# 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/T0359/ # command:# Making conformation for sequence T0359 numbered 1 through 97 Created new target T0359 from T0359.a2m # command:# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/T0359/ # command:Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0359//projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0359/manyalignments-good-all.under or /projects/compbio/experiments/protein-predict/casp7/T0359//projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0359/manyalignments-good-all.under.gz for input Trying /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0359/manyalignments-good-all.under # reading script from file /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0359/manyalignments-good-all.under # Reading fragments from alignment file # Attempting to read fragment alignments from file 1vj6A/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/T0359/1vj6A/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0359/1vj6A/merged-good-all-a2m.gz for input Trying 1vj6A/merged-good-all-a2m Error: Couldn't open file 1vj6A/merged-good-all-a2m or 1vj6A/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 2fneA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2fneA expands to /projects/compbio/data/pdb/2fne.pdb.gz 2fneA:Skipped atom 15, because occupancy 0.5 <= existing 0.500 in 2fneA Skipped atom 19, because occupancy 0.500 <= existing 0.500 in 2fneA Skipped atom 21, because occupancy 0.500 <= existing 0.500 in 2fneA Skipped atom 23, because occupancy 0.500 <= existing 0.500 in 2fneA Skipped atom 25, because occupancy 0.500 <= existing 0.500 in 2fneA Skipped atom 27, because occupancy 0.500 <= existing 0.500 in 2fneA Skipped atom 658, because occupancy 0.500 <= existing 0.500 in 2fneA Skipped atom 662, because occupancy 0.500 <= existing 0.500 in 2fneA Skipped atom 664, because occupancy 0.500 <= existing 0.500 in 2fneA Skipped atom 666, because occupancy 0.500 <= existing 0.500 in 2fneA Skipped atom 668, because occupancy 0.500 <= existing 0.500 in 2fneA # T0359 read from 2fneA/merged-good-all-a2m # 2fneA read from 2fneA/merged-good-all-a2m # adding 2fneA to template set # found chain 2fneA in template set Warning: unaligning (T0359)M2 because first residue in template chain is (2fneA)M1954 T0359 3 :SETFDVELTKNVQGLGITIAGYIGD 2fneA 1955 :PQCKSITLERGPDGLGFSIVGGYGS # choosing archetypes in rotamer library T0359 29 :KLEPSGIFVKSITKSSAVEHDGRIQIGDQIIAVDGTNLQGFTNQQAVEVLRHTGQTVLLTLMRRGE 2fneA 1980 :PHGDLPIYVKTVFAKGAASEDGRLKRGDQIIAVNGQSLEGVTHEEAVAILKRTKGTVTLMVLSSDE Number of specific fragments extracted= 2 number of extra gaps= 0 total=2 Number of alignments=1 # 2fneA read from 2fneA/merged-good-all-a2m # found chain 2fneA in template set Warning: unaligning (T0359)M2 because first residue in template chain is (2fneA)M1954 T0359 3 :SETFDVELTKNVQGLGITIAGYIGDKK 2fneA 1955 :PQCKSITLERGPDGLGFSIVGGYGSPH T0359 31 :EPSGIFVKSITKSSAVEHDGRIQIGDQIIAVDGTNLQGFTNQQAVEVLRHTGQTVLLTLMRRGETS 2fneA 1982 :GDLPIYVKTVFAKGAASEDGRLKRGDQIIAVNGQSLEGVTHEEAVAILKRTKGTVTLMVLSSDETS Number of specific fragments extracted= 2 number of extra gaps= 0 total=4 Number of alignments=2 # 2fneA read from 2fneA/merged-good-all-a2m # found chain 2fneA in template set Warning: unaligning (T0359)M2 because first residue in template chain is (2fneA)M1954 T0359 3 :SETFDVELTKNVQGLGITIAGYIGD 2fneA 1955 :PQCKSITLERGPDGLGFSIVGGYGS T0359 29 :KLEPSGIFVKSITKSSAVEHDGRIQIGDQIIAVDGTNLQGFTNQQAVEVLRHTGQTVLLTLMRRGETS 2fneA 1980 :PHGDLPIYVKTVFAKGAASEDGRLKRGDQIIAVNGQSLEGVTHEEAVAILKRTKGTVTLMVLSSDETS 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 2bygA/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/T0359/2bygA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0359/2bygA/merged-good-all-a2m.gz for input Trying 2bygA/merged-good-all-a2m Error: Couldn't open file 2bygA/merged-good-all-a2m or 2bygA/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1y8tA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1y8tA expands to /projects/compbio/data/pdb/1y8t.pdb.gz 1y8tA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0359 read from 1y8tA/merged-good-all-a2m # 1y8tA read from 1y8tA/merged-good-all-a2m # adding 1y8tA to template set # found chain 1y8tA in template set Warning: unaligning (T0359)G23 because of BadResidue code BAD_PEPTIDE in next template residue (1y8tA)D238 Warning: unaligning (T0359)K29 because of BadResidue code BAD_PEPTIDE at template residue (1y8tA)D238 Warning: unaligning (T0359)L30 because of BadResidue code TOO_FEW_ATOMS+BAD_PEPTIDE in next template residue (1y8tA)D240 Warning: unaligning (T0359)E31 because of BadResidue code TOO_FEW_ATOMS+BAD_PEPTIDE at template residue (1y8tA)D240 Warning: unaligning (T0359)P32 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1y8tA)T241 Warning: unaligning (T0359)S33 because of BadResidue code BAD_PEPTIDE at template residue (1y8tA)L242 Warning: unaligning (T0359)S44 because of BadResidue code BAD_PEPTIDE in next template residue (1y8tA)A254 Warning: unaligning (T0359)A45 because of BadResidue code BAD_PEPTIDE at template residue (1y8tA)A254 Warning: unaligning (T0359)H48 because of BadResidue code BAD_PEPTIDE in next template residue (1y8tA)A258 Warning: unaligning (T0359)D49 because of BadResidue code BAD_PEPTIDE at template residue (1y8tA)A258 Warning: unaligning (T0359)G50 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1y8tA)V260 Warning: unaligning (T0359)I52 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1y8tA)V260 Warning: unaligning (T0359)G63 because of BadResidue code TOO_FEW_ATOMS+BAD_PEPTIDE in next template residue (1y8tA)R272 Warning: unaligning (T0359)T64 because of BadResidue code TOO_FEW_ATOMS+BAD_PEPTIDE at template residue (1y8tA)R272 Warning: unaligning (T0359)N65 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1y8tA)P273 Warning: unaligning (T0359)R91 because of BadResidue code BAD_PEPTIDE in next template residue (1y8tA)P300 Warning: unaligning (T0359)R92 because of BadResidue code BAD_PEPTIDE at template residue (1y8tA)P300 Warning: unaligning (T0359)G93 because of BadResidue code BAD_PEPTIDE at template residue (1y8tA)S301 T0359 16 :GLGITIA 1y8tA 230 :SLGVQVT T0359 34 :GIFVKSITKS 1y8tA 243 :GAKIVEVVAG T0359 46 :VE 1y8tA 255 :AA T0359 53 :QIGDQIIAVD 1y8tA 261 :PKGVVVTKVD T0359 66 :LQG 1y8tA 274 :INS T0359 71 :NQQAVEVLRHT 1y8tA 277 :ADALVAAVRSK T0359 82 :GQTVLLTLM 1y8tA 290 :GATVALTFQ T0359 94 :E 1y8tA 302 :G Number of specific fragments extracted= 8 number of extra gaps= 5 total=14 Number of alignments=4 # 1y8tA read from 1y8tA/merged-good-all-a2m # found chain 1y8tA in template set Warning: unaligning (T0359)G23 because of BadResidue code BAD_PEPTIDE in next template residue (1y8tA)D238 Warning: unaligning (T0359)Y24 because of BadResidue code BAD_PEPTIDE at template residue (1y8tA)D238 Warning: unaligning (T0359)I25 because of BadResidue code TOO_FEW_ATOMS+BAD_PEPTIDE in next template residue (1y8tA)D240 Warning: unaligning (T0359)G26 because of BadResidue code TOO_FEW_ATOMS+BAD_PEPTIDE at template residue (1y8tA)D240 Warning: unaligning (T0359)P32 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1y8tA)T241 Warning: unaligning (T0359)S33 because of BadResidue code BAD_PEPTIDE at template residue (1y8tA)L242 Warning: unaligning (T0359)S44 because of BadResidue code BAD_PEPTIDE in next template residue (1y8tA)A254 Warning: unaligning (T0359)A45 because of BadResidue code BAD_PEPTIDE at template residue (1y8tA)A254 Warning: unaligning (T0359)H48 because of BadResidue code BAD_PEPTIDE in next template residue (1y8tA)A258 Warning: unaligning (T0359)D49 because of BadResidue code BAD_PEPTIDE at template residue (1y8tA)A258 Warning: unaligning (T0359)G50 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1y8tA)V260 Warning: unaligning (T0359)I52 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1y8tA)V260 Warning: unaligning (T0359)G63 because of BadResidue code TOO_FEW_ATOMS+BAD_PEPTIDE in next template residue (1y8tA)R272 Warning: unaligning (T0359)T64 because of BadResidue code TOO_FEW_ATOMS+BAD_PEPTIDE at template residue (1y8tA)R272 Warning: unaligning (T0359)N65 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1y8tA)P273 Warning: unaligning (T0359)R91 because of BadResidue code BAD_PEPTIDE in next template residue (1y8tA)P300 Warning: unaligning (T0359)R92 because of BadResidue code BAD_PEPTIDE at template residue (1y8tA)P300 Warning: unaligning (T0359)G93 because of BadResidue code BAD_PEPTIDE at template residue (1y8tA)S301 T0359 16 :GLGITIA 1y8tA 230 :SLGVQVT T0359 34 :GIFVKSITKS 1y8tA 243 :GAKIVEVVAG T0359 46 :VE 1y8tA 255 :AA T0359 53 :QIGDQIIAVD 1y8tA 261 :PKGVVVTKVD T0359 66 :LQG 1y8tA 274 :INS T0359 71 :NQQAVEVLRHT 1y8tA 277 :ADALVAAVRSK T0359 82 :GQTVLLTLM 1y8tA 290 :GATVALTFQ T0359 94 :ETS 1y8tA 302 :GGS Number of specific fragments extracted= 8 number of extra gaps= 5 total=22 Number of alignments=5 # 1y8tA read from 1y8tA/merged-good-all-a2m # found chain 1y8tA in template set Warning: unaligning (T0359)G23 because of BadResidue code BAD_PEPTIDE in next template residue (1y8tA)D238 Warning: unaligning (T0359)Y24 because of BadResidue code BAD_PEPTIDE at template residue (1y8tA)D238 Warning: unaligning (T0359)I25 because of BadResidue code TOO_FEW_ATOMS+BAD_PEPTIDE in next template residue (1y8tA)D240 Warning: unaligning (T0359)G26 because of BadResidue code TOO_FEW_ATOMS+BAD_PEPTIDE at template residue (1y8tA)D240 Warning: unaligning (T0359)D27 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1y8tA)T241 Warning: unaligning (T0359)S33 because of BadResidue code BAD_PEPTIDE at template residue (1y8tA)L242 Warning: unaligning (T0359)S44 because of BadResidue code BAD_PEPTIDE in next template residue (1y8tA)A254 Warning: unaligning (T0359)A45 because of BadResidue code BAD_PEPTIDE at template residue (1y8tA)A254 Warning: unaligning (T0359)H48 because of BadResidue code BAD_PEPTIDE in next template residue (1y8tA)A258 Warning: unaligning (T0359)D49 because of BadResidue code BAD_PEPTIDE at template residue (1y8tA)A258 Warning: unaligning (T0359)G50 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1y8tA)V260 Warning: unaligning (T0359)I52 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1y8tA)V260 Warning: unaligning (T0359)G63 because of BadResidue code TOO_FEW_ATOMS+BAD_PEPTIDE in next template residue (1y8tA)R272 Warning: unaligning (T0359)T64 because of BadResidue code TOO_FEW_ATOMS+BAD_PEPTIDE at template residue (1y8tA)R272 Warning: unaligning (T0359)N65 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1y8tA)P273 Warning: unaligning (T0359)R91 because of BadResidue code BAD_PEPTIDE in next template residue (1y8tA)P300 Warning: unaligning (T0359)R92 because of BadResidue code BAD_PEPTIDE at template residue (1y8tA)P300 Warning: unaligning (T0359)G93 because of BadResidue code BAD_PEPTIDE at template residue (1y8tA)S301 T0359 16 :GLGITIA 1y8tA 230 :SLGVQVT T0359 34 :GIFVKSITKS 1y8tA 243 :GAKIVEVVAG T0359 46 :VE 1y8tA 255 :AA T0359 53 :QIGDQIIAVD 1y8tA 261 :PKGVVVTKVD T0359 66 :LQG 1y8tA 274 :INS T0359 71 :NQQAVEVLRHT 1y8tA 277 :ADALVAAVRSK T0359 82 :GQTVLLTLM 1y8tA 290 :GATVALTFQ T0359 94 :ET 1y8tA 302 :GG Number of specific fragments extracted= 8 number of extra gaps= 5 total=30 Number of alignments=6 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1qauA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0359 read from 1qauA/merged-good-all-a2m # 1qauA read from 1qauA/merged-good-all-a2m # found chain 1qauA in training set Warning: unaligning (T0359)E4 because first residue in template chain is (1qauA)N14 T0359 5 :TFDVELTKNVQ 1qauA 15 :VISVRLFKRKV T0359 16 :GLGITIAGY 1qauA 27 :GLGFLVKER T0359 30 :LEPSGIFVKSITKSSAVEHDGRIQIGDQIIAVDGTNLQGFTNQQAVEVLRHT 1qauA 36 :VSKPPVIISDLIRGGAAEQSGLIQAGDIILAVNDRPLVDLSYDSALEVLRGI T0359 82 :GQTVLLTLMRRGE 1qauA 90 :ETHVVLILRGPEG Number of specific fragments extracted= 4 number of extra gaps= 0 total=34 Number of alignments=7 # 1qauA read from 1qauA/merged-good-all-a2m # found chain 1qauA in training set Warning: unaligning (T0359)E4 because first residue in template chain is (1qauA)N14 T0359 5 :TFDVELTKNV 1qauA 15 :VISVRLFKRK T0359 15 :QGLGITIAGYIG 1qauA 26 :GGLGFLVKERVS T0359 32 :PSGIFVKSITKSSAVEHDGRIQIGDQIIAVDGTNLQGFTNQQAVEVLRHT 1qauA 38 :KPPVIISDLIRGGAAEQSGLIQAGDIILAVNDRPLVDLSYDSALEVLRGI T0359 82 :GQTVLLTLMRRGETS 1qauA 90 :ETHVVLILRGPEGFT Number of specific fragments extracted= 4 number of extra gaps= 0 total=38 Number of alignments=8 # 1qauA read from 1qauA/merged-good-all-a2m # found chain 1qauA in training set Warning: unaligning (T0359)E4 because first residue in template chain is (1qauA)N14 T0359 5 :TFDVELT 1qauA 15 :VISVRLF T0359 12 :KNVQGLGITIAGYIGD 1qauA 23 :RKVGGLGFLVKERVSK T0359 33 :SGIFVKSITKSSAVEHDGRIQIGDQIIAVDGTNLQGFTNQQAVEVLRHTGQ 1qauA 39 :PPVIISDLIRGGAAEQSGLIQAGDIILAVNDRPLVDLSYDSALEVLRGIAS T0359 84 :TVLLTLMRRGET 1qauA 92 :HVVLILRGPEGF Number of specific fragments extracted= 4 number of extra gaps= 0 total=42 Number of alignments=9 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2h2bA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2h2bA expands to /projects/compbio/data/pdb/2h2b.pdb.gz 2h2bA:# T0359 read from 2h2bA/merged-good-all-a2m # 2h2bA read from 2h2bA/merged-good-all-a2m # adding 2h2bA to template set # found chain 2h2bA in template set T0359 2 :MSETFDVELTKNVQ 2h2bA 18 :IWEQHTVTLHRAPG T0359 16 :GLGITIAGYIG 2h2bA 33 :GFGIAISGGRD T0359 27 :DKKLEPSGIFVKSITKSSAVE 2h2bA 46 :HFQSGETSIVISDVLKGGPAE T0359 50 :GRIQIGDQIIAVDGTNLQGFTNQQAVEVLRHTGQTVLLTLMRRGE 2h2bA 67 :GQLQENDRVAMVNGVSMDNVEHAFAVQQLRKSGKNAKITIRRKKG T0359 96 :SV 2h2bA 116 :RT Number of specific fragments extracted= 5 number of extra gaps= 0 total=47 Number of alignments=10 # 2h2bA read from 2h2bA/merged-good-all-a2m # found chain 2h2bA in template set T0359 2 :MSETFDVELTKNVQ 2h2bA 18 :IWEQHTVTLHRAPG T0359 16 :GLGITIAGYIGD 2h2bA 33 :GFGIAISGGRDN T0359 28 :KKLEPSGIFVKSITKSSAVE 2h2bA 47 :FQSGETSIVISDVLKGGPAE T0359 50 :GRIQIGDQIIAVDGTNLQGFTNQQAVEVLRHTGQTVLLTLMRRGETS 2h2bA 67 :GQLQENDRVAMVNGVSMDNVEHAFAVQQLRKSGKNAKITIRRKKGGG Number of specific fragments extracted= 4 number of extra gaps= 0 total=51 Number of alignments=11 # 2h2bA read from 2h2bA/merged-good-all-a2m # found chain 2h2bA in template set T0359 2 :MSETFDVELTK 2h2bA 18 :IWEQHTVTLHR T0359 13 :NVQGLGITIAGYIG 2h2bA 30 :PGFGFGIAISGGRD T0359 27 :DKKLEPSGIFVKSITKSSAVE 2h2bA 46 :HFQSGETSIVISDVLKGGPAE T0359 50 :GRIQIGDQIIAVDGTNLQGFTNQQAVEVLRHTGQTVLLTLMRRGETSV 2h2bA 67 :GQLQENDRVAMVNGVSMDNVEHAFAVQQLRKSGKNAKITIRRKKGGGW Number of specific fragments extracted= 4 number of extra gaps= 0 total=55 Number of alignments=12 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1i16/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1i16 expands to /projects/compbio/data/pdb/1i16.pdb.gz 1i16:Warning: there is no chain 1i16 will retry with 1i16A # T0359 read from 1i16/merged-good-all-a2m # 1i16 read from 1i16/merged-good-all-a2m # adding 1i16 to template set # found chain 1i16 in template set T0359 5 :TFDVELTKNVQGLGITIAGYIGDK 1i16 30 :VCTVTLEKMSAGLGFSLEGGKGSL T0359 30 :LEPSGIFVKSITKSSAVEHDGRIQIGDQIIAVDGTNLQGFTNQQAVEVLRHT 1i16 54 :HGDKPLTINRIFKGAASEQSETVQPGDEILQLGGTAMQGLTRFEAWNIIKAL T0359 82 :GQTVLLTLMRRGE 1i16 107 :DGPVTIVIRRKSL T0359 96 :S 1i16 122 :K Number of specific fragments extracted= 4 number of extra gaps= 0 total=59 Number of alignments=13 # 1i16 read from 1i16/merged-good-all-a2m # found chain 1i16 in template set T0359 4 :ETFDVELTKNVQGLGITIAGYIGDKK 1i16 29 :TVCTVTLEKMSAGLGFSLEGGKGSLH T0359 31 :EPSGIFVKSITKSSAVEHDGRIQIGDQIIAVDGTNLQGFTNQQAVEVLRHT 1i16 55 :GDKPLTINRIFKGAASEQSETVQPGDEILQLGGTAMQGLTRFEAWNIIKAL T0359 82 :GQTVLLTLMRRGETS 1i16 107 :DGPVTIVIRRKSLQS Number of specific fragments extracted= 3 number of extra gaps= 0 total=62 Number of alignments=14 # 1i16 read from 1i16/merged-good-all-a2m # found chain 1i16 in template set T0359 3 :SETFDVELTKNVQGLGITIAGYIGD 1i16 28 :ATVCTVTLEKMSAGLGFSLEGGKGS T0359 29 :KLEPSGIFVKSITKSSAVEHDGRIQIGDQIIAVDGTNLQGFTNQQAVEVLRHTG 1i16 53 :LHGDKPLTINRIFKGAASEQSETVQPGDEILQLGGTAMQGLTRFEAWNIIKALP T0359 83 :QTVLLTLMRRGETSV 1i16 108 :GPVTIVIRRKSLQSK Number of specific fragments extracted= 3 number of extra gaps= 0 total=65 Number of alignments=15 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1v5lA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1v5lA expands to /projects/compbio/data/pdb/1v5l.pdb.gz 1v5lA:# T0359 read from 1v5lA/merged-good-all-a2m # 1v5lA read from 1v5lA/merged-good-all-a2m # adding 1v5lA to template set # found chain 1v5lA in template set T0359 2 :MSETFDVELTKN 1v5lA 3 :SGSSGNVVLPGP T0359 15 :QGLGITIAGYIGD 1v5lA 15 :APWGFRLSGGIDF T0359 32 :PSGIFVKSITKSSAVEHDG 1v5lA 28 :NQPLVITRITPGSKAAAAN T0359 52 :IQIGDQIIAVDGTNLQGFTNQQAVEVLRHTGQTVLLTLMRRGE 1v5lA 47 :LCPGDVILAIDGFGTESMTHADAQDRIKAASYQLCLKIDRAET T0359 95 :TS 1v5lA 94 :PQ Number of specific fragments extracted= 5 number of extra gaps= 0 total=70 Number of alignments=16 # 1v5lA read from 1v5lA/merged-good-all-a2m # found chain 1v5lA in template set T0359 4 :ETFDVELTKN 1v5lA 5 :SSGNVVLPGP T0359 15 :QGLGITIAGYIGD 1v5lA 15 :APWGFRLSGGIDF T0359 32 :PSGIFVKSITKSSAVEHDG 1v5lA 28 :NQPLVITRITPGSKAAAAN T0359 52 :IQIGDQIIAVDGTNLQGFTNQQAVEVLRHTGQTVLLTLMRRGE 1v5lA 47 :LCPGDVILAIDGFGTESMTHADAQDRIKAASYQLCLKIDRAET Number of specific fragments extracted= 4 number of extra gaps= 0 total=74 Number of alignments=17 # 1v5lA read from 1v5lA/merged-good-all-a2m # found chain 1v5lA in template set T0359 12 :KNVQGLGITIAGYIGD 1v5lA 12 :PGPAPWGFRLSGGIDF T0359 32 :PSGIFVKSITKSSAVEHDG 1v5lA 28 :NQPLVITRITPGSKAAAAN T0359 52 :IQIGDQIIAVDGTNLQGFTNQQAVEVLRHTGQTVLLTLMRRGE 1v5lA 47 :LCPGDVILAIDGFGTESMTHADAQDRIKAASYQLCLKIDRAET Number of specific fragments extracted= 3 number of extra gaps= 0 total=77 Number of alignments=18 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1tp5A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1tp5A expands to /projects/compbio/data/pdb/1tp5.pdb.gz 1tp5A:# T0359 read from 1tp5A/merged-good-all-a2m # 1tp5A read from 1tp5A/merged-good-all-a2m # adding 1tp5A to template set # found chain 1tp5A in template set Warning: unaligning (T0359)L87 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1tp5A)I389 Warning: unaligning (T0359)T88 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1tp5A)I389 T0359 2 :MSETFDVELTKNVQGLGITIAGY 1tp5A 308 :PREPRRIVIHRGSTGLGFNIVGG T0359 30 :LEPSGIFVKSITKSSAVEHDGRIQIGDQIIAVDGTNLQGFTNQQAVEVLRHTGQTVL 1tp5A 331 :EDGEGIFISFILAGGPADLSGELRKGDQILSVNGVDLRNASHEQAAIALKNAGQTVT T0359 89 :LMRR 1tp5A 390 :AQYK Number of specific fragments extracted= 3 number of extra gaps= 1 total=80 Number of alignments=19 # 1tp5A read from 1tp5A/merged-good-all-a2m # found chain 1tp5A in template set Warning: unaligning (T0359)L87 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1tp5A)I389 Warning: unaligning (T0359)T88 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1tp5A)I389 T0359 2 :MSETFDVELTKNVQGLGITIAGYIG 1tp5A 308 :PREPRRIVIHRGSTGLGFNIVGGED T0359 32 :PSGIFVKSITKSSAVEHDGRIQIGDQIIAVDGTNLQGFTNQQAVEVLRHTGQTVL 1tp5A 333 :GEGIFISFILAGGPADLSGELRKGDQILSVNGVDLRNASHEQAAIALKNAGQTVT T0359 89 :LMRR 1tp5A 390 :AQYK Number of specific fragments extracted= 3 number of extra gaps= 1 total=83 Number of alignments=20 # 1tp5A read from 1tp5A/merged-good-all-a2m # found chain 1tp5A in template set Warning: unaligning (T0359)L87 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1tp5A)I389 Warning: unaligning (T0359)T88 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1tp5A)I389 T0359 2 :MSETFDVELTKNVQGLGITIAGYIGD 1tp5A 308 :PREPRRIVIHRGSTGLGFNIVGGEDG T0359 33 :SGIFVKSITKSSAVEHDGRIQIGDQIIAVDGTNLQGFTNQQAVEVLRHTGQTVL 1tp5A 334 :EGIFISFILAGGPADLSGELRKGDQILSVNGVDLRNASHEQAAIALKNAGQTVT T0359 89 :LMRR 1tp5A 390 :AQYK Number of specific fragments extracted= 3 number of extra gaps= 1 total=86 Number of alignments=21 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1i92A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1i92A expands to /projects/compbio/data/pdb/1i92.pdb.gz 1i92A:Skipped atom 533, because occupancy 0.500 <= existing 0.500 in 1i92A Skipped atom 543, because occupancy 0.500 <= existing 0.500 in 1i92A Skipped atom 545, because occupancy 0.500 <= existing 0.500 in 1i92A Skipped atom 547, because occupancy 0.500 <= existing 0.500 in 1i92A Skipped atom 549, because occupancy 0.500 <= existing 0.500 in 1i92A Skipped atom 551, because occupancy 0.500 <= existing 0.500 in 1i92A Skipped atom 553, because occupancy 0.500 <= existing 0.500 in 1i92A Skipped atom 555, because occupancy 0.500 <= existing 0.500 in 1i92A Skipped atom 557, because occupancy 0.500 <= existing 0.500 in 1i92A Skipped atom 559, because occupancy 0.500 <= existing 0.500 in 1i92A Skipped atom 561, because occupancy 0.500 <= existing 0.500 in 1i92A Skipped atom 563, because occupancy 0.500 <= existing 0.500 in 1i92A Skipped atom 565, because occupancy 0.500 <= existing 0.500 in 1i92A Skipped atom 567, because occupancy 0.500 <= existing 0.500 in 1i92A Skipped atom 569, because occupancy 0.500 <= existing 0.500 in 1i92A Skipped atom 571, because occupancy 0.500 <= existing 0.500 in 1i92A Skipped atom 573, because occupancy 0.500 <= existing 0.500 in 1i92A Skipped atom 575, because occupancy 0.500 <= existing 0.500 in 1i92A Skipped atom 577, because occupancy 0.500 <= existing 0.500 in 1i92A Skipped atom 579, because occupancy 0.500 <= existing 0.500 in 1i92A Skipped atom 581, because occupancy 0.500 <= existing 0.500 in 1i92A Skipped atom 583, because occupancy 0.500 <= existing 0.500 in 1i92A # T0359 read from 1i92A/merged-good-all-a2m # 1i92A read from 1i92A/merged-good-all-a2m # adding 1i92A to template set # found chain 1i92A in template set Warning: unaligning (T0359)M2 because first residue in template chain is (1i92A)G9 Warning: unaligning (T0359)G82 because of BadResidue code TOO_FEW_ATOMS+NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1i92A)N84 Warning: unaligning (T0359)Q83 because of BadResidue code TOO_FEW_ATOMS+NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1i92A)N84 T0359 3 :SETFDVELTKNVQGLGITIAG 1i92A 10 :MLPRLCCLEKGPNGYGFHLHG T0359 29 :KLEPSGIFVKSITKSSAVEHDG 1i92A 31 :EKGKLGQYIRLVEPGSPAEKAG T0359 52 :IQIGDQIIAVDGTNLQGFTNQQAVEVLRHT 1i92A 53 :LLAGDRLVEVNGENVEKETHQQVVSRIRAA T0359 84 :TVLLTLMRRGE 1i92A 85 :AVRLLVVDPEQ T0359 95 :TS 1i92A 97 :TR Number of specific fragments extracted= 5 number of extra gaps= 1 total=91 Number of alignments=22 # 1i92A read from 1i92A/merged-good-all-a2m # found chain 1i92A in template set Warning: unaligning (T0359)M2 because first residue in template chain is (1i92A)G9 Warning: unaligning (T0359)G82 because of BadResidue code TOO_FEW_ATOMS+NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1i92A)N84 Warning: unaligning (T0359)Q83 because of BadResidue code TOO_FEW_ATOMS+NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1i92A)N84 T0359 3 :SETFDVELTKNVQGLGITIAGYIG 1i92A 10 :MLPRLCCLEKGPNGYGFHLHGEKG T0359 32 :PSGIFVKSITKSSAVEHDG 1i92A 34 :KLGQYIRLVEPGSPAEKAG T0359 52 :IQIGDQIIAVDGTNLQGFTNQQAVEVLRHT 1i92A 53 :LLAGDRLVEVNGENVEKETHQQVVSRIRAA T0359 84 :TVLLTLMRRGETS 1i92A 85 :AVRLLVVDPEQDT Number of specific fragments extracted= 4 number of extra gaps= 1 total=95 Number of alignments=23 # 1i92A read from 1i92A/merged-good-all-a2m # found chain 1i92A in template set Warning: unaligning (T0359)G82 because of BadResidue code TOO_FEW_ATOMS+NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1i92A)N84 Warning: unaligning (T0359)Q83 because of BadResidue code TOO_FEW_ATOMS+NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1i92A)N84 T0359 3 :SETFDVELTKNVQGLGITIAGYIGD 1i92A 10 :MLPRLCCLEKGPNGYGFHLHGEKGK T0359 33 :SGIFVKSITKSSAVEHDG 1i92A 35 :LGQYIRLVEPGSPAEKAG T0359 52 :IQIGDQIIAVDGTNLQGFTNQQAVEVLRHT 1i92A 53 :LLAGDRLVEVNGENVEKETHQQVVSRIRAA T0359 84 :TVLLTLMRRGETSV 1i92A 85 :AVRLLVVDPEQDTR Number of specific fragments extracted= 4 number of extra gaps= 1 total=99 Number of alignments=24 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1bfeA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1bfeA expands to /projects/compbio/data/pdb/1bfe.pdb.gz 1bfeA:# T0359 read from 1bfeA/merged-good-all-a2m # 1bfeA read from 1bfeA/merged-good-all-a2m # adding 1bfeA to template set # found chain 1bfeA in template set T0359 2 :MSETFDVELTKNVQGLGITIAGYI 1bfeA 308 :PREPRRIVIHRGSTGLGFNIIGGE T0359 31 :EPSGIFVKSITKSSAVEHDGRIQIGDQIIAVDGTNLQGFTNQQAVEVLRHTGQTVLLTLMRR 1bfeA 332 :DGEGIFISFILAGGPADLSGELRKGDQILSVNGVDLRNASHEQAAIALKNAGQTVTIIAQYK Number of specific fragments extracted= 2 number of extra gaps= 0 total=101 Number of alignments=25 # 1bfeA read from 1bfeA/merged-good-all-a2m # found chain 1bfeA in template set T0359 2 :MSETFDVELTKNVQGLGITIAGYIG 1bfeA 308 :PREPRRIVIHRGSTGLGFNIIGGED T0359 32 :PSGIFVKSITKSSAVEHDGRIQIGDQIIAVDGTNLQGFTNQQAVEVLRHTGQTVLLTLMRR 1bfeA 333 :GEGIFISFILAGGPADLSGELRKGDQILSVNGVDLRNASHEQAAIALKNAGQTVTIIAQYK Number of specific fragments extracted= 2 number of extra gaps= 0 total=103 Number of alignments=26 # 1bfeA read from 1bfeA/merged-good-all-a2m # found chain 1bfeA in template set T0359 2 :MSETFDVELTKNVQGLGITIAGYIG 1bfeA 308 :PREPRRIVIHRGSTGLGFNIIGGED T0359 32 :PSGIFVKSITKSSAVEHDGRIQIGDQIIAVDGTNLQGFTNQQAVEVLRHTGQTVLLTLMRR 1bfeA 333 :GEGIFISFILAGGPADLSGELRKGDQILSVNGVDLRNASHEQAAIALKNAGQTVTIIAQYK Number of specific fragments extracted= 2 number of extra gaps= 0 total=105 Number of alignments=27 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1fc6A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0359 read from 1fc6A/merged-good-all-a2m # 1fc6A read from 1fc6A/merged-good-all-a2m # found chain 1fc6A in training set T0359 13 :NVQ 1fc6A 157 :AGS T0359 16 :GLGITIAGY 1fc6A 162 :GVGLEITYD T0359 29 :KLEPSGIFVKSITKSSAVEHDG 1fc6A 171 :GGSGKDVVVLTPAPGGPAEKAG T0359 52 :IQIGDQIIAVDGTNLQGFTNQQAVEVL 1fc6A 193 :ARAGDVIVTVDGTAVKGMSLYDVSDLL T0359 81 :TGQTVLLTLMRRG 1fc6A 223 :ADSQVEVVLHAPG Number of specific fragments extracted= 5 number of extra gaps= 0 total=110 Number of alignments=28 # 1fc6A read from 1fc6A/merged-good-all-a2m # found chain 1fc6A in training set T0359 13 :NVQ 1fc6A 157 :AGS T0359 16 :GLGITIAGYIG 1fc6A 162 :GVGLEITYDGG T0359 31 :EPSGIFVKSITKSSAVEHDG 1fc6A 173 :SGKDVVVLTPAPGGPAEKAG T0359 52 :IQIGDQIIAVDGTNLQGFTNQQAVEVL 1fc6A 193 :ARAGDVIVTVDGTAVKGMSLYDVSDLL T0359 81 :TGQTVLLTLMRRG 1fc6A 223 :ADSQVEVVLHAPG Number of specific fragments extracted= 5 number of extra gaps= 0 total=115 Number of alignments=29 # 1fc6A read from 1fc6A/merged-good-all-a2m # found chain 1fc6A in training set T0359 12 :KNVQGLGITIAGYIGD 1fc6A 158 :GSVTGVGLEITYDGGS T0359 32 :PSGIFVKSITKSSAVEHDG 1fc6A 174 :GKDVVVLTPAPGGPAEKAG T0359 52 :IQIGDQIIAVDGTNLQGFTNQQAVEVL 1fc6A 193 :ARAGDVIVTVDGTAVKGMSLYDVSDLL T0359 79 :RHTGQTVLLTLMR 1fc6A 221 :GEADSQVEVVLHA Number of specific fragments extracted= 4 number of extra gaps= 0 total=119 Number of alignments=30 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1gm1A/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/T0359/1gm1A/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0359/1gm1A/merged-good-all-a2m.gz for input Trying 1gm1A/merged-good-all-a2m Error: Couldn't open file 1gm1A/merged-good-all-a2m or 1gm1A/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1kefA/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/T0359/1kefA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0359/1kefA/merged-good-all-a2m.gz for input Trying 1kefA/merged-good-all-a2m Error: Couldn't open file 1kefA/merged-good-all-a2m or 1kefA/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1nf3C/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1nf3C expands to /projects/compbio/data/pdb/1nf3.pdb.gz 1nf3C:# T0359 read from 1nf3C/merged-good-all-a2m # 1nf3C read from 1nf3C/merged-good-all-a2m # adding 1nf3C to template set # found chain 1nf3C in template set Warning: unaligning (T0359)S96 because last residue in template chain is (1nf3C)N253 T0359 2 :MSETFDVELTKNVQ 1nf3C 152 :PETHRRVRLCKYGT T0359 16 :GLGITIAGYIG 1nf3C 168 :PLGFYIRDGSS T0359 27 :DKKLEP 1nf3C 183 :PHGLEK T0359 33 :SGIFVKSITKSSAVEHDGRIQIGDQIIAVDGTNLQGFTNQQAVEVLRHTGQTVLLTLMRRGET 1nf3C 190 :PGIFISRLVPGGLAQSTGLLAVNDEVLEVNGIEVSGKSLDQVTDMMIANSRNLIITVRPANQR Number of specific fragments extracted= 4 number of extra gaps= 0 total=123 Number of alignments=31 # 1nf3C read from 1nf3C/merged-good-all-a2m # found chain 1nf3C in template set Warning: unaligning (T0359)S96 because last residue in template chain is (1nf3C)N253 T0359 2 :MSETFDVELTKNV 1nf3C 152 :PETHRRVRLCKYG T0359 15 :QGLGITIAGYI 1nf3C 167 :KPLGFYIRDGS T0359 26 :GDKKLEPSGIFVKSITKSSAVEHDGRIQIGDQIIAVDGTNLQGFTNQQAVEVLRHTGQTVLLTLMRRGET 1nf3C 183 :PHGLEKVPGIFISRLVPGGLAQSTGLLAVNDEVLEVNGIEVSGKSLDQVTDMMIANSRNLIITVRPANQR Number of specific fragments extracted= 3 number of extra gaps= 0 total=126 Number of alignments=32 # 1nf3C read from 1nf3C/merged-good-all-a2m # found chain 1nf3C in template set Warning: unaligning (T0359)S96 because last residue in template chain is (1nf3C)N253 T0359 4 :ETFDVELT 1nf3C 154 :THRRVRLC T0359 12 :KNVQGLGITIAGYIG 1nf3C 164 :GTEKPLGFYIRDGSS T0359 27 :DKKLEPSGIFVKSITKSSAVEHDGRIQIGDQIIAVDGTNLQGFTNQQAVEVLRHTGQTVLLTLMRRGET 1nf3C 184 :HGLEKVPGIFISRLVPGGLAQSTGLLAVNDEVLEVNGIEVSGKSLDQVTDMMIANSRNLIITVRPANQR Number of specific fragments extracted= 3 number of extra gaps= 0 total=129 Number of alignments=33 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1wf7A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1wf7A expands to /projects/compbio/data/pdb/1wf7.pdb.gz 1wf7A:# T0359 read from 1wf7A/merged-good-all-a2m # 1wf7A read from 1wf7A/merged-good-all-a2m # adding 1wf7A to template set # found chain 1wf7A in template set T0359 2 :MSETFDVELT 1wf7A 3 :SGSSGSVSLV T0359 13 :NVQGLGITIAGYIGD 1wf7A 13 :GPAPWGFRLQGGKDF T0359 32 :PSGIFVKSITKSSAVEHDG 1wf7A 28 :NMPLTISSLKDGGKASQAH T0359 52 :IQIGDQIIAVDGTNLQGFTNQQAVEVLRHTGQTVLLTLMRRGE 1wf7A 47 :VRIGDVVLSIDGISAQGMTHLEAQNKIKACTGSLNMTLQRASA T0359 97 :V 1wf7A 94 :E Number of specific fragments extracted= 5 number of extra gaps= 0 total=134 Number of alignments=34 # 1wf7A read from 1wf7A/merged-good-all-a2m # found chain 1wf7A in template set T0359 2 :MSETFDVELT 1wf7A 3 :SGSSGSVSLV T0359 13 :NVQGLGITIAGYIGD 1wf7A 13 :GPAPWGFRLQGGKDF T0359 32 :PSGIFVKSITKSSAVEHDG 1wf7A 28 :NMPLTISSLKDGGKASQAH T0359 52 :IQIGDQIIAVDGTNLQGFTNQQAVEVLRHTGQTVLLTLMRRGETS 1wf7A 47 :VRIGDVVLSIDGISAQGMTHLEAQNKIKACTGSLNMTLQRASAAA Number of specific fragments extracted= 4 number of extra gaps= 0 total=138 Number of alignments=35 # 1wf7A read from 1wf7A/merged-good-all-a2m # found chain 1wf7A in template set T0359 3 :SETFDVELTKNVQGLGITIAGYIGD 1wf7A 3 :SGSSGSVSLVGPAPWGFRLQGGKDF T0359 32 :PSGIFVKSITKSSAVEHDG 1wf7A 28 :NMPLTISSLKDGGKASQAH T0359 52 :IQIGDQIIAVDGTNLQGFTNQQAVEVLRHTGQTVLLTLMRRGETSV 1wf7A 47 :VRIGDVVLSIDGISAQGMTHLEAQNKIKACTGSLNMTLQRASAAAK Number of specific fragments extracted= 3 number of extra gaps= 0 total=141 Number of alignments=36 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1um7A/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/T0359/1um7A/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0359/1um7A/merged-good-all-a2m.gz for input Trying 1um7A/merged-good-all-a2m Error: Couldn't open file 1um7A/merged-good-all-a2m or 1um7A/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 2f0aA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2f0aA expands to /projects/compbio/data/pdb/2f0a.pdb.gz 2f0aA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0359 read from 2f0aA/merged-good-all-a2m # 2f0aA read from 2f0aA/merged-good-all-a2m # adding 2f0aA to template set # found chain 2f0aA in template set Warning: unaligning (T0359)E4 because first residue in template chain is (2f0aA)M251 Warning: unaligning (T0359)Q15 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2f0aA)N263 Warning: unaligning (T0359)G93 because last residue in template chain is (2f0aA)E342 T0359 5 :TFDVELT 2f0aA 252 :IITVTLN T0359 16 :GLGITIAGYIG 2f0aA 264 :FLGISIVGQSN T0359 29 :KLEPSGIFVKSITKSSAVEHDGRIQIGDQIIAVDGTNLQGFTNQQAVEVLRHT 2f0aA 275 :ERGDGGIYIGSIMKGGAVAADGRIEPGDMLLQVNDINFENMSNDDAVRVLRDI T0359 82 :GQTVLLTLMRR 2f0aA 331 :PGPIVLTVAKL Number of specific fragments extracted= 4 number of extra gaps= 1 total=145 Number of alignments=37 # 2f0aA read from 2f0aA/merged-good-all-a2m # found chain 2f0aA in template set Warning: unaligning (T0359)Q15 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2f0aA)N263 Warning: unaligning (T0359)G93 because last residue in template chain is (2f0aA)E342 T0359 5 :TFDVELT 2f0aA 252 :IITVTLN T0359 16 :GLGITIAGYIGDK 2f0aA 264 :FLGISIVGQSNER T0359 31 :EPSGIFVKSITKSSAVEHDGRIQIGDQIIAVDGTNLQGFTNQQAVEVLRHT 2f0aA 277 :GDGGIYIGSIMKGGAVAADGRIEPGDMLLQVNDINFENMSNDDAVRVLRDI T0359 82 :GQTVLLTLMRR 2f0aA 331 :PGPIVLTVAKL Number of specific fragments extracted= 4 number of extra gaps= 1 total=149 Number of alignments=38 # 2f0aA read from 2f0aA/merged-good-all-a2m # found chain 2f0aA in template set Warning: unaligning (T0359)E4 because first residue in template chain is (2f0aA)M251 Warning: unaligning (T0359)Q15 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2f0aA)N263 Warning: unaligning (T0359)G93 because last residue in template chain is (2f0aA)E342 T0359 5 :TFDVEL 2f0aA 252 :IITVTL T0359 16 :GLGITIAGYIGD 2f0aA 264 :FLGISIVGQSNE T0359 30 :LEPSGIFVKSITKSSAVEHDGRIQIGDQIIAVDGTNLQGFTNQQAVEVLRHT 2f0aA 276 :RGDGGIYIGSIMKGGAVAADGRIEPGDMLLQVNDINFENMSNDDAVRVLRDI T0359 82 :GQTVLLTLMRR 2f0aA 331 :PGPIVLTVAKL Number of specific fragments extracted= 4 number of extra gaps= 1 total=153 Number of alignments=39 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1n7eA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1n7eA expands to /projects/compbio/data/pdb/1n7e.pdb.gz 1n7eA:# T0359 read from 1n7eA/merged-good-all-a2m # 1n7eA read from 1n7eA/merged-good-all-a2m # adding 1n7eA to template set # found chain 1n7eA in template set Warning: unaligning (T0359)M2 because first residue in template chain is (1n7eA)G667 T0359 3 :SETFDVELTKNVQGLGITIAGY 1n7eA 668 :AIIYTVELKRYGGPLGITISGT T0359 29 :KLEPSGIFVKSITKSSAVEHDGRIQIGDQIIAVDGTNLQGFTNQQAVEVLRHTGQTVLLTLMRRGE 1n7eA 690 :EEPFDPIIISSLTKGGLAERTGAIHIGDRILAINSSSLKGKPLSEAIHLLQMAGETVTLKIKKQTD T0359 96 :SV 1n7eA 758 :PA Number of specific fragments extracted= 3 number of extra gaps= 0 total=156 Number of alignments=40 # 1n7eA read from 1n7eA/merged-good-all-a2m # found chain 1n7eA in template set Warning: unaligning (T0359)M2 because first residue in template chain is (1n7eA)G667 T0359 3 :SETFDVELTKNVQGLGITIAGYIG 1n7eA 668 :AIIYTVELKRYGGPLGITISGTEE T0359 31 :EPSGIFVKSITKSSAVEHDGRIQIGDQIIAVDGTNLQGFTNQQAVEVLRHTGQTVLLTLMRRGETSV 1n7eA 692 :PFDPIIISSLTKGGLAERTGAIHIGDRILAINSSSLKGKPLSEAIHLLQMAGETVTLKIKKQTDAQP Number of specific fragments extracted= 2 number of extra gaps= 0 total=158 Number of alignments=41 # 1n7eA read from 1n7eA/merged-good-all-a2m # found chain 1n7eA in template set Warning: unaligning (T0359)M2 because first residue in template chain is (1n7eA)G667 T0359 3 :SETFDVELTKNVQGLGITIAGYIGD 1n7eA 668 :AIIYTVELKRYGGPLGITISGTEEP T0359 32 :PSGIFVKSITKSSAVEHDGRIQIGDQIIAVDGTNLQGFTNQQAVEVLRHTGQTVLLTLMRRGETSV 1n7eA 693 :FDPIIISSLTKGGLAERTGAIHIGDRILAINSSSLKGKPLSEAIHLLQMAGETVTLKIKKQTDAQP Number of specific fragments extracted= 2 number of extra gaps= 0 total=160 Number of alignments=42 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ky9A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1ky9A expands to /projects/compbio/data/pdb/1ky9.pdb.gz 1ky9A:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0359 read from 1ky9A/merged-good-all-a2m # 1ky9A read from 1ky9A/merged-good-all-a2m # adding 1ky9A to template set # found chain 1ky9A in template set T0359 32 :PSGIFVKSITKSSAVEHDG 1ky9A 285 :QRGAFVSQVLPNSSAAKAG T0359 52 :IQIGDQIIAVDGTNLQGF 1ky9A 304 :IKAGDVITSLNGKPISSF T0359 72 :QQAVEVLRHT 1ky9A 322 :AALRAQVGTM T0359 82 :GQTVLLTLMRRGE 1ky9A 334 :GSKLTLGLLRDGK T0359 95 :TS 1ky9A 350 :VN Number of specific fragments extracted= 5 number of extra gaps= 0 total=165 Number of alignments=43 # 1ky9A read from 1ky9A/merged-good-all-a2m # found chain 1ky9A in template set T0359 26 :G 1ky9A 283 :D T0359 31 :EPSGIFVKSITKSSAVEHDG 1ky9A 284 :AQRGAFVSQVLPNSSAAKAG T0359 52 :IQIGDQIIAVDGTNLQGF 1ky9A 304 :IKAGDVITSLNGKPISSF T0359 72 :QQAVEVLRHT 1ky9A 322 :AALRAQVGTM T0359 82 :GQTVLLTLMRRGE 1ky9A 334 :GSKLTLGLLRDGK Number of specific fragments extracted= 5 number of extra gaps= 0 total=170 Number of alignments=44 # 1ky9A read from 1ky9A/merged-good-all-a2m # found chain 1ky9A in template set T0359 30 :LEPSGIFVKSITKSSAVEHDG 1ky9A 283 :DAQRGAFVSQVLPNSSAAKAG T0359 52 :IQIGDQIIAVDGTNLQGF 1ky9A 304 :IKAGDVITSLNGKPISSF T0359 72 :QQAVEVLRHT 1ky9A 322 :AALRAQVGTM T0359 82 :GQTVLLTLMRRG 1ky9A 334 :GSKLTLGLLRDG Number of specific fragments extracted= 4 number of extra gaps= 0 total=174 Number of alignments=45 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ky9B/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1ky9B expands to /projects/compbio/data/pdb/1ky9.pdb.gz 1ky9B:# T0359 read from 1ky9B/merged-good-all-a2m # 1ky9B read from 1ky9B/merged-good-all-a2m # adding 1ky9B to template set # found chain 1ky9B in template set Warning: unaligning (T0359)D27 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ky9B)K281 Warning: unaligning (T0359)K29 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ky9B)K281 Warning: unaligning (T0359)H80 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ky9B)P332 T0359 30 :LEPS 1ky9B 282 :VDAQ T0359 34 :GIFVKSITKSSAVEHDG 1ky9B 287 :GAFVSQVLPNSSAAKAG T0359 52 :IQIGDQIIAVDGTNLQG 1ky9B 304 :IKAGDVITSLNGKPISS T0359 71 :NQQAVEVLR 1ky9B 321 :FAALRAQVG T0359 82 :GQTVLLTLMRRGE 1ky9B 334 :GSKLTLGLLRDGK Number of specific fragments extracted= 5 number of extra gaps= 0 total=179 Number of alignments=46 # 1ky9B read from 1ky9B/merged-good-all-a2m # found chain 1ky9B in template set Warning: unaligning (T0359)I21 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ky9B)G269 Warning: unaligning (T0359)G23 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ky9B)G269 Warning: unaligning (T0359)D27 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ky9B)K281 Warning: unaligning (T0359)K29 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ky9B)K281 Warning: unaligning (T0359)H80 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ky9B)P332 T0359 18 :G 1ky9B 266 :G T0359 24 :YI 1ky9B 270 :TE T0359 30 :L 1ky9B 282 :V T0359 31 :EPSGIFVKSITKSSAVEHDG 1ky9B 284 :AQRGAFVSQVLPNSSAAKAG T0359 52 :IQIGDQIIAVDGTNLQG 1ky9B 304 :IKAGDVITSLNGKPISS T0359 71 :NQQAVEVLR 1ky9B 321 :FAALRAQVG T0359 82 :GQTVLLTLMRRGET 1ky9B 334 :GSKLTLGLLRDGKQ Number of specific fragments extracted= 7 number of extra gaps= 0 total=186 Number of alignments=47 # 1ky9B read from 1ky9B/merged-good-all-a2m # found chain 1ky9B in template set Warning: unaligning (T0359)I21 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ky9B)G269 Warning: unaligning (T0359)G23 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ky9B)G269 Warning: unaligning (T0359)H80 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ky9B)P332 T0359 19 :IT 1ky9B 265 :LG T0359 24 :YIGDKK 1ky9B 270 :TELNSE T0359 30 :LEPSGIFVKSITKSSAVEHDG 1ky9B 283 :DAQRGAFVSQVLPNSSAAKAG T0359 52 :IQIGDQIIAVDGTNLQG 1ky9B 304 :IKAGDVITSLNGKPISS T0359 71 :NQQAVEVLR 1ky9B 321 :FAALRAQVG T0359 81 :TGQTVLLTLMRRG 1ky9B 333 :VGSKLTLGLLRDG Number of specific fragments extracted= 6 number of extra gaps= 0 total=192 Number of alignments=48 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1zokA/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/T0359/1zokA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0359/1zokA/merged-good-all-a2m.gz for input Trying 1zokA/merged-good-all-a2m Error: Couldn't open file 1zokA/merged-good-all-a2m or 1zokA/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1mfgA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0359 read from 1mfgA/merged-good-all-a2m # 1mfgA read from 1mfgA/merged-good-all-a2m # found chain 1mfgA in training set Warning: unaligning (T0359)Q83 because of BadResidue code BAD_PEPTIDE in next template residue (1mfgA)T1360 Warning: unaligning (T0359)T84 because of BadResidue code BAD_PEPTIDE at template residue (1mfgA)T1360 Warning: unaligning (T0359)L87 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (1mfgA)I1364 Warning: unaligning (T0359)T88 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (1mfgA)I1364 Warning: unaligning (T0359)T95 because last residue in template chain is (1mfgA)S1371 T0359 5 :TFDVELTKNV 1mfgA 1280 :EIRVRVEKDP T0359 16 :GLGITIAGYIG 1mfgA 1290 :ELGFSISGGVG T0359 27 :DKKLEPSGIFVKSITKSSAVEH 1mfgA 1305 :PFRPDDDGIFVTRVQPEGPASK T0359 51 :RIQIGDQIIAVDGTNLQGFTNQQAVEVLRHTG 1mfgA 1327 :LLQPGDKIIQANGYSFINIEHGQAVSLLKTFQ T0359 85 :VL 1mfgA 1361 :VE T0359 89 :LMRRGE 1mfgA 1365 :IVREVS Number of specific fragments extracted= 6 number of extra gaps= 2 total=198 Number of alignments=49 # 1mfgA read from 1mfgA/merged-good-all-a2m # found chain 1mfgA in training set Warning: unaligning (T0359)M2 because first residue in template chain is (1mfgA)G1277 Warning: unaligning (T0359)Q83 because of BadResidue code BAD_PEPTIDE in next template residue (1mfgA)T1360 Warning: unaligning (T0359)T84 because of BadResidue code BAD_PEPTIDE at template residue (1mfgA)T1360 Warning: unaligning (T0359)L87 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (1mfgA)I1364 Warning: unaligning (T0359)T88 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (1mfgA)I1364 Warning: unaligning (T0359)T95 because last residue in template chain is (1mfgA)S1371 T0359 3 :SETFDVELTKNV 1mfgA 1278 :SMEIRVRVEKDP T0359 16 :GLGITIAGYIGDKKL 1mfgA 1290 :ELGFSISGGVGGRGN T0359 31 :EPSGIFVKSITKSSAVE 1mfgA 1309 :DDDGIFVTRVQPEGPAS T0359 50 :GRIQIGDQIIAVDGTNLQGFTNQQAVEVLRHTG 1mfgA 1326 :KLLQPGDKIIQANGYSFINIEHGQAVSLLKTFQ T0359 85 :VL 1mfgA 1361 :VE T0359 89 :LMRRGE 1mfgA 1365 :IVREVS Number of specific fragments extracted= 6 number of extra gaps= 2 total=204 Number of alignments=50 # 1mfgA read from 1mfgA/merged-good-all-a2m # found chain 1mfgA in training set Warning: unaligning (T0359)Q83 because of BadResidue code BAD_PEPTIDE in next template residue (1mfgA)T1360 Warning: unaligning (T0359)T84 because of BadResidue code BAD_PEPTIDE at template residue (1mfgA)T1360 Warning: unaligning (T0359)L87 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (1mfgA)I1364 Warning: unaligning (T0359)T88 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (1mfgA)I1364 Warning: unaligning (T0359)T95 because last residue in template chain is (1mfgA)S1371 T0359 3 :SETFDVELTKNVQ 1mfgA 1278 :SMEIRVRVEKDPE T0359 17 :LGITIAGYIG 1mfgA 1291 :LGFSISGGVG T0359 27 :DKKLEPSGIFVKSITKSSAV 1mfgA 1305 :PFRPDDDGIFVTRVQPEGPA T0359 49 :DGRIQIGDQIIAVDGTNLQGFTNQQAVEVLRHTG 1mfgA 1325 :SKLLQPGDKIIQANGYSFINIEHGQAVSLLKTFQ T0359 85 :VL 1mfgA 1361 :VE T0359 89 :LMRRGE 1mfgA 1365 :IVREVS Number of specific fragments extracted= 6 number of extra gaps= 2 total=210 Number of alignments=51 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1b8qA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1b8qA expands to /projects/compbio/data/pdb/1b8q.pdb.gz 1b8qA:# T0359 read from 1b8qA/merged-good-all-a2m # 1b8qA read from 1b8qA/merged-good-all-a2m # adding 1b8qA to template set # found chain 1b8qA in template set T0359 4 :ETFDVELTKNV 1b8qA 8 :NVISVRLFKRK T0359 15 :QGLGITIAGYI 1b8qA 20 :GGLGFLVKERV T0359 31 :EPSGIFVKSITKSSAVEHDGRIQIGDQIIAVDGTNLQGFTNQQAVEVLRHT 1b8qA 31 :SKPPVIISDLIRGGAAEQSGLIQAGDIILAVNDRPLVDLSYDSALEVLRGI T0359 82 :GQTVLLTLMRRGE 1b8qA 84 :ETHVVLILRGPEG Number of specific fragments extracted= 4 number of extra gaps= 0 total=214 Number of alignments=52 # 1b8qA read from 1b8qA/merged-good-all-a2m # found chain 1b8qA in template set T0359 1 :SMSET 1b8qA 1 :GSHMI T0359 6 :FDVELTK 1b8qA 10 :ISVRLFK T0359 13 :NVQGLGITIAGYIG 1b8qA 18 :KVGGLGFLVKERVS T0359 32 :PSGIFVKSITKSSAVEHDGRIQIGDQIIAVDGTNLQGFTNQQAVEVLRHT 1b8qA 32 :KPPVIISDLIRGGAAEQSGLIQAGDIILAVNDRPLVDLSYDSALEVLRGI T0359 82 :GQTVLLTLMRRGETS 1b8qA 84 :ETHVVLILRGPEGFT Number of specific fragments extracted= 5 number of extra gaps= 0 total=219 Number of alignments=53 # 1b8qA read from 1b8qA/merged-good-all-a2m # found chain 1b8qA in template set T0359 2 :MSETFDVELTK 1b8qA 6 :EPNVISVRLFK T0359 13 :NVQGLGITIAGYIGD 1b8qA 18 :KVGGLGFLVKERVSK T0359 33 :SGIFVKSITKSSAVEHDGRIQIGDQIIAVDGTNLQGFTNQQAVEVLRHTGQTVLLTLMRRGET 1b8qA 33 :PPVIISDLIRGGAAEQSGLIQAGDIILAVNDRPLVDLSYDSALEVLRGIASETHVVLILRGPE Number of specific fragments extracted= 3 number of extra gaps= 0 total=222 Number of alignments=54 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1nteA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1nteA expands to /projects/compbio/data/pdb/1nte.pdb.gz 1nteA:Skipped atom 107, because occupancy 0.500 <= existing 0.500 in 1nteA Skipped atom 281, because occupancy 0.400 <= existing 0.600 in 1nteA Skipped atom 283, because occupancy 0.400 <= existing 0.600 in 1nteA Skipped atom 285, because occupancy 0.400 <= existing 0.600 in 1nteA Skipped atom 287, because occupancy 0.400 <= existing 0.600 in 1nteA Skipped atom 289, because occupancy 0.400 <= existing 0.600 in 1nteA Skipped atom 291, because occupancy 0.400 <= existing 0.600 in 1nteA Skipped atom 332, because occupancy 0.500 <= existing 0.500 in 1nteA Skipped atom 334, because occupancy 0.500 <= existing 0.500 in 1nteA Skipped atom 336, because occupancy 0.500 <= existing 0.500 in 1nteA Skipped atom 338, because occupancy 0.500 <= existing 0.500 in 1nteA Skipped atom 340, because occupancy 0.500 <= existing 0.500 in 1nteA Skipped atom 373, because occupancy 0.500 <= existing 0.500 in 1nteA Skipped atom 595, because occupancy 0.300 <= existing 0.700 in 1nteA Skipped atom 597, because occupancy 0.300 <= existing 0.700 in 1nteA Skipped atom 599, because occupancy 0.300 <= existing 0.700 in 1nteA Skipped atom 601, because occupancy 0.300 <= existing 0.700 in 1nteA # T0359 read from 1nteA/merged-good-all-a2m # 1nteA read from 1nteA/merged-good-all-a2m # adding 1nteA to template set # found chain 1nteA in template set Warning: unaligning (T0359)S3 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1nteA)D195 Warning: unaligning (T0359)E4 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1nteA)D195 T0359 1 :SM 1nteA 192 :GA T0359 5 :TFDVELTKNVQG 1nteA 196 :PRTITMHKDSTG T0359 17 :LGITIA 1nteA 209 :VGFIFK T0359 32 :PS 1nteA 215 :NG T0359 36 :FVKSITKSSAVEHDG 1nteA 217 :KITSIVKDSSAARNG T0359 52 :IQIGDQIIAVDGTNLQGFTNQQAVEVLRHTGQTVLLTLMRR 1nteA 232 :LLTEHNICEINGQNVIGLKDSQIADILSTSGTVVTITIMPA Number of specific fragments extracted= 6 number of extra gaps= 1 total=228 Number of alignments=55 # 1nteA read from 1nteA/merged-good-all-a2m # found chain 1nteA in template set Warning: unaligning (T0359)S3 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1nteA)D195 Warning: unaligning (T0359)E4 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1nteA)D195 T0359 1 :SM 1nteA 192 :GA T0359 5 :TFDVELTKNVQG 1nteA 196 :PRTITMHKDSTG T0359 17 :LGITIA 1nteA 209 :VGFIFK T0359 32 :PS 1nteA 215 :NG T0359 36 :FVKSITKSSAVEHDG 1nteA 217 :KITSIVKDSSAARNG T0359 52 :IQIGDQIIAVDGTNLQGFTNQQAVEVLRHTGQTVLLTLMRR 1nteA 232 :LLTEHNICEINGQNVIGLKDSQIADILSTSGTVVTITIMPA Number of specific fragments extracted= 6 number of extra gaps= 1 total=234 Number of alignments=56 # 1nteA read from 1nteA/merged-good-all-a2m # found chain 1nteA in template set Warning: unaligning (T0359)S3 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1nteA)D195 Warning: unaligning (T0359)E4 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1nteA)D195 T0359 5 :TFDVELT 1nteA 196 :PRTITMH T0359 12 :KNVQGLGITIAGY 1nteA 204 :DSTGHVGFIFKNG T0359 36 :FVKSITKSSAVEHDG 1nteA 217 :KITSIVKDSSAARNG T0359 52 :IQIGDQIIAVDGTNLQGFTNQQAVEVLRHTGQTVLLTLMRR 1nteA 232 :LLTEHNICEINGQNVIGLKDSQIADILSTSGTVVTITIMPA Number of specific fragments extracted= 4 number of extra gaps= 1 total=238 Number of alignments=57 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2fe5A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2fe5A expands to /projects/compbio/data/pdb/2fe5.pdb.gz 2fe5A:Skipped atom 9, because occupancy 0.300 <= existing 0.700 in 2fe5A Skipped atom 13, because occupancy 0.300 <= existing 0.700 in 2fe5A Skipped atom 15, because occupancy 0.300 <= existing 0.700 in 2fe5A Skipped atom 17, because occupancy 0.300 <= existing 0.700 in 2fe5A Skipped atom 19, because occupancy 0.300 <= existing 0.700 in 2fe5A Skipped atom 42, because occupancy 0.500 <= existing 0.500 in 2fe5A Skipped atom 44, because occupancy 0.500 <= existing 0.500 in 2fe5A Skipped atom 47, because occupancy 0.300 <= existing 0.700 in 2fe5A Skipped atom 51, because occupancy 0.300 <= existing 0.700 in 2fe5A Skipped atom 53, because occupancy 0.300 <= existing 0.700 in 2fe5A Skipped atom 55, because occupancy 0.300 <= existing 0.700 in 2fe5A Skipped atom 57, because occupancy 0.300 <= existing 0.700 in 2fe5A Skipped atom 59, because occupancy 0.300 <= existing 0.700 in 2fe5A Skipped atom 294, because occupancy 0.400 <= existing 0.600 in 2fe5A Skipped atom 296, because occupancy 0.400 <= existing 0.600 in 2fe5A Skipped atom 298, because occupancy 0.400 <= existing 0.600 in 2fe5A Skipped atom 300, because occupancy 0.400 <= existing 0.600 in 2fe5A Skipped atom 302, because occupancy 0.400 <= existing 0.600 in 2fe5A Skipped atom 317, because occupancy 0.300 <= existing 0.700 in 2fe5A Skipped atom 320, because occupancy 0.300 <= existing 0.700 in 2fe5A Skipped atom 431, because occupancy 0.300 <= existing 0.700 in 2fe5A Skipped atom 433, because occupancy 0.300 <= existing 0.700 in 2fe5A Skipped atom 435, because occupancy 0.300 <= existing 0.700 in 2fe5A Skipped atom 437, because occupancy 0.300 <= existing 0.700 in 2fe5A Skipped atom 439, because occupancy 0.300 <= existing 0.700 in 2fe5A Skipped atom 441, because occupancy 0.300 <= existing 0.700 in 2fe5A Skipped atom 443, because occupancy 0.300 <= existing 0.700 in 2fe5A Skipped atom 593, because occupancy 0.250 <= existing 0.750 in 2fe5A Skipped atom 597, because occupancy 0.250 <= existing 0.750 in 2fe5A Skipped atom 599, because occupancy 0.250 <= existing 0.750 in 2fe5A Skipped atom 618, because occupancy 0.500 <= existing 0.500 in 2fe5A Skipped atom 620, because occupancy 0.500 <= existing 0.500 in 2fe5A Skipped atom 622, because occupancy 0.500 <= existing 0.500 in 2fe5A Skipped atom 624, because occupancy 0.500 <= existing 0.500 in 2fe5A Skipped atom 626, because occupancy 0.500 <= existing 0.500 in 2fe5A Skipped atom 628, because occupancy 0.500 <= existing 0.500 in 2fe5A Skipped atom 630, because occupancy 0.500 <= existing 0.500 in 2fe5A Skipped atom 632, because occupancy 0.500 <= existing 0.500 in 2fe5A Skipped atom 634, because occupancy 0.500 <= existing 0.500 in 2fe5A Skipped atom 636, because occupancy 0.500 <= existing 0.500 in 2fe5A Skipped atom 638, because occupancy 0.500 <= existing 0.500 in 2fe5A Skipped atom 640, because occupancy 0.500 <= existing 0.500 in 2fe5A Skipped atom 642, because occupancy 0.500 <= existing 0.500 in 2fe5A Skipped atom 644, because occupancy 0.500 <= existing 0.500 in 2fe5A Skipped atom 646, because occupancy 0.500 <= existing 0.500 in 2fe5A Skipped atom 648, because occupancy 0.500 <= existing 0.500 in 2fe5A Skipped atom 650, because occupancy 0.500 <= existing 0.500 in 2fe5A Skipped atom 652, because occupancy 0.500 <= existing 0.500 in 2fe5A Skipped atom 654, because occupancy 0.500 <= existing 0.500 in 2fe5A Skipped atom 656, because occupancy 0.500 <= existing 0.500 in 2fe5A Skipped atom 658, because occupancy 0.500 <= existing 0.500 in 2fe5A Skipped atom 660, because occupancy 0.500 <= existing 0.500 in 2fe5A Skipped atom 662, because occupancy 0.500 <= existing 0.500 in 2fe5A # T0359 read from 2fe5A/merged-good-all-a2m # 2fe5A read from 2fe5A/merged-good-all-a2m # adding 2fe5A to template set # found chain 2fe5A in template set Warning: unaligning (T0359)E94 because last residue in template chain is (2fe5A)S314 T0359 3 :SETFDVELTKNVQGLGITIAGYIGDKKL 2fe5A 222 :MTIMEVNLLKGPKGLGFSIAGGIGNQHI T0359 31 :EPSGIFVKSITKSSAVEHDGRIQIGDQIIAVDGTNLQGFTNQQAVEVLRHTGQTVLLTLMRRG 2fe5A 251 :GDNSIYITKIIEGGAAQKDGRLQIGDRLLAVNNTNLQDVRHEEAVASLKNTSDMVYLKVAKPG Number of specific fragments extracted= 2 number of extra gaps= 0 total=240 Number of alignments=58 # 2fe5A read from 2fe5A/merged-good-all-a2m # found chain 2fe5A in template set Warning: unaligning (T0359)M2 because first residue in template chain is (2fe5A)S221 T0359 3 :SETFDVELTKNVQGLGITIAGYIGDKKL 2fe5A 222 :MTIMEVNLLKGPKGLGFSIAGGIGNQHI T0359 31 :EPSGIFVKSITKSSAVEHDGRIQIGDQIIAVDGTNLQGFTNQQAVEVLRHTGQTVLLTLMRRG 2fe5A 251 :GDNSIYITKIIEGGAAQKDGRLQIGDRLLAVNNTNLQDVRHEEAVASLKNTSDMVYLKVAKPG Number of specific fragments extracted= 2 number of extra gaps= 0 total=242 Number of alignments=59 # 2fe5A read from 2fe5A/merged-good-all-a2m # found chain 2fe5A in template set T0359 3 :SETFDVELTKNVQGLGITIAGYIG 2fe5A 222 :MTIMEVNLLKGPKGLGFSIAGGIG T0359 27 :DKKLEPSGIFVKSITKSSAVEHDGRIQIGDQIIAVDGTNLQGFTNQQAVEVLRHTGQTVLLTLMRRG 2fe5A 247 :QHIPGDNSIYITKIIEGGAAQKDGRLQIGDRLLAVNNTNLQDVRHEEAVASLKNTSDMVYLKVAKPG Number of specific fragments extracted= 2 number of extra gaps= 0 total=244 Number of alignments=60 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1r6jA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0359 read from 1r6jA/merged-good-all-a2m # 1r6jA read from 1r6jA/merged-good-all-a2m # found chain 1r6jA in training set T0359 1 :SMSETFDVELTKNVQ 1r6jA 192 :GAMDPRTITMHKDST T0359 16 :GLGITIAGY 1r6jA 208 :HVGFIFKNG T0359 36 :FVKSITKSSAVEHDG 1r6jA 217 :KITSIVKDSSAARNG T0359 52 :IQIGDQIIAVDGTNLQGFTNQQAVEVLRHTGQTVLLTLMRR 1r6jA 232 :LLTEHNICEINGQNVIGLKDSQIADILSTSGTVVTITIMPA Number of specific fragments extracted= 4 number of extra gaps= 0 total=248 Number of alignments=61 # 1r6jA read from 1r6jA/merged-good-all-a2m # found chain 1r6jA in training set T0359 1 :SMSETFDVELTKNVQG 1r6jA 192 :GAMDPRTITMHKDSTG T0359 17 :LGITIAGY 1r6jA 209 :VGFIFKNG T0359 36 :FVKSITKSSAVEHDG 1r6jA 217 :KITSIVKDSSAARNG T0359 52 :IQIGDQIIAVDGTNLQGFTNQQAVEVLRHTGQTVLLTLMR 1r6jA 232 :LLTEHNICEINGQNVIGLKDSQIADILSTSGTVVTITIMP Number of specific fragments extracted= 4 number of extra gaps= 0 total=252 Number of alignments=62 # 1r6jA read from 1r6jA/merged-good-all-a2m # found chain 1r6jA in training set T0359 3 :SETFDVELT 1r6jA 194 :MDPRTITMH T0359 12 :KNVQGLGITIAGY 1r6jA 204 :DSTGHVGFIFKNG T0359 36 :FVKSITKSSAVEHDG 1r6jA 217 :KITSIVKDSSAARNG T0359 52 :IQIGDQIIAVDGTNLQGFTNQQAVEVLRHTGQTVLLTLMRR 1r6jA 232 :LLTEHNICEINGQNVIGLKDSQIADILSTSGTVVTITIMPA Number of specific fragments extracted= 4 number of extra gaps= 0 total=256 Number of alignments=63 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1qavA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1qavA expands to /projects/compbio/data/pdb/1qav.pdb.gz 1qavA:# T0359 read from 1qavA/merged-good-all-a2m # 1qavA read from 1qavA/merged-good-all-a2m # adding 1qavA to template set # found chain 1qavA in template set T0359 2 :MSETFDVELTKNVQ 1qavA 76 :SLQRRRVTVRKADA T0359 16 :GLGITIAGY 1qavA 91 :GLGISIKGG T0359 29 :KLEPSGIFVKSITKSSAVEHDGRIQIGDQIIAVDGTNLQGFTNQQAVEVLRHTGQTVLLTLMR 1qavA 100 :RENKMPILISKIFKGLAADQTEALFVGDAILSVNGEDLSSATHDEAVQALKKTGKEVVLEVKY Number of specific fragments extracted= 3 number of extra gaps= 0 total=259 Number of alignments=64 # 1qavA read from 1qavA/merged-good-all-a2m # found chain 1qavA in template set T0359 1 :SMSETFDVELTKNVQG 1qavA 75 :GSLQRRRVTVRKADAG T0359 17 :LGITIAGYIG 1qavA 92 :LGISIKGGRE T0359 31 :EPSGIFVKSITKSSAVEHDGRIQIGDQIIAVDGTNLQGFTNQQAVEVLRHTGQTVLLTLMR 1qavA 102 :NKMPILISKIFKGLAADQTEALFVGDAILSVNGEDLSSATHDEAVQALKKTGKEVVLEVKY Number of specific fragments extracted= 3 number of extra gaps= 0 total=262 Number of alignments=65 # 1qavA read from 1qavA/merged-good-all-a2m # found chain 1qavA in template set T0359 2 :MSETFDVELT 1qavA 76 :SLQRRRVTVR T0359 12 :KNVQGLGITIAGYIGD 1qavA 87 :ADAGGLGISIKGGREN T0359 32 :PSGIFVKSITKSSAVEHDGRIQIGDQIIAVDGTNLQGFTNQQAVEVLRHTGQTVLLTLMR 1qavA 103 :KMPILISKIFKGLAADQTEALFVGDAILSVNGEDLSSATHDEAVQALKKTGKEVVLEVKY Number of specific fragments extracted= 3 number of extra gaps= 0 total=265 Number of alignments=66 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1qavB/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1qavB expands to /projects/compbio/data/pdb/1qav.pdb.gz 1qavB:# T0359 read from 1qavB/merged-good-all-a2m # 1qavB read from 1qavB/merged-good-all-a2m # adding 1qavB to template set # found chain 1qavB in template set Warning: unaligning (T0359)M2 because first residue in template chain is (1qavB)Q1012 T0359 3 :SETFDVELTKNVQ 1qavB 1013 :PNVISVRLFKRKV T0359 16 :GLGITIAGY 1qavB 1027 :GLGFLVKER T0359 30 :LEPSGIFVKSITKSSAVEHDGRIQIGDQIIAVDGTNLQGFTNQQAVEVLRHT 1qavB 1036 :VSKPPVIISDLIRGGAAEQSGLIQAGDIILAVNDRPLVDLSYDSALEVLRGI T0359 82 :GQTVLLTLMRRGE 1qavB 1090 :ETHVVLILRGPEG Number of specific fragments extracted= 4 number of extra gaps= 0 total=269 Number of alignments=67 # 1qavB read from 1qavB/merged-good-all-a2m # found chain 1qavB in template set Warning: unaligning (T0359)M2 because first residue in template chain is (1qavB)Q1012 T0359 3 :SETFDVELTKNV 1qavB 1013 :PNVISVRLFKRK T0359 15 :QGLGITIAGYIG 1qavB 1026 :GGLGFLVKERVS T0359 32 :PSGIFVKSITKSSAVEHDGRIQIGDQIIAVDGTNLQGFTNQQAVEVLRHT 1qavB 1038 :KPPVIISDLIRGGAAEQSGLIQAGDIILAVNDRPLVDLSYDSALEVLRGI T0359 82 :GQTVLLTLMRRGET 1qavB 1090 :ETHVVLILRGPEGF Number of specific fragments extracted= 4 number of extra gaps= 0 total=273 Number of alignments=68 # 1qavB read from 1qavB/merged-good-all-a2m # found chain 1qavB in template set T0359 3 :SETFDVELT 1qavB 1013 :PNVISVRLF T0359 12 :KNVQGLGITIAGYIGD 1qavB 1023 :RKVGGLGFLVKERVSK T0359 33 :SGIFVKSITKSSAVEHDGRIQIGDQIIAVDGTNLQGFTNQQAVEVLRHTGQT 1qavB 1039 :PPVIISDLIRGGAAEQSGLIQAGDIILAVNDRPLVDLSYDSALEVLRGIASE T0359 85 :VLLTLMRRGE 1qavB 1093 :VVLILRGPEG Number of specific fragments extracted= 4 number of extra gaps= 0 total=277 Number of alignments=69 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1m5zA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1m5zA expands to /projects/compbio/data/pdb/1m5z.pdb.gz 1m5zA:# T0359 read from 1m5zA/merged-good-all-a2m # 1m5zA read from 1m5zA/merged-good-all-a2m # adding 1m5zA to template set # found chain 1m5zA in template set T0359 1 :SMSE 1m5zA 16 :SPTP T0359 5 :TFDVELTKNVQ 1m5zA 22 :LHKVTLYKDSG T0359 16 :GLGITIAGY 1m5zA 35 :DFGFSVADG T0359 30 :LEPSGIFVKSITKSSAVEHDG 1m5zA 44 :LLEKGVYVKNIRPAGPGDLGG T0359 52 :IQIGDQIIAVDGTNLQGFTNQQAVEVLRHTGQTVLLTLMRR 1m5zA 65 :LKPYDRLLQVNHVRTRDFDCCLVVPLIAESGNKLDLVISRN Number of specific fragments extracted= 5 number of extra gaps= 0 total=282 Number of alignments=70 # 1m5zA read from 1m5zA/merged-good-all-a2m # found chain 1m5zA in template set T0359 1 :SMS 1m5zA 16 :SPT T0359 4 :ETFDVELTKNVQ 1m5zA 21 :ELHKVTLYKDSG T0359 16 :GLGITIAGYIG 1m5zA 35 :DFGFSVADGLL T0359 32 :PSGIFVKSITKSSAVEHDG 1m5zA 46 :EKGVYVKNIRPAGPGDLGG T0359 52 :IQIGDQIIAVDGTNLQGFTNQQAVEVLRHTGQTVLLTLMRR 1m5zA 65 :LKPYDRLLQVNHVRTRDFDCCLVVPLIAESGNKLDLVISRN Number of specific fragments extracted= 5 number of extra gaps= 0 total=287 Number of alignments=71 # 1m5zA read from 1m5zA/merged-good-all-a2m # found chain 1m5zA in template set T0359 2 :MSETFDVELTKNV 1m5zA 19 :PVELHKVTLYKDS T0359 15 :QGLGITIAGYIGD 1m5zA 34 :EDFGFSVADGLLE T0359 33 :SGIFVKSITKSSAVEHDG 1m5zA 47 :KGVYVKNIRPAGPGDLGG T0359 52 :IQIGDQIIAVDGTNLQGFTNQQAVEVLRHTGQTVLLTLMRR 1m5zA 65 :LKPYDRLLQVNHVRTRDFDCCLVVPLIAESGNKLDLVISRN Number of specific fragments extracted= 4 number of extra gaps= 0 total=291 Number of alignments=72 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1be9A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1be9A expands to /projects/compbio/data/pdb/1be9.pdb.gz 1be9A:# T0359 read from 1be9A/merged-good-all-a2m # 1be9A read from 1be9A/merged-good-all-a2m # adding 1be9A to template set # found chain 1be9A in template set T0359 2 :MSETFDVELTKNVQGLGITIAGYI 1be9A 308 :PREPRRIVIHRGSTGLGFNIIGGE T0359 31 :EPSGIFVKSITKSSAVEHDGRIQIGDQIIAVDGTNLQGFTNQQAVEVLRHTGQTVLLTLMRR 1be9A 332 :DGEGIFISFILAGGPADLSGELRKGDQILSVNGVDLRNASHEQAAIALKNAGQTVTIIAQYK Number of specific fragments extracted= 2 number of extra gaps= 0 total=293 Number of alignments=73 # 1be9A read from 1be9A/merged-good-all-a2m # found chain 1be9A in template set T0359 2 :MSETFDVELTKNVQGLGITIAGYIG 1be9A 308 :PREPRRIVIHRGSTGLGFNIIGGED T0359 32 :PSGIFVKSITKSSAVEHDGRIQIGDQIIAVDGTNLQGFTNQQAVEVLRHTGQTVLLTLMRR 1be9A 333 :GEGIFISFILAGGPADLSGELRKGDQILSVNGVDLRNASHEQAAIALKNAGQTVTIIAQYK Number of specific fragments extracted= 2 number of extra gaps= 0 total=295 Number of alignments=74 # 1be9A read from 1be9A/merged-good-all-a2m # found chain 1be9A in template set T0359 2 :MSETFDVELTKNVQGLGITIAGYIG 1be9A 308 :PREPRRIVIHRGSTGLGFNIIGGED T0359 32 :PSGIFVKSITKSSAVEHDGRIQIGDQIIAVDGTNLQGFTNQQAVEVLRHTGQTVLLTLMRR 1be9A 333 :GEGIFISFILAGGPADLSGELRKGDQILSVNGVDLRNASHEQAAIALKNAGQTVTIIAQYK Number of specific fragments extracted= 2 number of extra gaps= 0 total=297 Number of alignments=75 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1d5gA/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/T0359/1d5gA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0359/1d5gA/merged-good-all-a2m.gz for input Trying 1d5gA/merged-good-all-a2m Error: Couldn't open file 1d5gA/merged-good-all-a2m or 1d5gA/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1te0A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1te0A expands to /projects/compbio/data/pdb/1te0.pdb.gz 1te0A:# T0359 read from 1te0A/merged-good-all-a2m # 1te0A read from 1te0A/merged-good-all-a2m # adding 1te0A to template set # found chain 1te0A in template set Warning: unaligning (T0359)G26 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1te0A)L269 Warning: unaligning (T0359)D27 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1te0A)L269 Warning: unaligning (T0359)L30 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1te0A)G273 Warning: unaligning (T0359)E31 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1te0A)G273 Warning: unaligning (T0359)P32 because of BadResidue code BAD_PEPTIDE in next template residue (1te0A)G275 Warning: unaligning (T0359)K38 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1te0A)E286 Warning: unaligning (T0359)S39 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1te0A)E286 Warning: unaligning (T0359)S43 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1te0A)G291 Warning: unaligning (T0359)S44 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1te0A)G291 Warning: unaligning (T0359)E47 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (1te0A)N295 Warning: unaligning (T0359)H48 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (1te0A)N295 Warning: unaligning (T0359)D49 because of BadResidue code BAD_PEPTIDE in next template residue (1te0A)G297 Warning: unaligning (T0359)G50 because of BadResidue code BAD_PEPTIDE at template residue (1te0A)G297 Warning: unaligning (T0359)D56 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1te0A)L303 Warning: unaligning (T0359)Q57 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1te0A)L303 Warning: unaligning (T0359)L66 because of BadResidue code BAD_PEPTIDE in next template residue (1te0A)I313 Warning: unaligning (T0359)Q67 because of BadResidue code BAD_PEPTIDE at template residue (1te0A)I313 T0359 18 :GITIAGYI 1te0A 260 :GIGGREIA T0359 28 :KK 1te0A 270 :HA T0359 33 :SGIFV 1te0A 280 :QGIVV T0359 40 :ITK 1te0A 287 :VSP T0359 45 :AV 1te0A 292 :PA T0359 52 :IQIG 1te0A 298 :IQVN T0359 58 :IIAVDGTN 1te0A 304 :IISVDNKP T0359 70 :TNQQAVEVLRHT 1te0A 314 :SALETMDQVAEI T0359 82 :GQTVLLTLMRRGE 1te0A 328 :GSVIPVVVMRDDK Number of specific fragments extracted= 9 number of extra gaps= 7 total=306 Number of alignments=76 # 1te0A read from 1te0A/merged-good-all-a2m # found chain 1te0A in template set Warning: unaligning (T0359)G26 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1te0A)L269 Warning: unaligning (T0359)D27 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1te0A)L269 Warning: unaligning (T0359)L30 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1te0A)G273 Warning: unaligning (T0359)E31 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1te0A)G273 Warning: unaligning (T0359)P32 because of BadResidue code BAD_PEPTIDE in next template residue (1te0A)G275 Warning: unaligning (T0359)S33 because of BadResidue code BAD_PEPTIDE at template residue (1te0A)G275 Warning: unaligning (T0359)K38 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1te0A)E286 Warning: unaligning (T0359)S39 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1te0A)E286 Warning: unaligning (T0359)S43 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1te0A)G291 Warning: unaligning (T0359)S44 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1te0A)G291 Warning: unaligning (T0359)E47 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (1te0A)N295 Warning: unaligning (T0359)H48 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (1te0A)N295 Warning: unaligning (T0359)D49 because of BadResidue code BAD_PEPTIDE in next template residue (1te0A)G297 Warning: unaligning (T0359)G50 because of BadResidue code BAD_PEPTIDE at template residue (1te0A)G297 Warning: unaligning (T0359)D56 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1te0A)L303 Warning: unaligning (T0359)Q57 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1te0A)L303 Warning: unaligning (T0359)L66 because of BadResidue code BAD_PEPTIDE in next template residue (1te0A)I313 Warning: unaligning (T0359)Q67 because of BadResidue code BAD_PEPTIDE at template residue (1te0A)I313 T0359 17 :LGITIAGYI 1te0A 259 :IGIGGREIA T0359 28 :KK 1te0A 270 :HA T0359 34 :GIFV 1te0A 281 :GIVV T0359 40 :ITK 1te0A 287 :VSP T0359 45 :AV 1te0A 292 :PA T0359 52 :IQIG 1te0A 298 :IQVN T0359 58 :IIAVDGTN 1te0A 304 :IISVDNKP T0359 70 :TNQQAVEVLRHT 1te0A 314 :SALETMDQVAEI T0359 82 :GQTVLLTLMRRGE 1te0A 328 :GSVIPVVVMRDDK Number of specific fragments extracted= 9 number of extra gaps= 7 total=315 Number of alignments=77 # 1te0A read from 1te0A/merged-good-all-a2m # found chain 1te0A in template set Warning: unaligning (T0359)I25 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1te0A)G273 Warning: unaligning (T0359)G26 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1te0A)G273 Warning: unaligning (T0359)D27 because of BadResidue code BAD_PEPTIDE in next template residue (1te0A)G275 Warning: unaligning (T0359)K28 because of BadResidue code BAD_PEPTIDE at template residue (1te0A)G275 Warning: unaligning (T0359)K29 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1te0A)D277 Warning: unaligning (T0359)L30 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1te0A)D277 Warning: unaligning (T0359)K38 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1te0A)E286 Warning: unaligning (T0359)S39 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1te0A)E286 Warning: unaligning (T0359)S43 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1te0A)G291 Warning: unaligning (T0359)S44 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1te0A)G291 Warning: unaligning (T0359)E47 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (1te0A)N295 Warning: unaligning (T0359)H48 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (1te0A)N295 Warning: unaligning (T0359)D49 because of BadResidue code BAD_PEPTIDE in next template residue (1te0A)G297 Warning: unaligning (T0359)G50 because of BadResidue code BAD_PEPTIDE at template residue (1te0A)G297 Warning: unaligning (T0359)D56 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1te0A)L303 Warning: unaligning (T0359)Q57 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1te0A)L303 Warning: unaligning (T0359)L66 because of BadResidue code BAD_PEPTIDE in next template residue (1te0A)I313 Warning: unaligning (T0359)Q67 because of BadResidue code BAD_PEPTIDE at template residue (1te0A)I313 T0359 31 :EPSGIFV 1te0A 278 :QLQGIVV T0359 40 :ITK 1te0A 287 :VSP T0359 45 :AV 1te0A 292 :PA T0359 52 :IQIG 1te0A 298 :IQVN T0359 58 :IIAVDGTN 1te0A 304 :IISVDNKP T0359 70 :TNQQAVEVLRHT 1te0A 314 :SALETMDQVAEI T0359 82 :GQTVLLTLMRRGE 1te0A 328 :GSVIPVVVMRDDK Number of specific fragments extracted= 7 number of extra gaps= 6 total=322 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2h3lA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2h3lA expands to /projects/compbio/data/pdb/2h3l.pdb.gz 2h3lA:# T0359 read from 2h3lA/merged-good-all-a2m # 2h3lA read from 2h3lA/merged-good-all-a2m # adding 2h3lA to template set # found chain 2h3lA in template set Warning: unaligning (T0359)E94 because of BadResidue code HAS_OXT+BAD_PEPTIDE in next template residue (2h3lA)S1412 T0359 5 :TFDVELTKNV 2h3lA 1321 :EIRVRVEKDP T0359 16 :GLGITIAGYIG 2h3lA 1331 :ELGFSISGGVG T0359 27 :DKKLEPSGIFVKSITKSSAVEH 2h3lA 1346 :PFRPDDDGIFVTRVQPEGPASK T0359 51 :RIQIGDQIIAVDGTNLQGFTNQQAVEVLRHTGQTVLLTLMRRG 2h3lA 1368 :LLQPGDKIIQANGYSFINIEHGQAVSLLKTFQNTVELIIVREV Number of specific fragments extracted= 4 number of extra gaps= 1 total=326 Number of alignments=78 # 2h3lA read from 2h3lA/merged-good-all-a2m # found chain 2h3lA in template set Warning: unaligning (T0359)E94 because of BadResidue code HAS_OXT+BAD_PEPTIDE in next template residue (2h3lA)S1412 T0359 4 :ETFDVELTKNV 2h3lA 1320 :QEIRVRVEKDP T0359 16 :GLGITIAGYIGDKKL 2h3lA 1331 :ELGFSISGGVGGRGN T0359 31 :EPSGIFVKSITKSSAVE 2h3lA 1350 :DDDGIFVTRVQPEGPAS T0359 50 :GRIQIGDQIIAVDGTNLQGFTNQQAVEVLRHTGQTVLLTLMRRG 2h3lA 1367 :KLLQPGDKIIQANGYSFINIEHGQAVSLLKTFQNTVELIIVREV Number of specific fragments extracted= 4 number of extra gaps= 1 total=330 Number of alignments=79 # 2h3lA read from 2h3lA/merged-good-all-a2m # found chain 2h3lA in template set T0359 2 :MSETFDVELTKNVQ 2h3lA 1318 :AKQEIRVRVEKDPE T0359 17 :LGITIAGYIG 2h3lA 1332 :LGFSISGGVG T0359 27 :DKKLEPSGIFVKSITKSSAV 2h3lA 1346 :PFRPDDDGIFVTRVQPEGPA T0359 49 :DGRIQIGDQIIAVDGTNLQGFTNQQAVEVLRHTGQTVLLTLMRR 2h3lA 1366 :SKLLQPGDKIIQANGYSFINIEHGQAVSLLKTFQNTVELIIVRE Number of specific fragments extracted= 4 number of extra gaps= 0 total=334 Number of alignments=80 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2fcfA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2fcfA expands to /projects/compbio/data/pdb/2fcf.pdb.gz 2fcfA:Skipped atom 598, because occupancy 0.500 <= existing 0.500 in 2fcfA Skipped atom 602, because occupancy 0.500 <= existing 0.500 in 2fcfA Skipped atom 604, because occupancy 0.500 <= existing 0.500 in 2fcfA Skipped atom 606, because occupancy 0.500 <= existing 0.500 in 2fcfA # T0359 read from 2fcfA/merged-good-all-a2m # 2fcfA read from 2fcfA/merged-good-all-a2m # adding 2fcfA to template set # found chain 2fcfA in template set Warning: unaligning (T0359)V14 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2fcfA)K1160 Warning: unaligning (T0359)I25 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2fcfA)G1184 Warning: unaligning (T0359)G26 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2fcfA)G1184 T0359 1 :SMSETFDVELTKN 2fcfA 1145 :QSMQPRRVELWRE T0359 16 :GLGITIAGY 2fcfA 1161 :SLGISIVGG T0359 35 :IFVKSITKSSAVEHDGRIQIGDQIIAVDGTNLQGFTNQQAVEVLRHTGQTVLLTLMRRGETSV 2fcfA 1185 :IFIKHVLEDSPAGKNGTLKPGDRIVEVDGMDLRDASHEQAVEAIRKAGNPVVFMVQSIISTRL Number of specific fragments extracted= 3 number of extra gaps= 1 total=337 Number of alignments=81 # 2fcfA read from 2fcfA/merged-good-all-a2m # found chain 2fcfA in template set Warning: unaligning (T0359)V14 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2fcfA)K1160 Warning: unaligning (T0359)Q15 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2fcfA)K1160 Warning: unaligning (T0359)I25 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2fcfA)G1184 Warning: unaligning (T0359)G26 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2fcfA)G1184 T0359 1 :SMSETFDVELTKN 2fcfA 1145 :QSMQPRRVELWRE T0359 16 :GLGITIAGY 2fcfA 1161 :SLGISIVGG T0359 35 :IFVKSITKSSAVEHDGRIQIGDQIIAVDGTNLQGFTNQQAVEVLRHTGQTVLLTLMRRGETSV 2fcfA 1185 :IFIKHVLEDSPAGKNGTLKPGDRIVEVDGMDLRDASHEQAVEAIRKAGNPVVFMVQSIISTRL Number of specific fragments extracted= 3 number of extra gaps= 1 total=340 Number of alignments=82 # 2fcfA read from 2fcfA/merged-good-all-a2m # found chain 2fcfA in template set Warning: unaligning (T0359)N13 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2fcfA)K1160 Warning: unaligning (T0359)Q15 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2fcfA)K1160 Warning: unaligning (T0359)I25 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2fcfA)G1184 Warning: unaligning (T0359)G26 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2fcfA)G1184 T0359 2 :MSETFDVELT 2fcfA 1146 :SMQPRRVELW T0359 12 :K 2fcfA 1157 :E T0359 16 :GLGITIAGY 2fcfA 1161 :SLGISIVGG T0359 35 :IFVKSITKSSAVEHDGRIQIGDQIIAVDGTNLQGFTNQQAVEVLRHTGQTVLLTLMRRGETSV 2fcfA 1185 :IFIKHVLEDSPAGKNGTLKPGDRIVEVDGMDLRDASHEQAVEAIRKAGNPVVFMVQSIISTRL Number of specific fragments extracted= 4 number of extra gaps= 1 total=344 Number of alignments=83 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1rgrA/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/T0359/1rgrA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0359/1rgrA/merged-good-all-a2m.gz for input Trying 1rgrA/merged-good-all-a2m Error: Couldn't open file 1rgrA/merged-good-all-a2m or 1rgrA/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1lcyA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1lcyA expands to /projects/compbio/data/pdb/1lcy.pdb.gz 1lcyA:# T0359 read from 1lcyA/merged-good-all-a2m # 1lcyA read from 1lcyA/merged-good-all-a2m # adding 1lcyA to template set # found chain 1lcyA in template set T0359 26 :GDKKLEP 1lcyA 247 :REPSFPD T0359 33 :SGIFVKSITKSSAVEHDG 1lcyA 256 :HGVLIHKVILGSPAHRAG T0359 52 :IQIGDQIIAVDGTNLQG 1lcyA 274 :LRPGDVILAIGEQMVQN T0359 71 :NQQAVEVLRHTG 1lcyA 291 :AEDVYEAVRTQS T0359 84 :TVLLTLMRRGE 1lcyA 303 :QLAVQIRRGRE Number of specific fragments extracted= 5 number of extra gaps= 0 total=349 Number of alignments=84 # 1lcyA read from 1lcyA/merged-good-all-a2m # found chain 1lcyA in template set T0359 16 :GLGITIAG 1lcyA 228 :YIGVMMLT T0359 24 :YIGDKKL 1lcyA 245 :QLREPSF T0359 31 :EPSGIFVKSITKSSAVEHDG 1lcyA 254 :VQHGVLIHKVILGSPAHRAG T0359 52 :IQIGDQIIAVDGTNLQG 1lcyA 274 :LRPGDVILAIGEQMVQN T0359 71 :NQQAVEVLRHTGQ 1lcyA 291 :AEDVYEAVRTQSQ T0359 85 :VLLTLMRRGET 1lcyA 304 :LAVQIRRGRET Number of specific fragments extracted= 6 number of extra gaps= 0 total=355 Number of alignments=85 # 1lcyA read from 1lcyA/merged-good-all-a2m # found chain 1lcyA in template set T0359 27 :DK 1lcyA 250 :SF T0359 30 :LEPSGIFVKSITKSSAVEHDG 1lcyA 253 :DVQHGVLIHKVILGSPAHRAG T0359 52 :IQIGDQIIAVDGTNLQG 1lcyA 274 :LRPGDVILAIGEQMVQN T0359 71 :NQQAVEVLRHTG 1lcyA 291 :AEDVYEAVRTQS T0359 84 :TVLLTLMRRGE 1lcyA 303 :QLAVQIRRGRE Number of specific fragments extracted= 5 number of extra gaps= 0 total=360 Number of alignments=86 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1sotA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1sotA expands to /projects/compbio/data/pdb/1sot.pdb.gz 1sotA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0359 read from 1sotA/merged-good-all-a2m # 1sotA read from 1sotA/merged-good-all-a2m # adding 1sotA to template set # found chain 1sotA in template set Warning: unaligning (T0359)G34 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1sotA)G281 T0359 35 :IFVKSITKSSAVEHDG 1sotA 282 :IVVNEVSPDGPAANAG T0359 52 :IQIGDQIIAVDGTNLQG 1sotA 298 :IQVNDLIISVDNKPAIS T0359 71 :NQQAVEVLRHT 1sotA 315 :ALETMDQVAEI T0359 82 :GQTVLL 1sotA 328 :GSVIPV Number of specific fragments extracted= 4 number of extra gaps= 0 total=364 Number of alignments=87 # 1sotA read from 1sotA/merged-good-all-a2m # found chain 1sotA in template set Warning: unaligning (T0359)G34 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1sotA)G281 Warning: unaligning (T0359)L89 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1sotA)Q341 Warning: unaligning (T0359)T95 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1sotA)Q341 T0359 35 :IFVKSITKSSAVEHDG 1sotA 282 :IVVNEVSPDGPAANAG T0359 52 :IQIGDQIIAVDGTNLQ 1sotA 298 :IQVNDLIISVDNKPAI T0359 70 :TNQQAVEVLRHT 1sotA 314 :SALETMDQVAEI T0359 82 :GQTVLLT 1sotA 328 :GSVIPVV T0359 96 :S 1sotA 342 :L Number of specific fragments extracted= 5 number of extra gaps= 0 total=369 Number of alignments=88 # 1sotA read from 1sotA/merged-good-all-a2m # found chain 1sotA in template set Warning: unaligning (T0359)G34 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1sotA)G281 Warning: unaligning (T0359)R91 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1sotA)Q341 T0359 35 :IFVKSITKSSAVEHDG 1sotA 282 :IVVNEVSPDGPAANAG T0359 52 :IQIGDQIIAVDGTNLQ 1sotA 298 :IQVNDLIISVDNKPAI T0359 70 :TNQQAVEVLRHTGQTVLLTLM 1sotA 314 :SALETMDQVAEIRPGSVIPVV Number of specific fragments extracted= 3 number of extra gaps= 0 total=372 Number of alignments=89 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2f5yA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2f5yA expands to /projects/compbio/data/pdb/2f5y.pdb.gz 2f5yA:Skipped atom 397, because occupancy 0.500 <= existing 0.500 in 2f5yA Skipped atom 401, because occupancy 0.500 <= existing 0.500 in 2f5yA Skipped atom 403, because occupancy 0.500 <= existing 0.500 in 2f5yA Skipped atom 405, because occupancy 0.500 <= existing 0.500 in 2f5yA Skipped atom 407, because occupancy 0.500 <= existing 0.500 in 2f5yA Skipped atom 409, because occupancy 0.500 <= existing 0.500 in 2f5yA Skipped atom 411, because occupancy 0.500 <= existing 0.500 in 2f5yA Skipped atom 413, because occupancy 0.500 <= existing 0.500 in 2f5yA # T0359 read from 2f5yA/merged-good-all-a2m # 2f5yA read from 2f5yA/merged-good-all-a2m # adding 2f5yA to template set # found chain 2f5yA in template set Warning: unaligning (T0359)S3 because first residue in template chain is (2f5yA)M14 Warning: unaligning (T0359)E4 because of BadResidue code BAD_PEPTIDE at template residue (2f5yA)R15 Warning: unaligning (T0359)Q67 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2f5yA)H70 Warning: unaligning (T0359)G68 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2f5yA)H70 Warning: unaligning (T0359)G93 because last residue in template chain is (2f5yA)V95 T0359 5 :TFDVELTKNVQGLGITIAG 2f5yA 16 :YRQITIPRGKDGFGFTICC T0359 32 :PSGIFVKSITKSSAVEHDG 2f5yA 35 :DSPVRVQAVDSGGPAERAG T0359 52 :IQIGDQIIAVDGTNL 2f5yA 54 :LQQLDTVLQLNERPV T0359 69 :FTNQQAVEVLRHTGQTVLLTLMRR 2f5yA 71 :WKCVELAHEIRSCPSEIILLVWRM Number of specific fragments extracted= 4 number of extra gaps= 1 total=376 Number of alignments=90 # 2f5yA read from 2f5yA/merged-good-all-a2m # found chain 2f5yA in template set Warning: unaligning (T0359)S3 because first residue in template chain is (2f5yA)M14 Warning: unaligning (T0359)E4 because of BadResidue code BAD_PEPTIDE at template residue (2f5yA)R15 Warning: unaligning (T0359)Q67 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2f5yA)H70 Warning: unaligning (T0359)G68 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2f5yA)H70 Warning: unaligning (T0359)G93 because last residue in template chain is (2f5yA)V95 T0359 5 :TFDVELTKNVQGLGITIA 2f5yA 16 :YRQITIPRGKDGFGFTIC T0359 31 :EPSGIFVKSITKSSAVEHDG 2f5yA 34 :CDSPVRVQAVDSGGPAERAG T0359 52 :IQIGDQIIAVDGTNL 2f5yA 54 :LQQLDTVLQLNERPV T0359 69 :FTNQQAVEVLRHTGQTVLLTLMRR 2f5yA 71 :WKCVELAHEIRSCPSEIILLVWRM Number of specific fragments extracted= 4 number of extra gaps= 1 total=380 Number of alignments=91 # 2f5yA read from 2f5yA/merged-good-all-a2m # found chain 2f5yA in template set Warning: unaligning (T0359)S3 because first residue in template chain is (2f5yA)M14 Warning: unaligning (T0359)E4 because of BadResidue code BAD_PEPTIDE at template residue (2f5yA)R15 Warning: unaligning (T0359)Q67 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2f5yA)H70 Warning: unaligning (T0359)G68 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2f5yA)H70 Warning: unaligning (T0359)G93 because last residue in template chain is (2f5yA)V95 T0359 5 :TFDVELTKNVQGLGITIAG 2f5yA 16 :YRQITIPRGKDGFGFTICC T0359 32 :PSGIFVKSITKSSAVEHDG 2f5yA 35 :DSPVRVQAVDSGGPAERAG T0359 52 :IQIGDQIIAVDGTNL 2f5yA 54 :LQQLDTVLQLNERPV T0359 69 :FTNQQAVEVLRHTGQTVLLTLMRR 2f5yA 71 :WKCVELAHEIRSCPSEIILLVWRM Number of specific fragments extracted= 4 number of extra gaps= 1 total=384 Number of alignments=92 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1kwaA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1kwaA expands to /projects/compbio/data/pdb/1kwa.pdb.gz 1kwaA:# T0359 read from 1kwaA/merged-good-all-a2m # 1kwaA read from 1kwaA/merged-good-all-a2m # adding 1kwaA to template set # found chain 1kwaA in template set Warning: unaligning (T0359)E4 because first residue in template chain is (1kwaA)R487 Warning: unaligning (T0359)S96 because last residue in template chain is (1kwaA)F574 T0359 5 :TFDVELTKNVQ 1kwaA 488 :SRLVQFQKNTD T0359 16 :GLGITIAG 1kwaA 500 :PMGITLKM T0359 26 :G 1kwaA 508 :N T0359 29 :KLEP 1kwaA 509 :ELNH T0359 35 :IFVKSITKSSAVEHDGRIQIGDQIIAVDGTNLQGFTNQQAVEVLRHTGQTVLLTLMRRGET 1kwaA 513 :CIVARIMHGGMIHRQGTLHVGDEIREINGISVANQTVEQLQKMLREMRGSITFKIVPSYRE Number of specific fragments extracted= 5 number of extra gaps= 0 total=389 Number of alignments=93 # 1kwaA read from 1kwaA/merged-good-all-a2m # found chain 1kwaA in template set Warning: unaligning (T0359)E4 because first residue in template chain is (1kwaA)R487 Warning: unaligning (T0359)S96 because last residue in template chain is (1kwaA)F574 T0359 5 :TFDVELTKNVQ 1kwaA 488 :SRLVQFQKNTD T0359 16 :GLGITIAGY 1kwaA 500 :PMGITLKMN T0359 27 :D 1kwaA 509 :E T0359 32 :PSGIFVKSITKSSAVEHDGRIQIGDQIIAVDGTNLQGFTNQQAVEVLRHTGQTVLLTLMRRGET 1kwaA 510 :LNHCIVARIMHGGMIHRQGTLHVGDEIREINGISVANQTVEQLQKMLREMRGSITFKIVPSYRE Number of specific fragments extracted= 4 number of extra gaps= 0 total=393 Number of alignments=94 # 1kwaA read from 1kwaA/merged-good-all-a2m # found chain 1kwaA in template set Warning: unaligning (T0359)S96 because last residue in template chain is (1kwaA)F574 T0359 5 :TFDVELT 1kwaA 488 :SRLVQFQ T0359 12 :KNVQGLGITIAGYIGD 1kwaA 496 :NTDEPMGITLKMNELN T0359 34 :GIFVKSITKSSAVEHDGRIQIGDQIIAVDGTNLQGFTNQQAVEVLRHTGQTVLLTLMRRGET 1kwaA 512 :HCIVARIMHGGMIHRQGTLHVGDEIREINGISVANQTVEQLQKMLREMRGSITFKIVPSYRE Number of specific fragments extracted= 3 number of extra gaps= 0 total=396 Number of alignments=95 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1kwaB/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1kwaB expands to /projects/compbio/data/pdb/1kwa.pdb.gz 1kwaB:# T0359 read from 1kwaB/merged-good-all-a2m # 1kwaB read from 1kwaB/merged-good-all-a2m # adding 1kwaB to template set # found chain 1kwaB in template set Warning: unaligning (T0359)E4 because first residue in template chain is (1kwaB)R487 Warning: unaligning (T0359)G23 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1kwaB)L510 Warning: unaligning (T0359)P32 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1kwaB)L510 T0359 5 :TFDVELTKNVQ 1kwaB 488 :SRLVQFQKNTD T0359 16 :GLGITIA 1kwaB 500 :PMGITLK T0359 33 :SGIFVKSITKSSAVEHDGRIQIGDQIIAVDGTNLQGFTNQQAVEVLRHTGQTVLLTLMRRG 1kwaB 511 :NHCIVARIMHGGMIHRQGTLHVGDEIREINGISVANQTVEQLQKMLREMRGSITFKIVPSY Number of specific fragments extracted= 3 number of extra gaps= 1 total=399 Number of alignments=96 # 1kwaB read from 1kwaB/merged-good-all-a2m # found chain 1kwaB in template set Warning: unaligning (T0359)E4 because first residue in template chain is (1kwaB)R487 Warning: unaligning (T0359)G23 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1kwaB)L510 Warning: unaligning (T0359)P32 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1kwaB)L510 Warning: unaligning (T0359)S96 because last residue in template chain is (1kwaB)F574 T0359 5 :TFDVELTKNVQ 1kwaB 488 :SRLVQFQKNTD T0359 16 :GLGITIA 1kwaB 500 :PMGITLK T0359 33 :SGIFVKSITKSSAVEHDGRIQIGDQIIAVDGTNLQGFTNQQAVEVLRHTGQTVLLTLMRRGET 1kwaB 511 :NHCIVARIMHGGMIHRQGTLHVGDEIREINGISVANQTVEQLQKMLREMRGSITFKIVPSYRE Number of specific fragments extracted= 3 number of extra gaps= 1 total=402 Number of alignments=97 # 1kwaB read from 1kwaB/merged-good-all-a2m # found chain 1kwaB in template set Warning: unaligning (T0359)G23 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1kwaB)L510 Warning: unaligning (T0359)P32 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1kwaB)L510 T0359 5 :TFDVELT 1kwaB 488 :SRLVQFQ T0359 12 :KNVQGLGITIA 1kwaB 496 :NTDEPMGITLK T0359 33 :SGIFVKSITKSSAVEHDGRIQIGDQIIAVDGTNLQGFTNQQAVEVLRHTGQTVLLTLMRR 1kwaB 511 :NHCIVARIMHGGMIHRQGTLHVGDEIREINGISVANQTVEQLQKMLREMRGSITFKIVPS Number of specific fragments extracted= 3 number of extra gaps= 1 total=405 Number of alignments=98 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1pdr/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1pdr expands to /projects/compbio/data/pdb/1pdr.pdb.gz 1pdr:Warning: there is no chain 1pdr will retry with 1pdrA # T0359 read from 1pdr/merged-good-all-a2m # 1pdr read from 1pdr/merged-good-all-a2m # adding 1pdr to template set # found chain 1pdr in template set T0359 1 :SMSETFDVELTKNVQGLGITIAGY 1pdr 460 :ITREPRKVVLHRGSTGLGFNIVGG T0359 30 :LEPSGIFVKSITKSSAVEHDGRIQIGDQIIAVDGTNLQGFTNQQAVEVLRHTGQTVLLTLMRR 1pdr 484 :EDGEGIFISFILAGGPADLSGELRKGDRIISVNSVDLRAASHEQAAAALKNAGQAVTIVAQYR Number of specific fragments extracted= 2 number of extra gaps= 0 total=407 Number of alignments=99 # 1pdr read from 1pdr/merged-good-all-a2m # found chain 1pdr in template set T0359 2 :MSETFDVELTKNVQGLGITIAGYIG 1pdr 461 :TREPRKVVLHRGSTGLGFNIVGGED T0359 32 :PSGIFVKSITKSSAVEHDGRIQIGDQIIAVDGTNLQGFTNQQAVEVLRHTGQTVLLTLMRR 1pdr 486 :GEGIFISFILAGGPADLSGELRKGDRIISVNSVDLRAASHEQAAAALKNAGQAVTIVAQYR Number of specific fragments extracted= 2 number of extra gaps= 0 total=409 Number of alignments=100 # 1pdr read from 1pdr/merged-good-all-a2m # found chain 1pdr in template set T0359 2 :MSETFDVELTKNVQGLGITIAGYIGD 1pdr 461 :TREPRKVVLHRGSTGLGFNIVGGEDG T0359 33 :SGIFVKSITKSSAVEHDGRIQIGDQIIAVDGTNLQGFTNQQAVEVLRHTGQTVLLTLMRR 1pdr 487 :EGIFISFILAGGPADLSGELRKGDRIISVNSVDLRAASHEQAAAALKNAGQAVTIVAQYR Number of specific fragments extracted= 2 number of extra gaps= 0 total=411 Number of alignments=101 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1iu0A/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/T0359/1iu0A/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0359/1iu0A/merged-good-all-a2m.gz for input Trying 1iu0A/merged-good-all-a2m Error: Couldn't open file 1iu0A/merged-good-all-a2m or 1iu0A/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1n99A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1n99A expands to /projects/compbio/data/pdb/1n99.pdb.gz 1n99A:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0359 read from 1n99A/merged-good-all-a2m # 1n99A read from 1n99A/merged-good-all-a2m # adding 1n99A to template set # found chain 1n99A in template set Warning: unaligning (T0359)T5 because first residue in template chain is (1n99A)P112 Warning: unaligning (T0359)T88 because of BadResidue code BAD_PEPTIDE in next template residue (1n99A)I190 Warning: unaligning (T0359)L89 because of BadResidue code BAD_PEPTIDE at template residue (1n99A)I190 T0359 6 :FDVELTKNVQG 1n99A 113 :REVILCKDQDG T0359 17 :LGITIAGY 1n99A 125 :IGLRLKSI T0359 32 :PSGIFVKSITKSSAVEHDG 1n99A 133 :DNGIFVQLVQANSPASLVG T0359 52 :IQIGDQIIAVDGTNLQGFTNQQAVEVLRHT 1n99A 152 :LRFGDQVLQINGENCAGWSSDKAHKVLKQA T0359 82 :GQTVLL 1n99A 183 :GEKITM T0359 90 :MRR 1n99A 191 :RDR Number of specific fragments extracted= 6 number of extra gaps= 1 total=417 Number of alignments=102 # 1n99A read from 1n99A/merged-good-all-a2m # found chain 1n99A in template set Warning: unaligning (T0359)T5 because first residue in template chain is (1n99A)P112 Warning: unaligning (T0359)T88 because of BadResidue code BAD_PEPTIDE in next template residue (1n99A)I190 Warning: unaligning (T0359)L89 because of BadResidue code BAD_PEPTIDE at template residue (1n99A)I190 T0359 6 :FDVELTKNVQG 1n99A 113 :REVILCKDQDG T0359 17 :LGITIAGY 1n99A 125 :IGLRLKSI T0359 32 :PSGIFVKSITKSSAVEHDG 1n99A 133 :DNGIFVQLVQANSPASLVG T0359 52 :IQIGDQIIAVDGTNLQGFTNQQAVEVLRHT 1n99A 152 :LRFGDQVLQINGENCAGWSSDKAHKVLKQA T0359 82 :GQTVLL 1n99A 183 :GEKITM T0359 90 :MRRGE 1n99A 191 :RDRPF Number of specific fragments extracted= 6 number of extra gaps= 1 total=423 Number of alignments=103 # 1n99A read from 1n99A/merged-good-all-a2m # found chain 1n99A in template set Warning: unaligning (T0359)T5 because first residue in template chain is (1n99A)P112 Warning: unaligning (T0359)T88 because of BadResidue code BAD_PEPTIDE in next template residue (1n99A)I190 Warning: unaligning (T0359)L89 because of BadResidue code BAD_PEPTIDE at template residue (1n99A)I190 T0359 6 :FDVELT 1n99A 113 :REVILC T0359 12 :KNVQGLGITIAGY 1n99A 120 :DQDGKIGLRLKSI T0359 32 :PSGIFVKSITKSSAVEHDG 1n99A 133 :DNGIFVQLVQANSPASLVG T0359 52 :IQIGDQIIAVDGTNLQGFTNQQAVEVLRHTGQ 1n99A 152 :LRFGDQVLQINGENCAGWSSDKAHKVLKQAFG T0359 84 :TVLL 1n99A 185 :KITM T0359 90 :MRRGE 1n99A 191 :RDRPF Number of specific fragments extracted= 6 number of extra gaps= 1 total=429 Number of alignments=104 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1g9oA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0359 read from 1g9oA/merged-good-all-a2m # 1g9oA read from 1g9oA/merged-good-all-a2m # found chain 1g9oA in training set Warning: unaligning (T0359)M2 because first residue in template chain is (1g9oA)R9 T0359 3 :SETFDVELTKNVQGLGITIAGY 1g9oA 10 :MLPRLCCLEKGPNGYGFHLHGE T0359 30 :LEPSGIFVKSITKSSAVEHDG 1g9oA 32 :KGKLGQYIRLVEPGSPAEKAG T0359 52 :IQIGDQIIAVDGTNLQGFTNQQAVEVLRHTGQTVLLTLMRRGE 1g9oA 53 :LLAGDRLVEVNGENVEKETHQQVVSRIRAALNAVRLLVVDPET T0359 95 :TSV 1g9oA 97 :EQL Number of specific fragments extracted= 4 number of extra gaps= 0 total=433 Number of alignments=105 # 1g9oA read from 1g9oA/merged-good-all-a2m # found chain 1g9oA in training set T0359 3 :SETFDVELTKNVQGLGITIAGYIG 1g9oA 10 :MLPRLCCLEKGPNGYGFHLHGEKG T0359 32 :PSGIFVKSITKSSAVEHDG 1g9oA 34 :KLGQYIRLVEPGSPAEKAG T0359 52 :IQIGDQIIAVDGTNLQGFTNQQAVEVLRHTGQTVLLTLMRRGETSV 1g9oA 53 :LLAGDRLVEVNGENVEKETHQQVVSRIRAALNAVRLLVVDPETDEQ Number of specific fragments extracted= 3 number of extra gaps= 0 total=436 Number of alignments=106 # 1g9oA read from 1g9oA/merged-good-all-a2m # found chain 1g9oA in training set T0359 3 :SETFDVELTKNVQGLGITIAGYIGD 1g9oA 10 :MLPRLCCLEKGPNGYGFHLHGEKGK T0359 33 :SGIFVKSITKSSAVEHDG 1g9oA 35 :LGQYIRLVEPGSPAEKAG T0359 52 :IQIGDQIIAVDGTNLQGFTNQQAVEVLRHTGQTVLLTLMRRGETSV 1g9oA 53 :LLAGDRLVEVNGENVEKETHQQVVSRIRAALNAVRLLVVDPETDEQ Number of specific fragments extracted= 3 number of extra gaps= 0 total=439 Number of alignments=107 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1l6oA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1l6oA expands to /projects/compbio/data/pdb/1l6o.pdb.gz 1l6oA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0359 read from 1l6oA/merged-good-all-a2m # 1l6oA read from 1l6oA/merged-good-all-a2m # adding 1l6oA to template set # found chain 1l6oA in template set Warning: unaligning (T0359)E4 because first residue in template chain is (1l6oA)M251 Warning: unaligning (T0359)V8 because of BadResidue code BAD_PEPTIDE in next template residue (1l6oA)T256 Warning: unaligning (T0359)E9 because of BadResidue code BAD_PEPTIDE at template residue (1l6oA)T256 Warning: unaligning (T0359)N13 because of BadResidue code BAD_PEPTIDE in next template residue (1l6oA)K261 Warning: unaligning (T0359)V14 because of BadResidue code BAD_PEPTIDE at template residue (1l6oA)K261 Warning: unaligning (T0359)Q15 because of BadResidue code BAD_PEPTIDE at template residue (1l6oA)N263 Warning: unaligning (T0359)G16 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1l6oA)L265 Warning: unaligning (T0359)L17 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1l6oA)L265 Warning: unaligning (T0359)I19 because of BadResidue code BAD_PEPTIDE in next template residue (1l6oA)S268 Warning: unaligning (T0359)T20 because of BadResidue code BAD_PEPTIDE at template residue (1l6oA)S268 Warning: unaligning (T0359)I25 because of BadResidue code BAD_PEPTIDE in next template residue (1l6oA)N274 Warning: unaligning (T0359)G26 because of BadResidue code BAD_PEPTIDE at template residue (1l6oA)N274 Warning: unaligning (T0359)P32 because of BadResidue code BAD_PEPTIDE in next template residue (1l6oA)G279 Warning: unaligning (T0359)S33 because of BadResidue code BAD_PEPTIDE at template residue (1l6oA)G279 Warning: unaligning (T0359)G34 because of BadResidue code BAD_PEPTIDE at template residue (1l6oA)G280 Warning: unaligning (T0359)V46 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1l6oA)A293 Warning: unaligning (T0359)E47 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1l6oA)A293 Warning: unaligning (T0359)D62 because of BadResidue code BAD_PEPTIDE in next template residue (1l6oA)D309 Warning: unaligning (T0359)G63 because of BadResidue code BAD_PEPTIDE at template residue (1l6oA)D309 Warning: unaligning (T0359)N65 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1l6oA)F312 Warning: unaligning (T0359)L66 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1l6oA)F312 Warning: unaligning (T0359)G68 because of BadResidue code BAD_PEPTIDE in next template residue (1l6oA)M315 Warning: unaligning (T0359)F69 because of BadResidue code BAD_PEPTIDE at template residue (1l6oA)M315 Warning: unaligning (T0359)T70 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1l6oA)S316 Warning: unaligning (T0359)R79 because of BadResidue code BAD_PEPTIDE in next template residue (1l6oA)D326 Warning: unaligning (T0359)H80 because of BadResidue code BAD_PEPTIDE at template residue (1l6oA)D326 Warning: unaligning (T0359)L87 because of BadResidue code BAD_PEPTIDE in next template residue (1l6oA)T337 Warning: unaligning (T0359)T88 because of BadResidue code BAD_PEPTIDE at template residue (1l6oA)T337 Warning: unaligning (T0359)L89 because of BadResidue code BAD_PEPTIDE in next template residue (1l6oA)A339 Warning: unaligning (T0359)M90 because of BadResidue code BAD_PEPTIDE at template residue (1l6oA)A339 Warning: unaligning (T0359)R92 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (1l6oA)E342 Warning: unaligning (T0359)G93 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (1l6oA)E342 Warning: unaligning (T0359)E94 because of BadResidue code BAD_PEPTIDE in next template residue (1l6oA)H344 Warning: unaligning (T0359)T95 because of BadResidue code BAD_PEPTIDE at template residue (1l6oA)H344 Warning: unaligning (T0359)S96 because last residue in template chain is (1l6oA)H345 T0359 5 :TFD 1l6oA 252 :IIT T0359 10 :LTK 1l6oA 257 :LNM T0359 18 :G 1l6oA 266 :G T0359 21 :IAGY 1l6oA 269 :IVGQ T0359 29 :KLE 1l6oA 275 :ERG T0359 35 :IFVKSITKSSA 1l6oA 281 :IYIGSIMKGGA T0359 48 :HDGRIQIGDQIIAV 1l6oA 294 :ADGRIEPGDMLLQV T0359 64 :T 1l6oA 310 :I T0359 67 :Q 1l6oA 313 :E T0359 71 :NQQAVEVL 1l6oA 317 :NDDAVRVL T0359 81 :T 1l6oA 327 :I T0359 82 :GQTVL 1l6oA 331 :PGPIV T0359 91 :R 1l6oA 340 :K Number of specific fragments extracted= 13 number of extra gaps= 13 total=452 # 1l6oA read from 1l6oA/merged-good-all-a2m # found chain 1l6oA in template set Warning: unaligning (T0359)V8 because of BadResidue code BAD_PEPTIDE in next template residue (1l6oA)T256 Warning: unaligning (T0359)E9 because of BadResidue code BAD_PEPTIDE at template residue (1l6oA)T256 Warning: unaligning (T0359)N13 because of BadResidue code BAD_PEPTIDE in next template residue (1l6oA)K261 Warning: unaligning (T0359)V14 because of BadResidue code BAD_PEPTIDE at template residue (1l6oA)K261 Warning: unaligning (T0359)Q15 because of BadResidue code BAD_PEPTIDE at template residue (1l6oA)N263 Warning: unaligning (T0359)G16 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1l6oA)L265 Warning: unaligning (T0359)L17 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1l6oA)L265 Warning: unaligning (T0359)I19 because of BadResidue code BAD_PEPTIDE in next template residue (1l6oA)S268 Warning: unaligning (T0359)T20 because of BadResidue code BAD_PEPTIDE at template residue (1l6oA)S268 Warning: unaligning (T0359)I25 because of BadResidue code BAD_PEPTIDE in next template residue (1l6oA)N274 Warning: unaligning (T0359)G26 because of BadResidue code BAD_PEPTIDE at template residue (1l6oA)N274 Warning: unaligning (T0359)P32 because of BadResidue code BAD_PEPTIDE in next template residue (1l6oA)G279 Warning: unaligning (T0359)S33 because of BadResidue code BAD_PEPTIDE at template residue (1l6oA)G279 Warning: unaligning (T0359)G34 because of BadResidue code BAD_PEPTIDE at template residue (1l6oA)G280 Warning: unaligning (T0359)V46 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1l6oA)A293 Warning: unaligning (T0359)E47 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1l6oA)A293 Warning: unaligning (T0359)D62 because of BadResidue code BAD_PEPTIDE in next template residue (1l6oA)D309 Warning: unaligning (T0359)G63 because of BadResidue code BAD_PEPTIDE at template residue (1l6oA)D309 Warning: unaligning (T0359)N65 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1l6oA)F312 Warning: unaligning (T0359)L66 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1l6oA)F312 Warning: unaligning (T0359)G68 because of BadResidue code BAD_PEPTIDE in next template residue (1l6oA)M315 Warning: unaligning (T0359)F69 because of BadResidue code BAD_PEPTIDE at template residue (1l6oA)M315 Warning: unaligning (T0359)T70 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1l6oA)S316 Warning: unaligning (T0359)R79 because of BadResidue code BAD_PEPTIDE in next template residue (1l6oA)D326 Warning: unaligning (T0359)H80 because of BadResidue code BAD_PEPTIDE at template residue (1l6oA)D326 Warning: unaligning (T0359)L87 because of BadResidue code BAD_PEPTIDE in next template residue (1l6oA)T337 Warning: unaligning (T0359)T88 because of BadResidue code BAD_PEPTIDE at template residue (1l6oA)T337 Warning: unaligning (T0359)L89 because of BadResidue code BAD_PEPTIDE in next template residue (1l6oA)A339 Warning: unaligning (T0359)M90 because of BadResidue code BAD_PEPTIDE at template residue (1l6oA)A339 Warning: unaligning (T0359)R92 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (1l6oA)E342 Warning: unaligning (T0359)G93 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (1l6oA)E342 Warning: unaligning (T0359)E94 because of BadResidue code BAD_PEPTIDE in next template residue (1l6oA)H344 Warning: unaligning (T0359)T95 because of BadResidue code BAD_PEPTIDE at template residue (1l6oA)H344 Warning: unaligning (T0359)S96 because last residue in template chain is (1l6oA)H345 T0359 5 :TFD 1l6oA 252 :IIT T0359 10 :LTK 1l6oA 257 :LNM T0359 18 :G 1l6oA 266 :G T0359 21 :IAGY 1l6oA 269 :IVGQ T0359 27 :DK 1l6oA 275 :ER T0359 31 :E 1l6oA 277 :G T0359 35 :IFVKSITKSSA 1l6oA 281 :IYIGSIMKGGA T0359 48 :HDGRIQIGDQIIAV 1l6oA 294 :ADGRIEPGDMLLQV T0359 64 :T 1l6oA 310 :I T0359 67 :Q 1l6oA 313 :E T0359 71 :NQQAVEVL 1l6oA 317 :NDDAVRVL T0359 81 :T 1l6oA 327 :I T0359 82 :GQTVL 1l6oA 331 :PGPIV T0359 91 :R 1l6oA 340 :K Number of specific fragments extracted= 14 number of extra gaps= 13 total=466 # 1l6oA read from 1l6oA/merged-good-all-a2m # found chain 1l6oA in template set Warning: unaligning (T0359)E4 because first residue in template chain is (1l6oA)M251 Warning: unaligning (T0359)V8 because of BadResidue code BAD_PEPTIDE in next template residue (1l6oA)T256 Warning: unaligning (T0359)E9 because of BadResidue code BAD_PEPTIDE at template residue (1l6oA)T256 Warning: unaligning (T0359)K12 because of BadResidue code BAD_PEPTIDE in next template residue (1l6oA)K261 Warning: unaligning (T0359)N13 because of BadResidue code BAD_PEPTIDE at template residue (1l6oA)K261 Warning: unaligning (T0359)V14 because of BadResidue code BAD_PEPTIDE in next template residue (1l6oA)N263 Warning: unaligning (T0359)Q15 because of BadResidue code BAD_PEPTIDE at template residue (1l6oA)N263 Warning: unaligning (T0359)G16 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1l6oA)L265 Warning: unaligning (T0359)L17 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1l6oA)L265 Warning: unaligning (T0359)I19 because of BadResidue code BAD_PEPTIDE in next template residue (1l6oA)S268 Warning: unaligning (T0359)T20 because of BadResidue code BAD_PEPTIDE at template residue (1l6oA)S268 Warning: unaligning (T0359)I25 because of BadResidue code BAD_PEPTIDE in next template residue (1l6oA)N274 Warning: unaligning (T0359)G26 because of BadResidue code BAD_PEPTIDE at template residue (1l6oA)N274 Warning: unaligning (T0359)P32 because of BadResidue code BAD_PEPTIDE in next template residue (1l6oA)G279 Warning: unaligning (T0359)S33 because of BadResidue code BAD_PEPTIDE at template residue (1l6oA)G279 Warning: unaligning (T0359)G34 because of BadResidue code BAD_PEPTIDE at template residue (1l6oA)G280 Warning: unaligning (T0359)V46 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1l6oA)A293 Warning: unaligning (T0359)E47 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1l6oA)A293 Warning: unaligning (T0359)D62 because of BadResidue code BAD_PEPTIDE in next template residue (1l6oA)D309 Warning: unaligning (T0359)G63 because of BadResidue code BAD_PEPTIDE at template residue (1l6oA)D309 Warning: unaligning (T0359)N65 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1l6oA)F312 Warning: unaligning (T0359)L66 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1l6oA)F312 Warning: unaligning (T0359)G68 because of BadResidue code BAD_PEPTIDE in next template residue (1l6oA)M315 Warning: unaligning (T0359)F69 because of BadResidue code BAD_PEPTIDE at template residue (1l6oA)M315 Warning: unaligning (T0359)T70 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1l6oA)S316 Warning: unaligning (T0359)R79 because of BadResidue code BAD_PEPTIDE in next template residue (1l6oA)D326 Warning: unaligning (T0359)H80 because of BadResidue code BAD_PEPTIDE at template residue (1l6oA)D326 Warning: unaligning (T0359)L87 because of BadResidue code BAD_PEPTIDE in next template residue (1l6oA)T337 Warning: unaligning (T0359)T88 because of BadResidue code BAD_PEPTIDE at template residue (1l6oA)T337 Warning: unaligning (T0359)L89 because of BadResidue code BAD_PEPTIDE in next template residue (1l6oA)A339 Warning: unaligning (T0359)M90 because of BadResidue code BAD_PEPTIDE at template residue (1l6oA)A339 Warning: unaligning (T0359)R92 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (1l6oA)E342 Warning: unaligning (T0359)G93 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (1l6oA)E342 Warning: unaligning (T0359)E94 because of BadResidue code BAD_PEPTIDE in next template residue (1l6oA)H344 Warning: unaligning (T0359)T95 because of BadResidue code BAD_PEPTIDE at template residue (1l6oA)H344 Warning: unaligning (T0359)S96 because last residue in template chain is (1l6oA)H345 T0359 5 :TFD 1l6oA 252 :IIT T0359 10 :LT 1l6oA 257 :LN T0359 18 :G 1l6oA 266 :G T0359 21 :IAGY 1l6oA 269 :IVGQ T0359 27 :D 1l6oA 275 :E T0359 30 :LE 1l6oA 276 :RG T0359 35 :IFVKSITKSSA 1l6oA 281 :IYIGSIMKGGA T0359 48 :HDGRIQIGDQIIAV 1l6oA 294 :ADGRIEPGDMLLQV T0359 64 :T 1l6oA 310 :I T0359 67 :Q 1l6oA 313 :E T0359 71 :NQQAVEVL 1l6oA 317 :NDDAVRVL T0359 81 :T 1l6oA 327 :I T0359 82 :GQTVL 1l6oA 331 :PGPIV T0359 91 :R 1l6oA 340 :K Number of specific fragments extracted= 14 number of extra gaps= 12 total=480 Number of alignments=108 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1q3oA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0359 read from 1q3oA/merged-good-all-a2m # 1q3oA read from 1q3oA/merged-good-all-a2m # found chain 1q3oA in training set Warning: unaligning (T0359)T95 because last residue in template chain is (1q3oA)H687 T0359 6 :FDVELTKNVQ 1q3oA 590 :KTVLLQKKDS T0359 16 :GLGITIAGYIGDKKLEPS 1q3oA 601 :GFGFVLRGAKAQTPIEEF T0359 34 :GIFVKSITKSSAVEHDG 1q3oA 627 :LQYLESVDEGGVAWRAG T0359 52 :IQIGDQIIAVDGTNLQGFTNQQAVEVLRHTGQTVLLTLMRRGE 1q3oA 644 :LRMGDFLIEVNGQNVVKVGHRQVVNMIRQGGNTLMVKVVMVTR Number of specific fragments extracted= 4 number of extra gaps= 0 total=484 Number of alignments=109 # 1q3oA read from 1q3oA/merged-good-all-a2m # found chain 1q3oA in training set Warning: unaligning (T0359)T95 because last residue in template chain is (1q3oA)H687 T0359 6 :FDVELTKNVQG 1q3oA 590 :KTVLLQKKDSE T0359 17 :LGITIAGYIGDKKLEPS 1q3oA 602 :FGFVLRGAKAQTPIEEF T0359 34 :GIFVKSITKSSAVEHDG 1q3oA 627 :LQYLESVDEGGVAWRAG T0359 52 :IQIGDQIIAVDGTNLQGFTNQQAVEVLRHTGQTVLLTLMRRGE 1q3oA 644 :LRMGDFLIEVNGQNVVKVGHRQVVNMIRQGGNTLMVKVVMVTR Number of specific fragments extracted= 4 number of extra gaps= 0 total=488 Number of alignments=110 # 1q3oA read from 1q3oA/merged-good-all-a2m # found chain 1q3oA in training set Warning: unaligning (T0359)T95 because last residue in template chain is (1q3oA)H687 T0359 5 :TFDVELT 1q3oA 589 :EKTVLLQ T0359 12 :KNVQGLGITIAGYIGDKKLEPS 1q3oA 597 :KDSEGFGFVLRGAKAQTPIEEF T0359 34 :GIFVKSITKSSAVEHDG 1q3oA 627 :LQYLESVDEGGVAWRAG T0359 52 :IQIGDQIIAVDGTNLQGFTNQQAVEVLRHTGQTVLLTLMRRGE 1q3oA 644 :LRMGDFLIEVNGQNVVKVGHRQVVNMIRQGGNTLMVKVVMVTR Number of specific fragments extracted= 4 number of extra gaps= 0 total=492 Number of alignments=111 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1n7fA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0359 read from 1n7fA/merged-good-all-a2m # 1n7fA read from 1n7fA/merged-good-all-a2m # found chain 1n7fA in training set Warning: unaligning (T0359)S3 because first residue in template chain is (1n7fA)A668 Warning: unaligning (T0359)R92 because last residue in template chain is (1n7fA)Q753 T0359 4 :ETFDVELTKNVQGLGITIAGY 1n7fA 669 :IIYTVELKRYGGPLGITISGT T0359 29 :KLEPSGIFVKSITKSSAVEHDGRIQIGDQIIAVDGTNLQGFTNQQAVEVLRHTGQTVLLTLMR 1n7fA 690 :EEPFDPIIISSLTKGGLAERTGAIHIGDRILAINSSSLKGKPLSEAIHLLQMAGETVTLKIKK Number of specific fragments extracted= 2 number of extra gaps= 0 total=494 Number of alignments=112 # 1n7fA read from 1n7fA/merged-good-all-a2m # found chain 1n7fA in training set Warning: unaligning (T0359)S3 because first residue in template chain is (1n7fA)A668 Warning: unaligning (T0359)R92 because last residue in template chain is (1n7fA)Q753 T0359 4 :ETFDVELTKNVQGLGITIAGYIG 1n7fA 669 :IIYTVELKRYGGPLGITISGTEE T0359 31 :EPSGIFVKSITKSSAVEHDGRIQIGDQIIAVDGTNLQGFTNQQAVEVLRHTGQTVLLTLMR 1n7fA 692 :PFDPIIISSLTKGGLAERTGAIHIGDRILAINSSSLKGKPLSEAIHLLQMAGETVTLKIKK Number of specific fragments extracted= 2 number of extra gaps= 0 total=496 Number of alignments=113 # 1n7fA read from 1n7fA/merged-good-all-a2m # found chain 1n7fA in training set Warning: unaligning (T0359)S3 because first residue in template chain is (1n7fA)A668 Warning: unaligning (T0359)R92 because last residue in template chain is (1n7fA)Q753 T0359 4 :ETFDVELTKNVQGLGITIAGYIGD 1n7fA 669 :IIYTVELKRYGGPLGITISGTEEP T0359 32 :PSGIFVKSITKSSAVEHDGRIQIGDQIIAVDGTNLQGFTNQQAVEVLRHTGQTVLLTLMR 1n7fA 693 :FDPIIISSLTKGGLAERTGAIHIGDRILAINSSSLKGKPLSEAIHLLQMAGETVTLKIKK Number of specific fragments extracted= 2 number of extra gaps= 0 total=498 Number of alignments=114 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ihjA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0359 read from 1ihjA/merged-good-all-a2m # 1ihjA read from 1ihjA/merged-good-all-a2m # found chain 1ihjA in training set Warning: unaligning (T0359)D27 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ihjA)P41 Warning: unaligning (T0359)K28 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ihjA)P41 Warning: unaligning (T0359)K29 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ihjA)N42 Warning: unaligning (T0359)R92 because last residue in template chain is (1ihjA)F105 T0359 4 :ETFDVELTKNV 1ihjA 14 :LIHMVTLDKTG T0359 15 :QGLGITIAGYI 1ihjA 26 :KSFGICIVRGE T0359 26 :G 1ihjA 39 :D T0359 30 :LEPSGIFVKSITKSSAVEHDGRIQIGDQIIAVDGTNLQGFTNQQAVEVLRHTGQTVLLTLMR 1ihjA 43 :TKTTGIFIKGIVPDSPAHLCGRLKVGDRILSLNGKDVRNSTEQAVIDLIKEADFKIELEIQT Number of specific fragments extracted= 4 number of extra gaps= 1 total=502 Number of alignments=115 # 1ihjA read from 1ihjA/merged-good-all-a2m # found chain 1ihjA in training set Warning: unaligning (T0359)M2 because first residue in template chain is (1ihjA)G12 Warning: unaligning (T0359)D27 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ihjA)P41 Warning: unaligning (T0359)K28 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ihjA)P41 Warning: unaligning (T0359)K29 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ihjA)N42 Warning: unaligning (T0359)R92 because last residue in template chain is (1ihjA)F105 T0359 3 :SETFDVELTKNV 1ihjA 13 :ELIHMVTLDKTG T0359 15 :QGLGITIAGYI 1ihjA 26 :KSFGICIVRGE T0359 26 :G 1ihjA 39 :D T0359 30 :LEPSGIFVKSITKSSAVEHDGRIQIGDQIIAVDGTNLQGFTNQQAVEVLRHTGQTVLLTLMR 1ihjA 43 :TKTTGIFIKGIVPDSPAHLCGRLKVGDRILSLNGKDVRNSTEQAVIDLIKEADFKIELEIQT Number of specific fragments extracted= 4 number of extra gaps= 1 total=506 Number of alignments=116 # 1ihjA read from 1ihjA/merged-good-all-a2m # found chain 1ihjA in training set Warning: unaligning (T0359)M2 because first residue in template chain is (1ihjA)G12 Warning: unaligning (T0359)D27 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ihjA)P41 Warning: unaligning (T0359)K28 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ihjA)P41 Warning: unaligning (T0359)K29 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ihjA)N42 Warning: unaligning (T0359)R92 because last residue in template chain is (1ihjA)F105 T0359 3 :SETFDVELTKNV 1ihjA 13 :ELIHMVTLDKTG T0359 15 :QGLGITIAGYIG 1ihjA 26 :KSFGICIVRGEV T0359 30 :LEPSGIFVKSITKSSAVEHDGRIQIGDQIIAVDGTNLQGFTNQQAVEVLRHTGQTVLLTLMR 1ihjA 43 :TKTTGIFIKGIVPDSPAHLCGRLKVGDRILSLNGKDVRNSTEQAVIDLIKEADFKIELEIQT Number of specific fragments extracted= 3 number of extra gaps= 1 total=509 Number of alignments=117 # command:Using radius: 8.0000 Alignment mode NUMB_ALIGNS: 117 Adding 547 constraints to all.constraints Done adding distance constraints # command:Reading probabilities from probabilities.dat Reading constraints from ConstraintSet all.constraints maxweight: 1.0000 Optimizing... Probability sum: -169.5306, CN propb: -169.5306 weights: 0.5271 constraints: 233 # command:Found ConstraintSet # PrintContacts align.constraints_v3 Number of constraints in align.constraints 233 # command:Found ConstraintSet # PrintContacts align_bonus.constraints_v3 Number of constraints in align.constraints.bonus 233 # command:Found ConstraintSet # PrintContacts rejected.constraints_v3 Number of constraints in rejected.constraints 314 # command:Found ConstraintSet # PrintContacts rejected_bonus.constraints_v3 Number of constraints in rejected.constraints.bonus 314 # command:Found ConstraintSet # PrintContacts non_contacts.constraints_v3 Number of constraints in noncontact.constraints 0 # command:Found ConstraintSet # PrintContacts non_contacts_bonus.constraints_v3 Number of constraints in noncontact.constraints.bonus 0 # command:Found ConstraintSet # PrintContacts all.constraints_v3 Number of constraints in all.constraints 547 # command: