# 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/T0366/ # command:# Making conformation for sequence T0366 numbered 1 through 106 Created new target T0366 from T0366.a2m # command:# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/T0366/ # command:Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0366//projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0366/manyalignments-good-all.under or /projects/compbio/experiments/protein-predict/casp7/T0366//projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0366/manyalignments-good-all.under.gz for input Trying /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0366/manyalignments-good-all.under # reading script from file /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0366/manyalignments-good-all.under # Reading fragments from alignment file # Attempting to read fragment alignments from file 1vj6A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0366/1vj6A/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0366/1vj6A/merged-good-all-a2m.gz for input Trying 1vj6A/merged-good-all-a2m Error: Couldn't open file 1vj6A/merged-good-all-a2m or 1vj6A/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 2fneA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2fneA expands to /projects/compbio/data/pdb/2fne.pdb.gz 2fneA:Skipped atom 15, because occupancy 0.5 <= existing 0.500 in 2fneA Skipped atom 19, because occupancy 0.500 <= existing 0.500 in 2fneA Skipped atom 21, because occupancy 0.500 <= existing 0.500 in 2fneA Skipped atom 23, because occupancy 0.500 <= existing 0.500 in 2fneA Skipped atom 25, because occupancy 0.500 <= existing 0.500 in 2fneA Skipped atom 27, because occupancy 0.500 <= existing 0.500 in 2fneA Skipped atom 658, because occupancy 0.500 <= existing 0.500 in 2fneA Skipped atom 662, because occupancy 0.500 <= existing 0.500 in 2fneA Skipped atom 664, because occupancy 0.500 <= existing 0.500 in 2fneA Skipped atom 666, because occupancy 0.500 <= existing 0.500 in 2fneA Skipped atom 668, because occupancy 0.500 <= existing 0.500 in 2fneA # T0366 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 (T0366)S8 because first residue in template chain is (2fneA)M1954 T0366 9 :MGLRTVEMKKG 2fneA 1955 :PQCKSITLERG # choosing archetypes in rotamer library T0366 21 :TDSLGISIAGGVGSPLGDVPIFIAMMHPTGVAAQTQKLRVGDRIVTICGTSTEGMTHTQAVNLLKNASGSIEMQVVAGGDV 2fneA 1966 :PDGLGFSIVGGYGSPHGDLPIYVKTVFAKGAASEDGRLKRGDQIIAVNGQSLEGVTHEEAVAILKRTKGTVTLMVLSSDET Number of specific fragments extracted= 2 number of extra gaps= 0 total=2 Number of alignments=1 # 2fneA read from 2fneA/merged-good-all-a2m # found chain 2fneA in template set Warning: unaligning (T0366)S8 because first residue in template chain is (2fneA)M1954 T0366 9 :MGLRTVEMKKG 2fneA 1955 :PQCKSITLERG T0366 21 :TDSLGISIAGGVGSPLGDVPIFIAMMHPTGVAAQTQKLRVGDRIVTICGTSTEGMTHTQAVNLLKNASGSIEMQVVAGGDV 2fneA 1966 :PDGLGFSIVGGYGSPHGDLPIYVKTVFAKGAASEDGRLKRGDQIIAVNGQSLEGVTHEEAVAILKRTKGTVTLMVLSSDET Number of specific fragments extracted= 2 number of extra gaps= 0 total=4 Number of alignments=2 # 2fneA read from 2fneA/merged-good-all-a2m # found chain 2fneA in template set Warning: unaligning (T0366)M9 because first residue in template chain is (2fneA)M1954 T0366 10 :GLRTVEMKKGPTDSLGISIAGGVGSPLGDVPIFIAMMHPTGVAAQTQKLRVGDRIVTICGTSTEGMTHTQAVNLLKNASGSIEMQVVAGGD 2fneA 1955 :PQCKSITLERGPDGLGFSIVGGYGSPHGDLPIYVKTVFAKGAASEDGRLKRGDQIIAVNGQSLEGVTHEEAVAILKRTKGTVTLMVLSSDE Number of specific fragments extracted= 1 number of extra gaps= 0 total=5 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/T0366/2bygA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0366/2bygA/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 # T0366 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 (T0366)G30 because of BadResidue code BAD_PEPTIDE in next template residue (1y8tA)D238 Warning: unaligning (T0366)G31 because of BadResidue code BAD_PEPTIDE at template residue (1y8tA)D238 Warning: unaligning (T0366)V32 because of BadResidue code TOO_FEW_ATOMS+BAD_PEPTIDE in next template residue (1y8tA)D240 Warning: unaligning (T0366)G33 because of BadResidue code TOO_FEW_ATOMS+BAD_PEPTIDE at template residue (1y8tA)D240 Warning: unaligning (T0366)D38 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1y8tA)T241 Warning: unaligning (T0366)V39 because of BadResidue code BAD_PEPTIDE at template residue (1y8tA)L242 Warning: unaligning (T0366)G50 because of BadResidue code BAD_PEPTIDE in next template residue (1y8tA)A254 Warning: unaligning (T0366)V51 because of BadResidue code BAD_PEPTIDE at template residue (1y8tA)A254 Warning: unaligning (T0366)Q54 because of BadResidue code BAD_PEPTIDE in next template residue (1y8tA)A258 Warning: unaligning (T0366)T55 because of BadResidue code BAD_PEPTIDE at template residue (1y8tA)A258 Warning: unaligning (T0366)Q56 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1y8tA)V260 Warning: unaligning (T0366)L58 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1y8tA)V260 Warning: unaligning (T0366)G69 because of BadResidue code TOO_FEW_ATOMS+BAD_PEPTIDE in next template residue (1y8tA)R272 Warning: unaligning (T0366)T70 because of BadResidue code TOO_FEW_ATOMS+BAD_PEPTIDE at template residue (1y8tA)R272 Warning: unaligning (T0366)S71 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1y8tA)P273 Warning: unaligning (T0366)A97 because of BadResidue code BAD_PEPTIDE in next template residue (1y8tA)P300 Warning: unaligning (T0366)G98 because of BadResidue code BAD_PEPTIDE at template residue (1y8tA)P300 Warning: unaligning (T0366)G99 because of BadResidue code BAD_PEPTIDE at template residue (1y8tA)S301 T0366 23 :SLGISIA 1y8tA 230 :SLGVQVT T0366 40 :PIFIAMMHPT 1y8tA 243 :GAKIVEVVAG T0366 52 :AA 1y8tA 255 :AA T0366 59 :RVGDRIVTIC 1y8tA 261 :PKGVVVTKVD T0366 72 :TEG 1y8tA 274 :INS T0366 77 :HTQAVNLLKNA 1y8tA 277 :ADALVAAVRSK T0366 88 :SGSIEMQVV 1y8tA 290 :GATVALTFQ T0366 100 :DV 1y8tA 302 :GG Number of specific fragments extracted= 8 number of extra gaps= 5 total=13 Number of alignments=4 # 1y8tA read from 1y8tA/merged-good-all-a2m # found chain 1y8tA in template set Warning: unaligning (T0366)G30 because of BadResidue code BAD_PEPTIDE in next template residue (1y8tA)D238 Warning: unaligning (T0366)G31 because of BadResidue code BAD_PEPTIDE at template residue (1y8tA)D238 Warning: unaligning (T0366)V32 because of BadResidue code TOO_FEW_ATOMS+BAD_PEPTIDE in next template residue (1y8tA)D240 Warning: unaligning (T0366)G37 because of BadResidue code TOO_FEW_ATOMS+BAD_PEPTIDE at template residue (1y8tA)D240 Warning: unaligning (T0366)D38 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1y8tA)T241 Warning: unaligning (T0366)V39 because of BadResidue code BAD_PEPTIDE at template residue (1y8tA)L242 Warning: unaligning (T0366)G50 because of BadResidue code BAD_PEPTIDE in next template residue (1y8tA)A254 Warning: unaligning (T0366)V51 because of BadResidue code BAD_PEPTIDE at template residue (1y8tA)A254 Warning: unaligning (T0366)Q54 because of BadResidue code BAD_PEPTIDE in next template residue (1y8tA)A258 Warning: unaligning (T0366)T55 because of BadResidue code BAD_PEPTIDE at template residue (1y8tA)A258 Warning: unaligning (T0366)Q56 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1y8tA)V260 Warning: unaligning (T0366)L58 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1y8tA)V260 Warning: unaligning (T0366)G69 because of BadResidue code TOO_FEW_ATOMS+BAD_PEPTIDE in next template residue (1y8tA)R272 Warning: unaligning (T0366)T70 because of BadResidue code TOO_FEW_ATOMS+BAD_PEPTIDE at template residue (1y8tA)R272 Warning: unaligning (T0366)S71 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1y8tA)P273 Warning: unaligning (T0366)A97 because of BadResidue code BAD_PEPTIDE in next template residue (1y8tA)P300 Warning: unaligning (T0366)G98 because of BadResidue code BAD_PEPTIDE at template residue (1y8tA)P300 Warning: unaligning (T0366)G99 because of BadResidue code BAD_PEPTIDE at template residue (1y8tA)S301 T0366 23 :SLGISIA 1y8tA 230 :SLGVQVT T0366 40 :PIFIAMMHPT 1y8tA 243 :GAKIVEVVAG T0366 52 :AA 1y8tA 255 :AA T0366 59 :RVGDRIVTIC 1y8tA 261 :PKGVVVTKVD T0366 72 :TEG 1y8tA 274 :INS T0366 77 :HTQAVNLLKNA 1y8tA 277 :ADALVAAVRSK T0366 88 :SGSIEMQVV 1y8tA 290 :GATVALTFQ T0366 100 :DVS 1y8tA 302 :GGS Number of specific fragments extracted= 8 number of extra gaps= 5 total=21 Number of alignments=5 # 1y8tA read from 1y8tA/merged-good-all-a2m # found chain 1y8tA in template set Warning: unaligning (T0366)G30 because of BadResidue code BAD_PEPTIDE in next template residue (1y8tA)D238 Warning: unaligning (T0366)G31 because of BadResidue code BAD_PEPTIDE at template residue (1y8tA)D238 Warning: unaligning (T0366)V32 because of BadResidue code TOO_FEW_ATOMS+BAD_PEPTIDE in next template residue (1y8tA)D240 Warning: unaligning (T0366)G33 because of BadResidue code TOO_FEW_ATOMS+BAD_PEPTIDE at template residue (1y8tA)D240 Warning: unaligning (T0366)D38 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1y8tA)T241 Warning: unaligning (T0366)V39 because of BadResidue code BAD_PEPTIDE at template residue (1y8tA)L242 Warning: unaligning (T0366)G50 because of BadResidue code BAD_PEPTIDE in next template residue (1y8tA)A254 Warning: unaligning (T0366)V51 because of BadResidue code BAD_PEPTIDE at template residue (1y8tA)A254 Warning: unaligning (T0366)Q54 because of BadResidue code BAD_PEPTIDE in next template residue (1y8tA)A258 Warning: unaligning (T0366)T55 because of BadResidue code BAD_PEPTIDE at template residue (1y8tA)A258 Warning: unaligning (T0366)Q56 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1y8tA)V260 Warning: unaligning (T0366)L58 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1y8tA)V260 Warning: unaligning (T0366)G69 because of BadResidue code TOO_FEW_ATOMS+BAD_PEPTIDE in next template residue (1y8tA)R272 Warning: unaligning (T0366)T70 because of BadResidue code TOO_FEW_ATOMS+BAD_PEPTIDE at template residue (1y8tA)R272 Warning: unaligning (T0366)S71 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1y8tA)P273 Warning: unaligning (T0366)A97 because of BadResidue code BAD_PEPTIDE in next template residue (1y8tA)P300 Warning: unaligning (T0366)G98 because of BadResidue code BAD_PEPTIDE at template residue (1y8tA)P300 Warning: unaligning (T0366)G99 because of BadResidue code BAD_PEPTIDE at template residue (1y8tA)S301 T0366 23 :SLGISIA 1y8tA 230 :SLGVQVT T0366 40 :PIFIAMMHPT 1y8tA 243 :GAKIVEVVAG T0366 52 :AA 1y8tA 255 :AA T0366 59 :RVGDRIVTIC 1y8tA 261 :PKGVVVTKVD T0366 72 :TEG 1y8tA 274 :INS T0366 77 :HTQAVNLLKNA 1y8tA 277 :ADALVAAVRSK T0366 88 :SGSIEMQVV 1y8tA 290 :GATVALTFQ T0366 100 :D 1y8tA 302 :G Number of specific fragments extracted= 8 number of extra gaps= 5 total=29 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 # T0366 read from 1qauA/merged-good-all-a2m # 1qauA read from 1qauA/merged-good-all-a2m # found chain 1qauA in training set T0366 11 :LRTVEMKKGPTDSLGISIAGGVG 1qauA 15 :VISVRLFKRKVGGLGFLVKERVS T0366 38 :DVPIFIAMMHPTGVAAQTQKLRVGDRIVTICGTSTEGMTHTQAVNLLKNA 1qauA 38 :KPPVIISDLIRGGAAEQSGLIQAGDIILAVNDRPLVDLSYDSALEVLRGI T0366 88 :SGSIEMQVVAGGDVS 1qauA 90 :ETHVVLILRGPEGFT Number of specific fragments extracted= 3 number of extra gaps= 0 total=32 Number of alignments=7 # 1qauA read from 1qauA/merged-good-all-a2m # found chain 1qauA in training set Warning: unaligning (T0366)G10 because first residue in template chain is (1qauA)N14 T0366 11 :LRTVEMKKGPTDSLGISIAGGV 1qauA 15 :VISVRLFKRKVGGLGFLVKERV T0366 37 :GDVPIFIAMMHPTGVAAQTQKLRVGDRIVTICGTSTEGMTHTQAVNLLKNA 1qauA 37 :SKPPVIISDLIRGGAAEQSGLIQAGDIILAVNDRPLVDLSYDSALEVLRGI T0366 88 :SGSIEMQVVAGGDVS 1qauA 90 :ETHVVLILRGPEGFT Number of specific fragments extracted= 3 number of extra gaps= 0 total=35 Number of alignments=8 # 1qauA read from 1qauA/merged-good-all-a2m # found chain 1qauA in training set T0366 11 :LRTVEMKKGPTDSLGISIAGGVG 1qauA 15 :VISVRLFKRKVGGLGFLVKERVS T0366 38 :DVPIFIAMMHPTGVAAQTQKLRVGDRIVTICGTSTEGMTHTQAVNLLKNA 1qauA 38 :KPPVIISDLIRGGAAEQSGLIQAGDIILAVNDRPLVDLSYDSALEVLRGI T0366 88 :SGSIEMQVVAGGDV 1qauA 90 :ETHVVLILRGPEGF Number of specific fragments extracted= 3 number of extra gaps= 0 total=38 Number of alignments=9 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2h2bA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2h2bA expands to /projects/compbio/data/pdb/2h2b.pdb.gz 2h2bA:# T0366 read from 2h2bA/merged-good-all-a2m # 2h2bA read from 2h2bA/merged-good-all-a2m # adding 2h2bA to template set # found chain 2h2bA in template set T0366 5 :YFQSMGLRTVEMKKGPTDSLGISIAGGV 2h2bA 15 :SHMIWEQHTVTLHRAPGFGFGIAISGGR T0366 33 :GSPLGDVPIFIAMMHPTGVAA 2h2bA 46 :HFQSGETSIVISDVLKGGPAE T0366 56 :QKLRVGDRIVTICGTSTEGMTHTQAVNLLKNASGSIEMQVVAGGDVSE 2h2bA 67 :GQLQENDRVAMVNGVSMDNVEHAFAVQQLRKSGKNAKITIRRKKGGGW T0366 104 :T 2h2bA 117 :T Number of specific fragments extracted= 4 number of extra gaps= 0 total=42 Number of alignments=10 # 2h2bA read from 2h2bA/merged-good-all-a2m # found chain 2h2bA in template set Warning: unaligning (T0366)L4 because first residue in template chain is (2h2bA)G14 T0366 5 :YFQSMGLRTVEMKKGPTDSLGISIAGGVGS 2h2bA 15 :SHMIWEQHTVTLHRAPGFGFGIAISGGRDN T0366 35 :PLGDVPIFIAMMHPTGVAA 2h2bA 48 :QSGETSIVISDVLKGGPAE T0366 56 :QKLRVGDRIVTICGTSTEGMTHTQAVNLLKNASGSIEMQVVAGGDVS 2h2bA 67 :GQLQENDRVAMVNGVSMDNVEHAFAVQQLRKSGKNAKITIRRKKGGG T0366 104 :TSV 2h2bA 116 :RTT Number of specific fragments extracted= 4 number of extra gaps= 0 total=46 Number of alignments=11 # 2h2bA read from 2h2bA/merged-good-all-a2m # found chain 2h2bA in template set T0366 7 :QSMGLRTVEMKKGPTDSLGISIAGGVG 2h2bA 17 :MIWEQHTVTLHRAPGFGFGIAISGGRD T0366 34 :SPLGDVPIFIAMMHPTGVAA 2h2bA 47 :FQSGETSIVISDVLKGGPAE T0366 56 :QKLRVGDRIVTICGTSTEGMTHTQAVNLLKNASGSIEMQVVAGGDVSETSV 2h2bA 67 :GQLQENDRVAMVNGVSMDNVEHAFAVQQLRKSGKNAKITIRRKKGGGWRRT Number of specific fragments extracted= 3 number of extra gaps= 0 total=49 Number of alignments=12 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1i16/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1i16 expands to /projects/compbio/data/pdb/1i16.pdb.gz 1i16:Warning: there is no chain 1i16 will retry with 1i16A # T0366 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 T0366 3 :NLYFQ 1i16 19 :DVSVE T0366 11 :LRTVEMKKG 1i16 30 :VCTVTLEKM T0366 21 :TDSLGISIAGGVGSPLGDVPIFIAMMHPTGVAAQTQKLRVGDRIVTICGTSTEGMTHTQAVNLLKNA 1i16 39 :SAGLGFSLEGGKGSLHGDKPLTINRIFKGAASEQSETVQPGDEILQLGGTAMQGLTRFEAWNIIKAL T0366 88 :SGSIEMQVVAGGDVSE 1i16 107 :DGPVTIVIRRKSLQSK T0366 105 :S 1i16 125 :T Number of specific fragments extracted= 5 number of extra gaps= 0 total=54 Number of alignments=13 # 1i16 read from 1i16/merged-good-all-a2m # found chain 1i16 in template set T0366 2 :ENLYFQ 1i16 18 :SDVSVE T0366 11 :LRTVEMKKG 1i16 30 :VCTVTLEKM T0366 21 :TDSLGISIAGGVGSPLGDVPIFIAMMHPTGVAAQTQKLRVGDRIVTICGTSTEGMTHTQAVNLLKNA 1i16 39 :SAGLGFSLEGGKGSLHGDKPLTINRIFKGAASEQSETVQPGDEILQLGGTAMQGLTRFEAWNIIKAL T0366 88 :SGSIEMQVVAGGDVS 1i16 107 :DGPVTIVIRRKSLQS T0366 103 :ETS 1i16 123 :ETT Number of specific fragments extracted= 5 number of extra gaps= 0 total=59 Number of alignments=14 # 1i16 read from 1i16/merged-good-all-a2m # found chain 1i16 in template set T0366 8 :SMGLRTVEMKKGPTDSLGISIAGGVGSPLGDVPIFIAMMHPTGVAAQTQKLRVGDRIVTICGTSTEGMTHTQAVNLLKNAS 1i16 26 :AEATVCTVTLEKMSAGLGFSLEGGKGSLHGDKPLTINRIFKGAASEQSETVQPGDEILQLGGTAMQGLTRFEAWNIIKALP T0366 89 :GSIEMQVVAGGDVSETS 1i16 108 :GPVTIVIRRKSLQSKET Number of specific fragments extracted= 2 number of extra gaps= 0 total=61 Number of alignments=15 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1v5lA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1v5lA expands to /projects/compbio/data/pdb/1v5l.pdb.gz 1v5lA:# T0366 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 T0366 2 :ENLYFQS 1v5lA 2 :SSGSSGN T0366 14 :VEMKKG 1v5lA 9 :VVLPGP T0366 22 :DSLGISIAGGVGS 1v5lA 15 :APWGFRLSGGIDF T0366 38 :DVPIFIAMMHPTGVAAQTQ 1v5lA 28 :NQPLVITRITPGSKAAAAN T0366 58 :LRVGDRIVTICGTSTEGMTHTQAVNLLKNASGSIEMQVVAGGDVSE 1v5lA 47 :LCPGDVILAIDGFGTESMTHADAQDRIKAASYQLCLKIDRAETRLW T0366 104 :TS 1v5lA 94 :PQ Number of specific fragments extracted= 6 number of extra gaps= 0 total=67 Number of alignments=16 # 1v5lA read from 1v5lA/merged-good-all-a2m # found chain 1v5lA in template set T0366 2 :ENLYFQS 1v5lA 2 :SSGSSGN T0366 14 :VEMKK 1v5lA 9 :VVLPG T0366 21 :TDSLGISIAGGVG 1v5lA 14 :PAPWGFRLSGGID T0366 37 :GDVPIFIAMMHPTGVAAQTQ 1v5lA 27 :FNQPLVITRITPGSKAAAAN T0366 58 :LRVGDRIVTICGTSTEGMTHTQAVNLLKNASGSIEMQVVAGGDVS 1v5lA 47 :LCPGDVILAIDGFGTESMTHADAQDRIKAASYQLCLKIDRAETRL T0366 105 :SV 1v5lA 94 :PQ Number of specific fragments extracted= 6 number of extra gaps= 0 total=73 Number of alignments=17 # 1v5lA read from 1v5lA/merged-good-all-a2m # found chain 1v5lA in template set T0366 17 :KKGPTDSLGISIAGGVG 1v5lA 10 :VLPGPAPWGFRLSGGID T0366 37 :GDVPIFIAMMHPTGVAAQTQ 1v5lA 27 :FNQPLVITRITPGSKAAAAN T0366 58 :LRVGDRIVTICGTSTEGMTHTQAVNLLKNASGSIEMQVVAGGDVSETSV 1v5lA 47 :LCPGDVILAIDGFGTESMTHADAQDRIKAASYQLCLKIDRAETRLWSPQ Number of specific fragments extracted= 3 number of extra gaps= 0 total=76 Number of alignments=18 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1tp5A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1tp5A expands to /projects/compbio/data/pdb/1tp5.pdb.gz 1tp5A:# T0366 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 (T0366)M93 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1tp5A)I389 Warning: unaligning (T0366)Q94 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1tp5A)I389 T0366 1 :TENLYFQSMGLRTVEMKKG 1tp5A 301 :FLGEEDIPREPRRIVIHRG T0366 21 :TDSLGISIAGGVG 1tp5A 320 :STGLGFNIVGGED T0366 38 :DVPIFIAMMHPTGVAAQTQKLRVGDRIVTICGTSTEGMTHTQAVNLLKNASGSIE 1tp5A 333 :GEGIFISFILAGGPADLSGELRKGDQILSVNGVDLRNASHEQAAIALKNAGQTVT T0366 95 :VVAG 1tp5A 390 :AQYK Number of specific fragments extracted= 4 number of extra gaps= 1 total=80 Number of alignments=19 # 1tp5A read from 1tp5A/merged-good-all-a2m # found chain 1tp5A in template set Warning: unaligning (T0366)M93 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1tp5A)I389 Warning: unaligning (T0366)Q94 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1tp5A)I389 T0366 1 :TENLYFQSMGLRTVEMKKG 1tp5A 301 :FLGEEDIPREPRRIVIHRG T0366 21 :TDSLGISIAGGV 1tp5A 320 :STGLGFNIVGGE T0366 37 :GDVPIFIAMMHPTGVAAQTQKLRVGDRIVTICGTSTEGMTHTQAVNLLKNASGSIE 1tp5A 332 :DGEGIFISFILAGGPADLSGELRKGDQILSVNGVDLRNASHEQAAIALKNAGQTVT T0366 95 :VVAG 1tp5A 390 :AQYK Number of specific fragments extracted= 4 number of extra gaps= 1 total=84 Number of alignments=20 # 1tp5A read from 1tp5A/merged-good-all-a2m # found chain 1tp5A in template set Warning: unaligning (T0366)M93 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1tp5A)I389 Warning: unaligning (T0366)Q94 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1tp5A)I389 T0366 7 :QSMGLRTVEMKKGPTDSLGISIAGGVG 1tp5A 306 :DIPREPRRIVIHRGSTGLGFNIVGGED T0366 38 :DVPIFIAMMHPTGVAAQTQKLRVGDRIVTICGTSTEGMTHTQAVNLLKNASGSIE 1tp5A 333 :GEGIFISFILAGGPADLSGELRKGDQILSVNGVDLRNASHEQAAIALKNAGQTVT T0366 95 :VVAG 1tp5A 390 :AQYK Number of specific fragments extracted= 3 number of extra gaps= 1 total=87 Number of alignments=21 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1i92A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1i92A expands to /projects/compbio/data/pdb/1i92.pdb.gz 1i92A:Skipped atom 533, because occupancy 0.500 <= existing 0.500 in 1i92A Skipped atom 543, because occupancy 0.500 <= existing 0.500 in 1i92A Skipped atom 545, because occupancy 0.500 <= existing 0.500 in 1i92A Skipped atom 547, because occupancy 0.500 <= existing 0.500 in 1i92A Skipped atom 549, because occupancy 0.500 <= existing 0.500 in 1i92A Skipped atom 551, because occupancy 0.500 <= existing 0.500 in 1i92A Skipped atom 553, because occupancy 0.500 <= existing 0.500 in 1i92A Skipped atom 555, because occupancy 0.500 <= existing 0.500 in 1i92A Skipped atom 557, because occupancy 0.500 <= existing 0.500 in 1i92A Skipped atom 559, because occupancy 0.500 <= existing 0.500 in 1i92A Skipped atom 561, because occupancy 0.500 <= existing 0.500 in 1i92A Skipped atom 563, because occupancy 0.500 <= existing 0.500 in 1i92A Skipped atom 565, because occupancy 0.500 <= existing 0.500 in 1i92A Skipped atom 567, because occupancy 0.500 <= existing 0.500 in 1i92A Skipped atom 569, because occupancy 0.500 <= existing 0.500 in 1i92A Skipped atom 571, because occupancy 0.500 <= existing 0.500 in 1i92A Skipped atom 573, because occupancy 0.500 <= existing 0.500 in 1i92A Skipped atom 575, because occupancy 0.500 <= existing 0.500 in 1i92A Skipped atom 577, because occupancy 0.500 <= existing 0.500 in 1i92A Skipped atom 579, because occupancy 0.500 <= existing 0.500 in 1i92A Skipped atom 581, because occupancy 0.500 <= existing 0.500 in 1i92A Skipped atom 583, because occupancy 0.500 <= existing 0.500 in 1i92A # T0366 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 (T0366)S8 because first residue in template chain is (1i92A)G9 Warning: unaligning (T0366)S88 because of BadResidue code TOO_FEW_ATOMS+NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1i92A)N84 Warning: unaligning (T0366)G89 because of BadResidue code TOO_FEW_ATOMS+NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1i92A)N84 T0366 9 :MGLRTVEMKKG 1i92A 10 :MLPRLCCLEKG T0366 21 :TDSLGISIAGGVG 1i92A 21 :PNGYGFHLHGEKG T0366 38 :DVPIFIAMMHPTGVAAQTQ 1i92A 34 :KLGQYIRLVEPGSPAEKAG T0366 58 :LRVGDRIVTICGTSTEGMTHTQAVNLLKNA 1i92A 53 :LLAGDRLVEVNGENVEKETHQQVVSRIRAA T0366 90 :SIEMQVVAGGDVSE 1i92A 85 :AVRLLVVDPEQDTR Number of specific fragments extracted= 5 number of extra gaps= 1 total=92 Number of alignments=22 # 1i92A read from 1i92A/merged-good-all-a2m # found chain 1i92A in template set Warning: unaligning (T0366)S8 because first residue in template chain is (1i92A)G9 Warning: unaligning (T0366)S88 because of BadResidue code TOO_FEW_ATOMS+NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1i92A)N84 Warning: unaligning (T0366)G89 because of BadResidue code TOO_FEW_ATOMS+NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1i92A)N84 T0366 9 :MGLRTVEMKKG 1i92A 10 :MLPRLCCLEKG T0366 21 :TDSLGISIAGGV 1i92A 21 :PNGYGFHLHGEK T0366 37 :GDVPIFIAMMHPTGVAAQTQ 1i92A 33 :GKLGQYIRLVEPGSPAEKAG T0366 58 :LRVGDRIVTICGTSTEGMTHTQAVNLLKNA 1i92A 53 :LLAGDRLVEVNGENVEKETHQQVVSRIRAA T0366 90 :SIEMQVVAGGDVS 1i92A 85 :AVRLLVVDPEQDT Number of specific fragments extracted= 5 number of extra gaps= 1 total=97 Number of alignments=23 # 1i92A read from 1i92A/merged-good-all-a2m # found chain 1i92A in template set Warning: unaligning (T0366)S88 because of BadResidue code TOO_FEW_ATOMS+NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1i92A)N84 Warning: unaligning (T0366)G89 because of BadResidue code TOO_FEW_ATOMS+NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1i92A)N84 T0366 10 :GLRTVEMKKGPTDSLGISIAGGVG 1i92A 10 :MLPRLCCLEKGPNGYGFHLHGEKG T0366 38 :DVPIFIAMMHPTGVAAQTQ 1i92A 34 :KLGQYIRLVEPGSPAEKAG T0366 58 :LRVGDRIVTICGTSTEGMTHTQAVNLLKNA 1i92A 53 :LLAGDRLVEVNGENVEKETHQQVVSRIRAA T0366 90 :SIEMQVVAGGDVSE 1i92A 85 :AVRLLVVDPEQDTR Number of specific fragments extracted= 4 number of extra gaps= 1 total=101 Number of alignments=24 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1bfeA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1bfeA expands to /projects/compbio/data/pdb/1bfe.pdb.gz 1bfeA:# T0366 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 Warning: unaligning (T0366)F6 because first residue in template chain is (1bfeA)D306 T0366 7 :QSMGLRTVEMKKG 1bfeA 307 :IPREPRRIVIHRG T0366 21 :TDSLGISIAGGVG 1bfeA 320 :STGLGFNIIGGED T0366 38 :DVPIFIAMMHPTGVAAQTQKLRVGDRIVTICGTSTEGMTHTQAVNLLKNASGSIEMQVVAG 1bfeA 333 :GEGIFISFILAGGPADLSGELRKGDQILSVNGVDLRNASHEQAAIALKNAGQTVTIIAQYK Number of specific fragments extracted= 3 number of extra gaps= 0 total=104 Number of alignments=25 # 1bfeA read from 1bfeA/merged-good-all-a2m # found chain 1bfeA in template set Warning: unaligning (T0366)F6 because first residue in template chain is (1bfeA)D306 T0366 7 :QSMGLRTVEMKKG 1bfeA 307 :IPREPRRIVIHRG T0366 21 :TDSLGISIAGGV 1bfeA 320 :STGLGFNIIGGE T0366 37 :GDVPIFIAMMHPTGVAAQTQKLRVGDRIVTICGTSTEGMTHTQAVNLLKNASGSIEMQVVAG 1bfeA 332 :DGEGIFISFILAGGPADLSGELRKGDQILSVNGVDLRNASHEQAAIALKNAGQTVTIIAQYK Number of specific fragments extracted= 3 number of extra gaps= 0 total=107 Number of alignments=26 # 1bfeA read from 1bfeA/merged-good-all-a2m # found chain 1bfeA in template set Warning: unaligning (T0366)Q7 because first residue in template chain is (1bfeA)D306 T0366 8 :SMGLRTVEMKKGPTDSLGISIAGGVG 1bfeA 307 :IPREPRRIVIHRGSTGLGFNIIGGED T0366 38 :DVPIFIAMMHPTGVAAQTQKLRVGDRIVTICGTSTEGMTHTQAVNLLKNASGSIEMQVVAG 1bfeA 333 :GEGIFISFILAGGPADLSGELRKGDQILSVNGVDLRNASHEQAAIALKNAGQTVTIIAQYK Number of specific fragments extracted= 2 number of extra gaps= 0 total=109 Number of alignments=27 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1fc6A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0366 read from 1fc6A/merged-good-all-a2m # 1fc6A read from 1fc6A/merged-good-all-a2m # found chain 1fc6A in training set T0366 22 :DSLGISIAGGVGS 1fc6A 161 :TGVGLEITYDGGS T0366 38 :DVPIFIAMMHPTGVAAQTQ 1fc6A 174 :GKDVVVLTPAPGGPAEKAG T0366 58 :LRVGDRIVTICGTSTEGMTHTQAVNLL 1fc6A 193 :ARAGDVIVTVDGTAVKGMSLYDVSDLL T0366 87 :ASGSIEMQVVAGGD 1fc6A 223 :ADSQVEVVLHAPGA Number of specific fragments extracted= 4 number of extra gaps= 0 total=113 Number of alignments=28 # 1fc6A read from 1fc6A/merged-good-all-a2m # found chain 1fc6A in training set T0366 21 :TDSLGISIAGGVG 1fc6A 160 :VTGVGLEITYDGG T0366 37 :GDVPIFIAMMHPTGVAAQTQ 1fc6A 173 :SGKDVVVLTPAPGGPAEKAG T0366 58 :LRVGDRIVTICGTSTEGMTHTQAVNLL 1fc6A 193 :ARAGDVIVTVDGTAVKGMSLYDVSDLL T0366 86 :NASGSIEMQVVAGGDV 1fc6A 222 :EADSQVEVVLHAPGAP Number of specific fragments extracted= 4 number of extra gaps= 0 total=117 Number of alignments=29 # 1fc6A read from 1fc6A/merged-good-all-a2m # found chain 1fc6A in training set T0366 19 :GPTDSLGISIAGGVG 1fc6A 158 :GSVTGVGLEITYDGG T0366 37 :GDVPIFIAMMHPTGVAAQTQ 1fc6A 173 :SGKDVVVLTPAPGGPAEKAG T0366 58 :LRVGDRIVTICGTSTEGMTHTQAVNLL 1fc6A 193 :ARAGDVIVTVDGTAVKGMSLYDVSDLL T0366 85 :KNASGSIEMQVVA 1fc6A 221 :GEADSQVEVVLHA Number of specific fragments extracted= 4 number of extra gaps= 0 total=121 Number of alignments=30 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1gm1A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0366/1gm1A/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0366/1gm1A/merged-good-all-a2m.gz for input Trying 1gm1A/merged-good-all-a2m Error: Couldn't open file 1gm1A/merged-good-all-a2m or 1gm1A/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1kefA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0366/1kefA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0366/1kefA/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:# T0366 read from 1nf3C/merged-good-all-a2m # 1nf3C read from 1nf3C/merged-good-all-a2m # adding 1nf3C to template set # found chain 1nf3C in template set Warning: unaligning (T0366)S102 because last residue in template chain is (1nf3C)N253 T0366 3 :NLYFQSMGLRTVEMKK 1nf3C 147 :DVDILPETHRRVRLCK T0366 19 :GPTDSLGISIAGG 1nf3C 164 :GTEKPLGFYIRDG T0366 32 :VGSPLGD 1nf3C 180 :RVTPHGL T0366 39 :VPIFIAMMHPTGVAAQTQKLRVGDRIVTICGTSTEGMTHTQAVNLLKNASGSIEMQVVAGGDV 1nf3C 190 :PGIFISRLVPGGLAQSTGLLAVNDEVLEVNGIEVSGKSLDQVTDMMIANSRNLIITVRPANQR Number of specific fragments extracted= 4 number of extra gaps= 0 total=125 Number of alignments=31 # 1nf3C read from 1nf3C/merged-good-all-a2m # found chain 1nf3C in template set Warning: unaligning (T0366)S102 because last residue in template chain is (1nf3C)N253 T0366 3 :NLYFQSMGLRTVEMKK 1nf3C 147 :DVDILPETHRRVRLCK T0366 19 :GPTDSLGISIAGGV 1nf3C 164 :GTEKPLGFYIRDGS T0366 33 :GSPLGDV 1nf3C 181 :VTPHGLE T0366 40 :PIFIAMMHPTGVAAQTQKLRVGDRIVTICGTSTEGMTHTQAVNLLKNASGSIEMQVVAGGDV 1nf3C 191 :GIFISRLVPGGLAQSTGLLAVNDEVLEVNGIEVSGKSLDQVTDMMIANSRNLIITVRPANQR Number of specific fragments extracted= 4 number of extra gaps= 0 total=129 Number of alignments=32 # 1nf3C read from 1nf3C/merged-good-all-a2m # found chain 1nf3C in template set Warning: unaligning (T0366)S102 because last residue in template chain is (1nf3C)N253 T0366 7 :QSMGLRTVEMKK 1nf3C 151 :LPETHRRVRLCK T0366 19 :GPTDSLGISIAGGVG 1nf3C 164 :GTEKPLGFYIRDGSS T0366 34 :SPLGD 1nf3C 182 :TPHGL T0366 39 :VPIFIAMMHPTGVAAQTQKLRVGDRIVTICGTSTEGMTHTQAVNLLKNASGSIEMQVVAGGDV 1nf3C 190 :PGIFISRLVPGGLAQSTGLLAVNDEVLEVNGIEVSGKSLDQVTDMMIANSRNLIITVRPANQR Number of specific fragments extracted= 4 number of extra gaps= 0 total=133 Number of alignments=33 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1wf7A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1wf7A expands to /projects/compbio/data/pdb/1wf7.pdb.gz 1wf7A:# T0366 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 T0366 7 :QSMGLRTVEMKK 1wf7A 2 :SSGSSGSVSLVG T0366 21 :TDSLGISIAGGVGS 1wf7A 14 :PAPWGFRLQGGKDF T0366 38 :DVPIFIAMMHPTGVAAQTQ 1wf7A 28 :NMPLTISSLKDGGKASQAH T0366 58 :LRVGDRIVTICGTSTEGMTHTQAVNLLKNASGSIEMQVVAGGDVSE 1wf7A 47 :VRIGDVVLSIDGISAQGMTHLEAQNKIKACTGSLNMTLQRASAAAK T0366 105 :SV 1wf7A 94 :EP Number of specific fragments extracted= 5 number of extra gaps= 0 total=138 Number of alignments=34 # 1wf7A read from 1wf7A/merged-good-all-a2m # found chain 1wf7A in template set T0366 7 :QSMGLRTVEMKK 1wf7A 2 :SSGSSGSVSLVG T0366 21 :TDSLGISIAGGVG 1wf7A 14 :PAPWGFRLQGGKD T0366 37 :GDVPIFIAMMHPTGVAAQTQ 1wf7A 27 :FNMPLTISSLKDGGKASQAH T0366 58 :LRVGDRIVTICGTSTEGMTHTQAVNLLKNASGSIEMQVVAGGDVS 1wf7A 47 :VRIGDVVLSIDGISAQGMTHLEAQNKIKACTGSLNMTLQRASAAA T0366 103 :ET 1wf7A 95 :PV Number of specific fragments extracted= 5 number of extra gaps= 0 total=143 Number of alignments=35 # 1wf7A read from 1wf7A/merged-good-all-a2m # found chain 1wf7A in template set T0366 12 :RTVEMKKGPTDSLGISIAGGVG 1wf7A 5 :SSGSVSLVGPAPWGFRLQGGKD T0366 37 :GDVPIFIAMMHPTGVAAQTQ 1wf7A 27 :FNMPLTISSLKDGGKASQAH T0366 58 :LRVGDRIVTICGTSTEGMTHTQAVNLLKNASGSIEMQVVAGGDVSETSV 1wf7A 47 :VRIGDVVLSIDGISAQGMTHLEAQNKIKACTGSLNMTLQRASAAAKSEP Number of specific fragments extracted= 3 number of extra gaps= 0 total=146 Number of alignments=36 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1um7A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0366/1um7A/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0366/1um7A/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 # T0366 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 (T0366)G10 because first residue in template chain is (2f0aA)M251 Warning: unaligning (T0366)D22 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2f0aA)N263 Warning: unaligning (T0366)G99 because last residue in template chain is (2f0aA)E342 T0366 11 :LRTVEMK 2f0aA 252 :IITVTLN T0366 23 :SLGISIAGG 2f0aA 264 :FLGISIVGQ T0366 33 :GSPLGDVPIFIAMMHPTGVAAQTQKLRVGDRIVTICGTSTEGMTHTQAVNLLKNA 2f0aA 273 :SNERGDGGIYIGSIMKGGAVAADGRIEPGDMLLQVNDINFENMSNDDAVRVLRDI T0366 88 :SGSIEMQVVAG 2f0aA 331 :PGPIVLTVAKL Number of specific fragments extracted= 4 number of extra gaps= 1 total=150 Number of alignments=37 # 2f0aA read from 2f0aA/merged-good-all-a2m # found chain 2f0aA in template set Warning: unaligning (T0366)G10 because first residue in template chain is (2f0aA)M251 Warning: unaligning (T0366)D22 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2f0aA)N263 Warning: unaligning (T0366)G99 because last residue in template chain is (2f0aA)E342 T0366 11 :LRTVEMK 2f0aA 252 :IITVTLN T0366 23 :SLGISIAG 2f0aA 264 :FLGISIVG T0366 32 :VGSPLGDVPIFIAMMHPTGVAAQTQKLRVGDRIVTICGTSTEGMTHTQAVNLLKNA 2f0aA 272 :QSNERGDGGIYIGSIMKGGAVAADGRIEPGDMLLQVNDINFENMSNDDAVRVLRDI T0366 88 :SGSIEMQVVAG 2f0aA 331 :PGPIVLTVAKL Number of specific fragments extracted= 4 number of extra gaps= 1 total=154 Number of alignments=38 # 2f0aA read from 2f0aA/merged-good-all-a2m # found chain 2f0aA in template set Warning: unaligning (T0366)D22 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2f0aA)N263 Warning: unaligning (T0366)G99 because last residue in template chain is (2f0aA)E342 T0366 23 :SLGISIAGGVG 2f0aA 264 :FLGISIVGQSN T0366 35 :PLGDVPIFIAMMHPTGVAAQTQKLRVGDRIVTICGTSTEGMTHTQAVNLLKNA 2f0aA 275 :ERGDGGIYIGSIMKGGAVAADGRIEPGDMLLQVNDINFENMSNDDAVRVLRDI T0366 88 :SGSIEMQVVAG 2f0aA 331 :PGPIVLTVAKL Number of specific fragments extracted= 3 number of extra gaps= 1 total=157 Number of alignments=39 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1n7eA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1n7eA expands to /projects/compbio/data/pdb/1n7e.pdb.gz 1n7eA:# T0366 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 (T0366)S8 because first residue in template chain is (1n7eA)G667 T0366 9 :MGLRTVEMKKG 1n7eA 668 :AIIYTVELKRY T0366 21 :TDSLGISIAGGVGS 1n7eA 679 :GGPLGITISGTEEP T0366 38 :DVPIFIAMMHPTGVAAQTQKLRVGDRIVTICGTSTEGMTHTQAVNLLKNASGSIEMQVVAGGDVSETSV 1n7eA 693 :FDPIIISSLTKGGLAERTGAIHIGDRILAINSSSLKGKPLSEAIHLLQMAGETVTLKIKKQTDAQPASS Number of specific fragments extracted= 3 number of extra gaps= 0 total=160 Number of alignments=40 # 1n7eA read from 1n7eA/merged-good-all-a2m # found chain 1n7eA in template set Warning: unaligning (T0366)S8 because first residue in template chain is (1n7eA)G667 T0366 9 :MGLRTVEMKKG 1n7eA 668 :AIIYTVELKRY T0366 21 :TDSLGISIAGGVG 1n7eA 679 :GGPLGITISGTEE T0366 37 :GDVPIFIAMMHPTGVAAQTQKLRVGDRIVTICGTSTEGMTHTQAVNLLKNASGSIEMQVVAGGDVSETSV 1n7eA 692 :PFDPIIISSLTKGGLAERTGAIHIGDRILAINSSSLKGKPLSEAIHLLQMAGETVTLKIKKQTDAQPASS Number of specific fragments extracted= 3 number of extra gaps= 0 total=163 Number of alignments=41 # 1n7eA read from 1n7eA/merged-good-all-a2m # found chain 1n7eA in template set Warning: unaligning (T0366)M9 because first residue in template chain is (1n7eA)G667 T0366 10 :GLRTVEMKKGPTDSLGISIAGGVG 1n7eA 668 :AIIYTVELKRYGGPLGITISGTEE T0366 37 :GDVPIFIAMMHPTGVAAQTQKLRVGDRIVTICGTSTEGMTHTQAVNLLKNASGSIEMQVVAGGDVSETSV 1n7eA 692 :PFDPIIISSLTKGGLAERTGAIHIGDRILAINSSSLKGKPLSEAIHLLQMAGETVTLKIKKQTDAQPASS Number of specific fragments extracted= 2 number of extra gaps= 0 total=165 Number of alignments=42 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ky9A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1ky9A expands to /projects/compbio/data/pdb/1ky9.pdb.gz 1ky9A:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0366 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 T0366 34 :SPL 1ky9A 282 :VDA T0366 38 :DVPIFIAMMHPTGVAAQTQ 1ky9A 285 :QRGAFVSQVLPNSSAAKAG T0366 58 :LRVGDRIVTICGTSTEGM 1ky9A 304 :IKAGDVITSLNGKPISSF T0366 78 :TQAVNLLKNA 1ky9A 322 :AALRAQVGTM T0366 88 :SGSIEMQVVAGGDVSETSV 1ky9A 334 :GSKLTLGLLRDGKQVNVNL Number of specific fragments extracted= 5 number of extra gaps= 0 total=170 Number of alignments=43 # 1ky9A read from 1ky9A/merged-good-all-a2m # found chain 1ky9A in template set T0366 38 :DVPIFIAMMHPTGVAAQTQ 1ky9A 285 :QRGAFVSQVLPNSSAAKAG T0366 58 :LRVGDRIVTICGTSTEGM 1ky9A 304 :IKAGDVITSLNGKPISSF T0366 78 :TQAVNLLKNA 1ky9A 322 :AALRAQVGTM T0366 88 :SGSIEMQVVAGGDVS 1ky9A 334 :GSKLTLGLLRDGKQV T0366 105 :S 1ky9A 351 :N Number of specific fragments extracted= 5 number of extra gaps= 0 total=175 Number of alignments=44 # 1ky9A read from 1ky9A/merged-good-all-a2m # found chain 1ky9A in template set T0366 37 :GDVPIFIAMMHPTGVAAQTQ 1ky9A 284 :AQRGAFVSQVLPNSSAAKAG T0366 58 :LRVGDRIVTICGTSTEG 1ky9A 304 :IKAGDVITSLNGKPISS T0366 77 :HTQAVNLLKNA 1ky9A 321 :FAALRAQVGTM T0366 88 :SGSIEMQVVAGGD 1ky9A 334 :GSKLTLGLLRDGK Number of specific fragments extracted= 4 number of extra gaps= 0 total=179 Number of alignments=45 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ky9B/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1ky9B expands to /projects/compbio/data/pdb/1ky9.pdb.gz 1ky9B:# T0366 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 (T0366)N86 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ky9B)P332 T0366 35 :PL 1ky9B 273 :NS T0366 37 :GDVPIFIAMMHPTGVAAQTQ 1ky9B 284 :AQRGAFVSQVLPNSSAAKAG T0366 58 :LRVGDRIVTICGTSTEG 1ky9B 304 :IKAGDVITSLNGKPISS T0366 77 :HTQAVNLLK 1ky9B 321 :FAALRAQVG T0366 88 :SGSIEMQVVAGGDVSETS 1ky9B 334 :GSKLTLGLLRDGKQVNVN Number of specific fragments extracted= 5 number of extra gaps= 0 total=184 Number of alignments=46 # 1ky9B read from 1ky9B/merged-good-all-a2m # found chain 1ky9B in template set Warning: unaligning (T0366)I28 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ky9B)G269 Warning: unaligning (T0366)G30 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ky9B)G269 Warning: unaligning (T0366)N86 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ky9B)P332 T0366 24 :L 1ky9B 265 :L T0366 27 :S 1ky9B 266 :G T0366 38 :DVPIFIAMMHPTGVAAQTQ 1ky9B 285 :QRGAFVSQVLPNSSAAKAG T0366 58 :LRVGDRIVTICGTSTEG 1ky9B 304 :IKAGDVITSLNGKPISS T0366 77 :HTQAVNLLK 1ky9B 321 :FAALRAQVG T0366 88 :SGSIEMQVVAGGDVSETS 1ky9B 334 :GSKLTLGLLRDGKQVNVN Number of specific fragments extracted= 6 number of extra gaps= 0 total=190 Number of alignments=47 # 1ky9B read from 1ky9B/merged-good-all-a2m # found chain 1ky9B in template set Warning: unaligning (T0366)N86 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ky9B)P332 T0366 37 :GDVPIFIAMMHPTGVAAQTQ 1ky9B 284 :AQRGAFVSQVLPNSSAAKAG T0366 58 :LRVGDRIVTICGTSTEG 1ky9B 304 :IKAGDVITSLNGKPISS T0366 77 :HTQAVNLLK 1ky9B 321 :FAALRAQVG T0366 87 :ASGSIEMQVVAGGDVSETS 1ky9B 333 :VGSKLTLGLLRDGKQVNVN Number of specific fragments extracted= 4 number of extra gaps= 0 total=194 Number of alignments=48 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1zokA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0366/1zokA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0366/1zokA/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 # T0366 read from 1mfgA/merged-good-all-a2m # 1mfgA read from 1mfgA/merged-good-all-a2m # found chain 1mfgA in training set Warning: unaligning (T0366)S8 because first residue in template chain is (1mfgA)G1277 Warning: unaligning (T0366)G89 because of BadResidue code BAD_PEPTIDE in next template residue (1mfgA)T1360 Warning: unaligning (T0366)S90 because of BadResidue code BAD_PEPTIDE at template residue (1mfgA)T1360 Warning: unaligning (T0366)M93 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (1mfgA)I1364 Warning: unaligning (T0366)Q94 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (1mfgA)I1364 Warning: unaligning (T0366)V101 because last residue in template chain is (1mfgA)S1371 T0366 9 :MGLRTVEMKKG 1mfgA 1278 :SMEIRVRVEKD T0366 22 :DSLGISIAGGVGSPL 1mfgA 1289 :PELGFSISGGVGGRG T0366 37 :GDVPIFIAMMHPTGVAA 1mfgA 1309 :DDDGIFVTRVQPEGPAS T0366 56 :QKLRVGDRIVTICGTSTEGMTHTQAVNLLKNAS 1mfgA 1326 :KLLQPGDKIIQANGYSFINIEHGQAVSLLKTFQ T0366 91 :IE 1mfgA 1361 :VE T0366 95 :VVAGGD 1mfgA 1365 :IVREVS Number of specific fragments extracted= 6 number of extra gaps= 2 total=200 Number of alignments=49 # 1mfgA read from 1mfgA/merged-good-all-a2m # found chain 1mfgA in training set Warning: unaligning (T0366)G89 because of BadResidue code BAD_PEPTIDE in next template residue (1mfgA)T1360 Warning: unaligning (T0366)S90 because of BadResidue code BAD_PEPTIDE at template residue (1mfgA)T1360 Warning: unaligning (T0366)M93 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (1mfgA)I1364 Warning: unaligning (T0366)Q94 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (1mfgA)I1364 Warning: unaligning (T0366)V101 because last residue in template chain is (1mfgA)S1371 T0366 9 :MGLRTVEMKKG 1mfgA 1278 :SMEIRVRVEKD T0366 22 :DSLGISIAGGV 1mfgA 1289 :PELGFSISGGV T0366 33 :GSPLGDVPIFIAMMHPTGVAA 1mfgA 1305 :PFRPDDDGIFVTRVQPEGPAS T0366 56 :QKLRVGDRIVTICGTSTEGMTHTQAVNLLKNAS 1mfgA 1326 :KLLQPGDKIIQANGYSFINIEHGQAVSLLKTFQ T0366 91 :IE 1mfgA 1361 :VE T0366 95 :VVAGGD 1mfgA 1365 :IVREVS Number of specific fragments extracted= 6 number of extra gaps= 2 total=206 Number of alignments=50 # 1mfgA read from 1mfgA/merged-good-all-a2m # found chain 1mfgA in training set Warning: unaligning (T0366)G10 because first residue in template chain is (1mfgA)G1277 Warning: unaligning (T0366)G89 because of BadResidue code BAD_PEPTIDE in next template residue (1mfgA)T1360 Warning: unaligning (T0366)S90 because of BadResidue code BAD_PEPTIDE at template residue (1mfgA)T1360 Warning: unaligning (T0366)M93 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (1mfgA)I1364 Warning: unaligning (T0366)Q94 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (1mfgA)I1364 T0366 11 :LRTVEMKKGPTDSLGISIAGGVGSPL 1mfgA 1278 :SMEIRVRVEKDPELGFSISGGVGGRG T0366 37 :GDVPIFIAMMHPTGVA 1mfgA 1309 :DDDGIFVTRVQPEGPA T0366 55 :TQKLRVGDRIVTICGTSTEGMTHTQAVNLLKNAS 1mfgA 1325 :SKLLQPGDKIIQANGYSFINIEHGQAVSLLKTFQ T0366 91 :IE 1mfgA 1361 :VE T0366 95 :VVAGGD 1mfgA 1365 :IVREVS Number of specific fragments extracted= 5 number of extra gaps= 2 total=211 Number of alignments=51 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1b8qA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1b8qA expands to /projects/compbio/data/pdb/1b8q.pdb.gz 1b8qA:# T0366 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 T0366 4 :LYFQSMGLRTVEMKKGPTDSLGISIAGGVG 1b8qA 2 :SHMIEPNVISVRLFKRKVGGLGFLVKERVS T0366 38 :DVPIFIAMMHPTGVAAQTQKLRVGDRIVTICGTSTEGMTHTQAVNLLKNA 1b8qA 32 :KPPVIISDLIRGGAAEQSGLIQAGDIILAVNDRPLVDLSYDSALEVLRGI T0366 88 :SGSIEMQVVAGGDVSE 1b8qA 84 :ETHVVLILRGPEGFTT Number of specific fragments extracted= 3 number of extra gaps= 0 total=214 Number of alignments=52 # 1b8qA read from 1b8qA/merged-good-all-a2m # found chain 1b8qA in template set Warning: unaligning (T0366)N3 because first residue in template chain is (1b8qA)G1 T0366 4 :LYFQSMGLRTVEMKKGPTDSLGISIAGGV 1b8qA 2 :SHMIEPNVISVRLFKRKVGGLGFLVKERV T0366 37 :GDVPIFIAMMHPTGVAAQTQKLRVGDRIVTICGTSTEGMTHTQAVNLLKNA 1b8qA 31 :SKPPVIISDLIRGGAAEQSGLIQAGDIILAVNDRPLVDLSYDSALEVLRGI T0366 88 :SGSIEMQVVAGGDVS 1b8qA 84 :ETHVVLILRGPEGFT T0366 103 :ETSV 1b8qA 100 :HLET Number of specific fragments extracted= 4 number of extra gaps= 0 total=218 Number of alignments=53 # 1b8qA read from 1b8qA/merged-good-all-a2m # found chain 1b8qA in template set T0366 10 :GLRTVEMKKGPTDSLGISIAGGVG 1b8qA 8 :NVISVRLFKRKVGGLGFLVKERVS T0366 38 :DVPIFIAMMHPTGVAAQTQKLRVGDRIVTICGTSTEGMTHTQAVNLLKNASGSIEMQVVAGGDV 1b8qA 32 :KPPVIISDLIRGGAAEQSGLIQAGDIILAVNDRPLVDLSYDSALEVLRGIASETHVVLILRGPE Number of specific fragments extracted= 2 number of extra gaps= 0 total=220 Number of alignments=54 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1nteA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1nteA expands to /projects/compbio/data/pdb/1nte.pdb.gz 1nteA:Skipped atom 107, because occupancy 0.500 <= existing 0.500 in 1nteA Skipped atom 281, because occupancy 0.400 <= existing 0.600 in 1nteA Skipped atom 283, because occupancy 0.400 <= existing 0.600 in 1nteA Skipped atom 285, because occupancy 0.400 <= existing 0.600 in 1nteA Skipped atom 287, because occupancy 0.400 <= existing 0.600 in 1nteA Skipped atom 289, because occupancy 0.400 <= existing 0.600 in 1nteA Skipped atom 291, because occupancy 0.400 <= existing 0.600 in 1nteA Skipped atom 332, because occupancy 0.500 <= existing 0.500 in 1nteA Skipped atom 334, because occupancy 0.500 <= existing 0.500 in 1nteA Skipped atom 336, because occupancy 0.500 <= existing 0.500 in 1nteA Skipped atom 338, because occupancy 0.500 <= existing 0.500 in 1nteA Skipped atom 340, because occupancy 0.500 <= existing 0.500 in 1nteA Skipped atom 373, because occupancy 0.500 <= existing 0.500 in 1nteA Skipped atom 595, because occupancy 0.300 <= existing 0.700 in 1nteA Skipped atom 597, because occupancy 0.300 <= existing 0.700 in 1nteA Skipped atom 599, because occupancy 0.300 <= existing 0.700 in 1nteA Skipped atom 601, because occupancy 0.300 <= existing 0.700 in 1nteA # T0366 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 (T0366)Q7 because first residue in template chain is (1nteA)G192 Warning: unaligning (T0366)M9 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1nteA)D195 Warning: unaligning (T0366)G10 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1nteA)D195 T0366 8 :S 1nteA 193 :A T0366 11 :LRTVEMKKGPTDSLGISIAGG 1nteA 196 :PRTITMHKDSTGHVGFIFKNG T0366 42 :FIAMMHPTGVAAQTQ 1nteA 217 :KITSIVKDSSAARNG T0366 58 :LRVGDRIVTICGTSTEGMTHTQAVNLLKNASGSIEMQVVAG 1nteA 232 :LLTEHNICEINGQNVIGLKDSQIADILSTSGTVVTITIMPA Number of specific fragments extracted= 4 number of extra gaps= 1 total=224 Number of alignments=55 # 1nteA read from 1nteA/merged-good-all-a2m # found chain 1nteA in template set Warning: unaligning (T0366)Q7 because first residue in template chain is (1nteA)G192 Warning: unaligning (T0366)M9 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1nteA)D195 Warning: unaligning (T0366)G10 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1nteA)D195 T0366 8 :S 1nteA 193 :A T0366 11 :LRTVEMKKGPTDSLGISIAGG 1nteA 196 :PRTITMHKDSTGHVGFIFKNG T0366 42 :FIAMMHPTGVAAQTQ 1nteA 217 :KITSIVKDSSAARNG T0366 58 :LRVGDRIVTICGTSTEGMTHTQAVNLLKNASGSIEMQVVAG 1nteA 232 :LLTEHNICEINGQNVIGLKDSQIADILSTSGTVVTITIMPA Number of specific fragments extracted= 4 number of extra gaps= 1 total=228 Number of alignments=56 # 1nteA read from 1nteA/merged-good-all-a2m # found chain 1nteA in template set Warning: unaligning (T0366)M9 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1nteA)D195 Warning: unaligning (T0366)G10 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1nteA)D195 T0366 11 :LRTVEMKKGPTDSLGISIAGG 1nteA 196 :PRTITMHKDSTGHVGFIFKNG T0366 42 :FIAMMHPTGVAAQTQ 1nteA 217 :KITSIVKDSSAARNG T0366 58 :LRVGDRIVTICGTSTEGMTHTQAVNLLKNASGSIEMQVVAG 1nteA 232 :LLTEHNICEINGQNVIGLKDSQIADILSTSGTVVTITIMPA Number of specific fragments extracted= 3 number of extra gaps= 1 total=231 Number of alignments=57 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2fe5A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2fe5A expands to /projects/compbio/data/pdb/2fe5.pdb.gz 2fe5A:Skipped atom 9, because occupancy 0.300 <= existing 0.700 in 2fe5A Skipped atom 13, because occupancy 0.300 <= existing 0.700 in 2fe5A Skipped atom 15, because occupancy 0.300 <= existing 0.700 in 2fe5A Skipped atom 17, because occupancy 0.300 <= existing 0.700 in 2fe5A Skipped atom 19, because occupancy 0.300 <= existing 0.700 in 2fe5A Skipped atom 42, because occupancy 0.500 <= existing 0.500 in 2fe5A Skipped atom 44, because occupancy 0.500 <= existing 0.500 in 2fe5A Skipped atom 47, because occupancy 0.300 <= existing 0.700 in 2fe5A Skipped atom 51, because occupancy 0.300 <= existing 0.700 in 2fe5A Skipped atom 53, because occupancy 0.300 <= existing 0.700 in 2fe5A Skipped atom 55, because occupancy 0.300 <= existing 0.700 in 2fe5A Skipped atom 57, because occupancy 0.300 <= existing 0.700 in 2fe5A Skipped atom 59, because occupancy 0.300 <= existing 0.700 in 2fe5A Skipped atom 294, because occupancy 0.400 <= existing 0.600 in 2fe5A Skipped atom 296, because occupancy 0.400 <= existing 0.600 in 2fe5A Skipped atom 298, because occupancy 0.400 <= existing 0.600 in 2fe5A Skipped atom 300, because occupancy 0.400 <= existing 0.600 in 2fe5A Skipped atom 302, because occupancy 0.400 <= existing 0.600 in 2fe5A Skipped atom 317, because occupancy 0.300 <= existing 0.700 in 2fe5A Skipped atom 320, because occupancy 0.300 <= existing 0.700 in 2fe5A Skipped atom 431, because occupancy 0.300 <= existing 0.700 in 2fe5A Skipped atom 433, because occupancy 0.300 <= existing 0.700 in 2fe5A Skipped atom 435, because occupancy 0.300 <= existing 0.700 in 2fe5A Skipped atom 437, because occupancy 0.300 <= existing 0.700 in 2fe5A Skipped atom 439, because occupancy 0.300 <= existing 0.700 in 2fe5A Skipped atom 441, because occupancy 0.300 <= existing 0.700 in 2fe5A Skipped atom 443, because occupancy 0.300 <= existing 0.700 in 2fe5A Skipped atom 593, because occupancy 0.250 <= existing 0.750 in 2fe5A Skipped atom 597, because occupancy 0.250 <= existing 0.750 in 2fe5A Skipped atom 599, because occupancy 0.250 <= existing 0.750 in 2fe5A Skipped atom 618, because occupancy 0.500 <= existing 0.500 in 2fe5A Skipped atom 620, because occupancy 0.500 <= existing 0.500 in 2fe5A Skipped atom 622, because occupancy 0.500 <= existing 0.500 in 2fe5A Skipped atom 624, because occupancy 0.500 <= existing 0.500 in 2fe5A Skipped atom 626, because occupancy 0.500 <= existing 0.500 in 2fe5A Skipped atom 628, because occupancy 0.500 <= existing 0.500 in 2fe5A Skipped atom 630, because occupancy 0.500 <= existing 0.500 in 2fe5A Skipped atom 632, because occupancy 0.500 <= existing 0.500 in 2fe5A Skipped atom 634, because occupancy 0.500 <= existing 0.500 in 2fe5A Skipped atom 636, because occupancy 0.500 <= existing 0.500 in 2fe5A Skipped atom 638, because occupancy 0.500 <= existing 0.500 in 2fe5A Skipped atom 640, because occupancy 0.500 <= existing 0.500 in 2fe5A Skipped atom 642, because occupancy 0.500 <= existing 0.500 in 2fe5A Skipped atom 644, because occupancy 0.500 <= existing 0.500 in 2fe5A Skipped atom 646, because occupancy 0.500 <= existing 0.500 in 2fe5A Skipped atom 648, because occupancy 0.500 <= existing 0.500 in 2fe5A Skipped atom 650, because occupancy 0.500 <= existing 0.500 in 2fe5A Skipped atom 652, because occupancy 0.500 <= existing 0.500 in 2fe5A Skipped atom 654, because occupancy 0.500 <= existing 0.500 in 2fe5A Skipped atom 656, because occupancy 0.500 <= existing 0.500 in 2fe5A Skipped atom 658, because occupancy 0.500 <= existing 0.500 in 2fe5A Skipped atom 660, because occupancy 0.500 <= existing 0.500 in 2fe5A Skipped atom 662, because occupancy 0.500 <= existing 0.500 in 2fe5A # T0366 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 (T0366)S8 because first residue in template chain is (2fe5A)S221 T0366 9 :MGLRTVEMKKG 2fe5A 222 :MTIMEVNLLKG T0366 21 :TDSLGISIAGGVG 2fe5A 233 :PKGLGFSIAGGIG T0366 34 :SPLGDVPIFIAMMHPTGVAAQTQKLRVGDRIVTICGTSTEGMTHTQAVNLLKNASGSIEMQVVAGG 2fe5A 248 :HIPGDNSIYITKIIEGGAAQKDGRLQIGDRLLAVNNTNLQDVRHEEAVASLKNTSDMVYLKVAKPG Number of specific fragments extracted= 3 number of extra gaps= 0 total=234 Number of alignments=58 # 2fe5A read from 2fe5A/merged-good-all-a2m # found chain 2fe5A in template set Warning: unaligning (T0366)S8 because first residue in template chain is (2fe5A)S221 T0366 9 :MGLRTVEMKKG 2fe5A 222 :MTIMEVNLLKG T0366 21 :TDSLGISIAGGVG 2fe5A 233 :PKGLGFSIAGGIG T0366 34 :SPLGDVPIFIAMMHPTGVAAQTQKLRVGDRIVTICGTSTEGMTHTQAVNLLKNASGSIEMQVVAGG 2fe5A 248 :HIPGDNSIYITKIIEGGAAQKDGRLQIGDRLLAVNNTNLQDVRHEEAVASLKNTSDMVYLKVAKPG Number of specific fragments extracted= 3 number of extra gaps= 0 total=237 Number of alignments=59 # 2fe5A read from 2fe5A/merged-good-all-a2m # found chain 2fe5A in template set T0366 11 :LRTVEMKKGPTDSLGISIAGGVGSPL 2fe5A 223 :TIMEVNLLKGPKGLGFSIAGGIGNQH T0366 37 :GDVPIFIAMMHPTGVAAQTQKLRVGDRIVTICGTSTEGMTHTQAVNLLKNASGSIEMQVVAGG 2fe5A 251 :GDNSIYITKIIEGGAAQKDGRLQIGDRLLAVNNTNLQDVRHEEAVASLKNTSDMVYLKVAKPG Number of specific fragments extracted= 2 number of extra gaps= 0 total=239 Number of alignments=60 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1r6jA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0366 read from 1r6jA/merged-good-all-a2m # 1r6jA read from 1r6jA/merged-good-all-a2m # found chain 1r6jA in training set Warning: unaligning (T0366)Q7 because first residue in template chain is (1r6jA)G192 T0366 8 :SMGLRTVEMKKGPTDSLGISIAGG 1r6jA 193 :AMDPRTITMHKDSTGHVGFIFKNG T0366 42 :FIAMMHPTGVAAQTQ 1r6jA 217 :KITSIVKDSSAARNG T0366 58 :LRVGDRIVTICGTSTEGMTHTQAVNLLKNASGSIEMQVVAG 1r6jA 232 :LLTEHNICEINGQNVIGLKDSQIADILSTSGTVVTITIMPA Number of specific fragments extracted= 3 number of extra gaps= 0 total=242 Number of alignments=61 # 1r6jA read from 1r6jA/merged-good-all-a2m # found chain 1r6jA in training set Warning: unaligning (T0366)Q7 because first residue in template chain is (1r6jA)G192 T0366 8 :SMGLRTVEMKKGPTDSLGISIAGG 1r6jA 193 :AMDPRTITMHKDSTGHVGFIFKNG T0366 42 :FIAMMHPTGVAAQTQ 1r6jA 217 :KITSIVKDSSAARNG T0366 58 :LRVGDRIVTICGTSTEGMTHTQAVNLLKNASGSIEMQVVA 1r6jA 232 :LLTEHNICEINGQNVIGLKDSQIADILSTSGTVVTITIMP Number of specific fragments extracted= 3 number of extra gaps= 0 total=245 Number of alignments=62 # 1r6jA read from 1r6jA/merged-good-all-a2m # found chain 1r6jA in training set T0366 9 :MGLRTVEMKKGPTDSLGISIAGG 1r6jA 194 :MDPRTITMHKDSTGHVGFIFKNG T0366 42 :FIAMMHPTGVAAQTQ 1r6jA 217 :KITSIVKDSSAARNG T0366 58 :LRVGDRIVTICGTSTEGMTHTQAVNLLKNASGSIEMQVVA 1r6jA 232 :LLTEHNICEINGQNVIGLKDSQIADILSTSGTVVTITIMP Number of specific fragments extracted= 3 number of extra gaps= 0 total=248 Number of alignments=63 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1qavA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1qavA expands to /projects/compbio/data/pdb/1qav.pdb.gz 1qavA:# T0366 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 T0366 8 :SMGLRTVEMKKGPTDSLGISIAGGVGS 1qavA 76 :SLQRRRVTVRKADAGGLGISIKGGREN T0366 38 :DVPIFIAMMHPTGVAAQTQKLRVGDRIVTICGTSTEGMTHTQAVNLLKNASGSIEMQVVA 1qavA 103 :KMPILISKIFKGLAADQTEALFVGDAILSVNGEDLSSATHDEAVQALKKTGKEVVLEVKY Number of specific fragments extracted= 2 number of extra gaps= 0 total=250 Number of alignments=64 # 1qavA read from 1qavA/merged-good-all-a2m # found chain 1qavA in template set T0366 8 :SMGLRTVEMKKGPTDSLGISIAGGVG 1qavA 76 :SLQRRRVTVRKADAGGLGISIKGGRE T0366 37 :GDVPIFIAMMHPTGVAAQTQKLRVGDRIVTICGTSTEGMTHTQAVNLLKNASGSIEMQVVA 1qavA 102 :NKMPILISKIFKGLAADQTEALFVGDAILSVNGEDLSSATHDEAVQALKKTGKEVVLEVKY Number of specific fragments extracted= 2 number of extra gaps= 0 total=252 Number of alignments=65 # 1qavA read from 1qavA/merged-good-all-a2m # found chain 1qavA in template set T0366 8 :SMGLRTVEMKKGPTDSLGISIAGGVG 1qavA 76 :SLQRRRVTVRKADAGGLGISIKGGRE T0366 37 :GDVPIFIAMMHPTGVAAQTQKLRVGDRIVTICGTSTEGMTHTQAVNLLKNASGSIEMQVVA 1qavA 102 :NKMPILISKIFKGLAADQTEALFVGDAILSVNGEDLSSATHDEAVQALKKTGKEVVLEVKY Number of specific fragments extracted= 2 number of extra gaps= 0 total=254 Number of alignments=66 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1qavB/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1qavB expands to /projects/compbio/data/pdb/1qav.pdb.gz 1qavB:# T0366 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 T0366 9 :MGLRTVEMKKGPTDSLGISIAGGVG 1qavB 1013 :PNVISVRLFKRKVGGLGFLVKERVS T0366 38 :DVPIFIAMMHPTGVAAQTQKLRVGDRIVTICGTSTEGMTHTQAVNLLKNA 1qavB 1038 :KPPVIISDLIRGGAAEQSGLIQAGDIILAVNDRPLVDLSYDSALEVLRGI T0366 88 :SGSIEMQVVAGGDVS 1qavB 1090 :ETHVVLILRGPEGFT Number of specific fragments extracted= 3 number of extra gaps= 0 total=257 Number of alignments=67 # 1qavB read from 1qavB/merged-good-all-a2m # found chain 1qavB in template set T0366 9 :MGLRTVEMKKGPTDSLGISIAGGV 1qavB 1013 :PNVISVRLFKRKVGGLGFLVKERV T0366 37 :GDVPIFIAMMHPTGVAAQTQKLRVGDRIVTICGTSTEGMTHTQAVNLLKNA 1qavB 1037 :SKPPVIISDLIRGGAAEQSGLIQAGDIILAVNDRPLVDLSYDSALEVLRGI T0366 88 :SGSIEMQVVAGGDVS 1qavB 1090 :ETHVVLILRGPEGFT Number of specific fragments extracted= 3 number of extra gaps= 0 total=260 Number of alignments=68 # 1qavB read from 1qavB/merged-good-all-a2m # found chain 1qavB in template set T0366 10 :GLRTVEMKKGPTDSLGISIAGGVG 1qavB 1014 :NVISVRLFKRKVGGLGFLVKERVS T0366 38 :DVPIFIAMMHPTGVAAQTQKLRVGDRIVTICGTSTEGMTHTQAVNLLKNASGS 1qavB 1038 :KPPVIISDLIRGGAAEQSGLIQAGDIILAVNDRPLVDLSYDSALEVLRGIASE T0366 91 :IEMQVVAGGD 1qavB 1093 :VVLILRGPEG Number of specific fragments extracted= 3 number of extra gaps= 0 total=263 Number of alignments=69 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1m5zA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1m5zA expands to /projects/compbio/data/pdb/1m5z.pdb.gz 1m5zA:# T0366 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 (T0366)Y5 because first residue in template chain is (1m5zA)S16 T0366 6 :FQSMGLRTVEMKKGPT 1m5zA 17 :PTPVELHKVTLYKDSG T0366 22 :DSLGISIAGGVG 1m5zA 34 :EDFGFSVADGLL T0366 38 :DVPIFIAMMHPTGVAAQTQ 1m5zA 46 :EKGVYVKNIRPAGPGDLGG T0366 58 :LRVGDRIVTICGTSTEGMTHTQAVNLLKNASGSIEMQVVAG 1m5zA 65 :LKPYDRLLQVNHVRTRDFDCCLVVPLIAESGNKLDLVISRN Number of specific fragments extracted= 4 number of extra gaps= 0 total=267 Number of alignments=70 # 1m5zA read from 1m5zA/merged-good-all-a2m # found chain 1m5zA in template set Warning: unaligning (T0366)Y5 because first residue in template chain is (1m5zA)S16 T0366 6 :FQSMGLRTVEMKKGPT 1m5zA 17 :PTPVELHKVTLYKDSG T0366 22 :DSLGISIAGGV 1m5zA 34 :EDFGFSVADGL T0366 37 :GDVPIFIAMMHPTGVAAQTQ 1m5zA 45 :LEKGVYVKNIRPAGPGDLGG T0366 58 :LRVGDRIVTICGTSTEGMTHTQAVNLLKNASGSIEMQVVAG 1m5zA 65 :LKPYDRLLQVNHVRTRDFDCCLVVPLIAESGNKLDLVISRN Number of specific fragments extracted= 4 number of extra gaps= 0 total=271 Number of alignments=71 # 1m5zA read from 1m5zA/merged-good-all-a2m # found chain 1m5zA in template set T0366 11 :LRTVEMKKGPT 1m5zA 22 :LHKVTLYKDSG T0366 22 :DSLGISIAGGVG 1m5zA 34 :EDFGFSVADGLL T0366 38 :DVPIFIAMMHPTGVAAQTQ 1m5zA 46 :EKGVYVKNIRPAGPGDLGG T0366 58 :LRVGDRIVTICGTSTEGMTHTQAVNLLKNASGSIEMQVVAG 1m5zA 65 :LKPYDRLLQVNHVRTRDFDCCLVVPLIAESGNKLDLVISRN Number of specific fragments extracted= 4 number of extra gaps= 0 total=275 Number of alignments=72 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1be9A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1be9A expands to /projects/compbio/data/pdb/1be9.pdb.gz 1be9A:# T0366 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 T0366 1 :TENLYFQSMGLRTVEMKKG 1be9A 301 :FLGEEDIPREPRRIVIHRG T0366 21 :TDSLGISIAGGVG 1be9A 320 :STGLGFNIIGGED T0366 38 :DVPIFIAMMHPTGVAAQTQKLRVGDRIVTICGTSTEGMTHTQAVNLLKNASGSIEMQVVAG 1be9A 333 :GEGIFISFILAGGPADLSGELRKGDQILSVNGVDLRNASHEQAAIALKNAGQTVTIIAQYK Number of specific fragments extracted= 3 number of extra gaps= 0 total=278 Number of alignments=73 # 1be9A read from 1be9A/merged-good-all-a2m # found chain 1be9A in template set T0366 1 :TENLYFQSMGLRTVEMKKG 1be9A 301 :FLGEEDIPREPRRIVIHRG T0366 21 :TDSLGISIAGGV 1be9A 320 :STGLGFNIIGGE T0366 37 :GDVPIFIAMMHPTGVAAQTQKLRVGDRIVTICGTSTEGMTHTQAVNLLKNASGSIEMQVVAG 1be9A 332 :DGEGIFISFILAGGPADLSGELRKGDQILSVNGVDLRNASHEQAAIALKNAGQTVTIIAQYK Number of specific fragments extracted= 3 number of extra gaps= 0 total=281 Number of alignments=74 # 1be9A read from 1be9A/merged-good-all-a2m # found chain 1be9A in template set T0366 8 :SMGLRTVEMKKGPTDSLGISIAGGVG 1be9A 307 :IPREPRRIVIHRGSTGLGFNIIGGED T0366 38 :DVPIFIAMMHPTGVAAQTQKLRVGDRIVTICGTSTEGMTHTQAVNLLKNASGSIEMQVVAG 1be9A 333 :GEGIFISFILAGGPADLSGELRKGDQILSVNGVDLRNASHEQAAIALKNAGQTVTIIAQYK Number of specific fragments extracted= 2 number of extra gaps= 0 total=283 Number of alignments=75 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1d5gA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0366/1d5gA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0366/1d5gA/merged-good-all-a2m.gz for input Trying 1d5gA/merged-good-all-a2m Error: Couldn't open file 1d5gA/merged-good-all-a2m or 1d5gA/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1te0A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1te0A expands to /projects/compbio/data/pdb/1te0.pdb.gz 1te0A:# T0366 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 (T0366)G33 because of BadResidue code BAD_PEPTIDE in next template residue (1te0A)G275 Warning: unaligning (T0366)S34 because of BadResidue code BAD_PEPTIDE at template residue (1te0A)G275 Warning: unaligning (T0366)P35 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1te0A)D277 Warning: unaligning (T0366)L36 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1te0A)D277 Warning: unaligning (T0366)A44 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1te0A)E286 Warning: unaligning (T0366)M45 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1te0A)E286 Warning: unaligning (T0366)T49 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1te0A)G291 Warning: unaligning (T0366)G50 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1te0A)G291 Warning: unaligning (T0366)A53 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (1te0A)N295 Warning: unaligning (T0366)Q54 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (1te0A)N295 Warning: unaligning (T0366)T55 because of BadResidue code BAD_PEPTIDE in next template residue (1te0A)G297 Warning: unaligning (T0366)Q56 because of BadResidue code BAD_PEPTIDE at template residue (1te0A)G297 Warning: unaligning (T0366)D62 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1te0A)L303 Warning: unaligning (T0366)R63 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1te0A)L303 Warning: unaligning (T0366)T72 because of BadResidue code BAD_PEPTIDE in next template residue (1te0A)I313 Warning: unaligning (T0366)E73 because of BadResidue code BAD_PEPTIDE at template residue (1te0A)I313 Warning: unaligning (T0366)S102 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1te0A)T343 Warning: unaligning (T0366)E103 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1te0A)T343 T0366 37 :GDVPIFI 1te0A 278 :QLQGIVV T0366 46 :MHP 1te0A 287 :VSP T0366 51 :VA 1te0A 292 :PA T0366 58 :LRVG 1te0A 298 :IQVN T0366 64 :IVTICGTS 1te0A 304 :IISVDNKP T0366 76 :THTQAVNLLKNA 1te0A 314 :SALETMDQVAEI T0366 88 :SGSIEMQVVAGGDV 1te0A 328 :GSVIPVVVMRDDKQ Number of specific fragments extracted= 7 number of extra gaps= 7 total=290 # 1te0A read from 1te0A/merged-good-all-a2m # found chain 1te0A in template set Warning: unaligning (T0366)T21 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1te0A)G273 Warning: unaligning (T0366)D22 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1te0A)G273 Warning: unaligning (T0366)S23 because of BadResidue code BAD_PEPTIDE in next template residue (1te0A)G275 Warning: unaligning (T0366)G31 because of BadResidue code BAD_PEPTIDE at template residue (1te0A)G275 Warning: unaligning (T0366)V32 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1te0A)D277 Warning: unaligning (T0366)G33 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1te0A)D277 Warning: unaligning (T0366)A44 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1te0A)E286 Warning: unaligning (T0366)M45 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1te0A)E286 Warning: unaligning (T0366)T49 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1te0A)G291 Warning: unaligning (T0366)G50 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1te0A)G291 Warning: unaligning (T0366)A53 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (1te0A)N295 Warning: unaligning (T0366)Q54 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (1te0A)N295 Warning: unaligning (T0366)T55 because of BadResidue code BAD_PEPTIDE in next template residue (1te0A)G297 Warning: unaligning (T0366)Q56 because of BadResidue code BAD_PEPTIDE at template residue (1te0A)G297 Warning: unaligning (T0366)D62 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1te0A)L303 Warning: unaligning (T0366)R63 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1te0A)L303 Warning: unaligning (T0366)T72 because of BadResidue code BAD_PEPTIDE in next template residue (1te0A)I313 Warning: unaligning (T0366)E73 because of BadResidue code BAD_PEPTIDE at template residue (1te0A)I313 Warning: unaligning (T0366)S102 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1te0A)T343 T0366 37 :GDVPIFI 1te0A 278 :QLQGIVV T0366 46 :MHP 1te0A 287 :VSP T0366 51 :VA 1te0A 292 :PA T0366 58 :LRVG 1te0A 298 :IQVN T0366 64 :IVTICGTS 1te0A 304 :IISVDNKP T0366 76 :THTQAVNLLKNA 1te0A 314 :SALETMDQVAEI T0366 88 :SGSIEMQVVAGGDV 1te0A 328 :GSVIPVVVMRDDKQ Number of specific fragments extracted= 7 number of extra gaps= 7 total=297 # 1te0A read from 1te0A/merged-good-all-a2m # found chain 1te0A in template set Warning: unaligning (T0366)D22 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1te0A)G273 Warning: unaligning (T0366)G30 because of BadResidue code BAD_PEPTIDE in next template residue (1te0A)G275 Warning: unaligning (T0366)G31 because of BadResidue code BAD_PEPTIDE at template residue (1te0A)G275 Warning: unaligning (T0366)V32 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1te0A)D277 Warning: unaligning (T0366)G33 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1te0A)D277 Warning: unaligning (T0366)A44 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1te0A)E286 Warning: unaligning (T0366)M45 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1te0A)E286 Warning: unaligning (T0366)T49 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1te0A)G291 Warning: unaligning (T0366)G50 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1te0A)G291 Warning: unaligning (T0366)A53 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (1te0A)N295 Warning: unaligning (T0366)Q54 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (1te0A)N295 Warning: unaligning (T0366)T55 because of BadResidue code BAD_PEPTIDE in next template residue (1te0A)G297 Warning: unaligning (T0366)Q56 because of BadResidue code BAD_PEPTIDE at template residue (1te0A)G297 Warning: unaligning (T0366)D62 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1te0A)L303 Warning: unaligning (T0366)R63 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1te0A)L303 Warning: unaligning (T0366)T72 because of BadResidue code BAD_PEPTIDE in next template residue (1te0A)I313 Warning: unaligning (T0366)E73 because of BadResidue code BAD_PEPTIDE at template residue (1te0A)I313 T0366 37 :GDVPIFI 1te0A 278 :QLQGIVV T0366 46 :MHP 1te0A 287 :VSP T0366 51 :VA 1te0A 292 :PA T0366 58 :LRVG 1te0A 298 :IQVN T0366 64 :IVTICGTS 1te0A 304 :IISVDNKP T0366 76 :THTQAVNLLKNA 1te0A 314 :SALETMDQVAEI T0366 88 :SGSIEMQVVAGGD 1te0A 328 :GSVIPVVVMRDDK Number of specific fragments extracted= 7 number of extra gaps= 6 total=304 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2h3lA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2h3lA expands to /projects/compbio/data/pdb/2h3l.pdb.gz 2h3lA:# T0366 read from 2h3lA/merged-good-all-a2m # 2h3lA read from 2h3lA/merged-good-all-a2m # adding 2h3lA to template set # found chain 2h3lA in template set Warning: unaligning (T0366)D100 because of BadResidue code HAS_OXT+BAD_PEPTIDE in next template residue (2h3lA)S1412 T0366 3 :NLYFQSMGLRTVEMKKG 2h3lA 1313 :MGHELAKQEIRVRVEKD T0366 22 :DSLGISIAGGVG 2h3lA 1330 :PELGFSISGGVG T0366 34 :SPLGDVPIFIAMMHPTGVAA 2h3lA 1347 :FRPDDDGIFVTRVQPEGPAS T0366 56 :QKLRVGDRIVTICGTSTEGMTHTQAVNLLKNASGSIEMQVVAGG 2h3lA 1367 :KLLQPGDKIIQANGYSFINIEHGQAVSLLKTFQNTVELIIVREV Number of specific fragments extracted= 4 number of extra gaps= 1 total=308 Number of alignments=76 # 2h3lA read from 2h3lA/merged-good-all-a2m # found chain 2h3lA in template set Warning: unaligning (T0366)D100 because of BadResidue code HAS_OXT+BAD_PEPTIDE in next template residue (2h3lA)S1412 T0366 3 :NLYFQSMGLRTVEMKKG 2h3lA 1313 :MGHELAKQEIRVRVEKD T0366 22 :DSLGISIAGGV 2h3lA 1330 :PELGFSISGGV T0366 33 :GSPLGDVPIFIAMMHPTGVAA 2h3lA 1346 :PFRPDDDGIFVTRVQPEGPAS T0366 56 :QKLRVGDRIVTICGTSTEGMTHTQAVNLLKNASGSIEMQVVAGG 2h3lA 1367 :KLLQPGDKIIQANGYSFINIEHGQAVSLLKTFQNTVELIIVREV Number of specific fragments extracted= 4 number of extra gaps= 1 total=312 Number of alignments=77 # 2h3lA read from 2h3lA/merged-good-all-a2m # found chain 2h3lA in template set T0366 11 :LRTVEMKKGPTDSLGISIAGGVG 2h3lA 1319 :KQEIRVRVEKDPELGFSISGGVG T0366 34 :SPLGDVPIFIAMMHPTGVA 2h3lA 1347 :FRPDDDGIFVTRVQPEGPA T0366 55 :TQKLRVGDRIVTICGTSTEGMTHTQAVNLLKNASGSIEMQVVAG 2h3lA 1366 :SKLLQPGDKIIQANGYSFINIEHGQAVSLLKTFQNTVELIIVRE Number of specific fragments extracted= 3 number of extra gaps= 0 total=315 Number of alignments=78 # 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 # T0366 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 (T0366)Q7 because first residue in template chain is (2fcfA)Q1145 Warning: unaligning (T0366)P20 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2fcfA)K1160 Warning: unaligning (T0366)D22 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2fcfA)K1160 Warning: unaligning (T0366)V32 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2fcfA)G1184 Warning: unaligning (T0366)G33 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2fcfA)G1184 T0366 8 :SMGLRTVEMKKG 2fcfA 1146 :SMQPRRVELWRE T0366 23 :SLGISIAGG 2fcfA 1161 :SLGISIVGG T0366 41 :IFIAMMHPTGVAAQTQKLRVGDRIVTICGTSTEGMTHTQAVNLLKNASGSIEMQVVAGGDVS 2fcfA 1185 :IFIKHVLEDSPAGKNGTLKPGDRIVEVDGMDLRDASHEQAVEAIRKAGNPVVFMVQSIISTR Number of specific fragments extracted= 3 number of extra gaps= 1 total=318 Number of alignments=79 # 2fcfA read from 2fcfA/merged-good-all-a2m # found chain 2fcfA in template set Warning: unaligning (T0366)Q7 because first residue in template chain is (2fcfA)Q1145 Warning: unaligning (T0366)P20 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2fcfA)K1160 Warning: unaligning (T0366)D22 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2fcfA)K1160 Warning: unaligning (T0366)V32 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2fcfA)G1184 Warning: unaligning (T0366)G33 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2fcfA)G1184 T0366 8 :SMGLRTVEMKKG 2fcfA 1146 :SMQPRRVELWRE T0366 23 :SLGISIAGG 2fcfA 1161 :SLGISIVGG T0366 41 :IFIAMMHPTGVAAQTQKLRVGDRIVTICGTSTEGMTHTQAVNLLKNASGSIEMQVVAGGDVS 2fcfA 1185 :IFIKHVLEDSPAGKNGTLKPGDRIVEVDGMDLRDASHEQAVEAIRKAGNPVVFMVQSIISTR Number of specific fragments extracted= 3 number of extra gaps= 1 total=321 Number of alignments=80 # 2fcfA read from 2fcfA/merged-good-all-a2m # found chain 2fcfA in template set Warning: unaligning (T0366)P20 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2fcfA)K1160 Warning: unaligning (T0366)D22 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2fcfA)K1160 Warning: unaligning (T0366)V32 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2fcfA)G1184 Warning: unaligning (T0366)G33 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2fcfA)G1184 T0366 8 :SMGLRTVEMKKG 2fcfA 1146 :SMQPRRVELWRE T0366 23 :SLGISIAGG 2fcfA 1161 :SLGISIVGG T0366 41 :IFIAMMHPTGVAAQTQKLRVGDRIVTICGTSTEGMTHTQAVNLLKNASGSIEMQVVAGGDVS 2fcfA 1185 :IFIKHVLEDSPAGKNGTLKPGDRIVEVDGMDLRDASHEQAVEAIRKAGNPVVFMVQSIISTR Number of specific fragments extracted= 3 number of extra gaps= 1 total=324 Number of alignments=81 # 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/T0366/1rgrA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0366/1rgrA/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:# T0366 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 T0366 32 :VGS 1lcyA 252 :PDV T0366 38 :DVPIFIAMMHPTGVAAQTQ 1lcyA 255 :QHGVLIHKVILGSPAHRAG T0366 58 :LRVGDRIVTICGTSTEG 1lcyA 274 :LRPGDVILAIGEQMVQN T0366 77 :HTQAVNLLKNAS 1lcyA 291 :AEDVYEAVRTQS T0366 90 :SIEMQVVAGGDVSE 1lcyA 303 :QLAVQIRRGRETLT Number of specific fragments extracted= 5 number of extra gaps= 0 total=329 Number of alignments=82 # 1lcyA read from 1lcyA/merged-good-all-a2m # found chain 1lcyA in template set T0366 22 :DSLGISIAG 1lcyA 227 :RYIGVMMLT T0366 31 :GVGSPLG 1lcyA 245 :QLREPSF T0366 38 :DVPIFIAMMHPTGVAAQTQ 1lcyA 255 :QHGVLIHKVILGSPAHRAG T0366 58 :LRVGDRIVTICGTSTEG 1lcyA 274 :LRPGDVILAIGEQMVQN T0366 77 :HTQAVNLLKNA 1lcyA 291 :AEDVYEAVRTQ T0366 89 :GSIEMQVVAGGDVS 1lcyA 302 :SQLAVQIRRGRETL Number of specific fragments extracted= 6 number of extra gaps= 0 total=335 Number of alignments=83 # 1lcyA read from 1lcyA/merged-good-all-a2m # found chain 1lcyA in template set T0366 32 :VGSPLGDVPIFIAMMHPTGVAAQTQ 1lcyA 249 :PSFPDVQHGVLIHKVILGSPAHRAG T0366 58 :LRVGDRIVTICGTSTEG 1lcyA 274 :LRPGDVILAIGEQMVQN T0366 77 :HTQAVNLLKNA 1lcyA 291 :AEDVYEAVRTQ T0366 89 :GSIEMQVVAGGD 1lcyA 302 :SQLAVQIRRGRE Number of specific fragments extracted= 4 number of extra gaps= 0 total=339 Number of alignments=84 # 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 # T0366 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 (T0366)M9 because first residue in template chain is (2f5yA)M14 Warning: unaligning (T0366)G10 because of BadResidue code BAD_PEPTIDE at template residue (2f5yA)R15 Warning: unaligning (T0366)E73 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2f5yA)H70 Warning: unaligning (T0366)G74 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2f5yA)H70 Warning: unaligning (T0366)G99 because last residue in template chain is (2f5yA)V95 T0366 11 :LRTVEMKKG 2f5yA 16 :YRQITIPRG T0366 21 :TDSLGISIAG 2f5yA 25 :KDGFGFTICC T0366 38 :DVPIFIAMMHPTGVAAQTQ 2f5yA 35 :DSPVRVQAVDSGGPAERAG T0366 58 :LRVGDRIVTICGTST 2f5yA 54 :LQQLDTVLQLNERPV T0366 75 :MTHTQAVNLLKNASGSIEMQVVAG 2f5yA 71 :WKCVELAHEIRSCPSEIILLVWRM Number of specific fragments extracted= 5 number of extra gaps= 1 total=344 Number of alignments=85 # 2f5yA read from 2f5yA/merged-good-all-a2m # found chain 2f5yA in template set Warning: unaligning (T0366)M9 because first residue in template chain is (2f5yA)M14 Warning: unaligning (T0366)G10 because of BadResidue code BAD_PEPTIDE at template residue (2f5yA)R15 Warning: unaligning (T0366)E73 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2f5yA)H70 Warning: unaligning (T0366)G74 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2f5yA)H70 Warning: unaligning (T0366)G99 because last residue in template chain is (2f5yA)V95 T0366 11 :LRTVEMKKG 2f5yA 16 :YRQITIPRG T0366 21 :TDSLGISIA 2f5yA 25 :KDGFGFTIC T0366 37 :GDVPIFIAMMHPTGVAAQTQ 2f5yA 34 :CDSPVRVQAVDSGGPAERAG T0366 58 :LRVGDRIVTICGTST 2f5yA 54 :LQQLDTVLQLNERPV T0366 75 :MTHTQAVNLLKNASGSIEMQVVAG 2f5yA 71 :WKCVELAHEIRSCPSEIILLVWRM Number of specific fragments extracted= 5 number of extra gaps= 1 total=349 Number of alignments=86 # 2f5yA read from 2f5yA/merged-good-all-a2m # found chain 2f5yA in template set Warning: unaligning (T0366)G10 because first residue in template chain is (2f5yA)M14 Warning: unaligning (T0366)L11 because of BadResidue code BAD_PEPTIDE at template residue (2f5yA)R15 Warning: unaligning (T0366)E73 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2f5yA)H70 Warning: unaligning (T0366)G74 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2f5yA)H70 Warning: unaligning (T0366)G99 because last residue in template chain is (2f5yA)V95 T0366 12 :RTVEMKKGPTDSLGISIAGG 2f5yA 16 :YRQITIPRGKDGFGFTICCD T0366 39 :VPIFIAMMHPTGVAAQTQ 2f5yA 36 :SPVRVQAVDSGGPAERAG T0366 58 :LRVGDRIVTICGTST 2f5yA 54 :LQQLDTVLQLNERPV T0366 75 :MTHTQAVNLLKNASGSIEMQVVAG 2f5yA 71 :WKCVELAHEIRSCPSEIILLVWRM Number of specific fragments extracted= 4 number of extra gaps= 1 total=353 Number of alignments=87 # 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:# T0366 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 (T0366)G10 because first residue in template chain is (1kwaA)R487 Warning: unaligning (T0366)S102 because last residue in template chain is (1kwaA)F574 T0366 11 :LRTVEMKKGPTDSLGISIA 1kwaA 488 :SRLVQFQKNTDEPMGITLK T0366 32 :VGSPLG 1kwaA 507 :MNELNH T0366 41 :IFIAMMHPTGVAAQTQKLRVGDRIVTICGTSTEGMTHTQAVNLLKNASGSIEMQVVAGGDV 1kwaA 513 :CIVARIMHGGMIHRQGTLHVGDEIREINGISVANQTVEQLQKMLREMRGSITFKIVPSYRE Number of specific fragments extracted= 3 number of extra gaps= 0 total=356 Number of alignments=88 # 1kwaA read from 1kwaA/merged-good-all-a2m # found chain 1kwaA in template set Warning: unaligning (T0366)G10 because first residue in template chain is (1kwaA)R487 Warning: unaligning (T0366)S102 because last residue in template chain is (1kwaA)F574 T0366 11 :LRTVEMKKGPTDSLGISIAGGV 1kwaA 488 :SRLVQFQKNTDEPMGITLKMNE T0366 36 :LGD 1kwaA 510 :LNH T0366 41 :IFIAMMHPTGVAAQTQKLRVGDRIVTICGTSTEGMTHTQAVNLLKNASGSIEMQVVAGGDV 1kwaA 513 :CIVARIMHGGMIHRQGTLHVGDEIREINGISVANQTVEQLQKMLREMRGSITFKIVPSYRE Number of specific fragments extracted= 3 number of extra gaps= 0 total=359 Number of alignments=89 # 1kwaA read from 1kwaA/merged-good-all-a2m # found chain 1kwaA in template set Warning: unaligning (T0366)G10 because first residue in template chain is (1kwaA)R487 T0366 11 :LRTVEMKKGPTDSLGISIAGGVGSP 1kwaA 488 :SRLVQFQKNTDEPMGITLKMNELNH T0366 41 :IFIAMMHPTGVAAQTQKLRVGDRIVTICGTSTEGMTHTQAVNLLKNASGSIEMQVVAGGDV 1kwaA 513 :CIVARIMHGGMIHRQGTLHVGDEIREINGISVANQTVEQLQKMLREMRGSITFKIVPSYRE Number of specific fragments extracted= 2 number of extra gaps= 0 total=361 Number of alignments=90 # 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:# T0366 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 (T0366)G10 because first residue in template chain is (1kwaB)R487 Warning: unaligning (T0366)G30 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1kwaB)L510 Warning: unaligning (T0366)D38 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1kwaB)L510 Warning: unaligning (T0366)S102 because last residue in template chain is (1kwaB)F574 T0366 11 :LRTVEMKKGPTDSLGISIA 1kwaB 488 :SRLVQFQKNTDEPMGITLK T0366 39 :VPIFIAMMHPTGVAAQTQKLRVGDRIVTICGTSTEGMTHTQAVNLLKNASGSIEMQVVAGGDV 1kwaB 511 :NHCIVARIMHGGMIHRQGTLHVGDEIREINGISVANQTVEQLQKMLREMRGSITFKIVPSYRE Number of specific fragments extracted= 2 number of extra gaps= 1 total=363 # 1kwaB read from 1kwaB/merged-good-all-a2m # found chain 1kwaB in template set Warning: unaligning (T0366)G10 because first residue in template chain is (1kwaB)R487 Warning: unaligning (T0366)G37 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1kwaB)L510 Warning: unaligning (T0366)D38 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1kwaB)L510 Warning: unaligning (T0366)S102 because last residue in template chain is (1kwaB)F574 T0366 11 :LRTVEMKKGPTDSLGISIA 1kwaB 488 :SRLVQFQKNTDEPMGITLK T0366 39 :VPIFIAMMHPTGVAAQTQKLRVGDRIVTICGTSTEGMTHTQAVNLLKNASGSIEMQVVAGGDV 1kwaB 511 :NHCIVARIMHGGMIHRQGTLHVGDEIREINGISVANQTVEQLQKMLREMRGSITFKIVPSYRE Number of specific fragments extracted= 2 number of extra gaps= 1 total=365 # 1kwaB read from 1kwaB/merged-good-all-a2m # found chain 1kwaB in template set Warning: unaligning (T0366)G10 because first residue in template chain is (1kwaB)R487 Warning: unaligning (T0366)G30 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1kwaB)L510 Warning: unaligning (T0366)G31 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1kwaB)L510 T0366 11 :LRTVEMKKGPTDSLGISIA 1kwaB 488 :SRLVQFQKNTDEPMGITLK T0366 39 :VPIFIAMMHPTGVAAQTQKLRVGDRIVTICGTSTEGMTHTQAVNLLKNASGSIEMQVVAG 1kwaB 511 :NHCIVARIMHGGMIHRQGTLHVGDEIREINGISVANQTVEQLQKMLREMRGSITFKIVPS Number of specific fragments extracted= 2 number of extra gaps= 1 total=367 # 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 # T0366 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 Warning: unaligning (T0366)Q7 because first residue in template chain is (1pdr)I460 T0366 8 :SMGLRTVEMKKG 1pdr 461 :TREPRKVVLHRG T0366 21 :TDSLGISIAGGVG 1pdr 473 :STGLGFNIVGGED T0366 38 :DVPIFIAMMHPTGVAAQTQKLRVGDRIVTICGTSTEGMTHTQAVNLLKNASGSIEMQVVAG 1pdr 486 :GEGIFISFILAGGPADLSGELRKGDRIISVNSVDLRAASHEQAAAALKNAGQAVTIVAQYR Number of specific fragments extracted= 3 number of extra gaps= 0 total=370 Number of alignments=91 # 1pdr read from 1pdr/merged-good-all-a2m # found chain 1pdr in template set Warning: unaligning (T0366)Q7 because first residue in template chain is (1pdr)I460 T0366 8 :SMGLRTVEMKKG 1pdr 461 :TREPRKVVLHRG T0366 21 :TDSLGISIAGGV 1pdr 473 :STGLGFNIVGGE T0366 37 :GDVPIFIAMMHPTGVAAQTQKLRVGDRIVTICGTSTEGMTHTQAVNLLKNASGSIEMQVVAG 1pdr 485 :DGEGIFISFILAGGPADLSGELRKGDRIISVNSVDLRAASHEQAAAALKNAGQAVTIVAQYR Number of specific fragments extracted= 3 number of extra gaps= 0 total=373 Number of alignments=92 # 1pdr read from 1pdr/merged-good-all-a2m # found chain 1pdr in template set Warning: unaligning (T0366)S8 because first residue in template chain is (1pdr)I460 T0366 9 :MGLRTVEMKKGPTDSLGISIAGGVG 1pdr 461 :TREPRKVVLHRGSTGLGFNIVGGED T0366 38 :DVPIFIAMMHPTGVAAQTQKLRVGDRIVTICGTSTEGMTHTQAVNLLKNASGSIEMQVVAG 1pdr 486 :GEGIFISFILAGGPADLSGELRKGDRIISVNSVDLRAASHEQAAAALKNAGQAVTIVAQYR Number of specific fragments extracted= 2 number of extra gaps= 0 total=375 Number of alignments=93 # 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/T0366/1iu0A/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0366/1iu0A/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 # T0366 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 (T0366)L11 because first residue in template chain is (1n99A)P112 Warning: unaligning (T0366)Q94 because of BadResidue code BAD_PEPTIDE in next template residue (1n99A)I190 Warning: unaligning (T0366)V95 because of BadResidue code BAD_PEPTIDE at template residue (1n99A)I190 T0366 12 :RTVEMKKGPTDSLGISIAGG 1n99A 113 :REVILCKDQDGKIGLRLKSI T0366 38 :DVPIFIAMMHPTGVAAQTQ 1n99A 133 :DNGIFVQLVQANSPASLVG T0366 58 :LRVGDRIVTICGTSTEGMTHTQAVNLLKNA 1n99A 152 :LRFGDQVLQINGENCAGWSSDKAHKVLKQA T0366 88 :SGSIEM 1n99A 183 :GEKITM T0366 96 :VAGGDVSE 1n99A 191 :RDRPFERT Number of specific fragments extracted= 5 number of extra gaps= 1 total=380 Number of alignments=94 # 1n99A read from 1n99A/merged-good-all-a2m # found chain 1n99A in template set Warning: unaligning (T0366)L11 because first residue in template chain is (1n99A)P112 Warning: unaligning (T0366)Q94 because of BadResidue code BAD_PEPTIDE in next template residue (1n99A)I190 Warning: unaligning (T0366)V95 because of BadResidue code BAD_PEPTIDE at template residue (1n99A)I190 T0366 12 :RTVEMKKGPTDSLGISIAG 1n99A 113 :REVILCKDQDGKIGLRLKS T0366 37 :GDVPIFIAMMHPTGVAAQTQ 1n99A 132 :IDNGIFVQLVQANSPASLVG T0366 58 :LRVGDRIVTICGTSTEGMTHTQAVNLLKNA 1n99A 152 :LRFGDQVLQINGENCAGWSSDKAHKVLKQA T0366 88 :SGSIEM 1n99A 183 :GEKITM T0366 96 :VAGGDVS 1n99A 191 :RDRPFER Number of specific fragments extracted= 5 number of extra gaps= 1 total=385 Number of alignments=95 # 1n99A read from 1n99A/merged-good-all-a2m # found chain 1n99A in template set Warning: unaligning (T0366)L11 because first residue in template chain is (1n99A)P112 Warning: unaligning (T0366)Q94 because of BadResidue code BAD_PEPTIDE in next template residue (1n99A)I190 Warning: unaligning (T0366)V95 because of BadResidue code BAD_PEPTIDE at template residue (1n99A)I190 T0366 12 :RTVEMKKGPTDSLGISIAGGVG 1n99A 113 :REVILCKDQDGKIGLRLKSIDN T0366 40 :PIFIAMMHPTGVAAQTQ 1n99A 135 :GIFVQLVQANSPASLVG T0366 58 :LRVGDRIVTICGTSTEGMTHTQAVNLLKNA 1n99A 152 :LRFGDQVLQINGENCAGWSSDKAHKVLKQA T0366 88 :SGSIEM 1n99A 183 :GEKITM T0366 96 :VAGG 1n99A 191 :RDRP Number of specific fragments extracted= 5 number of extra gaps= 1 total=390 Number of alignments=96 # 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 # T0366 read from 1g9oA/merged-good-all-a2m # 1g9oA read from 1g9oA/merged-good-all-a2m # found chain 1g9oA in training set Warning: unaligning (T0366)T104 because last residue in template chain is (1g9oA)L99 T0366 9 :MGLRTVEMKKG 1g9oA 10 :MLPRLCCLEKG T0366 21 :TDSLGISIAGGVG 1g9oA 21 :PNGYGFHLHGEKG T0366 38 :DVPIFIAMMHPTGVAAQTQ 1g9oA 34 :KLGQYIRLVEPGSPAEKAG T0366 58 :LRVGDRIVTICGTSTEGMTHTQAVNLLKNASGSIEMQVVAGGDVSE 1g9oA 53 :LLAGDRLVEVNGENVEKETHQQVVSRIRAALNAVRLLVVDPETDEQ Number of specific fragments extracted= 4 number of extra gaps= 0 total=394 Number of alignments=97 # 1g9oA read from 1g9oA/merged-good-all-a2m # found chain 1g9oA in training set Warning: unaligning (T0366)T104 because last residue in template chain is (1g9oA)L99 T0366 9 :MGLRTVEMKKG 1g9oA 10 :MLPRLCCLEKG T0366 21 :TDSLGISIAGGV 1g9oA 21 :PNGYGFHLHGEK T0366 37 :GDVPIFIAMMHPTGVAAQTQ 1g9oA 33 :GKLGQYIRLVEPGSPAEKAG T0366 58 :LRVGDRIVTICGTSTEGMTHTQAVNLLKNASGSIEMQVVAGGDVSE 1g9oA 53 :LLAGDRLVEVNGENVEKETHQQVVSRIRAALNAVRLLVVDPETDEQ Number of specific fragments extracted= 4 number of extra gaps= 0 total=398 Number of alignments=98 # 1g9oA read from 1g9oA/merged-good-all-a2m # found chain 1g9oA in training set T0366 10 :GLRTVEMKKGPTDSLGISIAGGVG 1g9oA 10 :MLPRLCCLEKGPNGYGFHLHGEKG T0366 38 :DVPIFIAMMHPTGVAAQTQ 1g9oA 34 :KLGQYIRLVEPGSPAEKAG T0366 58 :LRVGDRIVTICGTSTEGMTHTQAVNLLKNASGSIEMQVVAGGDVSE 1g9oA 53 :LLAGDRLVEVNGENVEKETHQQVVSRIRAALNAVRLLVVDPETDEQ Number of specific fragments extracted= 3 number of extra gaps= 0 total=401 Number of alignments=99 # 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 # T0366 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 (T0366)G10 because first residue in template chain is (1l6oA)M251 Warning: unaligning (T0366)V14 because of BadResidue code BAD_PEPTIDE in next template residue (1l6oA)T256 Warning: unaligning (T0366)E15 because of BadResidue code BAD_PEPTIDE at template residue (1l6oA)T256 Warning: unaligning (T0366)G19 because of BadResidue code BAD_PEPTIDE in next template residue (1l6oA)K261 Warning: unaligning (T0366)P20 because of BadResidue code BAD_PEPTIDE at template residue (1l6oA)K261 Warning: unaligning (T0366)T21 because of BadResidue code BAD_PEPTIDE in next template residue (1l6oA)N263 Warning: unaligning (T0366)D22 because of BadResidue code BAD_PEPTIDE at template residue (1l6oA)N263 Warning: unaligning (T0366)S23 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1l6oA)L265 Warning: unaligning (T0366)L24 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1l6oA)L265 Warning: unaligning (T0366)I26 because of BadResidue code BAD_PEPTIDE in next template residue (1l6oA)S268 Warning: unaligning (T0366)S27 because of BadResidue code BAD_PEPTIDE at template residue (1l6oA)S268 Warning: unaligning (T0366)G33 because of BadResidue code BAD_PEPTIDE in next template residue (1l6oA)N274 Warning: unaligning (T0366)S34 because of BadResidue code BAD_PEPTIDE at template residue (1l6oA)N274 Warning: unaligning (T0366)D38 because of BadResidue code BAD_PEPTIDE in next template residue (1l6oA)G279 Warning: unaligning (T0366)V39 because of BadResidue code BAD_PEPTIDE at template residue (1l6oA)G279 Warning: unaligning (T0366)P40 because of BadResidue code BAD_PEPTIDE at template residue (1l6oA)G280 Warning: unaligning (T0366)A52 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1l6oA)A293 Warning: unaligning (T0366)A53 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1l6oA)A293 Warning: unaligning (T0366)C68 because of BadResidue code BAD_PEPTIDE in next template residue (1l6oA)D309 Warning: unaligning (T0366)G69 because of BadResidue code BAD_PEPTIDE at template residue (1l6oA)D309 Warning: unaligning (T0366)S71 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1l6oA)F312 Warning: unaligning (T0366)T72 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1l6oA)F312 Warning: unaligning (T0366)G74 because of BadResidue code BAD_PEPTIDE in next template residue (1l6oA)M315 Warning: unaligning (T0366)M75 because of BadResidue code BAD_PEPTIDE at template residue (1l6oA)M315 Warning: unaligning (T0366)T76 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1l6oA)S316 Warning: unaligning (T0366)K85 because of BadResidue code BAD_PEPTIDE in next template residue (1l6oA)D326 Warning: unaligning (T0366)N86 because of BadResidue code BAD_PEPTIDE at template residue (1l6oA)D326 Warning: unaligning (T0366)M93 because of BadResidue code BAD_PEPTIDE in next template residue (1l6oA)T337 Warning: unaligning (T0366)Q94 because of BadResidue code BAD_PEPTIDE at template residue (1l6oA)T337 Warning: unaligning (T0366)V95 because of BadResidue code BAD_PEPTIDE in next template residue (1l6oA)A339 Warning: unaligning (T0366)V96 because of BadResidue code BAD_PEPTIDE at template residue (1l6oA)A339 Warning: unaligning (T0366)G98 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (1l6oA)E342 Warning: unaligning (T0366)G99 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (1l6oA)E342 Warning: unaligning (T0366)D100 because of BadResidue code BAD_PEPTIDE in next template residue (1l6oA)H344 Warning: unaligning (T0366)V101 because of BadResidue code BAD_PEPTIDE at template residue (1l6oA)H344 Warning: unaligning (T0366)S102 because last residue in template chain is (1l6oA)H345 T0366 11 :LRT 1l6oA 252 :IIT T0366 16 :MKK 1l6oA 257 :LNM T0366 25 :G 1l6oA 266 :G T0366 28 :IAGG 1l6oA 269 :IVGQ T0366 35 :PLG 1l6oA 275 :ERG T0366 41 :IFIAMMHPTGV 1l6oA 281 :IYIGSIMKGGA T0366 54 :QTQKLRVGDRIVTI 1l6oA 294 :ADGRIEPGDMLLQV T0366 70 :T 1l6oA 310 :I T0366 73 :E 1l6oA 313 :E T0366 77 :HTQAVNLL 1l6oA 317 :NDDAVRVL T0366 87 :A 1l6oA 327 :I T0366 88 :SGSIE 1l6oA 331 :PGPIV T0366 97 :A 1l6oA 340 :K Number of specific fragments extracted= 13 number of extra gaps= 12 total=414 # 1l6oA read from 1l6oA/merged-good-all-a2m # found chain 1l6oA in template set Warning: unaligning (T0366)G10 because first residue in template chain is (1l6oA)M251 Warning: unaligning (T0366)V14 because of BadResidue code BAD_PEPTIDE in next template residue (1l6oA)T256 Warning: unaligning (T0366)E15 because of BadResidue code BAD_PEPTIDE at template residue (1l6oA)T256 Warning: unaligning (T0366)G19 because of BadResidue code BAD_PEPTIDE in next template residue (1l6oA)K261 Warning: unaligning (T0366)P20 because of BadResidue code BAD_PEPTIDE at template residue (1l6oA)K261 Warning: unaligning (T0366)T21 because of BadResidue code BAD_PEPTIDE in next template residue (1l6oA)N263 Warning: unaligning (T0366)D22 because of BadResidue code BAD_PEPTIDE at template residue (1l6oA)N263 Warning: unaligning (T0366)S23 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1l6oA)L265 Warning: unaligning (T0366)L24 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1l6oA)L265 Warning: unaligning (T0366)I26 because of BadResidue code BAD_PEPTIDE in next template residue (1l6oA)S268 Warning: unaligning (T0366)S27 because of BadResidue code BAD_PEPTIDE at template residue (1l6oA)S268 Warning: unaligning (T0366)V32 because of BadResidue code BAD_PEPTIDE in next template residue (1l6oA)N274 Warning: unaligning (T0366)G33 because of BadResidue code BAD_PEPTIDE at template residue (1l6oA)N274 Warning: unaligning (T0366)D38 because of BadResidue code BAD_PEPTIDE in next template residue (1l6oA)G279 Warning: unaligning (T0366)V39 because of BadResidue code BAD_PEPTIDE at template residue (1l6oA)G279 Warning: unaligning (T0366)P40 because of BadResidue code BAD_PEPTIDE at template residue (1l6oA)G280 Warning: unaligning (T0366)A52 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1l6oA)A293 Warning: unaligning (T0366)A53 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1l6oA)A293 Warning: unaligning (T0366)C68 because of BadResidue code BAD_PEPTIDE in next template residue (1l6oA)D309 Warning: unaligning (T0366)G69 because of BadResidue code BAD_PEPTIDE at template residue (1l6oA)D309 Warning: unaligning (T0366)S71 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1l6oA)F312 Warning: unaligning (T0366)T72 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1l6oA)F312 Warning: unaligning (T0366)G74 because of BadResidue code BAD_PEPTIDE in next template residue (1l6oA)M315 Warning: unaligning (T0366)M75 because of BadResidue code BAD_PEPTIDE at template residue (1l6oA)M315 Warning: unaligning (T0366)T76 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1l6oA)S316 Warning: unaligning (T0366)K85 because of BadResidue code BAD_PEPTIDE in next template residue (1l6oA)D326 Warning: unaligning (T0366)N86 because of BadResidue code BAD_PEPTIDE at template residue (1l6oA)D326 Warning: unaligning (T0366)M93 because of BadResidue code BAD_PEPTIDE in next template residue (1l6oA)T337 Warning: unaligning (T0366)Q94 because of BadResidue code BAD_PEPTIDE at template residue (1l6oA)T337 Warning: unaligning (T0366)V95 because of BadResidue code BAD_PEPTIDE in next template residue (1l6oA)A339 Warning: unaligning (T0366)V96 because of BadResidue code BAD_PEPTIDE at template residue (1l6oA)A339 Warning: unaligning (T0366)G98 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (1l6oA)E342 Warning: unaligning (T0366)G99 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (1l6oA)E342 Warning: unaligning (T0366)D100 because of BadResidue code BAD_PEPTIDE in next template residue (1l6oA)H344 Warning: unaligning (T0366)V101 because of BadResidue code BAD_PEPTIDE at template residue (1l6oA)H344 Warning: unaligning (T0366)S102 because last residue in template chain is (1l6oA)H345 T0366 11 :LRT 1l6oA 252 :IIT T0366 16 :MKK 1l6oA 257 :LNM T0366 25 :G 1l6oA 266 :G T0366 28 :IAGG 1l6oA 269 :IVGQ T0366 35 :PLG 1l6oA 275 :ERG T0366 41 :IFIAMMHPTGV 1l6oA 281 :IYIGSIMKGGA T0366 54 :QTQKLRVGDRIVTI 1l6oA 294 :ADGRIEPGDMLLQV T0366 70 :T 1l6oA 310 :I T0366 73 :E 1l6oA 313 :E T0366 77 :HTQAVNLL 1l6oA 317 :NDDAVRVL T0366 87 :A 1l6oA 327 :I T0366 88 :SGSIE 1l6oA 331 :PGPIV T0366 97 :A 1l6oA 340 :K Number of specific fragments extracted= 13 number of extra gaps= 12 total=427 # 1l6oA read from 1l6oA/merged-good-all-a2m # found chain 1l6oA in template set Warning: unaligning (T0366)G10 because first residue in template chain is (1l6oA)M251 Warning: unaligning (T0366)V14 because of BadResidue code BAD_PEPTIDE in next template residue (1l6oA)T256 Warning: unaligning (T0366)E15 because of BadResidue code BAD_PEPTIDE at template residue (1l6oA)T256 Warning: unaligning (T0366)G19 because of BadResidue code BAD_PEPTIDE in next template residue (1l6oA)K261 Warning: unaligning (T0366)P20 because of BadResidue code BAD_PEPTIDE at template residue (1l6oA)K261 Warning: unaligning (T0366)T21 because of BadResidue code BAD_PEPTIDE in next template residue (1l6oA)N263 Warning: unaligning (T0366)D22 because of BadResidue code BAD_PEPTIDE at template residue (1l6oA)N263 Warning: unaligning (T0366)S23 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1l6oA)L265 Warning: unaligning (T0366)L24 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1l6oA)L265 Warning: unaligning (T0366)I26 because of BadResidue code BAD_PEPTIDE in next template residue (1l6oA)S268 Warning: unaligning (T0366)S27 because of BadResidue code BAD_PEPTIDE at template residue (1l6oA)S268 Warning: unaligning (T0366)V32 because of BadResidue code BAD_PEPTIDE in next template residue (1l6oA)N274 Warning: unaligning (T0366)G33 because of BadResidue code BAD_PEPTIDE at template residue (1l6oA)N274 Warning: unaligning (T0366)D38 because of BadResidue code BAD_PEPTIDE in next template residue (1l6oA)G279 Warning: unaligning (T0366)V39 because of BadResidue code BAD_PEPTIDE at template residue (1l6oA)G279 Warning: unaligning (T0366)P40 because of BadResidue code BAD_PEPTIDE at template residue (1l6oA)G280 Warning: unaligning (T0366)A52 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1l6oA)A293 Warning: unaligning (T0366)A53 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1l6oA)A293 Warning: unaligning (T0366)C68 because of BadResidue code BAD_PEPTIDE in next template residue (1l6oA)D309 Warning: unaligning (T0366)G69 because of BadResidue code BAD_PEPTIDE at template residue (1l6oA)D309 Warning: unaligning (T0366)S71 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1l6oA)F312 Warning: unaligning (T0366)T72 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1l6oA)F312 Warning: unaligning (T0366)G74 because of BadResidue code BAD_PEPTIDE in next template residue (1l6oA)M315 Warning: unaligning (T0366)M75 because of BadResidue code BAD_PEPTIDE at template residue (1l6oA)M315 Warning: unaligning (T0366)T76 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1l6oA)S316 Warning: unaligning (T0366)K85 because of BadResidue code BAD_PEPTIDE in next template residue (1l6oA)D326 Warning: unaligning (T0366)N86 because of BadResidue code BAD_PEPTIDE at template residue (1l6oA)D326 Warning: unaligning (T0366)M93 because of BadResidue code BAD_PEPTIDE in next template residue (1l6oA)T337 Warning: unaligning (T0366)Q94 because of BadResidue code BAD_PEPTIDE at template residue (1l6oA)T337 Warning: unaligning (T0366)V95 because of BadResidue code BAD_PEPTIDE in next template residue (1l6oA)A339 Warning: unaligning (T0366)V96 because of BadResidue code BAD_PEPTIDE at template residue (1l6oA)A339 Warning: unaligning (T0366)G98 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (1l6oA)E342 Warning: unaligning (T0366)G99 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (1l6oA)E342 Warning: unaligning (T0366)D100 because of BadResidue code BAD_PEPTIDE in next template residue (1l6oA)H344 Warning: unaligning (T0366)V101 because of BadResidue code BAD_PEPTIDE at template residue (1l6oA)H344 Warning: unaligning (T0366)S102 because last residue in template chain is (1l6oA)H345 T0366 11 :LRT 1l6oA 252 :IIT T0366 16 :MKK 1l6oA 257 :LNM T0366 25 :G 1l6oA 266 :G T0366 28 :IAGG 1l6oA 269 :IVGQ T0366 35 :PLG 1l6oA 275 :ERG T0366 41 :IFIAMMHPTGV 1l6oA 281 :IYIGSIMKGGA T0366 54 :QTQKLRVGDRIVTI 1l6oA 294 :ADGRIEPGDMLLQV T0366 70 :T 1l6oA 310 :I T0366 73 :E 1l6oA 313 :E T0366 77 :HTQAVNLL 1l6oA 317 :NDDAVRVL T0366 87 :A 1l6oA 327 :I T0366 88 :SGSIE 1l6oA 331 :PGPIV T0366 97 :A 1l6oA 340 :K Number of specific fragments extracted= 13 number of extra gaps= 12 total=440 # 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 # T0366 read from 1q3oA/merged-good-all-a2m # 1q3oA read from 1q3oA/merged-good-all-a2m # found chain 1q3oA in training set Warning: unaligning (T0366)V101 because last residue in template chain is (1q3oA)H687 T0366 11 :LRTVEMKKGPTDSLGISIAGGVGSPL 1q3oA 589 :EKTVLLQKKDSEGFGFVLRGAKAQTP T0366 37 :GDVPIFIAMMHPTGVAAQTQ 1q3oA 624 :FPALQYLESVDEGGVAWRAG T0366 58 :LRVGDRIVTICGTSTEGMTHTQAVNLLKNASGSIEMQVVAGGD 1q3oA 644 :LRMGDFLIEVNGQNVVKVGHRQVVNMIRQGGNTLMVKVVMVTR Number of specific fragments extracted= 3 number of extra gaps= 0 total=443 Number of alignments=100 # 1q3oA read from 1q3oA/merged-good-all-a2m # found chain 1q3oA in training set Warning: unaligning (T0366)V101 because last residue in template chain is (1q3oA)H687 T0366 10 :GLRTVEMKKGPTDSLGISIAGGVGSPLG 1q3oA 588 :KEKTVLLQKKDSEGFGFVLRGAKAQTPI T0366 38 :DVPIFIAMMHPTGVAAQTQ 1q3oA 625 :PALQYLESVDEGGVAWRAG T0366 58 :LRVGDRIVTICGTSTEGMTHTQAVNLLKNASGSIEMQVVAGGD 1q3oA 644 :LRMGDFLIEVNGQNVVKVGHRQVVNMIRQGGNTLMVKVVMVTR Number of specific fragments extracted= 3 number of extra gaps= 0 total=446 Number of alignments=101 # 1q3oA read from 1q3oA/merged-good-all-a2m # found chain 1q3oA in training set Warning: unaligning (T0366)V101 because last residue in template chain is (1q3oA)H687 T0366 12 :RTVEMKKGPTDSLGISIAGGVGSPL 1q3oA 590 :KTVLLQKKDSEGFGFVLRGAKAQTP T0366 37 :GDVPIFIAMMHPTGVAAQTQ 1q3oA 624 :FPALQYLESVDEGGVAWRAG T0366 58 :LRVGDRIVTICGTSTEGMTHTQAVNLLKNASGSIEMQVVAGGD 1q3oA 644 :LRMGDFLIEVNGQNVVKVGHRQVVNMIRQGGNTLMVKVVMVTR Number of specific fragments extracted= 3 number of extra gaps= 0 total=449 Number of alignments=102 # 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 # T0366 read from 1n7fA/merged-good-all-a2m # 1n7fA read from 1n7fA/merged-good-all-a2m # found chain 1n7fA in training set Warning: unaligning (T0366)M9 because first residue in template chain is (1n7fA)A668 Warning: unaligning (T0366)G98 because last residue in template chain is (1n7fA)Q753 T0366 10 :GLRTVEMKKG 1n7fA 669 :IIYTVELKRY T0366 21 :TDSLGISIAGGVGS 1n7fA 679 :GGPLGITISGTEEP T0366 38 :DVPIFIAMMHPTGVAAQTQKLRVGDRIVTICGTSTEGMTHTQAVNLLKNASGSIEMQVVA 1n7fA 693 :FDPIIISSLTKGGLAERTGAIHIGDRILAINSSSLKGKPLSEAIHLLQMAGETVTLKIKK Number of specific fragments extracted= 3 number of extra gaps= 0 total=452 Number of alignments=103 # 1n7fA read from 1n7fA/merged-good-all-a2m # found chain 1n7fA in training set Warning: unaligning (T0366)M9 because first residue in template chain is (1n7fA)A668 Warning: unaligning (T0366)G98 because last residue in template chain is (1n7fA)Q753 T0366 10 :GLRTVEMKKG 1n7fA 669 :IIYTVELKRY T0366 21 :TDSLGISIAGGVG 1n7fA 679 :GGPLGITISGTEE T0366 37 :GDVPIFIAMMHPTGVAAQTQKLRVGDRIVTICGTSTEGMTHTQAVNLLKNASGSIEMQVVA 1n7fA 692 :PFDPIIISSLTKGGLAERTGAIHIGDRILAINSSSLKGKPLSEAIHLLQMAGETVTLKIKK Number of specific fragments extracted= 3 number of extra gaps= 0 total=455 Number of alignments=104 # 1n7fA read from 1n7fA/merged-good-all-a2m # found chain 1n7fA in training set Warning: unaligning (T0366)G10 because first residue in template chain is (1n7fA)A668 Warning: unaligning (T0366)G98 because last residue in template chain is (1n7fA)Q753 T0366 11 :LRTVEMKKGPTDSLGISIAGGVG 1n7fA 669 :IIYTVELKRYGGPLGITISGTEE T0366 37 :GDVPIFIAMMHPTGVAAQTQKLRVGDRIVTICGTSTEGMTHTQAVNLLKNASGSIEMQVVA 1n7fA 692 :PFDPIIISSLTKGGLAERTGAIHIGDRILAINSSSLKGKPLSEAIHLLQMAGETVTLKIKK Number of specific fragments extracted= 2 number of extra gaps= 0 total=457 Number of alignments=105 # 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 # T0366 read from 1ihjA/merged-good-all-a2m # 1ihjA read from 1ihjA/merged-good-all-a2m # found chain 1ihjA in training set Warning: unaligning (T0366)S8 because first residue in template chain is (1ihjA)G12 Warning: unaligning (T0366)L36 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ihjA)P41 Warning: unaligning (T0366)G37 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ihjA)P41 Warning: unaligning (T0366)D38 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ihjA)N42 Warning: unaligning (T0366)G98 because last residue in template chain is (1ihjA)F105 T0366 9 :MGLRTVEMKKGPTDSLGISIAGGVGSP 1ihjA 13 :ELIHMVTLDKTGKKSFGICIVRGEVKD T0366 39 :V 1ihjA 43 :T T0366 40 :PIFIAMMHPTGVAAQTQKLRVGDRIVTICGTSTEGMTHTQAVNLLKNASGSIEMQVVA 1ihjA 47 :GIFIKGIVPDSPAHLCGRLKVGDRILSLNGKDVRNSTEQAVIDLIKEADFKIELEIQT Number of specific fragments extracted= 3 number of extra gaps= 1 total=460 Number of alignments=106 # 1ihjA read from 1ihjA/merged-good-all-a2m # found chain 1ihjA in training set Warning: unaligning (T0366)S8 because first residue in template chain is (1ihjA)G12 Warning: unaligning (T0366)S34 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ihjA)P41 Warning: unaligning (T0366)P35 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ihjA)P41 Warning: unaligning (T0366)L36 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ihjA)N42 Warning: unaligning (T0366)G98 because last residue in template chain is (1ihjA)F105 T0366 9 :MGLRTVEMKKGPTDSLGISIAGGV 1ihjA 13 :ELIHMVTLDKTGKKSFGICIVRGE T0366 33 :G 1ihjA 39 :D T0366 37 :GD 1ihjA 43 :TK T0366 40 :PIFIAMMHPTGVAAQTQKLRVGDRIVTICGTSTEGMTHTQAVNLLKNASGSIEMQVVA 1ihjA 47 :GIFIKGIVPDSPAHLCGRLKVGDRILSLNGKDVRNSTEQAVIDLIKEADFKIELEIQT Number of specific fragments extracted= 4 number of extra gaps= 1 total=464 Number of alignments=107 # 1ihjA read from 1ihjA/merged-good-all-a2m # found chain 1ihjA in training set Warning: unaligning (T0366)G33 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ihjA)P41 Warning: unaligning (T0366)S34 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ihjA)P41 Warning: unaligning (T0366)P35 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ihjA)N42 Warning: unaligning (T0366)G98 because last residue in template chain is (1ihjA)F105 T0366 9 :MGLRTVEMKKGPTDSLGISIAGGV 1ihjA 13 :ELIHMVTLDKTGKKSFGICIVRGE T0366 36 :LGDVPIFIAMMHPTGVAAQTQKLRVGDRIVTICGTSTEGMTHTQAVNLLKNASGSIEMQVVA 1ihjA 43 :TKTTGIFIKGIVPDSPAHLCGRLKVGDRILSLNGKDVRNSTEQAVIDLIKEADFKIELEIQT Number of specific fragments extracted= 2 number of extra gaps= 1 total=466 Number of alignments=108 # command:Using radius: 8.0000 Alignment mode NUMB_ALIGNS: 108 Adding 609 constraints to all.constraints Done adding distance constraints # command:Reading probabilities from probabilities.dat Reading constraints from ConstraintSet all.constraints maxweight: 1.0000 Optimizing... Probability sum: -194.2669, CN propb: -194.2669 weights: 0.5039 constraints: 253 # command:Found ConstraintSet # PrintContacts align.constraints_v3 Number of constraints in align.constraints 253 # command:Found ConstraintSet # PrintContacts align_bonus.constraints_v3 Number of constraints in align.constraints.bonus 253 # command:Found ConstraintSet # PrintContacts rejected.constraints_v3 Number of constraints in rejected.constraints 356 # command:Found ConstraintSet # PrintContacts rejected_bonus.constraints_v3 Number of constraints in rejected.constraints.bonus 356 # command:Found ConstraintSet # PrintContacts non_contacts.constraints_v3 Number of constraints in noncontact.constraints 0 # command:Found ConstraintSet # PrintContacts non_contacts_bonus.constraints_v3 Number of constraints in noncontact.constraints.bonus 0 # command:Found ConstraintSet # PrintContacts all.constraints_v3 Number of constraints in all.constraints 609 # command: