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/T0313/ # command:# Making conformation for sequence T0313 numbered 1 through 322 Created new target T0313 from T0313.a2m # command:# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/T0313/ # command:Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0313//projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0313/manyalignments-good-all.under or /projects/compbio/experiments/protein-predict/casp7/T0313//projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0313/manyalignments-good-all.under.gz for input Trying /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0313/manyalignments-good-all.under # reading script from file /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0313/manyalignments-good-all.under # Reading fragments from alignment file # Attempting to read fragment alignments from file 3kinB/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 3kinB expands to /projects/compbio/data/pdb/3kin.pdb.gz 3kinB:# T0313 read from 3kinB/merged-good-all-a2m # 3kinB read from 3kinB/merged-good-all-a2m # adding 3kinB to template set # found chain 3kinB in template set T0313 256 :SLSALGDVIAALRSRQG 3kinB 258 :SLSALGNVISALAEGTK # choosing archetypes in rotamer library T0313 273 :HVPFRNSKLTYLLQDSLSGDSKTLMVVQVSPVEKNTSETLYSLKFAERVR 3kinB 276 :HVPYRDSKMTRILQDSLGGNCRTTIVICCSPSVFNEAETKSTLMFGQRAK Number of specific fragments extracted= 2 number of extra gaps= 0 total=2 Number of alignments=1 # 3kinB read from 3kinB/merged-good-all-a2m # found chain 3kinB in template set T0313 256 :SLSALGDVIAALRSRQG 3kinB 258 :SLSALGNVISALAEGTK T0313 273 :HVPFRNSKLTYLLQDSLSGDSKTLMVVQVSPVEKNTSETLYSLKFAERVR 3kinB 276 :HVPYRDSKMTRILQDSLGGNCRTTIVICCSPSVFNEAETKSTLMFGQRAK Number of specific fragments extracted= 2 number of extra gaps= 0 total=4 Number of alignments=2 # 3kinB read from 3kinB/merged-good-all-a2m # found chain 3kinB in template set T0313 256 :SLSALGDVIAALRS 3kinB 258 :SLSALGNVISALAE T0313 270 :RQGHVPFRNSKLTYLLQDSLSGDSKTLMVVQVSPVEKNTSETLYSLKFAERVR 3kinB 273 :TKTHVPYRDSKMTRILQDSLGGNCRTTIVICCSPSVFNEAETKSTLMFGQRAK Number of specific fragments extracted= 2 number of extra gaps= 0 total=6 Number of alignments=3 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2ncdA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2ncdA expands to /projects/compbio/data/pdb/2ncd.pdb.gz 2ncdA:# T0313 read from 2ncdA/merged-good-all-a2m # 2ncdA read from 2ncdA/merged-good-all-a2m # adding 2ncdA to template set # found chain 2ncdA in template set Warning: unaligning (T0313)G241 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2ncdA)N598 Warning: unaligning (T0313)H252 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2ncdA)N598 T0313 2 :IRVIARVRPVTKEDGEGP 2ncdA 349 :IRVFCRIRPPLESEENRM T0313 21 :ATNAVTFDADDDSIIHLL 2ncdA 367 :CCTWTYHDESTVELQSID T0313 39 :HKGKPVSFELDKVFSPQASQQDVFQEVQALVTSCIDGFNVCIFAYGQTGAGKTYTMEGTAENPGINQRALQLLFSEVQEKAS 2ncdA 389 :SKMGQQIFSFDQVFHPLSSQSDIFEMVSPLIQSALDGYNICIFAYGQTGSGKTYTMDGVPESVGVIPRTVDLLFDSIRGYRN T0313 121 :DWEYTITVSAAEIYNEVLRDLLGKEPQ 2ncdA 472 :GWEYEIKATFLEIYNEVLYDLLSNEQK T0313 149 :KLEIRLCPDGSGQLYVPGLTEFQVQSVDDINKVFEFGHTNRTTEFTNLNEHSSRSHALLIVTVRGVDCSTGLRTTGKLNLVDLAGSE 2ncdA 499 :DMEIRMAKNNKNDIYVSNITEETVLDPNHLRHLMHTAKMNRATASTAGNERSSRSHAVTKLELIGRHAEKQEISVGSINLVDLAGSE T0313 240 :S 2ncdA 586 :S T0313 253 :INKSLSALGDVIAALRSRQGHVPFRNSKLTYLLQDSLSGDSKTLMVVQVSPVEKNTSETLYSLKFAERV 2ncdA 599 :INRSLSELTNVILALLQKQDHIPYRNSKLTHLLMPSLGGNSKTLMFINVSPFQDCFQESVKSLRFAASV Number of specific fragments extracted= 7 number of extra gaps= 0 total=13 Number of alignments=4 # 2ncdA read from 2ncdA/merged-good-all-a2m # found chain 2ncdA in template set Warning: unaligning (T0313)G241 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2ncdA)N598 Warning: unaligning (T0313)H252 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2ncdA)N598 T0313 1 :NIRVIARVRPVTKEDG 2ncdA 348 :NIRVFCRIRPPLESEE T0313 19 :PEATNAVTFDADDDSIIHLL 2ncdA 364 :NRMCCTWTYHDESTVELQSI T0313 39 :HKGKPVSFELDKVFSPQASQQDVFQEVQALVTSCIDGFNVCIFAYGQTGAGKTYTMEGTAENPGINQRALQLLFSEVQEKAS 2ncdA 389 :SKMGQQIFSFDQVFHPLSSQSDIFEMVSPLIQSALDGYNICIFAYGQTGSGKTYTMDGVPESVGVIPRTVDLLFDSIRGYRN T0313 121 :DWEYTITVSAAEIYNEVLRDLLGKEPQE 2ncdA 472 :GWEYEIKATFLEIYNEVLYDLLSNEQKD T0313 152 :IRLCPDG 2ncdA 500 :MEIRMAK T0313 159 :SGQLYVPGLTEFQVQSVDDINKVFEFGHTNRTTEFTNLNEHSSRSHALLIVTVRGVDCSTGLRTTGKLNLVDLAGSER 2ncdA 509 :KNDIYVSNITEETVLDPNHLRHLMHTAKMNRATASTAGNERSSRSHAVTKLELIGRHAEKQEISVGSINLVDLAGSES T0313 253 :INKSLSALGDVIAALRSRQGHVPFRNSKLTYLLQDSLSGDSKTLMVVQVSPVEKNTSETLYSLKFAERV 2ncdA 599 :INRSLSELTNVILALLQKQDHIPYRNSKLTHLLMPSLGGNSKTLMFINVSPFQDCFQESVKSLRFAASV Number of specific fragments extracted= 7 number of extra gaps= 0 total=20 Number of alignments=5 # 2ncdA read from 2ncdA/merged-good-all-a2m # found chain 2ncdA in template set Warning: unaligning (T0313)G241 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2ncdA)N598 Warning: unaligning (T0313)H252 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2ncdA)N598 T0313 1 :NIRVIARVRPVTKEDGEGPEAT 2ncdA 348 :NIRVFCRIRPPLESEENRMCCT T0313 25 :VTFDADDDSIIHLL 2ncdA 370 :WTYHDESTVELQSI T0313 39 :HKGKPVSFELDKVFSPQASQQDVFQEVQALVTSCIDGFNVCIFAYGQTGAGKTYTMEGTAENPGINQRALQLLFSEVQE 2ncdA 389 :SKMGQQIFSFDQVFHPLSSQSDIFEMVSPLIQSALDGYNICIFAYGQTGSGKTYTMDGVPESVGVIPRTVDLLFDSIRG T0313 118 :KASDWEYTITVSAAEIYNEVLRDLLGKEPQE 2ncdA 469 :RNLGWEYEIKATFLEIYNEVLYDLLSNEQKD T0313 150 :LEIRLCPDGSGQLYVPGLTEFQVQSVDDINKVFEFGHTNRTTEFTNLNEHSSRSHALLIVTVRGVDCSTGLRTTGKLNLVDLAGSE 2ncdA 500 :MEIRMAKNNKNDIYVSNITEETVLDPNHLRHLMHTAKMNRATASTAGNERSSRSHAVTKLELIGRHAEKQEISVGSINLVDLAGSE T0313 240 :S 2ncdA 586 :S T0313 253 :INKSLSALGDVIAALRSRQGHVPFRNSKLTYLLQDSLSGDSKTLMVVQVSPVEKNTSETLYSLKFAERV 2ncdA 599 :INRSLSELTNVILALLQKQDHIPYRNSKLTHLLMPSLGGNSKTLMFINVSPFQDCFQESVKSLRFAASV Number of specific fragments extracted= 7 number of extra gaps= 0 total=27 Number of alignments=6 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2kinA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2kinA expands to /projects/compbio/data/pdb/2kin.pdb.gz 2kinA:Skipped atom 1516, because occupancy 0.5 <= existing 0.500 in 2kinA Skipped atom 1518, because occupancy 0.500 <= existing 0.500 in 2kinA Skipped atom 1520, because occupancy 0.500 <= existing 0.500 in 2kinA Skipped atom 1522, because occupancy 0.500 <= existing 0.500 in 2kinA Skipped atom 1524, because occupancy 0.500 <= existing 0.500 in 2kinA Skipped atom 1526, because occupancy 0.500 <= existing 0.500 in 2kinA Skipped atom 1528, because occupancy 0.500 <= existing 0.500 in 2kinA Skipped atom 1636, because occupancy 0.500 <= existing 0.500 in 2kinA Skipped atom 1638, because occupancy 0.500 <= existing 0.500 in 2kinA # T0313 read from 2kinA/merged-good-all-a2m # 2kinA read from 2kinA/merged-good-all-a2m # adding 2kinA to template set # found chain 2kinA in template set Warning: unaligning (T0313)T86 because of BadResidue code BAD_PEPTIDE in next template residue (2kinA)S89 Warning: unaligning (T0313)G87 because of BadResidue code BAD_PEPTIDE at template residue (2kinA)S89 T0313 3 :RVIARVRPVTKEDGEGPEATNAVTFDADDDSI 2kinA 10 :KVMCRFRPLNEAEILRGDKFIPKFKGEETVVI T0313 39 :HKGKP 2kinA 42 :GQGKP T0313 46 :FELDKVFSPQASQQDVFQEV 2kinA 47 :YVFDRVLPPNTTQEQVYNAC T0313 66 :QALVTSCIDGFNVCIFAYGQ 2kinA 68 :KQIVKDVLEGYNGTIFAYGQ T0313 88 :AGKTYTMEG 2kinA 90 :SGKTHTMEG T0313 97 :TAENPGINQRALQLLFSEVQEKASDWEYTITVSAAEIYNEVLRDLLGKEPQ 2kinA 102 :DPQLMGIIPRIAHDIFDHIYSMDENLEFHIKVSYFEIYLDKIRDLLDVSKT T0313 151 :EIRLCPDGSGQLYVPGLTEFQVQSVDDINKVFEFGHTNRTTEFTNLNEHSSRSHALLIVTVRGVDCSTGLRTTGKLNLVDLAGSER 2kinA 153 :NLAVHEDKNRVPYVKGCTERFVSSPEEVMDVIDEGKANRHVAVTNMNEHSSRSHSIFLINIKQENVETEKKLSGKLYLVDLAGSEK Number of specific fragments extracted= 7 number of extra gaps= 1 total=34 Number of alignments=7 # 2kinA read from 2kinA/merged-good-all-a2m # found chain 2kinA in template set Warning: unaligning (T0313)T86 because of BadResidue code BAD_PEPTIDE in next template residue (2kinA)S89 Warning: unaligning (T0313)G87 because of BadResidue code BAD_PEPTIDE at template residue (2kinA)S89 T0313 2 :IRVIARVRPVTKEDGEGPEATNAVTFDADDDSI 2kinA 9 :IKVMCRFRPLNEAEILRGDKFIPKFKGEETVVI T0313 41 :GKPVSFELDKVFSPQASQQDVFQEV 2kinA 42 :GQGKPYVFDRVLPPNTTQEQVYNAC T0313 66 :QALVTSCIDGFNVCIFAYGQ 2kinA 68 :KQIVKDVLEGYNGTIFAYGQ T0313 88 :AGKTYTMEGTAENP 2kinA 90 :SGKTHTMEGKLHDP T0313 102 :GINQRALQLLFSEVQEKASDWEYTITVSAAEIYNEVLRDLLGKEPQE 2kinA 107 :GIIPRIAHDIFDHIYSMDENLEFHIKVSYFEIYLDKIRDLLDVSKTN T0313 152 :IRLCPDGSGQLYVPGLTEFQVQSVDDINKVFEFGHTNRTTEFTNLNEHSSRSHALLIVTVRGVDCSTGLRTTGKLNLVDLAGSER 2kinA 154 :LAVHEDKNRVPYVKGCTERFVSSPEEVMDVIDEGKANRHVAVTNMNEHSSRSHSIFLINIKQENVETEKKLSGKLYLVDLAGSEK Number of specific fragments extracted= 6 number of extra gaps= 1 total=40 Number of alignments=8 # 2kinA read from 2kinA/merged-good-all-a2m # found chain 2kinA in template set Warning: unaligning (T0313)T86 because of BadResidue code BAD_PEPTIDE in next template residue (2kinA)S89 Warning: unaligning (T0313)G87 because of BadResidue code BAD_PEPTIDE at template residue (2kinA)S89 T0313 3 :RVIARVRPVTKEDGEGPEATNAVTFDADDDSI 2kinA 10 :KVMCRFRPLNEAEILRGDKFIPKFKGEETVVI T0313 41 :GKPVSFELDKVFSPQASQQDVFQ 2kinA 42 :GQGKPYVFDRVLPPNTTQEQVYN T0313 64 :EVQALVTSCIDGFNVCIFAYGQ 2kinA 66 :CAKQIVKDVLEGYNGTIFAYGQ T0313 88 :AGKTYTMEG 2kinA 90 :SGKTHTMEG T0313 97 :TAENPGINQRALQLLFSEVQEKASDWEYTITVSAAEIYNEVLRDLLGKEPQE 2kinA 102 :DPQLMGIIPRIAHDIFDHIYSMDENLEFHIKVSYFEIYLDKIRDLLDVSKTN T0313 152 :IRLCPDGSGQLYVPGLTEFQVQSVDDINKVFEFGHTNRTTEFTNLNEHSSRSHALLIVTVRGVDCSTGLRTTGKLNLVDLAGSER 2kinA 154 :LAVHEDKNRVPYVKGCTERFVSSPEEVMDVIDEGKANRHVAVTNMNEHSSRSHSIFLINIKQENVETEKKLSGKLYLVDLAGSEK Number of specific fragments extracted= 6 number of extra gaps= 1 total=46 Number of alignments=9 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1v8kA/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/T0313/1v8kA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0313/1v8kA/merged-good-all-a2m.gz for input Trying 1v8kA/merged-good-all-a2m Error: Couldn't open file 1v8kA/merged-good-all-a2m or 1v8kA/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1t5cA/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/T0313/1t5cA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0313/1t5cA/merged-good-all-a2m.gz for input Trying 1t5cA/merged-good-all-a2m Error: Couldn't open file 1t5cA/merged-good-all-a2m or 1t5cA/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1gojA/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/T0313/1gojA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0313/1gojA/merged-good-all-a2m.gz for input Trying 1gojA/merged-good-all-a2m Error: Couldn't open file 1gojA/merged-good-all-a2m or 1gojA/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1bg2/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0313 read from 1bg2/merged-good-all-a2m # 1bg2 read from 1bg2/merged-good-all-a2m # found chain 1bg2 in training set T0313 2 :IRVIARVRPVTKEDGEGPEATNAVTFDADDDSII 1bg2 9 :IKVMCRFRPLNESEVNRGDKYIAKFQGEDTVVIA T0313 43 :PVSFELDKVFSPQASQQDVFQEV 1bg2 43 :SKPYAFDRVFQSSTSQEQVYNDC T0313 66 :QALVTSCIDGFNVCIFAYGQTGAGKTYTMEG 1bg2 67 :KKIVKDVLEGYNGTIFAYGQTSSGKTHTMEG T0313 97 :TAENPGINQRALQLLFSEVQEKASDWEYTITVSAAEIYNEVLRDLLGKEPQ 1bg2 101 :DPEGMGIIPRIVQDIFNYIYSMDENLEFHIKVSYFEIYLDKIRDLLDVSKT T0313 151 :EIRLCPDGSGQLYVPGLTEFQVQSVDDINKVFEFGHTNRTTEFTNLNEHSSRSHALLIVTVRGVDCSTGLRTTGKLNLVDLAGSERVGKSGAEGS 1bg2 152 :NLSVHEDKNRVPYVKGCTERFVCSPDEVMDTIDEGKSNRHVAVTNMNEHSSRSHSIFLINVKQENTQTEQKLSGKLYLVDLAGSEKVSKTGAEGA T0313 246 :R 1bg2 254 :I T0313 254 :NKSLSALGDVIAALRSRQGHVPFRNSKLTYLLQDSLSGDSKTLMVVQVSPVEKNTSETLYSLKFAERVR 1bg2 255 :NKSLSALGNVISALAEGSTYVPYRDSKMTRILQDSLGGNCRTTIVICCSPSSYNESETKSTLLFGQRAK Number of specific fragments extracted= 7 number of extra gaps= 0 total=53 Number of alignments=10 # 1bg2 read from 1bg2/merged-good-all-a2m # found chain 1bg2 in training set T0313 1 :NIRVIARVRPVTKEDGEGPEATNAVTFDADDDSI 1bg2 8 :NIKVMCRFRPLNESEVNRGDKYIAKFQGEDTVVI T0313 42 :KPVSFELDKVFSPQASQQDVFQEV 1bg2 42 :ASKPYAFDRVFQSSTSQEQVYNDC T0313 66 :QALVTSCIDGFNVCIFAYGQTGAGKTYTMEG 1bg2 67 :KKIVKDVLEGYNGTIFAYGQTSSGKTHTMEG T0313 97 :TAENPGINQRALQLLFSEVQEKASDWEYTITVSAAEIYNEVLRDLLGKEPQE 1bg2 101 :DPEGMGIIPRIVQDIFNYIYSMDENLEFHIKVSYFEIYLDKIRDLLDVSKTN T0313 152 :IRLCPDGSGQLYVPGLTEFQVQSVDDINKVFEFGHTNRTTEFTNLNEHSSRSHALLIVTVRGVDCSTGLRTTGKLNLVDLAGSERVGKSGAEGSRLREAQHINKSLSALGDVIAALRSRQGHVPFRNSKLTYLLQDSLSGDSKTLMVVQVSPVEKNTSETLYSLKFAERVR 1bg2 153 :LSVHEDKNRVPYVKGCTERFVCSPDEVMDTIDEGKSNRHVAVTNMNEHSSRSHSIFLINVKQENTQTEQKLSGKLYLVDLAGSEKVSKTGAEGAVLDEAKNINKSLSALGNVISALAEGSTYVPYRDSKMTRILQDSLGGNCRTTIVICCSPSSYNESETKSTLLFGQRAK Number of specific fragments extracted= 5 number of extra gaps= 0 total=58 Number of alignments=11 # 1bg2 read from 1bg2/merged-good-all-a2m # found chain 1bg2 in training set T0313 1 :NIRVIARVRPVTKEDGEGPEATNAVTFDADDDSII 1bg2 8 :NIKVMCRFRPLNESEVNRGDKYIAKFQGEDTVVIA T0313 43 :PVSFELDKVFSPQASQQDVFQ 1bg2 43 :SKPYAFDRVFQSSTSQEQVYN T0313 64 :EVQALVTSCIDGFNVCIFAYGQTGAGKTYTMEG 1bg2 65 :CAKKIVKDVLEGYNGTIFAYGQTSSGKTHTMEG T0313 97 :TAENPGINQRALQLLFSEVQEKASDWEYTITVSAAEIYNEVLRDLLGKEPQE 1bg2 101 :DPEGMGIIPRIVQDIFNYIYSMDENLEFHIKVSYFEIYLDKIRDLLDVSKTN T0313 152 :IRLCPDGSGQLYVPGLTEFQVQSVDDINKVFEFGHTNRTTEFTNLNEHSSRSHALLIVTVRGVDCSTGLRTTGKLNLVDLAGSERVGKSGAEG 1bg2 153 :LSVHEDKNRVPYVKGCTERFVCSPDEVMDTIDEGKSNRHVAVTNMNEHSSRSHSIFLINVKQENTQTEQKLSGKLYLVDLAGSEKVSKTGAEG T0313 254 :NKSLSALGDVIAALRSRQGHVPFRNSKLTYLLQDSLSGDSKTLMVVQVSPVEKNTSETLYSLKFAERVR 1bg2 255 :NKSLSALGNVISALAEGSTYVPYRDSKMTRILQDSLGGNCRTTIVICCSPSSYNESETKSTLLFGQRAK Number of specific fragments extracted= 6 number of extra gaps= 0 total=64 Number of alignments=12 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2kinB/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2kinB expands to /projects/compbio/data/pdb/2kin.pdb.gz 2kinB:# T0313 read from 2kinB/merged-good-all-a2m # 2kinB read from 2kinB/merged-good-all-a2m # adding 2kinB to template set # found chain 2kinB in template set Warning: unaligning (T0313)G272 because of BadResidue code BAD_PEPTIDE in next template residue (2kinB)T275 T0313 255 :KSLSALGDVIAALRSRQ 2kinB 257 :KSLSALGNVISALAEGT T0313 273 :HVPFRNSKLTYLLQDSLSGDSKTLMVVQVSPVEKNTSETLYSLKFAERVR 2kinB 276 :HVPYRDSKMTRILQDSLDGNCRTTIVICCSPSVFNEAETKSTLMFGQRAK Number of specific fragments extracted= 2 number of extra gaps= 1 total=66 # 2kinB read from 2kinB/merged-good-all-a2m # found chain 2kinB in template set Warning: unaligning (T0313)G272 because of BadResidue code BAD_PEPTIDE at template residue (2kinB)T275 T0313 255 :KSLSALGDVIAALRSRQ 2kinB 257 :KSLSALGNVISALAEGT T0313 273 :HVPFRNSKLTYLLQDSLSGDSKTLMVVQVSPVEKNTSETLYSLKFAERVR 2kinB 276 :HVPYRDSKMTRILQDSLDGNCRTTIVICCSPSVFNEAETKSTLMFGQRAK Number of specific fragments extracted= 2 number of extra gaps= 1 total=68 # 2kinB read from 2kinB/merged-good-all-a2m # found chain 2kinB in template set Warning: unaligning (T0313)Q271 because of BadResidue code BAD_PEPTIDE in next template residue (2kinB)T275 Warning: unaligning (T0313)G272 because of BadResidue code BAD_PEPTIDE at template residue (2kinB)T275 T0313 255 :KSLSALGDVIAALRS 2kinB 257 :KSLSALGNVISALAE T0313 270 :R 2kinB 273 :T T0313 273 :HVPFRNSKLTYLLQDSLSGDSKTLMVVQVSPVEKNTSETLYSLKFAERVR 2kinB 276 :HVPYRDSKMTRILQDSLDGNCRTTIVICCSPSVFNEAETKSTLMFGQRAK Number of specific fragments extracted= 3 number of extra gaps= 1 total=71 Number of alignments=13 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1mkjA/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/T0313/1mkjA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0313/1mkjA/merged-good-all-a2m.gz for input Trying 1mkjA/merged-good-all-a2m Error: Couldn't open file 1mkjA/merged-good-all-a2m or 1mkjA/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 2gryA/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/T0313/2gryA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0313/2gryA/merged-good-all-a2m.gz for input Trying 2gryA/merged-good-all-a2m Error: Couldn't open file 2gryA/merged-good-all-a2m or 2gryA/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1x88A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1x88A expands to /projects/compbio/data/pdb/1x88.pdb.gz 1x88A:# T0313 read from 1x88A/merged-good-all-a2m # 1x88A read from 1x88A/merged-good-all-a2m # adding 1x88A to template set # found chain 1x88A in template set Warning: unaligning (T0313)R236 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1x88A)N287 Warning: unaligning (T0313)H252 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1x88A)N287 T0313 1 :NIRVIARVRPVTKEDGEGPEATNAVTFDADDDSIIH 1x88A 18 :NIQVVVRCRPFNLAERKASAHSIVECDPVRKEVSVR T0313 37 :LLHKGKPVSFELDKVFSPQASQQDVFQEV 1x88A 57 :LADKSSRKTYTFDMVFGASTKQIDVYRSV T0313 66 :QALVTSCIDGFNVCIFAYGQTGAGKTYTMEGTAENP 1x88A 87 :CPILDEVIMGYNCTIFAYGQTGTGKTFTMEGERSPN T0313 102 :GINQRALQLLFSEV 1x88A 134 :GIIPRTLHQIFEKL T0313 118 :KASDWEYTITVSAAEIYNEVLRDLLGKEPQEKLEIRLCPDGS 1x88A 148 :TDNGTEFSVKVSLLEIYNEELFDLLNPSSDVSERLQMFDDPR T0313 160 :GQLYVPGLTEFQVQSVDDINKVFEFGHTNRTTEFTNLNEHSSRSHALLIVTVRGVDC 1x88A 192 :RGVIIKGLEEITVHNKDEVYQILEKGAAKRTTAATLMNAYSSRSHSVFSVTIHMKET T0313 217 :STG 1x88A 250 :IDG T0313 220 :LRTTGKLNLVDLAGSE 1x88A 255 :LVKIGKLNLVDLAGSE T0313 253 :INKSLSALGDVIAALRSRQGHVPFRNSKLTYLLQDSLSGDSKTLMVVQVSPVEKNTSETLYSLKFAERVR 1x88A 288 :INQSLLTLGRVITALVERTPHVPYRESKLTRILQDSLGGRTRTSIIATISPASLNLEETLSTLEYAHRAK Number of specific fragments extracted= 9 number of extra gaps= 0 total=80 Number of alignments=14 # 1x88A read from 1x88A/merged-good-all-a2m # found chain 1x88A in template set Warning: unaligning (T0313)R236 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1x88A)N287 Warning: unaligning (T0313)H252 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1x88A)N287 T0313 1 :NIRVIARVRPVTKEDGEGPEATNAVTFDADDDSIIHLLHKGKP 1x88A 18 :NIQVVVRCRPFNLAERKASAHSIVECDPVRKEVSVRTGGLADK T0313 44 :VSFELDKVFSPQASQQDVFQE 1x88A 64 :KTYTFDMVFGASTKQIDVYRS T0313 65 :VQALVTSCIDGFNVCIFAYGQTGAGKTYTMEGT 1x88A 86 :VCPILDEVIMGYNCTIFAYGQTGTGKTFTMEGE T0313 98 :AENP 1x88A 128 :EEDP T0313 102 :GINQRALQLLFSEV 1x88A 134 :GIIPRTLHQIFEKL T0313 118 :KASDWEYTITVSAAEIYNEVLRDLLGKEPQEKLEIRLCPDGSG 1x88A 148 :TDNGTEFSVKVSLLEIYNEELFDLLNPSSDVSERLQMFDDPRN T0313 161 :QLYVPGLTEFQVQSVDDINKVFEFGHTNRTTEFTNLNEHSSRSHALLIVTVRGVDC 1x88A 193 :GVIIKGLEEITVHNKDEVYQILEKGAAKRTTAATLMNAYSSRSHSVFSVTIHMKET T0313 217 :STG 1x88A 250 :IDG T0313 220 :LRTTGKLNLVDLAGSE 1x88A 255 :LVKIGKLNLVDLAGSE T0313 253 :INKSLSALGDVIAALRSRQGHVPFRNSKLTYLLQDSLSGDSKTLMVVQVSPVEKNTSETLYSLKFAERVR 1x88A 288 :INQSLLTLGRVITALVERTPHVPYRESKLTRILQDSLGGRTRTSIIATISPASLNLEETLSTLEYAHRAK Number of specific fragments extracted= 10 number of extra gaps= 0 total=90 Number of alignments=15 # 1x88A read from 1x88A/merged-good-all-a2m # found chain 1x88A in template set Warning: unaligning (T0313)R236 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1x88A)N287 Warning: unaligning (T0313)H252 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1x88A)N287 T0313 1 :NIRVIARVRPVTKEDGEGPEATNAVTFDADDDSIIHLLHKGK 1x88A 18 :NIQVVVRCRPFNLAERKASAHSIVECDPVRKEVSVRTGGLAD T0313 43 :PVSFELDKVFSPQASQQDVFQ 1x88A 63 :RKTYTFDMVFGASTKQIDVYR T0313 64 :EVQALVTSCIDGFNVCIFAYGQTGAGKTYTMEG 1x88A 85 :VVCPILDEVIMGYNCTIFAYGQTGTGKTFTMEG T0313 97 :TAENPGINQRALQLLFSEV 1x88A 129 :EDPLAGIIPRTLHQIFEKL T0313 118 :KASDWEYTITVSAAEIYNEVLRDLLGKEPQEKLEIRLCPDGS 1x88A 148 :TDNGTEFSVKVSLLEIYNEELFDLLNPSSDVSERLQMFDDPR T0313 160 :GQLYVPGLTEFQVQSVDDINKVFEFGHTNRTTEFTNLNEHSSRSHALLIVTVRGVDCSTGL 1x88A 192 :RGVIIKGLEEITVHNKDEVYQILEKGAAKRTTAATLMNAYSSRSHSVFSVTIHMKETTIDG T0313 221 :RTTGKLNLVDLAGSE 1x88A 256 :VKIGKLNLVDLAGSE T0313 253 :INKSLSALGDVIAALRSRQGHVPFRNSKLTYLLQDSLSGDSKTLMVVQVSPVEKNTSETLYSLKFAERVR 1x88A 288 :INQSLLTLGRVITALVERTPHVPYRESKLTRILQDSLGGRTRTSIIATISPASLNLEETLSTLEYAHRAK Number of specific fragments extracted= 8 number of extra gaps= 0 total=98 Number of alignments=16 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3kar/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 3kar expands to /projects/compbio/data/pdb/3kar.pdb.gz 3kar:Warning: there is no chain 3kar will retry with 3karA # T0313 read from 3kar/merged-good-all-a2m # 3kar read from 3kar/merged-good-all-a2m # adding 3kar to template set # found chain 3kar in template set Warning: unaligning (T0313)K144 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (3kar)L545 Warning: unaligning (T0313)L150 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (3kar)L545 Warning: unaligning (T0313)S240 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (3kar)D641 Warning: unaligning (T0313)S245 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (3kar)D641 T0313 1 :NIRVIARVRPVTKEDGEGPEATNAVT 3kar 386 :NIRVYCRIRPALKNLENSDTSLINVN T0313 27 :FDADDDSIIH 3kar 414 :DDNSGVQSME T0313 37 :LLHKGKPVSFELDKVFSPQASQQDVFQEVQALVTSCIDGFNVCIFAYGQTGAGKTYTME 3kar 427 :IQNTAQVHEFKFDKIFDQQDTNVDVFKEVGQLVQSSLDGYNVCIFAYGQTGSGKTFTML T0313 98 :AENPGINQRALQLLFSEVQEK 3kar 486 :NPGDGIIPSTISHIFNWINKL T0313 119 :ASDWEYTITVSAAEIYNEVLRDLLG 3kar 508 :TKGWDYKVNCEFIEIYNENIVDLLR T0313 151 :EIRLCPDGS 3kar 546 :KHEIRHDQE T0313 160 :GQLYVPGLTEFQVQSVDDINKVFEFGHTNRTTEFTNLNEHSSRSHALLIVTVRGVDCSTGLRTTGKLNLVDLAGSERVGK 3kar 556 :KTTTITNVTSCKLESEEMVEIILKKANKLRSTASTASNEHSSRSHSIFIIHLSGSNAKTGAHSYGTLNLVDLAGSERINV T0313 246 :RLREAQHINKSLSALGDVIAALRS 3kar 642 :RLRETQNINKSLSCLGDVIHALGQ T0313 270 :RQGHVPFRNSKLTYLLQDSLSGDSKTLMVVQVSPVEKNTSETLYSLKFAERV 3kar 669 :TKRHIPFRNSKLTYLLQYSLTGDSKTLMFVNISPSSSHINETLNSLRFASKV Number of specific fragments extracted= 9 number of extra gaps= 0 total=107 Number of alignments=17 # 3kar read from 3kar/merged-good-all-a2m # found chain 3kar in template set Warning: unaligning (T0313)K144 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (3kar)L545 Warning: unaligning (T0313)L150 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (3kar)L545 Warning: unaligning (T0313)S240 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (3kar)D641 Warning: unaligning (T0313)S245 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (3kar)D641 T0313 1 :NIRVIARVRPVTKEDGEGPEATNAVT 3kar 386 :NIRVYCRIRPALKNLENSDTSLINVN T0313 27 :FDADDDSIIHLLHKGKP 3kar 414 :DDNSGVQSMEVTKIQNT T0313 44 :VSFELDKVFSPQASQQDVFQEVQALVTSCIDGFNVCIFAYGQTGAGKTYTMEGTA 3kar 434 :HEFKFDKIFDQQDTNVDVFKEVGQLVQSSLDGYNVCIFAYGQTGSGKTFTMLNPG T0313 101 :PGINQRALQLLFSEVQEK 3kar 489 :DGIIPSTISHIFNWINKL T0313 119 :ASDWEYTITVSAAEIYNEVLRDLLG 3kar 508 :TKGWDYKVNCEFIEIYNENIVDLLR T0313 151 :EIRLCPDGSGQ 3kar 546 :KHEIRHDQETK T0313 162 :LYVPGLTEFQVQSVDDINKVFEFGHTNRTTEFTNLNEHSSRSHALLIVTVRGVDCSTGLRTTGKLNLVDLAGSERVGK 3kar 558 :TTITNVTSCKLESEEMVEIILKKANKLRSTASTASNEHSSRSHSIFIIHLSGSNAKTGAHSYGTLNLVDLAGSERINV T0313 246 :RLREAQHINKSLSALGDVIAALRS 3kar 642 :RLRETQNINKSLSCLGDVIHALGQ T0313 270 :RQGHVPFRNSKLTYLLQDSLSGDSKTLMVVQVSPVEKNTSETLYSLKFAERV 3kar 669 :TKRHIPFRNSKLTYLLQYSLTGDSKTLMFVNISPSSSHINETLNSLRFASKV Number of specific fragments extracted= 9 number of extra gaps= 0 total=116 Number of alignments=18 # 3kar read from 3kar/merged-good-all-a2m # found chain 3kar in template set Warning: unaligning (T0313)E148 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (3kar)L545 Warning: unaligning (T0313)S240 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (3kar)D641 Warning: unaligning (T0313)S245 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (3kar)D641 T0313 1 :NIRVIARVRPVTKEDGEGPEATNAV 3kar 386 :NIRVYCRIRPALKNLENSDTSLINV T0313 26 :TFDADDDSI 3kar 412 :EFDDNSGVQ T0313 35 :IHLLHKGKPVSFELDKVFSPQASQQDVFQEVQALVTSCIDGFNVCIFAYGQTGAGKTYTME 3kar 425 :TKIQNTAQVHEFKFDKIFDQQDTNVDVFKEVGQLVQSSLDGYNVCIFAYGQTGSGKTFTML T0313 98 :AENPGINQRALQLLFSEVQE 3kar 486 :NPGDGIIPSTISHIFNWINK T0313 118 :KASDWEYTITVSAAEIYNEVLRDLL 3kar 507 :KTKGWDYKVNCEFIEIYNENIVDLL T0313 149 :KLEIRL 3kar 546 :KHEIRH T0313 156 :PDGSGQLYVPGLTEFQVQSVDDINKVFEFGHTNRTTEFTNLNEHSSRSHALLIVTVRGVDCSTGLRTTGKLNLVDLAGSERVGK 3kar 552 :DQETKTTTITNVTSCKLESEEMVEIILKKANKLRSTASTASNEHSSRSHSIFIIHLSGSNAKTGAHSYGTLNLVDLAGSERINV T0313 246 :RLREAQHINKSLSALGDVIAALRS 3kar 642 :RLRETQNINKSLSCLGDVIHALGQ T0313 270 :RQGHVPFRNSKLTYLLQDSLSGDSKTLMVVQVSPVEKNTSETLYSLKFAERV 3kar 669 :TKRHIPFRNSKLTYLLQYSLTGDSKTLMFVNISPSSSHINETLNSLRFASKV Number of specific fragments extracted= 9 number of extra gaps= 0 total=125 Number of alignments=19 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1sdmA/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/T0313/1sdmA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0313/1sdmA/merged-good-all-a2m.gz for input Trying 1sdmA/merged-good-all-a2m Error: Couldn't open file 1sdmA/merged-good-all-a2m or 1sdmA/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1q0bA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1q0bA expands to /projects/compbio/data/pdb/1q0b.pdb.gz 1q0bA:# T0313 read from 1q0bA/merged-good-all-a2m # 1q0bA read from 1q0bA/merged-good-all-a2m # adding 1q0bA to template set # found chain 1q0bA in template set Warning: unaligning (T0313)R236 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1q0bA)I288 Warning: unaligning (T0313)V237 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1q0bA)I288 T0313 2 :IRVIARVRPVTKEDGEGPEATNAVTFD 1q0bA 19 :IQVVVRCRPFNLAERKASAHSIVECDP T0313 29 :ADDDSIIHLLHKGKP 1q0bA 47 :RKEVSVRTGGLADKS T0313 44 :VSFELDKVFSPQASQQDVFQEV 1q0bA 64 :KTYTFDMVFGASTKQIDVYRSV T0313 66 :QALVTSCIDGFNVCIFAYGQTGAGKTYTMEG 1q0bA 87 :CPILDEVIMGYNCTIFAYGQTGTGKTFTMEG T0313 102 :GINQRALQLLFSEVQE 1q0bA 134 :GIIPRTLHQIFEKLTD T0313 120 :SDWEYTITVSAAEIYNEVLRDLLGKEPQEKLEIRLCPDG 1q0bA 150 :NGTEFSVKVSLLEIYNEELFDLLNPSSDVSERLQMFDDP T0313 159 :SGQLYVPGLTEFQVQSVDDINKVFEFGHTNRTTEFTNLNEHSSRSHALLIVTVRGV 1q0bA 191 :KRGVIIKGLEEITVHNKDEVYQILEKGAAKRTTAATLMNAYSSRSHSVFSVTIHMK T0313 215 :DCSTG 1q0bA 248 :TTIDG T0313 220 :LRTTGKLNLVDLAGSE 1q0bA 255 :LVKIGKLNLVDLAGSE T0313 254 :NKSLSALGDVIAALRSRQGHVPFRNSKLTYLLQDSLSGDSKTLMVVQVSPVEKNTSETLYSLKFAERVR 1q0bA 289 :NQSLLTLGRVITALVERTPHVPYRESKLTRILQDSLGGRTRTSIIATISPASLNLEETLSTLEYAHRAK Number of specific fragments extracted= 10 number of extra gaps= 1 total=135 Number of alignments=20 # 1q0bA read from 1q0bA/merged-good-all-a2m # found chain 1q0bA in template set Warning: unaligning (T0313)R236 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1q0bA)I288 Warning: unaligning (T0313)V237 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1q0bA)I288 T0313 1 :NIRVIARVRPVTKEDGEGPEATNAVTFDADDDSIIHLLHKGKP 1q0bA 18 :NIQVVVRCRPFNLAERKASAHSIVECDPVRKEVSVRTGGLADK T0313 44 :VSFELDKVFSPQASQQDVFQE 1q0bA 64 :KTYTFDMVFGASTKQIDVYRS T0313 65 :VQALVTSCIDGFNVCIFAYGQTGAGKTYTMEGT 1q0bA 86 :VCPILDEVIMGYNCTIFAYGQTGTGKTFTMEGE T0313 98 :AENP 1q0bA 128 :EEDP T0313 102 :GINQRALQLLFSEVQE 1q0bA 134 :GIIPRTLHQIFEKLTD T0313 120 :SDWEYTITVSAAEIYNEVLRDLLGKEPQEKLEIRLCPDG 1q0bA 150 :NGTEFSVKVSLLEIYNEELFDLLNPSSDVSERLQMFDDP T0313 159 :SGQLYVPGLTEFQVQSVDDINKVFEFGHTNRTTEFTNLNEHSSRSHALLIVTVRGVDC 1q0bA 191 :KRGVIIKGLEEITVHNKDEVYQILEKGAAKRTTAATLMNAYSSRSHSVFSVTIHMKET T0313 217 :STG 1q0bA 250 :IDG T0313 220 :LRTTGKLNLVDLAGSE 1q0bA 255 :LVKIGKLNLVDLAGSE T0313 254 :NKSLSALGDVIAALRSRQGHVPFRNSKLTYLLQDSLSGDSKTLMVVQVSPVEKNTSETLYSLKFAERVR 1q0bA 289 :NQSLLTLGRVITALVERTPHVPYRESKLTRILQDSLGGRTRTSIIATISPASLNLEETLSTLEYAHRAK Number of specific fragments extracted= 10 number of extra gaps= 1 total=145 Number of alignments=21 # 1q0bA read from 1q0bA/merged-good-all-a2m # found chain 1q0bA in template set Warning: unaligning (T0313)R236 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1q0bA)I288 Warning: unaligning (T0313)V237 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1q0bA)I288 T0313 2 :IRVIARVRPVTKEDGEGPEATNAVTFDADDDSIIHLLHKGK 1q0bA 19 :IQVVVRCRPFNLAERKASAHSIVECDPVRKEVSVRTGGLAD T0313 43 :PVSFELDKVFSPQASQQDVFQ 1q0bA 63 :RKTYTFDMVFGASTKQIDVYR T0313 64 :EVQALVTSCIDGFNVCIFAYGQTGAGKTYTMEG 1q0bA 85 :VVCPILDEVIMGYNCTIFAYGQTGTGKTFTMEG T0313 97 :TAENPGINQRALQLLFSEVQE 1q0bA 129 :EDPLAGIIPRTLHQIFEKLTD T0313 120 :SDWEYTITVSAAEIYNEVLRDLLGKEPQEKLEIRLCPDG 1q0bA 150 :NGTEFSVKVSLLEIYNEELFDLLNPSSDVSERLQMFDDP T0313 159 :SGQLYVPGLTEFQVQSVDDINKVFEFGHTNRTTEFTNLNEHSSRSHALLIVTVRGVDCSTGL 1q0bA 191 :KRGVIIKGLEEITVHNKDEVYQILEKGAAKRTTAATLMNAYSSRSHSVFSVTIHMKETTIDG T0313 221 :RTTGKLNLVDLAGSE 1q0bA 256 :VKIGKLNLVDLAGSE T0313 254 :NKSLSALGDVIAALRSRQGHVPFRNSKLTYLLQDSLSGDSKTLMVVQVSPVEKNTSETLYSLKFAERVR 1q0bA 289 :NQSLLTLGRVITALVERTPHVPYRESKLTRILQDSLGGRTRTSIIATISPASLNLEETLSTLEYAHRAK Number of specific fragments extracted= 8 number of extra gaps= 1 total=153 Number of alignments=22 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1vfvA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1vfvA expands to /projects/compbio/data/pdb/1vfv.pdb.gz 1vfvA:# T0313 read from 1vfvA/merged-good-all-a2m # 1vfvA read from 1vfvA/merged-good-all-a2m # adding 1vfvA to template set # found chain 1vfvA in template set Warning: unaligning (T0313)T190 because of BadResidue code BAD_PEPTIDE in next template residue (1vfvA)V205 Warning: unaligning (T0313)T191 because of BadResidue code BAD_PEPTIDE at template residue (1vfvA)V205 Warning: unaligning (T0313)H199 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1vfvA)T213 Warning: unaligning (T0313)S201 because of BadResidue code BAD_PEPTIDE in next template residue (1vfvA)R216 Warning: unaligning (T0313)R202 because of BadResidue code BAD_PEPTIDE at template residue (1vfvA)R216 Warning: unaligning (T0313)G219 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1vfvA)T234 Warning: unaligning (T0313)E235 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1vfvA)A269 Warning: unaligning (T0313)Q251 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1vfvA)A269 Warning: unaligning (T0313)H273 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1vfvA)F303 T0313 2 :IRVIARVRPVTKEDGEGPEATNA 1vfvA 6 :VKVAVRVRPFNSREMSRDSKCII T0313 26 :TFDADDDSIIHLLHKGKP 1vfvA 29 :QMSGSTTTIVNPKQPKET T0313 44 :VSFELDKVF 1vfvA 48 :KSFSFDYSY T0313 53 :SPQ 1vfvA 61 :SPE T0313 56 :ASQQDVFQEV 1vfvA 68 :ASQKQVYRDI T0313 66 :QALVTSCIDGFNVCIFAYGQTGAGKTYTMEG 1vfvA 79 :EEMLQHAFEGYNVCIFAYGQTGAGKSYTMMG T0313 97 :TAENPGINQRALQLLFSEVQEKA 1vfvA 112 :EKDQQGIIPQLCEDLFSRINDTT T0313 120 :SDWEYTITVSAAEIYNEVLRDLLGKEPQE 1vfvA 136 :DNMSYSVEVSYMEIYCERVRDLLNPKNKG T0313 151 :EIRLCPDGSGQLYVPGLTEFQVQSVDDINKVFEFGHTNR 1vfvA 165 :NLRVREHPLLGPYVEDLSKLAVTSYNDIQDLMDSGNKPR T0313 200 :S 1vfvA 214 :S T0313 203 :SHALLIVTVRGVDCST 1vfvA 217 :SHAVFNIIFTQKRHDA T0313 220 :LRTTGKLNLVDLAGS 1vfvA 238 :TEKVSKISLVDLAGS T0313 252 :HINKSLSALGDVIAAL 1vfvA 270 :NINKSLTTLGKVISAL T0313 274 :VPFRNSKLTYLLQDSLSGDSKTLMVVQVSPVEKNTSETLYSLKFAERVR 1vfvA 304 :IPYRDSVLTWLLRENLGGNSRTAMVAALSPADINYDETLSTLRYADRAK Number of specific fragments extracted= 14 number of extra gaps= 3 total=167 Number of alignments=23 # 1vfvA read from 1vfvA/merged-good-all-a2m # found chain 1vfvA in template set Warning: unaligning (T0313)T190 because of BadResidue code BAD_PEPTIDE in next template residue (1vfvA)V205 Warning: unaligning (T0313)T191 because of BadResidue code BAD_PEPTIDE at template residue (1vfvA)V205 Warning: unaligning (T0313)H199 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1vfvA)T213 Warning: unaligning (T0313)S201 because of BadResidue code BAD_PEPTIDE in next template residue (1vfvA)R216 Warning: unaligning (T0313)R202 because of BadResidue code BAD_PEPTIDE at template residue (1vfvA)R216 Warning: unaligning (T0313)G219 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1vfvA)T234 Warning: unaligning (T0313)L220 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1vfvA)T234 Warning: unaligning (T0313)E235 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1vfvA)A269 Warning: unaligning (T0313)Q251 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1vfvA)A269 Warning: unaligning (T0313)H273 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1vfvA)F303 T0313 1 :NIRVIARVRPVTKEDGEGPEATNAVT 1vfvA 5 :SVKVAVRVRPFNSREMSRDSKCIIQM T0313 28 :DADDDSIIHLLHKGKP 1vfvA 31 :SGSTTTIVNPKQPKET T0313 44 :VSFELDKVF 1vfvA 48 :KSFSFDYSY T0313 53 :SPQ 1vfvA 61 :SPE T0313 56 :ASQQDVFQEV 1vfvA 68 :ASQKQVYRDI T0313 66 :QALVTSCIDGFNVCIFAYGQTGAGKTYTMEG 1vfvA 79 :EEMLQHAFEGYNVCIFAYGQTGAGKSYTMMG T0313 97 :TAENPGINQRALQLLFSEVQEKA 1vfvA 112 :EKDQQGIIPQLCEDLFSRINDTT T0313 120 :SDWEYTITVSAAEIYNEVLRDLLGKEPQEK 1vfvA 136 :DNMSYSVEVSYMEIYCERVRDLLNPKNKGN T0313 152 :IRLCPDGSGQLYVPGLTEFQVQSVDDINKVFEFGHTNR 1vfvA 166 :LRVREHPLLGPYVEDLSKLAVTSYNDIQDLMDSGNKPR T0313 200 :S 1vfvA 214 :S T0313 203 :SHALLIVTVRGVDCST 1vfvA 217 :SHAVFNIIFTQKRHDA T0313 222 :TTGKLNLVDLAGS 1vfvA 240 :KVSKISLVDLAGS T0313 252 :HINKSLSALGDVIAALR 1vfvA 270 :NINKSLTTLGKVISALA T0313 274 :VPFRNSKLTYLLQDSLSGDSKTLMVVQVSPVEKNTSETLYSLKFAERVR 1vfvA 304 :IPYRDSVLTWLLRENLGGNSRTAMVAALSPADINYDETLSTLRYADRAK Number of specific fragments extracted= 14 number of extra gaps= 3 total=181 Number of alignments=24 # 1vfvA read from 1vfvA/merged-good-all-a2m # found chain 1vfvA in template set Warning: unaligning (T0313)T190 because of BadResidue code BAD_PEPTIDE in next template residue (1vfvA)V205 Warning: unaligning (T0313)T191 because of BadResidue code BAD_PEPTIDE at template residue (1vfvA)V205 Warning: unaligning (T0313)H199 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1vfvA)T213 Warning: unaligning (T0313)S201 because of BadResidue code BAD_PEPTIDE in next template residue (1vfvA)R216 Warning: unaligning (T0313)R202 because of BadResidue code BAD_PEPTIDE at template residue (1vfvA)R216 Warning: unaligning (T0313)G219 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1vfvA)T234 Warning: unaligning (T0313)L220 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1vfvA)T234 Warning: unaligning (T0313)E235 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1vfvA)A269 Warning: unaligning (T0313)Q251 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1vfvA)A269 Warning: unaligning (T0313)H273 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1vfvA)F303 T0313 2 :IRVIARVRPVTKEDGEGPEATNAVTFDADDDSIIHLLHKGKPVSFELDKVF 1vfvA 6 :VKVAVRVRPFNSREMSRDSKCIIQMSGSTTTIVNPKQPKETPKSFSFDYSY T0313 53 :SPQ 1vfvA 61 :SPE T0313 56 :ASQQDVFQ 1vfvA 68 :ASQKQVYR T0313 64 :EVQALVTSCIDGFNVCIFAYGQTGAGKTYTMEG 1vfvA 77 :IGEEMLQHAFEGYNVCIFAYGQTGAGKSYTMMG T0313 97 :TAENPGINQRALQLLFSEVQEKA 1vfvA 112 :EKDQQGIIPQLCEDLFSRINDTT T0313 120 :SDWEYTITVSAAEIYNEVLRDLLGKEPQEK 1vfvA 136 :DNMSYSVEVSYMEIYCERVRDLLNPKNKGN T0313 152 :IRLCPDGSGQLYVPGLTEFQVQSVDDINKVFEFGHTNR 1vfvA 166 :LRVREHPLLGPYVEDLSKLAVTSYNDIQDLMDSGNKPR T0313 200 :S 1vfvA 214 :S T0313 203 :SHALLIVTVRGVDCST 1vfvA 217 :SHAVFNIIFTQKRHDA T0313 221 :RTTGKLNLVDLAGS 1vfvA 239 :EKVSKISLVDLAGS T0313 252 :HINKSLSALGDVIAALRS 1vfvA 270 :NINKSLTTLGKVISALAE T0313 274 :VPFRNSKLTYLLQDSLSGDSKTLMVVQVSPVEKNTSETLYSLKFAERVR 1vfvA 304 :IPYRDSVLTWLLRENLGGNSRTAMVAALSPADINYDETLSTLRYADRAK Number of specific fragments extracted= 12 number of extra gaps= 3 total=193 Number of alignments=25 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1n6mA/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/T0313/1n6mA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0313/1n6mA/merged-good-all-a2m.gz for input Trying 1n6mA/merged-good-all-a2m Error: Couldn't open file 1n6mA/merged-good-all-a2m or 1n6mA/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ia0K/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/T0313/1ia0K/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0313/1ia0K/merged-good-all-a2m.gz for input Trying 1ia0K/merged-good-all-a2m Error: Couldn't open file 1ia0K/merged-good-all-a2m or 1ia0K/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1i5sA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1i5sA expands to /projects/compbio/data/pdb/1i5s.pdb.gz 1i5sA:Skipped atom 226, because occupancy 0.500 <= existing 0.500 in 1i5sA Skipped atom 228, because occupancy 0.500 <= existing 0.500 in 1i5sA Skipped atom 230, because occupancy 0.500 <= existing 0.500 in 1i5sA Skipped atom 232, because occupancy 0.500 <= existing 0.500 in 1i5sA Skipped atom 234, because occupancy 0.500 <= existing 0.500 in 1i5sA Skipped atom 236, because occupancy 0.500 <= existing 0.500 in 1i5sA Skipped atom 598, because occupancy 0.500 <= existing 0.500 in 1i5sA Skipped atom 600, because occupancy 0.500 <= existing 0.500 in 1i5sA Skipped atom 602, because occupancy 0.500 <= existing 0.500 in 1i5sA Skipped atom 604, because occupancy 0.500 <= existing 0.500 in 1i5sA Skipped atom 606, because occupancy 0.500 <= existing 0.500 in 1i5sA Skipped atom 608, because occupancy 0.500 <= existing 0.500 in 1i5sA Skipped atom 610, because occupancy 0.500 <= existing 0.500 in 1i5sA Skipped atom 612, because occupancy 0.500 <= existing 0.500 in 1i5sA Skipped atom 661, because occupancy 0.500 <= existing 0.500 in 1i5sA Skipped atom 663, because occupancy 0.500 <= existing 0.500 in 1i5sA Skipped atom 665, because occupancy 0.500 <= existing 0.500 in 1i5sA Skipped atom 667, because occupancy 0.500 <= existing 0.500 in 1i5sA Skipped atom 669, because occupancy 0.500 <= existing 0.500 in 1i5sA Skipped atom 671, because occupancy 0.500 <= existing 0.500 in 1i5sA Skipped atom 673, because occupancy 0.500 <= existing 0.500 in 1i5sA Skipped atom 675, because occupancy 0.500 <= existing 0.500 in 1i5sA Skipped atom 677, because occupancy 0.500 <= existing 0.500 in 1i5sA Skipped atom 679, because occupancy 0.500 <= existing 0.500 in 1i5sA Skipped atom 884, because occupancy 0.500 <= existing 0.500 in 1i5sA Skipped atom 886, because occupancy 0.500 <= existing 0.500 in 1i5sA Skipped atom 888, because occupancy 0.500 <= existing 0.500 in 1i5sA Skipped atom 890, because occupancy 0.500 <= existing 0.500 in 1i5sA Skipped atom 892, because occupancy 0.500 <= existing 0.500 in 1i5sA Skipped atom 894, because occupancy 0.500 <= existing 0.500 in 1i5sA Skipped atom 896, because occupancy 0.500 <= existing 0.500 in 1i5sA Skipped atom 898, because occupancy 0.500 <= existing 0.500 in 1i5sA Skipped atom 900, because occupancy 0.500 <= existing 0.500 in 1i5sA Skipped atom 928, because occupancy 0.500 <= existing 0.500 in 1i5sA Skipped atom 930, because occupancy 0.500 <= existing 0.500 in 1i5sA Skipped atom 932, because occupancy 0.500 <= existing 0.500 in 1i5sA Skipped atom 934, because occupancy 0.500 <= existing 0.500 in 1i5sA Skipped atom 936, because occupancy 0.500 <= existing 0.500 in 1i5sA Skipped atom 938, because occupancy 0.500 <= existing 0.500 in 1i5sA Skipped atom 940, because occupancy 0.500 <= existing 0.500 in 1i5sA Skipped atom 942, because occupancy 0.500 <= existing 0.500 in 1i5sA Skipped atom 944, because occupancy 0.500 <= existing 0.500 in 1i5sA Skipped atom 1166, because occupancy 0.500 <= existing 0.500 in 1i5sA Skipped atom 1168, because occupancy 0.500 <= existing 0.500 in 1i5sA Skipped atom 1170, because occupancy 0.500 <= existing 0.500 in 1i5sA Skipped atom 1172, because occupancy 0.500 <= existing 0.500 in 1i5sA Skipped atom 1174, because occupancy 0.500 <= existing 0.500 in 1i5sA Skipped atom 1176, because occupancy 0.500 <= existing 0.500 in 1i5sA Skipped atom 1923, because occupancy 0.500 <= existing 0.500 in 1i5sA Skipped atom 1925, because occupancy 0.500 <= existing 0.500 in 1i5sA Skipped atom 1927, because occupancy 0.500 <= existing 0.500 in 1i5sA Skipped atom 1929, because occupancy 0.500 <= existing 0.500 in 1i5sA Skipped atom 1931, because occupancy 0.500 <= existing 0.500 in 1i5sA Skipped atom 1933, because occupancy 0.500 <= existing 0.500 in 1i5sA Skipped atom 1935, because occupancy 0.500 <= existing 0.500 in 1i5sA Skipped atom 1937, because occupancy 0.500 <= existing 0.500 in 1i5sA Skipped atom 1939, because occupancy 0.500 <= existing 0.500 in 1i5sA Skipped atom 2425, because occupancy 0.500 <= existing 0.500 in 1i5sA Skipped atom 2427, because occupancy 0.500 <= existing 0.500 in 1i5sA Skipped atom 2429, because occupancy 0.500 <= existing 0.500 in 1i5sA Skipped atom 2431, because occupancy 0.500 <= existing 0.500 in 1i5sA Skipped atom 2433, because occupancy 0.500 <= existing 0.500 in 1i5sA Skipped atom 2435, because occupancy 0.500 <= existing 0.500 in 1i5sA # T0313 read from 1i5sA/merged-good-all-a2m # 1i5sA read from 1i5sA/merged-good-all-a2m # adding 1i5sA to template set # found chain 1i5sA in template set Warning: unaligning (T0313)K42 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1i5sA)T46 Warning: unaligning (T0313)P43 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1i5sA)T46 Warning: unaligning (T0313)E99 because of BadResidue code BAD_PEPTIDE in next template residue (1i5sA)Q115 Warning: unaligning (T0313)N100 because of BadResidue code BAD_PEPTIDE at template residue (1i5sA)Q115 Warning: unaligning (T0313)P146 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1i5sA)K163 Warning: unaligning (T0313)Q147 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1i5sA)K163 Warning: unaligning (T0313)V237 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1i5sA)K261 Warning: unaligning (T0313)E243 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1i5sA)K261 Warning: unaligning (T0313)Q271 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1i5sA)I304 Warning: unaligning (T0313)V274 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1i5sA)I304 Warning: unaligning (T0313)P303 because of BadResidue code BAD_PEPTIDE in next template residue (1i5sA)A334 Warning: unaligning (T0313)V304 because of BadResidue code BAD_PEPTIDE at template residue (1i5sA)A334 T0313 1 :NIRVIARVRPVTKEDGEGPEAT 1i5sA 5 :SVKVAVRVRPFNSREMSRDSKC T0313 24 :AVTFDADDDSIIHLLHKG 1i5sA 27 :IIQMSGSTTTIVNPKQPK T0313 44 :VSFELDKVF 1i5sA 48 :KSFSFDYSY T0313 53 :SPQ 1i5sA 61 :SPE T0313 56 :ASQQDVFQEV 1i5sA 68 :ASQKQVYRDI T0313 66 :QALVTSCIDGFNVCIFAYGQTGAGKTYTMEG 1i5sA 79 :EEMLQHAFEGYNVCIFAYGQTGAGKSYTMMG T0313 97 :TA 1i5sA 112 :EK T0313 101 :PGINQRALQLLFSEVQEKA 1i5sA 116 :QGIIPQLCEDLFSRINDTT T0313 120 :SDWEYTITVSAAEIYNEVLRDLLGKE 1i5sA 136 :DNMSYSVEVSYMEIYCERVRDLLNPK T0313 148 :E 1i5sA 164 :G T0313 151 :EIRLCPDGSGQLYVPGLTEFQVQSVDDINKVFEFGHTNRTTEFTNLNEHSSRSHALLIVTVRGVDCSTG 1i5sA 165 :NLRVREHPLLGPYVEDLSKLAVTSYNDIQDLMDSGNKARTVAATNMNETSSRSHAVFNIIFTQKRHDAE T0313 220 :LRTTGKLNLVDLAGSER 1i5sA 238 :TEKVSKISLVDLAGSER T0313 244 :GSRLREAQHINKSLSALGDVIAALRSR 1i5sA 262 :GTRLKEGANINKSLTTLGKVISALAEM T0313 275 :PFRNSKLTYLLQDSLSGDSKTLMVVQVS 1i5sA 305 :PYRDSVLTWLLRENLGGNSRTAMVAALS T0313 305 :EKNTSETLYSLKFAERVR 1i5sA 335 :DINYDETLSTLRYADRAK Number of specific fragments extracted= 15 number of extra gaps= 4 total=208 Number of alignments=26 # 1i5sA read from 1i5sA/merged-good-all-a2m # found chain 1i5sA in template set Warning: unaligning (T0313)K42 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1i5sA)T46 Warning: unaligning (T0313)P43 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1i5sA)T46 Warning: unaligning (T0313)E99 because of BadResidue code BAD_PEPTIDE in next template residue (1i5sA)Q115 Warning: unaligning (T0313)N100 because of BadResidue code BAD_PEPTIDE at template residue (1i5sA)Q115 Warning: unaligning (T0313)P146 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1i5sA)K163 Warning: unaligning (T0313)Q147 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1i5sA)K163 Warning: unaligning (T0313)V237 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1i5sA)K261 Warning: unaligning (T0313)E243 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1i5sA)K261 Warning: unaligning (T0313)Q271 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1i5sA)I304 Warning: unaligning (T0313)V274 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1i5sA)I304 Warning: unaligning (T0313)P303 because of BadResidue code BAD_PEPTIDE in next template residue (1i5sA)A334 Warning: unaligning (T0313)V304 because of BadResidue code BAD_PEPTIDE at template residue (1i5sA)A334 T0313 1 :NIRVIARVRPVTKEDGEGPEATNAVT 1i5sA 5 :SVKVAVRVRPFNSREMSRDSKCIIQM T0313 28 :DADDDSIIHLLHKG 1i5sA 31 :SGSTTTIVNPKQPK T0313 44 :VSFELDKVF 1i5sA 48 :KSFSFDYSY T0313 53 :SPQ 1i5sA 61 :SPE T0313 56 :ASQQDVFQE 1i5sA 68 :ASQKQVYRD T0313 65 :VQALVTSCIDGFNVCIFAYGQTGAGKTYTMEG 1i5sA 78 :GEEMLQHAFEGYNVCIFAYGQTGAGKSYTMMG T0313 97 :TA 1i5sA 112 :EK T0313 101 :PGINQRALQLLFSEVQEKA 1i5sA 116 :QGIIPQLCEDLFSRINDTT T0313 120 :SDWEYTITVSAAEIYNEVLRDLLGKE 1i5sA 136 :DNMSYSVEVSYMEIYCERVRDLLNPK T0313 148 :EK 1i5sA 164 :GN T0313 152 :IRLCPDGSGQLYVPGLTEFQVQSVDDINKVFEFGHTNRTTEFTNLNEHSSRSHALLIVTVRGVDCSTG 1i5sA 166 :LRVREHPLLGPYVEDLSKLAVTSYNDIQDLMDSGNKARTVAATNMNETSSRSHAVFNIIFTQKRHDAE T0313 220 :LRTTGKLNLVDLAGSER 1i5sA 238 :TEKVSKISLVDLAGSER T0313 244 :GSRLREAQHINKSLSALGDVIAALRSR 1i5sA 262 :GTRLKEGANINKSLTTLGKVISALAEM T0313 275 :PFRNSKLTYLLQDSLSGDSKTLMVVQVS 1i5sA 305 :PYRDSVLTWLLRENLGGNSRTAMVAALS T0313 305 :EKNTSETLYSLKFAERVR 1i5sA 335 :DINYDETLSTLRYADRAK Number of specific fragments extracted= 15 number of extra gaps= 4 total=223 Number of alignments=27 # 1i5sA read from 1i5sA/merged-good-all-a2m # found chain 1i5sA in template set Warning: unaligning (T0313)K42 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1i5sA)T46 Warning: unaligning (T0313)E99 because of BadResidue code BAD_PEPTIDE in next template residue (1i5sA)Q115 Warning: unaligning (T0313)N100 because of BadResidue code BAD_PEPTIDE at template residue (1i5sA)Q115 Warning: unaligning (T0313)P146 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1i5sA)K163 Warning: unaligning (T0313)Q147 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1i5sA)K163 Warning: unaligning (T0313)L220 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1i5sA)N235 Warning: unaligning (T0313)V237 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1i5sA)K261 Warning: unaligning (T0313)E243 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1i5sA)K261 Warning: unaligning (T0313)V274 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1i5sA)I304 Warning: unaligning (T0313)P303 because of BadResidue code BAD_PEPTIDE in next template residue (1i5sA)A334 Warning: unaligning (T0313)V304 because of BadResidue code BAD_PEPTIDE at template residue (1i5sA)A334 T0313 1 :NIRVIARVRPVTKEDGEGPEATNA 1i5sA 5 :SVKVAVRVRPFNSREMSRDSKCII T0313 26 :TFDADDDSIIHLLHKG 1i5sA 29 :QMSGSTTTIVNPKQPK T0313 43 :PVSFELDKVF 1i5sA 47 :PKSFSFDYSY T0313 53 :SPQ 1i5sA 61 :SPE T0313 56 :ASQQDVFQ 1i5sA 68 :ASQKQVYR T0313 64 :EVQALVTSCIDGFNVCIFAYGQTGAGKTYTMEG 1i5sA 77 :IGEEMLQHAFEGYNVCIFAYGQTGAGKSYTMMG T0313 97 :TA 1i5sA 112 :EK T0313 101 :PGINQRALQLLFSEVQE 1i5sA 116 :QGIIPQLCEDLFSRIND T0313 118 :KASDWEYTITVSAAEIYNEVLRDLLGKE 1i5sA 134 :TNDNMSYSVEVSYMEIYCERVRDLLNPK T0313 148 :EK 1i5sA 164 :GN T0313 152 :IRLCPDGSGQLYVPGLTEFQVQSVDDINKVFEFGHTNRTTEFTNLNEHSSRSHALLIVTVRGVDCSTG 1i5sA 166 :LRVREHPLLGPYVEDLSKLAVTSYNDIQDLMDSGNKARTVAATNMNETSSRSHAVFNIIFTQKRHDAE T0313 221 :RTTGKLNLVDLAGSER 1i5sA 239 :EKVSKISLVDLAGSER T0313 244 :GSRLREAQHINKSLSALGDVIAALRS 1i5sA 262 :GTRLKEGANINKSLTTLGKVISALAE T0313 275 :PFRNSKLTYLLQDSLSGDSKTLMVVQVS 1i5sA 305 :PYRDSVLTWLLRENLGGNSRTAMVAALS T0313 305 :EKNTSETLYSLKFAERVR 1i5sA 335 :DINYDETLSTLRYADRAK Number of specific fragments extracted= 15 number of extra gaps= 5 total=238 Number of alignments=28 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1f9tA/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/T0313/1f9tA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0313/1f9tA/merged-good-all-a2m.gz for input Trying 1f9tA/merged-good-all-a2m Error: Couldn't open file 1f9tA/merged-good-all-a2m or 1f9tA/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ry6A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0313 read from 1ry6A/merged-good-all-a2m # 1ry6A read from 1ry6A/merged-good-all-a2m # found chain 1ry6A in training set Warning: unaligning (T0313)G143 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ry6A)K168 Warning: unaligning (T0313)K144 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ry6A)K168 Warning: unaligning (T0313)R270 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1ry6A)K278 Warning: unaligning (T0313)Q271 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1ry6A)K278 T0313 2 :IRVIARVRPVTKEDGEGPEATNAVTFDADDDSIIH 1ry6A 2 :IKVVVRKRPLSELEKKKKDSDIITVKNNCTLYIDE T0313 37 :LLHKGKPVSFELDKVFSPQASQQDVFQEV 1ry6A 43 :MTKYIERHEFIVDKVFDDTVDNFTVYENT T0313 66 :QALVTSCI 1ry6A 73 :KPLIIDLY T0313 74 :DGFNVCIFAYGQTGAGKTYTMEG 1ry6A 82 :NGCVCSCFAYGQTGSGKTYTMLG T0313 97 :TAE 1ry6A 110 :QSD T0313 102 :GINQRALQLLFSEVQEKASDWEYTITVSAAEIYNEVLRDLL 1ry6A 115 :GIFQYAAGDIFTFLNIYDKDNTKGIFISFYEIYCGKLYDLL T0313 160 :GQLYVPGLTEFQVQSVDDINKVFEFGHTNRTTEFTNLNEHSSRSHALLIVTVRGV 1ry6A 169 :KEVVVKDLKILRVLTKEELILKMIDGVLLRKIGVNSQNDESSRSHAILNIDLKDI T0313 218 :TGLRTTGKLNLVDLAGSERVGKSGAEGSR 1ry6A 224 :NKNTSLGKIAFIDLAGSERGADTVSQNKQ T0313 247 :LREAQHINKSLSALGDVIAALRS 1ry6A 254 :QTDGANINRSLLALKECIRAMDS T0313 272 :GHVPFRNSKLTYLLQDSLSGDSKTLMVVQVSPVEKNTSETLYSLKFAERVR 1ry6A 279 :NHIPFRDSELTKVLRDIFVGKSKSIMIANISPTISCCEQTLNTLRYSSRVK Number of specific fragments extracted= 10 number of extra gaps= 2 total=248 Number of alignments=29 # 1ry6A read from 1ry6A/merged-good-all-a2m # found chain 1ry6A in training set Warning: unaligning (T0313)G143 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ry6A)K168 Warning: unaligning (T0313)K144 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ry6A)K168 Warning: unaligning (T0313)R270 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1ry6A)K278 Warning: unaligning (T0313)Q271 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1ry6A)K278 T0313 1 :NIRVIARVRPVTKEDGEGPEATNAVTFDADDDSI 1ry6A 1 :MIKVVVRKRPLSELEKKKKDSDIITVKNNCTLYI T0313 35 :IHLLHKGKP 1ry6A 36 :EPRYKVDMT T0313 44 :VSFELDKVFSPQASQQDVFQE 1ry6A 50 :HEFIVDKVFDDTVDNFTVYEN T0313 65 :VQALVTSCI 1ry6A 72 :IKPLIIDLY T0313 74 :DGFNVCIFAYGQTGAGKTYTMEGT 1ry6A 82 :NGCVCSCFAYGQTGSGKTYTMLGS T0313 98 :AENPGINQRALQLLFSEVQEKASDWEYTITVSAAEIYNEVLRDLL 1ry6A 111 :SDTPGIFQYAAGDIFTFLNIYDKDNTKGIFISFYEIYCGKLYDLL T0313 160 :GQLYVPGLTEFQVQSVDDINKVFEFGHTNRTTEFTNLNEHSSRSHALLIVTVRG 1ry6A 169 :KEVVVKDLKILRVLTKEELILKMIDGVLLRKIGVNSQNDESSRSHAILNIDLKD T0313 217 :STGLRTTGKLNLVDLAGSERVGKSGAEGS 1ry6A 223 :INKNTSLGKIAFIDLAGSERGADTVSQNK T0313 246 :RLREAQHINKSLSALGDVIAALRS 1ry6A 253 :TQTDGANINRSLLALKECIRAMDS T0313 272 :GHVPFRNSKLTYLLQDSLSGDSKTLMVVQVSPVEKNTSETLYSLKFAERVR 1ry6A 279 :NHIPFRDSELTKVLRDIFVGKSKSIMIANISPTISCCEQTLNTLRYSSRVK Number of specific fragments extracted= 10 number of extra gaps= 2 total=258 Number of alignments=30 # 1ry6A read from 1ry6A/merged-good-all-a2m # found chain 1ry6A in training set Warning: unaligning (T0313)G143 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ry6A)K168 Warning: unaligning (T0313)K144 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ry6A)K168 Warning: unaligning (T0313)R270 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1ry6A)K278 Warning: unaligning (T0313)Q271 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1ry6A)K278 T0313 2 :IRVIARVRPVTKEDGEGPEATNAVTFDADDDSI 1ry6A 2 :IKVVVRKRPLSELEKKKKDSDIITVKNNCTLYI T0313 35 :IHLLHKGK 1ry6A 37 :PRYKVDMT T0313 43 :PVSFELDKVFSPQASQQDVFQ 1ry6A 49 :RHEFIVDKVFDDTVDNFTVYE T0313 64 :EVQALVTSCI 1ry6A 71 :TIKPLIIDLY T0313 74 :DGFNVCIFAYGQTGAGKTYTMEG 1ry6A 82 :NGCVCSCFAYGQTGSGKTYTMLG T0313 97 :TAENPGINQRALQLLFSEVQEKASDWEYTITVSAAEIYNEVLRDLL 1ry6A 110 :QSDTPGIFQYAAGDIFTFLNIYDKDNTKGIFISFYEIYCGKLYDLL T0313 160 :GQLYVPGLTEFQVQSVDDINKVFEFGHTNRTTEFTNLNEHSSRSHALLIVTVRGV 1ry6A 169 :KEVVVKDLKILRVLTKEELILKMIDGVLLRKIGVNSQNDESSRSHAILNIDLKDI T0313 218 :TGLRTTGKLNLVDLAGSERVGKSGAEG 1ry6A 224 :NKNTSLGKIAFIDLAGSERGADTVSQN T0313 245 :SRLREAQHINKSLSALGDVIAALRS 1ry6A 252 :QTQTDGANINRSLLALKECIRAMDS T0313 272 :GHVPFRNSKLTYLLQDSLSGDSKTLMVVQVSPVEKNTSETLYSLKFAERVR 1ry6A 279 :NHIPFRDSELTKVLRDIFVGKSKSIMIANISPTISCCEQTLNTLRYSSRVK Number of specific fragments extracted= 10 number of extra gaps= 2 total=268 Number of alignments=31 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1f9uA/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/T0313/1f9uA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0313/1f9uA/merged-good-all-a2m.gz for input Trying 1f9uA/merged-good-all-a2m Error: Couldn't open file 1f9uA/merged-good-all-a2m or 1f9uA/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1cz7A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1cz7A expands to /projects/compbio/data/pdb/1cz7.pdb.gz 1cz7A:# T0313 read from 1cz7A/merged-good-all-a2m # 1cz7A read from 1cz7A/merged-good-all-a2m # adding 1cz7A to template set # found chain 1cz7A in template set Warning: unaligning (T0313)G241 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1cz7A)I599 Warning: unaligning (T0313)I253 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1cz7A)I599 T0313 2 :IRVIARVRPVTKEDGE 1cz7A 349 :IRVFCRIRPPLESEEN T0313 19 :PEATNAVTFDADDDSIIH 1cz7A 365 :RMCCTWTYHDESTVELQS T0313 37 :LLHKGKPVSFELDKVFSPQASQQDVFQEVQALVTSCIDGFNVCIFAYGQTGAGKTYTMEGTAENPGINQRALQLLFSEVQEKAS 1cz7A 387 :AKSKMGQQIFSFDQVFHPLSSQSDIFEMVSPLIQSALDGYNICIFAYGQTGSGKTYTMDGVPESVGVIPRTVDLLFDSIRGYRN T0313 121 :DWEYTITVSAAEIYNEVLRDLLGKEPQ 1cz7A 472 :GWEYEIKATFLEIYNEVLYDLLSNEQK T0313 149 :KLEIRLCPDGSGQLYVPGLTEFQVQSVDDINKVFEFGHTNRTTEFTNLNEHSSRSHALLIVTVRGVDCSTGLRTTGKLNLVDLAGSE 1cz7A 499 :DMEIRMAKNNKNDIYVSNITEETVLDPNHLRHLMHTAKMNRATASTAGNERSSRSHAVTKLELIGRHAEKQEISVGSINLVDLAGSE T0313 240 :S 1cz7A 586 :S T0313 254 :NKSLSALGDVIAALRSRQGHVPFRNSKLTYLLQDSLSGDSKTLMVVQVSPVEKNTSETLYSLKFAERVR 1cz7A 600 :NRSLSELTNVILALLQKQDHIPYRNSKLTHLLMPSLGGNSKTLMFINVSPFQDCFQESVKSLRFAASVN Number of specific fragments extracted= 7 number of extra gaps= 0 total=275 Number of alignments=32 # 1cz7A read from 1cz7A/merged-good-all-a2m # found chain 1cz7A in template set Warning: unaligning (T0313)G241 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1cz7A)I599 Warning: unaligning (T0313)I253 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1cz7A)I599 T0313 2 :IRVIARVRPVTKEDG 1cz7A 349 :IRVFCRIRPPLESEE T0313 19 :PEATNAVTFDADDDSIIHLLHKG 1cz7A 364 :NRMCCTWTYHDESTVELQSIDAQ T0313 42 :KPVSFELDKVFSPQASQQDVFQEVQALVTSCIDGFNVCIFAYGQTGAGKTYTMEGTAENPGINQRALQLLFSEVQEKAS 1cz7A 392 :GQQIFSFDQVFHPLSSQSDIFEMVSPLIQSALDGYNICIFAYGQTGSGKTYTMDGVPESVGVIPRTVDLLFDSIRGYRN T0313 121 :DWEYTITVSAAEIYNEVLRDLLGKEPQE 1cz7A 472 :GWEYEIKATFLEIYNEVLYDLLSNEQKD T0313 152 :IRLCPDGSGQ 1cz7A 500 :MEIRMAKNNK T0313 162 :LYVPGLTEFQVQSVDDINKVFEFGHTNRTTEFTNLNEHSSRSHALLIVTVRGVDCSTGLRTTGKLNLVDLAGSE 1cz7A 512 :IYVSNITEETVLDPNHLRHLMHTAKMNRATASTAGNERSSRSHAVTKLELIGRHAEKQEISVGSINLVDLAGSE T0313 240 :S 1cz7A 586 :S T0313 254 :NKSLSALGDVIAALRSRQGHVPFRNSKLTYLLQDSLSGDSKTLMVVQVSPVEKNTSETLYSLKFAERV 1cz7A 600 :NRSLSELTNVILALLQKQDHIPYRNSKLTHLLMPSLGGNSKTLMFINVSPFQDCFQESVKSLRFAASV Number of specific fragments extracted= 8 number of extra gaps= 0 total=283 Number of alignments=33 # 1cz7A read from 1cz7A/merged-good-all-a2m # found chain 1cz7A in template set Warning: unaligning (T0313)G241 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1cz7A)I599 Warning: unaligning (T0313)I253 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1cz7A)I599 T0313 1 :NIRVIARVRPVTKEDGEGPEA 1cz7A 348 :NIRVFCRIRPPLESEENRMCC T0313 24 :AVTFDADDDSIIHLL 1cz7A 369 :TWTYHDESTVELQSI T0313 39 :HKGKPVSFELDKVFSPQASQQDVFQEVQALVTSCIDGFNVCIFAYGQTGAGKTYTMEGTAENPGINQRALQLLFSEVQEKAS 1cz7A 389 :SKMGQQIFSFDQVFHPLSSQSDIFEMVSPLIQSALDGYNICIFAYGQTGSGKTYTMDGVPESVGVIPRTVDLLFDSIRGYRN T0313 121 :DWEYTITVSAAEIYNEVLRDLLGKEPQE 1cz7A 472 :GWEYEIKATFLEIYNEVLYDLLSNEQKD T0313 150 :LEIRLCPDGSGQLYVPGLTEFQVQSVDDINKVFEFGHTNRTTEFTNLNEHSSRSHALLIVTVRGVDCSTGLRTTGKLNLVDLAGSE 1cz7A 500 :MEIRMAKNNKNDIYVSNITEETVLDPNHLRHLMHTAKMNRATASTAGNERSSRSHAVTKLELIGRHAEKQEISVGSINLVDLAGSE T0313 240 :S 1cz7A 586 :S T0313 254 :NKSLSALGDVIAALRSRQGHVPFRNSKLTYLLQDSLSGDSKTLMVVQVSPVEKNTSETLYSLKFAERV 1cz7A 600 :NRSLSELTNVILALLQKQDHIPYRNSKLTHLLMPSLGGNSKTLMFINVSPFQDCFQESVKSLRFAASV Number of specific fragments extracted= 7 number of extra gaps= 0 total=290 Number of alignments=34 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ii6A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1ii6A expands to /projects/compbio/data/pdb/1ii6.pdb.gz 1ii6A:# T0313 read from 1ii6A/merged-good-all-a2m # 1ii6A read from 1ii6A/merged-good-all-a2m # adding 1ii6A to template set # found chain 1ii6A in template set Warning: unaligning (T0313)E235 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ii6A)R281 Warning: unaligning (T0313)R246 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ii6A)R281 T0313 1 :NIRVIARVRPVTKEDGEGPEATNAVTFDADDDSIIHLLHKGKP 1ii6A 18 :NIQVVVRCRPFNLAERKASAHSIVECDPVRKEVSVRTGGLADK T0313 44 :VSFELDKVFSPQASQQDVFQEV 1ii6A 64 :KTYTFDMVFGASTKQIDVYRSV T0313 66 :QALVTSCIDGFNVCIFAYGQTGAGKTYTMEG 1ii6A 87 :CPILDEVIMGYNCTIFAYGQTGTGKTFTMEG T0313 97 :TAENP 1ii6A 120 :SPNEE T0313 102 :GINQRALQLLFSEVQE 1ii6A 134 :GIIPRTLHQIFEKLTD T0313 120 :SDWEYTITVSAAEIYNEVLRDLLGKEPQEKLEIRLCPDG 1ii6A 150 :NGTEFSVKVSLLEIYNEELFDLLNPSSDVSERLQMFDDP T0313 159 :SGQLYVPGLTEFQVQSVDDINKVFEFGHTNRTTEFTNLNEHSSRSHALLIVTVRGVDC 1ii6A 191 :KRGVIIKGLEEITVHNKDEVYQILEKGAAKRTTAATLMNAYSSRSHSVFSVTIHMKET T0313 217 :STG 1ii6A 250 :IDG T0313 220 :LRTTGKLNLVDLAGS 1ii6A 255 :LVKIGKLNLVDLAGS T0313 247 :LREAQHINKSLSALGDVIAALRSRQGHVPFRNSKLTYLLQDSLSGDSKTLMVVQVSPVEKNTSETLYSLKFAERVR 1ii6A 282 :AREAGNINQSLLTLGRVITALVERTPHVPYRESKLTRILQDSLGGRTRTSIIATISPASLNLEETLSTLEYAHRAK Number of specific fragments extracted= 10 number of extra gaps= 0 total=300 Number of alignments=35 # 1ii6A read from 1ii6A/merged-good-all-a2m # found chain 1ii6A in template set Warning: unaligning (T0313)E235 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ii6A)R281 Warning: unaligning (T0313)R246 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ii6A)R281 T0313 1 :NIRVIARVRPVTKEDGEGPEATNAVTFDADDDSIIHLLHKGKP 1ii6A 18 :NIQVVVRCRPFNLAERKASAHSIVECDPVRKEVSVRTGGLADK T0313 44 :VSFELDKVFSPQASQQDVFQE 1ii6A 64 :KTYTFDMVFGASTKQIDVYRS T0313 65 :VQALVTSCIDGFNVCIFAYGQTGAGKTYTMEG 1ii6A 86 :VCPILDEVIMGYNCTIFAYGQTGTGKTFTMEG T0313 102 :GINQRALQLLFSEVQE 1ii6A 134 :GIIPRTLHQIFEKLTD T0313 120 :SDWEYTITVSAAEIYNEVLRDLLGKEPQEKLEIRLCPDG 1ii6A 150 :NGTEFSVKVSLLEIYNEELFDLLNPSSDVSERLQMFDDP T0313 159 :SGQLYVPGLTEFQVQSVDDINKVFEFGHTNRTTEFTNLNEHSSRSHALLIVTVRGVDCSTG 1ii6A 191 :KRGVIIKGLEEITVHNKDEVYQILEKGAAKRTTAATLMNAYSSRSHSVFSVTIHMKETTID T0313 220 :LRTTGKLNLVDLAGS 1ii6A 255 :LVKIGKLNLVDLAGS T0313 247 :LREAQHINKSLSALGDVIAALRSRQGHVPFRNSKLTYLLQDSLSGDSKTLMVVQVSPVEKNTSETLYSLKFAERVR 1ii6A 282 :AREAGNINQSLLTLGRVITALVERTPHVPYRESKLTRILQDSLGGRTRTSIIATISPASLNLEETLSTLEYAHRAK Number of specific fragments extracted= 8 number of extra gaps= 0 total=308 Number of alignments=36 # 1ii6A read from 1ii6A/merged-good-all-a2m # found chain 1ii6A in template set Warning: unaligning (T0313)E235 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ii6A)R281 Warning: unaligning (T0313)R246 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ii6A)R281 T0313 1 :NIRVIARVRPVTKEDGEGPEATNAVTFDADDDSIIHLLHKGK 1ii6A 18 :NIQVVVRCRPFNLAERKASAHSIVECDPVRKEVSVRTGGLAD T0313 43 :PVSFELDKVFSPQASQQDVFQ 1ii6A 63 :RKTYTFDMVFGASTKQIDVYR T0313 64 :EVQALVTSCIDGFNVCIFAYGQTGAGKTYTMEG 1ii6A 85 :VVCPILDEVIMGYNCTIFAYGQTGTGKTFTMEG T0313 97 :TAENPGINQRALQLLFSEVQE 1ii6A 129 :EDPLAGIIPRTLHQIFEKLTD T0313 120 :SDWEYTITVSAAEIYNEVLRDLLGKEPQEKLEIRLCPDG 1ii6A 150 :NGTEFSVKVSLLEIYNEELFDLLNPSSDVSERLQMFDDP T0313 159 :SGQLYVPGLTEFQVQSVDDINKVFEFGHTNRTTEFTNLNEHSSRSHALLIVTVRGVDCSTGL 1ii6A 191 :KRGVIIKGLEEITVHNKDEVYQILEKGAAKRTTAATLMNAYSSRSHSVFSVTIHMKETTIDG T0313 221 :RTTGKLNLVDLAGS 1ii6A 256 :VKIGKLNLVDLAGS T0313 247 :LREAQHINKSLSALGDVIAALRSRQGHVPFRNSKLTYLLQDSLSGDSKTLMVVQVSPVEKNTSETLYSLKFAERVR 1ii6A 282 :AREAGNINQSLLTLGRVITALVERTPHVPYRESKLTRILQDSLGGRTRTSIIATISPASLNLEETLSTLEYAHRAK Number of specific fragments extracted= 8 number of extra gaps= 0 total=316 Number of alignments=37 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1i6iA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1i6iA expands to /projects/compbio/data/pdb/1i6i.pdb.gz 1i6iA:Skipped atom 113, because occupancy 0.500 <= existing 0.500 in 1i6iA Skipped atom 115, because occupancy 0.500 <= existing 0.500 in 1i6iA Skipped atom 117, because occupancy 0.500 <= existing 0.500 in 1i6iA Skipped atom 119, because occupancy 0.500 <= existing 0.500 in 1i6iA Skipped atom 121, because occupancy 0.500 <= existing 0.500 in 1i6iA Skipped atom 123, because occupancy 0.500 <= existing 0.500 in 1i6iA Skipped atom 125, because occupancy 0.500 <= existing 0.500 in 1i6iA Skipped atom 127, because occupancy 0.500 <= existing 0.500 in 1i6iA Skipped atom 129, because occupancy 0.500 <= existing 0.500 in 1i6iA Skipped atom 131, because occupancy 0.500 <= existing 0.500 in 1i6iA Skipped atom 133, because occupancy 0.500 <= existing 0.500 in 1i6iA Skipped atom 158, because occupancy 0.500 <= existing 0.500 in 1i6iA Skipped atom 160, because occupancy 0.500 <= existing 0.500 in 1i6iA Skipped atom 162, because occupancy 0.500 <= existing 0.500 in 1i6iA Skipped atom 164, because occupancy 0.500 <= existing 0.500 in 1i6iA Skipped atom 166, because occupancy 0.500 <= existing 0.500 in 1i6iA Skipped atom 168, because occupancy 0.500 <= existing 0.500 in 1i6iA Skipped atom 170, because occupancy 0.500 <= existing 0.500 in 1i6iA Skipped atom 172, because occupancy 0.500 <= existing 0.500 in 1i6iA Skipped atom 174, because occupancy 0.500 <= existing 0.500 in 1i6iA Skipped atom 176, because occupancy 0.500 <= existing 0.500 in 1i6iA Skipped atom 178, because occupancy 0.500 <= existing 0.500 in 1i6iA Skipped atom 571, because occupancy 0.500 <= existing 0.500 in 1i6iA Skipped atom 573, because occupancy 0.500 <= existing 0.500 in 1i6iA Skipped atom 575, because occupancy 0.500 <= existing 0.500 in 1i6iA Skipped atom 577, because occupancy 0.500 <= existing 0.500 in 1i6iA Skipped atom 579, because occupancy 0.500 <= existing 0.500 in 1i6iA Skipped atom 581, because occupancy 0.500 <= existing 0.500 in 1i6iA Skipped atom 583, because occupancy 0.500 <= existing 0.500 in 1i6iA Skipped atom 585, because occupancy 0.500 <= existing 0.500 in 1i6iA Skipped atom 587, because occupancy 0.500 <= existing 0.500 in 1i6iA Skipped atom 627, because occupancy 0.500 <= existing 0.500 in 1i6iA Skipped atom 629, because occupancy 0.500 <= existing 0.500 in 1i6iA Skipped atom 631, because occupancy 0.500 <= existing 0.500 in 1i6iA Skipped atom 633, because occupancy 0.500 <= existing 0.500 in 1i6iA Skipped atom 635, because occupancy 0.500 <= existing 0.500 in 1i6iA Skipped atom 637, because occupancy 0.500 <= existing 0.500 in 1i6iA Skipped atom 639, because occupancy 0.500 <= existing 0.500 in 1i6iA Skipped atom 641, because occupancy 0.500 <= existing 0.500 in 1i6iA Skipped atom 681, because occupancy 0.500 <= existing 0.500 in 1i6iA Skipped atom 683, because occupancy 0.500 <= existing 0.500 in 1i6iA Skipped atom 685, because occupancy 0.500 <= existing 0.500 in 1i6iA Skipped atom 687, because occupancy 0.500 <= existing 0.500 in 1i6iA Skipped atom 689, because occupancy 0.500 <= existing 0.500 in 1i6iA Skipped atom 691, because occupancy 0.500 <= existing 0.500 in 1i6iA Skipped atom 693, because occupancy 0.500 <= existing 0.500 in 1i6iA Skipped atom 695, because occupancy 0.500 <= existing 0.500 in 1i6iA Skipped atom 697, because occupancy 0.500 <= existing 0.500 in 1i6iA Skipped atom 1176, because occupancy 0.500 <= existing 0.500 in 1i6iA Skipped atom 1178, because occupancy 0.500 <= existing 0.500 in 1i6iA Skipped atom 1180, because occupancy 0.500 <= existing 0.500 in 1i6iA Skipped atom 1182, because occupancy 0.500 <= existing 0.500 in 1i6iA Skipped atom 1184, because occupancy 0.500 <= existing 0.500 in 1i6iA Skipped atom 1186, because occupancy 0.500 <= existing 0.500 in 1i6iA Skipped atom 1699, because occupancy 0.500 <= existing 0.500 in 1i6iA Skipped atom 1701, because occupancy 0.500 <= existing 0.500 in 1i6iA Skipped atom 1703, because occupancy 0.500 <= existing 0.500 in 1i6iA Skipped atom 1705, because occupancy 0.500 <= existing 0.500 in 1i6iA Skipped atom 1707, because occupancy 0.500 <= existing 0.500 in 1i6iA Skipped atom 1709, because occupancy 0.500 <= existing 0.500 in 1i6iA Skipped atom 1711, because occupancy 0.500 <= existing 0.500 in 1i6iA Skipped atom 1713, because occupancy 0.500 <= existing 0.500 in 1i6iA Skipped atom 1966, because occupancy 0.500 <= existing 0.500 in 1i6iA Skipped atom 1968, because occupancy 0.500 <= existing 0.500 in 1i6iA Skipped atom 1970, because occupancy 0.500 <= existing 0.500 in 1i6iA Skipped atom 1972, because occupancy 0.500 <= existing 0.500 in 1i6iA Skipped atom 1974, because occupancy 0.500 <= existing 0.500 in 1i6iA Skipped atom 1976, because occupancy 0.500 <= existing 0.500 in 1i6iA Skipped atom 1995, because occupancy 0.500 <= existing 0.500 in 1i6iA Skipped atom 1997, because occupancy 0.500 <= existing 0.500 in 1i6iA Skipped atom 1999, because occupancy 0.500 <= existing 0.500 in 1i6iA Skipped atom 2001, because occupancy 0.500 <= existing 0.500 in 1i6iA Skipped atom 2003, because occupancy 0.500 <= existing 0.500 in 1i6iA Skipped atom 2005, because occupancy 0.500 <= existing 0.500 in 1i6iA Skipped atom 2504, because occupancy 0.500 <= existing 0.500 in 1i6iA Skipped atom 2506, because occupancy 0.500 <= existing 0.500 in 1i6iA Skipped atom 2508, because occupancy 0.500 <= existing 0.500 in 1i6iA Skipped atom 2510, because occupancy 0.500 <= existing 0.500 in 1i6iA Skipped atom 2512, because occupancy 0.500 <= existing 0.500 in 1i6iA Skipped atom 2514, because occupancy 0.500 <= existing 0.500 in 1i6iA Skipped atom 2516, because occupancy 0.500 <= existing 0.500 in 1i6iA Skipped atom 2518, because occupancy 0.500 <= existing 0.500 in 1i6iA Skipped atom 2520, because occupancy 0.500 <= existing 0.500 in 1i6iA # T0313 read from 1i6iA/merged-good-all-a2m # 1i6iA read from 1i6iA/merged-good-all-a2m # adding 1i6iA to template set # found chain 1i6iA in template set Warning: unaligning (T0313)T97 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1i6iA)K113 Warning: unaligning (T0313)A98 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1i6iA)K113 Warning: unaligning (T0313)E148 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1i6iA)N165 Warning: unaligning (T0313)E151 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1i6iA)N165 Warning: unaligning (T0313)E235 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1i6iA)A269 Warning: unaligning (T0313)Q251 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1i6iA)A269 Warning: unaligning (T0313)H273 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1i6iA)F303 T0313 2 :IRVIARVRPVTKEDGEGPEATNA 1i6iA 6 :VKVAVRVRPFNSREMSRDSKCII T0313 26 :TFDADDDSIIH 1i6iA 29 :QMSGSTTTIVN T0313 37 :LLHKGKPVSFELDKVF 1i6iA 41 :KQPKETPKSFSFDYSY T0313 53 :SPQ 1i6iA 61 :SPE T0313 56 :ASQQDVFQEV 1i6iA 68 :ASQKQVYRDI T0313 66 :QALVTSCIDGFNVCIFAYGQTGAGKTYTMEG 1i6iA 79 :EEMLQHAFEGYNVCIFAYGQTGAGKSYTMMG T0313 99 :ENPGINQRALQLLFSEVQEKA 1i6iA 114 :DQQGIIPQLCEDLFSRINDTT T0313 120 :SDWEYTITVSAAEIYNEVLRDLLGKEPQ 1i6iA 136 :DNMSYSVEVSYMEIYCERVRDLLNPKNK T0313 152 :IRLCPDGSGQLYVPGLTEFQVQSVDDINKVFEFGHTNRTTEFTNLNEHSSRSHALLIVTVRGVDCSTG 1i6iA 166 :LRVREHPLLGPYVEDLSKLAVTSYNDIQDLMDSGNKARTVAATNMNETSSRSHAVFNIIFTQKRHDAE T0313 220 :LRTTGKLNLVDLAGS 1i6iA 238 :TEKVSKISLVDLAGS T0313 252 :HINKSLSALGDVIAAL 1i6iA 270 :NINKSLTTLGKVISAL T0313 274 :VPFRNSKLTYLLQDSLSGDSKTLMVVQVSPVEKNTSETLYSLKFAERVR 1i6iA 304 :IPYRDSVLTWLLRENLGGNSRTAMVAALSPADINYDETLSTLRYADRAK Number of specific fragments extracted= 12 number of extra gaps= 2 total=328 Number of alignments=38 # 1i6iA read from 1i6iA/merged-good-all-a2m # found chain 1i6iA in template set Warning: unaligning (T0313)T97 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1i6iA)K113 Warning: unaligning (T0313)A98 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1i6iA)K113 Warning: unaligning (T0313)E148 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1i6iA)N165 Warning: unaligning (T0313)K149 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1i6iA)N165 Warning: unaligning (T0313)E235 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1i6iA)A269 Warning: unaligning (T0313)Q251 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1i6iA)A269 Warning: unaligning (T0313)H273 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1i6iA)F303 T0313 1 :NIRVIARVRPVTKEDGEGPEATNAVT 1i6iA 5 :SVKVAVRVRPFNSREMSRDSKCIIQM T0313 28 :DADDDSIIHLLHKGKP 1i6iA 31 :SGSTTTIVNPKQPKET T0313 44 :VSFELDKVF 1i6iA 48 :KSFSFDYSY T0313 53 :SPQ 1i6iA 61 :SPE T0313 56 :ASQQDVFQEV 1i6iA 68 :ASQKQVYRDI T0313 66 :QALVTSCIDGFNVCIFAYGQTGAGKTYTMEG 1i6iA 79 :EEMLQHAFEGYNVCIFAYGQTGAGKSYTMMG T0313 99 :ENPGINQRALQLLFSEVQEKA 1i6iA 114 :DQQGIIPQLCEDLFSRINDTT T0313 120 :SDWEYTITVSAAEIYNEVLRDLLGKEPQ 1i6iA 136 :DNMSYSVEVSYMEIYCERVRDLLNPKNK T0313 152 :IRLCPDGSGQLYVPGLTEFQVQSVDDINKVFEFGHTNRTTEFTNLNEHSSRSHALLIVTVRGVDCSTG 1i6iA 166 :LRVREHPLLGPYVEDLSKLAVTSYNDIQDLMDSGNKARTVAATNMNETSSRSHAVFNIIFTQKRHDAE T0313 220 :LRTTGKLNLVDLAGS 1i6iA 238 :TEKVSKISLVDLAGS T0313 252 :HINKSLSALGDVIAALR 1i6iA 270 :NINKSLTTLGKVISALA T0313 274 :VPFRNSKLTYLLQDSLSGDSKTLMVVQVSPVEKNTSETLYSLKFAERVR 1i6iA 304 :IPYRDSVLTWLLRENLGGNSRTAMVAALSPADINYDETLSTLRYADRAK Number of specific fragments extracted= 12 number of extra gaps= 2 total=340 Number of alignments=39 # 1i6iA read from 1i6iA/merged-good-all-a2m # found chain 1i6iA in template set Warning: unaligning (T0313)T97 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1i6iA)K113 Warning: unaligning (T0313)A98 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1i6iA)K113 Warning: unaligning (T0313)E148 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1i6iA)N165 Warning: unaligning (T0313)K149 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1i6iA)N165 Warning: unaligning (T0313)E235 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1i6iA)A269 Warning: unaligning (T0313)Q251 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1i6iA)A269 Warning: unaligning (T0313)H273 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1i6iA)F303 T0313 2 :IRVIARVRPVTKEDGEGPEATNAVTFDADDDSIIHLLHKGKPVSFELDKVF 1i6iA 6 :VKVAVRVRPFNSREMSRDSKCIIQMSGSTTTIVNPKQPKETPKSFSFDYSY T0313 53 :SPQ 1i6iA 61 :SPE T0313 56 :ASQQDVFQ 1i6iA 68 :ASQKQVYR T0313 64 :EVQALVTSCIDGFNVCIFAYGQTGAGKTYTMEG 1i6iA 77 :IGEEMLQHAFEGYNVCIFAYGQTGAGKSYTMMG T0313 99 :ENPGINQRALQLLFSEVQEKA 1i6iA 114 :DQQGIIPQLCEDLFSRINDTT T0313 120 :SDWEYTITVSAAEIYNEVLRDLLGKEPQ 1i6iA 136 :DNMSYSVEVSYMEIYCERVRDLLNPKNK T0313 152 :IRLCPDGSGQLYVPGLTEFQVQSVDDINKVFEFGHTNRTTEFTNLNEHSSRSHALLIVTVRGVDCSTGL 1i6iA 166 :LRVREHPLLGPYVEDLSKLAVTSYNDIQDLMDSGNKARTVAATNMNETSSRSHAVFNIIFTQKRHDAET T0313 221 :RTTGKLNLVDLAGS 1i6iA 239 :EKVSKISLVDLAGS T0313 252 :HINKSLSALGDVIAALRS 1i6iA 270 :NINKSLTTLGKVISALAE T0313 274 :VPFRNSKLTYLLQDSLSGDSKTLMVVQVSPVEKNTSETLYSLKFAERVR 1i6iA 304 :IPYRDSVLTWLLRENLGGNSRTAMVAALSPADINYDETLSTLRYADRAK Number of specific fragments extracted= 10 number of extra gaps= 2 total=350 Number of alignments=40 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1f9vA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0313 read from 1f9vA/merged-good-all-a2m # 1f9vA read from 1f9vA/merged-good-all-a2m # found chain 1f9vA in training set Warning: unaligning (T0313)E151 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1f9vA)K546 Warning: unaligning (T0313)H186 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1f9vA)E594 Warning: unaligning (T0313)E198 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1f9vA)E594 Warning: unaligning (T0313)C216 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1f9vA)G615 Warning: unaligning (T0313)G219 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1f9vA)G615 Warning: unaligning (T0313)Q271 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1f9vA)R671 T0313 2 :IRVIARVRPVTKEDGEGPEATNAVT 1f9vA 387 :IRVYCRIRPALKNLENSDTSLINVN T0313 27 :FDAD 1f9vA 414 :DDNS T0313 31 :DDSIIHLLHKGKPVSFELDKVFSPQASQQDVFQEVQALVTSCIDGFNVCIFAYGQTGAGKTYTME 1f9vA 421 :SMEVTKIQNTAQVHEFKFDKIFDQQDTNVDVFKEVGQLVQSSLDGYNVCIFAYGQTGSGKTFTML T0313 98 :AENPGINQRALQLLFSEVQEKA 1f9vA 486 :NPGDGIIPSTISHIFNWINKLK T0313 120 :SDWEYTITVSAAEIYNEVLRDLL 1f9vA 509 :KGWDYKVNCEFIEIYNENIVDLL T0313 152 :IRLC 1f9vA 547 :HEIR T0313 156 :PDGSGQLYVPGLTEFQVQSVDDINKVFEFG 1f9vA 552 :DQETKTTTITNVTSCKLESEEMVEIILKKA T0313 199 :HSSRSHALLIVTVRGVD 1f9vA 595 :HSSASHSIFIIHLSGSN T0313 220 :LRTTGKLNLVDLAGSERVGKSGAEGSRLREAQHINKSLSALGDVIAALRSR 1f9vA 616 :AHSYGTLNLVDLAGSERINVSQVVGDRLRETQNINKSLSCLGDVIHALGQP T0313 273 :HVPFRNSKLTYLLQDSLSGDSKTLMVVQVSPVEKNTSETLYSLKFAERVR 1f9vA 672 :HIPFRNSKLTYLLQYSLTGDSKTLMFVNISPSSSHINETLNSLRFASKVN Number of specific fragments extracted= 10 number of extra gaps= 0 total=360 Number of alignments=41 # 1f9vA read from 1f9vA/merged-good-all-a2m # found chain 1f9vA in training set Warning: unaligning (T0313)G143 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1f9vA)K546 Warning: unaligning (T0313)E151 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1f9vA)K546 Warning: unaligning (T0313)H186 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1f9vA)E594 Warning: unaligning (T0313)E198 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1f9vA)E594 Warning: unaligning (T0313)C216 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1f9vA)G615 Warning: unaligning (T0313)G219 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1f9vA)G615 Warning: unaligning (T0313)Q271 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1f9vA)R671 T0313 1 :NIRVIARVRPVTKEDGEGPEATNAVT 1f9vA 386 :NIRVYCRIRPALKNLENSDTSLINVN T0313 27 :FDADD 1f9vA 414 :DDNSG T0313 32 :DSIIHLLHKGKPVSFELDKVFSPQASQQDVFQEVQALVTSCIDGFNVCIFAYGQTGAGKTYTMEGTA 1f9vA 422 :MEVTKIQNTAQVHEFKFDKIFDQQDTNVDVFKEVGQLVQSSLDGYNVCIFAYGQTGSGKTFTMLNPG T0313 101 :PGINQRALQLLFSEVQEKA 1f9vA 489 :DGIIPSTISHIFNWINKLK T0313 120 :SDWEYTITVSAAEIYNEVLRDLL 1f9vA 509 :KGWDYKVNCEFIEIYNENIVDLL T0313 152 :IRLCPDGS 1f9vA 547 :HEIRHDQE T0313 160 :GQLYVPGLTEFQVQSVDDINKVFEFG 1f9vA 556 :KTTTITNVTSCKLESEEMVEIILKKA T0313 199 :HSSRSHALLIVTVRGVD 1f9vA 595 :HSSASHSIFIIHLSGSN T0313 220 :LRTTGKLNLVDLAGSERVGKSGAEGSRLREAQHINKSLSALGDVIAALRSR 1f9vA 616 :AHSYGTLNLVDLAGSERINVSQVVGDRLRETQNINKSLSCLGDVIHALGQP T0313 273 :HVPFRNSKLTYLLQDSLSGDSKTLMVVQVSPVEKNTSETLYSLKFAERVR 1f9vA 672 :HIPFRNSKLTYLLQYSLTGDSKTLMFVNISPSSSHINETLNSLRFASKVN Number of specific fragments extracted= 10 number of extra gaps= 0 total=370 Number of alignments=42 # 1f9vA read from 1f9vA/merged-good-all-a2m # found chain 1f9vA in training set Warning: unaligning (T0313)K149 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1f9vA)K546 Warning: unaligning (T0313)H186 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1f9vA)E594 Warning: unaligning (T0313)E198 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1f9vA)E594 Warning: unaligning (T0313)C216 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1f9vA)G615 Warning: unaligning (T0313)G219 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1f9vA)G615 Warning: unaligning (T0313)G272 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1f9vA)R671 T0313 1 :NIRVIARVRPVTKEDGEGPEATNAV 1f9vA 386 :NIRVYCRIRPALKNLENSDTSLINV T0313 26 :TFDADDDSI 1f9vA 412 :EFDDNSGVQ T0313 35 :IHLLHKGKPVSFELDKVFSPQASQQDVFQEVQALVTSCIDGFNVCIFAYGQTGAGKTYTME 1f9vA 425 :TKIQNTAQVHEFKFDKIFDQQDTNVDVFKEVGQLVQSSLDGYNVCIFAYGQTGSGKTFTML T0313 98 :AENPGINQRALQLLFSEVQEKAS 1f9vA 486 :NPGDGIIPSTISHIFNWINKLKT T0313 121 :DWEYTITVSAAEIYNEVLRDLL 1f9vA 510 :GWDYKVNCEFIEIYNENIVDLL T0313 150 :LEIRL 1f9vA 547 :HEIRH T0313 156 :PDGSGQLYVPGLTEFQVQSVDDINKVFEFG 1f9vA 552 :DQETKTTTITNVTSCKLESEEMVEIILKKA T0313 199 :HSSRSHALLIVTVRGVD 1f9vA 595 :HSSASHSIFIIHLSGSN T0313 220 :LRTTGKLNLVDLAGSERVGKSGAEGSRLREAQHINKSLSALGDVIAALRS 1f9vA 616 :AHSYGTLNLVDLAGSERINVSQVVGDRLRETQNINKSLSCLGDVIHALGQ T0313 273 :HVPFRNSKLTYLLQDSLSGDSKTLMVVQVSPVEKNTSETLYSLKFAERV 1f9vA 672 :HIPFRNSKLTYLLQYSLTGDSKTLMFVNISPSSSHINETLNSLRFASKV Number of specific fragments extracted= 10 number of extra gaps= 0 total=380 Number of alignments=43 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1f9wA/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/T0313/1f9wA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0313/1f9wA/merged-good-all-a2m.gz for input Trying 1f9wA/merged-good-all-a2m Error: Couldn't open file 1f9wA/merged-good-all-a2m or 1f9wA/merged-good-all-a2m.gz for input # command:# PrintAlignmentsContacts allconstraints.under Using radius: 8.0000 NUMB_ALIGNS: 43 Done printing distance constraints # command: