaligning (T0298)A73 because of BadResidue code BAD_PEPTIDE in next template residue (1dih)T80 Warning: unaligning (T0298)A74 because of BadResidue code BAD_PEPTIDE at template residue (1dih)T80 Warning: unaligning (T0298)C149 because of BadResidue code BAD_PEPTIDE in next template residue (1dih)T151 Warning: unaligning (T0298)R150 because of BadResidue code BAD_PEPTIDE at template residue (1dih)T151 Warning: unaligning (T0298)P230 because of BadResidue code BAD_PEPTIDE in next template residue (1dih)I206 Warning: unaligning (T0298)L231 because of BadResidue code BAD_PEPTIDE at template residue (1dih)I206 T0298 3 :QPLNVAVVGATGSVGEALVGLLDERDFPLHRLHLLASAESA 1dih 4 :ANIRVAIAGAGGRMGRQLIQAALALEGVQLGAALEREGSSL T0298 46 :R 1dih 47 :S T0298 47 :MGFAESSLRVGDVDSFDFSSVGLAFF 1dih 53 :AGAGKTGVTVQSSLDAVKDDFDVFID T0298 75 :AAEVSRAHAERARAAGCSVIDLSGALE 1dih 81 :RPEGTLNHLAFCRQHGKGMVIGTTGFD T0298 113 :NAERLASQ 1dih 110 :GKQAIRDA T0298 121 :AAPFLLSSPCAV 1dih 119 :ADIAIVFAANFS T0298 134 :AELCEVLAPLLATLD 1dih 131 :VGVNVMLKLLEKAAK T0298 151 :QLNLTACL 1dih 152 :DIEIIEAH T0298 162 :SLGREGVKELARQTAELLNARPLEPRLFDRQ 1dih 165 :DAPSGTALAMGEAIAHALDKDLKDCAVYSRE T0298 203 :AVDAEGH 1dih 196 :GHTGERV T0298 228 :IG 1dih 203 :PG T0298 232 :NVTCIQ 1dih 207 :GFATVR T0298 276 :EGDYP 1dih 213 :AGDIV T0298 292 :TYVGRVRAGQADPCQVN 1dih 218 :GEHTAMFADIGERLEIT T0298 317 :RKGAALNAVLLGELL 1dih 240 :RMTFANGAVRSALWL Number of specific fragments extracted= 15 number of extra gaps= 5 total=2081 Will force an alignment to be made, even if fragment is small Number of alignments=117 # command:CPU_time= 50.152 sec, elapsed time= 54.856 sec. # command:Using radius: 8.000 NUMB_ALIGNS: 117 Adding 56280 constraints to all_contacts Done adding distance constraints # command:CPU_time= 50.432 sec, elapsed time= 55.160 sec. # command:Reading probabilities from T0298.t06.CB8-sep9.rdb Reading constraints from ConstraintSet all_contacts maxweight: 45.721 Optimizing... Probability sum: -587.091, CN propb: -587.091 weights: 0.362 constraints: 1259 # command:CPU_time= 956.349 sec, elapsed time= 961.672 sec. # command:Found ConstraintSet # PrintContacts log_align.constraints Number of constraints in align 1259 # command:Found ConstraintSet # PrintContacts log_align_bonus.constraints Number of constraints in align.bonus 1259 # command:Found ConstraintSet # PrintContacts log_rejected.constraints Number of constraints in rejected 4309 # command:Found ConstraintSet # PrintContacts log_rejected_bonus.constraints Number of constraints in rejected.bonus 4309 # command:Found ConstraintSet # PrintContacts log_noncontact.constraints Number of constraints in noncontact 48060 # command:Found ConstraintSet # PrintContacts log_noncontact_bonus.constraints Number of constraints in noncontact.bonus 48060 # command:CPU_time= 957.338 sec, elapsed time= 963.321 sec. # command: