parameters: 0.6 1.3 0.5 200 50 # command:# Prefix for input files set to /projects/compbio/experiments/undertaker/atoms-inputs/ # command:# reading dunbrack-2191.atoms # #computed average backbone with maximum peptide_sq_deviance = 0.002 # computed average trans backbone unit from 53157 examples # computed average trans backbone unit before proline from 2010 examples # computed average cis backbone unit from 97 examples # trans (non-proline) backbone unit: # CA= -2.2087 1.0126 -0.0030 # O= -0.1499 2.2440 0.0016 # C= -0.6889 1.1368 -0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4581 -0.0000 0.0000 # cis backbone unit: # CA= -0.1436 2.4534 -0.0002 # O= -2.0284 0.9742 0.0015 # C= -0.8018 1.0771 -0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4668 0.0000 0.0000 # trans backbone unit before proline: # CA= -2.2100 1.0631 -0.0014 # O= -0.1236 2.2458 0.0075 # C= -0.6872 1.1517 -0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4660 0.0000 0.0000 # After reading dunbrack-2191.atoms have 2191 chains in training database # Count of chains,residues,atoms: 2191,500310,3902258 # 493341 residues have no bad marker # 3226 residues lack atoms needed to compute omega # 1453 residues have cis peptide # number of each bad type: # NON_STANDARD_RESIDUE 4 # HAS_OXT 1167 # TOO_MANY_ATOMS 1 # TOO_FEW_ATOMS 3052 # HAS_UNKNOWN_ATOMS 9 # HAS_DUPLICATE_ATOMS 0 # CHAIN_BREAK_BEFORE 979 # NON_PLANAR_PEPTIDE 888 # BAD_PEPTIDE 2680 # Note: may sum to more than number of residues, # because one residue may have multiple problems # command:# Reading rotamer library from dunbrack-2191.rot # command:# Prefix for input files set to /projects/compbio/experiments/undertaker/spots/ # command:# ReadAtomType exp-pdb.types Read AtomType exp-pdb with 49 types. # command:# ReadClashTable exp-pdb-2191-2symm.clash # Read ClashTable exp-pdb-2191-2symm checking bonds symmetric at MaxSep 2 # command:# command:# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/T0340/ # command:# Making conformation for sequence T0340 numbered 1 through 90 Created new target T0340 from T0340.a2m # command:# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/T0340/ # command:Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0340//projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0340/manyalignments-good-all.under or /projects/compbio/experiments/protein-predict/casp7/T0340//projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0340/manyalignments-good-all.under.gz for input Trying /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0340/manyalignments-good-all.under # reading script from file /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0340/manyalignments-good-all.under # 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 # T0340 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 (T0340)M2 because first residue in template chain is (2fneA)M1954 T0340 3 :LRPRLCHLRKGPQGYGFNLHSDK 2fneA 1955 :PQCKSITLERGPDGLGFSIVGGY # choosing archetypes in rotamer library T0340 26 :SRPGQYIRSVDPGSPAARSG 2fneA 1982 :GDLPIYVKTVFAKGAASEDG T0340 46 :LRAQDRLIEVNGQNVEGLRHAEVVASIKAREDEARLLVVGPST 2fneA 2003 :LKRGDQIIAVNGQSLEGVTHEEAVAILKRTKGTVTLMVLSSDE Number of specific fragments extracted= 3 number of extra gaps= 0 total=3 Number of alignments=1 # 2fneA read from 2fneA/merged-good-all-a2m # found chain 2fneA in template set Warning: unaligning (T0340)M2 because first residue in template chain is (2fneA)M1954 T0340 3 :LRPRLCHLRKGPQGYGFNLHSDKS 2fneA 1955 :PQCKSITLERGPDGLGFSIVGGYG T0340 27 :RPGQYIRSVDPGSPAARSG 2fneA 1983 :DLPIYVKTVFAKGAASEDG T0340 46 :LRAQDRLIEVNGQNVEGLRHAEVVASIKAREDEARLLVVGPST 2fneA 2003 :LKRGDQIIAVNGQSLEGVTHEEAVAILKRTKGTVTLMVLSSDE Number of specific fragments extracted= 3 number of extra gaps= 0 total=6 Number of alignments=2 # 2fneA read from 2fneA/merged-good-all-a2m # found chain 2fneA in template set Warning: unaligning (T0340)M2 because first residue in template chain is (2fneA)M1954 T0340 3 :LRPRLCHLRKGPQGYGFNLHSDKS 2fneA 1955 :PQCKSITLERGPDGLGFSIVGGYG T0340 27 :RPGQYIRSVDPGSPAARSG 2fneA 1983 :DLPIYVKTVFAKGAASEDG T0340 46 :LRAQDRLIEVNGQNVEGLRHAEVVASIKAREDEARLLVVGPST 2fneA 2003 :LKRGDQIIAVNGQSLEGVTHEEAVAILKRTKGTVTLMVLSSDE Number of specific fragments extracted= 3 number of extra gaps= 0 total=9 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/T0340/2bygA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0340/2bygA/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 # T0340 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 (T0340)S23 because of BadResidue code BAD_PEPTIDE in next template residue (1y8tA)D238 Warning: unaligning (T0340)D24 because of BadResidue code BAD_PEPTIDE at template residue (1y8tA)D238 Warning: unaligning (T0340)K25 because of BadResidue code TOO_FEW_ATOMS+BAD_PEPTIDE in next template residue (1y8tA)D240 Warning: unaligning (T0340)S26 because of BadResidue code TOO_FEW_ATOMS+BAD_PEPTIDE at template residue (1y8tA)D240 Warning: unaligning (T0340)R27 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1y8tA)T241 Warning: unaligning (T0340)P28 because of BadResidue code BAD_PEPTIDE at template residue (1y8tA)L242 Warning: unaligning (T0340)S39 because of BadResidue code BAD_PEPTIDE in next template residue (1y8tA)A254 Warning: unaligning (T0340)P40 because of BadResidue code BAD_PEPTIDE at template residue (1y8tA)A254 Warning: unaligning (T0340)R43 because of BadResidue code BAD_PEPTIDE in next template residue (1y8tA)A258 Warning: unaligning (T0340)S44 because of BadResidue code BAD_PEPTIDE at template residue (1y8tA)A258 Warning: unaligning (T0340)G45 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1y8tA)V260 Warning: unaligning (T0340)L46 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1y8tA)V260 Warning: unaligning (T0340)G57 because of BadResidue code TOO_FEW_ATOMS+BAD_PEPTIDE in next template residue (1y8tA)R272 Warning: unaligning (T0340)Q58 because of BadResidue code TOO_FEW_ATOMS+BAD_PEPTIDE at template residue (1y8tA)R272 Warning: unaligning (T0340)N59 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1y8tA)P273 Warning: unaligning (T0340)G85 because of BadResidue code BAD_PEPTIDE in next template residue (1y8tA)P300 Warning: unaligning (T0340)P86 because of BadResidue code BAD_PEPTIDE at template residue (1y8tA)P300 Warning: unaligning (T0340)S87 because of BadResidue code BAD_PEPTIDE at template residue (1y8tA)S301 T0340 16 :GYGFNLH 1y8tA 230 :SLGVQVT T0340 29 :GQYIRSVDPG 1y8tA 243 :GAKIVEVVAG T0340 41 :AA 1y8tA 255 :AA T0340 47 :RAQDRLIEVN 1y8tA 261 :PKGVVVTKVD T0340 60 :VEG 1y8tA 274 :INS T0340 65 :HAEVVASIKAR 1y8tA 277 :ADALVAAVRSK T0340 76 :EDEARLLVV 1y8tA 290 :GATVALTFQ T0340 88 :TR 1y8tA 302 :GG Number of specific fragments extracted= 8 number of extra gaps= 5 total=17 Number of alignments=4 # 1y8tA read from 1y8tA/merged-good-all-a2m # found chain 1y8tA in template set Warning: unaligning (T0340)S23 because of BadResidue code BAD_PEPTIDE in next template residue (1y8tA)D238 Warning: unaligning (T0340)D24 because of BadResidue code BAD_PEPTIDE at template residue (1y8tA)D238 Warning: unaligning (T0340)K25 because of BadResidue code TOO_FEW_ATOMS+BAD_PEPTIDE in next template residue (1y8tA)D240 Warning: unaligning (T0340)S26 because of BadResidue code TOO_FEW_ATOMS+BAD_PEPTIDE at template residue (1y8tA)D240 Warning: unaligning (T0340)R27 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1y8tA)T241 Warning: unaligning (T0340)P28 because of BadResidue code BAD_PEPTIDE at template residue (1y8tA)L242 Warning: unaligning (T0340)S39 because of BadResidue code BAD_PEPTIDE in next template residue (1y8tA)A254 Warning: unaligning (T0340)P40 because of BadResidue code BAD_PEPTIDE at template residue (1y8tA)A254 Warning: unaligning (T0340)R43 because of BadResidue code BAD_PEPTIDE in next template residue (1y8tA)A258 Warning: unaligning (T0340)S44 because of BadResidue code BAD_PEPTIDE at template residue (1y8tA)A258 Warning: unaligning (T0340)G45 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1y8tA)V260 Warning: unaligning (T0340)L46 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1y8tA)V260 Warning: unaligning (T0340)G57 because of BadResidue code TOO_FEW_ATOMS+BAD_PEPTIDE in next template residue (1y8tA)R272 Warning: unaligning (T0340)Q58 because of BadResidue code TOO_FEW_ATOMS+BAD_PEPTIDE at template residue (1y8tA)R272 Warning: unaligning (T0340)N59 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1y8tA)P273 Warning: unaligning (T0340)G85 because of BadResidue code BAD_PEPTIDE in next template residue (1y8tA)P300 Warning: unaligning (T0340)P86 because of BadResidue code BAD_PEPTIDE at template residue (1y8tA)P300 Warning: unaligning (T0340)S87 because of BadResidue code BAD_PEPTIDE at template residue (1y8tA)S301 T0340 16 :GYGFNLH 1y8tA 230 :SLGVQVT T0340 29 :GQYIRSVDPG 1y8tA 243 :GAKIVEVVAG T0340 41 :AA 1y8tA 255 :AA T0340 47 :RAQDRLIEVN 1y8tA 261 :PKGVVVTKVD T0340 60 :VEG 1y8tA 274 :INS T0340 65 :HAEVVASIKAR 1y8tA 277 :ADALVAAVRSK T0340 76 :EDEARLLVV 1y8tA 290 :GATVALTFQ T0340 88 :TR 1y8tA 302 :GG Number of specific fragments extracted= 8 number of extra gaps= 5 total=25 Number of alignments=5 # 1y8tA read from 1y8tA/merged-good-all-a2m # found chain 1y8tA in template set Warning: unaligning (T0340)S23 because of BadResidue code BAD_PEPTIDE in next template residue (1y8tA)D238 Warning: unaligning (T0340)D24 because of BadResidue code BAD_PEPTIDE at template residue (1y8tA)D238 Warning: unaligning (T0340)K25 because of BadResidue code TOO_FEW_ATOMS+BAD_PEPTIDE in next template residue (1y8tA)D240 Warning: unaligning (T0340)S26 because of BadResidue code TOO_FEW_ATOMS+BAD_PEPTIDE at template residue (1y8tA)D240 Warning: unaligning (T0340)R27 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1y8tA)T241 Warning: unaligning (T0340)P28 because of BadResidue code BAD_PEPTIDE at template residue (1y8tA)L242 Warning: unaligning (T0340)S39 because of BadResidue code BAD_PEPTIDE in next template residue (1y8tA)A254 Warning: unaligning (T0340)P40 because of BadResidue code BAD_PEPTIDE at template residue (1y8tA)A254 Warning: unaligning (T0340)R43 because of BadResidue code BAD_PEPTIDE in next template residue (1y8tA)A258 Warning: unaligning (T0340)S44 because of BadResidue code BAD_PEPTIDE at template residue (1y8tA)A258 Warning: unaligning (T0340)G45 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1y8tA)V260 Warning: unaligning (T0340)L46 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1y8tA)V260 Warning: unaligning (T0340)G57 because of BadResidue code TOO_FEW_ATOMS+BAD_PEPTIDE in next template residue (1y8tA)R272 Warning: unaligning (T0340)Q58 because of BadResidue code TOO_FEW_ATOMS+BAD_PEPTIDE at template residue (1y8tA)R272 Warning: unaligning (T0340)N59 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1y8tA)P273 Warning: unaligning (T0340)R75 because of BadResidue code BAD_PEPTIDE at template residue (1y8tA)P289 Warning: unaligning (T0340)G85 because of BadResidue code BAD_PEPTIDE in next template residue (1y8tA)P300 Warning: unaligning (T0340)P86 because of BadResidue code BAD_PEPTIDE at template residue (1y8tA)P300 Warning: unaligning (T0340)S87 because of BadResidue code BAD_PEPTIDE at template residue (1y8tA)S301 T0340 16 :GYGFNLH 1y8tA 230 :SLGVQVT T0340 29 :GQYIRSVDPG 1y8tA 243 :GAKIVEVVAG T0340 41 :AA 1y8tA 255 :AA T0340 47 :RAQDRLIEVN 1y8tA 261 :PKGVVVTKVD T0340 60 :VEG 1y8tA 274 :INS T0340 65 :HAEVVASIKA 1y8tA 277 :ADALVAAVRS T0340 76 :EDEARLLVV 1y8tA 290 :GATVALTFQ T0340 88 :TR 1y8tA 302 :GG Number of specific fragments extracted= 8 number of extra gaps= 6 total=33 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 # T0340 read from 1qauA/merged-good-all-a2m # 1qauA read from 1qauA/merged-good-all-a2m # found chain 1qauA in training set Warning: unaligning (T0340)R4 because first residue in template chain is (1qauA)N14 T0340 5 :PRLCHLRKGPQ 1qauA 15 :VISVRLFKRKV T0340 16 :GYGFNLHSDKSRPGQYIRSVDPGSPAARSG 1qauA 27 :GLGFLVKERVSKPPVIISDLIRGGAAEQSG T0340 46 :LRAQDRLIEVNGQNVEGLRHAEVVASIKAR 1qauA 58 :IQAGDIILAVNDRPLVDLSYDSALEVLRGI T0340 76 :EDEARLLVVGPS 1qauA 90 :ETHVVLILRGPE Number of specific fragments extracted= 4 number of extra gaps= 0 total=37 Number of alignments=7 # 1qauA read from 1qauA/merged-good-all-a2m # found chain 1qauA in training set Warning: unaligning (T0340)R4 because first residue in template chain is (1qauA)N14 T0340 5 :PRLCHLRKGP 1qauA 15 :VISVRLFKRK T0340 15 :QGYGFNLHSDKSRPGQYIRSVDPGSPAARSG 1qauA 26 :GGLGFLVKERVSKPPVIISDLIRGGAAEQSG T0340 46 :LRAQDRLIEVNGQNVEGLRHAEVVASIKAR 1qauA 58 :IQAGDIILAVNDRPLVDLSYDSALEVLRGI T0340 76 :EDEARLLVVGPSTR 1qauA 90 :ETHVVLILRGPEGF Number of specific fragments extracted= 4 number of extra gaps= 0 total=41 Number of alignments=8 # 1qauA read from 1qauA/merged-good-all-a2m # found chain 1qauA in training set Warning: unaligning (T0340)R4 because first residue in template chain is (1qauA)N14 T0340 5 :PRLCHLR 1qauA 15 :VISVRLF T0340 12 :KGPQGYGFNLHSDKSRPGQYIRSVDPGSPAARSG 1qauA 23 :RKVGGLGFLVKERVSKPPVIISDLIRGGAAEQSG T0340 46 :LRAQDRLIEVNGQNVEGLRHAEVVASIKA 1qauA 58 :IQAGDIILAVNDRPLVDLSYDSALEVLRG T0340 75 :REDEARLLVVGPST 1qauA 89 :SETHVVLILRGPEG Number of specific fragments extracted= 4 number of extra gaps= 0 total=45 Number of alignments=9 # 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 # T0340 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 T0340 3 :LRPRLCHLRKGPQGYGFNLHSDK 1i16 28 :ATVCTVTLEKMSAGLGFSLEGGK T0340 26 :SRPGQYIRSVDPGSPAARSG 1i16 55 :GDKPLTINRIFKGAASEQSE T0340 46 :LRAQDRLIEVNGQNVEGLRHAEVVASIKAR 1i16 76 :VQPGDEILQLGGTAMQGLTRFEAWNIIKAL T0340 76 :EDEARLLVVGPSTRL 1i16 107 :DGPVTIVIRRKSLQS Number of specific fragments extracted= 4 number of extra gaps= 0 total=49 Number of alignments=10 # 1i16 read from 1i16/merged-good-all-a2m # found chain 1i16 in template set T0340 3 :LRPRLCHLRKGPQGYGFNLHSDKS 1i16 28 :ATVCTVTLEKMSAGLGFSLEGGKG T0340 27 :RPGQYIRSVDPGSPAARSG 1i16 56 :DKPLTINRIFKGAASEQSE T0340 46 :LRAQDRLIEVNGQNVEGLRHAEVVASIKAR 1i16 76 :VQPGDEILQLGGTAMQGLTRFEAWNIIKAL T0340 76 :EDEARLLVVGPSTR 1i16 107 :DGPVTIVIRRKSLQ Number of specific fragments extracted= 4 number of extra gaps= 0 total=53 Number of alignments=11 # 1i16 read from 1i16/merged-good-all-a2m # found chain 1i16 in template set T0340 3 :LRPRLCHLRKGPQGYGFNLHSDKS 1i16 28 :ATVCTVTLEKMSAGLGFSLEGGKG T0340 27 :RPGQYIRSVDPGSPAARSG 1i16 56 :DKPLTINRIFKGAASEQSE T0340 46 :LRAQDRLIEVNGQNVEGLRHAEVVASIKARE 1i16 76 :VQPGDEILQLGGTAMQGLTRFEAWNIIKALP T0340 77 :DEARLLVVGPSTRL 1i16 108 :GPVTIVIRRKSLQS Number of specific fragments extracted= 4 number of extra gaps= 0 total=57 Number of alignments=12 # 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:# T0340 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 T0340 3 :LRPRLCHLR 1v5lA 4 :GSSGNVVLP T0340 13 :GPQGYGFNLHSDKSRP 1v5lA 13 :GPAPWGFRLSGGIDFN T0340 29 :GQYIRSVDPGSPAARSGLRAQDRLIEVNGQNVEGLRHAEVVASIKAREDEARLLVVGPS 1v5lA 30 :PLVITRITPGSKAAAANLCPGDVILAIDGFGTESMTHADAQDRIKAASYQLCLKIDRAE T0340 88 :TR 1v5lA 94 :PQ Number of specific fragments extracted= 4 number of extra gaps= 0 total=61 Number of alignments=13 # 1v5lA read from 1v5lA/merged-good-all-a2m # found chain 1v5lA in template set T0340 8 :CHLR 1v5lA 9 :VVLP T0340 13 :GPQGYGFNLHSDKS 1v5lA 13 :GPAPWGFRLSGGID T0340 27 :RPGQYIRSVDPGSPAARSGLRAQDRLIEVNGQNVEGLRHAEVVASIKAREDEARLLVVGP 1v5lA 28 :NQPLVITRITPGSKAAAANLCPGDVILAIDGFGTESMTHADAQDRIKAASYQLCLKIDRA Number of specific fragments extracted= 3 number of extra gaps= 0 total=64 Number of alignments=14 # 1v5lA read from 1v5lA/merged-good-all-a2m # found chain 1v5lA in template set T0340 12 :KGPQGYGFNLHSDKS 1v5lA 12 :PGPAPWGFRLSGGID T0340 27 :RPGQYIRSVDPGSPAARSGLRAQDRLIEVNGQNVEGLRHAEVVASIKAREDEARLLVVGPST 1v5lA 28 :NQPLVITRITPGSKAAAANLCPGDVILAIDGFGTESMTHADAQDRIKAASYQLCLKIDRAET Number of specific fragments extracted= 2 number of extra gaps= 0 total=66 Number of alignments=15 # 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:# T0340 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 (T0340)L81 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1tp5A)I389 Warning: unaligning (T0340)L82 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1tp5A)I389 T0340 2 :MLRPRLCHLRKGPQGYGFNLHSDKSRPGQYIRSVDPGSPAARSG 1tp5A 308 :PREPRRIVIHRGSTGLGFNIVGGEDGEGIFISFILAGGPADLSG T0340 46 :LRAQDRLIEVNGQNVEGLRHAEVVASIKAREDEAR 1tp5A 353 :LRKGDQILSVNGVDLRNASHEQAAIALKNAGQTVT T0340 83 :VVGP 1tp5A 390 :AQYK Number of specific fragments extracted= 3 number of extra gaps= 1 total=69 Number of alignments=16 # 1tp5A read from 1tp5A/merged-good-all-a2m # found chain 1tp5A in template set Warning: unaligning (T0340)L81 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1tp5A)I389 Warning: unaligning (T0340)L82 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1tp5A)I389 T0340 2 :MLRPRLCHLRKGPQGYGFNLHSDKSRPGQYIRSVDPGSPAARSG 1tp5A 308 :PREPRRIVIHRGSTGLGFNIVGGEDGEGIFISFILAGGPADLSG T0340 46 :LRAQDRLIEVNGQNVEGLRHAEVVASIKAREDEAR 1tp5A 353 :LRKGDQILSVNGVDLRNASHEQAAIALKNAGQTVT T0340 83 :VVGP 1tp5A 390 :AQYK Number of specific fragments extracted= 3 number of extra gaps= 1 total=72 Number of alignments=17 # 1tp5A read from 1tp5A/merged-good-all-a2m # found chain 1tp5A in template set Warning: unaligning (T0340)L81 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1tp5A)I389 Warning: unaligning (T0340)L82 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1tp5A)I389 T0340 2 :MLRPRLCHLRKGPQGYGFNLHSDKSRPGQYIRSVDPGSPAARSG 1tp5A 308 :PREPRRIVIHRGSTGLGFNIVGGEDGEGIFISFILAGGPADLSG T0340 46 :LRAQDRLIEVNGQNVEGLRHAEVVASIKAREDEAR 1tp5A 353 :LRKGDQILSVNGVDLRNASHEQAAIALKNAGQTVT T0340 83 :VVG 1tp5A 390 :AQY Number of specific fragments extracted= 3 number of extra gaps= 1 total=75 Number of alignments=18 # 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 # T0340 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 (T0340)M2 because first residue in template chain is (1i92A)G9 Warning: unaligning (T0340)E76 because of BadResidue code TOO_FEW_ATOMS+NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1i92A)N84 Warning: unaligning (T0340)D77 because of BadResidue code TOO_FEW_ATOMS+NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1i92A)N84 T0340 3 :LRPRLCHLRKGPQGYGFNLHSDKSRPGQYIRSVDPGSPAARSGLRAQDRLIEVNGQNVEGLRHAEVVASIKAR 1i92A 10 :MLPRLCCLEKGPNGYGFHLHGEKGKLGQYIRLVEPGSPAEKAGLLAGDRLVEVNGENVEKETHQQVVSRIRAA T0340 78 :EARLLVVGPS 1i92A 85 :AVRLLVVDPE T0340 89 :R 1i92A 97 :T Number of specific fragments extracted= 3 number of extra gaps= 1 total=78 Number of alignments=19 # 1i92A read from 1i92A/merged-good-all-a2m # found chain 1i92A in template set Warning: unaligning (T0340)M2 because first residue in template chain is (1i92A)G9 Warning: unaligning (T0340)E76 because of BadResidue code TOO_FEW_ATOMS+NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1i92A)N84 Warning: unaligning (T0340)D77 because of BadResidue code TOO_FEW_ATOMS+NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1i92A)N84 T0340 3 :LRPRLCHLRKGPQGYGFNLHSDKSRPGQYIRSVDPGSPAARSGLRAQDRLIEVNGQNVEGLRHAEVVASIKAR 1i92A 10 :MLPRLCCLEKGPNGYGFHLHGEKGKLGQYIRLVEPGSPAEKAGLLAGDRLVEVNGENVEKETHQQVVSRIRAA T0340 78 :EARLLVVGPSTRL 1i92A 85 :AVRLLVVDPEQDT Number of specific fragments extracted= 2 number of extra gaps= 1 total=80 Number of alignments=20 # 1i92A read from 1i92A/merged-good-all-a2m # found chain 1i92A in template set Warning: unaligning (T0340)E76 because of BadResidue code TOO_FEW_ATOMS+NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1i92A)N84 Warning: unaligning (T0340)D77 because of BadResidue code TOO_FEW_ATOMS+NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1i92A)N84 T0340 4 :RPRLCHLRKGPQGYGFNLHSDKSRPGQYIRSVDPGSPAARSGLRAQDRLIEVNGQNVEGLRHAEVVASIKAR 1i92A 11 :LPRLCCLEKGPNGYGFHLHGEKGKLGQYIRLVEPGSPAEKAGLLAGDRLVEVNGENVEKETHQQVVSRIRAA T0340 78 :EARLLVVGPSTRL 1i92A 85 :AVRLLVVDPEQDT Number of specific fragments extracted= 2 number of extra gaps= 1 total=82 Number of alignments=21 # 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:# T0340 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 T0340 2 :MLRPRLCHLRKGPQGYGFNLHSDKSRPGQYIRSVDPGSPAARSG 1bfeA 308 :PREPRRIVIHRGSTGLGFNIIGGEDGEGIFISFILAGGPADLSG T0340 46 :LRAQDRLIEVNGQNVEGLRHAEVVASIKAREDEARLLVVGP 1bfeA 353 :LRKGDQILSVNGVDLRNASHEQAAIALKNAGQTVTIIAQYK Number of specific fragments extracted= 2 number of extra gaps= 0 total=84 Number of alignments=22 # 1bfeA read from 1bfeA/merged-good-all-a2m # found chain 1bfeA in template set T0340 2 :MLRPRLCHLRKGPQGYGFNLHSDKSRPGQYIRSVDPGSPAARSG 1bfeA 308 :PREPRRIVIHRGSTGLGFNIIGGEDGEGIFISFILAGGPADLSG T0340 46 :LRAQDRLIEVNGQNVEGLRHAEVVASIKAREDEARLLVVGP 1bfeA 353 :LRKGDQILSVNGVDLRNASHEQAAIALKNAGQTVTIIAQYK Number of specific fragments extracted= 2 number of extra gaps= 0 total=86 Number of alignments=23 # 1bfeA read from 1bfeA/merged-good-all-a2m # found chain 1bfeA in template set T0340 3 :LRPRLCHLRKGPQGYGFNLHSDKSRPGQYIRSVDPGSPAARSG 1bfeA 309 :REPRRIVIHRGSTGLGFNIIGGEDGEGIFISFILAGGPADLSG T0340 46 :LRAQDRLIEVNGQNVEGLRHAEVVASIKAREDEARLLVVGP 1bfeA 353 :LRKGDQILSVNGVDLRNASHEQAAIALKNAGQTVTIIAQYK Number of specific fragments extracted= 2 number of extra gaps= 0 total=88 Number of alignments=24 # 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 # T0340 read from 1fc6A/merged-good-all-a2m # 1fc6A read from 1fc6A/merged-good-all-a2m # found chain 1fc6A in training set T0340 13 :GPQ 1fc6A 157 :AGS T0340 16 :GYGFNLHSDKSRP 1fc6A 162 :GVGLEITYDGGSG T0340 29 :GQYIRSVDPGSPAARSGLRAQDRLIEVNGQNVEGLRHAEVVASI 1fc6A 176 :DVVVLTPAPGGPAEKAGARAGDVIVTVDGTAVKGMSLYDVSDLL T0340 74 :AREDEARLLVVGPS 1fc6A 222 :EADSQVEVVLHAPG Number of specific fragments extracted= 4 number of extra gaps= 0 total=92 Number of alignments=25 # 1fc6A read from 1fc6A/merged-good-all-a2m # found chain 1fc6A in training set T0340 13 :GPQ 1fc6A 157 :AGS T0340 16 :GYGFNLHSDKS 1fc6A 162 :GVGLEITYDGG T0340 27 :RPGQYIRSVDPGSPAARSGLRAQDRLIEVNGQNVEGLRHAEVVASI 1fc6A 174 :GKDVVVLTPAPGGPAEKAGARAGDVIVTVDGTAVKGMSLYDVSDLL T0340 73 :KAREDEARLLVVGP 1fc6A 221 :GEADSQVEVVLHAP Number of specific fragments extracted= 4 number of extra gaps= 0 total=96 Number of alignments=26 # 1fc6A read from 1fc6A/merged-good-all-a2m # found chain 1fc6A in training set T0340 13 :GPQGYGFNLHSDKS 1fc6A 159 :SVTGVGLEITYDGG T0340 27 :RPGQYIRSVDPGSPAARSGLRAQDRLIEVNGQNVEGLRHAEVVASIKA 1fc6A 174 :GKDVVVLTPAPGGPAEKAGARAGDVIVTVDGTAVKGMSLYDVSDLLQG T0340 75 :REDEARLLVVGPS 1fc6A 223 :ADSQVEVVLHAPG Number of specific fragments extracted= 3 number of extra gaps= 0 total=99 Number of alignments=27 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1gq4A/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/T0340/1gq4A/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0340/1gq4A/merged-good-all-a2m.gz for input Trying 1gq4A/merged-good-all-a2m Error: Couldn't open file 1gq4A/merged-good-all-a2m or 1gq4A/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/T0340/1kefA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0340/1kefA/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:# T0340 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 T0340 2 :MLRPRLCHLRKGPQ 1nf3C 152 :PETHRRVRLCKYGT T0340 16 :GYGFNLHSDK 1nf3C 168 :PLGFYIRDGS T0340 26 :SRP 1nf3C 184 :HGL T0340 29 :GQYIRSVDPGSPAARSG 1nf3C 191 :GIFISRLVPGGLAQSTG T0340 46 :LRAQDRLIEVNGQNVEGLRHAEVVASIKAREDEARLLVVGPSTRL 1nf3C 209 :LAVNDEVLEVNGIEVSGKSLDQVTDMMIANSRNLIITVRPANQRN Number of specific fragments extracted= 5 number of extra gaps= 0 total=104 Number of alignments=28 # 1nf3C read from 1nf3C/merged-good-all-a2m # found chain 1nf3C in template set T0340 2 :MLRPRLCHLRKGPQ 1nf3C 152 :PETHRRVRLCKYGT T0340 16 :GYGFNLHSDKS 1nf3C 168 :PLGFYIRDGSS T0340 30 :QYIRSVDPGSPAARSG 1nf3C 192 :IFISRLVPGGLAQSTG T0340 46 :LRAQDRLIEVNGQNVEGLRHAEVVASIKAREDEARLLVVGPSTRL 1nf3C 209 :LAVNDEVLEVNGIEVSGKSLDQVTDMMIANSRNLIITVRPANQRN Number of specific fragments extracted= 4 number of extra gaps= 0 total=108 Number of alignments=29 # 1nf3C read from 1nf3C/merged-good-all-a2m # found chain 1nf3C in template set T0340 4 :RPRLCHLR 1nf3C 154 :THRRVRLC T0340 12 :KGPQGYGFNLHSDKS 1nf3C 164 :GTEKPLGFYIRDGSS T0340 27 :RPGQYIRSVDPGSPAARSG 1nf3C 189 :VPGIFISRLVPGGLAQSTG T0340 46 :LRAQDRLIEVNGQNVEGLRHAEVVASIKAREDEARLLVVGPSTRL 1nf3C 209 :LAVNDEVLEVNGIEVSGKSLDQVTDMMIANSRNLIITVRPANQRN Number of specific fragments extracted= 4 number of extra gaps= 0 total=112 Number of alignments=30 # 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:# T0340 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 T0340 1 :SMLRPRLCHLR 1wf7A 2 :SSGSSGSVSLV T0340 13 :GPQGYGFNLHSDKSRP 1wf7A 13 :GPAPWGFRLQGGKDFN T0340 29 :GQYIRSVDPGSPAARSGLRAQDRLIEVNGQNVEGLRHAEVVASIKAREDEARLLVVGPS 1wf7A 30 :PLTISSLKDGGKASQAHVRIGDVVLSIDGISAQGMTHLEAQNKIKACTGSLNMTLQRAS Number of specific fragments extracted= 3 number of extra gaps= 0 total=115 Number of alignments=31 # 1wf7A read from 1wf7A/merged-good-all-a2m # found chain 1wf7A in template set T0340 1 :SMLRPRLCHLR 1wf7A 2 :SSGSSGSVSLV T0340 13 :GPQGYGFNLHSDKS 1wf7A 13 :GPAPWGFRLQGGKD T0340 27 :RPGQYIRSVDPGSPAARSGLRAQDRLIEVNGQNVEGLRHAEVVASIKAREDEARLLVVGP 1wf7A 28 :NMPLTISSLKDGGKASQAHVRIGDVVLSIDGISAQGMTHLEAQNKIKACTGSLNMTLQRA T0340 87 :STR 1wf7A 94 :EPV Number of specific fragments extracted= 4 number of extra gaps= 0 total=119 Number of alignments=32 # 1wf7A read from 1wf7A/merged-good-all-a2m # found chain 1wf7A in template set T0340 8 :CHLRKGPQGYGFNLHSDKS 1wf7A 8 :SVSLVGPAPWGFRLQGGKD T0340 27 :RPGQYIRSVDPGSPAARSGLRAQDRLIEVNGQNVEGLRHAEVVASIKAREDEARLLVVGPST 1wf7A 28 :NMPLTISSLKDGGKASQAHVRIGDVVLSIDGISAQGMTHLEAQNKIKACTGSLNMTLQRASA Number of specific fragments extracted= 2 number of extra gaps= 0 total=121 Number of alignments=33 # 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/T0340/1um7A/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0340/1um7A/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 # T0340 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 (T0340)R4 because first residue in template chain is (2f0aA)M251 Warning: unaligning (T0340)Q15 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2f0aA)N263 Warning: unaligning (T0340)S87 because last residue in template chain is (2f0aA)E342 T0340 5 :PRLCHLR 2f0aA 252 :IITVTLN T0340 16 :GYGFNLHS 2f0aA 264 :FLGISIVG T0340 24 :DKSRPGQYIRSVDPGSPAARSG 2f0aA 275 :ERGDGGIYIGSIMKGGAVAADG T0340 46 :LRAQDRLIEVNGQNVEGLRHAEVVASIKAR 2f0aA 298 :IEPGDMLLQVNDINFENMSNDDAVRVLRDI T0340 76 :EDEARLLVVGP 2f0aA 331 :PGPIVLTVAKL Number of specific fragments extracted= 5 number of extra gaps= 1 total=126 Number of alignments=34 # 2f0aA read from 2f0aA/merged-good-all-a2m # found chain 2f0aA in template set Warning: unaligning (T0340)Q15 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2f0aA)N263 Warning: unaligning (T0340)S87 because last residue in template chain is (2f0aA)E342 T0340 5 :PRLCHLR 2f0aA 252 :IITVTLN T0340 16 :GYGFNLHS 2f0aA 264 :FLGISIVG T0340 24 :DKSRPGQYIRSVDPGSPAARSG 2f0aA 275 :ERGDGGIYIGSIMKGGAVAADG T0340 46 :LRAQDRLIEVNGQNVEGLRHAEVVASIKAR 2f0aA 298 :IEPGDMLLQVNDINFENMSNDDAVRVLRDI T0340 76 :EDEARLLVVGP 2f0aA 331 :PGPIVLTVAKL Number of specific fragments extracted= 5 number of extra gaps= 1 total=131 Number of alignments=35 # 2f0aA read from 2f0aA/merged-good-all-a2m # found chain 2f0aA in template set Warning: unaligning (T0340)Q15 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2f0aA)N263 Warning: unaligning (T0340)S87 because last residue in template chain is (2f0aA)E342 T0340 16 :GYGFNLHS 2f0aA 264 :FLGISIVG T0340 24 :DKSRPGQYIRSVDPGSPAARSG 2f0aA 275 :ERGDGGIYIGSIMKGGAVAADG T0340 46 :LRAQDRLIEVNGQNVEGLRHAEVVASIKA 2f0aA 298 :IEPGDMLLQVNDINFENMSNDDAVRVLRD T0340 75 :REDEARLLVVGP 2f0aA 330 :KPGPIVLTVAKL Number of specific fragments extracted= 4 number of extra gaps= 1 total=135 Number of alignments=36 # 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:# T0340 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 (T0340)M2 because first residue in template chain is (1n7eA)G667 T0340 3 :LRPRLCHLRKGPQGYGFNLHSDKSRP 1n7eA 668 :AIIYTVELKRYGGPLGITISGTEEPF T0340 29 :GQYIRSVDPGSPAARSG 1n7eA 695 :PIIISSLTKGGLAERTG T0340 46 :LRAQDRLIEVNGQNVEGLRHAEVVASIKAREDEARLLVVGPS 1n7eA 713 :IHIGDRILAINSSSLKGKPLSEAIHLLQMAGETVTLKIKKQT T0340 88 :TR 1n7eA 758 :PA Number of specific fragments extracted= 4 number of extra gaps= 0 total=139 Number of alignments=37 # 1n7eA read from 1n7eA/merged-good-all-a2m # found chain 1n7eA in template set Warning: unaligning (T0340)M2 because first residue in template chain is (1n7eA)G667 T0340 3 :LRPRLCHLRKGPQGYGFNLHSDKS 1n7eA 668 :AIIYTVELKRYGGPLGITISGTEE T0340 27 :RPGQYIRSVDPGSPAARSG 1n7eA 693 :FDPIIISSLTKGGLAERTG T0340 46 :LRAQDRLIEVNGQNVEGLRHAEVVASIKAREDEARLLVVGP 1n7eA 713 :IHIGDRILAINSSSLKGKPLSEAIHLLQMAGETVTLKIKKQ T0340 87 :STRL 1n7eA 757 :QPAS Number of specific fragments extracted= 4 number of extra gaps= 0 total=143 Number of alignments=38 # 1n7eA read from 1n7eA/merged-good-all-a2m # found chain 1n7eA in template set T0340 3 :LRPRLCHLRKGPQGYGFNLHSDKS 1n7eA 668 :AIIYTVELKRYGGPLGITISGTEE T0340 27 :RPGQYIRSVDPGSPAARSG 1n7eA 693 :FDPIIISSLTKGGLAERTG T0340 46 :LRAQDRLIEVNGQNVEGLRHAEVVASIKAREDEARLLVVGPSTRL 1n7eA 713 :IHIGDRILAINSSSLKGKPLSEAIHLLQMAGETVTLKIKKQTDAQ Number of specific fragments extracted= 3 number of extra gaps= 0 total=146 Number of alignments=39 # 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 # T0340 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 T0340 25 :KSRPGQYIRSVDPGSPAARSGLRAQDRLIEVNGQNVEGL 1ky9A 283 :DAQRGAFVSQVLPNSSAAKAGIKAGDVITSLNGKPISSF T0340 66 :AEVVASIKAR 1ky9A 322 :AALRAQVGTM T0340 76 :EDEARLLVVGPS 1ky9A 334 :GSKLTLGLLRDG T0340 88 :TRL 1ky9A 350 :VNL Number of specific fragments extracted= 4 number of extra gaps= 0 total=150 Number of alignments=40 # 1ky9A read from 1ky9A/merged-good-all-a2m # found chain 1ky9A in template set T0340 26 :S 1ky9A 283 :D T0340 27 :RPGQYIRSVDPGSPAARSGLRAQDRLIEVNGQNVEGL 1ky9A 285 :QRGAFVSQVLPNSSAAKAGIKAGDVITSLNGKPISSF T0340 66 :AEVVASIKAR 1ky9A 322 :AALRAQVGTM T0340 76 :EDEARLLVVGPS 1ky9A 334 :GSKLTLGLLRDG Number of specific fragments extracted= 4 number of extra gaps= 0 total=154 Number of alignments=41 # 1ky9A read from 1ky9A/merged-good-all-a2m # found chain 1ky9A in template set T0340 24 :DKSRPGQYIRSVDPGSPAARSGLRAQDRLIEVNGQNVEGL 1ky9A 282 :VDAQRGAFVSQVLPNSSAAKAGIKAGDVITSLNGKPISSF T0340 66 :AEVVASIKA 1ky9A 322 :AALRAQVGT T0340 75 :REDEARLLVVGPS 1ky9A 333 :VGSKLTLGLLRDG Number of specific fragments extracted= 3 number of extra gaps= 0 total=157 Number of alignments=42 # 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:# T0340 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 (T0340)L21 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ky9B)G269 Warning: unaligning (T0340)S23 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ky9B)G269 Warning: unaligning (T0340)A74 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ky9B)P332 T0340 24 :DK 1ky9B 270 :TE T0340 26 :SRPGQYIRSVDPGSPAARSGLRAQDRLIEVNGQNVEG 1ky9B 284 :AQRGAFVSQVLPNSSAAKAGIKAGDVITSLNGKPISS T0340 65 :HAEVVASIK 1ky9B 321 :FAALRAQVG T0340 76 :EDEARLLVVGPS 1ky9B 334 :GSKLTLGLLRDG Number of specific fragments extracted= 4 number of extra gaps= 0 total=161 Number of alignments=43 # 1ky9B read from 1ky9B/merged-good-all-a2m # found chain 1ky9B in template set Warning: unaligning (T0340)L21 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ky9B)G269 Warning: unaligning (T0340)S23 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ky9B)G269 Warning: unaligning (T0340)A74 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ky9B)P332 T0340 24 :DKS 1ky9B 270 :TEL T0340 27 :RPGQYIRSVDPGSPAARSGLRAQDRLIEVNGQNVEG 1ky9B 285 :QRGAFVSQVLPNSSAAKAGIKAGDVITSLNGKPISS T0340 65 :HAEVVASIK 1ky9B 321 :FAALRAQVG T0340 76 :EDEARLLVVGPST 1ky9B 334 :GSKLTLGLLRDGK Number of specific fragments extracted= 4 number of extra gaps= 0 total=165 Number of alignments=44 # 1ky9B read from 1ky9B/merged-good-all-a2m # found chain 1ky9B in template set T0340 25 :KSRPGQYIRSVDPGSPAARSGLRAQDRLIEVNGQNVEG 1ky9B 283 :DAQRGAFVSQVLPNSSAAKAGIKAGDVITSLNGKPISS T0340 65 :HAEVVASIK 1ky9B 321 :FAALRAQVG Number of specific fragments extracted= 2 number of extra gaps= 0 total=167 Number of alignments=45 # 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/T0340/1zokA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0340/1zokA/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 # T0340 read from 1mfgA/merged-good-all-a2m # 1mfgA read from 1mfgA/merged-good-all-a2m # found chain 1mfgA in training set Warning: unaligning (T0340)M2 because first residue in template chain is (1mfgA)G1277 Warning: unaligning (T0340)D77 because of BadResidue code BAD_PEPTIDE in next template residue (1mfgA)T1360 Warning: unaligning (T0340)E78 because of BadResidue code BAD_PEPTIDE at template residue (1mfgA)T1360 Warning: unaligning (T0340)L81 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (1mfgA)I1364 Warning: unaligning (T0340)L82 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (1mfgA)I1364 Warning: unaligning (T0340)R89 because last residue in template chain is (1mfgA)S1371 T0340 3 :LRPRLCHLRKGPQ 1mfgA 1278 :SMEIRVRVEKDPE T0340 17 :YGFNLHSDK 1mfgA 1291 :LGFSISGGV T0340 26 :SRPGQYIRSVDPGSPA 1mfgA 1309 :DDDGIFVTRVQPEGPA T0340 44 :SG 1mfgA 1325 :SK T0340 46 :LRAQDRLIEVNGQNVEGLRHAEVVASIKARE 1mfgA 1328 :LQPGDKIIQANGYSFINIEHGQAVSLLKTFQ T0340 79 :AR 1mfgA 1361 :VE T0340 83 :VVGPST 1mfgA 1365 :IVREVS Number of specific fragments extracted= 7 number of extra gaps= 2 total=174 Number of alignments=46 # 1mfgA read from 1mfgA/merged-good-all-a2m # found chain 1mfgA in training set Warning: unaligning (T0340)M2 because first residue in template chain is (1mfgA)G1277 Warning: unaligning (T0340)D77 because of BadResidue code BAD_PEPTIDE in next template residue (1mfgA)T1360 Warning: unaligning (T0340)E78 because of BadResidue code BAD_PEPTIDE at template residue (1mfgA)T1360 Warning: unaligning (T0340)L81 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (1mfgA)I1364 Warning: unaligning (T0340)L82 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (1mfgA)I1364 Warning: unaligning (T0340)T88 because last residue in template chain is (1mfgA)S1371 T0340 3 :LRPRLCHLRKGP 1mfgA 1278 :SMEIRVRVEKDP T0340 16 :GYGFNLHSDKS 1mfgA 1290 :ELGFSISGGVG T0340 27 :RPGQYIRSVDPGSPAA 1mfgA 1310 :DDGIFVTRVQPEGPAS T0340 45 :G 1mfgA 1326 :K T0340 46 :LRAQDRLIEVNGQNVEGLRHAEVVASIKARE 1mfgA 1328 :LQPGDKIIQANGYSFINIEHGQAVSLLKTFQ T0340 79 :AR 1mfgA 1361 :VE T0340 83 :VVGP 1mfgA 1365 :IVRE T0340 87 :S 1mfgA 1370 :S Number of specific fragments extracted= 8 number of extra gaps= 2 total=182 Number of alignments=47 # 1mfgA read from 1mfgA/merged-good-all-a2m # found chain 1mfgA in training set Warning: unaligning (T0340)D77 because of BadResidue code BAD_PEPTIDE in next template residue (1mfgA)T1360 Warning: unaligning (T0340)E78 because of BadResidue code BAD_PEPTIDE at template residue (1mfgA)T1360 Warning: unaligning (T0340)L81 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (1mfgA)I1364 Warning: unaligning (T0340)L82 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (1mfgA)I1364 Warning: unaligning (T0340)R89 because last residue in template chain is (1mfgA)S1371 T0340 3 :LRPRLCHLRKGPQ 1mfgA 1278 :SMEIRVRVEKDPE T0340 17 :YGFNLHSDKS 1mfgA 1291 :LGFSISGGVG T0340 27 :RPGQYIRSVDPGSPAA 1mfgA 1310 :DDGIFVTRVQPEGPAS T0340 45 :G 1mfgA 1326 :K T0340 46 :LRAQDRLIEVNGQNVEGLRHAEVVASIKARE 1mfgA 1328 :LQPGDKIIQANGYSFINIEHGQAVSLLKTFQ T0340 79 :AR 1mfgA 1361 :VE T0340 83 :VVGPST 1mfgA 1365 :IVREVS Number of specific fragments extracted= 7 number of extra gaps= 2 total=189 Number of alignments=48 # 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:# T0340 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 T0340 4 :RPRLCHLRKGP 1b8qA 8 :NVISVRLFKRK T0340 15 :QGYGFNLHSDKSRPGQYIRSVDPGSPAARSG 1b8qA 20 :GGLGFLVKERVSKPPVIISDLIRGGAAEQSG T0340 46 :LRAQDRLIEVNGQNVEGLRHAEVVASIKAR 1b8qA 52 :IQAGDIILAVNDRPLVDLSYDSALEVLRGI T0340 76 :EDEARLLVVGPS 1b8qA 84 :ETHVVLILRGPE Number of specific fragments extracted= 4 number of extra gaps= 0 total=193 Number of alignments=49 # 1b8qA read from 1b8qA/merged-good-all-a2m # found chain 1b8qA in template set T0340 2 :MLRP 1b8qA 2 :SHMI T0340 6 :RLCHLRKGP 1b8qA 10 :ISVRLFKRK T0340 15 :QGYGFNLHSDKSRPGQYIRSVDPGSPAARSG 1b8qA 20 :GGLGFLVKERVSKPPVIISDLIRGGAAEQSG T0340 46 :LRAQDRLIEVNGQNVEGLRHAEVVASIKAR 1b8qA 52 :IQAGDIILAVNDRPLVDLSYDSALEVLRGI T0340 76 :EDEARLLVVGP 1b8qA 84 :ETHVVLILRGP Number of specific fragments extracted= 5 number of extra gaps= 0 total=198 Number of alignments=50 # 1b8qA read from 1b8qA/merged-good-all-a2m # found chain 1b8qA in template set T0340 2 :MLRPRLCHLR 1b8qA 6 :EPNVISVRLF T0340 12 :KGPQGYGFNLHSDKSRPGQYIRSVDPGSPAARSG 1b8qA 17 :RKVGGLGFLVKERVSKPPVIISDLIRGGAAEQSG T0340 46 :LRAQDRLIEVNGQNVEGLRHAEVVASIKAREDEARLLVVGPSTR 1b8qA 52 :IQAGDIILAVNDRPLVDLSYDSALEVLRGIASETHVVLILRGPE Number of specific fragments extracted= 3 number of extra gaps= 0 total=201 Number of alignments=51 # 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 # T0340 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 (T0340)L3 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1nteA)D195 Warning: unaligning (T0340)R4 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1nteA)D195 T0340 1 :SM 1nteA 192 :GA T0340 5 :PRLCHLRKGPQG 1nteA 196 :PRTITMHKDSTG T0340 17 :YGFNLHSD 1nteA 209 :VGFIFKNG T0340 31 :YIRSVDPGSPAARSGLRAQDRLIEVNGQNVEGLRHAEVVASIKAREDEARLLVVGP 1nteA 217 :KITSIVKDSSAARNGLLTEHNICEINGQNVIGLKDSQIADILSTSGTVVTITIMPA Number of specific fragments extracted= 4 number of extra gaps= 1 total=205 Number of alignments=52 # 1nteA read from 1nteA/merged-good-all-a2m # found chain 1nteA in template set Warning: unaligning (T0340)L3 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1nteA)D195 Warning: unaligning (T0340)R4 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1nteA)D195 T0340 1 :SM 1nteA 192 :GA T0340 5 :PRLCHLRKGPQG 1nteA 196 :PRTITMHKDSTG T0340 17 :YGFNLHSD 1nteA 209 :VGFIFKNG T0340 31 :YIRSVDPGSPAARSGLRAQDRLIEVNGQNVEGLRHAEVVASIKAREDEARLLVVGP 1nteA 217 :KITSIVKDSSAARNGLLTEHNICEINGQNVIGLKDSQIADILSTSGTVVTITIMPA Number of specific fragments extracted= 4 number of extra gaps= 1 total=209 Number of alignments=53 # 1nteA read from 1nteA/merged-good-all-a2m # found chain 1nteA in template set Warning: unaligning (T0340)L3 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1nteA)D195 Warning: unaligning (T0340)R4 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1nteA)D195 T0340 2 :M 1nteA 193 :A T0340 5 :PRLCHLRKGPQG 1nteA 196 :PRTITMHKDSTG T0340 17 :YGF 1nteA 209 :VGF T0340 22 :HSDKS 1nteA 212 :IFKNG T0340 31 :YIRSVDPGSPAARSGLRAQDRLIEVNGQNVEGLRHAEVVASIKAREDEARLLVVG 1nteA 217 :KITSIVKDSSAARNGLLTEHNICEINGQNVIGLKDSQIADILSTSGTVVTITIMP Number of specific fragments extracted= 5 number of extra gaps= 1 total=214 Number of alignments=54 # 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 # T0340 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 (T0340)M2 because first residue in template chain is (2fe5A)S221 T0340 3 :LRPRLCHLRKGPQGYGFNLHSDK 2fe5A 222 :MTIMEVNLLKGPKGLGFSIAGGI T0340 26 :SRPGQYIRSVDPGSPAARSG 2fe5A 251 :GDNSIYITKIIEGGAAQKDG T0340 46 :LRAQDRLIEVNGQNVEGLRHAEVVASIKAREDEARLLVVGPS 2fe5A 272 :LQIGDRLLAVNNTNLQDVRHEEAVASLKNTSDMVYLKVAKPG Number of specific fragments extracted= 3 number of extra gaps= 0 total=217 Number of alignments=55 # 2fe5A read from 2fe5A/merged-good-all-a2m # found chain 2fe5A in template set Warning: unaligning (T0340)M2 because first residue in template chain is (2fe5A)S221 T0340 3 :LRPRLCHLRKGPQGYGFNLHSDKS 2fe5A 222 :MTIMEVNLLKGPKGLGFSIAGGIG T0340 27 :RPGQYIRSVDPGSPAARSG 2fe5A 252 :DNSIYITKIIEGGAAQKDG T0340 46 :LRAQDRLIEVNGQNVEGLRHAEVVASIKAREDEARLLVVGPS 2fe5A 272 :LQIGDRLLAVNNTNLQDVRHEEAVASLKNTSDMVYLKVAKPG Number of specific fragments extracted= 3 number of extra gaps= 0 total=220 Number of alignments=56 # 2fe5A read from 2fe5A/merged-good-all-a2m # found chain 2fe5A in template set T0340 3 :LRPRLCHLRKGPQGYGFNLHSDKS 2fe5A 222 :MTIMEVNLLKGPKGLGFSIAGGIG T0340 27 :RPGQYIRSVDPGSPAARSG 2fe5A 252 :DNSIYITKIIEGGAAQKDG T0340 46 :LRAQDRLIEVNGQNVEGLRHAEVVASIKAREDEARLLVVGPS 2fe5A 272 :LQIGDRLLAVNNTNLQDVRHEEAVASLKNTSDMVYLKVAKPG Number of specific fragments extracted= 3 number of extra gaps= 0 total=223 Number of alignments=57 # 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 # T0340 read from 1r6jA/merged-good-all-a2m # 1r6jA read from 1r6jA/merged-good-all-a2m # found chain 1r6jA in training set T0340 1 :SMLRPRLCHLRKGPQG 1r6jA 192 :GAMDPRTITMHKDSTG T0340 17 :YGFNLHSD 1r6jA 209 :VGFIFKNG T0340 31 :YIRSVDPGSPAARSGLRAQDRLIEVNGQNVEGLRHAEVVASIKAREDEARLLVVG 1r6jA 217 :KITSIVKDSSAARNGLLTEHNICEINGQNVIGLKDSQIADILSTSGTVVTITIMP Number of specific fragments extracted= 3 number of extra gaps= 0 total=226 Number of alignments=58 # 1r6jA read from 1r6jA/merged-good-all-a2m # found chain 1r6jA in training set T0340 1 :SMLRPRLCHLRKGPQG 1r6jA 192 :GAMDPRTITMHKDSTG T0340 17 :YGFNLHSD 1r6jA 209 :VGFIFKNG T0340 31 :YIRSVDPGSPAARSGLRAQDRLIEVNGQNVEGLRHAEVVASIKAREDEARLLVVG 1r6jA 217 :KITSIVKDSSAARNGLLTEHNICEINGQNVIGLKDSQIADILSTSGTVVTITIMP Number of specific fragments extracted= 3 number of extra gaps= 0 total=229 Number of alignments=59 # 1r6jA read from 1r6jA/merged-good-all-a2m # found chain 1r6jA in training set T0340 2 :MLRPRLCHLRK 1r6jA 193 :AMDPRTITMHK T0340 13 :GPQGYGFNLHSD 1r6jA 205 :STGHVGFIFKNG T0340 31 :YIRSVDPGSPAARSGLRAQDRLIEVNGQNVEGLRHAEVVASIKAREDEARLLVVG 1r6jA 217 :KITSIVKDSSAARNGLLTEHNICEINGQNVIGLKDSQIADILSTSGTVVTITIMP Number of specific fragments extracted= 3 number of extra gaps= 0 total=232 Number of alignments=60 # 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:# T0340 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 T0340 2 :MLRPRLCHLRKGPQ 1qavA 76 :SLQRRRVTVRKADA T0340 16 :GYGFNLHSDKSRP 1qavA 91 :GLGISIKGGRENK T0340 29 :GQYIRSVDPGSPAARSG 1qavA 105 :PILISKIFKGLAADQTE T0340 46 :LRAQDRLIEVNGQNVEGLRHAEVVASIKAREDEARLLVVG 1qavA 123 :LFVGDAILSVNGEDLSSATHDEAVQALKKTGKEVVLEVKY Number of specific fragments extracted= 4 number of extra gaps= 0 total=236 Number of alignments=61 # 1qavA read from 1qavA/merged-good-all-a2m # found chain 1qavA in template set T0340 1 :SMLRPRLCHLRKGPQ 1qavA 75 :GSLQRRRVTVRKADA T0340 16 :GYGFNLHSDKS 1qavA 91 :GLGISIKGGRE T0340 27 :RPGQYIRSVDPGSPAARSG 1qavA 103 :KMPILISKIFKGLAADQTE T0340 46 :LRAQDRLIEVNGQNVEGLRHAEVVASIKAREDEARLLVVG 1qavA 123 :LFVGDAILSVNGEDLSSATHDEAVQALKKTGKEVVLEVKY Number of specific fragments extracted= 4 number of extra gaps= 0 total=240 Number of alignments=62 # 1qavA read from 1qavA/merged-good-all-a2m # found chain 1qavA in template set T0340 3 :LRPRLCHLRK 1qavA 77 :LQRRRVTVRK T0340 13 :GPQGYGFNLHSDKS 1qavA 88 :DAGGLGISIKGGRE T0340 27 :RPGQYIRSVDPGSPAARSG 1qavA 103 :KMPILISKIFKGLAADQTE T0340 46 :LRAQDRLIEVNGQNVEGLRHAEVVASIKAREDEARLLVVG 1qavA 123 :LFVGDAILSVNGEDLSSATHDEAVQALKKTGKEVVLEVKY Number of specific fragments extracted= 4 number of extra gaps= 0 total=244 Number of alignments=63 # 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:# T0340 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 (T0340)M2 because first residue in template chain is (1qavB)Q1012 T0340 3 :LRPRLCHLRKGPQ 1qavB 1013 :PNVISVRLFKRKV T0340 16 :GYGFNLHSDKSRPGQYIRSVDPGSPAARSG 1qavB 1027 :GLGFLVKERVSKPPVIISDLIRGGAAEQSG T0340 46 :LRAQDRLIEVNGQNVEGLRHAEVVASIKAR 1qavB 1058 :IQAGDIILAVNDRPLVDLSYDSALEVLRGI T0340 76 :EDEARLLVVGPS 1qavB 1090 :ETHVVLILRGPE Number of specific fragments extracted= 4 number of extra gaps= 0 total=248 Number of alignments=64 # 1qavB read from 1qavB/merged-good-all-a2m # found chain 1qavB in template set Warning: unaligning (T0340)M2 because first residue in template chain is (1qavB)Q1012 T0340 3 :LRPRLCHLRKGP 1qavB 1013 :PNVISVRLFKRK T0340 15 :QGYGFNLHSDKSRPGQYIRSVDPGSPAARSG 1qavB 1026 :GGLGFLVKERVSKPPVIISDLIRGGAAEQSG T0340 46 :LRAQDRLIEVNGQNVEGLRHAEVVASIKAR 1qavB 1058 :IQAGDIILAVNDRPLVDLSYDSALEVLRGI T0340 76 :EDEARLLVVGPSTR 1qavB 1090 :ETHVVLILRGPEGF Number of specific fragments extracted= 4 number of extra gaps= 0 total=252 Number of alignments=65 # 1qavB read from 1qavB/merged-good-all-a2m # found chain 1qavB in template set T0340 3 :LRPRLCHLR 1qavB 1013 :PNVISVRLF T0340 12 :KGPQGYGFNLHSDKSRPGQYIRSVDPGSPAARSG 1qavB 1023 :RKVGGLGFLVKERVSKPPVIISDLIRGGAAEQSG T0340 46 :LRAQDRLIEVNGQNVEGLRHAEVVASIKARED 1qavB 1058 :IQAGDIILAVNDRPLVDLSYDSALEVLRGIAS T0340 78 :EARLLVVGPST 1qavB 1092 :HVVLILRGPEG Number of specific fragments extracted= 4 number of extra gaps= 0 total=256 Number of alignments=66 # 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:# T0340 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 Warning: unaligning (T0340)S87 because last residue in template chain is (1m5zA)P106 T0340 1 :SMLRPRLCHLRKGPQ 1m5zA 18 :TPVELHKVTLYKDSG T0340 16 :GYGFNLHSDKSRPGQYIRSVDPGSPAARSGLRAQDRLIEVNGQNVEGLRHAEVVASIKAREDEARLLVVGP 1m5zA 35 :DFGFSVADGLLEKGVYVKNIRPAGPGDLGGLKPYDRLLQVNHVRTRDFDCCLVVPLIAESGNKLDLVISRN Number of specific fragments extracted= 2 number of extra gaps= 0 total=258 Number of alignments=67 # 1m5zA read from 1m5zA/merged-good-all-a2m # found chain 1m5zA in template set T0340 1 :SMLRPRLCHLRKGPQ 1m5zA 18 :TPVELHKVTLYKDSG T0340 16 :GYGFNLHSDKSRPGQYIRSVDPGSPAARSGLRAQDRLIEVNGQNVEGLRHAEVVASIKAREDEARLLVVGP 1m5zA 35 :DFGFSVADGLLEKGVYVKNIRPAGPGDLGGLKPYDRLLQVNHVRTRDFDCCLVVPLIAESGNKLDLVISRN Number of specific fragments extracted= 2 number of extra gaps= 0 total=260 Number of alignments=68 # 1m5zA read from 1m5zA/merged-good-all-a2m # found chain 1m5zA in template set T0340 2 :MLRPRLCHLRKGP 1m5zA 19 :PVELHKVTLYKDS T0340 15 :QGYGFNLHSDKSRPGQYIRSVDPGSPAARSGLRAQDRLIEVNGQNVEGLRHAEVVASIKAREDEARLLVVGP 1m5zA 34 :EDFGFSVADGLLEKGVYVKNIRPAGPGDLGGLKPYDRLLQVNHVRTRDFDCCLVVPLIAESGNKLDLVISRN Number of specific fragments extracted= 2 number of extra gaps= 0 total=262 Number of alignments=69 # 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:# T0340 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 T0340 2 :MLRPRLCHLRKGPQGYGFNLHSDKSRPGQYIRSVDPGSPAARSG 1be9A 308 :PREPRRIVIHRGSTGLGFNIIGGEDGEGIFISFILAGGPADLSG T0340 46 :LRAQDRLIEVNGQNVEGLRHAEVVASIKAREDEARLLVVGP 1be9A 353 :LRKGDQILSVNGVDLRNASHEQAAIALKNAGQTVTIIAQYK Number of specific fragments extracted= 2 number of extra gaps= 0 total=264 Number of alignments=70 # 1be9A read from 1be9A/merged-good-all-a2m # found chain 1be9A in template set T0340 2 :MLRPRLCHLRKGPQGYGFNLHSDKSRPGQYIRSVDPGSPAARSG 1be9A 308 :PREPRRIVIHRGSTGLGFNIIGGEDGEGIFISFILAGGPADLSG T0340 46 :LRAQDRLIEVNGQNVEGLRHAEVVASIKAREDEARLLVVGP 1be9A 353 :LRKGDQILSVNGVDLRNASHEQAAIALKNAGQTVTIIAQYK Number of specific fragments extracted= 2 number of extra gaps= 0 total=266 Number of alignments=71 # 1be9A read from 1be9A/merged-good-all-a2m # found chain 1be9A in template set T0340 2 :MLRPRLCHLRKGPQGYGFNLHSDKSRPGQYIRSVDPGSPAARSG 1be9A 308 :PREPRRIVIHRGSTGLGFNIIGGEDGEGIFISFILAGGPADLSG T0340 46 :LRAQDRLIEVNGQNVEGLRHAEVVASIKAREDEARLLVVG 1be9A 353 :LRKGDQILSVNGVDLRNASHEQAAIALKNAGQTVTIIAQY Number of specific fragments extracted= 2 number of extra gaps= 0 total=268 Number of alignments=72 # 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:# T0340 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 (T0340)Q15 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1te0A)G273 Warning: unaligning (T0340)G16 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1te0A)G273 Warning: unaligning (T0340)S23 because of BadResidue code BAD_PEPTIDE in next template residue (1te0A)G275 Warning: unaligning (T0340)D24 because of BadResidue code BAD_PEPTIDE at template residue (1te0A)G275 Warning: unaligning (T0340)K25 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1te0A)D277 Warning: unaligning (T0340)S26 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1te0A)D277 Warning: unaligning (T0340)R33 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1te0A)E286 Warning: unaligning (T0340)S34 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1te0A)E286 Warning: unaligning (T0340)G38 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1te0A)G291 Warning: unaligning (T0340)S39 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1te0A)G291 Warning: unaligning (T0340)A42 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (1te0A)N295 Warning: unaligning (T0340)R43 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (1te0A)N295 Warning: unaligning (T0340)S44 because of BadResidue code BAD_PEPTIDE in next template residue (1te0A)G297 Warning: unaligning (T0340)G45 because of BadResidue code BAD_PEPTIDE at template residue (1te0A)G297 Warning: unaligning (T0340)D50 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1te0A)L303 Warning: unaligning (T0340)R51 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1te0A)L303 Warning: unaligning (T0340)V60 because of BadResidue code BAD_PEPTIDE in next template residue (1te0A)I313 Warning: unaligning (T0340)E61 because of BadResidue code BAD_PEPTIDE at template residue (1te0A)I313 T0340 27 :RP 1te0A 278 :QL T0340 29 :GQYI 1te0A 281 :GIVV T0340 35 :VDP 1te0A 287 :VSP T0340 40 :PA 1te0A 292 :PA T0340 46 :LRAQ 1te0A 298 :IQVN T0340 52 :LIEVNGQN 1te0A 304 :IISVDNKP T0340 64 :RHAEVVASIKAR 1te0A 314 :SALETMDQVAEI T0340 76 :EDEARLLVVGPS 1te0A 328 :GSVIPVVVMRDD Number of specific fragments extracted= 8 number of extra gaps= 6 total=276 Number of alignments=73 # 1te0A read from 1te0A/merged-good-all-a2m # found chain 1te0A in template set Warning: unaligning (T0340)P14 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1te0A)G273 Warning: unaligning (T0340)Q15 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1te0A)G273 Warning: unaligning (T0340)S23 because of BadResidue code BAD_PEPTIDE in next template residue (1te0A)G275 Warning: unaligning (T0340)D24 because of BadResidue code BAD_PEPTIDE at template residue (1te0A)G275 Warning: unaligning (T0340)K25 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1te0A)D277 Warning: unaligning (T0340)S26 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1te0A)D277 Warning: unaligning (T0340)R33 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1te0A)E286 Warning: unaligning (T0340)S34 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1te0A)E286 Warning: unaligning (T0340)G38 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1te0A)G291 Warning: unaligning (T0340)S39 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1te0A)G291 Warning: unaligning (T0340)A42 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (1te0A)N295 Warning: unaligning (T0340)R43 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (1te0A)N295 Warning: unaligning (T0340)S44 because of BadResidue code BAD_PEPTIDE in next template residue (1te0A)G297 Warning: unaligning (T0340)G45 because of BadResidue code BAD_PEPTIDE at template residue (1te0A)G297 Warning: unaligning (T0340)D50 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1te0A)L303 Warning: unaligning (T0340)R51 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1te0A)L303 Warning: unaligning (T0340)V60 because of BadResidue code BAD_PEPTIDE in next template residue (1te0A)I313 Warning: unaligning (T0340)E61 because of BadResidue code BAD_PEPTIDE at template residue (1te0A)I313 T0340 27 :RPGQYI 1te0A 279 :LQGIVV T0340 35 :VDP 1te0A 287 :VSP T0340 40 :PA 1te0A 292 :PA T0340 46 :LRAQ 1te0A 298 :IQVN T0340 52 :LIEVNGQN 1te0A 304 :IISVDNKP T0340 64 :RHAEVVASIKAR 1te0A 314 :SALETMDQVAEI T0340 76 :EDEARLLVVGPST 1te0A 328 :GSVIPVVVMRDDK Number of specific fragments extracted= 7 number of extra gaps= 6 total=283 # 1te0A read from 1te0A/merged-good-all-a2m # found chain 1te0A in template set Warning: unaligning (T0340)S23 because of BadResidue code BAD_PEPTIDE at template residue (1te0A)G275 Warning: unaligning (T0340)D24 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1te0A)D277 Warning: unaligning (T0340)K25 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1te0A)D277 Warning: unaligning (T0340)R33 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1te0A)E286 Warning: unaligning (T0340)S34 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1te0A)E286 Warning: unaligning (T0340)G38 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1te0A)G291 Warning: unaligning (T0340)S39 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1te0A)G291 Warning: unaligning (T0340)A42 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (1te0A)N295 Warning: unaligning (T0340)R43 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (1te0A)N295 Warning: unaligning (T0340)S44 because of BadResidue code BAD_PEPTIDE in next template residue (1te0A)G297 Warning: unaligning (T0340)G45 because of BadResidue code BAD_PEPTIDE at template residue (1te0A)G297 Warning: unaligning (T0340)D50 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1te0A)L303 Warning: unaligning (T0340)R51 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1te0A)L303 Warning: unaligning (T0340)V60 because of BadResidue code BAD_PEPTIDE in next template residue (1te0A)I313 Warning: unaligning (T0340)E61 because of BadResidue code BAD_PEPTIDE at template residue (1te0A)I313 T0340 26 :SRPGQYI 1te0A 278 :QLQGIVV T0340 35 :VDP 1te0A 287 :VSP T0340 40 :PA 1te0A 292 :PA T0340 46 :LRAQ 1te0A 298 :IQVN T0340 52 :LIEVNGQN 1te0A 304 :IISVDNKP T0340 64 :RHAEVVASIKA 1te0A 314 :SALETMDQVAE T0340 75 :REDEARLLVVGPST 1te0A 327 :PGSVIPVVVMRDDK Number of specific fragments extracted= 7 number of extra gaps= 6 total=290 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1gq5A/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/T0340/1gq5A/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0340/1gq5A/merged-good-all-a2m.gz for input Trying 1gq5A/merged-good-all-a2m Error: Couldn't open file 1gq5A/merged-good-all-a2m or 1gq5A/merged-good-all-a2m.gz for input # 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 # T0340 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 (T0340)P14 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2fcfA)K1160 Warning: unaligning (T0340)Q15 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2fcfA)K1160 Warning: unaligning (T0340)K25 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2fcfA)G1184 T0340 1 :SMLRPRLCHLRKG 2fcfA 1145 :QSMQPRRVELWRE T0340 16 :GYGFNLHSD 2fcfA 1161 :SLGISIVGG T0340 30 :QYIRSVDPGSPAARSG 2fcfA 1185 :IFIKHVLEDSPAGKNG T0340 46 :LRAQDRLIEVNGQNVEGLRHAEVVASIKAREDEARLLVVGPS 2fcfA 1202 :LKPGDRIVEVDGMDLRDASHEQAVEAIRKAGNPVVFMVQSII T0340 88 :TR 2fcfA 1245 :TR Number of specific fragments extracted= 5 number of extra gaps= 1 total=295 Number of alignments=74 # 2fcfA read from 2fcfA/merged-good-all-a2m # found chain 2fcfA in template set Warning: unaligning (T0340)P14 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2fcfA)K1160 Warning: unaligning (T0340)Q15 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2fcfA)K1160 Warning: unaligning (T0340)K25 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2fcfA)G1184 Warning: unaligning (T0340)S26 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2fcfA)G1184 T0340 1 :SMLRPRLCHLRKG 2fcfA 1145 :QSMQPRRVELWRE T0340 16 :GYGFNLHSD 2fcfA 1161 :SLGISIVGG T0340 30 :QYIRSVDPGSPAARSG 2fcfA 1185 :IFIKHVLEDSPAGKNG T0340 46 :LRAQDRLIEVNGQNVEGLRHAEVVASIKAREDEARLLVVGP 2fcfA 1202 :LKPGDRIVEVDGMDLRDASHEQAVEAIRKAGNPVVFMVQSI T0340 87 :STRL 2fcfA 1244 :STRL Number of specific fragments extracted= 5 number of extra gaps= 1 total=300 Number of alignments=75 # 2fcfA read from 2fcfA/merged-good-all-a2m # found chain 2fcfA in template set Warning: unaligning (T0340)P14 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2fcfA)K1160 Warning: unaligning (T0340)Q15 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2fcfA)K1160 Warning: unaligning (T0340)K25 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2fcfA)G1184 Warning: unaligning (T0340)S26 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2fcfA)G1184 T0340 3 :LRPRLCHLRKG 2fcfA 1147 :MQPRRVELWRE T0340 16 :GYGFNLHSD 2fcfA 1161 :SLGISIVGG T0340 30 :QYIRSVDPGSPAARSG 2fcfA 1185 :IFIKHVLEDSPAGKNG T0340 46 :LRAQDRLIEVNGQNVEGLRHAEVVASIKAREDEARLLVVGP 2fcfA 1202 :LKPGDRIVEVDGMDLRDASHEQAVEAIRKAGNPVVFMVQSI Number of specific fragments extracted= 4 number of extra gaps= 1 total=304 Number of alignments=76 # 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/T0340/1rgrA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0340/1rgrA/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:# T0340 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 T0340 27 :RPGQYIRSVDPGSPAARSGLRAQDRLIEVNGQNVEG 1lcyA 255 :QHGVLIHKVILGSPAHRAGLRPGDVILAIGEQMVQN T0340 65 :HAEVVASIKARE 1lcyA 291 :AEDVYEAVRTQS T0340 78 :EARLLVVGPS 1lcyA 303 :QLAVQIRRGR Number of specific fragments extracted= 3 number of extra gaps= 0 total=307 Number of alignments=77 # 1lcyA read from 1lcyA/merged-good-all-a2m # found chain 1lcyA in template set T0340 24 :DKS 1lcyA 248 :EPS T0340 27 :RPGQYIRSVDPGSPAARSGLRAQDRLIEVNGQNVEG 1lcyA 255 :QHGVLIHKVILGSPAHRAGLRPGDVILAIGEQMVQN T0340 65 :HAEVVASIKARE 1lcyA 291 :AEDVYEAVRTQS T0340 78 :EARLLVVGPST 1lcyA 303 :QLAVQIRRGRE Number of specific fragments extracted= 4 number of extra gaps= 0 total=311 Number of alignments=78 # 1lcyA read from 1lcyA/merged-good-all-a2m # found chain 1lcyA in template set T0340 25 :KSRPGQYIRSVDPGSPAARSGLRAQDRLIEVNGQNVEG 1lcyA 253 :DVQHGVLIHKVILGSPAHRAGLRPGDVILAIGEQMVQN T0340 65 :HAEVVASIKARE 1lcyA 291 :AEDVYEAVRTQS T0340 78 :EARLLVVGPS 1lcyA 303 :QLAVQIRRGR Number of specific fragments extracted= 3 number of extra gaps= 0 total=314 Number of alignments=79 # 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 # T0340 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 (T0340)G29 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1sotA)G281 Warning: unaligning (T0340)V83 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1sotA)Q341 Warning: unaligning (T0340)R89 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1sotA)Q341 T0340 30 :QYIRSVDPGSPAARSGLRAQDRLIEVNGQNVE 1sotA 282 :IVVNEVSPDGPAANAGIQVNDLIISVDNKPAI T0340 64 :RHAEVVASIKAR 1sotA 314 :SALETMDQVAEI T0340 76 :EDEARLL 1sotA 328 :GSVIPVV Number of specific fragments extracted= 3 number of extra gaps= 0 total=317 Number of alignments=80 # 1sotA read from 1sotA/merged-good-all-a2m # found chain 1sotA in template set Warning: unaligning (T0340)G29 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1sotA)G281 Warning: unaligning (T0340)V83 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1sotA)Q341 Warning: unaligning (T0340)T88 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1sotA)Q341 T0340 30 :QYIRSVDPGSPAARSGLRAQDRLIEVNGQNVE 1sotA 282 :IVVNEVSPDGPAANAGIQVNDLIISVDNKPAI T0340 64 :RHAEVVASIKAR 1sotA 314 :SALETMDQVAEI T0340 76 :EDEARLL 1sotA 328 :GSVIPVV T0340 89 :R 1sotA 342 :L Number of specific fragments extracted= 4 number of extra gaps= 0 total=321 Number of alignments=81 # 1sotA read from 1sotA/merged-good-all-a2m # found chain 1sotA in template set Warning: unaligning (T0340)G29 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1sotA)G281 T0340 30 :QYIRSVDPGSPAARSGLRAQDRLIEVNGQNVE 1sotA 282 :IVVNEVSPDGPAANAGIQVNDLIISVDNKPAI T0340 64 :RHAEVVASIKAREDEARL 1sotA 314 :SALETMDQVAEIRPGSVI Number of specific fragments extracted= 2 number of extra gaps= 0 total=323 Number of alignments=82 # 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 # T0340 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 (T0340)L3 because first residue in template chain is (2f5yA)M14 Warning: unaligning (T0340)R4 because of BadResidue code BAD_PEPTIDE at template residue (2f5yA)R15 Warning: unaligning (T0340)E61 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2f5yA)H70 Warning: unaligning (T0340)G62 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2f5yA)H70 Warning: unaligning (T0340)S87 because last residue in template chain is (2f5yA)V95 T0340 5 :PRLCHLRKGPQGYGFNLHS 2f5yA 16 :YRQITIPRGKDGFGFTICC T0340 27 :RPGQYIRSVDPGSPAARSGLRAQDRLIEVNGQNV 2f5yA 35 :DSPVRVQAVDSGGPAERAGLQQLDTVLQLNERPV T0340 63 :LRHAEVVASIKAREDEARLLVVGP 2f5yA 71 :WKCVELAHEIRSCPSEIILLVWRM Number of specific fragments extracted= 3 number of extra gaps= 1 total=326 Number of alignments=83 # 2f5yA read from 2f5yA/merged-good-all-a2m # found chain 2f5yA in template set Warning: unaligning (T0340)L3 because first residue in template chain is (2f5yA)M14 Warning: unaligning (T0340)R4 because of BadResidue code BAD_PEPTIDE at template residue (2f5yA)R15 Warning: unaligning (T0340)E61 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2f5yA)H70 Warning: unaligning (T0340)G62 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2f5yA)H70 T0340 5 :PRLCHLRKGPQGYGFNLHS 2f5yA 16 :YRQITIPRGKDGFGFTICC T0340 27 :RPGQYIRSVDPGSPAARSGLRAQDRLIEVNGQNV 2f5yA 35 :DSPVRVQAVDSGGPAERAGLQQLDTVLQLNERPV T0340 63 :LRHAEVVASIKAREDEARLLVVGP 2f5yA 71 :WKCVELAHEIRSCPSEIILLVWRM Number of specific fragments extracted= 3 number of extra gaps= 1 total=329 Number of alignments=84 # 2f5yA read from 2f5yA/merged-good-all-a2m # found chain 2f5yA in template set Warning: unaligning (T0340)L3 because first residue in template chain is (2f5yA)M14 Warning: unaligning (T0340)R4 because of BadResidue code BAD_PEPTIDE at template residue (2f5yA)R15 Warning: unaligning (T0340)E61 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2f5yA)H70 Warning: unaligning (T0340)G62 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2f5yA)H70 T0340 5 :PRLCHLRKGPQGYGFNLHS 2f5yA 16 :YRQITIPRGKDGFGFTICC T0340 27 :RPGQYIRSVDPGSPAARSGLRAQDRLIEVNGQNV 2f5yA 35 :DSPVRVQAVDSGGPAERAGLQQLDTVLQLNERPV T0340 63 :LRHAEVVASIKAREDEARLLVVGP 2f5yA 71 :WKCVELAHEIRSCPSEIILLVWRM Number of specific fragments extracted= 3 number of extra gaps= 1 total=332 Number of alignments=85 # 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:# T0340 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 (T0340)R4 because first residue in template chain is (1kwaA)R487 T0340 5 :PRLCHLRKGPQ 1kwaA 488 :SRLVQFQKNTD T0340 16 :GYGFNLHSD 1kwaA 500 :PMGITLKMN T0340 26 :SRPGQYIRSVDPGSPAARSG 1kwaA 509 :ELNHCIVARIMHGGMIHRQG T0340 46 :LRAQDRLIEVNGQNVEGLRHAEVVASIKAREDEARLLVVGPSTRL 1kwaA 530 :LHVGDEIREINGISVANQTVEQLQKMLREMRGSITFKIVPSYREF Number of specific fragments extracted= 4 number of extra gaps= 0 total=336 Number of alignments=86 # 1kwaA read from 1kwaA/merged-good-all-a2m # found chain 1kwaA in template set Warning: unaligning (T0340)R4 because first residue in template chain is (1kwaA)R487 T0340 5 :PRLCHLRKGPQ 1kwaA 488 :SRLVQFQKNTD T0340 16 :GYGFNLHSD 1kwaA 500 :PMGITLKMN T0340 26 :SRPGQYIRSVDPGSPAARSG 1kwaA 509 :ELNHCIVARIMHGGMIHRQG T0340 46 :LRAQDRLIEVNGQNVEGLRHAEVVASIKAREDEARLLVVGP 1kwaA 530 :LHVGDEIREINGISVANQTVEQLQKMLREMRGSITFKIVPS T0340 88 :TRL 1kwaA 572 :REF Number of specific fragments extracted= 5 number of extra gaps= 0 total=341 Number of alignments=87 # 1kwaA read from 1kwaA/merged-good-all-a2m # found chain 1kwaA in template set T0340 5 :PRLCHLRK 1kwaA 488 :SRLVQFQK T0340 13 :GPQGYGFNLHSDKS 1kwaA 497 :TDEPMGITLKMNEL T0340 28 :PGQYIRSVDPGSPAARSG 1kwaA 511 :NHCIVARIMHGGMIHRQG T0340 46 :LRAQDRLIEVNGQNVEGLRHAEVVASIKAREDEARLLVVGPSTRL 1kwaA 530 :LHVGDEIREINGISVANQTVEQLQKMLREMRGSITFKIVPSYREF Number of specific fragments extracted= 4 number of extra gaps= 0 total=345 Number of alignments=88 # 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:# T0340 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 (T0340)R4 because first residue in template chain is (1kwaB)R487 Warning: unaligning (T0340)S23 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1kwaB)L510 Warning: unaligning (T0340)R27 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1kwaB)L510 T0340 5 :PRLCHLRKGPQ 1kwaB 488 :SRLVQFQKNTD T0340 16 :GYGFNLH 1kwaB 500 :PMGITLK T0340 28 :PGQYIRSVDPGSPAARSG 1kwaB 511 :NHCIVARIMHGGMIHRQG T0340 46 :LRAQDRLIEVNGQNVEGLRHAEVVASIKAREDEARLLVVGPS 1kwaB 530 :LHVGDEIREINGISVANQTVEQLQKMLREMRGSITFKIVPSY Number of specific fragments extracted= 4 number of extra gaps= 1 total=349 Number of alignments=89 # 1kwaB read from 1kwaB/merged-good-all-a2m # found chain 1kwaB in template set Warning: unaligning (T0340)R4 because first residue in template chain is (1kwaB)R487 Warning: unaligning (T0340)S23 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1kwaB)L510 Warning: unaligning (T0340)R27 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1kwaB)L510 T0340 5 :PRLCHLRKGPQ 1kwaB 488 :SRLVQFQKNTD T0340 16 :GYGFNLH 1kwaB 500 :PMGITLK T0340 28 :PGQYIRSVDPGSPAARSG 1kwaB 511 :NHCIVARIMHGGMIHRQG T0340 46 :LRAQDRLIEVNGQNVEGLRHAEVVASIKAREDEARLLVVGP 1kwaB 530 :LHVGDEIREINGISVANQTVEQLQKMLREMRGSITFKIVPS Number of specific fragments extracted= 4 number of extra gaps= 1 total=353 Number of alignments=90 # 1kwaB read from 1kwaB/merged-good-all-a2m # found chain 1kwaB in template set Warning: unaligning (T0340)S23 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1kwaB)L510 Warning: unaligning (T0340)D24 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1kwaB)L510 T0340 5 :PRLCHLRK 1kwaB 488 :SRLVQFQK T0340 13 :GPQGYGFNLH 1kwaB 497 :TDEPMGITLK T0340 28 :PGQYIRSVDPGSPAARSG 1kwaB 511 :NHCIVARIMHGGMIHRQG T0340 46 :LRAQDRLIEVNGQNVEGLRHAEVVASIKAREDEARLLVVG 1kwaB 530 :LHVGDEIREINGISVANQTVEQLQKMLREMRGSITFKIVP Number of specific fragments extracted= 4 number of extra gaps= 1 total=357 Number of alignments=91 # 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 # T0340 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 T0340 1 :SMLRPRLCHLRKGPQGYGFNLHSDKSRPGQYIRSVDPGSPAARSG 1pdr 460 :ITREPRKVVLHRGSTGLGFNIVGGEDGEGIFISFILAGGPADLSG T0340 46 :LRAQDRLIEVNGQNVEGLRHAEVVASIKAREDEARLLVVGP 1pdr 506 :LRKGDRIISVNSVDLRAASHEQAAAALKNAGQAVTIVAQYR Number of specific fragments extracted= 2 number of extra gaps= 0 total=359 Number of alignments=92 # 1pdr read from 1pdr/merged-good-all-a2m # found chain 1pdr in template set T0340 2 :MLRPRLCHLRKGPQGYGFNLHSDKSRPGQYIRSVDPGSPAARSG 1pdr 461 :TREPRKVVLHRGSTGLGFNIVGGEDGEGIFISFILAGGPADLSG T0340 46 :LRAQDRLIEVNGQNVEGLRHAEVVASIKAREDEARLLVVGP 1pdr 506 :LRKGDRIISVNSVDLRAASHEQAAAALKNAGQAVTIVAQYR Number of specific fragments extracted= 2 number of extra gaps= 0 total=361 Number of alignments=93 # 1pdr read from 1pdr/merged-good-all-a2m # found chain 1pdr in template set T0340 3 :LRPRLCHLRKGPQGYGFNLHSDKSRPGQYIRSVDPGSPAARSG 1pdr 462 :REPRKVVLHRGSTGLGFNIVGGEDGEGIFISFILAGGPADLSG T0340 46 :LRAQDRLIEVNGQNVEGLRHAEVVASIKAREDEARLLVVGP 1pdr 506 :LRKGDRIISVNSVDLRAASHEQAAAALKNAGQAVTIVAQYR Number of specific fragments extracted= 2 number of extra gaps= 0 total=363 Number of alignments=94 # 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/T0340/1iu0A/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0340/1iu0A/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 # T0340 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 (T0340)P5 because first residue in template chain is (1n99A)P112 Warning: unaligning (T0340)L82 because of BadResidue code BAD_PEPTIDE in next template residue (1n99A)I190 Warning: unaligning (T0340)V83 because of BadResidue code BAD_PEPTIDE at template residue (1n99A)I190 T0340 6 :RLCHLRKGPQG 1n99A 113 :REVILCKDQDG T0340 17 :YGFNLHSD 1n99A 125 :IGLRLKSI T0340 27 :RPGQYIRSVDPGSPAARSGLRAQDRLIEVNGQNVEGLRHAEVVASIKAR 1n99A 133 :DNGIFVQLVQANSPASLVGLRFGDQVLQINGENCAGWSSDKAHKVLKQA T0340 76 :EDEARL 1n99A 183 :GEKITM T0340 84 :VGPS 1n99A 191 :RDRP Number of specific fragments extracted= 5 number of extra gaps= 1 total=368 Number of alignments=95 # 1n99A read from 1n99A/merged-good-all-a2m # found chain 1n99A in template set Warning: unaligning (T0340)P5 because first residue in template chain is (1n99A)P112 Warning: unaligning (T0340)L82 because of BadResidue code BAD_PEPTIDE in next template residue (1n99A)I190 Warning: unaligning (T0340)V83 because of BadResidue code BAD_PEPTIDE at template residue (1n99A)I190 T0340 6 :RLCHLRKGPQG 1n99A 113 :REVILCKDQDG T0340 17 :YGFNLHSD 1n99A 125 :IGLRLKSI T0340 27 :RPGQYIRSVDPGSPAARSGLRAQDRLIEVNGQNVEGLRHAEVVASIKAR 1n99A 133 :DNGIFVQLVQANSPASLVGLRFGDQVLQINGENCAGWSSDKAHKVLKQA T0340 76 :EDEARL 1n99A 183 :GEKITM T0340 84 :VGPS 1n99A 191 :RDRP Number of specific fragments extracted= 5 number of extra gaps= 1 total=373 Number of alignments=96 # 1n99A read from 1n99A/merged-good-all-a2m # found chain 1n99A in template set Warning: unaligning (T0340)P5 because first residue in template chain is (1n99A)P112 Warning: unaligning (T0340)V83 because of BadResidue code BAD_PEPTIDE in next template residue (1n99A)I190 Warning: unaligning (T0340)V84 because of BadResidue code BAD_PEPTIDE at template residue (1n99A)I190 T0340 6 :RLCHLRKGPQG 1n99A 113 :REVILCKDQDG T0340 19 :FNLHSDKSRPGQYIRSVDPGSPAARSGLRAQDRLIEVNGQNVEGLRHAEVVASIKAREDEARLL 1n99A 125 :IGLRLKSIDNGIFVQLVQANSPASLVGLRFGDQVLQINGENCAGWSSDKAHKVLKQAFGEKITM T0340 85 :GP 1n99A 191 :RD Number of specific fragments extracted= 3 number of extra gaps= 1 total=376 Number of alignments=97 # 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 # T0340 read from 1g9oA/merged-good-all-a2m # 1g9oA read from 1g9oA/merged-good-all-a2m # found chain 1g9oA in training set Warning: unaligning (T0340)M2 because first residue in template chain is (1g9oA)R9 T0340 3 :LRPRLCHLRKGPQGYGFNLHSDKSRPGQYIRSVDPGSPAARSGLRAQDRLIEVNGQNVEGLRHAEVVASIKAREDEARLLVVGPS 1g9oA 10 :MLPRLCCLEKGPNGYGFHLHGEKGKLGQYIRLVEPGSPAEKAGLLAGDRLVEVNGENVEKETHQQVVSRIRAALNAVRLLVVDPE T0340 88 :TR 1g9oA 97 :EQ Number of specific fragments extracted= 2 number of extra gaps= 0 total=378 Number of alignments=98 # 1g9oA read from 1g9oA/merged-good-all-a2m # found chain 1g9oA in training set Warning: unaligning (T0340)M2 because first residue in template chain is (1g9oA)R9 T0340 3 :LRPRLCHLRKGPQGYGFNLHSDKSRPGQYIRSVDPGSPAARSGLRAQDRLIEVNGQNVEGLRHAEVVASIKAREDEARLLVVGP 1g9oA 10 :MLPRLCCLEKGPNGYGFHLHGEKGKLGQYIRLVEPGSPAEKAGLLAGDRLVEVNGENVEKETHQQVVSRIRAALNAVRLLVVDP T0340 87 :STRL 1g9oA 96 :DEQL Number of specific fragments extracted= 2 number of extra gaps= 0 total=380 Number of alignments=99 # 1g9oA read from 1g9oA/merged-good-all-a2m # found chain 1g9oA in training set T0340 4 :RPRLCHLRKGPQGYGFNLHSDKSRPGQYIRSVDPGSPAARSGLRAQDRLIEVNGQNVEGLRHAEVVASIKAREDEARLLVVGPSTRL 1g9oA 11 :LPRLCCLEKGPNGYGFHLHGEKGKLGQYIRLVEPGSPAEKAGLLAGDRLVEVNGENVEKETHQQVVSRIRAALNAVRLLVVDPETDE Number of specific fragments extracted= 1 number of extra gaps= 0 total=381 Number of alignments=100 # 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 # T0340 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 (T0340)R4 because first residue in template chain is (1l6oA)M251 Warning: unaligning (T0340)C8 because of BadResidue code BAD_PEPTIDE in next template residue (1l6oA)T256 Warning: unaligning (T0340)H9 because of BadResidue code BAD_PEPTIDE at template residue (1l6oA)T256 Warning: unaligning (T0340)G13 because of BadResidue code BAD_PEPTIDE in next template residue (1l6oA)K261 Warning: unaligning (T0340)P14 because of BadResidue code BAD_PEPTIDE at template residue (1l6oA)K261 Warning: unaligning (T0340)Q15 because of BadResidue code BAD_PEPTIDE at template residue (1l6oA)N263 Warning: unaligning (T0340)G16 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1l6oA)L265 Warning: unaligning (T0340)Y17 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1l6oA)L265 Warning: unaligning (T0340)F19 because of BadResidue code BAD_PEPTIDE in next template residue (1l6oA)S268 Warning: unaligning (T0340)N20 because of BadResidue code BAD_PEPTIDE at template residue (1l6oA)S268 Warning: unaligning (T0340)R27 because of BadResidue code BAD_PEPTIDE in next template residue (1l6oA)G279 Warning: unaligning (T0340)P28 because of BadResidue code BAD_PEPTIDE at template residue (1l6oA)G279 Warning: unaligning (T0340)G29 because of BadResidue code BAD_PEPTIDE at template residue (1l6oA)G280 Warning: unaligning (T0340)A41 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1l6oA)A293 Warning: unaligning (T0340)A42 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1l6oA)A293 Warning: unaligning (T0340)N56 because of BadResidue code BAD_PEPTIDE in next template residue (1l6oA)D309 Warning: unaligning (T0340)G57 because of BadResidue code BAD_PEPTIDE at template residue (1l6oA)D309 Warning: unaligning (T0340)N59 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1l6oA)F312 Warning: unaligning (T0340)V60 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1l6oA)F312 Warning: unaligning (T0340)G62 because of BadResidue code BAD_PEPTIDE in next template residue (1l6oA)M315 Warning: unaligning (T0340)L63 because of BadResidue code BAD_PEPTIDE at template residue (1l6oA)M315 Warning: unaligning (T0340)R64 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1l6oA)S316 Warning: unaligning (T0340)K73 because of BadResidue code BAD_PEPTIDE in next template residue (1l6oA)D326 Warning: unaligning (T0340)A74 because of BadResidue code BAD_PEPTIDE at template residue (1l6oA)D326 Warning: unaligning (T0340)L81 because of BadResidue code BAD_PEPTIDE in next template residue (1l6oA)T337 Warning: unaligning (T0340)L82 because of BadResidue code BAD_PEPTIDE at template residue (1l6oA)T337 Warning: unaligning (T0340)V83 because of BadResidue code BAD_PEPTIDE in next template residue (1l6oA)A339 Warning: unaligning (T0340)V84 because of BadResidue code BAD_PEPTIDE at template residue (1l6oA)A339 Warning: unaligning (T0340)P86 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (1l6oA)E342 Warning: unaligning (T0340)S87 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (1l6oA)E342 Warning: unaligning (T0340)T88 because of BadResidue code BAD_PEPTIDE in next template residue (1l6oA)H344 Warning: unaligning (T0340)R89 because of BadResidue code BAD_PEPTIDE at template residue (1l6oA)H344 T0340 5 :PRL 1l6oA 252 :IIT T0340 10 :LRK 1l6oA 257 :LNM T0340 18 :G 1l6oA 266 :G T0340 21 :LHS 1l6oA 269 :IVG T0340 24 :DKS 1l6oA 275 :ERG T0340 30 :QYIRSVDPGSP 1l6oA 281 :IYIGSIMKGGA T0340 43 :RSG 1l6oA 294 :ADG T0340 46 :LRAQDRLIEV 1l6oA 298 :IEPGDMLLQV T0340 58 :Q 1l6oA 310 :I T0340 61 :E 1l6oA 313 :E T0340 65 :HAEVVASI 1l6oA 317 :NDDAVRVL T0340 75 :R 1l6oA 327 :I T0340 76 :EDEAR 1l6oA 331 :PGPIV T0340 85 :G 1l6oA 340 :K Number of specific fragments extracted= 14 number of extra gaps= 12 total=395 Number of alignments=101 # 1l6oA read from 1l6oA/merged-good-all-a2m # found chain 1l6oA in template set Warning: unaligning (T0340)C8 because of BadResidue code BAD_PEPTIDE in next template residue (1l6oA)T256 Warning: unaligning (T0340)H9 because of BadResidue code BAD_PEPTIDE at template residue (1l6oA)T256 Warning: unaligning (T0340)G13 because of BadResidue code BAD_PEPTIDE in next template residue (1l6oA)K261 Warning: unaligning (T0340)P14 because of BadResidue code BAD_PEPTIDE at template residue (1l6oA)K261 Warning: unaligning (T0340)Q15 because of BadResidue code BAD_PEPTIDE at template residue (1l6oA)N263 Warning: unaligning (T0340)G16 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1l6oA)L265 Warning: unaligning (T0340)Y17 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1l6oA)L265 Warning: unaligning (T0340)F19 because of BadResidue code BAD_PEPTIDE in next template residue (1l6oA)S268 Warning: unaligning (T0340)N20 because of BadResidue code BAD_PEPTIDE at template residue (1l6oA)S268 Warning: unaligning (T0340)R27 because of BadResidue code BAD_PEPTIDE in next template residue (1l6oA)G279 Warning: unaligning (T0340)P28 because of BadResidue code BAD_PEPTIDE at template residue (1l6oA)G279 Warning: unaligning (T0340)G29 because of BadResidue code BAD_PEPTIDE at template residue (1l6oA)G280 Warning: unaligning (T0340)A41 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1l6oA)A293 Warning: unaligning (T0340)A42 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1l6oA)A293 Warning: unaligning (T0340)N56 because of BadResidue code BAD_PEPTIDE in next template residue (1l6oA)D309 Warning: unaligning (T0340)G57 because of BadResidue code BAD_PEPTIDE at template residue (1l6oA)D309 Warning: unaligning (T0340)N59 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1l6oA)F312 Warning: unaligning (T0340)V60 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1l6oA)F312 Warning: unaligning (T0340)G62 because of BadResidue code BAD_PEPTIDE in next template residue (1l6oA)M315 Warning: unaligning (T0340)L63 because of BadResidue code BAD_PEPTIDE at template residue (1l6oA)M315 Warning: unaligning (T0340)R64 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1l6oA)S316 Warning: unaligning (T0340)K73 because of BadResidue code BAD_PEPTIDE in next template residue (1l6oA)D326 Warning: unaligning (T0340)A74 because of BadResidue code BAD_PEPTIDE at template residue (1l6oA)D326 Warning: unaligning (T0340)L81 because of BadResidue code BAD_PEPTIDE in next template residue (1l6oA)T337 Warning: unaligning (T0340)L82 because of BadResidue code BAD_PEPTIDE at template residue (1l6oA)T337 Warning: unaligning (T0340)V83 because of BadResidue code BAD_PEPTIDE in next template residue (1l6oA)A339 Warning: unaligning (T0340)V84 because of BadResidue code BAD_PEPTIDE at template residue (1l6oA)A339 Warning: unaligning (T0340)P86 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (1l6oA)E342 Warning: unaligning (T0340)S87 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (1l6oA)E342 Warning: unaligning (T0340)T88 because of BadResidue code BAD_PEPTIDE in next template residue (1l6oA)H344 Warning: unaligning (T0340)R89 because of BadResidue code BAD_PEPTIDE at template residue (1l6oA)H344 T0340 5 :PRL 1l6oA 252 :IIT T0340 10 :LRK 1l6oA 257 :LNM T0340 18 :G 1l6oA 266 :G T0340 21 :LHS 1l6oA 269 :IVG T0340 24 :DKS 1l6oA 275 :ERG T0340 30 :QYIRSVDPGSP 1l6oA 281 :IYIGSIMKGGA T0340 43 :RSG 1l6oA 294 :ADG T0340 46 :LRAQDRLIEV 1l6oA 298 :IEPGDMLLQV T0340 58 :Q 1l6oA 310 :I T0340 61 :E 1l6oA 313 :E T0340 65 :HAEVVASI 1l6oA 317 :NDDAVRVL T0340 75 :R 1l6oA 327 :I T0340 76 :EDEAR 1l6oA 331 :PGPIV T0340 85 :G 1l6oA 340 :K Number of specific fragments extracted= 14 number of extra gaps= 12 total=409 Number of alignments=102 # 1l6oA read from 1l6oA/merged-good-all-a2m # found chain 1l6oA in template set Warning: unaligning (T0340)C8 because of BadResidue code BAD_PEPTIDE in next template residue (1l6oA)T256 Warning: unaligning (T0340)H9 because of BadResidue code BAD_PEPTIDE at template residue (1l6oA)T256 Warning: unaligning (T0340)G13 because of BadResidue code BAD_PEPTIDE in next template residue (1l6oA)K261 Warning: unaligning (T0340)P14 because of BadResidue code BAD_PEPTIDE at template residue (1l6oA)K261 Warning: unaligning (T0340)Q15 because of BadResidue code BAD_PEPTIDE at template residue (1l6oA)N263 Warning: unaligning (T0340)G16 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1l6oA)L265 Warning: unaligning (T0340)Y17 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1l6oA)L265 Warning: unaligning (T0340)F19 because of BadResidue code BAD_PEPTIDE in next template residue (1l6oA)S268 Warning: unaligning (T0340)N20 because of BadResidue code BAD_PEPTIDE at template residue (1l6oA)S268 Warning: unaligning (T0340)D24 because of BadResidue code BAD_PEPTIDE at template residue (1l6oA)N274 Warning: unaligning (T0340)R27 because of BadResidue code BAD_PEPTIDE in next template residue (1l6oA)G279 Warning: unaligning (T0340)P28 because of BadResidue code BAD_PEPTIDE at template residue (1l6oA)G279 Warning: unaligning (T0340)G29 because of BadResidue code BAD_PEPTIDE at template residue (1l6oA)G280 Warning: unaligning (T0340)A41 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1l6oA)A293 Warning: unaligning (T0340)A42 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1l6oA)A293 Warning: unaligning (T0340)N56 because of BadResidue code BAD_PEPTIDE in next template residue (1l6oA)D309 Warning: unaligning (T0340)G57 because of BadResidue code BAD_PEPTIDE at template residue (1l6oA)D309 Warning: unaligning (T0340)N59 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1l6oA)F312 Warning: unaligning (T0340)V60 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1l6oA)F312 Warning: unaligning (T0340)G62 because of BadResidue code BAD_PEPTIDE in next template residue (1l6oA)M315 Warning: unaligning (T0340)L63 because of BadResidue code BAD_PEPTIDE at template residue (1l6oA)M315 Warning: unaligning (T0340)R64 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1l6oA)S316 Warning: unaligning (T0340)K73 because of BadResidue code BAD_PEPTIDE in next template residue (1l6oA)D326 Warning: unaligning (T0340)L81 because of BadResidue code BAD_PEPTIDE in next template residue (1l6oA)T337 Warning: unaligning (T0340)L82 because of BadResidue code BAD_PEPTIDE at template residue (1l6oA)T337 Warning: unaligning (T0340)V83 because of BadResidue code BAD_PEPTIDE in next template residue (1l6oA)A339 Warning: unaligning (T0340)V84 because of BadResidue code BAD_PEPTIDE at template residue (1l6oA)A339 Warning: unaligning (T0340)P86 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (1l6oA)E342 Warning: unaligning (T0340)S87 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (1l6oA)E342 Warning: unaligning (T0340)T88 because of BadResidue code BAD_PEPTIDE in next template residue (1l6oA)H344 Warning: unaligning (T0340)R89 because of BadResidue code BAD_PEPTIDE at template residue (1l6oA)H344 T0340 5 :PRL 1l6oA 252 :IIT T0340 10 :LRK 1l6oA 257 :LNM T0340 18 :G 1l6oA 266 :G T0340 21 :LHS 1l6oA 269 :IVG T0340 25 :KS 1l6oA 275 :ER T0340 30 :QYIRSVDPGSP 1l6oA 281 :IYIGSIMKGGA T0340 43 :RSG 1l6oA 294 :ADG T0340 46 :LRAQDRLIEV 1l6oA 298 :IEPGDMLLQV T0340 58 :Q 1l6oA 310 :I T0340 61 :E 1l6oA 313 :E T0340 65 :HAEVVASI 1l6oA 317 :NDDAVRVL T0340 74 :AREDEAR 1l6oA 329 :HKPGPIV T0340 85 :G 1l6oA 340 :K Number of specific fragments extracted= 13 number of extra gaps= 13 total=422 # 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 # T0340 read from 1q3oA/merged-good-all-a2m # 1q3oA read from 1q3oA/merged-good-all-a2m # found chain 1q3oA in training set T0340 6 :RLCHLRKGPQ 1q3oA 590 :KTVLLQKKDS T0340 16 :GYGFNLHSDK 1q3oA 601 :GFGFVLRGAK T0340 30 :QYIRSVDPGSPAARSGLRAQDRLIEVNGQNVEGLRHAEVVASIKAREDEARLLVVGP 1q3oA 628 :QYLESVDEGGVAWRAGLRMGDFLIEVNGQNVVKVGHRQVVNMIRQGGNTLMVKVVMV Number of specific fragments extracted= 3 number of extra gaps= 0 total=425 Number of alignments=103 # 1q3oA read from 1q3oA/merged-good-all-a2m # found chain 1q3oA in training set T0340 6 :RLCHLRKGPQ 1q3oA 590 :KTVLLQKKDS T0340 16 :GYGFNLHSDKS 1q3oA 601 :GFGFVLRGAKA T0340 30 :QYIRSVDPGSPAARSGLRAQDRLIEVNGQNVEGLRHAEVVASIKAREDEARLLVVG 1q3oA 628 :QYLESVDEGGVAWRAGLRMGDFLIEVNGQNVVKVGHRQVVNMIRQGGNTLMVKVVM Number of specific fragments extracted= 3 number of extra gaps= 0 total=428 Number of alignments=104 # 1q3oA read from 1q3oA/merged-good-all-a2m # found chain 1q3oA in training set T0340 6 :RLCHLR 1q3oA 590 :KTVLLQ T0340 12 :KGPQGYGFNLHSDKS 1q3oA 597 :KDSEGFGFVLRGAKA T0340 27 :RPGQYIRSVDPGSPAARSGLRAQDRLIEVNGQNVEGLRHAEVVASIKAREDEARLLVVG 1q3oA 625 :PALQYLESVDEGGVAWRAGLRMGDFLIEVNGQNVVKVGHRQVVNMIRQGGNTLMVKVVM Number of specific fragments extracted= 3 number of extra gaps= 0 total=431 Number of alignments=105 # 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 # T0340 read from 1n7fA/merged-good-all-a2m # 1n7fA read from 1n7fA/merged-good-all-a2m # found chain 1n7fA in training set Warning: unaligning (T0340)L3 because first residue in template chain is (1n7fA)A668 Warning: unaligning (T0340)P86 because last residue in template chain is (1n7fA)Q753 T0340 4 :RPRLCHLRKGPQGYGFNLHSDKSRP 1n7fA 669 :IIYTVELKRYGGPLGITISGTEEPF T0340 29 :GQYIRSVDPGSPAARSG 1n7fA 695 :PIIISSLTKGGLAERTG T0340 46 :LRAQDRLIEVNGQNVEGLRHAEVVASIKAREDEARLLVVG 1n7fA 713 :IHIGDRILAINSSSLKGKPLSEAIHLLQMAGETVTLKIKK Number of specific fragments extracted= 3 number of extra gaps= 0 total=434 Number of alignments=106 # 1n7fA read from 1n7fA/merged-good-all-a2m # found chain 1n7fA in training set Warning: unaligning (T0340)L3 because first residue in template chain is (1n7fA)A668 Warning: unaligning (T0340)P86 because last residue in template chain is (1n7fA)Q753 T0340 4 :RPRLCHLRKGPQGYGFNLHSDKS 1n7fA 669 :IIYTVELKRYGGPLGITISGTEE T0340 27 :RPGQYIRSVDPGSPAARSG 1n7fA 693 :FDPIIISSLTKGGLAERTG T0340 46 :LRAQDRLIEVNGQNVEGLRHAEVVASIKAREDEARLLVVG 1n7fA 713 :IHIGDRILAINSSSLKGKPLSEAIHLLQMAGETVTLKIKK Number of specific fragments extracted= 3 number of extra gaps= 0 total=437 Number of alignments=107 # 1n7fA read from 1n7fA/merged-good-all-a2m # found chain 1n7fA in training set Warning: unaligning (T0340)L3 because first residue in template chain is (1n7fA)A668 Warning: unaligning (T0340)P86 because last residue in template chain is (1n7fA)Q753 T0340 4 :RPRLCHLRKGPQGYGFNLHSDKS 1n7fA 669 :IIYTVELKRYGGPLGITISGTEE T0340 27 :RPGQYIRSVDPGSPAARSG 1n7fA 693 :FDPIIISSLTKGGLAERTG T0340 46 :LRAQDRLIEVNGQNVEGLRHAEVVASIKAREDEARLLVVG 1n7fA 713 :IHIGDRILAINSSSLKGKPLSEAIHLLQMAGETVTLKIKK Number of specific fragments extracted= 3 number of extra gaps= 0 total=440 Number of alignments=108 # 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 # T0340 read from 1ihjA/merged-good-all-a2m # 1ihjA read from 1ihjA/merged-good-all-a2m # found chain 1ihjA in training set Warning: unaligning (T0340)M2 because first residue in template chain is (1ihjA)G12 Warning: unaligning (T0340)S26 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ihjA)N42 Warning: unaligning (T0340)P86 because last residue in template chain is (1ihjA)F105 T0340 3 :LRPRLCHLRKGP 1ihjA 13 :ELIHMVTLDKTG T0340 15 :QGYGFNLHSDK 1ihjA 26 :KSFGICIVRGE T0340 27 :RP 1ihjA 43 :TK T0340 29 :GQYIRSVDPGSPAARSG 1ihjA 47 :GIFIKGIVPDSPAHLCG T0340 46 :LRAQDRLIEVNGQNVEGLRHAEVVASIKAREDEARLLVVG 1ihjA 65 :LKVGDRILSLNGKDVRNSTEQAVIDLIKEADFKIELEIQT Number of specific fragments extracted= 5 number of extra gaps= 1 total=445 Number of alignments=109 # 1ihjA read from 1ihjA/merged-good-all-a2m # found chain 1ihjA in training set Warning: unaligning (T0340)M2 because first residue in template chain is (1ihjA)G12 Warning: unaligning (T0340)D24 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ihjA)P41 Warning: unaligning (T0340)K25 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ihjA)P41 Warning: unaligning (T0340)S26 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ihjA)N42 Warning: unaligning (T0340)P86 because last residue in template chain is (1ihjA)F105 T0340 3 :LRPRLCHLRKGP 1ihjA 13 :ELIHMVTLDKTG T0340 15 :QGYGFNLHS 1ihjA 26 :KSFGICIVR T0340 27 :RPGQYIRSVDPGSPAARSG 1ihjA 45 :TTGIFIKGIVPDSPAHLCG T0340 46 :LRAQDRLIEVNGQNVEGLRHAEVVASIKAREDEARLLVVG 1ihjA 65 :LKVGDRILSLNGKDVRNSTEQAVIDLIKEADFKIELEIQT Number of specific fragments extracted= 4 number of extra gaps= 1 total=449 Number of alignments=110 # 1ihjA read from 1ihjA/merged-good-all-a2m # found chain 1ihjA in training set Warning: unaligning (T0340)M2 because first residue in template chain is (1ihjA)G12 Warning: unaligning (T0340)P86 because last residue in template chain is (1ihjA)F105 T0340 3 :LRPRLCHLRKGP 1ihjA 13 :ELIHMVTLDKTG T0340 15 :QGYGFNLHSDKS 1ihjA 26 :KSFGICIVRGEV T0340 27 :RPGQYIRSVDPGSPAARSG 1ihjA 45 :TTGIFIKGIVPDSPAHLCG T0340 46 :LRAQDRLIEVNGQNVEGLRHAEVVASIKAREDEARLLVVG 1ihjA 65 :LKVGDRILSLNGKDVRNSTEQAVIDLIKEADFKIELEIQT Number of specific fragments extracted= 4 number of extra gaps= 0 total=453 Number of alignments=111 # command:# PrintAlignmentsContacts allconstraints.under Using radius: 8.0000 NUMB_ALIGNS: 111 Done printing distance constraints # command: