parameters: 0.6 1.3 0.5 200 50 # command:# Prefix for input files set to /projects/compbio/experiments/undertaker/atoms-inputs/ # command:# reading dunbrack-2191.atoms # #computed average backbone with maximum peptide_sq_deviance = 0.002 # computed average trans backbone unit from 53157 examples # computed average trans backbone unit before proline from 2010 examples # computed average cis backbone unit from 97 examples # trans (non-proline) backbone unit: # CA= -2.2087 1.0126 -0.0030 # O= -0.1499 2.2440 0.0016 # C= -0.6889 1.1368 -0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4581 -0.0000 0.0000 # cis backbone unit: # CA= -0.1436 2.4534 -0.0002 # O= -2.0284 0.9742 0.0015 # C= -0.8018 1.0771 -0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4668 0.0000 0.0000 # trans backbone unit before proline: # CA= -2.2100 1.0631 -0.0014 # O= -0.1236 2.2458 0.0075 # C= -0.6872 1.1517 -0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4660 0.0000 0.0000 # After reading dunbrack-2191.atoms have 2191 chains in training database # Count of chains,residues,atoms: 2191,500310,3902258 # 493341 residues have no bad marker # 3226 residues lack atoms needed to compute omega # 1453 residues have cis peptide # number of each bad type: # NON_STANDARD_RESIDUE 4 # HAS_OXT 1167 # TOO_MANY_ATOMS 1 # TOO_FEW_ATOMS 3052 # HAS_UNKNOWN_ATOMS 9 # HAS_DUPLICATE_ATOMS 0 # CHAIN_BREAK_BEFORE 979 # NON_PLANAR_PEPTIDE 888 # BAD_PEPTIDE 2680 # Note: may sum to more than number of residues, # because one residue may have multiple problems # command:# Reading rotamer library from dunbrack-2191.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 /projects/compbio/experiments/protein-predict/casp7/T0286/ # command:# Making conformation for sequence T0286 numbered 1 through 205 Created new target T0286 from T0286.a2m # command:# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/T0286/ # command:Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0286//projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0286/manyalignments-good-all.under or /projects/compbio/experiments/protein-predict/casp7/T0286//projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0286/manyalignments-good-all.under.gz for input Trying /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0286/manyalignments-good-all.under # reading script from file /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0286/manyalignments-good-all.under # Reading fragments from alignment file # Attempting to read fragment alignments from file 1yzfA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1yzfA expands to /projects/compbio/data/pdb/1yzf.pdb.gz 1yzfA:# T0286 read from 1yzfA/merged-good-all-a2m # 1yzfA read from 1yzfA/merged-good-all-a2m # adding 1yzfA to template set # found chain 1yzfA in template set T0286 6 :IKIMPVGDSCTEGMGG 1yzfA 2 :RKIVLFGDSITAGYLD # choosing archetypes in rotamer library T0286 22 :GEMGSYRTELYRLLTQAGL 1yzfA 19 :AVSPVLVDLVKRDIAAMGL T0286 41 :SIDFVGS 1yzfA 39 :EVAVINA T0286 62 :GHSGWTIPQIASNINNWLNTHNPDVVFLWIGGNDLLLNGNLN 1yzfA 46 :GMPGDTTEDGLKRLNKEVLIEKPDEVVIFFGANDASLDRNIT T0286 104 :ATGLSNLIDQI 1yzfA 92 :RENLETMIHEI T0286 120 :NVT 1yzfA 103 :GSE T0286 123 :LFVADYYPW 1yzfA 107 :VILITPPYA T0286 132 :PEAIKQYNAVIPGIVQQKANAG 1yzfA 121 :PERPQTRIKELVKVAQEVGAAH T0286 155 :KVYFVKLSEIQFD 1yzfA 143 :NLPVIDLYKAMTV T0286 168 :RNTDISWDGLHLSEIGYKKIANIWYKYTIDILRALA 1yzfA 159 :TDEFLQADGLHFSQVGYELLGALIVREIKGRLKPKQ Number of specific fragments extracted= 10 number of extra gaps= 0 total=10 Number of alignments=1 # 1yzfA read from 1yzfA/merged-good-all-a2m # found chain 1yzfA in template set Warning: unaligning (T0286)T5 because first residue in template chain is (1yzfA)M1 T0286 6 :IKIMPVGDSCTEGMGGGEMG 1yzfA 2 :RKIVLFGDSITAGYLDEAVS T0286 26 :SYRTELYRLLTQAGL 1yzfA 23 :VLVDLVKRDIAAMGL T0286 41 :SIDFVGS 1yzfA 39 :EVAVINA T0286 62 :GHSGWTIPQIASNINNWLNTHNPDVVFLWIGGND 1yzfA 46 :GMPGDTTEDGLKRLNKEVLIEKPDEVVIFFGAND T0286 96 :LLLNGNLNATGLSNLIDQI 1yzfA 84 :RNITVATFRENLETMIHEI T0286 120 :NVT 1yzfA 103 :GSE T0286 123 :LFVADYYPW 1yzfA 107 :VILITPPYA T0286 132 :PEAIKQYNAVIPGIVQQKANAG 1yzfA 121 :PERPQTRIKELVKVAQEVGAAH T0286 155 :KVYFVKLSEIQFDRNT 1yzfA 143 :NLPVIDLYKAMTVYPG T0286 171 :DISWDGLHLSEIGYKKIANIWYKYTIDILRALA 1yzfA 162 :FLQADGLHFSQVGYELLGALIVREIKGRLKPKQ Number of specific fragments extracted= 10 number of extra gaps= 0 total=20 Number of alignments=2 # 1yzfA read from 1yzfA/merged-good-all-a2m # found chain 1yzfA in template set T0286 6 :IKIMPVGDSCTEGMGGGE 1yzfA 2 :RKIVLFGDSITAGYLDEA T0286 24 :MGSYRTELYRLLTQAGL 1yzfA 21 :SPVLVDLVKRDIAAMGL T0286 41 :SIDFVGSQR 1yzfA 39 :EVAVINAGM T0286 64 :SGWTIPQIASNINNWLNTHNPDVVFLWIGGNDLLLNGNLNATGLSNLIDQIFTV 1yzfA 48 :PGDTTEDGLKRLNKEVLIEKPDEVVIFFGANDASLDRNITVATFRENLETMIHE T0286 118 :KPNVTLF 1yzfA 103 :GSEKVIL T0286 126 :ADYYP 1yzfA 110 :ITPPY T0286 131 :WPEAIKQYNAVIPGIVQQKANAGKKVYFV 1yzfA 120 :RPERPQTRIKELVKVAQEVGAAHNLPVID T0286 163 :EIQF 1yzfA 151 :KAMT T0286 167 :DRNTDISWDGLHLSEIGYKKIANIWYKYT 1yzfA 158 :GTDEFLQADGLHFSQVGYELLGALIVREI Number of specific fragments extracted= 9 number of extra gaps= 0 total=29 Number of alignments=3 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1j00A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0286/1j00A/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0286/1j00A/merged-good-all-a2m.gz for input Trying 1j00A/merged-good-all-a2m Error: Couldn't open file 1j00A/merged-good-all-a2m or 1j00A/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1esc/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1esc expands to /projects/compbio/data/pdb/1esc.pdb.gz 1esc:Warning: there is no chain 1esc will retry with 1escA # T0286 read from 1esc/merged-good-all-a2m # 1esc read from 1esc/merged-good-all-a2m # adding 1esc to template set # found chain 1esc in template set Warning: unaligning (T0286)K4 because first residue in template chain is (1esc)D4 Warning: unaligning (T0286)G12 because of BadResidue code BAD_PEPTIDE in next template residue (1esc)D13 Warning: unaligning (T0286)D13 because of BadResidue code BAD_PEPTIDE at template residue (1esc)D13 Warning: unaligning (T0286)A140 because of BadResidue code BAD_PEPTIDE in next template residue (1esc)R226 Warning: unaligning (T0286)V141 because of BadResidue code BAD_PEPTIDE at template residue (1esc)R226 T0286 5 :TIKIMPV 1esc 5 :PVPTVFF T0286 14 :SCTEGMGGGEMG 1esc 14 :SYTANFGIAPVT T0286 26 :SYRTELYRLLTQAGLSIDFVGS 1esc 40 :NYPAVATRSLADKGITLDVQAD T0286 61 :EGHSGWTIPQIA 1esc 62 :VSCGGALIHHFW T0286 73 :SNI 1esc 90 :DAL T0286 81 :THNPDVVFLWIGGNDLLLNGNLN 1esc 93 :KQDTQLTVGSLGGNTLGFNRILK T0286 104 :ATGLSNLIDQIFTVKPNVTLFVADYYPW 1esc 162 :GAELEELLDRIGYFAPDAKRVLVGYPRL T0286 132 :PEAIKQYN 1esc 217 :LPVLDQIQ T0286 142 :IPGIVQQKANAG 1esc 227 :LNDAMKKAAADG T0286 155 :KVYFVKLSEIQFD 1esc 239 :GADFVDLYAGTGA T0286 169 :NTDISWDGLHLSEIGYKKIANIWYKYTIDIL 1esc 274 :LGTKIPWYAHPNDKGRDIQAKQVADKIEEIL Number of specific fragments extracted= 11 number of extra gaps= 2 total=40 Number of alignments=4 # 1esc read from 1esc/merged-good-all-a2m # found chain 1esc in template set Warning: unaligning (T0286)K4 because first residue in template chain is (1esc)D4 Warning: unaligning (T0286)G12 because of BadResidue code BAD_PEPTIDE in next template residue (1esc)D13 Warning: unaligning (T0286)D13 because of BadResidue code BAD_PEPTIDE at template residue (1esc)D13 Warning: unaligning (T0286)A140 because of BadResidue code BAD_PEPTIDE in next template residue (1esc)R226 Warning: unaligning (T0286)V141 because of BadResidue code BAD_PEPTIDE at template residue (1esc)R226 T0286 5 :TIKIMPV 1esc 5 :PVPTVFF T0286 14 :SCTEGMGGGEMG 1esc 14 :SYTANFGIAPVT T0286 26 :SYRTELYRLLTQAGLSIDFVGSQ 1esc 40 :NYPAVATRSLADKGITLDVQADV T0286 62 :GHSGWTIPQIAS 1esc 63 :SCGGALIHHFWE T0286 74 :NINNWLNT 1esc 87 :PQQDALKQ T0286 83 :NPDVVFLWIGGND 1esc 95 :DTQLTVGSLGGNT T0286 96 :LLLN 1esc 134 :GDEP T0286 100 :GNLNATGLSNLIDQIFTVKPNVTLFVADYYPW 1esc 158 :FERVGAELEELLDRIGYFAPDAKRVLVGYPRL T0286 132 :PEAIKQYN 1esc 217 :LPVLDQIQ T0286 142 :IPGIVQQKANAG 1esc 227 :LNDAMKKAAADG T0286 155 :KVYFVKLSEIQFDRNT 1esc 239 :GADFVDLYAGTGANTA T0286 172 :ISW 1esc 278 :IPW T0286 176 :GLHLSEIGYKKIANIWYKYTIDIL 1esc 281 :YAHPNDKGRDIQAKQVADKIEEIL Number of specific fragments extracted= 13 number of extra gaps= 2 total=53 Number of alignments=5 # 1esc read from 1esc/merged-good-all-a2m # found chain 1esc in template set Warning: unaligning (T0286)K4 because first residue in template chain is (1esc)D4 Warning: unaligning (T0286)G12 because of BadResidue code BAD_PEPTIDE in next template residue (1esc)D13 Warning: unaligning (T0286)D13 because of BadResidue code BAD_PEPTIDE at template residue (1esc)D13 Warning: unaligning (T0286)A140 because of BadResidue code BAD_PEPTIDE in next template residue (1esc)R226 Warning: unaligning (T0286)V141 because of BadResidue code BAD_PEPTIDE at template residue (1esc)R226 T0286 5 :TIKIMPV 1esc 5 :PVPTVFF T0286 14 :SCTEGMGGGE 1esc 14 :SYTANFGIAP T0286 24 :MGSYRTELYRLLTQAGLSIDFVGSQRSGPSSLPDK 1esc 38 :KENYPAVATRSLADKGITLDVQADVSCGGALIHHF T0286 76 :NN 1esc 73 :WE T0286 78 :WLNTHNPDVVFLWIGGNDLLLNG 1esc 90 :DALKQDTQLTVGSLGGNTLGFNR T0286 101 :NLNATGLSNLIDQIFTVKPNVTLFVADYYP 1esc 159 :ERVGAELEELLDRIGYFAPDAKRVLVGYPR T0286 131 :WPEAIKQYN 1esc 216 :ALPVLDQIQ T0286 142 :IPGIVQQKANAGKKVYF 1esc 227 :LNDAMKKAAADGGADFV T0286 160 :KLSEIQFDR 1esc 244 :DLYAGTGAN T0286 169 :NTDISWDGLHLSEIGYKKIANIWYKYTIDI 1esc 274 :LGTKIPWYAHPNDKGRDIQAKQVADKIEEI Number of specific fragments extracted= 10 number of extra gaps= 2 total=63 Number of alignments=6 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2aebA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2aebA expands to /projects/compbio/data/pdb/2aeb.pdb.gz 2aebA:Skipped atom 2231, because occupancy 0.29 <= existing 0.710 in 2aebA Skipped atom 2233, because occupancy 0.290 <= existing 0.710 in 2aebA Skipped atom 2235, because occupancy 0.290 <= existing 0.710 in 2aebA Skipped atom 2237, because occupancy 0.290 <= existing 0.710 in 2aebA Skipped atom 2239, because occupancy 0.290 <= existing 0.710 in 2aebA # T0286 read from 2aebA/merged-good-all-a2m # 2aebA read from 2aebA/merged-good-all-a2m # adding 2aebA to template set # found chain 2aebA in template set Warning: unaligning (T0286)T5 because first residue in template chain is (2aebA)S5 Warning: unaligning (T0286)I6 because of BadResidue code BAD_PEPTIDE at template residue (2aebA)R6 Warning: unaligning (T0286)K7 because of BadResidue code BAD_PEPTIDE at template residue (2aebA)T7 Warning: unaligning (T0286)Q37 because of BadResidue code BAD_PEPTIDE in next template residue (2aebA)Q43 Warning: unaligning (T0286)A38 because of BadResidue code BAD_PEPTIDE at template residue (2aebA)Q43 Warning: unaligning (T0286)G39 because of BadResidue code BAD_PEPTIDE at template residue (2aebA)E44 Warning: unaligning (T0286)L40 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2aebA)C45 Warning: unaligning (T0286)S50 because of BadResidue code BAD_PEPTIDE in next template residue (2aebA)A56 Warning: unaligning (T0286)G51 because of BadResidue code BAD_PEPTIDE at template residue (2aebA)A56 Warning: unaligning (T0286)I91 because of BadResidue code BAD_PEPTIDE in next template residue (2aebA)G99 Warning: unaligning (T0286)G92 because of BadResidue code BAD_PEPTIDE at template residue (2aebA)G99 Warning: unaligning (T0286)Y128 because of BadResidue code BAD_PEPTIDE in next template residue (2aebA)H126 Warning: unaligning (T0286)Y129 because of BadResidue code BAD_PEPTIDE at template residue (2aebA)H126 Warning: unaligning (T0286)I182 because of BadResidue code BAD_PEPTIDE in next template residue (2aebA)E256 Warning: unaligning (T0286)G183 because of BadResidue code BAD_PEPTIDE at template residue (2aebA)E256 T0286 8 :IMPVGDSCTEGMGGGEMGSYRTELYR 2aebA 8 :IGIIGAPFSKGQPRGGVEEGPTVLRK T0286 34 :LLT 2aebA 39 :KLK T0286 41 :SIDFVGSQR 2aebA 46 :DVKDYGDLP T0286 52 :PSSLPDKDHEGHSGWTIPQIA 2aebA 57 :DIPNDSPFQIVKNPRSVGKAS T0286 73 :SNINNWLNTH 2aebA 82 :GKVAEVKKNG T0286 85 :DVVFLW 2aebA 92 :RISLVL T0286 93 :GNDLLLN 2aebA 100 :DHSLAIG T0286 110 :LIDQIFTVKPNVTLFVAD 2aebA 107 :SISGHARVHPDLGVIWVD T0286 130 :PW 2aebA 127 :TD T0286 132 :PEAIKQY 2aebA 200 :MTEVDRL T0286 139 :NAVIPGIVQQKANAGK 2aebA 208 :IGKVMEETLSYLLGRK T0286 155 :KVYFVKLS 2aebA 225 :RPIHLSFD T0286 163 :EIQ 2aebA 234 :DGL T0286 168 :RNTDISWDGL 2aebA 237 :DPSFTPATGT T0286 178 :HLSE 2aebA 251 :GLTY T0286 184 :YKKIANIWYK 2aebA 257 :GLYITEEIYK Number of specific fragments extracted= 16 number of extra gaps= 5 total=79 Number of alignments=7 # 2aebA read from 2aebA/merged-good-all-a2m # found chain 2aebA in template set Warning: unaligning (T0286)T5 because first residue in template chain is (2aebA)S5 Warning: unaligning (T0286)I6 because of BadResidue code BAD_PEPTIDE at template residue (2aebA)R6 Warning: unaligning (T0286)K7 because of BadResidue code BAD_PEPTIDE at template residue (2aebA)T7 Warning: unaligning (T0286)Q37 because of BadResidue code BAD_PEPTIDE in next template residue (2aebA)Q43 Warning: unaligning (T0286)A38 because of BadResidue code BAD_PEPTIDE at template residue (2aebA)Q43 Warning: unaligning (T0286)G39 because of BadResidue code BAD_PEPTIDE at template residue (2aebA)E44 Warning: unaligning (T0286)L40 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2aebA)C45 Warning: unaligning (T0286)S50 because of BadResidue code BAD_PEPTIDE in next template residue (2aebA)A56 Warning: unaligning (T0286)G51 because of BadResidue code BAD_PEPTIDE at template residue (2aebA)A56 Warning: unaligning (T0286)I91 because of BadResidue code BAD_PEPTIDE in next template residue (2aebA)G99 Warning: unaligning (T0286)G92 because of BadResidue code BAD_PEPTIDE at template residue (2aebA)G99 Warning: unaligning (T0286)Y128 because of BadResidue code BAD_PEPTIDE in next template residue (2aebA)H126 Warning: unaligning (T0286)Y129 because of BadResidue code BAD_PEPTIDE at template residue (2aebA)H126 Warning: unaligning (T0286)I182 because of BadResidue code BAD_PEPTIDE in next template residue (2aebA)E256 Warning: unaligning (T0286)G183 because of BadResidue code BAD_PEPTIDE at template residue (2aebA)E256 T0286 8 :IMPVGDSCTEGMGGGEMGSYRTELYR 2aebA 8 :IGIIGAPFSKGQPRGGVEEGPTVLRK T0286 34 :LLT 2aebA 39 :KLK T0286 41 :SIDFVGSQR 2aebA 46 :DVKDYGDLP T0286 52 :PSSLPDKDHEGHSGWTI 2aebA 57 :DIPNDSPFQIVKNPRSV T0286 69 :PQIASNINNWLNTH 2aebA 78 :EQLAGKVAEVKKNG T0286 85 :DVVFLW 2aebA 92 :RISLVL T0286 93 :GND 2aebA 100 :DHS T0286 110 :LIDQIFTVKPNVTLFVAD 2aebA 107 :SISGHARVHPDLGVIWVD T0286 130 :PW 2aebA 127 :TD T0286 132 :PEAIKQY 2aebA 200 :MTEVDRL T0286 139 :NAVIPGIVQQKANAGK 2aebA 208 :IGKVMEETLSYLLGRK T0286 155 :KVYFVKLS 2aebA 225 :RPIHLSFD T0286 163 :EIQFDRNT 2aebA 234 :DGLDPSFT T0286 175 :DGL 2aebA 246 :TPV T0286 178 :HLSE 2aebA 251 :GLTY T0286 184 :YKKIANIWYK 2aebA 257 :GLYITEEIYK Number of specific fragments extracted= 16 number of extra gaps= 5 total=95 Number of alignments=8 # 2aebA read from 2aebA/merged-good-all-a2m # found chain 2aebA in template set Warning: unaligning (T0286)T5 because first residue in template chain is (2aebA)S5 Warning: unaligning (T0286)I6 because of BadResidue code BAD_PEPTIDE at template residue (2aebA)R6 Warning: unaligning (T0286)K7 because of BadResidue code BAD_PEPTIDE at template residue (2aebA)T7 Warning: unaligning (T0286)Q37 because of BadResidue code BAD_PEPTIDE in next template residue (2aebA)Q43 Warning: unaligning (T0286)A38 because of BadResidue code BAD_PEPTIDE at template residue (2aebA)Q43 Warning: unaligning (T0286)G39 because of BadResidue code BAD_PEPTIDE at template residue (2aebA)E44 Warning: unaligning (T0286)L40 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2aebA)C45 Warning: unaligning (T0286)S50 because of BadResidue code BAD_PEPTIDE in next template residue (2aebA)A56 Warning: unaligning (T0286)I91 because of BadResidue code BAD_PEPTIDE in next template residue (2aebA)G99 Warning: unaligning (T0286)G92 because of BadResidue code BAD_PEPTIDE at template residue (2aebA)G99 Warning: unaligning (T0286)Y128 because of BadResidue code BAD_PEPTIDE in next template residue (2aebA)H126 Warning: unaligning (T0286)Y129 because of BadResidue code BAD_PEPTIDE at template residue (2aebA)H126 Warning: unaligning (T0286)I182 because of BadResidue code BAD_PEPTIDE in next template residue (2aebA)E256 Warning: unaligning (T0286)G183 because of BadResidue code BAD_PEPTIDE at template residue (2aebA)E256 T0286 8 :IMPVGDSCTEGMGGGEMGSYRTELYR 2aebA 8 :IGIIGAPFSKGQPRGGVEEGPTVLRK T0286 34 :LLT 2aebA 39 :KLK T0286 41 :SIDFVGSQR 2aebA 46 :DVKDYGDLP T0286 51 :GPSSLPDKDHEGHSGWTIPQIASNINNWLNTHN 2aebA 60 :NDSPFQIVKNPRSVGKASEQLAGKVAEVKKNGR T0286 86 :VVFLW 2aebA 93 :ISLVL T0286 93 :GNDLLLN 2aebA 100 :DHSLAIG T0286 110 :LIDQIFTVKPNVTLFVAD 2aebA 107 :SISGHARVHPDLGVIWVD T0286 130 :P 2aebA 127 :T T0286 131 :WPEAIKQY 2aebA 199 :SMTEVDRL T0286 139 :NAVIPGIVQQKANAGKKVYFVKLSEIQFDR 2aebA 209 :GKVMEETLSYLLGRKKRPIHLSFDVDGLDP T0286 169 :NTDISWDGL 2aebA 240 :FTPATGTPV T0286 179 :LSE 2aebA 252 :LTY T0286 184 :YKKIANIWYKY 2aebA 257 :GLYITEEIYKT Number of specific fragments extracted= 13 number of extra gaps= 5 total=108 Number of alignments=9 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1xel/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1xel expands to /projects/compbio/data/pdb/1xel.pdb.gz 1xel:Warning: there is no chain 1xel will retry with 1xelA # T0286 read from 1xel/merged-good-all-a2m # 1xel read from 1xel/merged-good-all-a2m # adding 1xel to template set # found chain 1xel in template set Warning: unaligning (T0286)I6 because first residue in template chain is (1xel)M1 T0286 7 :KIMPVGD 1xel 2 :RVLVTGG T0286 24 :MGSYRTELYRLLTQAGLSIDFVGSQ 1xel 9 :SGYIGSHTCVQLLQNGHDVIILDNL T0286 62 :GHSGWTIPQIA 1xel 34 :CNSKRSVLPVI T0286 73 :SNINNWLNTHNPDVVFLWIGGNDLL 1xel 63 :ALMTEILHDHAIDTVIHFAGLKAVG T0286 104 :ATGLSNLIDQIFTV 1xel 101 :VNGTLRLISAMRAA T0286 120 :NVTLFVADYYPW 1xel 115 :NVKNFIFSSSAT T0286 132 :PEAIKQYNAVIPGIVQQKANAGKKVYFV 1xel 146 :QSPYGKSKLMVEQILTDLQKAQPDWSIA T0286 160 :KLSEIQFD 1xel 176 :RYFNPVGA T0286 168 :RNTDISW 1xel 223 :PTEDGTG T0286 175 :DGLHLSE 1xel 232 :DYIHVMD T0286 182 :IGYKKIANIW 1xel 241 :DGHVVAMEKL T0286 192 :YKYTIDILRALAGE 1xel 269 :VLDVVNAFSKACGK Number of specific fragments extracted= 12 number of extra gaps= 0 total=120 Number of alignments=10 # 1xel read from 1xel/merged-good-all-a2m # found chain 1xel in template set Warning: unaligning (T0286)I6 because first residue in template chain is (1xel)M1 T0286 7 :KIMPVGDSCT 1xel 2 :RVLVTGGSGY T0286 27 :YRTELYRLLTQAGLSIDFVGSQ 1xel 12 :IGSHTCVQLLQNGHDVIILDNL T0286 62 :GHSGWTIPQIAS 1xel 34 :CNSKRSVLPVIE T0286 74 :NINNWLNTHNPDVVFLWIGGND 1xel 64 :LMTEILHDHAIDTVIHFAGLKA T0286 99 :NGNLNATG 1xel 92 :KPLEYYDN T0286 107 :LSNLIDQIFTV 1xel 104 :TLRLISAMRAA T0286 120 :NVTLFVADYYPW 1xel 115 :NVKNFIFSSSAT T0286 132 :PEAIKQYNAVIPGIVQQKANAGKKVYFV 1xel 146 :QSPYGKSKLMVEQILTDLQKAQPDWSIA T0286 160 :KLSEIQFDRNT 1xel 176 :RYFNPVGAHPS T0286 171 :DISWDGLHLS 1xel 228 :TGVRDYIHVM T0286 181 :EIGYKKIANIW 1xel 240 :ADGHVVAMEKL T0286 192 :YKYTIDILRALAGE 1xel 269 :VLDVVNAFSKACGK Number of specific fragments extracted= 12 number of extra gaps= 0 total=132 Number of alignments=11 # 1xel read from 1xel/merged-good-all-a2m # found chain 1xel in template set T0286 2 :ASKTIKIMP 1xel 23 :NGHDVIILD T0286 18 :GMGGGE 1xel 33 :LCNSKR T0286 24 :MGSYRTELYRLLTQAGLSIDFVGSQRS 1xel 58 :DIRNEALMTEILHDHAIDTVIHFAGLK T0286 67 :TIPQIASNINN 1xel 92 :KPLEYYDNNVN T0286 78 :WLNTHNPDVVFLWIGGNDLLLNG 1xel 110 :AMRAANVKNFIFSSSATVYGDNP T0286 101 :NLNATGLSNLIDQIFTV 1xel 147 :SPYGKSKLMVEQILTDL T0286 118 :KPNVTLFVADYYP 1xel 167 :QPDWSIALLRYFN T0286 131 :WPEAIK 1xel 197 :PNNLMP T0286 145 :IVQQKANAGKKVYFVKLSEIQFDRNT 1xel 203 :YIAQVAVGRRDSLAIFGNDYPTEDGT T0286 172 :ISWDGLH 1xel 229 :GVRDYIH T0286 184 :YKKIANIW 1xel 236 :VMDLADGH T0286 196 :IDILRALAG 1xel 244 :VVAMEKLAN Number of specific fragments extracted= 12 number of extra gaps= 0 total=144 Number of alignments=12 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1vbuA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1vbuA expands to /projects/compbio/data/pdb/1vbu.pdb.gz 1vbuA:# T0286 read from 1vbuA/merged-good-all-a2m # 1vbuA read from 1vbuA/merged-good-all-a2m # adding 1vbuA to template set # found chain 1vbuA in template set Warning: unaligning (T0286)D13 because of BadResidue code BAD_PEPTIDE in next template residue (1vbuA)T599 Warning: unaligning (T0286)S14 because of BadResidue code BAD_PEPTIDE at template residue (1vbuA)T599 Warning: unaligning (T0286)L202 because last residue in template chain is (1vbuA)R840 T0286 10 :PVG 1vbuA 595 :VHG T0286 15 :CTEGMGGGE 1vbuA 600 :LVWHNQLPG T0286 26 :SYRTELYRLLTQAGLSIDF 1vbuA 667 :EYIEKAFRWAKEADPDAIL T0286 45 :VGSQRS 1vbuA 687 :YNDYSI T0286 62 :GHSGWTIPQIASNINNWLNTH 1vbuA 693 :EEINAKSNFVYNMIKELKEKG T0286 83 :NPDVVFLWIGGN 1vbuA 715 :PVDGIGFQMHID T0286 99 :NGNLNATGLSNLIDQIFTV 1vbuA 727 :YRGLNYDSFRRNLERFAKL T0286 120 :NVTLFVADYYPW 1vbuA 746 :GLQIYITEMDVR T0286 132 :PEAIKQYNAVIPGIVQQKAN 1vbuA 761 :SGSEEYYLKKQAEVCAKIFD T0286 152 :AGKKVYFVKLSEIQFD 1vbuA 784 :DNPAVKAIQFWGFTDK T0286 169 :NTDISWDGLHLSE 1vbuA 812 :KALLFDENYNPKP T0286 187 :IANIWYKYTIDILRA 1vbuA 825 :CYYAIKEVLEKKIEE Number of specific fragments extracted= 12 number of extra gaps= 1 total=156 Number of alignments=13 # 1vbuA read from 1vbuA/merged-good-all-a2m # found chain 1vbuA in template set Warning: unaligning (T0286)V45 because of BadResidue code BAD_PEPTIDE in next template residue (1vbuA)T599 Warning: unaligning (T0286)G46 because of BadResidue code BAD_PEPTIDE at template residue (1vbuA)T599 Warning: unaligning (T0286)L202 because last residue in template chain is (1vbuA)R840 T0286 6 :IKIMPVG 1vbuA 528 :IYIGFAA T0286 17 :EGMGGGEMG 1vbuA 535 :INNFWSLSD T0286 26 :SYRTELYRLLTQAGLSIDF 1vbuA 579 :TPAEKHVEFAEENDMIVHG T0286 47 :SQRSGPSSLP 1vbuA 600 :LVWHNQLPGW T0286 74 :NINNWLNTHNP 1vbuA 705 :MIKELKEKGVP T0286 85 :DVVFLWIGGNDLLLNGNLN 1vbuA 717 :DGIGFQMHIDYRGLNYDSF T0286 108 :SNLIDQIFTV 1vbuA 736 :RRNLERFAKL T0286 120 :NVTLFVADYYPW 1vbuA 746 :GLQIYITEMDVR T0286 132 :PEAIKQYNAVIPGIVQQ 1vbuA 761 :SGSEEYYLKKQAEVCAK T0286 149 :KANAGKKVYFVKLSEIQFDRNT 1vbuA 781 :ICLDNPAVKAIQFWGFTDKYSW T0286 171 :DISWDGLHLSE 1vbuA 814 :LLFDENYNPKP T0286 187 :IANIWYKYTIDILRA 1vbuA 825 :CYYAIKEVLEKKIEE Number of specific fragments extracted= 12 number of extra gaps= 1 total=168 Number of alignments=14 # 1vbuA read from 1vbuA/merged-good-all-a2m # found chain 1vbuA in template set Warning: unaligning (T0286)V45 because of BadResidue code BAD_PEPTIDE in next template residue (1vbuA)T599 Warning: unaligning (T0286)G46 because of BadResidue code BAD_PEPTIDE at template residue (1vbuA)T599 T0286 29 :TELYRLLTQAGLSIDF 1vbuA 582 :EKHVEFAEENDMIVHG T0286 47 :SQRSGPSSLPDKDH 1vbuA 600 :LVWHNQLPGWITGR T0286 65 :GWTIPQIASNINN 1vbuA 614 :EWTKEELLNVLED T0286 78 :WLNTHNPDVVFLWIGGN 1vbuA 710 :KEKGVPVDGIGFQMHID T0286 101 :NLNATGLSNLIDQIFTV 1vbuA 729 :GLNYDSFRRNLERFAKL T0286 120 :NVTLFVADYYP 1vbuA 746 :GLQIYITEMDV T0286 131 :WPEAIKQYNAVIPGIVQQKANAGKKVYFVKLS 1vbuA 764 :EEYYLKKQAEVCAKIFDICLDNPAVKAIQFWG T0286 164 :IQ 1vbuA 796 :FT T0286 169 :NTDISWDGLHLSE 1vbuA 812 :KALLFDENYNPKP T0286 187 :IANIWYKYTIDILR 1vbuA 825 :CYYAIKEVLEKKIE Number of specific fragments extracted= 10 number of extra gaps= 1 total=178 Number of alignments=15 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1udc/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1udc expands to /projects/compbio/data/pdb/1udc.pdb.gz 1udc:Warning: there is no chain 1udc will retry with 1udcA # T0286 read from 1udc/merged-good-all-a2m # 1udc read from 1udc/merged-good-all-a2m # adding 1udc to template set # found chain 1udc in template set Warning: unaligning (T0286)I6 because first residue in template chain is (1udc)M1 T0286 7 :KIMPVGDS 1udc 2 :RVLVTGGS T0286 25 :GSYRTELYRLLTQAGLSIDFVGSQ 1udc 10 :GYIGSHTCVQLLQNGHDVIILDNL T0286 62 :GHSGWTIPQIA 1udc 34 :CNSKRSVLPVI T0286 73 :SNINNWLNTHNPDVVFLWIGGNDLL 1udc 63 :ALMTEILHDHAIDTVIHFAGLKAVG T0286 104 :ATGLSNLIDQIFTV 1udc 101 :VNGTLRLISAMRAA T0286 120 :NVTLFVADYYPW 1udc 115 :NVKNFIFSSSAT T0286 132 :PEAIKQYNAVIPGIVQQKANAGKKVYFV 1udc 146 :QSPYGKSKLMVEQILTDLQKAQPDWSIA T0286 160 :KLSEIQFD 1udc 176 :RYFNPVGA T0286 170 :TDISW 1udc 225 :EDGTG T0286 175 :DGLHLSE 1udc 232 :DYIHVMD T0286 182 :IGYKKIANIW 1udc 241 :DGHVVAMEKL T0286 192 :YKYTIDILRALAGE 1udc 269 :VLDVVNAFSKACGK Number of specific fragments extracted= 12 number of extra gaps= 0 total=190 Number of alignments=16 # 1udc read from 1udc/merged-good-all-a2m # found chain 1udc in template set Warning: unaligning (T0286)I6 because first residue in template chain is (1udc)M1 T0286 7 :KIMPVGDSCT 1udc 2 :RVLVTGGSGY T0286 27 :YRTELYRLLTQAGLSIDFVGSQ 1udc 12 :IGSHTCVQLLQNGHDVIILDNL T0286 62 :GHSGWTIPQIAS 1udc 34 :CNSKRSVLPVIE T0286 74 :NINNWLNTHNPDVVFLWIGGND 1udc 64 :LMTEILHDHAIDTVIHFAGLKA T0286 99 :NGNLNATG 1udc 92 :KPLEYYDN T0286 107 :LSNLIDQIFTV 1udc 104 :TLRLISAMRAA T0286 120 :NVTLFVADYYPW 1udc 115 :NVKNFIFSSSAT T0286 132 :PEAIKQYNAVIPGIVQQKANAGK 1udc 146 :QSPYGKSKLMVEQILTDLQKAQP T0286 155 :KVYFVKLSEIQFDRNT 1udc 171 :SIALLRYFNPVGAHPS T0286 171 :DISWDGLHLS 1udc 228 :TGVRDYIHVM T0286 181 :EIGYKKIANIW 1udc 240 :ADGHVVAMEKL T0286 192 :YKYTIDILRAL 1udc 269 :VLDVVNAFSKA Number of specific fragments extracted= 12 number of extra gaps= 0 total=202 Number of alignments=17 # 1udc read from 1udc/merged-good-all-a2m # found chain 1udc in template set T0286 2 :ASKTIKIMP 1udc 23 :NGHDVIILD T0286 18 :GMGGGE 1udc 33 :LCNSKR T0286 24 :MGSYRTELYRLLTQAGLSIDFVGSQRS 1udc 58 :DIRNEALMTEILHDHAIDTVIHFAGLK T0286 67 :TIPQIASNINN 1udc 92 :KPLEYYDNNVN T0286 78 :WLNTHNPDVVFLWIGGNDLLLNG 1udc 110 :AMRAANVKNFIFSSSATVYGDQP T0286 101 :NLNATGLSNLIDQIFTV 1udc 147 :SPYGKSKLMVEQILTDL T0286 118 :KPNVTLFVADYYP 1udc 167 :QPDWSIALLRYFN T0286 132 :PEAIK 1udc 198 :NNLMP T0286 145 :IVQQKANAGKKVYFVKLSEIQFDR 1udc 203 :YIAQVAVGRRDSLAIFGNDYPTED T0286 170 :TDISWDGLH 1udc 227 :GTGVRDYIH T0286 188 :ANIWYKYTIDILRALAGE 1udc 236 :VMDLADGHVVAMEKLANK Number of specific fragments extracted= 11 number of extra gaps= 0 total=213 Number of alignments=18 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1oy1A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1oy1A expands to /projects/compbio/data/pdb/1oy1.pdb.gz 1oy1A:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0286 read from 1oy1A/merged-good-all-a2m # 1oy1A read from 1oy1A/merged-good-all-a2m # adding 1oy1A to template set # found chain 1oy1A in template set T0286 6 :IKIMPVG 1oy1A 5 :KKIGVIL T0286 15 :CTEGMGGGEMGSYRTELYRLLTQAGLSIDFVGSQRSGPSSLPDKD 1oy1A 12 :SGCGVYDGSEIHEAVLTLLAISRSGAQAVCFAPDKQQVDVINHLT T0286 62 :GHSGWTIPQIASNINNWL 1oy1A 57 :GEAMTETRNVLIEAARIT T0286 80 :NTHN 1oy1A 82 :AQAD T0286 84 :PDVVFLWIGGNDLLLNGNLN 1oy1A 89 :LDALIVPGGFGAAKNLSNFA T0286 104 :ATGLSNLIDQIFTV 1oy1A 117 :DRELKALAQAMHQA T0286 120 :NVTLFVADYYPW 1oy1A 131 :GKPLGFMCIAPA T0286 132 :PEA 1oy1A 159 :DID T0286 146 :VQQKANAG 1oy1A 162 :TAEVLEEM T0286 155 :KVYFVKLS 1oy1A 170 :GAEHVPCP T0286 163 :EIQFD 1oy1A 180 :DIVVD T0286 177 :LHLSEIGYKKIANIWYKYTIDILR 1oy1A 197 :LAQNIAEAASGIDKLVSRVLVLAE Number of specific fragments extracted= 12 number of extra gaps= 0 total=225 Number of alignments=19 # 1oy1A read from 1oy1A/merged-good-all-a2m # found chain 1oy1A in template set Warning: unaligning (T0286)T5 because first residue in template chain is (1oy1A)M4 T0286 6 :IKIMPVGD 1oy1A 5 :KKIGVILS T0286 17 :EGMGGGEMGSYRTELYRLLTQAGLSIDFVGSQRSGPSSLPDKD 1oy1A 14 :CGVYDGSEIHEAVLTLLAISRSGAQAVCFAPDKQQVDVINHLT T0286 62 :GHSGWTIPQIASNINNWLNT 1oy1A 57 :GEAMTETRNVLIEAARITRG T0286 83 :N 1oy1A 77 :E T0286 84 :PDVVFLWIGGND 1oy1A 89 :LDALIVPGGFGA T0286 96 :LLLN 1oy1A 114 :CTVD T0286 105 :TGLSNLIDQIFTV 1oy1A 118 :RELKALAQAMHQA T0286 120 :NVTLFVADYYPW 1oy1A 131 :GKPLGFMCIAPA T0286 132 :PEA 1oy1A 159 :DID T0286 146 :VQQKANAG 1oy1A 162 :TAEVLEEM T0286 155 :KVYFVKLS 1oy1A 170 :GAEHVPCP T0286 163 :EIQFDRNT 1oy1A 180 :DIVVDEDN T0286 171 :DISWD 1oy1A 195 :YMLAQ T0286 180 :SEIGYKKIANIWYKYTIDIL 1oy1A 200 :NIAEAASGIDKLVSRVLVLA Number of specific fragments extracted= 14 number of extra gaps= 0 total=239 Number of alignments=20 # 1oy1A read from 1oy1A/merged-good-all-a2m # found chain 1oy1A in template set T0286 4 :KTIKIMPVG 1oy1A 5 :KKIGVILSG T0286 17 :EGMGGGEMGSYRTELYRLLTQAGLSIDFVGSQRSGPSSLPDKDHEGHSG 1oy1A 14 :CGVYDGSEIHEAVLTLLAISRSGAQAVCFAPDKQQVDVINHLTGEAMTE T0286 66 :WTIPQIASNINN 1oy1A 64 :RNVLIEAARITR T0286 78 :WLNTHNPDVVFLWIGGN 1oy1A 83 :QADAAELDALIVPGGFG T0286 96 :LLLNG 1oy1A 100 :AAKNL T0286 101 :NLNATGLSNLIDQIFT 1oy1A 114 :CTVDRELKALAQAMHQ T0286 119 :PNVTLFVADYYP 1oy1A 130 :AGKPLGFMCIAP T0286 131 :WPE 1oy1A 159 :DID T0286 146 :VQQKANAGKKVYFVKLSEIQF 1oy1A 162 :TAEVLEEMGAEHVPCPVDDIV T0286 169 :NTDISWDG 1oy1A 193 :PAYMLAQN T0286 181 :EIGYKKIANIWYKYT 1oy1A 205 :ASGIDKLVSRVLVLA Number of specific fragments extracted= 11 number of extra gaps= 0 total=250 Number of alignments=21 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ivnA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1ivnA expands to /projects/compbio/data/pdb/1ivn.pdb.gz 1ivnA:# T0286 read from 1ivnA/merged-good-all-a2m # 1ivnA read from 1ivnA/merged-good-all-a2m # adding 1ivnA to template set # found chain 1ivnA in template set Warning: unaligning (T0286)T5 because first residue in template chain is (1ivnA)A1 Warning: unaligning (T0286)L35 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ivnA)S33 Warning: unaligning (T0286)Q37 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ivnA)S33 T0286 6 :IKIMPVGDSCTEGMGGGEMGSYRTELYRL 1ivnA 2 :DTLLILGDSLSAGYRMSASAAWPALLNDK T0286 41 :SIDFVGS 1ivnA 34 :KTSVVNA T0286 62 :GHSGWTIPQIASNINNWLNTHNPDVVFLWIGGNDLLLNGNLN 1ivnA 41 :SISGDTSQQGLARLPALLKQHQPRWVLVELGGNDGLRGFQPQ T0286 104 :ATGLSNLIDQIFTV 1ivnA 85 :EQTLRQILQDVKAA T0286 120 :NVTLFVADYYPWPEAIKQYNAVIPGIVQQKANAGK 1ivnA 99 :NAEPLLMQIRLPANYGRRYNEAFSAIYPKLAKEFD T0286 156 :VYFVKLS 1ivnA 134 :VPLLPFF T0286 163 :EIQFDRNTDISWDGLHLSEIGYKKIANIWYKYTI 1ivnA 142 :EEVYLKPQWMQDDGIHPNRDAQPFIADWMAKQLQ Number of specific fragments extracted= 7 number of extra gaps= 0 total=257 Number of alignments=22 # 1ivnA read from 1ivnA/merged-good-all-a2m # found chain 1ivnA in template set Warning: unaligning (T0286)T5 because first residue in template chain is (1ivnA)A1 Warning: unaligning (T0286)L35 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ivnA)S33 Warning: unaligning (T0286)L40 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ivnA)S33 T0286 6 :IKIMPVGDSCTEGMGGGEMGSYRTELYRL 1ivnA 2 :DTLLILGDSLSAGYRMSASAAWPALLNDK T0286 41 :SIDFVGS 1ivnA 34 :KTSVVNA T0286 62 :GHSGWTIPQIASNINNWLNTHNPDVVFLWIGGND 1ivnA 41 :SISGDTSQQGLARLPALLKQHQPRWVLVELGGND T0286 96 :LLLNGNLNATGLSNLIDQIFTV 1ivnA 77 :RGFQPQQTEQTLRQILQDVKAA T0286 120 :NVTLFVADYYPWPEAIKQYNAVIPGIVQQKANAGK 1ivnA 99 :NAEPLLMQIRLPANYGRRYNEAFSAIYPKLAKEFD T0286 156 :VYFVKLS 1ivnA 134 :VPLLPFF T0286 163 :EIQFDRNTDISWDGLHLSEIGYKKIANIWYKYTI 1ivnA 142 :EEVYLKPQWMQDDGIHPNRDAQPFIADWMAKQLQ Number of specific fragments extracted= 7 number of extra gaps= 0 total=264 Number of alignments=23 # 1ivnA read from 1ivnA/merged-good-all-a2m # found chain 1ivnA in template set Warning: unaligning (T0286)L35 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ivnA)S33 Warning: unaligning (T0286)Q37 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ivnA)S33 T0286 7 :KIMPVGDSCTEGMGGGEMGSYRTELYRL 1ivnA 3 :TLLILGDSLSAGYRMSASAAWPALLNDK T0286 41 :SIDFVGSQR 1ivnA 34 :KTSVVNASI T0286 64 :SGWTIPQIASNINNWLNTHNPDVVFLWIGGNDLLLNG 1ivnA 43 :SGDTSQQGLARLPALLKQHQPRWVLVELGGNDGLRGF T0286 101 :NLNATGLSNLIDQIFT 1ivnA 82 :QQTEQTLRQILQDVKA T0286 119 :PNVTLFVADYYPWPEAIKQYNAVIPGIVQQKANAGKKVYFVKLSEIQFDRNTDISWDGLHLSEIGYKKIANIWYKYT 1ivnA 98 :ANAEPLLMQIRLPANYGRRYNEAFSAIYPKLAKEFDVPLLPFFMEEVYLKPQWMQDDGIHPNRDAQPFIADWMAKQL Number of specific fragments extracted= 5 number of extra gaps= 0 total=269 Number of alignments=24 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1he2A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1he2A expands to /projects/compbio/data/pdb/1he2.pdb.gz 1he2A:Skipped atom 40, because occupancy 0.410 <= existing 0.590 in 1he2A Skipped atom 42, because occupancy 0.410 <= existing 0.590 in 1he2A Skipped atom 44, because occupancy 0.410 <= existing 0.590 in 1he2A Skipped atom 46, because occupancy 0.410 <= existing 0.590 in 1he2A Skipped atom 48, because occupancy 0.410 <= existing 0.590 in 1he2A Skipped atom 78, because occupancy 0.480 <= existing 0.520 in 1he2A Skipped atom 80, because occupancy 0.480 <= existing 0.520 in 1he2A Skipped atom 82, because occupancy 0.480 <= existing 0.520 in 1he2A Skipped atom 84, because occupancy 0.480 <= existing 0.520 in 1he2A Skipped atom 86, because occupancy 0.480 <= existing 0.520 in 1he2A Skipped atom 637, because occupancy 0.320 <= existing 0.680 in 1he2A Skipped atom 639, because occupancy 0.320 <= existing 0.680 in 1he2A Skipped atom 1055, because occupancy 0.350 <= existing 0.640 in 1he2A Skipped atom 1057, because occupancy 0.350 <= existing 0.640 in 1he2A Skipped atom 1059, because occupancy 0.350 <= existing 0.640 in 1he2A Skipped atom 1534, because occupancy 0.330 <= existing 0.670 in 1he2A Skipped atom 1536, because occupancy 0.330 <= existing 0.670 in 1he2A Skipped atom 1538, because occupancy 0.330 <= existing 0.670 in 1he2A Skipped atom 1540, because occupancy 0.330 <= existing 0.670 in 1he2A Skipped atom 2145, because occupancy 0.320 <= existing 0.680 in 1he2A Skipped atom 2147, because occupancy 0.320 <= existing 0.680 in 1he2A Skipped atom 2149, because occupancy 0.320 <= existing 0.680 in 1he2A Skipped atom 2151, because occupancy 0.320 <= existing 0.680 in 1he2A Skipped atom 2345, because occupancy 0.430 <= existing 0.570 in 1he2A Skipped atom 2347, because occupancy 0.430 <= existing 0.570 in 1he2A Skipped atom 2349, because occupancy 0.430 <= existing 0.570 in 1he2A Skipped atom 2351, because occupancy 0.430 <= existing 0.570 in 1he2A Skipped atom 2381, because occupancy 0.230 <= existing 0.770 in 1he2A Skipped atom 2546, because occupancy 0.420 <= existing 0.580 in 1he2A Skipped atom 2548, because occupancy 0.420 <= existing 0.580 in 1he2A Skipped atom 2550, because occupancy 0.420 <= existing 0.580 in 1he2A Skipped atom 2552, because occupancy 0.420 <= existing 0.580 in 1he2A Skipped atom 2554, because occupancy 0.420 <= existing 0.580 in 1he2A Skipped atom 2556, because occupancy 0.420 <= existing 0.580 in 1he2A Skipped atom 2558, because occupancy 0.420 <= existing 0.580 in 1he2A Skipped atom 2641, because occupancy 0.200 <= existing 0.800 in 1he2A Skipped atom 2643, because occupancy 0.200 <= existing 0.800 in 1he2A Skipped atom 2645, because occupancy 0.200 <= existing 0.800 in 1he2A Skipped atom 2686, because occupancy 0.460 <= existing 0.540 in 1he2A Skipped atom 2688, because occupancy 0.460 <= existing 0.540 in 1he2A Skipped atom 2815, because occupancy 0.390 <= existing 0.610 in 1he2A Skipped atom 2817, because occupancy 0.390 <= existing 0.610 in 1he2A Skipped atom 2819, because occupancy 0.390 <= existing 0.610 in 1he2A # T0286 read from 1he2A/merged-good-all-a2m # 1he2A read from 1he2A/merged-good-all-a2m # adding 1he2A to template set # found chain 1he2A in template set T0286 6 :IKIMPVG 1he2A 4 :KKIAIFG T0286 23 :EMGSYRTELYRLLTQAGLSIDFVGSQRSGPSSLPDKDHEGHSGWTI 1he2A 11 :ATGQTGLTTLAQAVQAGYEVTVLVRDSSRLPSEGPRPAHVVVGDVL T0286 73 :SNINNWLNTH 1he2A 59 :ADVDKTVAGQ T0286 85 :DVVFLWIGGN 1he2A 69 :DAVIVLLGTR T0286 97 :LLNGNLN 1he2A 79 :NDLSPTT T0286 104 :ATGLSNLIDQIFTV 1he2A 88 :SEGARNIVAAMKAH T0286 120 :NVT 1he2A 102 :GVD T0286 123 :LFVADYYPW 1he2A 106 :VVACTSAFL T0286 132 :PEAIKQYNAVIPG 1he2A 122 :PPRLQAVTDDHIR T0286 146 :VQQKANAG 1he2A 135 :MHKVLRES T0286 155 :KVYFVKLS 1he2A 143 :GLKYVAVM T0286 163 :EIQFD 1he2A 152 :PHIGD T0286 168 :RNTDISWDGLHLS 1he2A 161 :GAYTVTLDGRGPS T0286 184 :YKKIANIWYK 1he2A 178 :KHDLGHFMLR Number of specific fragments extracted= 14 number of extra gaps= 0 total=283 Number of alignments=25 # 1he2A read from 1he2A/merged-good-all-a2m # found chain 1he2A in template set T0286 5 :TIKIMPVG 1he2A 3 :VKKIAIFG T0286 23 :EMGSYRTELYRLLTQAGLSIDFVGSQRSGPSSLPDKDHEGHSGWTIP 1he2A 11 :ATGQTGLTTLAQAVQAGYEVTVLVRDSSRLPSEGPRPAHVVVGDVLQ T0286 72 :ASNINNWLNTH 1he2A 58 :AADVDKTVAGQ T0286 85 :DVVFLWIGGNDLLLNGNLNATGLSNLIDQIFTV 1he2A 69 :DAVIVLLGTRNDLSPTTVMSEGARNIVAAMKAH T0286 120 :NVT 1he2A 102 :GVD T0286 123 :LFVADYYPW 1he2A 106 :VVACTSAFL T0286 132 :PEAIKQYNAVIPGIV 1he2A 122 :PPRLQAVTDDHIRMH T0286 148 :QKANAG 1he2A 137 :KVLRES T0286 155 :KVYFVKLS 1he2A 143 :GLKYVAVM T0286 163 :EIQFDRNT 1he2A 152 :PHIGDQPL T0286 171 :DISWDGLHLS 1he2A 164 :TVTLDGRGPS T0286 184 :YKKIANIWY 1he2A 178 :KHDLGHFML Number of specific fragments extracted= 12 number of extra gaps= 0 total=295 Number of alignments=26 # 1he2A read from 1he2A/merged-good-all-a2m # found chain 1he2A in template set T0286 7 :KIMPVG 1he2A 5 :KIAIFG T0286 23 :EMGSYRTELYRLLTQAGLSIDFVGSQRS 1he2A 11 :ATGQTGLTTLAQAVQAGYEVTVLVRDSS T0286 51 :GP 1he2A 53 :GD T0286 65 :GWTIPQIASNI 1he2A 55 :VLQAADVDKTV T0286 82 :HNPDVVFLWIGGN 1he2A 66 :AGQDAVIVLLGTR T0286 98 :LN 1he2A 79 :ND T0286 101 :NLNATGLSNLIDQIFTV 1he2A 85 :TVMSEGARNIVAAMKAH T0286 121 :V 1he2A 103 :V T0286 122 :TLFVADYYP 1he2A 105 :KVVACTSAF T0286 131 :WPEAIKQYNAVIPGIVQQKANAGKKVYFV 1he2A 121 :VPPRLQAVTDDHIRMHKVLRESGLKYVAV T0286 160 :KLSEIQFDRNTDISWDGL 1he2A 153 :HIGDQPLTGAYTVTLDGR Number of specific fragments extracted= 11 number of extra gaps= 0 total=306 Number of alignments=27 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1fxwF/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0286/1fxwF/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0286/1fxwF/merged-good-all-a2m.gz for input Trying 1fxwF/merged-good-all-a2m Error: Couldn't open file 1fxwF/merged-good-all-a2m or 1fxwF/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1bwp/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0286/1bwp/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0286/1bwp/merged-good-all-a2m.gz for input Trying 1bwp/merged-good-all-a2m Error: Couldn't open file 1bwp/merged-good-all-a2m or 1bwp/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1bwq/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0286/1bwq/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0286/1bwq/merged-good-all-a2m.gz for input Trying 1bwq/merged-good-all-a2m Error: Couldn't open file 1bwq/merged-good-all-a2m or 1bwq/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1vhqA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0286 read from 1vhqA/merged-good-all-a2m # 1vhqA read from 1vhqA/merged-good-all-a2m # found chain 1vhqA in training set Warning: unaligning (T0286)A126 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1vhqA)I139 Warning: unaligning (T0286)Y128 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1vhqA)I139 Warning: unaligning (T0286)R200 because last residue in template chain is (1vhqA)E220 T0286 6 :IKIMPVG 1vhqA 5 :KKIGVIL T0286 15 :CTEGMGGGEMGSYRTELYRLLTQAGLSIDFVGSQRSGPSSLPDKD 1vhqA 12 :SGCGVYDGSEIHEAVLTLLAISRSGAQAVCFAPDKQQVDVINHLT T0286 62 :GHSGWTIPQIA 1vhqA 57 :GEAMTETRNVL T0286 80 :NTHN 1vhqA 82 :AQAD T0286 84 :PDVVFLWIGGNDLLLNGNLN 1vhqA 89 :LDALIVPGGFGAAKNLSNFA T0286 104 :ATGLSNLIDQIFTV 1vhqA 117 :DRELKALAQAMHQA T0286 120 :NVTLFV 1vhqA 131 :GKPLGF T0286 129 :YPW 1vhqA 140 :APA T0286 132 :PEA 1vhqA 159 :DID T0286 146 :VQQKANAG 1vhqA 162 :TAEVLEEM T0286 155 :KVYFVKLS 1vhqA 170 :GAEHVPCP T0286 163 :EIQFD 1vhqA 180 :DIVVD T0286 169 :NTDIS 1vhqA 193 :PAYML T0286 178 :HLSEIGYKKIANIWYKYTIDIL 1vhqA 198 :AQNIAEAASGIDKLVSRVLVLA Number of specific fragments extracted= 14 number of extra gaps= 0 total=320 Number of alignments=28 # 1vhqA read from 1vhqA/merged-good-all-a2m # found chain 1vhqA in training set Warning: unaligning (T0286)T5 because first residue in template chain is (1vhqA)M4 Warning: unaligning (T0286)A126 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1vhqA)I139 Warning: unaligning (T0286)Y128 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1vhqA)I139 Warning: unaligning (T0286)R200 because last residue in template chain is (1vhqA)E220 T0286 6 :IKIMPVGD 1vhqA 5 :KKIGVILS T0286 17 :EGMGGGEMGSYRTELYRLLTQAGLSIDFVGSQRSGPSSLPDKD 1vhqA 14 :CGVYDGSEIHEAVLTLLAISRSGAQAVCFAPDKQQVDVINHLT T0286 62 :GHSGWTIPQIASNINNWL 1vhqA 57 :GEAMTETRNVLIEAARIT T0286 81 :THN 1vhqA 75 :RGE T0286 84 :PDVVFLWIG 1vhqA 89 :LDALIVPGG T0286 96 :LLLN 1vhqA 112 :SECT T0286 105 :TGLSNLIDQIFTV 1vhqA 118 :RELKALAQAMHQA T0286 120 :NVTLFV 1vhqA 131 :GKPLGF T0286 129 :YPW 1vhqA 140 :APA T0286 132 :PEA 1vhqA 159 :DID T0286 146 :VQQKANAG 1vhqA 162 :TAEVLEEM T0286 155 :KVYFVKLS 1vhqA 170 :GAEHVPCP T0286 163 :EIQFDRNT 1vhqA 180 :DIVVDEDN T0286 171 :DISWD 1vhqA 195 :YMLAQ T0286 180 :SEIGYKKIANIWYKYTIDIL 1vhqA 200 :NIAEAASGIDKLVSRVLVLA Number of specific fragments extracted= 15 number of extra gaps= 0 total=335 Number of alignments=29 # 1vhqA read from 1vhqA/merged-good-all-a2m # found chain 1vhqA in training set Warning: unaligning (T0286)A126 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1vhqA)I139 Warning: unaligning (T0286)Y128 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1vhqA)I139 T0286 4 :KTIKIMPVG 1vhqA 5 :KKIGVILSG T0286 17 :EGMGGGEMGSYRTELYRLLTQAGLSIDFVGSQRSGPSSLPDKDHEGHSGWT 1vhqA 14 :CGVYDGSEIHEAVLTLLAISRSGAQAVCFAPDKQQVDVINHLTGEAMTETR T0286 68 :IPQIASNINN 1vhqA 66 :VLIEAARITR T0286 78 :WLNTHNPDVVFLWIGGNDLLLNG 1vhqA 83 :QADAAELDALIVPGGFGAAKNLS T0286 101 :NLNATGLSNLIDQIFT 1vhqA 114 :CTVDRELKALAQAMHQ T0286 119 :PNVTLFV 1vhqA 130 :AGKPLGF T0286 129 :YP 1vhqA 140 :AP T0286 131 :WPEAIKQYNA 1vhqA 159 :DIDTAEVLEE T0286 153 :GKKVYFV 1vhqA 178 :VDDIVVD T0286 160 :KLSEIQFDRNTD 1vhqA 192 :TPAYMLAQNIAE T0286 180 :SEIGYKKIANIWYKYT 1vhqA 204 :AASGIDKLVSRVLVLA Number of specific fragments extracted= 11 number of extra gaps= 0 total=346 Number of alignments=30 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1bwr/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0286/1bwr/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0286/1bwr/merged-good-all-a2m.gz for input Trying 1bwr/merged-good-all-a2m Error: Couldn't open file 1bwr/merged-good-all-a2m or 1bwr/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1tmy/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1tmy expands to /projects/compbio/data/pdb/1tmy.pdb.gz 1tmy:Warning: there is no chain 1tmy will retry with 1tmyA # T0286 read from 1tmy/merged-good-all-a2m # 1tmy read from 1tmy/merged-good-all-a2m # adding 1tmy to template set # found chain 1tmy in template set Warning: unaligning (T0286)T5 because first residue in template chain is (1tmy)G2 T0286 6 :IKIMPVGD 1tmy 3 :KRVLIVDD T0286 24 :MGSYRTELYRLLTQA 1tmy 11 :AAFMRMMLKDIITKA T0286 41 :SIDFVGS 1tmy 26 :GYEVAGE T0286 62 :GH 1tmy 33 :AT T0286 67 :TIPQIASNIN 1tmy 35 :NGREAVEKYK T0286 81 :THNPDVVFLWIG 1tmy 45 :ELKPDIVTMDIT T0286 99 :NGNL 1tmy 57 :MPEM T0286 106 :GLSNLIDQIFTVKPNVTLFVADYYPWPEAIKQYNAV 1tmy 61 :NGIDAIKEIMKIDPNAKIIVCSAMGQQAMVIEAIKA T0286 143 :PGIVQQKANA 1tmy 108 :PSRVVEALNK Number of specific fragments extracted= 9 number of extra gaps= 0 total=355 Number of alignments=31 # 1tmy read from 1tmy/merged-good-all-a2m # found chain 1tmy in template set Warning: unaligning (T0286)T5 because first residue in template chain is (1tmy)G2 T0286 6 :IKIMPVGD 1tmy 3 :KRVLIVDD T0286 26 :SYRTELYRLLTQAGLSIDFVGS 1tmy 13 :FMRMMLKDIITKAGYEVAGEAT T0286 67 :TIPQIA 1tmy 35 :NGREAV T0286 77 :NWLNTHNPDVVFLWIG 1tmy 41 :EKYKELKPDIVTMDIT T0286 99 :NGNL 1tmy 57 :MPEM T0286 106 :GLSNLIDQIFTVKPNVTLFVADYYPWPEAIKQYNAV 1tmy 61 :NGIDAIKEIMKIDPNAKIIVCSAMGQQAMVIEAIKA T0286 143 :PGIVQQKANA 1tmy 108 :PSRVVEALNK Number of specific fragments extracted= 7 number of extra gaps= 0 total=362 Number of alignments=32 # 1tmy read from 1tmy/merged-good-all-a2m # found chain 1tmy in template set Warning: unaligning (T0286)S3 because first residue in template chain is (1tmy)G2 Warning: unaligning (T0286)Y157 because of BadResidue code BAD_PEPTIDE in next template residue (1tmy)I102 Warning: unaligning (T0286)F158 because of BadResidue code BAD_PEPTIDE at template residue (1tmy)I102 T0286 4 :KTIKIMP 1tmy 3 :KRVLIVD T0286 23 :EMGSYRTELYRLLTQAGLSIDFVGSQ 1tmy 10 :DAAFMRMMLKDIITKAGYEVAGEATN T0286 72 :ASNINNWLNTHNPDVVFLWI 1tmy 36 :GREAVEKYKELKPDIVTMDI T0286 104 :ATGLSNLIDQIFTVKPNVTLFVADYYPW 1tmy 59 :EMNGIDAIKEIMKIDPNAKIIVCSAMGQ T0286 143 :PGIVQQKANAGKKV 1tmy 87 :QAMVIEAIKAGAKD T0286 159 :V 1tmy 103 :V T0286 166 :FDR 1tmy 106 :FQP T0286 193 :KYTIDILRAL 1tmy 109 :SRVVEALNKV Number of specific fragments extracted= 8 number of extra gaps= 1 total=370 Number of alignments=33 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1es9A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0286 read from 1es9A/merged-good-all-a2m # 1es9A read from 1es9A/merged-good-all-a2m # found chain 1es9A in training set Warning: unaligning (T0286)Y32 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1es9A)Q54 Warning: unaligning (T0286)R33 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1es9A)Q54 Warning: unaligning (T0286)L34 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1es9A)C55 Warning: unaligning (T0286)L35 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1es9A)W58 Warning: unaligning (T0286)Q37 because of BadResidue code BAD_PEPTIDE in next template residue (1es9A)L61 Warning: unaligning (T0286)A38 because of BadResidue code BAD_PEPTIDE at template residue (1es9A)L61 Warning: unaligning (T0286)G39 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1es9A)F62 Warning: unaligning (T0286)N76 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1es9A)G87 Warning: unaligning (T0286)N77 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1es9A)G87 Warning: unaligning (T0286)D167 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1es9A)S181 Warning: unaligning (T0286)L199 because last residue in template chain is (1es9A)L216 T0286 3 :SKTIKIMPVGDSCTE 1es9A 36 :DKEPEVVFIGDSLVQ T0286 30 :EL 1es9A 51 :LM T0286 36 :T 1es9A 59 :R T0286 40 :LSIDFVGS 1es9A 63 :SPLHALNF T0286 62 :GHSGWTIPQIASNI 1es9A 71 :GIGGDSTQHVLWRL T0286 78 :WLNTHNPDVVFLWIGGN 1es9A 88 :ELEHIRPKIVVVWVGTN T0286 99 :NGNLN 1es9A 105 :NHGHT T0286 104 :ATGLSNLIDQIFTVKPNVTLFVADYYPW 1es9A 114 :TGGIKAIVQLVNERQPQARVVVLGLLPR T0286 132 :PEAIKQYNAVIPGIVQQKANAGKKVYFVKLSEIQF 1es9A 145 :PNPLREKNRRVNELVRAALAGHPRAHFLDADPGFV T0286 168 :RNTDISWDGLHLSEIGYKKIANIWYKYTIDI 1es9A 185 :ISHHDMYDYLHLSRLGYTPVCRALHSLLLRL Number of specific fragments extracted= 10 number of extra gaps= 5 total=380 Number of alignments=34 # 1es9A read from 1es9A/merged-good-all-a2m # found chain 1es9A in training set Warning: unaligning (T0286)Y32 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1es9A)Q54 Warning: unaligning (T0286)R33 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1es9A)Q54 Warning: unaligning (T0286)L34 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1es9A)C55 Warning: unaligning (T0286)L35 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1es9A)W58 Warning: unaligning (T0286)Q37 because of BadResidue code BAD_PEPTIDE in next template residue (1es9A)L61 Warning: unaligning (T0286)A38 because of BadResidue code BAD_PEPTIDE at template residue (1es9A)L61 Warning: unaligning (T0286)G39 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1es9A)F62 Warning: unaligning (T0286)N77 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1es9A)G87 Warning: unaligning (T0286)D167 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1es9A)S181 Warning: unaligning (T0286)R168 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1es9A)S181 Warning: unaligning (T0286)L199 because last residue in template chain is (1es9A)L216 T0286 3 :SKTIKIMPVGDSCT 1es9A 36 :DKEPEVVFIGDSLV T0286 29 :TEL 1es9A 50 :QLM T0286 36 :T 1es9A 59 :R T0286 40 :LSIDFVGS 1es9A 63 :SPLHALNF T0286 62 :GHSGWTIPQIASNIN 1es9A 71 :GIGGDSTQHVLWRLE T0286 78 :WLNTHNPDVVFLWIGGNDLLLNGNLNATGLSNLIDQIFTVKPNVTLFVADYYPW 1es9A 88 :ELEHIRPKIVVVWVGTNNHGHTAEQVTGGIKAIVQLVNERQPQARVVVLGLLPR T0286 132 :PEAIKQYNAVIPGIVQQKANAGKKVYFVKLSEIQF 1es9A 145 :PNPLREKNRRVNELVRAALAGHPRAHFLDADPGFV T0286 169 :NT 1es9A 182 :DG T0286 171 :DISWDGLHLSEIGYKKIANIWYKYTIDI 1es9A 188 :HDMYDYLHLSRLGYTPVCRALHSLLLRL Number of specific fragments extracted= 9 number of extra gaps= 5 total=389 Number of alignments=35 # 1es9A read from 1es9A/merged-good-all-a2m # found chain 1es9A in training set Warning: unaligning (T0286)N77 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1es9A)G87 T0286 19 :MGGGEMGSYRTELYRLLTQAGLSIDFVGSQ 1es9A 18 :QGDGKWMSLHHRFVADSKDKEPEVVFIGDS T0286 63 :HSGWTIPQIASNIN 1es9A 72 :IGGDSTQHVLWRLE T0286 78 :WLNTHNPDVVFLWIGGNDLLLNGNLNATGLSNLIDQIFTVKPNVTLFVADYYP 1es9A 88 :ELEHIRPKIVVVWVGTNNHGHTAEQVTGGIKAIVQLVNERQPQARVVVLGLLP T0286 131 :WPEAIKQYNAVIPGIVQQKANAGKKVYFVKLSEIQF 1es9A 144 :HPNPLREKNRRVNELVRAALAGHPRAHFLDADPGFV T0286 167 :DRNTDISWDGLHLSEIGYKKIANIWYKYTIDI 1es9A 184 :TISHHDMYDYLHLSRLGYTPVCRALHSLLLRL Number of specific fragments extracted= 5 number of extra gaps= 1 total=394 Number of alignments=36 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1deoA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1deoA expands to /projects/compbio/data/pdb/1deo.pdb.gz 1deoA:# T0286 read from 1deoA/merged-good-all-a2m # 1deoA read from 1deoA/merged-good-all-a2m # adding 1deoA to template set # found chain 1deoA in template set T0286 7 :KIMPVGDSCTEGMGG 1deoA 2 :TVYLAGDSTMAKNGG T0286 22 :GEMGSYRTELYRLL 1deoA 18 :SGTNGWGEYLASYL T0286 41 :SIDFVGS 1deoA 32 :SATVVND T0286 62 :GHSGWTIPQIA 1deoA 39 :AVAGRSARSYT T0286 73 :SNINNWLNTHN 1deoA 52 :GRFENIADVVT T0286 84 :PDVVFLWIGGNDLLLNGNLN 1deoA 64 :GDYVIVEFGHNDGGSLSTDN T0286 104 :ATGLSNLIDQIFTV 1deoA 111 :PAYLENAAKLFTAK T0286 120 :NVTLFVADYYPW 1deoA 125 :GAKVILSSQTPN T0286 139 :NAVIPGIVQQKANAG 1deoA 148 :PTRFVEYAELAAEVA T0286 155 :KVYFVKLSEIQFD 1deoA 163 :GVEYVDHWSYVDS T0286 168 :RNTDISWDGLHLSEIGYKKIANIWYKYTIDI 1deoA 185 :VNSYFPIDHTHTSPAGAEVVAEAFLKAVVCT T0286 199 :LRAL 1deoA 219 :LKSV Number of specific fragments extracted= 12 number of extra gaps= 0 total=406 Number of alignments=37 # 1deoA read from 1deoA/merged-good-all-a2m # found chain 1deoA in template set Warning: unaligning (T0286)I6 because first residue in template chain is (1deoA)T1 T0286 7 :KIMPVGDSCTEGMGGGEMG 1deoA 2 :TVYLAGDSTMAKNGGGSGT T0286 26 :SYRTELYRLL 1deoA 22 :GWGEYLASYL T0286 41 :SIDFVGS 1deoA 32 :SATVVND T0286 62 :GHSGWTIPQIAS 1deoA 39 :AVAGRSARSYTR T0286 74 :NINNWLNTHNP 1deoA 53 :RFENIADVVTA T0286 85 :DVVFLWIGGND 1deoA 65 :DYVIVEFGHND T0286 96 :LL 1deoA 91 :TG T0286 103 :NATGLSNLIDQIFTV 1deoA 110 :FPAYLENAAKLFTAK T0286 120 :NVTLFVADYYPW 1deoA 125 :GAKVILSSQTPN T0286 132 :PEAIKQYNAVIPGIV 1deoA 148 :PTRFVEYAELAAEVA T0286 155 :KVYFVKLSEIQFDRNT 1deoA 163 :GVEYVDHWSYVDSIYE T0286 171 :DISWDGLHLSEIGYKKIANIWYKYTID 1deoA 188 :YFPIDHTHTSPAGAEVVAEAFLKAVVC Number of specific fragments extracted= 12 number of extra gaps= 0 total=418 Number of alignments=38 # 1deoA read from 1deoA/merged-good-all-a2m # found chain 1deoA in template set T0286 7 :KIMPVGDSCTEGM 1deoA 2 :TVYLAGDSTMAKN T0286 20 :GGGEMGSYRTEL 1deoA 16 :GGSGTNGWGEYL T0286 40 :LSIDFVGSQRSG 1deoA 31 :LSATVVNDAVAG T0286 66 :WTIPQIA 1deoA 43 :RSARSYT T0286 73 :SNINNWLNTH 1deoA 55 :ENIADVVTAG T0286 85 :DVVFLWIGGND 1deoA 65 :DYVIVEFGHND T0286 99 :NG 1deoA 76 :GG T0286 101 :NLNATGLSNLIDQIFT 1deoA 108 :LTFPAYLENAAKLFTA T0286 119 :PNVTLFVADYYP 1deoA 124 :KGAKVILSSQTP T0286 131 :WP 1deoA 148 :PT T0286 137 :Q 1deoA 150 :R T0286 142 :IPGIVQQKANAGKKVYFV 1deoA 151 :FVEYAELAAEVAGVEYVD T0286 169 :NTDISWDGLHLSEIGYKKIANIWYKYTI 1deoA 186 :NSYFPIDHTHTSPAGAEVVAEAFLKAVV Number of specific fragments extracted= 13 number of extra gaps= 0 total=431 Number of alignments=39 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2apjA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2apjA expands to /projects/compbio/data/pdb/2apj.pdb.gz 2apjA:Bad short name: CI2 for alphabet: pdb_atoms Bad short name: CJ for alphabet: pdb_atoms Bad short name: CI1 for alphabet: pdb_atoms Bad short name: CH1 for alphabet: pdb_atoms Skipped atom 275, because occupancy 0.350 <= existing 0.650 in 2apjA Skipped atom 277, because occupancy 0.350 <= existing 0.650 in 2apjA Skipped atom 279, because occupancy 0.350 <= existing 0.650 in 2apjA Skipped atom 547, because occupancy 0.350 <= existing 0.650 in 2apjA Skipped atom 549, because occupancy 0.350 <= existing 0.650 in 2apjA Skipped atom 551, because occupancy 0.350 <= existing 0.650 in 2apjA Skipped atom 734, because occupancy 0.350 <= existing 0.650 in 2apjA Skipped atom 736, because occupancy 0.350 <= existing 0.650 in 2apjA Skipped atom 738, because occupancy 0.350 <= existing 0.650 in 2apjA Skipped atom 1623, because occupancy 0.350 <= existing 0.650 in 2apjA Skipped atom 1625, because occupancy 0.350 <= existing 0.650 in 2apjA Skipped atom 1627, because occupancy 0.350 <= existing 0.650 in 2apjA Skipped atom 1825, because occupancy 0.350 <= existing 0.650 in 2apjA Skipped atom 1827, because occupancy 0.350 <= existing 0.650 in 2apjA # T0286 read from 2apjA/merged-good-all-a2m # 2apjA read from 2apjA/merged-good-all-a2m # adding 2apjA to template set # found chain 2apjA in template set Warning: unaligning (T0286)D13 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2apjA)N32 Warning: unaligning (T0286)C15 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2apjA)N32 Warning: unaligning (T0286)T16 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2apjA)M33 T0286 1 :MASKTIKIMPVG 2apjA 18 :PIPPNQIFILSG T0286 17 :EGMGG 2apjA 34 :AGRGG T0286 22 :GEMG 2apjA 42 :DHHN T0286 26 :SYRTELYRLLTQAGLSIDFVGS 2apjA 97 :AFANAVKNRLETDSAVIGLVPC T0286 62 :GHSGWTIPQIA 2apjA 119 :ASGGTAIKEWE T0286 73 :SNI 2apjA 140 :KRT T0286 77 :NWLNTHNP 2apjA 143 :EESRKCGG T0286 85 :DVVFLWIGGNDLLLN 2apjA 153 :KAVLWYQGESDVLDI T0286 104 :ATGLSNLIDQIFTV 2apjA 174 :GNNMDRLIKNLRHD T0286 118 :KPNVTLFVADYYPWPEAI 2apjA 190 :LPSLPIIQVAIASGGGYI T0286 144 :GIVQQKANAGK 2apjA 208 :DKVREAQLGLK T0286 155 :KVYFVKL 2apjA 221 :NVVCVDA T0286 168 :RNTDISWDGLHLSEIGYKKIANIWYKYTIDIL 2apjA 228 :KGLPLKSDNLHLTTEAQVQLGLSLAQAYLSNF Number of specific fragments extracted= 13 number of extra gaps= 0 total=444 Number of alignments=40 # 2apjA read from 2apjA/merged-good-all-a2m # found chain 2apjA in template set Warning: unaligning (T0286)D13 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2apjA)N32 Warning: unaligning (T0286)C15 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2apjA)N32 Warning: unaligning (T0286)T16 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2apjA)M33 T0286 3 :SKTIKIMPVG 2apjA 20 :PPNQIFILSG T0286 17 :EGMGG 2apjA 34 :AGRGG T0286 22 :GEMG 2apjA 43 :HHNN T0286 26 :SYRTELYRLLTQAGLSIDFVGS 2apjA 97 :AFANAVKNRLETDSAVIGLVPC T0286 62 :GHSGWTIPQIAS 2apjA 119 :ASGGTAIKEWER T0286 74 :NINNWLN 2apjA 137 :RMVKRTE T0286 81 :THNP 2apjA 147 :KCGG T0286 85 :DVVFLWIGGND 2apjA 153 :KAVLWYQGESD T0286 96 :LL 2apjA 166 :DI T0286 100 :GNLNATGLSNLIDQIFTV 2apjA 170 :AESYGNNMDRLIKNLRHD T0286 118 :KPNVTLFVADYYPWPEA 2apjA 190 :LPSLPIIQVAIASGGGY T0286 143 :PGIVQQKANAGK 2apjA 207 :IDKVREAQLGLK T0286 155 :KVYFVKLSEI 2apjA 221 :NVVCVDAKGL T0286 171 :DISWDGLHLSEIGYKKIANIWYKYTIDIL 2apjA 231 :PLKSDNLHLTTEAQVQLGLSLAQAYLSNF Number of specific fragments extracted= 14 number of extra gaps= 0 total=458 Number of alignments=41 # 2apjA read from 2apjA/merged-good-all-a2m # found chain 2apjA in template set T0286 1 :MASKTIKIMPVGDSCTEGMGGGEMGSYRTELYRLLT 2apjA 108 :TDSAVIGLVPCASGGTAIKEWERGSHLYERMVKRTE T0286 77 :N 2apjA 144 :E T0286 78 :WLNTHNPDVVFLWIGGNDLLLNG 2apjA 146 :RKCGGEIKAVLWYQGESDVLDIH T0286 101 :NLNATGLSNLIDQIFTV 2apjA 171 :ESYGNNMDRLIKNLRHD T0286 118 :KPNVTLFVADYYPWPEAIKQYNAVIPG 2apjA 190 :LPSLPIIQVAIASGGGYIDKVREAQLG T0286 153 :GKKVYFVKLSE 2apjA 219 :LSNVVCVDAKG T0286 170 :TDISWDGLHLSEIGYKKIANIWYKYTIDIL 2apjA 230 :LPLKSDNLHLTTEAQVQLGLSLAQAYLSNF Number of specific fragments extracted= 7 number of extra gaps= 0 total=465 Number of alignments=42 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1w5fA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1w5fA expands to /projects/compbio/data/pdb/1w5f.pdb.gz 1w5fA:# T0286 read from 1w5fA/merged-good-all-a2m # 1w5fA read from 1w5fA/merged-good-all-a2m # adding 1w5fA to template set # found chain 1w5fA in template set Warning: unaligning (T0286)K4 because first residue in template chain is (1w5fA)L22 T0286 5 :TIKIMPVG 1w5fA 23 :KIKVIGVG T0286 26 :SYRTELYRLLTQAGL 1w5fA 31 :GAGNNAINRMIEIGI T0286 41 :SIDFVGS 1w5fA 47 :GVEFVAV T0286 66 :WTIPQIA 1w5fA 54 :NTDLQVL T0286 73 :SNINNWLNTH 1w5fA 97 :EKIREVLQDT T0286 85 :DVVFLWIGGN 1w5fA 107 :HMVFITAGFG T0286 100 :GNLNATGLSNLIDQIFTV 1w5fA 117 :GGTGTGASPVIAKIAKEM T0286 120 :NVT 1w5fA 135 :GIL T0286 123 :LFVADYYPW 1w5fA 140 :AIVTTPFYF T0286 132 :PEAIKQYNAVIPGIVQQ 1w5fA 150 :GPERLKKAIEGLKKLRK T0286 152 :AGKKVYFVKLSEIQFDRNTDISW 1w5fA 167 :HVDTLIKISNNKLMEELPRDVKI T0286 181 :EIGYKKIANIWYKYTIDILRALAGE 1w5fA 190 :KDAFLKADETLHQGVKGISELITKR Number of specific fragments extracted= 12 number of extra gaps= 0 total=477 Number of alignments=43 # 1w5fA read from 1w5fA/merged-good-all-a2m # found chain 1w5fA in template set Warning: unaligning (T0286)K4 because first residue in template chain is (1w5fA)L22 T0286 5 :TIKIMPVG 1w5fA 23 :KIKVIGVG T0286 26 :SYRTELYRLLTQAGL 1w5fA 31 :GAGNNAINRMIEIGI T0286 41 :SIDFVGS 1w5fA 47 :GVEFVAV T0286 62 :GH 1w5fA 54 :NT T0286 68 :IPQIAS 1w5fA 56 :DLQVLE T0286 74 :NINNWLNTH 1w5fA 98 :KIREVLQDT T0286 85 :DVVFLWIGGND 1w5fA 107 :HMVFITAGFGG T0286 105 :TGLSNLIDQIFTV 1w5fA 122 :GASPVIAKIAKEM T0286 120 :NVT 1w5fA 135 :GIL T0286 123 :LFVADYYPW 1w5fA 140 :AIVTTPFYF T0286 132 :PEAIKQYNAVIPGIVQQ 1w5fA 150 :GPERLKKAIEGLKKLRK T0286 152 :AGKKVYFVKLSEIQFDRNTDISW 1w5fA 167 :HVDTLIKISNNKLMEELPRDVKI T0286 181 :EIGYKKIANIWYKYTIDILRALAGE 1w5fA 190 :KDAFLKADETLHQGVKGISELITKR Number of specific fragments extracted= 13 number of extra gaps= 0 total=490 Number of alignments=44 # 1w5fA read from 1w5fA/merged-good-all-a2m # found chain 1w5fA in template set Warning: unaligning (T0286)K4 because first residue in template chain is (1w5fA)L22 T0286 5 :TIKIMPVG 1w5fA 23 :KIKVIGVG T0286 26 :SYRTELYRLLTQAGL 1w5fA 31 :GAGNNAINRMIEIGI T0286 41 :SIDFVGSQRS 1w5fA 47 :GVEFVAVNTD T0286 55 :LPDKDHEGHSGWTIPQIASNINN 1w5fA 72 :GENITRGLGAGGRPEIGEQAALE T0286 80 :NTHNPDVVFLWIGG 1w5fA 102 :VLQDTHMVFITAGF T0286 99 :NGNLNATGLSNLIDQIFTVKPNVTLFVA 1w5fA 116 :GGGTGTGASPVIAKIAKEMGILTVAIVT T0286 129 :YPWPEAIKQYNAVIPGIVQQKANAGKKVYFVKLSEIQFDRNTDIS 1w5fA 144 :TPFYFEGPERLKKAIEGLKKLRKHVDTLIKISNNKLMEELPRDVK T0286 180 :SEIGYKKIANIWYKYTIDILRALAGE 1w5fA 189 :IKDAFLKADETLHQGVKGISELITKR Number of specific fragments extracted= 8 number of extra gaps= 0 total=498 Number of alignments=45 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1orrA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0286 read from 1orrA/merged-good-all-a2m # 1orrA read from 1orrA/merged-good-all-a2m # found chain 1orrA in training set Warning: unaligning (T0286)Y194 because last residue in template chain is (1orrA)I339 T0286 7 :KIMPVGD 1orrA 3 :KLLITGG T0286 24 :MGSYRTELYRLLTQAGLSIDFVGS 1orrA 10 :CGFLGSNLASFALSQGIDLIVFDN T0286 63 :HSGWTIPQIA 1orrA 34 :LSRKGATDNL T0286 73 :SNINNWLNTHNPDVVFLWIGGNDLLLNGNLN 1orrA 63 :NDVTRLITKYMPDSCFHLAGQVAMTTSIDNP T0286 104 :ATGLSNLIDQIFTVKPNVTLFVADYYPW 1orrA 101 :VGGTLNLLEAVRQYNSNCNIIYSSTNKV T0286 132 :PEAIKQYNAVIPGIVQQKANAGK 1orrA 162 :HSPYGCSKGAADQYMLDYARIFG T0286 155 :KVYFVKLSEIQFD 1orrA 186 :NTVVFRHSSMYGG T0286 168 :RNTDIS 1orrA 319 :WSPKVS T0286 180 :SEIGYKKIANIWYK 1orrA 325 :AKDGVQKMYDWTSS Number of specific fragments extracted= 9 number of extra gaps= 0 total=507 Number of alignments=46 # 1orrA read from 1orrA/merged-good-all-a2m # found chain 1orrA in training set Warning: unaligning (T0286)I6 because first residue in template chain is (1orrA)A2 Warning: unaligning (T0286)Y194 because last residue in template chain is (1orrA)I339 T0286 7 :KIMPVGDSCT 1orrA 3 :KLLITGGCGF T0286 27 :YRTELYRLLTQAGLSIDFVGS 1orrA 13 :LGSNLASFALSQGIDLIVFDN T0286 63 :HSGWTIPQIAS 1orrA 34 :LSRKGATDNLH T0286 74 :NINNWLNTHNPDVVFLWIGG 1orrA 64 :DVTRLITKYMPDSCFHLAGQ T0286 98 :LNGNLNATG 1orrA 84 :VAMTTSIDN T0286 107 :LSNLIDQIFTVKPNVTLFVADYYPW 1orrA 104 :TLNLLEAVRQYNSNCNIIYSSTNKV T0286 132 :PEAIKQYNAVIPGIVQQKANAGK 1orrA 162 :HSPYGCSKGAADQYMLDYARIFG T0286 155 :KVYFVKLSEIQFDRNT 1orrA 186 :NTVVFRHSSMYGGRQF T0286 171 :DISWDG 1orrA 318 :DWSPKV T0286 179 :LSEIGYKKIANIWYK 1orrA 324 :SAKDGVQKMYDWTSS Number of specific fragments extracted= 10 number of extra gaps= 0 total=517 Number of alignments=47 # 1orrA read from 1orrA/merged-good-all-a2m # found chain 1orrA in training set T0286 2 :ASKTIKIMP 1orrA 24 :QGIDLIVFD T0286 19 :M 1orrA 34 :L T0286 24 :MGSYRTELYRLLTQAG 1orrA 35 :SRKGATDNLHWLSSLG T0286 41 :SIDFVGSQRS 1orrA 51 :NFEFVHGDIR T0286 60 :H 1orrA 61 :N T0286 72 :ASNINNWLNTHNPDVVFLWIGGNDLLLNG 1orrA 62 :KNDVTRLITKYMPDSCFHLAGQVAMTTSI T0286 101 :NLNATGLSNLIDQIFTVKPNVTLFVADYYP 1orrA 98 :EINVGGTLNLLEAVRQYNSNCNIIYSSTNK T0286 131 :WPEAIKQYNAVIPGIVQQKANAGKKVYFVKLSEIQFDRNTDISWDGL 1orrA 161 :FHSPYGCSKGAADQYMLDYARIFGLNTVVFRHSSMYGGRQFATYDQG T0286 187 :IANIWYKYTIDIL 1orrA 208 :WVGWFCQKAVEIK Number of specific fragments extracted= 9 number of extra gaps= 0 total=526 Number of alignments=48 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1k7cA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0286 read from 1k7cA/merged-good-all-a2m # 1k7cA read from 1k7cA/merged-good-all-a2m # found chain 1k7cA in training set Warning: unaligning (T0286)P130 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1k7cA)N136 Warning: unaligning (T0286)W131 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1k7cA)N136 T0286 7 :KIMPVGDSCTEGMGG 1k7cA 2 :TVYLAGDSTMAKNGG T0286 22 :GEMGSYRTELYRLL 1k7cA 18 :SGTNGWGEYLASYL T0286 41 :SIDFVGS 1k7cA 32 :SATVVND T0286 62 :GHSGWTIPQIA 1k7cA 39 :AVAGRSARSYT T0286 73 :SNINNWLNTHN 1k7cA 52 :GRFENIADVVT T0286 84 :PDVVFLWIGGNDLLLNGNLN 1k7cA 64 :GDYVIVEFGHNDGGSLSTDN T0286 104 :ATGLSNLIDQIFTV 1k7cA 111 :PAYLENAAKLFTAK T0286 120 :NVTLFVADYY 1k7cA 125 :GAKVILSSQT T0286 132 :PEAIKQYNAVIPGIV 1k7cA 148 :PTRFVEYAELAAEVA T0286 155 :KVYFVKLSEIQFD 1k7cA 163 :GVEYVDHWSYVDS T0286 168 :RNTDISWDGLHLSEIGYKKIANIWYKYTIDI 1k7cA 185 :VNSYFPIDHTHTSPAGAEVVAEAFLKAVVCT Number of specific fragments extracted= 11 number of extra gaps= 1 total=537 Number of alignments=49 # 1k7cA read from 1k7cA/merged-good-all-a2m # found chain 1k7cA in training set Warning: unaligning (T0286)I6 because first residue in template chain is (1k7cA)T1 Warning: unaligning (T0286)P130 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1k7cA)N136 Warning: unaligning (T0286)W131 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1k7cA)N136 T0286 7 :KIMPVGDSCTEGMGGGEMG 1k7cA 2 :TVYLAGDSTMAKNGGGSGT T0286 26 :SYRTELYRLL 1k7cA 22 :GWGEYLASYL T0286 41 :SIDFVGS 1k7cA 32 :SATVVND T0286 62 :GHSGWTIPQIAS 1k7cA 39 :AVAGRSARSYTR T0286 74 :NINNWLNTHNP 1k7cA 53 :RFENIADVVTA T0286 85 :DVVFLWIGGND 1k7cA 65 :DYVIVEFGHND T0286 96 :LL 1k7cA 91 :TG T0286 103 :NATGLSNLIDQIFTV 1k7cA 110 :FPAYLENAAKLFTAK T0286 120 :NVTLFVADYY 1k7cA 125 :GAKVILSSQT T0286 132 :PEAIKQYNAVIPGIV 1k7cA 148 :PTRFVEYAELAAEVA T0286 155 :KVYFVKLSEIQFDRNT 1k7cA 163 :GVEYVDHWSYVDSIYE T0286 171 :DISWDGLHLSEIGYKKIANIWYKYTI 1k7cA 188 :YFPIDHTHTSPAGAEVVAEAFLKAVV Number of specific fragments extracted= 12 number of extra gaps= 1 total=549 Number of alignments=50 # 1k7cA read from 1k7cA/merged-good-all-a2m # found chain 1k7cA in training set Warning: unaligning (T0286)P130 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1k7cA)N136 T0286 7 :KIMPVGDSCTEGMGGGE 1k7cA 2 :TVYLAGDSTMAKNGGGS T0286 24 :MGSYRTEL 1k7cA 20 :TNGWGEYL T0286 40 :LSIDFVGSQRSG 1k7cA 31 :LSATVVNDAVAG T0286 66 :WTIPQIA 1k7cA 43 :RSARSYT T0286 73 :SNINNWLNTH 1k7cA 55 :ENIADVVTAG T0286 85 :DVVFLWIGGND 1k7cA 65 :DYVIVEFGHND T0286 100 :G 1k7cA 77 :G T0286 101 :NLNATGLSNLIDQIFT 1k7cA 108 :LTFPAYLENAAKLFTA T0286 119 :PNVTLFVADYY 1k7cA 124 :KGAKVILSSQT T0286 132 :PEA 1k7cA 148 :PTR T0286 142 :IPGIVQQKANAGKKVYFV 1k7cA 151 :FVEYAELAAEVAGVEYVD T0286 169 :NTDISWDGLHLSEIGYKKIANIWYKYTID 1k7cA 186 :NSYFPIDHTHTSPAGAEVVAEAFLKAVVC Number of specific fragments extracted= 12 number of extra gaps= 1 total=561 Number of alignments=51 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1vjgA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1vjgA expands to /projects/compbio/data/pdb/1vjg.pdb.gz 1vjgA:Skipped atom 37, because occupancy 0.350 <= existing 0.650 in 1vjgA Skipped atom 39, because occupancy 0.350 <= existing 0.650 in 1vjgA Skipped atom 41, because occupancy 0.350 <= existing 0.650 in 1vjgA Skipped atom 43, because occupancy 0.350 <= existing 0.650 in 1vjgA Skipped atom 418, because occupancy 0.400 <= existing 0.600 in 1vjgA Skipped atom 422, because occupancy 0.400 <= existing 0.600 in 1vjgA Skipped atom 424, because occupancy 0.400 <= existing 0.600 in 1vjgA Skipped atom 490, because occupancy 0.500 <= existing 0.500 in 1vjgA Skipped atom 494, because occupancy 0.500 <= existing 0.500 in 1vjgA Skipped atom 496, because occupancy 0.500 <= existing 0.500 in 1vjgA Skipped atom 498, because occupancy 0.500 <= existing 0.500 in 1vjgA Skipped atom 500, because occupancy 0.500 <= existing 0.500 in 1vjgA Skipped atom 502, because occupancy 0.500 <= existing 0.500 in 1vjgA Skipped atom 521, because occupancy 0.500 <= existing 0.500 in 1vjgA Skipped atom 525, because occupancy 0.500 <= existing 0.500 in 1vjgA Skipped atom 527, because occupancy 0.500 <= existing 0.500 in 1vjgA Skipped atom 557, because occupancy 0.500 <= existing 0.500 in 1vjgA Skipped atom 561, because occupancy 0.500 <= existing 0.500 in 1vjgA Skipped atom 563, because occupancy 0.500 <= existing 0.500 in 1vjgA Skipped atom 565, because occupancy 0.500 <= existing 0.500 in 1vjgA Skipped atom 567, because occupancy 0.500 <= existing 0.500 in 1vjgA Skipped atom 569, because occupancy 0.500 <= existing 0.500 in 1vjgA Skipped atom 571, because occupancy 0.500 <= existing 0.500 in 1vjgA Skipped atom 878, because occupancy 0.500 <= existing 0.500 in 1vjgA Skipped atom 882, because occupancy 0.500 <= existing 0.500 in 1vjgA Skipped atom 884, because occupancy 0.500 <= existing 0.500 in 1vjgA Skipped atom 886, because occupancy 0.500 <= existing 0.500 in 1vjgA Skipped atom 888, because occupancy 0.500 <= existing 0.500 in 1vjgA Skipped atom 890, because occupancy 0.500 <= existing 0.500 in 1vjgA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0286 read from 1vjgA/merged-good-all-a2m # 1vjgA read from 1vjgA/merged-good-all-a2m # adding 1vjgA to template set # found chain 1vjgA in template set Warning: unaligning (T0286)A2 because first residue in template chain is (1vjgA)S5 Warning: unaligning (T0286)S3 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1vjgA)K6 Warning: unaligning (T0286)K118 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (1vjgA)P119 Warning: unaligning (T0286)P119 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (1vjgA)P119 T0286 4 :KTIKIMPVGDSCTEGMGGGEMGSYRTELYRLLTQAGLSIDFVGS 1vjgA 7 :TQIRICFVGDSFVNGTGDPECLGWTGRVCVNANKKGYDVTYYNL T0286 62 :GHSGWTIPQIASNINNWLNTH 1vjgA 51 :GIRRDTSSDIAKRWLQEVSLR T0286 84 :P 1vjgA 76 :Y T0286 85 :DVVFLWIGGNDLLLNGNLN 1vjgA 78 :SLVVFSFGLNDTTLENGKP T0286 104 :ATGLSNLIDQIFTV 1vjgA 104 :IKNTREILTQAKKL T0286 123 :LFVADYYPW 1vjgA 120 :VLMISPAPY T0286 132 :PEAIKQYNAVIPGIVQQKANAGK 1vjgA 133 :DPGRRRRTIDLSQQLALVCQDLD T0286 156 :VYFVKLSEIQFD 1vjgA 156 :VPYLDVFPLLEK T0286 174 :WDGLHLSEIGYKKIANIWYKY 1vjgA 178 :NDGVHPQAGGYTEFARIVENW T0286 197 :DILRAL 1vjgA 199 :DAWLNW Number of specific fragments extracted= 10 number of extra gaps= 1 total=571 Number of alignments=52 # 1vjgA read from 1vjgA/merged-good-all-a2m # found chain 1vjgA in template set Warning: unaligning (T0286)A2 because first residue in template chain is (1vjgA)S5 Warning: unaligning (T0286)S3 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1vjgA)K6 Warning: unaligning (T0286)K118 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (1vjgA)P119 Warning: unaligning (T0286)P119 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (1vjgA)P119 T0286 4 :KTIKIMPVGDSCTEGMGGGEMGSYRTELYRLLTQAGLSIDFVGS 1vjgA 7 :TQIRICFVGDSFVNGTGDPECLGWTGRVCVNANKKGYDVTYYNL T0286 62 :GHSGWTIPQIASNINNWLNTHN 1vjgA 51 :GIRRDTSSDIAKRWLQEVSLRL T0286 85 :DVVFLWIGGND 1vjgA 78 :SLVVFSFGLND T0286 96 :LLLNGNLNATGLSNLIDQIFTV 1vjgA 96 :PRVSIAETIKNTREILTQAKKL T0286 123 :LFVADYYPW 1vjgA 120 :VLMISPAPY T0286 132 :PEAIKQYNAVIPGIVQQKANAGK 1vjgA 133 :DPGRRRRTIDLSQQLALVCQDLD T0286 156 :VYFVKLSEIQFDRNT 1vjgA 156 :VPYLDVFPLLEKPSV T0286 174 :WDGLHLSEIGYKKIANIWY 1vjgA 178 :NDGVHPQAGGYTEFARIVE T0286 197 :DILRA 1vjgA 199 :DAWLN Number of specific fragments extracted= 9 number of extra gaps= 1 total=580 Number of alignments=53 # 1vjgA read from 1vjgA/merged-good-all-a2m # found chain 1vjgA in template set Warning: unaligning (T0286)S3 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1vjgA)K6 Warning: unaligning (T0286)V121 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (1vjgA)P119 Warning: unaligning (T0286)T122 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (1vjgA)P119 T0286 4 :KTIKIMPVGDSCTEGMGGGEMGSYRTELYRLLTQAGLSIDFVGSQR 1vjgA 7 :TQIRICFVGDSFVNGTGDPECLGWTGRVCVNANKKGYDVTYYNLGI T0286 64 :SGWTIPQIASNINN 1vjgA 53 :RRDTSSDIAKRWLQ T0286 78 :WLNTHNPDVVFLWIGGNDLLLNG 1vjgA 71 :RLHKEYNSLVVFSFGLNDTTLEN T0286 101 :NLNATGLSNLIDQIFTV 1vjgA 101 :AETIKNTREILTQAKKL T0286 123 :LFVADYYP 1vjgA 120 :VLMISPAP T0286 131 :WPEA 1vjgA 133 :DPGR T0286 136 :KQYNAVIPGIVQQKANAGKKVYFVKLSEIQFDR 1vjgA 137 :RRRTIDLSQQLALVCQDLDVPYLDVFPLLEKPS T0286 172 :ISWDGLHLSEIGYKKIANIWY 1vjgA 176 :KANDGVHPQAGGYTEFARIVE Number of specific fragments extracted= 8 number of extra gaps= 2 total=588 Number of alignments=54 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ek6A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0286 read from 1ek6A/merged-good-all-a2m # 1ek6A read from 1ek6A/merged-good-all-a2m # found chain 1ek6A in training set T0286 6 :IKIMPVGD 1ek6A 3 :EKVLVTGG T0286 24 :MGSYRTELYRLLTQAGLSIDFVGSQRS 1ek6A 11 :AGYIGSHTVLELLEAGYLPVVIDNFHN T0286 60 :HEGHSGWTIPQIA 1ek6A 38 :AFRGGGSLPESLR T0286 73 :SNINNWLNTHNPDVVFLWIGGNDLLLNGNLN 1ek6A 71 :GALQRLFKKYSFMAVIHFAGLKAVGESVQKP T0286 104 :ATGLSNLIDQIFTV 1ek6A 109 :LTGTIQLLEIMKAH T0286 120 :NVTLFVADYYPW 1ek6A 123 :GVKNLVFSSSAT T0286 132 :PEAIKQYNAVIPGIVQQKANAGK 1ek6A 154 :TNPYGKSKFFIEEMIRDLCQADK T0286 155 :KVYFVKLSEIQFD 1ek6A 179 :NAVLLRYFNPTGA T0286 168 :RNTDISW 1ek6A 231 :DTEDGTG T0286 175 :DGLHLSE 1ek6A 240 :DYIHVVD T0286 182 :IGYKKIANIW 1ek6A 249 :KGHIAALRKL T0286 192 :YKYTIDILRALA 1ek6A 277 :VLQMVQAMEKAS Number of specific fragments extracted= 12 number of extra gaps= 0 total=600 Number of alignments=55 # 1ek6A read from 1ek6A/merged-good-all-a2m # found chain 1ek6A in training set T0286 6 :IKIMPVGD 1ek6A 3 :EKVLVTGG T0286 14 :SCT 1ek6A 31 :VID T0286 17 :EGMGGGEMGSYRTELYRLLTQAGLSIDFVGS 1ek6A 35 :FHNAFRGGGSLPESLRRVQELTGRSVEFEEM T0286 74 :NINNWLNTHNPDVVFLWIGGND 1ek6A 72 :ALQRLFKKYSFMAVIHFAGLKA T0286 100 :GNLNATGLSNLIDQIFTV 1ek6A 105 :YRVNLTGTIQLLEIMKAH T0286 120 :NVTLFVADYYPW 1ek6A 123 :GVKNLVFSSSAT T0286 132 :PEAIKQYNAVIPGIVQQKANAGK 1ek6A 154 :TNPYGKSKFFIEEMIRDLCQADK T0286 155 :KVYFVKLSEIQFDRNT 1ek6A 179 :NAVLLRYFNPTGAHAS T0286 173 :SWDGLHLS 1ek6A 238 :VRDYIHVV T0286 181 :EIGYKKIANIW 1ek6A 248 :AKGHIAALRKL T0286 192 :YKYTIDILRALA 1ek6A 277 :VLQMVQAMEKAS Number of specific fragments extracted= 11 number of extra gaps= 0 total=611 Number of alignments=56 # 1ek6A read from 1ek6A/merged-good-all-a2m # found chain 1ek6A in training set T0286 7 :KIMPVGDS 1ek6A 4 :KVLVTGGA T0286 34 :LLTQAGLSIDFVGSQRSGPSSLPDKDH 1ek6A 21 :ELLEAGYLPVVIDNFHNAFRGGGSLPE T0286 71 :IASNIN 1ek6A 48 :SLRRVQ T0286 78 :WLNTHNPDV 1ek6A 54 :ELTGRSVEF T0286 96 :L 1ek6A 67 :I T0286 102 :LNATGLSNLIDQ 1ek6A 68 :LDQGALQRLFKK T0286 119 :PNVTLFVADYYP 1ek6A 80 :YSFMAVIHFAGL T0286 131 :WPEAIKQYNAVIPGIVQQKANAGKKVYFVKLSEIQFDRNTDISWDGLHLSE 1ek6A 101 :PLDYYRVNLTGTIQLLEIMKAHGVKNLVFSSSATVYGNPQYLPLDEAHPTG T0286 182 :IGYKKIANIWYKYTIDILRA 1ek6A 155 :NPYGKSKFFIEEMIRDLCQA Number of specific fragments extracted= 9 number of extra gaps= 0 total=620 Number of alignments=57 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1vcoA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1vcoA expands to /projects/compbio/data/pdb/1vco.pdb.gz 1vcoA:# T0286 read from 1vcoA/merged-good-all-a2m # 1vcoA read from 1vcoA/merged-good-all-a2m # adding 1vcoA to template set # found chain 1vcoA in template set Warning: unaligning (T0286)S3 because first residue in template chain is (1vcoA)R10 Warning: unaligning (T0286)I164 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1vcoA)A347 Warning: unaligning (T0286)D167 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1vcoA)A347 T0286 4 :KTIKIMPVG 1vcoA 11 :PRKYVFITG T0286 18 :GMGGGEMG 1vcoA 20 :GVVSSLGK T0286 26 :SYRTELYRLLTQAGLSIDFVGSQRSGPSSLPDKDHE 1vcoA 29 :ILTSSLGALLRARGYRVTAIKIDPYVNVDAGTMRPY T0286 62 :GHS 1vcoA 67 :GEV T0286 66 :WTIPQIA 1vcoA 70 :FVTADGA T0286 73 :SNINNWLNTHNPDVVFLWIGGN 1vcoA 134 :ERIRKVAEEQKAEIVVVEVGGT T0286 97 :LLNGNLN 1vcoA 156 :VGDIESL T0286 104 :ATGLSNLIDQIFTV 1vcoA 199 :TKPTQHSVATLRGV T0286 120 :NV 1vcoA 213 :GI T0286 122 :TLFVADYYPW 1vcoA 218 :ILVLRSARPV T0286 132 :PEAIKQYNA 1vcoA 284 :LSFWQEAVR T0286 149 :KANAGK 1vcoA 293 :VLKHPE T0286 155 :KVYFVKLSE 1vcoA 335 :EVKWVDAES T0286 181 :EIGYKKIANIWYK 1vcoA 370 :IEGKVRAAQYARE Number of specific fragments extracted= 14 number of extra gaps= 0 total=634 Number of alignments=58 # 1vcoA read from 1vcoA/merged-good-all-a2m # found chain 1vcoA in template set Warning: unaligning (T0286)S3 because first residue in template chain is (1vcoA)R10 Warning: unaligning (T0286)I164 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1vcoA)A347 Warning: unaligning (T0286)D167 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1vcoA)A347 T0286 4 :KTIKIMPVG 1vcoA 11 :PRKYVFITG T0286 18 :GMGGGEMG 1vcoA 20 :GVVSSLGK T0286 26 :SYRTELYRLLTQAGLSIDFV 1vcoA 29 :ILTSSLGALLRARGYRVTAI T0286 46 :GSQRSGPSSLP 1vcoA 52 :PYVNVDAGTMR T0286 59 :DHEGHSGWTIPQIASNINNWLNTHNPDVVFLWIGGNDLLLN 1vcoA 120 :QTVQVIPHITDEIKERIRKVAEEQKAEIVVVEVGGTVGDIE T0286 100 :GNLNATG 1vcoA 168 :IRQFRFD T0286 107 :LSNLIDQIFTV 1vcoA 202 :TQHSVATLRGV T0286 120 :NVT 1vcoA 213 :GIQ T0286 123 :LFVADYYPW 1vcoA 219 :LVLRSARPV T0286 132 :PEAIKQYNA 1vcoA 284 :LSFWQEAVR T0286 149 :KANAGK 1vcoA 293 :VLKHPE T0286 155 :KVYFVKLSE 1vcoA 335 :EVKWVDAES T0286 168 :RNT 1vcoA 348 :DLE T0286 172 :ISWDGLHLSEI 1vcoA 525 :FKSRPMRPSPP T0286 184 :YKKIANIWY 1vcoA 536 :FVGFVEAAL Number of specific fragments extracted= 15 number of extra gaps= 0 total=649 Number of alignments=59 # 1vcoA read from 1vcoA/merged-good-all-a2m # found chain 1vcoA in template set Warning: unaligning (T0286)K4 because first residue in template chain is (1vcoA)R10 T0286 5 :TIKIMP 1vcoA 11 :PRKYVF T0286 15 :CTEGMGGG 1vcoA 17 :ITGGVVSS T0286 23 :EMGSYRTELYRLLTQAGLSIDFV 1vcoA 26 :GKGILTSSLGALLRARGYRVTAI T0286 46 :GSQRS 1vcoA 51 :DPYVN T0286 51 :GPSSLPDKDHEGH 1vcoA 115 :GEYLSQTVQVIPH T0286 67 :TIPQIASNINNWLNTHNPDVVFLWIGGN 1vcoA 128 :ITDEIKERIRKVAEEQKAEIVVVEVGGT T0286 97 :LLNG 1vcoA 156 :VGDI T0286 101 :NLNATGLSNLIDQIFTV 1vcoA 196 :EFKTKPTQHSVATLRGV T0286 118 :KPNVTLFVADYY 1vcoA 215 :QPDILVLRSARP T0286 131 :WPEAIKQYNAVIP 1vcoA 228 :PEEVRRKVALFTN T0286 153 :GKK 1vcoA 241 :VRP T0286 156 :VYFVKLSEIQF 1vcoA 246 :VFSSPTVEHLY T0286 183 :GYKKIAN 1vcoA 258 :VPLLLEE T0286 190 :IWYKYTIDI 1vcoA 266 :GLGRAVERA Number of specific fragments extracted= 14 number of extra gaps= 0 total=663 Number of alignments=60 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1nf3A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1nf3A expands to /projects/compbio/data/pdb/1nf3.pdb.gz 1nf3A:# T0286 read from 1nf3A/merged-good-all-a2m # 1nf3A read from 1nf3A/merged-good-all-a2m # adding 1nf3A to template set # found chain 1nf3A in template set T0286 4 :KTIKIMPVGD 1nf3A 2 :QTIKCVVVGD T0286 24 :MG 1nf3A 12 :GA T0286 41 :SIDFVGS 1nf3A 52 :TLGLFDT T0286 66 :WTIPQIASNINNWLN 1nf3A 59 :AGLEDYDRLRPLSYP T0286 83 :NPDVVFLWIGGN 1nf3A 74 :QTDVFLVCFSVV T0286 101 :NL 1nf3A 86 :SP T0286 104 :ATGLSN 1nf3A 90 :FENVKE T0286 110 :LIDQIFTVKPNVTLFVADYYPW 1nf3A 97 :WVPEITHHCPKTPFLLVGTQID T0286 132 :PEAIKQYNAV 1nf3A 122 :DPSTIEKLAK T0286 143 :PGIVQQKANAGK 1nf3A 139 :PETAEKLARDLK T0286 156 :VYFVKLSEIQ 1nf3A 152 :VKYVECSALT T0286 167 :D 1nf3A 162 :Q T0286 182 :IGYKKIANIWYKYTI 1nf3A 163 :KGLKNVFDEAILAAL T0286 201 :ALAGE 1nf3A 178 :EPPEP Number of specific fragments extracted= 14 number of extra gaps= 0 total=677 Number of alignments=61 # 1nf3A read from 1nf3A/merged-good-all-a2m # found chain 1nf3A in template set T0286 4 :KTIKIMPVGD 1nf3A 2 :QTIKCVVVGD T0286 26 :SYRTELYRLL 1nf3A 15 :GKTCLLISYT T0286 37 :Q 1nf3A 25 :T T0286 46 :GSQRSGPSSLP 1nf3A 26 :NKFPSEYVPTV T0286 67 :TIPQIASNIN 1nf3A 60 :GLEDYDRLRP T0286 81 :THN 1nf3A 70 :LSY T0286 84 :PDVVFLWIGGND 1nf3A 75 :TDVFLVCFSVVS T0286 101 :NLNATGLSN 1nf3A 87 :PSSFENVKE T0286 110 :LIDQIFTVKPNVTLFVADYYPW 1nf3A 97 :WVPEITHHCPKTPFLLVGTQID T0286 132 :PEAIKQYNA 1nf3A 122 :DPSTIEKLA T0286 143 :PGIVQQKANAGK 1nf3A 139 :PETAEKLARDLK T0286 155 :K 1nf3A 153 :K T0286 158 :FVKL 1nf3A 154 :YVEC T0286 163 :EIQFDRN 1nf3A 158 :SALTQKG T0286 184 :YKKIANIWYKYTIDI 1nf3A 165 :LKNVFDEAILAALEP Number of specific fragments extracted= 15 number of extra gaps= 0 total=692 Number of alignments=62 # 1nf3A read from 1nf3A/merged-good-all-a2m # found chain 1nf3A in template set T0286 4 :KTIKIMPVGD 1nf3A 2 :QTIKCVVVGD T0286 24 :MGSYRTELYRLLTQAGL 1nf3A 12 :GAVGKTCLLISYTTNKF T0286 49 :RS 1nf3A 29 :PS T0286 53 :SSLPDKDH 1nf3A 59 :AGLEDYDR T0286 76 :NNWLNTHNPDVVFLWIG 1nf3A 67 :LRPLSYPQTDVFLVCFS T0286 97 :LLNGNLNATGLSNLIDQIFTVKPNVTLFVADYYP 1nf3A 84 :VVSPSSFENVKEKWVPEITHHCPKTPFLLVGTQI T0286 131 :WPEAIKQYNA 1nf3A 122 :DPSTIEKLAK T0286 143 :PGIVQQKANAGKKVYFVKLS 1nf3A 139 :PETAEKLARDLKAVKYVECS T0286 166 :F 1nf3A 159 :A T0286 179 :LSEIGYKKIANIWYKYTI 1nf3A 160 :LTQKGLKNVFDEAILAAL Number of specific fragments extracted= 10 number of extra gaps= 0 total=702 Number of alignments=63 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1jrlA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0286/1jrlA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0286/1jrlA/merged-good-all-a2m.gz for input Trying 1jrlA/merged-good-all-a2m Error: Couldn't open file 1jrlA/merged-good-all-a2m or 1jrlA/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1hdoA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0286 read from 1hdoA/merged-good-all-a2m # 1hdoA read from 1hdoA/merged-good-all-a2m # found chain 1hdoA in training set Warning: unaligning (T0286)G153 because of BadResidue code BAD_PEPTIDE in next template residue (1hdoA)G143 Warning: unaligning (T0286)K155 because of BadResidue code BAD_PEPTIDE at template residue (1hdoA)G143 T0286 6 :IKIMPVG 1hdoA 4 :KKIAIFG T0286 23 :EMGSYRTELYRLLTQAGLSIDFVGSQRSGPSSLPDKDHEGHSGWTI 1hdoA 11 :ATGQTGLTTLAQAVQAGYEVTVLVRDSSRLPSEGPRPAHVVVGDVL T0286 73 :SNINNWLNTH 1hdoA 59 :ADVDKTVAGQ T0286 85 :DVVFLWIGGN 1hdoA 69 :DAVIVLLGTR T0286 97 :LLNGNLN 1hdoA 79 :NDLSPTT T0286 104 :ATGLSNLIDQIFTV 1hdoA 88 :SEGARNIVAAMKAH T0286 120 :NV 1hdoA 102 :GV T0286 122 :TLFVADYYPW 1hdoA 105 :KVVACTSAFL T0286 132 :PEAIKQYNAVIPG 1hdoA 122 :PPRLQAVTDDHIR T0286 146 :VQQKANA 1hdoA 135 :MHKVLRE T0286 156 :VYFVKLS 1hdoA 144 :LKYVAVM T0286 163 :EIQFD 1hdoA 152 :PHIGD T0286 172 :ISWDGLHLS 1hdoA 165 :VTLDGRGPS T0286 184 :YKKIANIWYK 1hdoA 178 :KHDLGHFMLR Number of specific fragments extracted= 14 number of extra gaps= 1 total=716 Number of alignments=64 # 1hdoA read from 1hdoA/merged-good-all-a2m # found chain 1hdoA in training set Warning: unaligning (T0286)G153 because of BadResidue code BAD_PEPTIDE in next template residue (1hdoA)G143 Warning: unaligning (T0286)K155 because of BadResidue code BAD_PEPTIDE at template residue (1hdoA)G143 T0286 5 :TIKIMPVG 1hdoA 3 :VKKIAIFG T0286 23 :EMGSYRTELYRLLTQAGLSIDFVGSQRSGPSSLPDKDHEGHSGWTIP 1hdoA 11 :ATGQTGLTTLAQAVQAGYEVTVLVRDSSRLPSEGPRPAHVVVGDVLQ T0286 72 :ASNINNWLNTH 1hdoA 58 :AADVDKTVAGQ T0286 85 :DVVFLWIGGNDLLLNGNLNATGLSNLIDQIFTV 1hdoA 69 :DAVIVLLGTRNDLSPTTVMSEGARNIVAAMKAH T0286 120 :NVT 1hdoA 102 :GVD T0286 123 :LFVADYYPW 1hdoA 106 :VVACTSAFL T0286 132 :PEAIKQYNAVIPGIV 1hdoA 122 :PPRLQAVTDDHIRMH T0286 148 :QKANA 1hdoA 137 :KVLRE T0286 156 :VYFVKLS 1hdoA 144 :LKYVAVM T0286 163 :EIQFDRNT 1hdoA 152 :PHIGDQPL T0286 171 :DISWDGLHLS 1hdoA 164 :TVTLDGRGPS T0286 184 :YKKIANIWY 1hdoA 178 :KHDLGHFML Number of specific fragments extracted= 12 number of extra gaps= 1 total=728 Number of alignments=65 # 1hdoA read from 1hdoA/merged-good-all-a2m # found chain 1hdoA in training set Warning: unaligning (T0286)W131 because of BadResidue code BAD_PEPTIDE at template residue (1hdoA)V121 Warning: unaligning (T0286)A152 because of BadResidue code BAD_PEPTIDE in next template residue (1hdoA)G143 Warning: unaligning (T0286)G153 because of BadResidue code BAD_PEPTIDE at template residue (1hdoA)G143 T0286 7 :KIMPVG 1hdoA 5 :KIAIFG T0286 23 :EMGSYRTELYRLLTQAGLSIDFVGSQRS 1hdoA 11 :ATGQTGLTTLAQAVQAGYEVTVLVRDSS T0286 51 :GP 1hdoA 53 :GD T0286 65 :GWTIPQIASNI 1hdoA 55 :VLQAADVDKTV T0286 82 :HNPDVVFLWIGGN 1hdoA 66 :AGQDAVIVLLGTR T0286 98 :LN 1hdoA 79 :ND T0286 101 :NLNATGLSNLIDQIFTV 1hdoA 85 :TVMSEGARNIVAAMKAH T0286 122 :TLFVADYYP 1hdoA 105 :KVVACTSAF T0286 132 :PEAIKQYNAVIPGIVQQKAN 1hdoA 122 :PPRLQAVTDDHIRMHKVLRE T0286 154 :KKVYFV 1hdoA 144 :LKYVAV T0286 160 :KLSEIQFDRNTDISWDGLHL 1hdoA 153 :HIGDQPLTGAYTVTLDGRGP Number of specific fragments extracted= 11 number of extra gaps= 2 total=739 Number of alignments=66 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1a4rA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1a4rA expands to /projects/compbio/data/pdb/1a4r.pdb.gz 1a4rA:# T0286 read from 1a4rA/merged-good-all-a2m # 1a4rA read from 1a4rA/merged-good-all-a2m # adding 1a4rA to template set # found chain 1a4rA in template set T0286 4 :KTIKIMPVGD 1a4rA 2 :QTIKCVVVGD T0286 23 :EMGSYRTELYRLLTQ 1a4rA 12 :VAVGKTCLLISYTTN T0286 48 :QRSGPSSLPDKDHEGH 1a4rA 27 :KFPSEYVPTVFDNYAV T0286 64 :SGWT 1a4rA 57 :DTAG T0286 69 :PQIASNINNWLNT 1a4rA 62 :EDYDRLRPLSYPQ T0286 84 :PDVVFLWIGGN 1a4rA 75 :TDVFLVCFSVV T0286 101 :NLN 1a4rA 86 :SPS T0286 104 :ATGLSN 1a4rA 90 :FENVKE T0286 110 :LIDQIFTVKPNVTLFVADYYPW 1a4rA 97 :WVPEITHHCPKTPFLLVGTQID T0286 132 :PEAIKQYNAV 1a4rA 122 :DPSTIEKLAK T0286 143 :PGIVQQKANAGK 1a4rA 139 :PETAEKLARDLK T0286 155 :K 1a4rA 153 :K T0286 158 :FVKLS 1a4rA 154 :YVECS T0286 164 :IQFD 1a4rA 159 :ALTQ T0286 182 :IGYKKIANIWYKY 1a4rA 163 :KGLKNVFDEAILA T0286 199 :LRALAG 1a4rA 176 :ALEPPE Number of specific fragments extracted= 16 number of extra gaps= 0 total=755 Number of alignments=67 # 1a4rA read from 1a4rA/merged-good-all-a2m # found chain 1a4rA in template set T0286 5 :TIKIMPVGD 1a4rA 3 :TIKCVVVGD T0286 26 :SYRTELYRLLTQAGLS 1a4rA 15 :GKTCLLISYTTNKFPS T0286 51 :GPSSLP 1a4rA 31 :EYVPTV T0286 57 :DKDHE 1a4rA 57 :DTAGQ T0286 69 :PQIASNINNWLNT 1a4rA 62 :EDYDRLRPLSYPQ T0286 84 :PDVVFLWIGGND 1a4rA 75 :TDVFLVCFSVVS T0286 101 :NLNATGLSN 1a4rA 87 :PSSFENVKE T0286 110 :LIDQIFTVKPNVTLFVADYYPW 1a4rA 97 :WVPEITHHCPKTPFLLVGTQID T0286 132 :PEAIKQYNAV 1a4rA 122 :DPSTIEKLAK T0286 143 :PGIVQQKANAGK 1a4rA 139 :PETAEKLARDLK T0286 155 :K 1a4rA 153 :K T0286 158 :FVKL 1a4rA 154 :YVEC T0286 163 :EIQFDRN 1a4rA 158 :SALTQKG T0286 184 :YKKIANIWYKYT 1a4rA 165 :LKNVFDEAILAA Number of specific fragments extracted= 14 number of extra gaps= 0 total=769 Number of alignments=68 # 1a4rA read from 1a4rA/merged-good-all-a2m # found chain 1a4rA in template set T0286 4 :KTIKIMPVGD 1a4rA 2 :QTIKCVVVGD T0286 24 :MGSYRTELYRLLTQAGLSIDFVGSQRS 1a4rA 12 :VAVGKTCLLISYTTNKFPSEYVPTVFD T0286 51 :GPSSLPDKDH 1a4rA 57 :DTAGQEDYDR T0286 76 :NNWLNTHNPDVVFLWIG 1a4rA 67 :LRPLSYPQTDVFLVCFS T0286 97 :LLNGNLNATGLSNLIDQIFTVKPNVTLFVADYYP 1a4rA 84 :VVSPSSFENVKEKWVPEITHHCPKTPFLLVGTQI T0286 131 :WPEAIKQYNA 1a4rA 122 :DPSTIEKLAK T0286 143 :PGIVQQKANAGKKVYFVKLS 1a4rA 139 :PETAEKLARDLKAVKYVECS T0286 179 :LSEIGYKKIANIWYKYT 1a4rA 160 :LTQKGLKNVFDEAILAA Number of specific fragments extracted= 8 number of extra gaps= 0 total=777 Number of alignments=69 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1zmbA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1zmbA expands to /projects/compbio/data/pdb/1zmb.pdb.gz 1zmbA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0286 read from 1zmbA/merged-good-all-a2m # 1zmbA read from 1zmbA/merged-good-all-a2m # adding 1zmbA to template set # found chain 1zmbA in template set T0286 5 :TIKIMPVGDSCTEGMGGGEMG 1zmbA 2 :VKSFLMLGQSNMAGRGFINEV T0286 26 :SYRTELYRLLTQAGL 1zmbA 55 :SLAGSFADAWSQKNQ T0286 41 :SIDFVGS 1zmbA 72 :IIGLIPC T0286 62 :GHSGWTIPQIA 1zmbA 79 :AEGGSSIDEWA T0286 73 :SNINNWLNTHNPDVVFLWIGGNDLLLNGNLN 1zmbA 100 :TEAKFAMESSELTGILWHQGESDSLNGNYKV T0286 104 :ATGLSNLIDQIFTVK 1zmbA 132 :YKKLLLIIEALRKEL T0286 119 :PNVTLFVADYYPW 1zmbA 149 :PDIPIIIGGLGDF T0286 135 :IKQ 1zmbA 171 :CTE T0286 139 :NAVIPGIVQQKANAGKKVYFVKLSEIQ 1zmbA 174 :YNFINKELQKFAFEQDNCYFVTASGLT T0286 172 :ISWDGLHLSEIGYKKIANIWYKYTID 1zmbA 201 :CNPDGIHIDAISQRKFGLRYFEAFFN Number of specific fragments extracted= 10 number of extra gaps= 0 total=787 Number of alignments=70 # 1zmbA read from 1zmbA/merged-good-all-a2m # found chain 1zmbA in template set T0286 5 :TIKIMPVGDSCTEGMGGGEMG 1zmbA 2 :VKSFLMLGQSNMAGRGFINEV T0286 26 :SYRTELYRLLTQAGL 1zmbA 55 :SLAGSFADAWSQKNQ T0286 41 :SIDFVGS 1zmbA 72 :IIGLIPC T0286 62 :GHSGWTIPQIAS 1zmbA 79 :AEGGSSIDEWAL T0286 74 :NINNWLNTHNPDVVFLWIGGND 1zmbA 101 :EAKFAMESSELTGILWHQGESD T0286 96 :LLLNGNLNATGLSNLIDQIFTVK 1zmbA 124 :LNGNYKVYYKKLLLIIEALRKEL T0286 119 :PNVTLFVADYYPW 1zmbA 149 :PDIPIIIGGLGDF T0286 132 :PEAI 1zmbA 171 :CTEY T0286 140 :AVIPGIVQQKANAGKKVYFVKLSEI 1zmbA 175 :NFINKELQKFAFEQDNCYFVTASGL T0286 171 :DISWDGLHLSEIGYKKIANIWYKYTID 1zmbA 200 :TCNPDGIHIDAISQRKFGLRYFEAFFN Number of specific fragments extracted= 10 number of extra gaps= 0 total=797 Number of alignments=71 # 1zmbA read from 1zmbA/merged-good-all-a2m # found chain 1zmbA in template set T0286 2 :ASKTIKIMPVG 1zmbA 69 :QEDIIGLIPCA T0286 53 :SSLPDKDHEGHSGWTIPQIASNINNWLNTHNPDVVFLWIGGNDLLLNG 1zmbA 80 :EGGSSIDEWALDGVLFRHALTEAKFAMESSELTGILWHQGESDSLNGN T0286 101 :NLNATGLSNLIDQIFTV 1zmbA 129 :KVYYKKLLLIIEALRKE T0286 118 :KPNVTLFVADYYP 1zmbA 148 :VPDIPIIIGGLGD T0286 131 :WPEAIKQYNAVIPGIV 1zmbA 170 :GCTEYNFINKELQKFA T0286 151 :NAGKKVYFVKLSEI 1zmbA 186 :FEQDNCYFVTASGL T0286 171 :DISWDGLHLSEIGYKKIANIWYKYTID 1zmbA 200 :TCNPDGIHIDAISQRKFGLRYFEAFFN Number of specific fragments extracted= 7 number of extra gaps= 0 total=804 Number of alignments=72 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1u0sY/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1u0sY expands to /projects/compbio/data/pdb/1u0s.pdb.gz 1u0sY:Skipped atom 825, because occupancy 0.500 <= existing 0.500 in 1u0sY Skipped atom 827, because occupancy 0.500 <= existing 0.500 in 1u0sY Skipped atom 829, because occupancy 0.500 <= existing 0.500 in 1u0sY Skipped atom 831, because occupancy 0.500 <= existing 0.500 in 1u0sY Skipped atom 833, because occupancy 0.500 <= existing 0.500 in 1u0sY Skipped atom 835, because occupancy 0.500 <= existing 0.500 in 1u0sY Skipped atom 837, because occupancy 0.500 <= existing 0.500 in 1u0sY Skipped atom 839, because occupancy 0.500 <= existing 0.500 in 1u0sY Skipped atom 841, because occupancy 0.500 <= existing 0.500 in 1u0sY Skipped atom 843, because occupancy 0.500 <= existing 0.500 in 1u0sY Skipped atom 845, because occupancy 0.500 <= existing 0.500 in 1u0sY # T0286 read from 1u0sY/merged-good-all-a2m # 1u0sY read from 1u0sY/merged-good-all-a2m # adding 1u0sY to template set # found chain 1u0sY in template set Warning: unaligning (T0286)T5 because first residue in template chain is (1u0sY)G2 T0286 6 :IKIMPVGD 1u0sY 3 :KRVLIVDD T0286 24 :MGSYRTELYRLLTQA 1u0sY 11 :AAFMRMMLKDIITKA T0286 41 :SIDFVGS 1u0sY 26 :GYEVAGE T0286 62 :GHS 1u0sY 33 :ATN T0286 68 :IP 1u0sY 36 :GR T0286 74 :NINNWLNTHNPDVVFLWIGG 1u0sY 38 :EAVEKYKELKPDIVTMDITM T0286 100 :G 1u0sY 58 :P T0286 104 :ATGLSNLIDQIFTVKPNVTLFVADYYPWPEAIKQYNAV 1u0sY 59 :EMNGIDAIKEIMKIDPNAKIIVCSAMGQQAMVIEAIKA T0286 143 :PGIVQQKANA 1u0sY 108 :PSRVVEALNK Number of specific fragments extracted= 9 number of extra gaps= 0 total=813 Number of alignments=73 # 1u0sY read from 1u0sY/merged-good-all-a2m # found chain 1u0sY in template set Warning: unaligning (T0286)T5 because first residue in template chain is (1u0sY)G2 T0286 6 :IKIMPVGD 1u0sY 3 :KRVLIVDD T0286 26 :SYRTELYRLLTQAGLSIDFVGS 1u0sY 13 :FMRMMLKDIITKAGYEVAGEAT T0286 67 :TI 1u0sY 35 :NG T0286 73 :SNINNWLNTHNPDVVFLWIGG 1u0sY 37 :REAVEKYKELKPDIVTMDITM T0286 100 :GN 1u0sY 58 :PE T0286 106 :GLSNLIDQIFTVKPNVTLFVADYYPWPEAIKQYNAV 1u0sY 61 :NGIDAIKEIMKIDPNAKIIVCSAMGQQAMVIEAIKA T0286 143 :PGIVQQKANA 1u0sY 108 :PSRVVEALNK Number of specific fragments extracted= 7 number of extra gaps= 0 total=820 Number of alignments=74 # 1u0sY read from 1u0sY/merged-good-all-a2m # found chain 1u0sY in template set Warning: unaligning (T0286)S3 because first residue in template chain is (1u0sY)G2 T0286 4 :KTIKIMP 1u0sY 3 :KRVLIVD T0286 23 :EMGSYRTELYRLLTQAGLSIDFVGSQ 1u0sY 10 :DAAFMRMMLKDIITKAGYEVAGEATN T0286 72 :ASNINNWLNTHNPDVVFLWI 1u0sY 36 :GREAVEKYKELKPDIVTMDI T0286 101 :NL 1u0sY 59 :EM T0286 106 :GLSNLIDQIFTVKPNVTLFVADYYPW 1u0sY 61 :NGIDAIKEIMKIDPNAKIIVCSAMGQ T0286 143 :PGIVQQKANAGKKVYFV 1u0sY 87 :QAMVIEAIKAGAKDFIV T0286 188 :ANIWYKYTIDI 1u0sY 108 :PSRVVEALNKV Number of specific fragments extracted= 7 number of extra gaps= 0 total=827 Number of alignments=75 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1wab/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1wab expands to /projects/compbio/data/pdb/1wab.pdb.gz 1wab:Warning: there is no chain 1wab will retry with 1wabA # T0286 read from 1wab/merged-good-all-a2m # 1wab read from 1wab/merged-good-all-a2m # adding 1wab to template set # found chain 1wab in template set Warning: unaligning (T0286)R33 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1wab)C55 Warning: unaligning (T0286)L34 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1wab)C55 Warning: unaligning (T0286)L35 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1wab)W58 Warning: unaligning (T0286)A38 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1wab)F62 Warning: unaligning (T0286)G39 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1wab)F62 Warning: unaligning (T0286)L199 because last residue in template chain is (1wab)L216 T0286 3 :SKTIKIMPVGDSCTE 1wab 36 :DKEPEVVFIGDSLVQ T0286 30 :ELY 1wab 51 :LMH T0286 36 :TQ 1wab 59 :RE T0286 40 :LSIDFVGS 1wab 63 :SPLHALNF T0286 62 :GHSGWTIPQIASNI 1wab 71 :GIGGDSTQHVLWRL T0286 76 :NNWLNTHNPDVVFLWIGGN 1wab 86 :NGELEHIRPKIVVVWVGTN T0286 99 :NGNLN 1wab 105 :NHGHT T0286 104 :ATGLSNLIDQIFTVKPNVTLFVADYYPW 1wab 114 :TGGIKAIVQLVNERQPQARVVVLGLLPR T0286 132 :PEAIKQYNAVIPGIVQQKANAGKKVYFVKLSEIQFDRNTDISW 1wab 145 :PNPLREKNRRVNELVRAALAGHPRAHFLDADPGFVHSDGTISH T0286 175 :DGLHLSEIGYKKIANIWYKYTIDI 1wab 192 :DYLHLSRLGYTPVCRALHSLLLRL Number of specific fragments extracted= 10 number of extra gaps= 3 total=837 Number of alignments=76 # 1wab read from 1wab/merged-good-all-a2m # found chain 1wab in template set Warning: unaligning (T0286)R33 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1wab)C55 Warning: unaligning (T0286)L34 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1wab)C55 Warning: unaligning (T0286)L35 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1wab)W58 Warning: unaligning (T0286)A38 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1wab)F62 Warning: unaligning (T0286)G39 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1wab)F62 Warning: unaligning (T0286)L199 because last residue in template chain is (1wab)L216 T0286 4 :KTIKIMPVGDSCT 1wab 37 :KEPEVVFIGDSLV T0286 29 :TELY 1wab 50 :QLMH T0286 36 :TQ 1wab 59 :RE T0286 40 :LSIDFVGS 1wab 63 :SPLHALNF T0286 62 :GHSGWTIPQIASNINN 1wab 71 :GIGGDSTQHVLWRLEN T0286 78 :WLNTHNPDVVFLWIGGNDLLLNGNLNATGLSNLIDQIFTVKPNVTLFVADYYPW 1wab 88 :ELEHIRPKIVVVWVGTNNHGHTAEQVTGGIKAIVQLVNERQPQARVVVLGLLPR T0286 132 :PEAIKQYNAVIPGIVQQKANAGKKVYFVKLSEIQFDRNT 1wab 145 :PNPLREKNRRVNELVRAALAGHPRAHFLDADPGFVHSDG T0286 171 :DISWDGLHLSEIGYKKIANIWYKYTIDI 1wab 188 :HDMYDYLHLSRLGYTPVCRALHSLLLRL Number of specific fragments extracted= 8 number of extra gaps= 3 total=845 Number of alignments=77 # 1wab read from 1wab/merged-good-all-a2m # found chain 1wab in template set T0286 19 :MGGGEMGSYRTELYRLLTQAGLSIDFVGSQ 1wab 18 :QGDGRWMSLHHRFVADSKDKEPEVVFIGDS T0286 63 :HSGWTIPQIASNINN 1wab 72 :IGGDSTQHVLWRLEN T0286 78 :WLNTHNPDVVFLWIGGNDLLLNGNLNATGLSNLIDQIFTVKPNVTLFVADYYP 1wab 88 :ELEHIRPKIVVVWVGTNNHGHTAEQVTGGIKAIVQLVNERQPQARVVVLGLLP T0286 131 :WPEAIKQYNAVIPGIVQQKANAGKKVYFVKLSEIQF 1wab 144 :HPNPLREKNRRVNELVRAALAGHPRAHFLDADPGFV T0286 167 :DRNTDISWDGLHLSEIGYKKIANIWYKYTIDI 1wab 184 :TISHHDMYDYLHLSRLGYTPVCRALHSLLLRL Number of specific fragments extracted= 5 number of extra gaps= 0 total=850 Number of alignments=78 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1t2dA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0286 read from 1t2dA/merged-good-all-a2m # 1t2dA read from 1t2dA/merged-good-all-a2m # found chain 1t2dA in training set Warning: unaligning (T0286)S3 because first residue in template chain is (1t2dA)A1 Warning: unaligning (T0286)Y129 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1t2dA)V128 Warning: unaligning (T0286)P130 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1t2dA)V128 T0286 4 :KTIKIMPVG 1t2dA 2 :PKAKIVLVG T0286 24 :MGSYRTELYRLLTQAGL 1t2dA 11 :SGMIGGVMATLIVQKNL T0286 41 :SIDFVGS 1t2dA 29 :DVVLFDI T0286 64 :SGWTIPQIASNINNWL 1t2dA 36 :VKNMPHGKALDTSHTN T0286 80 :NTHN 1t2dA 67 :DDLA T0286 84 :PDVVFLWIGGN 1t2dA 72 :ADVVIVTAGFT T0286 98 :LNGNLN 1t2dA 83 :KAPGKS T0286 104 :ATGLSNLIDQIFTVKPNVTLFVADY 1t2dA 102 :NKIMIEIGGHIKKNCPNAFIIVVTN T0286 132 :PEAIKQYNAVIPGIVQQKANAGK 1t2dA 210 :DAELEAIFDRTVNTALEIVNLHA T0286 165 :QFD 1t2dA 233 :SPY T0286 168 :RNTDISWDGLHLSEIGYKK 1t2dA 282 :ANGVEQVIELQLNSEEKAK T0286 188 :ANIWYKYTIDILR 1t2dA 301 :FDEAIAETKRMKA Number of specific fragments extracted= 12 number of extra gaps= 1 total=862 Number of alignments=79 # 1t2dA read from 1t2dA/merged-good-all-a2m # found chain 1t2dA in training set Warning: unaligning (T0286)S3 because first residue in template chain is (1t2dA)A1 Warning: unaligning (T0286)Y129 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1t2dA)V128 T0286 4 :KTIKIMPVGD 1t2dA 2 :PKAKIVLVGS T0286 26 :SYRTELYRLLTQAGL 1t2dA 13 :MIGGVMATLIVQKNL T0286 41 :SIDFV 1t2dA 29 :DVVLF T0286 62 :GHSGWTIPQIASNINNWLNTHN 1t2dA 34 :DIVKNMPHGKALDTSHTNVMAY T0286 84 :PDVVFLWIGGND 1t2dA 72 :ADVVIVTAGFTK T0286 96 :LLLN 1t2dA 85 :PGKS T0286 100 :GNLNATGLSNLIDQIFTVKPNVTLFVADY 1t2dA 98 :LPLNNKIMIEIGGHIKKNCPNAFIIVVTN T0286 132 :PEAIKQYNAVIPGIVQQKANAGK 1t2dA 210 :DAELEAIFDRTVNTALEIVNLHA T0286 171 :DISW 1t2dA 287 :QVIE T0286 177 :LHLSEIGYKKI 1t2dA 291 :LQLNSEEKAKF T0286 189 :NIWYKYTIDILR 1t2dA 302 :DEAIAETKRMKA Number of specific fragments extracted= 11 number of extra gaps= 1 total=873 Number of alignments=80 # 1t2dA read from 1t2dA/merged-good-all-a2m # found chain 1t2dA in training set Warning: unaligning (T0286)Y129 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1t2dA)V128 Warning: unaligning (T0286)P130 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1t2dA)V128 T0286 4 :KTIKIMPVGD 1t2dA 2 :PKAKIVLVGS T0286 25 :GSYRTELYRLLTQAGL 1t2dA 12 :GMIGGVMATLIVQKNL T0286 41 :SIDFVGSQRS 1t2dA 29 :DVVLFDIVKN T0286 51 :GPSSLPD 1t2dA 62 :GSNTYDD T0286 81 :THNPDVVFLWIGGNDL 1t2dA 69 :LAGADVVIVTAGFTKA T0286 101 :NLNATGLSNLIDQIFTVKPNVTLFVADY 1t2dA 99 :PLNNKIMIEIGGHIKKNCPNAFIIVVTN T0286 131 :WP 1t2dA 234 :PY T0286 136 :KQYNAVIPGIVQQKANAGKKVYFV 1t2dA 236 :VAPAAAIIEMAESYLKDLKKVLIC T0286 160 :KLSEIQFDR 1t2dA 261 :TLLEGQYGH T0286 169 :NTDISWDGLHLSEIGYKKI 1t2dA 283 :NGVEQVIELQLNSEEKAKF T0286 189 :NIWYKYTIDILR 1t2dA 302 :DEAIAETKRMKA Number of specific fragments extracted= 11 number of extra gaps= 1 total=884 Number of alignments=81 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1mh1/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0286 read from 1mh1/merged-good-all-a2m # 1mh1 read from 1mh1/merged-good-all-a2m # found chain 1mh1 in training set T0286 2 :ASKTIKIMPVGD 1mh1 2A:SPQAIKCVVVGD T0286 23 :EMGSYRTELYRLLTQ 1mh1 12 :GAVGKTCLLISYTTN T0286 48 :QRSGPSSLPDKDHEGH 1mh1 27 :AFPGEYIPTVFDNYSA T0286 64 :SGWTI 1mh1 56 :WDTAG T0286 69 :PQIASNINNW 1mh1 62 :EDYDRLRPLS T0286 82 :HN 1mh1 72 :YP T0286 84 :PDVVFLWIGGN 1mh1 75 :TDVSLICFSLV T0286 100 :GN 1mh1 86 :SP T0286 104 :ATGLSN 1mh1 90 :FENVRA T0286 110 :LIDQIFTVKPNVTLFVADYYPW 1mh1 97 :WYPEVRHHCPNTPIILVGTKLD T0286 132 :PEAIKQYNAV 1mh1 122 :DKDTIEKLKE T0286 143 :PGIVQQKANAG 1mh1 139 :YPQGLAMAKEI T0286 155 :KVYFVKLSEIQFD 1mh1 150 :GAVKYLECSALTQ T0286 182 :IGYKKIANIWYKYT 1mh1 163 :RGLKTVFDEAIRAV Number of specific fragments extracted= 14 number of extra gaps= 0 total=898 Number of alignments=82 # 1mh1 read from 1mh1/merged-good-all-a2m # found chain 1mh1 in training set T0286 2 :ASKTIKIMPVGD 1mh1 2A:SPQAIKCVVVGD T0286 25 :GSYRTELYRLLTQAGLS 1mh1 14 :VGKTCLLISYTTNAFPG T0286 51 :GPSSLP 1mh1 31 :EYIPTV T0286 57 :DKDHE 1mh1 57 :DTAGQ T0286 69 :PQIASNINN 1mh1 62 :EDYDRLRPL T0286 81 :THN 1mh1 71 :SYP T0286 84 :PDVVFLWIGGND 1mh1 75 :TDVSLICFSLVS T0286 101 :NLNATGLSN 1mh1 87 :PASFENVRA T0286 110 :LIDQIFTVKPNVTLFVADYYPW 1mh1 97 :WYPEVRHHCPNTPIILVGTKLD T0286 132 :PEAIKQYNAV 1mh1 122 :DKDTIEKLKE T0286 143 :PGIVQQKANAG 1mh1 139 :YPQGLAMAKEI T0286 155 :KVYFVKLSEIQFDRN 1mh1 150 :GAVKYLECSALTQRG T0286 184 :YKKIANIWYKYT 1mh1 165 :LKTVFDEAIRAV Number of specific fragments extracted= 13 number of extra gaps= 0 total=911 Number of alignments=83 # 1mh1 read from 1mh1/merged-good-all-a2m # found chain 1mh1 in training set T0286 2 :ASKTIKIMPVGD 1mh1 2A:SPQAIKCVVVGD T0286 24 :MGSYRTELYRLLTQAGL 1mh1 12 :GAVGKTCLLISYTTNAF T0286 46 :GSQ 1mh1 30 :GEY T0286 51 :GPSSLPDKDH 1mh1 57 :DTAGQEDYDR T0286 76 :NNWLNTHNPDVVFLWIG 1mh1 67 :LRPLSYPQTDVSLICFS T0286 97 :LLNGNLNATGLSNLIDQIFTVKPNVTLFVADYYP 1mh1 84 :LVSPASFENVRAKWYPEVRHHCPNTPIILVGTKL T0286 131 :WPEAIKQYNAV 1mh1 122 :DKDTIEKLKEK T0286 143 :PGIVQQKANAGKKVYFVKLSE 1mh1 139 :YPQGLAMAKEIGAVKYLECSA T0286 179 :LSEIGYKKIANIWYKYT 1mh1 160 :LTQRGLKTVFDEAIRAV Number of specific fragments extracted= 9 number of extra gaps= 0 total=920 Number of alignments=84 # command:# PrintAlignmentsContacts allconstraints.under Using radius: 8.0000 NUMB_ALIGNS: 84 Done printing distance constraints # command: