# 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/T0288/ # command:# Making conformation for sequence T0288 numbered 1 through 93 Created new target T0288 from T0288.a2m # command:# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/T0288/ # command:Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0288//projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0288/manyalignments-good-all.under or /projects/compbio/experiments/protein-predict/casp7/T0288//projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0288/manyalignments-good-all.under.gz for input Trying /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0288/manyalignments-good-all.under # reading script from file /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0288/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/T0288/1vj6A/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0288/1vj6A/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 # T0288 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 T0288 2 :MVPGKVTLQKDAQN 2fneA 1955 :PQCKSITLERGPDG # choosing archetypes in rotamer library T0288 17 :IGISIGGGAQYCP 2fneA 1969 :LGFSIVGGYGSPH T0288 30 :CLYIVQVFDNTPAALDGTVAAGDEITGVNGRSIKGKTKVEVAKMIQEVKGEVTIHYNKLQY 2fneA 1985 :PIYVKTVFAKGAASEDGRLKRGDQIIAVNGQSLEGVTHEEAVAILKRTKGTVTLMVLSSDE Number of specific fragments extracted= 3 number of extra gaps= 0 total=3 Number of alignments=1 # 2fneA read from 2fneA/merged-good-all-a2m # found chain 2fneA in template set T0288 2 :MVPGKVTLQKDAQN 2fneA 1955 :PQCKSITLERGPDG T0288 17 :IGISIGGGA 2fneA 1969 :LGFSIVGGY T0288 26 :QYCPCLYIVQVFDNTPAALDGTVAAGDEITGVNGRSIKGKTKVEVAKMIQEVKGEVTIH 2fneA 1981 :HGDLPIYVKTVFAKGAASEDGRLKRGDQIIAVNGQSLEGVTHEEAVAILKRTKGTVTLM T0288 86 :NKLQ 2fneA 2043 :SDET Number of specific fragments extracted= 4 number of extra gaps= 0 total=7 Number of alignments=2 # 2fneA read from 2fneA/merged-good-all-a2m # found chain 2fneA in template set Warning: unaligning (T0288)M2 because first residue in template chain is (2fneA)M1954 T0288 3 :VPGKVTLQKDAQNLIGISIGGGAQ 2fneA 1955 :PQCKSITLERGPDGLGFSIVGGYG T0288 27 :YCPCLYIVQVFDNTPAALDGTVAAGDEITGVNGRSIKGKTKVEVAKMIQEVKGEVTIHYNKLQYYKV 2fneA 1982 :GDLPIYVKTVFAKGAASEDGRLKRGDQIIAVNGQSLEGVTHEEAVAILKRTKGTVTLMVLSSDETSV Number of specific fragments extracted= 2 number of extra gaps= 0 total=9 Number of alignments=3 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2bygA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0288/2bygA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0288/2bygA/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 # T0288 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 (T0288)G23 because of BadResidue code BAD_PEPTIDE in next template residue (1y8tA)D238 Warning: unaligning (T0288)G24 because of BadResidue code BAD_PEPTIDE at template residue (1y8tA)D238 Warning: unaligning (T0288)A25 because of BadResidue code TOO_FEW_ATOMS+BAD_PEPTIDE in next template residue (1y8tA)D240 Warning: unaligning (T0288)Q26 because of BadResidue code TOO_FEW_ATOMS+BAD_PEPTIDE at template residue (1y8tA)D240 Warning: unaligning (T0288)Y27 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1y8tA)T241 Warning: unaligning (T0288)P29 because of BadResidue code BAD_PEPTIDE at template residue (1y8tA)L242 Warning: unaligning (T0288)T40 because of BadResidue code BAD_PEPTIDE in next template residue (1y8tA)A254 Warning: unaligning (T0288)P41 because of BadResidue code BAD_PEPTIDE at template residue (1y8tA)A254 Warning: unaligning (T0288)L44 because of BadResidue code BAD_PEPTIDE in next template residue (1y8tA)A258 Warning: unaligning (T0288)D45 because of BadResidue code BAD_PEPTIDE at template residue (1y8tA)A258 Warning: unaligning (T0288)G46 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1y8tA)V260 Warning: unaligning (T0288)V48 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1y8tA)V260 Warning: unaligning (T0288)G59 because of BadResidue code TOO_FEW_ATOMS+BAD_PEPTIDE in next template residue (1y8tA)R272 Warning: unaligning (T0288)R60 because of BadResidue code TOO_FEW_ATOMS+BAD_PEPTIDE at template residue (1y8tA)R272 Warning: unaligning (T0288)S61 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1y8tA)P273 Warning: unaligning (T0288)K87 because of BadResidue code BAD_PEPTIDE in next template residue (1y8tA)P300 Warning: unaligning (T0288)L88 because of BadResidue code BAD_PEPTIDE at template residue (1y8tA)P300 Warning: unaligning (T0288)Q89 because of BadResidue code BAD_PEPTIDE at template residue (1y8tA)S301 T0288 16 :LIGISIG 1y8tA 230 :SLGVQVT T0288 30 :CLYIVQVFDN 1y8tA 243 :GAKIVEVVAG T0288 42 :AA 1y8tA 255 :AA T0288 49 :AAGDEITGVN 1y8tA 261 :PKGVVVTKVD T0288 62 :IKG 1y8tA 274 :INS T0288 67 :KVEVAKMIQEV 1y8tA 277 :ADALVAAVRSK T0288 78 :KGEVTIHYN 1y8tA 290 :GATVALTFQ T0288 90 :YY 1y8tA 302 :GG Number of specific fragments extracted= 8 number of extra gaps= 5 total=17 Number of alignments=4 # 1y8tA read from 1y8tA/merged-good-all-a2m # found chain 1y8tA in template set Warning: unaligning (T0288)G23 because of BadResidue code BAD_PEPTIDE in next template residue (1y8tA)D238 Warning: unaligning (T0288)G24 because of BadResidue code BAD_PEPTIDE at template residue (1y8tA)D238 Warning: unaligning (T0288)A25 because of BadResidue code TOO_FEW_ATOMS+BAD_PEPTIDE in next template residue (1y8tA)D240 Warning: unaligning (T0288)Q26 because of BadResidue code TOO_FEW_ATOMS+BAD_PEPTIDE at template residue (1y8tA)D240 Warning: unaligning (T0288)C28 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1y8tA)T241 Warning: unaligning (T0288)P29 because of BadResidue code BAD_PEPTIDE at template residue (1y8tA)L242 Warning: unaligning (T0288)T40 because of BadResidue code BAD_PEPTIDE in next template residue (1y8tA)A254 Warning: unaligning (T0288)P41 because of BadResidue code BAD_PEPTIDE at template residue (1y8tA)A254 Warning: unaligning (T0288)L44 because of BadResidue code BAD_PEPTIDE in next template residue (1y8tA)A258 Warning: unaligning (T0288)D45 because of BadResidue code BAD_PEPTIDE at template residue (1y8tA)A258 Warning: unaligning (T0288)G46 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1y8tA)V260 Warning: unaligning (T0288)V48 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1y8tA)V260 Warning: unaligning (T0288)G59 because of BadResidue code TOO_FEW_ATOMS+BAD_PEPTIDE in next template residue (1y8tA)R272 Warning: unaligning (T0288)R60 because of BadResidue code TOO_FEW_ATOMS+BAD_PEPTIDE at template residue (1y8tA)R272 Warning: unaligning (T0288)S61 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1y8tA)P273 T0288 16 :LIGISIG 1y8tA 230 :SLGVQVT T0288 30 :CLYIVQVFDN 1y8tA 243 :GAKIVEVVAG T0288 42 :AA 1y8tA 255 :AA T0288 49 :AAGDEITGVN 1y8tA 261 :PKGVVVTKVD T0288 62 :IKG 1y8tA 274 :INS T0288 67 :KVEVAKMIQEV 1y8tA 277 :ADALVAAVRSK T0288 78 :KGEVTIH 1y8tA 290 :GATVALT T0288 89 :Q 1y8tA 304 :S Number of specific fragments extracted= 8 number of extra gaps= 4 total=25 Number of alignments=5 # 1y8tA read from 1y8tA/merged-good-all-a2m # found chain 1y8tA in template set Warning: unaligning (T0288)G23 because of BadResidue code BAD_PEPTIDE in next template residue (1y8tA)D238 Warning: unaligning (T0288)G24 because of BadResidue code BAD_PEPTIDE at template residue (1y8tA)D238 Warning: unaligning (T0288)A25 because of BadResidue code TOO_FEW_ATOMS+BAD_PEPTIDE in next template residue (1y8tA)D240 Warning: unaligning (T0288)Q26 because of BadResidue code TOO_FEW_ATOMS+BAD_PEPTIDE at template residue (1y8tA)D240 Warning: unaligning (T0288)C28 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1y8tA)T241 Warning: unaligning (T0288)P29 because of BadResidue code BAD_PEPTIDE at template residue (1y8tA)L242 Warning: unaligning (T0288)T40 because of BadResidue code BAD_PEPTIDE in next template residue (1y8tA)A254 Warning: unaligning (T0288)P41 because of BadResidue code BAD_PEPTIDE at template residue (1y8tA)A254 Warning: unaligning (T0288)L44 because of BadResidue code BAD_PEPTIDE in next template residue (1y8tA)A258 Warning: unaligning (T0288)D45 because of BadResidue code BAD_PEPTIDE at template residue (1y8tA)A258 Warning: unaligning (T0288)G46 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1y8tA)V260 Warning: unaligning (T0288)V48 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1y8tA)V260 Warning: unaligning (T0288)G59 because of BadResidue code TOO_FEW_ATOMS+BAD_PEPTIDE in next template residue (1y8tA)R272 Warning: unaligning (T0288)R60 because of BadResidue code TOO_FEW_ATOMS+BAD_PEPTIDE at template residue (1y8tA)R272 Warning: unaligning (T0288)S61 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1y8tA)P273 Warning: unaligning (T0288)K78 because of BadResidue code BAD_PEPTIDE in next template residue (1y8tA)P289 Warning: unaligning (T0288)G79 because of BadResidue code BAD_PEPTIDE at template residue (1y8tA)P289 Warning: unaligning (T0288)Q89 because of BadResidue code BAD_PEPTIDE in next template residue (1y8tA)P300 Warning: unaligning (T0288)Y90 because of BadResidue code BAD_PEPTIDE at template residue (1y8tA)P300 Warning: unaligning (T0288)Y91 because of BadResidue code BAD_PEPTIDE at template residue (1y8tA)S301 T0288 16 :LIGISIG 1y8tA 230 :SLGVQVT T0288 30 :CLYIVQVFDN 1y8tA 243 :GAKIVEVVAG T0288 42 :AA 1y8tA 255 :AA T0288 49 :AAGDEITGVN 1y8tA 261 :PKGVVVTKVD T0288 62 :IKG 1y8tA 274 :INS T0288 67 :KVEVAKMIQEV 1y8tA 277 :ADALVAAVRSK T0288 80 :EVTIHYNKL 1y8tA 290 :GATVALTFQ T0288 92 :K 1y8tA 302 :G Number of specific fragments extracted= 8 number of extra gaps= 6 total=33 Number of alignments=6 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1qauA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0288 read from 1qauA/merged-good-all-a2m # 1qauA read from 1qauA/merged-good-all-a2m # found chain 1qauA in training set Warning: unaligning (T0288)V3 because first residue in template chain is (1qauA)N14 T0288 4 :PGKVTLQKDAQNLIGISIGGGAQYC 1qauA 15 :VISVRLFKRKVGGLGFLVKERVSKP T0288 30 :CLYIVQVFDNTPAALDGTVAAGDEITGVNGRSIKGKTKVEVAKMIQEV 1qauA 40 :PVIISDLIRGGAAEQSGLIQAGDIILAVNDRPLVDLSYDSALEVLRGI T0288 78 :KGEVTIHYNKLQYY 1qauA 90 :ETHVVLILRGPEGF Number of specific fragments extracted= 3 number of extra gaps= 0 total=36 Number of alignments=7 # 1qauA read from 1qauA/merged-good-all-a2m # found chain 1qauA in training set T0288 4 :PGKVTLQKDAQNLIGISIGGGAQ 1qauA 15 :VISVRLFKRKVGGLGFLVKERVS T0288 28 :CPCLYIVQVFDNTPAALDGTVAAGDEITGVNGRSIKGKTKVEVAKMIQEV 1qauA 38 :KPPVIISDLIRGGAAEQSGLIQAGDIILAVNDRPLVDLSYDSALEVLRGI T0288 78 :KGEVTIH 1qauA 90 :ETHVVLI T0288 85 :YNKLQY 1qauA 105 :THLETT Number of specific fragments extracted= 4 number of extra gaps= 0 total=40 Number of alignments=8 # 1qauA read from 1qauA/merged-good-all-a2m # found chain 1qauA in training set T0288 4 :PGKVTLQKDAQNLIGISIGGGAQ 1qauA 15 :VISVRLFKRKVGGLGFLVKERVS T0288 28 :CPCLYIVQVFDNTPAALDGTVAAGDEITGVNGRSIKGKTKVEVAKMIQEVK 1qauA 38 :KPPVIISDLIRGGAAEQSGLIQAGDIILAVNDRPLVDLSYDSALEVLRGIA T0288 79 :GEVTIHYNKLQYYKV 1qauA 91 :THVVLILRGPEGFTT Number of specific fragments extracted= 3 number of extra gaps= 0 total=43 Number of alignments=9 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1i16/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1i16 expands to /projects/compbio/data/pdb/1i16.pdb.gz 1i16:Warning: there is no chain 1i16 will retry with 1i16A # T0288 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 T0288 2 :MVPGKVTLQKDAQN 1i16 28 :ATVCTVTLEKMSAG T0288 17 :IGISIGGGAQYCP 1i16 42 :LGFSLEGGKGSLH T0288 30 :CLYIVQVFDNTPAALDGTVAAGDEITGVNGRSIKGKTKVEVAKMIQEV 1i16 58 :PLTINRIFKGAASEQSETVQPGDEILQLGGTAMQGLTRFEAWNIIKAL T0288 78 :KGEVTIHYNKLQYY 1i16 107 :DGPVTIVIRRKSLQ Number of specific fragments extracted= 4 number of extra gaps= 0 total=47 Number of alignments=10 # 1i16 read from 1i16/merged-good-all-a2m # found chain 1i16 in template set T0288 2 :MVPGKVTLQKDAQN 1i16 28 :ATVCTVTLEKMSAG T0288 17 :IGISIGGGAQYCP 1i16 42 :LGFSLEGGKGSLH T0288 30 :CLYIVQVFDNTPAALDGTVAAGDEITGVNGRSIKGKTKVEVAKMIQEV 1i16 58 :PLTINRIFKGAASEQSETVQPGDEILQLGGTAMQGLTRFEAWNIIKAL T0288 78 :KGEVTIH 1i16 107 :DGPVTIV T0288 85 :YNKLQYYK 1i16 115 :RRKSLQSK Number of specific fragments extracted= 5 number of extra gaps= 0 total=52 Number of alignments=11 # 1i16 read from 1i16/merged-good-all-a2m # found chain 1i16 in template set T0288 3 :VPGKVTLQKDAQNLIGISIGGGAQ 1i16 28 :ATVCTVTLEKMSAGLGFSLEGGKG T0288 27 :YCPCLYIVQVFDNTPAALDGTVAAGDEITGVNGRSIKGKTKVEVAKMIQEVKGE 1i16 55 :GDKPLTINRIFKGAASEQSETVQPGDEILQLGGTAMQGLTRFEAWNIIKALPDG T0288 81 :VTIHY 1i16 110 :VTIVI T0288 87 :KLQYYK 1i16 115 :RRKSLQ Number of specific fragments extracted= 4 number of extra gaps= 0 total=56 Number of alignments=12 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1v5lA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1v5lA expands to /projects/compbio/data/pdb/1v5l.pdb.gz 1v5lA:# T0288 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 T0288 6 :KVTL 1v5lA 8 :NVVL T0288 12 :DAQNLIGISIGGGAQYCPCLYIVQVFDNTPAALDG 1v5lA 12 :PGPAPWGFRLSGGIDFNQPLVITRITPGSKAAAAN T0288 48 :VAAGDEITGVNGRSIKGKTKVEVAKMIQEVKGEVTIHYNKLQYY 1v5lA 47 :LCPGDVILAIDGFGTESMTHADAQDRIKAASYQLCLKIDRAETR Number of specific fragments extracted= 3 number of extra gaps= 0 total=59 Number of alignments=13 # 1v5lA read from 1v5lA/merged-good-all-a2m # found chain 1v5lA in template set T0288 4 :PGKVTLQ 1v5lA 6 :SGNVVLP T0288 13 :AQNLIGISIGGGAQYCPCLYIVQVFDNTPAALDG 1v5lA 13 :GPAPWGFRLSGGIDFNQPLVITRITPGSKAAAAN T0288 48 :VAAGDEITGVNGRSIKGKTKVEVAKMIQEVKGEVTIH 1v5lA 47 :LCPGDVILAIDGFGTESMTHADAQDRIKAASYQLCLK T0288 87 :KLQYY 1v5lA 87 :AETRL Number of specific fragments extracted= 4 number of extra gaps= 0 total=63 Number of alignments=14 # 1v5lA read from 1v5lA/merged-good-all-a2m # found chain 1v5lA in template set T0288 10 :QKDAQNLIGISIGGGAQYCPCLYIVQVFDNTPAALDG 1v5lA 10 :VLPGPAPWGFRLSGGIDFNQPLVITRITPGSKAAAAN T0288 48 :VAAGDEITGVNGRSIKGKTKVEVAKMIQEVKGEVTIHYNKLQY 1v5lA 47 :LCPGDVILAIDGFGTESMTHADAQDRIKAASYQLCLKIDRAET Number of specific fragments extracted= 2 number of extra gaps= 0 total=65 Number of alignments=15 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1tp5A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1tp5A expands to /projects/compbio/data/pdb/1tp5.pdb.gz 1tp5A:# T0288 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 (T0288)I83 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1tp5A)I389 Warning: unaligning (T0288)H84 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1tp5A)I389 T0288 1 :SMVPGKVTLQKDAQN 1tp5A 308 :PREPRRIVIHRGSTG T0288 17 :IGISIGGGAQYC 1tp5A 323 :LGFNIVGGEDGE T0288 30 :CLYIVQVFDNTPAALDGTVAAGDEITGVNGRSIKGKTKVEVAKMIQEVKGEVT 1tp5A 335 :GIFISFILAGGPADLSGELRKGDQILSVNGVDLRNASHEQAAIALKNAGQTVT T0288 85 :YNKL 1tp5A 390 :AQYK Number of specific fragments extracted= 4 number of extra gaps= 1 total=69 Number of alignments=16 # 1tp5A read from 1tp5A/merged-good-all-a2m # found chain 1tp5A in template set Warning: unaligning (T0288)I83 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1tp5A)I389 Warning: unaligning (T0288)H84 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1tp5A)I389 T0288 1 :SMVPGKVTLQKDAQN 1tp5A 308 :PREPRRIVIHRGSTG T0288 17 :IGISIGGGAQY 1tp5A 323 :LGFNIVGGEDG T0288 29 :PCLYIVQVFDNTPAALDGTVAAGDEITGVNGRSIKGKTKVEVAKMIQEVKGEVT 1tp5A 334 :EGIFISFILAGGPADLSGELRKGDQILSVNGVDLRNASHEQAAIALKNAGQTVT Number of specific fragments extracted= 3 number of extra gaps= 1 total=72 Number of alignments=17 # 1tp5A read from 1tp5A/merged-good-all-a2m # found chain 1tp5A in template set Warning: unaligning (T0288)I83 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1tp5A)I389 Warning: unaligning (T0288)H84 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1tp5A)I389 T0288 2 :MVPGKVTLQKDAQNLIGISIGGGAQ 1tp5A 308 :PREPRRIVIHRGSTGLGFNIVGGED T0288 28 :CPCLYIVQVFDNTPAALDGTVAAGDEITGVNGRSIKGKTKVEVAKMIQEVKGEVT 1tp5A 333 :GEGIFISFILAGGPADLSGELRKGDQILSVNGVDLRNASHEQAAIALKNAGQTVT T0288 85 :YNK 1tp5A 390 :AQY Number of specific fragments extracted= 3 number of extra gaps= 1 total=75 Number of alignments=18 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1i92A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1i92A expands to /projects/compbio/data/pdb/1i92.pdb.gz 1i92A:Skipped atom 533, because occupancy 0.500 <= existing 0.500 in 1i92A Skipped atom 543, because occupancy 0.500 <= existing 0.500 in 1i92A Skipped atom 545, because occupancy 0.500 <= existing 0.500 in 1i92A Skipped atom 547, because occupancy 0.500 <= existing 0.500 in 1i92A Skipped atom 549, because occupancy 0.500 <= existing 0.500 in 1i92A Skipped atom 551, because occupancy 0.500 <= existing 0.500 in 1i92A Skipped atom 553, because occupancy 0.500 <= existing 0.500 in 1i92A Skipped atom 555, because occupancy 0.500 <= existing 0.500 in 1i92A Skipped atom 557, because occupancy 0.500 <= existing 0.500 in 1i92A Skipped atom 559, because occupancy 0.500 <= existing 0.500 in 1i92A Skipped atom 561, because occupancy 0.500 <= existing 0.500 in 1i92A Skipped atom 563, because occupancy 0.500 <= existing 0.500 in 1i92A Skipped atom 565, because occupancy 0.500 <= existing 0.500 in 1i92A Skipped atom 567, because occupancy 0.500 <= existing 0.500 in 1i92A Skipped atom 569, because occupancy 0.500 <= existing 0.500 in 1i92A Skipped atom 571, because occupancy 0.500 <= existing 0.500 in 1i92A Skipped atom 573, because occupancy 0.500 <= existing 0.500 in 1i92A Skipped atom 575, because occupancy 0.500 <= existing 0.500 in 1i92A Skipped atom 577, because occupancy 0.500 <= existing 0.500 in 1i92A Skipped atom 579, because occupancy 0.500 <= existing 0.500 in 1i92A Skipped atom 581, because occupancy 0.500 <= existing 0.500 in 1i92A Skipped atom 583, because occupancy 0.500 <= existing 0.500 in 1i92A # T0288 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 (T0288)K78 because of BadResidue code TOO_FEW_ATOMS+NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1i92A)N84 Warning: unaligning (T0288)G79 because of BadResidue code TOO_FEW_ATOMS+NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1i92A)N84 T0288 1 :SMVPGKVTLQKDAQN 1i92A 9 :GMLPRLCCLEKGPNG T0288 17 :IGISIGGGAQ 1i92A 24 :YGFHLHGEKG T0288 28 :CPCLYIVQVFDNTPAALDG 1i92A 34 :KLGQYIRLVEPGSPAEKAG T0288 48 :VAAGDEITGVNGRSIKGKTKVEVAKMIQEV 1i92A 53 :LLAGDRLVEVNGENVEKETHQQVVSRIRAA T0288 80 :EVTIHYNKLQYYKV 1i92A 85 :AVRLLVVDPEQDTR Number of specific fragments extracted= 5 number of extra gaps= 1 total=80 Number of alignments=19 # 1i92A read from 1i92A/merged-good-all-a2m # found chain 1i92A in template set Warning: unaligning (T0288)K78 because of BadResidue code TOO_FEW_ATOMS+NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1i92A)N84 Warning: unaligning (T0288)G79 because of BadResidue code TOO_FEW_ATOMS+NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1i92A)N84 T0288 1 :SMVPGKVTLQKDAQN 1i92A 9 :GMLPRLCCLEKGPNG T0288 17 :IGISIGGGAQ 1i92A 24 :YGFHLHGEKG T0288 28 :CPCLYIVQVFDNTPAALDG 1i92A 34 :KLGQYIRLVEPGSPAEKAG T0288 48 :VAAGDEITGVNGRSIKGKTKVEVAKMIQEV 1i92A 53 :LLAGDRLVEVNGENVEKETHQQVVSRIRAA T0288 80 :EVTIH 1i92A 85 :AVRLL T0288 85 :YN 1i92A 93 :PE Number of specific fragments extracted= 6 number of extra gaps= 1 total=86 Number of alignments=20 # 1i92A read from 1i92A/merged-good-all-a2m # found chain 1i92A in template set Warning: unaligning (T0288)K78 because of BadResidue code TOO_FEW_ATOMS+NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1i92A)N84 Warning: unaligning (T0288)G79 because of BadResidue code TOO_FEW_ATOMS+NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1i92A)N84 T0288 4 :PGKVTLQKDAQNLIGISIGGGAQ 1i92A 11 :LPRLCCLEKGPNGYGFHLHGEKG T0288 28 :CPCLYIVQVFDNTPAALDG 1i92A 34 :KLGQYIRLVEPGSPAEKAG T0288 48 :VAAGDEITGVNGRSIKGKTKVEVAKMIQEV 1i92A 53 :LLAGDRLVEVNGENVEKETHQQVVSRIRAA T0288 80 :EVTIHYNKLQYYKV 1i92A 85 :AVRLLVVDPEQDTR Number of specific fragments extracted= 4 number of extra gaps= 1 total=90 Number of alignments=21 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1bfeA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1bfeA expands to /projects/compbio/data/pdb/1bfe.pdb.gz 1bfeA:# T0288 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 T0288 2 :MVPGKVTLQKDAQN 1bfeA 309 :REPRRIVIHRGSTG T0288 17 :IGISIGGGAQYC 1bfeA 323 :LGFNIIGGEDGE T0288 30 :CLYIVQVFDNTPAALDGTVAAGDEITGVNGRSIKGKTKVEVAKMIQEVKGEVTIHYNKL 1bfeA 335 :GIFISFILAGGPADLSGELRKGDQILSVNGVDLRNASHEQAAIALKNAGQTVTIIAQYK Number of specific fragments extracted= 3 number of extra gaps= 0 total=93 Number of alignments=22 # 1bfeA read from 1bfeA/merged-good-all-a2m # found chain 1bfeA in template set T0288 2 :MVPGKVTLQKDAQN 1bfeA 309 :REPRRIVIHRGSTG T0288 17 :IGISIGGGAQY 1bfeA 323 :LGFNIIGGEDG T0288 29 :PCLYIVQVFDNTPAALDGTVAAGDEITGVNGRSIKGKTKVEVAKMIQEVKGEVTIH 1bfeA 334 :EGIFISFILAGGPADLSGELRKGDQILSVNGVDLRNASHEQAAIALKNAGQTVTII Number of specific fragments extracted= 3 number of extra gaps= 0 total=96 Number of alignments=23 # 1bfeA read from 1bfeA/merged-good-all-a2m # found chain 1bfeA in template set T0288 3 :VPGKVTLQKDAQNLIGISIGGGAQ 1bfeA 309 :REPRRIVIHRGSTGLGFNIIGGED T0288 28 :CPCLYIVQVFDNTPAALDGTVAAGDEITGVNGRSIKGKTKVEVAKMIQEVKGEVTIHYNK 1bfeA 333 :GEGIFISFILAGGPADLSGELRKGDQILSVNGVDLRNASHEQAAIALKNAGQTVTIIAQY Number of specific fragments extracted= 2 number of extra gaps= 0 total=98 Number of alignments=24 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1fc6A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0288 read from 1fc6A/merged-good-all-a2m # 1fc6A read from 1fc6A/merged-good-all-a2m # found chain 1fc6A in training set T0288 15 :NLIGISIGGGAQYCPCLYIVQVFDNTPAALDG 1fc6A 161 :TGVGLEITYDGGSGKDVVVLTPAPGGPAEKAG T0288 48 :VAAGDEITGVNGRSIKGKTKVEVAKMI 1fc6A 193 :ARAGDVIVTVDGTAVKGMSLYDVSDLL T0288 77 :VKGEVTIHYNKLQY 1fc6A 223 :ADSQVEVVLHAPGA Number of specific fragments extracted= 3 number of extra gaps= 0 total=101 Number of alignments=25 # 1fc6A read from 1fc6A/merged-good-all-a2m # found chain 1fc6A in training set T0288 15 :NLIGISIGGGAQYCPCLYIVQVFDNTPAALDG 1fc6A 161 :TGVGLEITYDGGSGKDVVVLTPAPGGPAEKAG T0288 48 :VAAGDEITGVNGRSIKGKTKVEVAKMI 1fc6A 193 :ARAGDVIVTVDGTAVKGMSLYDVSDLL T0288 77 :VKGEVTIH 1fc6A 223 :ADSQVEVV T0288 85 :YNKLQY 1fc6A 237 :PSNTRT Number of specific fragments extracted= 4 number of extra gaps= 0 total=105 Number of alignments=26 # 1fc6A read from 1fc6A/merged-good-all-a2m # found chain 1fc6A in training set T0288 13 :AQNLIGISIGGGAQYCPCLYIVQVFDNTPAALDG 1fc6A 159 :SVTGVGLEITYDGGSGKDVVVLTPAPGGPAEKAG T0288 48 :VAAGDEITGVNGRSIKGKTKVEVAKMI 1fc6A 193 :ARAGDVIVTVDGTAVKGMSLYDVSDLL T0288 77 :VKGEVTIHYNKLQY 1fc6A 223 :ADSQVEVVLHAPGA Number of specific fragments extracted= 3 number of extra gaps= 0 total=108 Number of alignments=27 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1t2mA/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/T0288/1t2mA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0288/1t2mA/merged-good-all-a2m.gz for input Trying 1t2mA/merged-good-all-a2m Error: Couldn't open file 1t2mA/merged-good-all-a2m or 1t2mA/merged-good-all-a2m.gz for input # 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/T0288/1gm1A/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0288/1gm1A/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/T0288/1kefA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0288/1kefA/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:# T0288 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 (T0288)K92 because last residue in template chain is (1nf3C)N253 T0288 2 :MVPGKVTLQK 1nf3C 153 :ETHRRVRLCK T0288 12 :DAQNLIGISIGGGAQYCP 1nf3C 164 :GTEKPLGFYIRDGSSVRV T0288 30 :CLYIVQVFDNTPAALDGTVAAGDEITGVNGRSIKGKTKVEVAKMIQEVKGEVTIHYNKLQYY 1nf3C 191 :GIFISRLVPGGLAQSTGLLAVNDEVLEVNGIEVSGKSLDQVTDMMIANSRNLIITVRPANQR Number of specific fragments extracted= 3 number of extra gaps= 0 total=111 Number of alignments=28 # 1nf3C read from 1nf3C/merged-good-all-a2m # found chain 1nf3C in template set T0288 2 :MVPGKVTLQK 1nf3C 153 :ETHRRVRLCK T0288 12 :DAQNLIGISIGGGAQYCP 1nf3C 164 :GTEKPLGFYIRDGSSVRV T0288 30 :CLYIVQVFDNTPAALDGTVAAGDEITGVNGRSIKGKTKVEVAKMIQEVKGEVTIH 1nf3C 191 :GIFISRLVPGGLAQSTGLLAVNDEVLEVNGIEVSGKSLDQVTDMMIANSRNLIIT T0288 85 :YNK 1nf3C 249 :ANQ Number of specific fragments extracted= 4 number of extra gaps= 0 total=115 Number of alignments=29 # 1nf3C read from 1nf3C/merged-good-all-a2m # found chain 1nf3C in template set Warning: unaligning (T0288)K92 because last residue in template chain is (1nf3C)N253 T0288 3 :VPGKVTLQKDAQNLIGISIGGGAQ 1nf3C 155 :HRRVRLCKYGTEKPLGFYIRDGSS T0288 27 :YCPCLYIVQVFDNTPAALDGTVAAGDEITGVNGRSIKGKTKVEVAKMIQEVKGEVTIHYNKLQYY 1nf3C 188 :KVPGIFISRLVPGGLAQSTGLLAVNDEVLEVNGIEVSGKSLDQVTDMMIANSRNLIITVRPANQR Number of specific fragments extracted= 2 number of extra gaps= 0 total=117 Number of alignments=30 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1wf7A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1wf7A expands to /projects/compbio/data/pdb/1wf7.pdb.gz 1wf7A:# T0288 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 T0288 2 :MVPGKVTLQ 1wf7A 4 :GSSGSVSLV T0288 13 :AQNLIGISIGGGAQYCPCLYIVQVFDNTPAALDG 1wf7A 13 :GPAPWGFRLQGGKDFNMPLTISSLKDGGKASQAH T0288 48 :VAAGDEITGVNGRSIKGKTKVEVAKMIQEVKGEVTIHYNKLQYY 1wf7A 47 :VRIGDVVLSIDGISAQGMTHLEAQNKIKACTGSLNMTLQRASAA Number of specific fragments extracted= 3 number of extra gaps= 0 total=120 Number of alignments=31 # 1wf7A read from 1wf7A/merged-good-all-a2m # found chain 1wf7A in template set T0288 1 :SMVPGKVTLQ 1wf7A 3 :SGSSGSVSLV T0288 13 :AQNLIGISIGGGAQYCPCLYIVQVFDNTPAALDG 1wf7A 13 :GPAPWGFRLQGGKDFNMPLTISSLKDGGKASQAH T0288 48 :VAAGDEITGVNGRSIKGKTKVEVAKMIQEVKGEVTIH 1wf7A 47 :VRIGDVVLSIDGISAQGMTHLEAQNKIKACTGSLNMT Number of specific fragments extracted= 3 number of extra gaps= 0 total=123 Number of alignments=32 # 1wf7A read from 1wf7A/merged-good-all-a2m # found chain 1wf7A in template set T0288 7 :VTLQKDAQNLIGISIGGGAQYCPCLYIVQVFDNTPAALDG 1wf7A 7 :GSVSLVGPAPWGFRLQGGKDFNMPLTISSLKDGGKASQAH T0288 48 :VAAGDEITGVNGRSIKGKTKVEVAKMIQEVKGEVTIHYNKLQYY 1wf7A 47 :VRIGDVVLSIDGISAQGMTHLEAQNKIKACTGSLNMTLQRASAA Number of specific fragments extracted= 2 number of extra gaps= 0 total=125 Number of alignments=33 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1um7A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0288/1um7A/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0288/1um7A/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 # T0288 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 (T0288)V3 because first residue in template chain is (2f0aA)M251 Warning: unaligning (T0288)N15 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2f0aA)N263 Warning: unaligning (T0288)Q89 because last residue in template chain is (2f0aA)E342 T0288 4 :PGKVTLQ 2f0aA 252 :IITVTLN T0288 16 :LIGISIGG 2f0aA 264 :FLGISIVG T0288 24 :GAQYCPCLYIVQVFDNTPAALDGTVAAGDEITGVNGRSIKGKTKVEVAKMIQEV 2f0aA 274 :NERGDGGIYIGSIMKGGAVAADGRIEPGDMLLQVNDINFENMSNDDAVRVLRDI T0288 78 :KGEVTIHYNKL 2f0aA 331 :PGPIVLTVAKL Number of specific fragments extracted= 4 number of extra gaps= 1 total=129 Number of alignments=34 # 2f0aA read from 2f0aA/merged-good-all-a2m # found chain 2f0aA in template set Warning: unaligning (T0288)V3 because first residue in template chain is (2f0aA)M251 Warning: unaligning (T0288)N15 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2f0aA)N263 Warning: unaligning (T0288)N86 because last residue in template chain is (2f0aA)E342 T0288 4 :PGKVTLQ 2f0aA 252 :IITVTLN T0288 16 :LIGISIGG 2f0aA 264 :FLGISIVG T0288 24 :GAQYCPCLYIVQVFDNTPAALDGTVAAGDEITGVNGRSIKGKTKVEVAKMIQEV 2f0aA 274 :NERGDGGIYIGSIMKGGAVAADGRIEPGDMLLQVNDINFENMSNDDAVRVLRDI T0288 78 :KGEVTIH 2f0aA 331 :PGPIVLT T0288 85 :Y 2f0aA 341 :L Number of specific fragments extracted= 5 number of extra gaps= 1 total=134 Number of alignments=35 # 2f0aA read from 2f0aA/merged-good-all-a2m # found chain 2f0aA in template set Warning: unaligning (T0288)N15 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2f0aA)N263 Warning: unaligning (T0288)Q89 because last residue in template chain is (2f0aA)E342 T0288 16 :LIGISIGGGAQ 2f0aA 264 :FLGISIVGQSN T0288 27 :YCPCLYIVQVFDNTPAALDGTVAAGDEITGVNGRSIKGKTKVEVAKMIQEV 2f0aA 277 :GDGGIYIGSIMKGGAVAADGRIEPGDMLLQVNDINFENMSNDDAVRVLRDI T0288 78 :KGEVTIHYNKL 2f0aA 331 :PGPIVLTVAKL Number of specific fragments extracted= 3 number of extra gaps= 1 total=137 Number of alignments=36 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1n7eA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1n7eA expands to /projects/compbio/data/pdb/1n7e.pdb.gz 1n7eA:# T0288 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 T0288 1 :SMVPGKVTLQKDAQN 1n7eA 667 :GAIIYTVELKRYGGP T0288 17 :IGISIGGGAQYCPCLYIVQVFDNTPAALDGTVAAGDEITGVNGRSIKGKTKVEVAKMIQEVKGEVTIHYNKLQYYKV 1n7eA 682 :LGITISGTEEPFDPIIISSLTKGGLAERTGAIHIGDRILAINSSSLKGKPLSEAIHLLQMAGETVTLKIKKQTDAQP Number of specific fragments extracted= 2 number of extra gaps= 0 total=139 Number of alignments=37 # 1n7eA read from 1n7eA/merged-good-all-a2m # found chain 1n7eA in template set T0288 1 :SMVPGKVTLQKDAQN 1n7eA 667 :GAIIYTVELKRYGGP T0288 17 :IGISIGGGAQYCPCLYIVQVFDNTPAALDGTVAAGDEITGVNGRSIKGKTKVEVAKMIQEVKGEVTIH 1n7eA 682 :LGITISGTEEPFDPIIISSLTKGGLAERTGAIHIGDRILAINSSSLKGKPLSEAIHLLQMAGETVTLK T0288 87 :KL 1n7eA 756 :AQ Number of specific fragments extracted= 3 number of extra gaps= 0 total=142 Number of alignments=38 # 1n7eA read from 1n7eA/merged-good-all-a2m # found chain 1n7eA in template set T0288 3 :VPGKVTLQKDAQNLIGISIGGGAQYCPCLYIVQVFDNTPAALDGTVAAGDEITGVNGRSIKGKTKVEVAKMIQEVKGEVTIHYNKLQYYKV 1n7eA 668 :AIIYTVELKRYGGPLGITISGTEEPFDPIIISSLTKGGLAERTGAIHIGDRILAINSSSLKGKPLSEAIHLLQMAGETVTLKIKKQTDAQP Number of specific fragments extracted= 1 number of extra gaps= 0 total=143 Number of alignments=39 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ky9A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1ky9A expands to /projects/compbio/data/pdb/1ky9.pdb.gz 1ky9A:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0288 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 T0288 30 :CLYIVQVFDNTPAALDG 1ky9A 287 :GAFVSQVLPNSSAAKAG T0288 48 :VAAGDEITGVNGRSIKGK 1ky9A 304 :IKAGDVITSLNGKPISSF T0288 68 :VEVAKMIQEV 1ky9A 322 :AALRAQVGTM T0288 78 :KGEVTIHYNKLQY 1ky9A 334 :GSKLTLGLLRDGK Number of specific fragments extracted= 4 number of extra gaps= 0 total=147 Number of alignments=40 # 1ky9A read from 1ky9A/merged-good-all-a2m # found chain 1ky9A in template set Warning: unaligning (T0288)A25 because of BadResidue code BAD_PEPTIDE in next template residue (1ky9A)P231 Warning: unaligning (T0288)Q26 because of BadResidue code BAD_PEPTIDE at template residue (1ky9A)P231 T0288 10 :QKDAQNLIGISIGGG 1ky9A 215 :VNLNGELIGINTAIL T0288 27 :YCP 1ky9A 232 :DGG T0288 30 :CLYIVQVFDNTPAALDG 1ky9A 287 :GAFVSQVLPNSSAAKAG T0288 48 :VAAGDEITGVNGRSIKGK 1ky9A 304 :IKAGDVITSLNGKPISSF T0288 68 :VEVAKMIQEV 1ky9A 322 :AALRAQVGTM T0288 78 :KGEVTIH 1ky9A 334 :GSKLTLG T0288 85 :YNKLQ 1ky9A 343 :RDGKQ Number of specific fragments extracted= 7 number of extra gaps= 1 total=154 Number of alignments=41 # 1ky9A read from 1ky9A/merged-good-all-a2m # found chain 1ky9A in template set T0288 24 :GAQYCPCLYIVQVFDNTPAALDG 1ky9A 281 :KVDAQRGAFVSQVLPNSSAAKAG T0288 48 :VAAGDEITGVNGRSIKGK 1ky9A 304 :IKAGDVITSLNGKPISSF T0288 68 :VEVAKMIQEVKGEVTIHYNKLQYY 1ky9A 322 :AALRAQVGTMPVGSKLTLGLLRDG Number of specific fragments extracted= 3 number of extra gaps= 0 total=157 Number of alignments=42 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ky9B/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1ky9B expands to /projects/compbio/data/pdb/1ky9.pdb.gz 1ky9B:# T0288 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 (T0288)E76 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ky9B)P332 T0288 30 :CLYIVQVFDNTPAALDG 1ky9B 287 :GAFVSQVLPNSSAAKAG T0288 48 :VAAGDEITGVNGRSIKG 1ky9B 304 :IKAGDVITSLNGKPISS T0288 67 :KVEVAKMIQ 1ky9B 321 :FAALRAQVG T0288 78 :KGEVTIHYNKLQY 1ky9B 334 :GSKLTLGLLRDGK Number of specific fragments extracted= 4 number of extra gaps= 0 total=161 Number of alignments=43 # 1ky9B read from 1ky9B/merged-good-all-a2m # found chain 1ky9B in template set Warning: unaligning (T0288)A25 because of BadResidue code BAD_PEPTIDE in next template residue (1ky9B)P231 Warning: unaligning (T0288)Q26 because of BadResidue code BAD_PEPTIDE at template residue (1ky9B)P231 Warning: unaligning (T0288)E76 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ky9B)P332 T0288 11 :KDAQNLIGISIGGG 1ky9B 216 :NLNGELIGINTAIL T0288 27 :YCP 1ky9B 232 :DGG T0288 30 :CLYIVQVFDNTPAALDG 1ky9B 287 :GAFVSQVLPNSSAAKAG T0288 48 :VAAGDEITGVNGRSIKG 1ky9B 304 :IKAGDVITSLNGKPISS T0288 67 :KVEVAKMIQ 1ky9B 321 :FAALRAQVG T0288 78 :KGEVTIH 1ky9B 334 :GSKLTLG T0288 85 :YNKLQYY 1ky9B 342 :LRDGKQV Number of specific fragments extracted= 7 number of extra gaps= 1 total=168 Number of alignments=44 # 1ky9B read from 1ky9B/merged-good-all-a2m # found chain 1ky9B in template set Warning: unaligning (T0288)I19 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ky9B)G269 Warning: unaligning (T0288)I21 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ky9B)G269 T0288 16 :LIG 1ky9B 264 :ELG T0288 22 :GGGAQ 1ky9B 270 :TELNS T0288 27 :YCPCLYIVQVFDNTPAALDG 1ky9B 284 :AQRGAFVSQVLPNSSAAKAG T0288 48 :VAAGDEITGVNGRSIKG 1ky9B 304 :IKAGDVITSLNGKPISS T0288 67 :KVEVAKM 1ky9B 321 :FAALRAQ Number of specific fragments extracted= 5 number of extra gaps= 0 total=173 Number of alignments=45 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1zokA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0288/1zokA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0288/1zokA/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 1xz9A/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/T0288/1xz9A/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0288/1xz9A/merged-good-all-a2m.gz for input Trying 1xz9A/merged-good-all-a2m Error: Couldn't open file 1xz9A/merged-good-all-a2m or 1xz9A/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 # T0288 read from 1mfgA/merged-good-all-a2m # 1mfgA read from 1mfgA/merged-good-all-a2m # found chain 1mfgA in training set Warning: unaligning (T0288)G79 because of BadResidue code BAD_PEPTIDE in next template residue (1mfgA)T1360 Warning: unaligning (T0288)E80 because of BadResidue code BAD_PEPTIDE at template residue (1mfgA)T1360 Warning: unaligning (T0288)I83 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (1mfgA)I1364 Warning: unaligning (T0288)H84 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (1mfgA)I1364 Warning: unaligning (T0288)Y91 because last residue in template chain is (1mfgA)S1371 T0288 1 :SMVPGKVTLQKDAQ 1mfgA 1277 :GSMEIRVRVEKDPE T0288 17 :IGISIGGGAQYCP 1mfgA 1291 :LGFSISGGVGGRG T0288 30 :CLYIVQVFDNTPA 1mfgA 1312 :GIFVTRVQPEGPA T0288 45 :DGTVAAGDEITGVNGRSIKGKTKVEVAKMIQEVK 1mfgA 1325 :SKLLQPGDKIIQANGYSFINIEHGQAVSLLKTFQ T0288 81 :VT 1mfgA 1361 :VE T0288 85 :YNKLQY 1mfgA 1365 :IVREVS Number of specific fragments extracted= 6 number of extra gaps= 2 total=179 Number of alignments=46 # 1mfgA read from 1mfgA/merged-good-all-a2m # found chain 1mfgA in training set Warning: unaligning (T0288)G79 because of BadResidue code BAD_PEPTIDE in next template residue (1mfgA)T1360 Warning: unaligning (T0288)E80 because of BadResidue code BAD_PEPTIDE at template residue (1mfgA)T1360 Warning: unaligning (T0288)I83 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (1mfgA)I1364 Warning: unaligning (T0288)H84 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (1mfgA)I1364 T0288 1 :SMVPGKVTLQKDAQ 1mfgA 1277 :GSMEIRVRVEKDPE T0288 17 :IGISIGGGAQYCP 1mfgA 1291 :LGFSISGGVGGRG T0288 30 :CLYIVQVFDNTPA 1mfgA 1312 :GIFVTRVQPEGPA T0288 45 :DGTVAAGDEITGVNGRSIKGKTKVEVAKMIQEVK 1mfgA 1325 :SKLLQPGDKIIQANGYSFINIEHGQAVSLLKTFQ T0288 81 :VT 1mfgA 1361 :VE T0288 85 :Y 1mfgA 1369 :V Number of specific fragments extracted= 6 number of extra gaps= 2 total=185 Number of alignments=47 # 1mfgA read from 1mfgA/merged-good-all-a2m # found chain 1mfgA in training set Warning: unaligning (T0288)G79 because of BadResidue code BAD_PEPTIDE in next template residue (1mfgA)T1360 Warning: unaligning (T0288)E80 because of BadResidue code BAD_PEPTIDE at template residue (1mfgA)T1360 Warning: unaligning (T0288)I83 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (1mfgA)I1364 Warning: unaligning (T0288)H84 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (1mfgA)I1364 T0288 4 :PGKVTLQKDAQNLIGISIGGGAQ 1mfgA 1278 :SMEIRVRVEKDPELGFSISGGVG T0288 27 :YCPCLYIVQVFDNTPA 1mfgA 1309 :DDDGIFVTRVQPEGPA T0288 45 :DGTVAAGDEITGVNGRSIKGKTKVEVAKMIQEVK 1mfgA 1325 :SKLLQPGDKIIQANGYSFINIEHGQAVSLLKTFQ T0288 81 :VT 1mfgA 1361 :VE T0288 85 :YNKLQY 1mfgA 1365 :IVREVS Number of specific fragments extracted= 5 number of extra gaps= 2 total=190 Number of alignments=48 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1b8qA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1b8qA expands to /projects/compbio/data/pdb/1b8q.pdb.gz 1b8qA:# T0288 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 T0288 5 :GKVTLQKDAQNLIGISIGGGAQYC 1b8qA 10 :ISVRLFKRKVGGLGFLVKERVSKP T0288 30 :CLYIVQVFDNTPAALDGTVAAGDEITGVNGRSIKGKTKVEVAKMIQEV 1b8qA 34 :PVIISDLIRGGAAEQSGLIQAGDIILAVNDRPLVDLSYDSALEVLRGI T0288 78 :KGEVTIHYNKLQYY 1b8qA 84 :ETHVVLILRGPEGF Number of specific fragments extracted= 3 number of extra gaps= 0 total=193 Number of alignments=49 # 1b8qA read from 1b8qA/merged-good-all-a2m # found chain 1b8qA in template set T0288 5 :GKVTLQKDAQNLIGISIGGGAQ 1b8qA 10 :ISVRLFKRKVGGLGFLVKERVS T0288 28 :CPCLYIVQVFDNTPAALDGTVAAGDEITGVNGRSIKGKTKVEVAKMIQEV 1b8qA 32 :KPPVIISDLIRGGAAEQSGLIQAGDIILAVNDRPLVDLSYDSALEVLRGI T0288 78 :KGEVTIH 1b8qA 84 :ETHVVLI T0288 86 :NKLQYY 1b8qA 94 :PEGFTT Number of specific fragments extracted= 4 number of extra gaps= 0 total=197 Number of alignments=50 # 1b8qA read from 1b8qA/merged-good-all-a2m # found chain 1b8qA in template set T0288 3 :VPGKVTLQKDAQNLIGISIGGGAQ 1b8qA 8 :NVISVRLFKRKVGGLGFLVKERVS T0288 28 :CPCLYIVQVFDNTPAALDGTVAAGDEITGVNGRSIKGKTKVEVAKMIQEVKGEVTIHYNKLQYYK 1b8qA 32 :KPPVIISDLIRGGAAEQSGLIQAGDIILAVNDRPLVDLSYDSALEVLRGIASETHVVLILRGPEG Number of specific fragments extracted= 2 number of extra gaps= 0 total=199 Number of alignments=51 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1nteA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1nteA expands to /projects/compbio/data/pdb/1nte.pdb.gz 1nteA:Skipped atom 107, because occupancy 0.500 <= existing 0.500 in 1nteA Skipped atom 281, because occupancy 0.400 <= existing 0.600 in 1nteA Skipped atom 283, because occupancy 0.400 <= existing 0.600 in 1nteA Skipped atom 285, because occupancy 0.400 <= existing 0.600 in 1nteA Skipped atom 287, because occupancy 0.400 <= existing 0.600 in 1nteA Skipped atom 289, because occupancy 0.400 <= existing 0.600 in 1nteA Skipped atom 291, because occupancy 0.400 <= existing 0.600 in 1nteA Skipped atom 332, because occupancy 0.500 <= existing 0.500 in 1nteA Skipped atom 334, because occupancy 0.500 <= existing 0.500 in 1nteA Skipped atom 336, because occupancy 0.500 <= existing 0.500 in 1nteA Skipped atom 338, because occupancy 0.500 <= existing 0.500 in 1nteA Skipped atom 340, because occupancy 0.500 <= existing 0.500 in 1nteA Skipped atom 373, because occupancy 0.500 <= existing 0.500 in 1nteA Skipped atom 595, because occupancy 0.300 <= existing 0.700 in 1nteA Skipped atom 597, because occupancy 0.300 <= existing 0.700 in 1nteA Skipped atom 599, because occupancy 0.300 <= existing 0.700 in 1nteA Skipped atom 601, because occupancy 0.300 <= existing 0.700 in 1nteA # T0288 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 (T0288)M2 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1nteA)D195 Warning: unaligning (T0288)V3 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1nteA)D195 T0288 1 :S 1nteA 193 :A T0288 4 :PGKVTLQKDAQNLIGISIGGG 1nteA 196 :PRTITMHKDSTGHVGFIFKNG T0288 32 :YIVQVFDNTPAALDG 1nteA 217 :KITSIVKDSSAARNG T0288 48 :VAAGDEITGVNGRSIKGKTKVEVAKMIQEVKGEVTIHYNKL 1nteA 232 :LLTEHNICEINGQNVIGLKDSQIADILSTSGTVVTITIMPA Number of specific fragments extracted= 4 number of extra gaps= 1 total=203 Number of alignments=52 # 1nteA read from 1nteA/merged-good-all-a2m # found chain 1nteA in template set Warning: unaligning (T0288)M2 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1nteA)D195 Warning: unaligning (T0288)V3 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1nteA)D195 T0288 1 :S 1nteA 193 :A T0288 4 :PGKVTLQKDAQNLIGISIGGG 1nteA 196 :PRTITMHKDSTGHVGFIFKNG T0288 32 :YIVQVFDNTPAALDG 1nteA 217 :KITSIVKDSSAARNG T0288 48 :VAAGDEITGVNGRSIKGKTKVEVAKMIQEVKGEVTIH 1nteA 232 :LLTEHNICEINGQNVIGLKDSQIADILSTSGTVVTIT Number of specific fragments extracted= 4 number of extra gaps= 1 total=207 Number of alignments=53 # 1nteA read from 1nteA/merged-good-all-a2m # found chain 1nteA in template set Warning: unaligning (T0288)V3 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1nteA)D195 T0288 4 :PGKVTLQKDAQNLIGISIGGG 1nteA 196 :PRTITMHKDSTGHVGFIFKNG T0288 32 :YIVQVFDNTPAALDG 1nteA 217 :KITSIVKDSSAARNG T0288 48 :VAAGDEITGVNGRSIKGKTKVEVAKMIQEVKGEVTIHYNKL 1nteA 232 :LLTEHNICEINGQNVIGLKDSQIADILSTSGTVVTITIMPA Number of specific fragments extracted= 3 number of extra gaps= 1 total=210 Number of alignments=54 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2fe5A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2fe5A expands to /projects/compbio/data/pdb/2fe5.pdb.gz 2fe5A:Skipped atom 9, because occupancy 0.300 <= existing 0.700 in 2fe5A Skipped atom 13, because occupancy 0.300 <= existing 0.700 in 2fe5A Skipped atom 15, because occupancy 0.300 <= existing 0.700 in 2fe5A Skipped atom 17, because occupancy 0.300 <= existing 0.700 in 2fe5A Skipped atom 19, because occupancy 0.300 <= existing 0.700 in 2fe5A Skipped atom 42, because occupancy 0.500 <= existing 0.500 in 2fe5A Skipped atom 44, because occupancy 0.500 <= existing 0.500 in 2fe5A Skipped atom 47, because occupancy 0.300 <= existing 0.700 in 2fe5A Skipped atom 51, because occupancy 0.300 <= existing 0.700 in 2fe5A Skipped atom 53, because occupancy 0.300 <= existing 0.700 in 2fe5A Skipped atom 55, because occupancy 0.300 <= existing 0.700 in 2fe5A Skipped atom 57, because occupancy 0.300 <= existing 0.700 in 2fe5A Skipped atom 59, because occupancy 0.300 <= existing 0.700 in 2fe5A Skipped atom 294, because occupancy 0.400 <= existing 0.600 in 2fe5A Skipped atom 296, because occupancy 0.400 <= existing 0.600 in 2fe5A Skipped atom 298, because occupancy 0.400 <= existing 0.600 in 2fe5A Skipped atom 300, because occupancy 0.400 <= existing 0.600 in 2fe5A Skipped atom 302, because occupancy 0.400 <= existing 0.600 in 2fe5A Skipped atom 317, because occupancy 0.300 <= existing 0.700 in 2fe5A Skipped atom 320, because occupancy 0.300 <= existing 0.700 in 2fe5A Skipped atom 431, because occupancy 0.300 <= existing 0.700 in 2fe5A Skipped atom 433, because occupancy 0.300 <= existing 0.700 in 2fe5A Skipped atom 435, because occupancy 0.300 <= existing 0.700 in 2fe5A Skipped atom 437, because occupancy 0.300 <= existing 0.700 in 2fe5A Skipped atom 439, because occupancy 0.300 <= existing 0.700 in 2fe5A Skipped atom 441, because occupancy 0.300 <= existing 0.700 in 2fe5A Skipped atom 443, because occupancy 0.300 <= existing 0.700 in 2fe5A Skipped atom 593, because occupancy 0.250 <= existing 0.750 in 2fe5A Skipped atom 597, because occupancy 0.250 <= existing 0.750 in 2fe5A Skipped atom 599, because occupancy 0.250 <= existing 0.750 in 2fe5A Skipped atom 618, because occupancy 0.500 <= existing 0.500 in 2fe5A Skipped atom 620, because occupancy 0.500 <= existing 0.500 in 2fe5A Skipped atom 622, because occupancy 0.500 <= existing 0.500 in 2fe5A Skipped atom 624, because occupancy 0.500 <= existing 0.500 in 2fe5A Skipped atom 626, because occupancy 0.500 <= existing 0.500 in 2fe5A Skipped atom 628, because occupancy 0.500 <= existing 0.500 in 2fe5A Skipped atom 630, because occupancy 0.500 <= existing 0.500 in 2fe5A Skipped atom 632, because occupancy 0.500 <= existing 0.500 in 2fe5A Skipped atom 634, because occupancy 0.500 <= existing 0.500 in 2fe5A Skipped atom 636, because occupancy 0.500 <= existing 0.500 in 2fe5A Skipped atom 638, because occupancy 0.500 <= existing 0.500 in 2fe5A Skipped atom 640, because occupancy 0.500 <= existing 0.500 in 2fe5A Skipped atom 642, because occupancy 0.500 <= existing 0.500 in 2fe5A Skipped atom 644, because occupancy 0.500 <= existing 0.500 in 2fe5A Skipped atom 646, because occupancy 0.500 <= existing 0.500 in 2fe5A Skipped atom 648, because occupancy 0.500 <= existing 0.500 in 2fe5A Skipped atom 650, because occupancy 0.500 <= existing 0.500 in 2fe5A Skipped atom 652, because occupancy 0.500 <= existing 0.500 in 2fe5A Skipped atom 654, because occupancy 0.500 <= existing 0.500 in 2fe5A Skipped atom 656, because occupancy 0.500 <= existing 0.500 in 2fe5A Skipped atom 658, because occupancy 0.500 <= existing 0.500 in 2fe5A Skipped atom 660, because occupancy 0.500 <= existing 0.500 in 2fe5A Skipped atom 662, because occupancy 0.500 <= existing 0.500 in 2fe5A # T0288 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 T0288 1 :SMVPGKVTLQKDAQN 2fe5A 221 :SMTIMEVNLLKGPKG T0288 17 :IGISIGGGAQYCP 2fe5A 236 :LGFSIAGGIGNQH T0288 30 :CLYIVQVFDNTPAALDGTVAAGDEITGVNGRSIKGKTKVEVAKMIQEVKGEVTIHYNKLQ 2fe5A 254 :SIYITKIIEGGAAQKDGRLQIGDRLLAVNNTNLQDVRHEEAVASLKNTSDMVYLKVAKPG Number of specific fragments extracted= 3 number of extra gaps= 0 total=213 Number of alignments=55 # 2fe5A read from 2fe5A/merged-good-all-a2m # found chain 2fe5A in template set T0288 1 :SMVPGKVTLQKDAQN 2fe5A 221 :SMTIMEVNLLKGPKG T0288 17 :IGISIGGGAQYCP 2fe5A 236 :LGFSIAGGIGNQH T0288 30 :CLYIVQVFDNTPAALDGTVAAGDEITGVNGRSIKGKTKVEVAKMIQEVKGEVTIH 2fe5A 254 :SIYITKIIEGGAAQKDGRLQIGDRLLAVNNTNLQDVRHEEAVASLKNTSDMVYLK Number of specific fragments extracted= 3 number of extra gaps= 0 total=216 Number of alignments=56 # 2fe5A read from 2fe5A/merged-good-all-a2m # found chain 2fe5A in template set T0288 3 :VPGKVTLQKDAQNLIGISIGGGAQ 2fe5A 222 :MTIMEVNLLKGPKGLGFSIAGGIG T0288 27 :YCPCLYIVQVFDNTPAALDGTVAAGDEITGVNGRSIKGKTKVEVAKMIQEVKGEVTIHYNKL 2fe5A 251 :GDNSIYITKIIEGGAAQKDGRLQIGDRLLAVNNTNLQDVRHEEAVASLKNTSDMVYLKVAKP Number of specific fragments extracted= 2 number of extra gaps= 0 total=218 Number of alignments=57 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1r6jA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0288 read from 1r6jA/merged-good-all-a2m # 1r6jA read from 1r6jA/merged-good-all-a2m # found chain 1r6jA in training set T0288 1 :SMVPGKVTLQKDAQNLIGISIGGG 1r6jA 193 :AMDPRTITMHKDSTGHVGFIFKNG T0288 32 :YIVQVFDNTPAALDG 1r6jA 217 :KITSIVKDSSAARNG T0288 48 :VAAGDEITGVNGRSIKGKTKVEVAKMIQEVKGEVTIHYNKL 1r6jA 232 :LLTEHNICEINGQNVIGLKDSQIADILSTSGTVVTITIMPA Number of specific fragments extracted= 3 number of extra gaps= 0 total=221 Number of alignments=58 # 1r6jA read from 1r6jA/merged-good-all-a2m # found chain 1r6jA in training set T0288 1 :SMVPGKVTLQKDAQNLIGISIGGG 1r6jA 193 :AMDPRTITMHKDSTGHVGFIFKNG T0288 32 :YIVQVFDNTPAALDG 1r6jA 217 :KITSIVKDSSAARNG T0288 48 :VAAGDEITGVNGRSIKGKTKVEVAKMIQEVKGEVTIH 1r6jA 232 :LLTEHNICEINGQNVIGLKDSQIADILSTSGTVVTIT Number of specific fragments extracted= 3 number of extra gaps= 0 total=224 Number of alignments=59 # 1r6jA read from 1r6jA/merged-good-all-a2m # found chain 1r6jA in training set T0288 2 :MVPGKVTLQKDAQNLIGISIGGG 1r6jA 194 :MDPRTITMHKDSTGHVGFIFKNG T0288 32 :YIVQVFDNTPAALDG 1r6jA 217 :KITSIVKDSSAARNG T0288 48 :VAAGDEITGVNGRSIKGKTKVEVAKMIQEVKGEVTIHYNKL 1r6jA 232 :LLTEHNICEINGQNVIGLKDSQIADILSTSGTVVTITIMPA Number of specific fragments extracted= 3 number of extra gaps= 0 total=227 Number of alignments=60 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1qavA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1qavA expands to /projects/compbio/data/pdb/1qav.pdb.gz 1qavA:# T0288 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 T0288 1 :SMVPGKVTLQKDAQNLIGISIGGGAQYCPCLYIVQVFDNTPAALDGTVAAGDEITGVNGRSIKGKTKVEVAKMIQEVKGEVTIHYNKL 1qavA 76 :SLQRRRVTVRKADAGGLGISIKGGRENKMPILISKIFKGLAADQTEALFVGDAILSVNGEDLSSATHDEAVQALKKTGKEVVLEVKYM Number of specific fragments extracted= 1 number of extra gaps= 0 total=228 Number of alignments=61 # 1qavA read from 1qavA/merged-good-all-a2m # found chain 1qavA in template set T0288 1 :SMVPGKVTLQKDAQNLIGISIGGGAQYCPCLYIVQVFDNTPAALDGTVAAGDEITGVNGRSIKGKTKVEVAKMIQEVKGEVTIHYNK 1qavA 76 :SLQRRRVTVRKADAGGLGISIKGGRENKMPILISKIFKGLAADQTEALFVGDAILSVNGEDLSSATHDEAVQALKKTGKEVVLEVKY Number of specific fragments extracted= 1 number of extra gaps= 0 total=229 Number of alignments=62 # 1qavA read from 1qavA/merged-good-all-a2m # found chain 1qavA in template set T0288 3 :VPGKVTLQKDAQNLIGISIGGGAQYCPCLYIVQVFDNTPAALDGTVAAGDEITGVNGRSIKGKTKVEVAKMIQEVKGEVTIHYNKL 1qavA 78 :QRRRVTVRKADAGGLGISIKGGRENKMPILISKIFKGLAADQTEALFVGDAILSVNGEDLSSATHDEAVQALKKTGKEVVLEVKYM Number of specific fragments extracted= 1 number of extra gaps= 0 total=230 Number of alignments=63 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1wfvA/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/T0288/1wfvA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0288/1wfvA/merged-good-all-a2m.gz for input Trying 1wfvA/merged-good-all-a2m Error: Couldn't open file 1wfvA/merged-good-all-a2m or 1wfvA/merged-good-all-a2m.gz for input # 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:# T0288 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 T0288 2 :MVPGKVTLQKDAQNLIGISIGGGAQYC 1qavB 1013 :PNVISVRLFKRKVGGLGFLVKERVSKP T0288 30 :CLYIVQVFDNTPAALDGTVAAGDEITGVNGRSIKGKTKVEVAKMIQEV 1qavB 1040 :PVIISDLIRGGAAEQSGLIQAGDIILAVNDRPLVDLSYDSALEVLRGI T0288 78 :KGEVTIHYNKLQYY 1qavB 1090 :ETHVVLILRGPEGF Number of specific fragments extracted= 3 number of extra gaps= 0 total=233 Number of alignments=64 # 1qavB read from 1qavB/merged-good-all-a2m # found chain 1qavB in template set T0288 2 :MVPGKVTLQKDAQNLIGISIGGGAQ 1qavB 1013 :PNVISVRLFKRKVGGLGFLVKERVS T0288 28 :CPCLYIVQVFDNTPAALDGTVAAGDEITGVNGRSIKGKTKVEVAKMIQEV 1qavB 1038 :KPPVIISDLIRGGAAEQSGLIQAGDIILAVNDRPLVDLSYDSALEVLRGI T0288 78 :KGEVTIH 1qavB 1090 :ETHVVLI Number of specific fragments extracted= 3 number of extra gaps= 0 total=236 Number of alignments=65 # 1qavB read from 1qavB/merged-good-all-a2m # found chain 1qavB in template set T0288 2 :MVPGKVTLQKDAQNLIGISIGGGAQ 1qavB 1013 :PNVISVRLFKRKVGGLGFLVKERVS T0288 28 :CPCLYIVQVFDNTPAALDGTVAAGDEITGVNGRSIKGKTKVEVAKMIQEVKGE 1qavB 1038 :KPPVIISDLIRGGAAEQSGLIQAGDIILAVNDRPLVDLSYDSALEVLRGIASE T0288 81 :VTIHYNKLQY 1qavB 1093 :VVLILRGPEG Number of specific fragments extracted= 3 number of extra gaps= 0 total=239 Number of alignments=66 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1m5zA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1m5zA expands to /projects/compbio/data/pdb/1m5z.pdb.gz 1m5zA:# T0288 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 T0288 1 :SMVPGKVTLQKDAQ 1m5zA 19 :PVELHKVTLYKDSG T0288 15 :NLIGISIGGGAQYC 1m5zA 34 :EDFGFSVADGLLEK T0288 30 :CLYIVQVFDNTPAALDG 1m5zA 48 :GVYVKNIRPAGPGDLGG T0288 48 :VAAGDEITGVNGRSIKGKTKVEVAKMIQEVKGEVTIHYNKL 1m5zA 65 :LKPYDRLLQVNHVRTRDFDCCLVVPLIAESGNKLDLVISRN Number of specific fragments extracted= 4 number of extra gaps= 0 total=243 Number of alignments=67 # 1m5zA read from 1m5zA/merged-good-all-a2m # found chain 1m5zA in template set T0288 1 :SMVPGKVTLQKDAQ 1m5zA 19 :PVELHKVTLYKDSG T0288 15 :NLIGISIGGGAQ 1m5zA 34 :EDFGFSVADGLL T0288 28 :CPCLYIVQVFDNTPAALDG 1m5zA 46 :EKGVYVKNIRPAGPGDLGG T0288 48 :VAAGDEITGVNGRSIKGKTKVEVAKMIQEVKGEVTIH 1m5zA 65 :LKPYDRLLQVNHVRTRDFDCCLVVPLIAESGNKLDLV Number of specific fragments extracted= 4 number of extra gaps= 0 total=247 Number of alignments=68 # 1m5zA read from 1m5zA/merged-good-all-a2m # found chain 1m5zA in template set T0288 2 :MVPGKVTLQKDAQ 1m5zA 20 :VELHKVTLYKDSG T0288 15 :NLIGISIGGGAQ 1m5zA 34 :EDFGFSVADGLL T0288 28 :CPCLYIVQVFDNTPAALDG 1m5zA 46 :EKGVYVKNIRPAGPGDLGG T0288 48 :VAAGDEITGVNGRSIKGKTKVEVAKMIQEVKGEVTIHYNK 1m5zA 65 :LKPYDRLLQVNHVRTRDFDCCLVVPLIAESGNKLDLVISR Number of specific fragments extracted= 4 number of extra gaps= 0 total=251 Number of alignments=69 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1be9A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1be9A expands to /projects/compbio/data/pdb/1be9.pdb.gz 1be9A:# T0288 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 T0288 2 :MVPGKVTLQKDAQN 1be9A 309 :REPRRIVIHRGSTG T0288 17 :IGISIGGGAQYC 1be9A 323 :LGFNIIGGEDGE T0288 30 :CLYIVQVFDNTPAALDGTVAAGDEITGVNGRSIKGKTKVEVAKMIQEVKGEVTIHYNKL 1be9A 335 :GIFISFILAGGPADLSGELRKGDQILSVNGVDLRNASHEQAAIALKNAGQTVTIIAQYK Number of specific fragments extracted= 3 number of extra gaps= 0 total=254 Number of alignments=70 # 1be9A read from 1be9A/merged-good-all-a2m # found chain 1be9A in template set T0288 2 :MVPGKVTLQKDAQN 1be9A 309 :REPRRIVIHRGSTG T0288 17 :IGISIGGGAQYC 1be9A 323 :LGFNIIGGEDGE T0288 30 :CLYIVQVFDNTPAALDGTVAAGDEITGVNGRSIKGKTKVEVAKMIQEVKGEVTIH 1be9A 335 :GIFISFILAGGPADLSGELRKGDQILSVNGVDLRNASHEQAAIALKNAGQTVTII Number of specific fragments extracted= 3 number of extra gaps= 0 total=257 Number of alignments=71 # 1be9A read from 1be9A/merged-good-all-a2m # found chain 1be9A in template set T0288 3 :VPGKVTLQKDAQNLIGISIGGGAQ 1be9A 309 :REPRRIVIHRGSTGLGFNIIGGED T0288 28 :CPCLYIVQVFDNTPAALDGTVAAGDEITGVNGRSIKGKTKVEVAKMIQEVKGEVTIHYNK 1be9A 333 :GEGIFISFILAGGPADLSGELRKGDQILSVNGVDLRNASHEQAAIALKNAGQTVTIIAQY Number of specific fragments extracted= 2 number of extra gaps= 0 total=259 Number of alignments=72 # 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/T0288/1d5gA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0288/1d5gA/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 1x6dA/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/T0288/1x6dA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0288/1x6dA/merged-good-all-a2m.gz for input Trying 1x6dA/merged-good-all-a2m Error: Couldn't open file 1x6dA/merged-good-all-a2m or 1x6dA/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:# T0288 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 (T0288)Q14 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1te0A)G273 Warning: unaligning (T0288)N15 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1te0A)G273 Warning: unaligning (T0288)G23 because of BadResidue code BAD_PEPTIDE in next template residue (1te0A)G275 Warning: unaligning (T0288)G24 because of BadResidue code BAD_PEPTIDE at template residue (1te0A)G275 Warning: unaligning (T0288)A25 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1te0A)D277 Warning: unaligning (T0288)Q26 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1te0A)D277 Warning: unaligning (T0288)V34 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1te0A)E286 Warning: unaligning (T0288)Q35 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1te0A)E286 Warning: unaligning (T0288)N39 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1te0A)G291 Warning: unaligning (T0288)T40 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1te0A)G291 Warning: unaligning (T0288)A43 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (1te0A)N295 Warning: unaligning (T0288)L44 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (1te0A)N295 Warning: unaligning (T0288)D45 because of BadResidue code BAD_PEPTIDE in next template residue (1te0A)G297 Warning: unaligning (T0288)G46 because of BadResidue code BAD_PEPTIDE at template residue (1te0A)G297 Warning: unaligning (T0288)D52 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1te0A)L303 Warning: unaligning (T0288)E53 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1te0A)L303 Warning: unaligning (T0288)I62 because of BadResidue code BAD_PEPTIDE in next template residue (1te0A)I313 Warning: unaligning (T0288)K63 because of BadResidue code BAD_PEPTIDE at template residue (1te0A)I313 T0288 12 :DA 1te0A 270 :HA T0288 27 :YCPCLYI 1te0A 278 :QLQGIVV T0288 36 :VFD 1te0A 287 :VSP T0288 41 :PA 1te0A 292 :PA T0288 48 :VAAG 1te0A 298 :IQVN T0288 54 :ITGVNGRS 1te0A 304 :IISVDNKP T0288 66 :TKVEVAKMIQEV 1te0A 314 :SALETMDQVAEI T0288 78 :KGEVTIHYNKLQY 1te0A 328 :GSVIPVVVMRDDK Number of specific fragments extracted= 8 number of extra gaps= 6 total=267 Number of alignments=73 # 1te0A read from 1te0A/merged-good-all-a2m # found chain 1te0A in template set Warning: unaligning (T0288)Q14 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1te0A)G273 Warning: unaligning (T0288)N15 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1te0A)G273 Warning: unaligning (T0288)G23 because of BadResidue code BAD_PEPTIDE in next template residue (1te0A)G275 Warning: unaligning (T0288)G24 because of BadResidue code BAD_PEPTIDE at template residue (1te0A)G275 Warning: unaligning (T0288)A25 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1te0A)D277 Warning: unaligning (T0288)Q26 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1te0A)D277 Warning: unaligning (T0288)V34 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1te0A)E286 Warning: unaligning (T0288)Q35 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1te0A)E286 Warning: unaligning (T0288)N39 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1te0A)G291 Warning: unaligning (T0288)T40 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1te0A)G291 Warning: unaligning (T0288)A43 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (1te0A)N295 Warning: unaligning (T0288)L44 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (1te0A)N295 Warning: unaligning (T0288)D45 because of BadResidue code BAD_PEPTIDE in next template residue (1te0A)G297 Warning: unaligning (T0288)G46 because of BadResidue code BAD_PEPTIDE at template residue (1te0A)G297 Warning: unaligning (T0288)D52 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1te0A)L303 Warning: unaligning (T0288)E53 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1te0A)L303 Warning: unaligning (T0288)I62 because of BadResidue code BAD_PEPTIDE in next template residue (1te0A)I313 Warning: unaligning (T0288)K65 because of BadResidue code BAD_PEPTIDE at template residue (1te0A)I313 Warning: unaligning (T0288)Y90 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1te0A)T343 T0288 8 :TLQK 1te0A 262 :GGRE T0288 12 :DA 1te0A 270 :HA T0288 27 :YCPCLYI 1te0A 278 :QLQGIVV T0288 36 :VFD 1te0A 287 :VSP T0288 41 :PA 1te0A 292 :PA T0288 48 :VAAG 1te0A 298 :IQVN T0288 54 :ITGVNGRS 1te0A 304 :IISVDNKP T0288 66 :TKVEVAKMIQEV 1te0A 314 :SALETMDQVAEI T0288 78 :KGEVTIH 1te0A 328 :GSVIPVV T0288 85 :YNKLQ 1te0A 337 :RDDKQ Number of specific fragments extracted= 10 number of extra gaps= 7 total=277 Number of alignments=74 # 1te0A read from 1te0A/merged-good-all-a2m # found chain 1te0A in template set Warning: unaligning (T0288)Q14 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1te0A)G273 Warning: unaligning (T0288)N15 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1te0A)G273 Warning: unaligning (T0288)G23 because of BadResidue code BAD_PEPTIDE in next template residue (1te0A)G275 Warning: unaligning (T0288)G24 because of BadResidue code BAD_PEPTIDE at template residue (1te0A)G275 Warning: unaligning (T0288)A25 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1te0A)D277 Warning: unaligning (T0288)Q26 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1te0A)D277 Warning: unaligning (T0288)V34 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1te0A)E286 Warning: unaligning (T0288)Q35 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1te0A)E286 Warning: unaligning (T0288)N39 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1te0A)G291 Warning: unaligning (T0288)T40 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1te0A)G291 Warning: unaligning (T0288)A43 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (1te0A)N295 Warning: unaligning (T0288)L44 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (1te0A)N295 Warning: unaligning (T0288)D45 because of BadResidue code BAD_PEPTIDE in next template residue (1te0A)G297 Warning: unaligning (T0288)G46 because of BadResidue code BAD_PEPTIDE at template residue (1te0A)G297 Warning: unaligning (T0288)D52 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1te0A)L303 Warning: unaligning (T0288)E53 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1te0A)L303 Warning: unaligning (T0288)I62 because of BadResidue code BAD_PEPTIDE in next template residue (1te0A)I313 Warning: unaligning (T0288)K63 because of BadResidue code BAD_PEPTIDE at template residue (1te0A)I313 T0288 12 :DA 1te0A 270 :HA T0288 27 :YCPCLYI 1te0A 278 :QLQGIVV T0288 36 :VFD 1te0A 287 :VSP T0288 41 :PA 1te0A 292 :PA T0288 48 :VAAG 1te0A 298 :IQVN T0288 54 :ITGVNGRS 1te0A 304 :IISVDNKP T0288 66 :TKVEVAKMIQEVKGEVTIHYNKLQYYK 1te0A 314 :SALETMDQVAEIRPGSVIPVVVMRDDK Number of specific fragments extracted= 7 number of extra gaps= 6 total=284 # 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 # T0288 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 (T0288)A13 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2fcfA)K1160 Warning: unaligning (T0288)N15 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2fcfA)K1160 Warning: unaligning (T0288)A25 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2fcfA)G1184 Warning: unaligning (T0288)Q26 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2fcfA)G1184 T0288 1 :SMVPGKVTLQKD 2fcfA 1146 :SMQPRRVELWRE T0288 16 :LIGISIGGG 2fcfA 1161 :SLGISIVGG T0288 31 :LYIVQVFDNTPAALDGTVAAGDEITGVNGRSIKGKTKVEVAKMIQEVKGEVTIHYNKLQYYKV 2fcfA 1185 :IFIKHVLEDSPAGKNGTLKPGDRIVEVDGMDLRDASHEQAVEAIRKAGNPVVFMVQSIISTRL Number of specific fragments extracted= 3 number of extra gaps= 1 total=287 Number of alignments=75 # 2fcfA read from 2fcfA/merged-good-all-a2m # found chain 2fcfA in template set Warning: unaligning (T0288)A13 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2fcfA)K1160 Warning: unaligning (T0288)N15 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2fcfA)K1160 Warning: unaligning (T0288)A25 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2fcfA)G1184 Warning: unaligning (T0288)Q26 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2fcfA)G1184 T0288 1 :SMVPGKVTLQKD 2fcfA 1146 :SMQPRRVELWRE T0288 16 :LIGISIGGG 2fcfA 1161 :SLGISIVGG T0288 31 :LYIVQVFDNTPAALDGTVAAGDEITGVNGRSIKGKTKVEVAKMIQEVKGEVTIHYNKLQYYK 2fcfA 1185 :IFIKHVLEDSPAGKNGTLKPGDRIVEVDGMDLRDASHEQAVEAIRKAGNPVVFMVQSIISTR Number of specific fragments extracted= 3 number of extra gaps= 1 total=290 Number of alignments=76 # 2fcfA read from 2fcfA/merged-good-all-a2m # found chain 2fcfA in template set Warning: unaligning (T0288)A13 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2fcfA)K1160 Warning: unaligning (T0288)N15 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2fcfA)K1160 Warning: unaligning (T0288)A25 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2fcfA)G1184 Warning: unaligning (T0288)Q26 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2fcfA)G1184 T0288 4 :PGKVTLQKD 2fcfA 1149 :PRRVELWRE T0288 16 :LIGISIGGG 2fcfA 1161 :SLGISIVGG T0288 31 :LYIVQVFDNTPAALDGTVAAGDEITGVNGRSIKGKTKVEVAKMIQEVKGEVTIHYNKLQYYKV 2fcfA 1185 :IFIKHVLEDSPAGKNGTLKPGDRIVEVDGMDLRDASHEQAVEAIRKAGNPVVFMVQSIISTRL Number of specific fragments extracted= 3 number of extra gaps= 1 total=293 Number of alignments=77 # 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/T0288/1rgrA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0288/1rgrA/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:# T0288 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 T0288 13 :AQ 1lcyA 249 :PS T0288 24 :GAQYCPCLYIVQVFDNTPAALDG 1lcyA 251 :FPDVQHGVLIHKVILGSPAHRAG T0288 48 :VAAGDEITGVNGRSIKG 1lcyA 274 :LRPGDVILAIGEQMVQN T0288 67 :KVEVAKMIQE 1lcyA 291 :AEDVYEAVRT T0288 78 :KGEVTIHYNKLQY 1lcyA 301 :QSQLAVQIRRGRE Number of specific fragments extracted= 5 number of extra gaps= 0 total=298 Number of alignments=78 # 1lcyA read from 1lcyA/merged-good-all-a2m # found chain 1lcyA in template set T0288 12 :DAQN 1lcyA 248 :EPSF T0288 25 :AQYCPCLYIVQVFDNTPAALDG 1lcyA 252 :PDVQHGVLIHKVILGSPAHRAG T0288 48 :VAAGDEITGVNGRSIKG 1lcyA 274 :LRPGDVILAIGEQMVQN T0288 67 :KVEVAKMIQEV 1lcyA 291 :AEDVYEAVRTQ T0288 79 :GEVTIH 1lcyA 302 :SQLAVQ Number of specific fragments extracted= 5 number of extra gaps= 0 total=303 Number of alignments=79 # 1lcyA read from 1lcyA/merged-good-all-a2m # found chain 1lcyA in template set T0288 24 :GAQYCPCLYIVQVFDNTPAALDG 1lcyA 251 :FPDVQHGVLIHKVILGSPAHRAG T0288 48 :VAAGDEITGVNGRSIKG 1lcyA 274 :LRPGDVILAIGEQMVQN T0288 67 :KVEVAKMIQEV 1lcyA 291 :AEDVYEAVRTQ T0288 79 :GEVTIHYNKLQY 1lcyA 302 :SQLAVQIRRGRE Number of specific fragments extracted= 4 number of extra gaps= 0 total=307 Number of alignments=80 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1sotA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1sotA expands to /projects/compbio/data/pdb/1sot.pdb.gz 1sotA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0288 read from 1sotA/merged-good-all-a2m # 1sotA read from 1sotA/merged-good-all-a2m # adding 1sotA to template set # found chain 1sotA in template set Warning: unaligning (T0288)C30 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1sotA)G281 T0288 31 :LYIVQVFDNTPAALDG 1sotA 282 :IVVNEVSPDGPAANAG T0288 48 :VAAGDEITGVNGRSIKG 1sotA 298 :IQVNDLIISVDNKPAIS T0288 67 :KVEVAKMIQEV 1sotA 315 :ALETMDQVAEI T0288 78 :KGEVTIH 1sotA 328 :GSVIPVV Number of specific fragments extracted= 4 number of extra gaps= 0 total=311 Number of alignments=81 # 1sotA read from 1sotA/merged-good-all-a2m # found chain 1sotA in template set Warning: unaligning (T0288)C30 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1sotA)G281 Warning: unaligning (T0288)N86 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1sotA)Q341 T0288 9 :LQKDAQNLIGISIG 1sotA 205 :LVNSLGELMGINTL T0288 31 :LYIVQVFDNTPAALDG 1sotA 282 :IVVNEVSPDGPAANAG T0288 48 :VAAGDEITGVNGRSIK 1sotA 298 :IQVNDLIISVDNKPAI T0288 66 :TKVEVAKMIQEV 1sotA 314 :SALETMDQVAEI T0288 78 :KGEVTIH 1sotA 328 :GSVIPVV T0288 87 :KLQYYK 1sotA 342 :LTLQVT Number of specific fragments extracted= 6 number of extra gaps= 0 total=317 Number of alignments=82 # 1sotA read from 1sotA/merged-good-all-a2m # found chain 1sotA in template set Warning: unaligning (T0288)C30 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1sotA)G281 Warning: unaligning (T0288)K87 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1sotA)Q341 T0288 31 :LYIVQVFDNTPAALDG 1sotA 282 :IVVNEVSPDGPAANAG T0288 48 :VAAGDEITGVNGRSIKG 1sotA 298 :IQVNDLIISVDNKPAIS T0288 67 :KVEVAKMIQEVKGEVTIHYN 1sotA 315 :ALETMDQVAEIRPGSVIPVV Number of specific fragments extracted= 3 number of extra gaps= 0 total=320 Number of alignments=83 # 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 # T0288 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 (T0288)M2 because first residue in template chain is (2f5yA)M14 Warning: unaligning (T0288)V3 because of BadResidue code BAD_PEPTIDE at template residue (2f5yA)R15 Warning: unaligning (T0288)K63 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2f5yA)H70 Warning: unaligning (T0288)G64 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2f5yA)H70 Warning: unaligning (T0288)Q89 because last residue in template chain is (2f5yA)V95 T0288 4 :PGKVTLQKDAQN 2f5yA 16 :YRQITIPRGKDG T0288 17 :IGISIGG 2f5yA 28 :FGFTICC T0288 28 :CPCLYIVQVFDNTPAALDG 2f5yA 35 :DSPVRVQAVDSGGPAERAG T0288 48 :VAAGDEITGVNGRSI 2f5yA 54 :LQQLDTVLQLNERPV T0288 65 :KTKVEVAKMIQEVKGEVTIHYNKL 2f5yA 71 :WKCVELAHEIRSCPSEIILLVWRM Number of specific fragments extracted= 5 number of extra gaps= 1 total=325 Number of alignments=84 # 2f5yA read from 2f5yA/merged-good-all-a2m # found chain 2f5yA in template set Warning: unaligning (T0288)M2 because first residue in template chain is (2f5yA)M14 Warning: unaligning (T0288)V3 because of BadResidue code BAD_PEPTIDE at template residue (2f5yA)R15 Warning: unaligning (T0288)K63 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2f5yA)H70 Warning: unaligning (T0288)G64 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2f5yA)H70 T0288 4 :PGKVTLQKDAQN 2f5yA 16 :YRQITIPRGKDG T0288 17 :IGISIGG 2f5yA 28 :FGFTICC T0288 28 :CPCLYIVQVFDNTPAALDG 2f5yA 35 :DSPVRVQAVDSGGPAERAG T0288 48 :VAAGDEITGVNGRSI 2f5yA 54 :LQQLDTVLQLNERPV T0288 65 :KTKVEVAKMIQEVKGEVTIH 2f5yA 71 :WKCVELAHEIRSCPSEIILL Number of specific fragments extracted= 5 number of extra gaps= 1 total=330 Number of alignments=85 # 2f5yA read from 2f5yA/merged-good-all-a2m # found chain 2f5yA in template set Warning: unaligning (T0288)V3 because first residue in template chain is (2f5yA)M14 Warning: unaligning (T0288)P4 because of BadResidue code BAD_PEPTIDE at template residue (2f5yA)R15 Warning: unaligning (T0288)K63 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2f5yA)H70 Warning: unaligning (T0288)G64 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2f5yA)H70 T0288 5 :GKVTLQKDAQNLIGISIGGG 2f5yA 16 :YRQITIPRGKDGFGFTICCD T0288 29 :PCLYIVQVFDNTPAALDG 2f5yA 36 :SPVRVQAVDSGGPAERAG T0288 48 :VAAGDEITGVNGRSI 2f5yA 54 :LQQLDTVLQLNERPV T0288 65 :KTKVEVAKMIQEVKGEVTIHYNKL 2f5yA 71 :WKCVELAHEIRSCPSEIILLVWRM Number of specific fragments extracted= 4 number of extra gaps= 1 total=334 Number of alignments=86 # 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:# T0288 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 (T0288)V3 because first residue in template chain is (1kwaA)R487 T0288 4 :PGKVTLQKDAQNLIGISIG 1kwaA 488 :SRLVQFQKNTDEPMGITLK T0288 23 :GGAQ 1kwaA 508 :NELN T0288 30 :CLYIVQVFDNTPAALDGTVAAGDEITGVNGRSIKGKTKVEVAKMIQEVKGEVTIHYNKLQYY 1kwaA 512 :HCIVARIMHGGMIHRQGTLHVGDEIREINGISVANQTVEQLQKMLREMRGSITFKIVPSYRE Number of specific fragments extracted= 3 number of extra gaps= 0 total=337 Number of alignments=87 # 1kwaA read from 1kwaA/merged-good-all-a2m # found chain 1kwaA in template set Warning: unaligning (T0288)V3 because first residue in template chain is (1kwaA)R487 T0288 4 :PGKVTLQKDAQNLIGISIG 1kwaA 488 :SRLVQFQKNTDEPMGITLK T0288 23 :GGAQ 1kwaA 508 :NELN T0288 30 :CLYIVQVFDNTPAALDGTVAAGDEITGVNGRSIKGKTKVEVAKMIQEVKGEVTIH 1kwaA 512 :HCIVARIMHGGMIHRQGTLHVGDEIREINGISVANQTVEQLQKMLREMRGSITFK Number of specific fragments extracted= 3 number of extra gaps= 0 total=340 Number of alignments=88 # 1kwaA read from 1kwaA/merged-good-all-a2m # found chain 1kwaA in template set Warning: unaligning (T0288)K92 because last residue in template chain is (1kwaA)F574 T0288 5 :GKVTLQKDAQNLIGISIGGGAQ 1kwaA 489 :RLVQFQKNTDEPMGITLKMNEL T0288 29 :PCLYIVQVFDNTPAALDGTVAAGDEITGVNGRSIKGKTKVEVAKMIQEVKGEVTIHYNKLQYY 1kwaA 511 :NHCIVARIMHGGMIHRQGTLHVGDEIREINGISVANQTVEQLQKMLREMRGSITFKIVPSYRE Number of specific fragments extracted= 2 number of extra gaps= 0 total=342 Number of alignments=89 # 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:# T0288 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 (T0288)V3 because first residue in template chain is (1kwaB)R487 Warning: unaligning (T0288)Y27 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1kwaB)L510 Warning: unaligning (T0288)C28 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1kwaB)L510 T0288 4 :PGKVTLQKDAQNLIGISIG 1kwaB 488 :SRLVQFQKNTDEPMGITLK T0288 29 :PCLYIVQVFDNTPAALDGTVAAGDEITGVNGRSIKGKTKVEVAKMIQEVKGEVTIHYNKLQY 1kwaB 511 :NHCIVARIMHGGMIHRQGTLHVGDEIREINGISVANQTVEQLQKMLREMRGSITFKIVPSYR Number of specific fragments extracted= 2 number of extra gaps= 1 total=344 # 1kwaB read from 1kwaB/merged-good-all-a2m # found chain 1kwaB in template set Warning: unaligning (T0288)V3 because first residue in template chain is (1kwaB)R487 Warning: unaligning (T0288)G23 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1kwaB)L510 Warning: unaligning (T0288)C28 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1kwaB)L510 Warning: unaligning (T0288)Y90 because last residue in template chain is (1kwaB)F574 T0288 4 :PGKVTLQKDAQNLIGISIG 1kwaB 488 :SRLVQFQKNTDEPMGITLK T0288 29 :PCLYIVQVFDNTPAALDGTVAAGDEITGVNGRSIKGKTKVEVAKMIQEVKGEVTIH 1kwaB 511 :NHCIVARIMHGGMIHRQGTLHVGDEIREINGISVANQTVEQLQKMLREMRGSITFK T0288 85 :YNKLQ 1kwaB 569 :PSYRE Number of specific fragments extracted= 3 number of extra gaps= 1 total=347 Number of alignments=90 # 1kwaB read from 1kwaB/merged-good-all-a2m # found chain 1kwaB in template set Warning: unaligning (T0288)G23 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1kwaB)L510 Warning: unaligning (T0288)G24 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1kwaB)L510 T0288 4 :PGKVTLQKDAQNLIGISIG 1kwaB 488 :SRLVQFQKNTDEPMGITLK T0288 29 :PCLYIVQVFDNTPAALDGTVAAGDEITGVNGRSIKGKTKVEVAKMIQEVKGEVTIHYNKLQYY 1kwaB 511 :NHCIVARIMHGGMIHRQGTLHVGDEIREINGISVANQTVEQLQKMLREMRGSITFKIVPSYRE Number of specific fragments extracted= 2 number of extra gaps= 1 total=349 # 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 # T0288 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 T0288 2 :MVPGKVTLQKDAQN 1pdr 462 :REPRKVVLHRGSTG T0288 17 :IGISIGGGAQYC 1pdr 476 :LGFNIVGGEDGE T0288 30 :CLYIVQVFDNTPAALDGTVAAGDEITGVNGRSIKGKTKVEVAKMIQEVKGEVTIHYNKL 1pdr 488 :GIFISFILAGGPADLSGELRKGDRIISVNSVDLRAASHEQAAAALKNAGQAVTIVAQYR Number of specific fragments extracted= 3 number of extra gaps= 0 total=352 Number of alignments=91 # 1pdr read from 1pdr/merged-good-all-a2m # found chain 1pdr in template set T0288 2 :MVPGKVTLQKDAQN 1pdr 462 :REPRKVVLHRGSTG T0288 17 :IGISIGGGAQ 1pdr 476 :LGFNIVGGED T0288 28 :CPCLYIVQVFDNTPAALDGTVAAGDEITGVNGRSIKGKTKVEVAKMIQEVKGEVTIH 1pdr 486 :GEGIFISFILAGGPADLSGELRKGDRIISVNSVDLRAASHEQAAAALKNAGQAVTIV T0288 85 :YNK 1pdr 545 :YRP Number of specific fragments extracted= 4 number of extra gaps= 0 total=356 Number of alignments=92 # 1pdr read from 1pdr/merged-good-all-a2m # found chain 1pdr in template set T0288 2 :MVPGKVTLQKDAQNLIGISIGGGAQ 1pdr 461 :TREPRKVVLHRGSTGLGFNIVGGED T0288 28 :CPCLYIVQVFDNTPAALDGTVAAGDEITGVNGRSIKGKTKVEVAKMIQEVKGEVTIHYNKL 1pdr 486 :GEGIFISFILAGGPADLSGELRKGDRIISVNSVDLRAASHEQAAAALKNAGQAVTIVAQYR Number of specific fragments extracted= 2 number of extra gaps= 0 total=358 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/T0288/1iu0A/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0288/1iu0A/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 # T0288 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 (T0288)P4 because first residue in template chain is (1n99A)P112 Warning: unaligning (T0288)H84 because of BadResidue code BAD_PEPTIDE in next template residue (1n99A)I190 Warning: unaligning (T0288)Y85 because of BadResidue code BAD_PEPTIDE at template residue (1n99A)I190 T0288 5 :GKVTLQKDAQNLIGISIGGGAQ 1n99A 113 :REVILCKDQDGKIGLRLKSIDN T0288 30 :CLYIVQVFDNTPAALDG 1n99A 135 :GIFVQLVQANSPASLVG T0288 48 :VAAGDEITGVNGRSIKGKTKVEVAKMIQEV 1n99A 152 :LRFGDQVLQINGENCAGWSSDKAHKVLKQA T0288 78 :KGEVTI 1n99A 183 :GEKITM T0288 86 :NKLQYY 1n99A 191 :RDRPFE Number of specific fragments extracted= 5 number of extra gaps= 1 total=363 Number of alignments=94 # 1n99A read from 1n99A/merged-good-all-a2m # found chain 1n99A in template set Warning: unaligning (T0288)P4 because first residue in template chain is (1n99A)P112 Warning: unaligning (T0288)H84 because of BadResidue code BAD_PEPTIDE in next template residue (1n99A)I190 T0288 5 :GKVTLQKDAQNLIGISIGGGAQ 1n99A 113 :REVILCKDQDGKIGLRLKSIDN T0288 30 :CLYIVQVFDNTPAALDG 1n99A 135 :GIFVQLVQANSPASLVG T0288 48 :VAAGDEITGVNGRSIKGKTKVEVAKMIQEV 1n99A 152 :LRFGDQVLQINGENCAGWSSDKAHKVLKQA T0288 78 :KGEVTI 1n99A 183 :GEKITM T0288 85 :YNKLQYY 1n99A 193 :RPFERTI Number of specific fragments extracted= 5 number of extra gaps= 1 total=368 Number of alignments=95 # 1n99A read from 1n99A/merged-good-all-a2m # found chain 1n99A in template set Warning: unaligning (T0288)P4 because first residue in template chain is (1n99A)P112 Warning: unaligning (T0288)H84 because of BadResidue code BAD_PEPTIDE in next template residue (1n99A)I190 Warning: unaligning (T0288)Y85 because of BadResidue code BAD_PEPTIDE at template residue (1n99A)I190 T0288 5 :GKVTLQKDAQNLIGISIGGGAQ 1n99A 113 :REVILCKDQDGKIGLRLKSIDN T0288 30 :CLYIVQVFDNTPAALDG 1n99A 135 :GIFVQLVQANSPASLVG T0288 48 :VAAGDEITGVNGRSIKGKTKVEVAKMIQEVKGE 1n99A 152 :LRFGDQVLQINGENCAGWSSDKAHKVLKQAFGE T0288 81 :VTI 1n99A 186 :ITM T0288 86 :NKLQYYK 1n99A 191 :RDRPFER Number of specific fragments extracted= 5 number of extra gaps= 1 total=373 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 # T0288 read from 1g9oA/merged-good-all-a2m # 1g9oA read from 1g9oA/merged-good-all-a2m # found chain 1g9oA in training set T0288 2 :MVPGKVTLQKDAQN 1g9oA 10 :MLPRLCCLEKGPNG T0288 17 :IGISIGGGAQ 1g9oA 24 :YGFHLHGEKG T0288 28 :CPCLYIVQVFDNTPAALDG 1g9oA 34 :KLGQYIRLVEPGSPAEKAG T0288 48 :VAAGDEITGVNGRSIKGKTKVEVAKMIQEVKGEVTIHYNKLQYYKV 1g9oA 53 :LLAGDRLVEVNGENVEKETHQQVVSRIRAALNAVRLLVVDPETDEQ Number of specific fragments extracted= 4 number of extra gaps= 0 total=377 Number of alignments=97 # 1g9oA read from 1g9oA/merged-good-all-a2m # found chain 1g9oA in training set T0288 1 :SMVPGKVTLQKDAQN 1g9oA 9 :RMLPRLCCLEKGPNG T0288 17 :IGISIGGGAQ 1g9oA 24 :YGFHLHGEKG T0288 28 :CPCLYIVQVFDNTPAALDG 1g9oA 34 :KLGQYIRLVEPGSPAEKAG T0288 48 :VAAGDEITGVNGRSIKGKTKVEVAKMIQEVKGEVTIH 1g9oA 53 :LLAGDRLVEVNGENVEKETHQQVVSRIRAALNAVRLL T0288 85 :YNKL 1g9oA 93 :PETD Number of specific fragments extracted= 5 number of extra gaps= 0 total=382 Number of alignments=98 # 1g9oA read from 1g9oA/merged-good-all-a2m # found chain 1g9oA in training set T0288 4 :PGKVTLQKDAQNLIGISIGGGAQ 1g9oA 11 :LPRLCCLEKGPNGYGFHLHGEKG T0288 28 :CPCLYIVQVFDNTPAALDG 1g9oA 34 :KLGQYIRLVEPGSPAEKAG T0288 48 :VAAGDEITGVNGRSIKGKTKVEVAKMIQEVKGEVTIHYNKLQYYKV 1g9oA 53 :LLAGDRLVEVNGENVEKETHQQVVSRIRAALNAVRLLVVDPETDEQ Number of specific fragments extracted= 3 number of extra gaps= 0 total=385 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 # T0288 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 (T0288)V3 because first residue in template chain is (1l6oA)M251 Warning: unaligning (T0288)V7 because of BadResidue code BAD_PEPTIDE in next template residue (1l6oA)T256 Warning: unaligning (T0288)T8 because of BadResidue code BAD_PEPTIDE at template residue (1l6oA)T256 Warning: unaligning (T0288)D12 because of BadResidue code BAD_PEPTIDE in next template residue (1l6oA)K261 Warning: unaligning (T0288)A13 because of BadResidue code BAD_PEPTIDE at template residue (1l6oA)K261 Warning: unaligning (T0288)Q14 because of BadResidue code BAD_PEPTIDE in next template residue (1l6oA)N263 Warning: unaligning (T0288)N15 because of BadResidue code BAD_PEPTIDE at template residue (1l6oA)N263 Warning: unaligning (T0288)L16 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1l6oA)L265 Warning: unaligning (T0288)I17 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1l6oA)L265 Warning: unaligning (T0288)I19 because of BadResidue code BAD_PEPTIDE in next template residue (1l6oA)S268 Warning: unaligning (T0288)S20 because of BadResidue code BAD_PEPTIDE at template residue (1l6oA)S268 Warning: unaligning (T0288)G24 because of BadResidue code BAD_PEPTIDE at template residue (1l6oA)N274 Warning: unaligning (T0288)C28 because of BadResidue code BAD_PEPTIDE in next template residue (1l6oA)G279 Warning: unaligning (T0288)P29 because of BadResidue code BAD_PEPTIDE at template residue (1l6oA)G279 Warning: unaligning (T0288)C30 because of BadResidue code BAD_PEPTIDE at template residue (1l6oA)G280 Warning: unaligning (T0288)A42 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1l6oA)A293 Warning: unaligning (T0288)A43 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1l6oA)A293 Warning: unaligning (T0288)N58 because of BadResidue code BAD_PEPTIDE in next template residue (1l6oA)D309 Warning: unaligning (T0288)G59 because of BadResidue code BAD_PEPTIDE at template residue (1l6oA)D309 Warning: unaligning (T0288)S61 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1l6oA)F312 Warning: unaligning (T0288)I62 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1l6oA)F312 Warning: unaligning (T0288)G64 because of BadResidue code BAD_PEPTIDE in next template residue (1l6oA)M315 Warning: unaligning (T0288)K65 because of BadResidue code BAD_PEPTIDE at template residue (1l6oA)M315 Warning: unaligning (T0288)T66 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1l6oA)S316 Warning: unaligning (T0288)Q75 because of BadResidue code BAD_PEPTIDE in next template residue (1l6oA)D326 Warning: unaligning (T0288)E76 because of BadResidue code BAD_PEPTIDE at template residue (1l6oA)D326 Warning: unaligning (T0288)I83 because of BadResidue code BAD_PEPTIDE in next template residue (1l6oA)T337 Warning: unaligning (T0288)H84 because of BadResidue code BAD_PEPTIDE at template residue (1l6oA)T337 Warning: unaligning (T0288)Y85 because of BadResidue code BAD_PEPTIDE in next template residue (1l6oA)A339 Warning: unaligning (T0288)N86 because of BadResidue code BAD_PEPTIDE at template residue (1l6oA)A339 Warning: unaligning (T0288)L88 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (1l6oA)E342 Warning: unaligning (T0288)Q89 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (1l6oA)E342 Warning: unaligning (T0288)Y90 because of BadResidue code BAD_PEPTIDE in next template residue (1l6oA)H344 Warning: unaligning (T0288)Y91 because of BadResidue code BAD_PEPTIDE at template residue (1l6oA)H344 Warning: unaligning (T0288)K92 because last residue in template chain is (1l6oA)H345 T0288 4 :PGK 1l6oA 252 :IIT T0288 9 :LQK 1l6oA 257 :LNM T0288 18 :G 1l6oA 266 :G T0288 21 :IGG 1l6oA 269 :IVG T0288 25 :AQY 1l6oA 275 :ERG T0288 31 :LYIVQVFDNTP 1l6oA 281 :IYIGSIMKGGA T0288 44 :LDGTVAAGDEITGV 1l6oA 294 :ADGRIEPGDMLLQV T0288 60 :R 1l6oA 310 :I T0288 63 :K 1l6oA 313 :E T0288 67 :KVEVAKMI 1l6oA 317 :NDDAVRVL T0288 77 :V 1l6oA 327 :I T0288 78 :KGEVT 1l6oA 331 :PGPIV T0288 87 :K 1l6oA 340 :K Number of specific fragments extracted= 13 number of extra gaps= 12 total=398 # 1l6oA read from 1l6oA/merged-good-all-a2m # found chain 1l6oA in template set Warning: unaligning (T0288)V3 because first residue in template chain is (1l6oA)M251 Warning: unaligning (T0288)V7 because of BadResidue code BAD_PEPTIDE in next template residue (1l6oA)T256 Warning: unaligning (T0288)T8 because of BadResidue code BAD_PEPTIDE at template residue (1l6oA)T256 Warning: unaligning (T0288)D12 because of BadResidue code BAD_PEPTIDE in next template residue (1l6oA)K261 Warning: unaligning (T0288)A13 because of BadResidue code BAD_PEPTIDE at template residue (1l6oA)K261 Warning: unaligning (T0288)Q14 because of BadResidue code BAD_PEPTIDE in next template residue (1l6oA)N263 Warning: unaligning (T0288)N15 because of BadResidue code BAD_PEPTIDE at template residue (1l6oA)N263 Warning: unaligning (T0288)L16 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1l6oA)L265 Warning: unaligning (T0288)I17 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1l6oA)L265 Warning: unaligning (T0288)I19 because of BadResidue code BAD_PEPTIDE in next template residue (1l6oA)S268 Warning: unaligning (T0288)S20 because of BadResidue code BAD_PEPTIDE at template residue (1l6oA)S268 Warning: unaligning (T0288)G24 because of BadResidue code BAD_PEPTIDE at template residue (1l6oA)N274 Warning: unaligning (T0288)C28 because of BadResidue code BAD_PEPTIDE in next template residue (1l6oA)G279 Warning: unaligning (T0288)P29 because of BadResidue code BAD_PEPTIDE at template residue (1l6oA)G279 Warning: unaligning (T0288)C30 because of BadResidue code BAD_PEPTIDE at template residue (1l6oA)G280 Warning: unaligning (T0288)A42 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1l6oA)A293 Warning: unaligning (T0288)A43 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1l6oA)A293 Warning: unaligning (T0288)N58 because of BadResidue code BAD_PEPTIDE in next template residue (1l6oA)D309 Warning: unaligning (T0288)G59 because of BadResidue code BAD_PEPTIDE at template residue (1l6oA)D309 Warning: unaligning (T0288)S61 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1l6oA)F312 Warning: unaligning (T0288)I62 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1l6oA)F312 Warning: unaligning (T0288)G64 because of BadResidue code BAD_PEPTIDE in next template residue (1l6oA)M315 Warning: unaligning (T0288)K65 because of BadResidue code BAD_PEPTIDE at template residue (1l6oA)M315 Warning: unaligning (T0288)T66 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1l6oA)S316 Warning: unaligning (T0288)Q75 because of BadResidue code BAD_PEPTIDE in next template residue (1l6oA)D326 Warning: unaligning (T0288)E76 because of BadResidue code BAD_PEPTIDE at template residue (1l6oA)D326 Warning: unaligning (T0288)I83 because of BadResidue code BAD_PEPTIDE in next template residue (1l6oA)T337 Warning: unaligning (T0288)H84 because of BadResidue code BAD_PEPTIDE at template residue (1l6oA)T337 Warning: unaligning (T0288)Y85 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (1l6oA)E342 Warning: unaligning (T0288)N86 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (1l6oA)E342 Warning: unaligning (T0288)K87 because of BadResidue code BAD_PEPTIDE in next template residue (1l6oA)H344 T0288 4 :PGK 1l6oA 252 :IIT T0288 9 :LQK 1l6oA 257 :LNM T0288 18 :G 1l6oA 266 :G T0288 21 :IGG 1l6oA 269 :IVG T0288 25 :AQY 1l6oA 275 :ERG T0288 31 :LYIVQVFDNTP 1l6oA 281 :IYIGSIMKGGA T0288 44 :LDGTVAAGDEITGV 1l6oA 294 :ADGRIEPGDMLLQV T0288 60 :R 1l6oA 310 :I T0288 63 :K 1l6oA 313 :E T0288 67 :KVEVAKMI 1l6oA 317 :NDDAVRVL T0288 77 :V 1l6oA 327 :I T0288 78 :KGEVT 1l6oA 331 :PGPIV Number of specific fragments extracted= 12 number of extra gaps= 12 total=410 # 1l6oA read from 1l6oA/merged-good-all-a2m # found chain 1l6oA in template set Warning: unaligning (T0288)V7 because of BadResidue code BAD_PEPTIDE in next template residue (1l6oA)T256 Warning: unaligning (T0288)T8 because of BadResidue code BAD_PEPTIDE at template residue (1l6oA)T256 Warning: unaligning (T0288)D12 because of BadResidue code BAD_PEPTIDE in next template residue (1l6oA)K261 Warning: unaligning (T0288)A13 because of BadResidue code BAD_PEPTIDE at template residue (1l6oA)K261 Warning: unaligning (T0288)Q14 because of BadResidue code BAD_PEPTIDE in next template residue (1l6oA)N263 Warning: unaligning (T0288)N15 because of BadResidue code BAD_PEPTIDE at template residue (1l6oA)N263 Warning: unaligning (T0288)L16 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1l6oA)L265 Warning: unaligning (T0288)I17 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1l6oA)L265 Warning: unaligning (T0288)I19 because of BadResidue code BAD_PEPTIDE in next template residue (1l6oA)S268 Warning: unaligning (T0288)S20 because of BadResidue code BAD_PEPTIDE at template residue (1l6oA)S268 Warning: unaligning (T0288)A25 because of BadResidue code BAD_PEPTIDE in next template residue (1l6oA)N274 Warning: unaligning (T0288)Q26 because of BadResidue code BAD_PEPTIDE at template residue (1l6oA)N274 Warning: unaligning (T0288)C28 because of BadResidue code BAD_PEPTIDE in next template residue (1l6oA)G279 Warning: unaligning (T0288)P29 because of BadResidue code BAD_PEPTIDE at template residue (1l6oA)G279 Warning: unaligning (T0288)C30 because of BadResidue code BAD_PEPTIDE at template residue (1l6oA)G280 Warning: unaligning (T0288)A42 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1l6oA)A293 Warning: unaligning (T0288)A43 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1l6oA)A293 Warning: unaligning (T0288)N58 because of BadResidue code BAD_PEPTIDE in next template residue (1l6oA)D309 Warning: unaligning (T0288)G59 because of BadResidue code BAD_PEPTIDE at template residue (1l6oA)D309 Warning: unaligning (T0288)S61 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1l6oA)F312 Warning: unaligning (T0288)I62 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1l6oA)F312 Warning: unaligning (T0288)G64 because of BadResidue code BAD_PEPTIDE in next template residue (1l6oA)M315 Warning: unaligning (T0288)K65 because of BadResidue code BAD_PEPTIDE at template residue (1l6oA)M315 Warning: unaligning (T0288)T66 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1l6oA)S316 Warning: unaligning (T0288)Q75 because of BadResidue code BAD_PEPTIDE in next template residue (1l6oA)D326 Warning: unaligning (T0288)E76 because of BadResidue code BAD_PEPTIDE at template residue (1l6oA)D326 Warning: unaligning (T0288)I83 because of BadResidue code BAD_PEPTIDE in next template residue (1l6oA)T337 Warning: unaligning (T0288)H84 because of BadResidue code BAD_PEPTIDE at template residue (1l6oA)T337 Warning: unaligning (T0288)Y85 because of BadResidue code BAD_PEPTIDE in next template residue (1l6oA)A339 Warning: unaligning (T0288)N86 because of BadResidue code BAD_PEPTIDE at template residue (1l6oA)A339 Warning: unaligning (T0288)L88 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (1l6oA)E342 Warning: unaligning (T0288)Q89 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (1l6oA)E342 Warning: unaligning (T0288)Y90 because of BadResidue code BAD_PEPTIDE in next template residue (1l6oA)H344 Warning: unaligning (T0288)Y91 because of BadResidue code BAD_PEPTIDE at template residue (1l6oA)H344 Warning: unaligning (T0288)K92 because last residue in template chain is (1l6oA)H345 T0288 4 :PGK 1l6oA 252 :IIT T0288 9 :LQK 1l6oA 257 :LNM T0288 18 :G 1l6oA 266 :G T0288 21 :IGGG 1l6oA 269 :IVGQ T0288 27 :Y 1l6oA 277 :G T0288 31 :LYIVQVFDNTP 1l6oA 281 :IYIGSIMKGGA T0288 44 :LDGTVAAGDEITGV 1l6oA 294 :ADGRIEPGDMLLQV T0288 60 :R 1l6oA 310 :I T0288 63 :K 1l6oA 313 :E T0288 67 :KVEVAKMI 1l6oA 317 :NDDAVRVL T0288 77 :V 1l6oA 327 :I T0288 78 :KGEVT 1l6oA 331 :PGPIV T0288 87 :K 1l6oA 340 :K Number of specific fragments extracted= 13 number of extra gaps= 12 total=423 # 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 # T0288 read from 1q3oA/merged-good-all-a2m # 1q3oA read from 1q3oA/merged-good-all-a2m # found chain 1q3oA in training set Warning: unaligning (T0288)Y91 because last residue in template chain is (1q3oA)H687 T0288 5 :GKVTLQKDAQNLIGISIGGGAQYCP 1q3oA 590 :KTVLLQKKDSEGFGFVLRGAKAQTP T0288 30 :CLYIVQVFDNTPAALDG 1q3oA 627 :LQYLESVDEGGVAWRAG T0288 48 :VAAGDEITGVNGRSIKGKTKVEVAKMIQEVKGEVTIHYNKLQY 1q3oA 644 :LRMGDFLIEVNGQNVVKVGHRQVVNMIRQGGNTLMVKVVMVTR Number of specific fragments extracted= 3 number of extra gaps= 0 total=426 Number of alignments=100 # 1q3oA read from 1q3oA/merged-good-all-a2m # found chain 1q3oA in training set Warning: unaligning (T0288)L88 because last residue in template chain is (1q3oA)H687 T0288 5 :GKVTLQKDAQNLIGISIGGGAQYCP 1q3oA 590 :KTVLLQKKDSEGFGFVLRGAKAQTP T0288 30 :CLYIVQVFDNTPAALDG 1q3oA 627 :LQYLESVDEGGVAWRAG T0288 48 :VAAGDEITGVNGRSIKGKTKVEVAKMIQEVKGEVTIH 1q3oA 644 :LRMGDFLIEVNGQNVVKVGHRQVVNMIRQGGNTLMVK T0288 85 :YNK 1q3oA 684 :VTR Number of specific fragments extracted= 4 number of extra gaps= 0 total=430 Number of alignments=101 # 1q3oA read from 1q3oA/merged-good-all-a2m # found chain 1q3oA in training set Warning: unaligning (T0288)Y91 because last residue in template chain is (1q3oA)H687 T0288 5 :GKVTLQKDAQNLIGISIGGGAQ 1q3oA 590 :KTVLLQKKDSEGFGFVLRGAKA T0288 27 :YCPCLYIVQVFDNTPAALDG 1q3oA 624 :FPALQYLESVDEGGVAWRAG T0288 48 :VAAGDEITGVNGRSIKGKTKVEVAKMIQEVKGEVTIHYNKLQY 1q3oA 644 :LRMGDFLIEVNGQNVVKVGHRQVVNMIRQGGNTLMVKVVMVTR Number of specific fragments extracted= 3 number of extra gaps= 0 total=433 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 # T0288 read from 1n7fA/merged-good-all-a2m # 1n7fA read from 1n7fA/merged-good-all-a2m # found chain 1n7fA in training set Warning: unaligning (T0288)M2 because first residue in template chain is (1n7fA)A668 Warning: unaligning (T0288)L88 because last residue in template chain is (1n7fA)Q753 T0288 3 :VPGKVTLQK 1n7fA 669 :IIYTVELKR T0288 13 :AQNLIGISIGGGAQYCPCLYIVQVFDNTPAALDGTVAAGDEITGVNGRSIKGKTKVEVAKMIQEVKGEVTIHYNK 1n7fA 678 :YGGPLGITISGTEEPFDPIIISSLTKGGLAERTGAIHIGDRILAINSSSLKGKPLSEAIHLLQMAGETVTLKIKK Number of specific fragments extracted= 2 number of extra gaps= 0 total=435 Number of alignments=103 # 1n7fA read from 1n7fA/merged-good-all-a2m # found chain 1n7fA in training set Warning: unaligning (T0288)M2 because first residue in template chain is (1n7fA)A668 T0288 3 :VPGKVTLQK 1n7fA 669 :IIYTVELKR T0288 13 :AQNLIGISIGGGAQYCPCLYIVQVFDNTPAALDGTVAAGDEITGVNGRSIKGKTKVEVAKMIQEVKGEVTIH 1n7fA 678 :YGGPLGITISGTEEPFDPIIISSLTKGGLAERTGAIHIGDRILAINSSSLKGKPLSEAIHLLQMAGETVTLK Number of specific fragments extracted= 2 number of extra gaps= 0 total=437 Number of alignments=104 # 1n7fA read from 1n7fA/merged-good-all-a2m # found chain 1n7fA in training set Warning: unaligning (T0288)V3 because first residue in template chain is (1n7fA)A668 Warning: unaligning (T0288)L88 because last residue in template chain is (1n7fA)Q753 T0288 4 :PGKVTLQKDAQNLIGISIGGGAQYCPCLYIVQVFDNTPAALDGTVAAGDEITGVNGRSIKGKTKVEVAKMIQEVKGEVTIHYNK 1n7fA 669 :IIYTVELKRYGGPLGITISGTEEPFDPIIISSLTKGGLAERTGAIHIGDRILAINSSSLKGKPLSEAIHLLQMAGETVTLKIKK Number of specific fragments extracted= 1 number of extra gaps= 0 total=438 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 # T0288 read from 1ihjA/merged-good-all-a2m # 1ihjA read from 1ihjA/merged-good-all-a2m # found chain 1ihjA in training set Warning: unaligning (T0288)Y27 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ihjA)P41 Warning: unaligning (T0288)C28 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ihjA)P41 Warning: unaligning (T0288)P29 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ihjA)N42 Warning: unaligning (T0288)L88 because last residue in template chain is (1ihjA)F105 T0288 1 :SMVPGKVTLQKDAQNLIGISIGGGA 1ihjA 12 :GELIHMVTLDKTGKKSFGICIVRGE T0288 26 :Q 1ihjA 39 :D T0288 30 :CLYIVQVFDNTPAALDGTVAAGDEITGVNGRSIKGKTKVEVAKMIQEVKGEVTIHYNK 1ihjA 47 :GIFIKGIVPDSPAHLCGRLKVGDRILSLNGKDVRNSTEQAVIDLIKEADFKIELEIQT Number of specific fragments extracted= 3 number of extra gaps= 1 total=441 Number of alignments=106 # 1ihjA read from 1ihjA/merged-good-all-a2m # found chain 1ihjA in training set Warning: unaligning (T0288)Y27 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ihjA)P41 Warning: unaligning (T0288)C28 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ihjA)P41 Warning: unaligning (T0288)P29 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ihjA)N42 T0288 1 :SMVPGKVTLQKDAQNLIGISIGGGA 1ihjA 12 :GELIHMVTLDKTGKKSFGICIVRGE T0288 26 :Q 1ihjA 39 :D T0288 30 :CLYIVQVFDNTPAALDGTVAAGDEITGVNGRSIKGKTKVEVAKMIQEVKGEVTIH 1ihjA 47 :GIFIKGIVPDSPAHLCGRLKVGDRILSLNGKDVRNSTEQAVIDLIKEADFKIELE Number of specific fragments extracted= 3 number of extra gaps= 1 total=444 Number of alignments=107 # 1ihjA read from 1ihjA/merged-good-all-a2m # found chain 1ihjA in training set Warning: unaligning (T0288)L88 because last residue in template chain is (1ihjA)F105 T0288 2 :MVPGKVTLQKDAQNLIGISIGGGAQ 1ihjA 13 :ELIHMVTLDKTGKKSFGICIVRGEV T0288 27 :YCPCLYIVQVFDNTPAALDGTVAAGDEITGVNGRSIKGKTKVEVAKMIQEVKGEVTIHYNK 1ihjA 44 :KTTGIFIKGIVPDSPAHLCGRLKVGDRILSLNGKDVRNSTEQAVIDLIKEADFKIELEIQT Number of specific fragments extracted= 2 number of extra gaps= 0 total=446 Number of alignments=108 # command:Using radius: 8.0000 Alignment mode NUMB_ALIGNS: 108 Adding 592 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: -170.7068, CN propb: -170.7068 weights: 0.4530 constraints: 238 # command:Found ConstraintSet # PrintContacts align.constraints_v3 Number of constraints in align.constraints 238 # command:Found ConstraintSet # PrintContacts align_bonus.constraints_v3 Number of constraints in align.constraints.bonus 238 # command:Found ConstraintSet # PrintContacts rejected.constraints_v3 Number of constraints in rejected.constraints 354 # command:Found ConstraintSet # PrintContacts rejected_bonus.constraints_v3 Number of constraints in rejected.constraints.bonus 354 # 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 592 # command: