# 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:Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0288//projects/compbio/experiments/protein-predict/casp7/T0288/align.constraints_v3.costfcn or /projects/compbio/experiments/protein-predict/casp7/T0288//projects/compbio/experiments/protein-predict/casp7/T0288/align.constraints_v3.costfcn.gz for input Trying /projects/compbio/experiments/protein-predict/casp7/T0288/align.constraints_v3.costfcn # reading script from file /projects/compbio/experiments/protein-predict/casp7/T0288/align.constraints_v3.costfcn # future Constraint commands -> align # future HelixConstraint commands -> align # future StrandConstraint commands -> align # future SheetConstraint commands -> align # future Hbond commands -> align # future SSbond commands -> align # Constraint # added constraint: constraint((T0288)V36.CB, (T0288)A50.CB) [> 3.7444 = 6.2407 < 8.1129] w=1.0000 to align # Constraint # added constraint: constraint((T0288)I33.CB, (T0288)I54.CB) [> 4.0383 = 6.7305 < 8.7497] w=1.0000 to align # Constraint # added constraint: constraint((T0288)I33.CB, (T0288)G51.CA) [> 3.2915 = 5.4859 < 7.1316] w=1.0000 to align # Constraint # added constraint: constraint((T0288)I33.CB, (T0288)A50.CB) [> 3.4221 = 5.7035 < 7.4146] w=1.0000 to align # Constraint # added constraint: constraint((T0288)Y32.CB, (T0288)G51.CA) [> 3.1841 = 5.3069 < 6.8990] w=1.0000 to align # Constraint # added constraint: constraint((T0288)I33.CB, (T0288)D52.CB) [> 2.8733 = 4.7888 < 6.2254] w=0.9802 to align # Constraint # added constraint: constraint((T0288)Y32.CB, (T0288)E53.CB) [> 3.3719 = 5.6199 < 7.3058] w=0.9802 to align # Constraint # added constraint: constraint((T0288)V36.CB, (T0288)V48.CB) [> 3.5279 = 5.8799 < 7.6438] w=0.9738 to align # Constraint # added constraint: constraint((T0288)I33.CB, (T0288)V48.CB) [> 3.6941 = 6.1569 < 8.0039] w=0.9738 to align # Constraint # added constraint: constraint((T0288)V57.CB, (T0288)M73.CB) [> 3.1499 = 5.2499 < 6.8248] w=0.9701 to align # Constraint # added constraint: constraint((T0288)N58.CB, (T0288)T82.CB) [> 3.2935 = 5.4892 < 7.1360] w=0.9670 to align # Constraint # added constraint: constraint((T0288)N58.CB, (T0288)V81.CB) [> 3.6972 = 6.1620 < 8.0106] w=0.9670 to align # Constraint # added constraint: constraint((T0288)V57.CB, (T0288)I74.CB) [> 3.8124 = 6.3539 < 8.2601] w=0.9632 to align # Constraint # added constraint: constraint((T0288)I33.CB, (T0288)A49.CB) [> 4.1709 = 6.9514 < 9.0369] w=0.9581 to align # Constraint # added constraint: constraint((T0288)Q35.CB, (T0288)A50.CB) [> 3.7416 = 6.2359 < 8.1067] w=0.9502 to align # Constraint # added constraint: constraint((T0288)V34.CB, (T0288)A50.CB) [> 3.8444 = 6.4073 < 8.3295] w=0.9401 to align # Constraint # added constraint: constraint((T0288)L31.CB, (T0288)I54.CB) [> 2.9331 = 4.8885 < 6.3551] w=0.9401 to align # Constraint # added constraint: constraint((T0288)V57.CB, (T0288)V81.CB) [> 3.9316 = 6.5527 < 8.5185] w=0.9370 to align # Constraint # added constraint: constraint((T0288)V57.CB, (T0288)I83.CB) [> 3.4609 = 5.7681 < 7.4985] w=0.9331 to align # Constraint # added constraint: constraint((T0288)Y32.CB, (T0288)I54.CB) [> 4.3651 = 7.2752 < 9.4578] w=0.9308 to align # Constraint # added constraint: constraint((T0288)Y32.CB, (T0288)D52.CB) [> 4.1339 = 6.8898 < 8.9568] w=0.9293 to align # Constraint # added constraint: constraint((T0288)R60.CB, (T0288)M73.CB) [> 3.7270 = 6.2117 < 8.0752] w=0.9220 to align # Constraint # added constraint: constraint((T0288)L31.CB, (T0288)I62.CB) [> 3.3128 = 5.5213 < 7.1777] w=0.9203 to align # Constraint # added constraint: constraint((T0288)G18.CA, (T0288)V36.CB) [> 3.9515 = 6.5859 < 8.5617] w=0.9143 to align # Constraint # added constraint: constraint((T0288)G18.CA, (T0288)F37.CB) [> 2.5517 = 4.2529 < 5.5287] w=0.9143 to align # Constraint # added constraint: constraint((T0288)G22.CA, (T0288)Y32.CB) [> 3.2515 = 5.4191 < 7.0449] w=0.9143 to align # Constraint # added constraint: constraint((T0288)G22.CA, (T0288)V34.CB) [> 3.1114 = 5.1857 < 6.7414] w=0.9143 to align # Constraint # added constraint: constraint((T0288)L31.CB, (T0288)V70.CB) [> 3.0703 = 5.1171 < 6.6523] w=0.9102 to align # Constraint # added constraint: constraint((T0288)I19.CB, (T0288)I33.CB) [> 3.2217 = 5.3695 < 6.9803] w=0.9073 to align # Constraint # added constraint: constraint((T0288)I19.CB, (T0288)V36.CB) [> 3.1530 = 5.2550 < 6.8315] w=0.9073 to align # Constraint # added constraint: constraint((T0288)I19.CB, (T0288)F37.CB) [> 4.1038 = 6.8397 < 8.8916] w=0.9073 to align # Constraint # added constraint: constraint((T0288)S20.CB, (T0288)I33.CB) [> 4.2595 = 7.0992 < 9.2289] w=0.9073 to align # Constraint # added constraint: constraint((T0288)S20.CB, (T0288)V34.CB) [> 2.8756 = 4.7927 < 6.2305] w=0.9073 to align # Constraint # added constraint: constraint((T0288)S20.CB, (T0288)Q35.CB) [> 2.6305 = 4.3843 < 5.6995] w=0.9073 to align # Constraint # added constraint: constraint((T0288)I21.CB, (T0288)Y32.CB) [> 3.9681 = 6.6135 < 8.5976] w=0.9073 to align # Constraint # added constraint: constraint((T0288)I21.CB, (T0288)I33.CB) [> 3.6511 = 6.0851 < 7.9107] w=0.9073 to align # Constraint # added constraint: constraint((T0288)I21.CB, (T0288)V34.CB) [> 3.8070 = 6.3450 < 8.2485] w=0.9073 to align # Constraint # added constraint: constraint((T0288)I21.CB, (T0288)I54.CB) [> 4.1369 = 6.8948 < 8.9633] w=0.9073 to align # Constraint # added constraint: constraint((T0288)I54.CB, (T0288)I83.CB) [> 3.5194 = 5.8656 < 7.6253] w=0.9071 to align # Constraint # added constraint: constraint((T0288)L31.CB, (T0288)K67.CB) [> 3.8984 = 6.4973 < 8.4465] w=0.8982 to align # Constraint # added constraint: constraint((T0288)N58.CB, (T0288)V77.CB) [> 3.6737 = 6.1228 < 7.9597] w=0.8909 to align # Constraint # added constraint: constraint((T0288)V34.CB, (T0288)G51.CA) [> 4.3900 = 7.3166 < 9.5116] w=0.8904 to align # Constraint # added constraint: constraint((T0288)L31.CB, (T0288)E53.CB) [> 4.1418 = 6.9029 < 8.9738] w=0.8904 to align # Constraint # added constraint: constraint((T0288)G56.CA, (T0288)H84.CB) [> 2.7659 = 4.6098 < 5.9927] w=0.8899 to align # Constraint # added constraint: constraint((T0288)G18.CA, (T0288)P41.CB) [> 3.5185 = 5.8642 < 7.6235] w=0.8881 to align # Constraint # added constraint: constraint((T0288)G18.CA, (T0288)T40.CB) [> 2.2671 = 3.7785 < 4.9121] w=0.8881 to align # Constraint # added constraint: constraint((T0288)G18.CA, (T0288)A42.CB) [> 2.8571 = 4.7619 < 6.1904] w=0.8843 to align # Constraint # added constraint: constraint((T0288)I17.CB, (T0288)A42.CB) [> 3.3939 = 5.6564 < 7.3533] w=0.8843 to align # Constraint # added constraint: constraint((T0288)I19.CB, (T0288)V48.CB) [> 3.7648 = 6.2746 < 8.1570] w=0.8811 to align # Constraint # added constraint: constraint((T0288)G23.CA, (T0288)K67.CB) [> 3.3033 = 5.5055 < 7.1571] w=0.8781 to align # Constraint # added constraint: constraint((T0288)I19.CB, (T0288)A42.CB) [> 2.6955 = 4.4925 < 5.8402] w=0.8773 to align # Constraint # added constraint: constraint((T0288)I19.CB, (T0288)Q35.CB) [> 3.9823 = 6.6372 < 8.6284] w=0.8773 to align # Constraint # added constraint: constraint((T0288)T55.CB, (T0288)H84.CB) [> 2.8818 = 4.8030 < 6.2439] w=0.8771 to align # Constraint # added constraint: constraint((T0288)I54.CB, (T0288)V70.CB) [> 4.1178 = 6.8629 < 8.9218] w=0.8703 to align # Constraint # added constraint: constraint((T0288)G23.CA, (T0288)Y32.CB) [> 3.6283 = 6.0472 < 7.8614] w=0.8582 to align # Constraint # added constraint: constraint((T0288)I17.CB, (T0288)P41.CB) [> 3.3012 = 5.5020 < 7.1526] w=0.8582 to align # Constraint # added constraint: constraint((T0288)G22.CA, (T0288)L31.CB) [> 3.6811 = 6.1351 < 7.9757] w=0.8544 to align # Constraint # added constraint: constraint((T0288)V57.CB, (T0288)T82.CB) [> 4.3604 = 7.2673 < 9.4475] w=0.8506 to align # Constraint # added constraint: constraint((T0288)V36.CB, (T0288)A49.CB) [> 4.1096 = 6.8493 < 8.9040] w=0.8503 to align # Constraint # added constraint: constraint((T0288)I17.CB, (T0288)I74.CB) [> 4.0042 = 6.6737 < 8.6758] w=0.8474 to align # Constraint # added constraint: constraint((T0288)I21.CB, (T0288)L31.CB) [> 3.1659 = 5.2764 < 6.8594] w=0.8474 to align # Constraint # added constraint: constraint((T0288)I17.CB, (T0288)V81.CB) [> 3.7443 = 6.2405 < 8.1127] w=0.8312 to align # Constraint # added constraint: constraint((T0288)I33.CB, (T0288)E53.CB) [> 4.6400 = 7.7333 < 10.0534] w=0.8305 to align # Constraint # added constraint: constraint((T0288)G59.CA, (T0288)T82.CB) [> 4.1447 = 6.9078 < 8.9801] w=0.8299 to align # Constraint # added constraint: constraint((T0288)I54.CB, (T0288)H84.CB) [> 4.3805 = 7.3008 < 9.4911] w=0.8273 to align # Constraint # added constraint: constraint((T0288)V57.CB, (T0288)V70.CB) [> 4.1305 = 6.8842 < 8.9495] w=0.8174 to align # Constraint # added constraint: constraint((T0288)G22.CA, (T0288)K67.CB) [> 3.5495 = 5.9158 < 7.6905] w=0.8145 to align # Constraint # added constraint: constraint((T0288)L9.CB, (T0288)V81.CB) [> 3.1115 = 5.1859 < 6.7416] w=0.8113 to align # Constraint # added constraint: constraint((T0288)T8.CB, (T0288)T82.CB) [> 3.1967 = 5.3279 < 6.9263] w=0.8113 to align # Constraint # added constraint: constraint((T0288)I21.CB, (T0288)V70.CB) [> 3.7044 = 6.1740 < 8.0261] w=0.8075 to align # Constraint # added constraint: constraint((T0288)V7.CB, (T0288)T82.CB) [> 4.2555 = 7.0925 < 9.2203] w=0.8013 to align # Constraint # added constraint: constraint((T0288)G18.CA, (T0288)A43.CB) [> 4.2571 = 7.0952 < 9.2238] w=0.7945 to align # Constraint # added constraint: constraint((T0288)I19.CB, (T0288)T40.CB) [> 4.2656 = 7.1094 < 9.2422] w=0.7913 to align # Constraint # added constraint: constraint((T0288)I21.CB, (T0288)A71.CB) [> 4.1272 = 6.8787 < 8.9423] w=0.7875 to align # Constraint # added constraint: constraint((T0288)V57.CB, (T0288)V77.CB) [> 4.1009 = 6.8349 < 8.8854] w=0.7813 to align # Constraint # added constraint: constraint((T0288)C30.CB, (T0288)E53.CB) [> 3.0114 = 5.0190 < 6.5247] w=0.7605 to align # Constraint # added constraint: constraint((T0288)L9.CB, (T0288)E80.CB) [> 4.1767 = 6.9612 < 9.0496] w=0.7514 to align # Constraint # added constraint: constraint((T0288)Q10.CB, (T0288)E80.CB) [> 3.4269 = 5.7114 < 7.4249] w=0.7514 to align # Constraint # added constraint: constraint((T0288)I21.CB, (T0288)K67.CB) [> 3.9149 = 6.5249 < 8.4824] w=0.7476 to align # Constraint # added constraint: constraint((T0288)Q10.CB, (T0288)P41.CB) [> 3.6256 = 6.0428 < 7.8556] w=0.7414 to align # Constraint # added constraint: constraint((T0288)V7.CB, (T0288)I83.CB) [> 3.1577 = 5.2629 < 6.8418] w=0.7414 to align # Constraint # added constraint: constraint((T0288)K6.CB, (T0288)H84.CB) [> 3.4547 = 5.7578 < 7.4851] w=0.7314 to align # Constraint # added constraint: constraint((T0288)G5.CA, (T0288)H84.CB) [> 3.7357 = 6.2261 < 8.0939] w=0.7115 to align # Constraint # added constraint: constraint((T0288)K11.CB, (T0288)G79.CA) [> 3.1886 = 5.3143 < 6.9086] w=0.6915 to align # Constraint # added constraint: constraint((T0288)L9.CB, (T0288)A42.CB) [> 3.7637 = 6.2728 < 8.1546] w=0.6905 to align # Constraint # added constraint: constraint((T0288)K6.CB, (T0288)T82.CB) [> 3.8886 = 6.4809 < 8.4252] w=0.6905 to align # Constraint # added constraint: constraint((T0288)T8.CB, (T0288)V81.CB) [> 4.2423 = 7.0704 < 9.1916] w=0.6905 to align # Constraint # added constraint: constraint((T0288)V7.CB, (T0288)V48.CB) [> 3.7301 = 6.2168 < 8.0818] w=0.6905 to align # Constraint # added constraint: constraint((T0288)N58.CB, (T0288)M73.CB) [> 4.2262 = 7.0437 < 9.1568] w=0.6846 to align # Constraint # added constraint: constraint((T0288)D52.CB, (T0288)Y85.CB) [> 2.7090 = 4.5149 < 5.8694] w=0.6812 to align # Constraint # added constraint: constraint((T0288)L9.CB, (T0288)P41.CB) [> 3.0381 = 5.0635 < 6.5825] w=0.6805 to align # Constraint # added constraint: constraint((T0288)L9.CB, (T0288)I83.CB) [> 4.1031 = 6.8386 < 8.8902] w=0.6716 to align # Constraint # added constraint: constraint((T0288)K11.CB, (T0288)V81.CB) [> 3.8776 = 6.4627 < 8.4015] w=0.6716 to align # Constraint # added constraint: constraint((T0288)I21.CB, (T0288)I74.CB) [> 4.4257 = 7.3761 < 9.5890] w=0.6616 to align # Constraint # added constraint: constraint((T0288)I54.CB, (T0288)Y85.CB) [> 3.5049 = 5.8415 < 7.5939] w=0.6533 to align # Constraint # added constraint: constraint((T0288)L31.CB, (T0288)K65.CB) [> 3.9038 = 6.5064 < 8.4583] w=0.6437 to align # Constraint # added constraint: constraint((T0288)T8.CB, (T0288)E80.CB) [> 3.6628 = 6.1046 < 7.9360] w=0.6406 to align # Constraint # added constraint: constraint((T0288)T55.CB, (T0288)Y85.CB) [> 4.0489 = 6.7481 < 8.7726] w=0.6373 to align # Constraint # added constraint: constraint((T0288)K6.CB, (T0288)I83.CB) [> 4.3422 = 7.2369 < 9.4080] w=0.6307 to align # Constraint # added constraint: constraint((T0288)G59.CA, (T0288)H84.CB) [> 4.3649 = 7.2749 < 9.4574] w=0.6110 to align # Constraint # added constraint: constraint((T0288)C30.CB, (T0288)K63.CB) [> 3.9267 = 6.5444 < 8.5077] w=0.6078 to align # Constraint # added constraint: constraint((T0288)G24.CA, (T0288)K67.CB) [> 3.1920 = 5.3201 < 6.9161] w=0.6017 to align # Constraint # added constraint: constraint((T0288)Q10.CB, (T0288)G79.CA) [> 3.6743 = 6.1238 < 7.9610] w=0.6007 to align # Constraint # added constraint: constraint((T0288)T8.CB, (T0288)I83.CB) [> 4.2622 = 7.1036 < 9.2347] w=0.5917 to align # Constraint # added constraint: constraint((T0288)V7.CB, (T0288)D45.CB) [> 3.3698 = 5.6163 < 7.3012] w=0.5708 to align # Constraint # added constraint: constraint((T0288)P4.CB, (T0288)T55.CB) [> 4.1470 = 6.9117 < 8.9852] w=0.5608 to align # Constraint # added constraint: constraint((T0288)G22.CA, (T0288)I33.CB) [> 4.6472 = 7.7453 < 10.0689] w=0.5558 to align # Constraint # added constraint: constraint((T0288)P4.CB, (T0288)H84.CB) [> 3.6638 = 6.1063 < 7.9382] w=0.5508 to align # Constraint # added constraint: constraint((T0288)V7.CB, (T0288)H84.CB) [> 4.2831 = 7.1385 < 9.2800] w=0.5299 to align # Constraint # added constraint: constraint((T0288)G5.CA, (T0288)Y85.CB) [> 3.5434 = 5.9056 < 7.6773] w=0.5209 to align # Constraint # added constraint: constraint((T0288)G5.CA, (T0288)N86.CB) [> 4.0513 = 6.7521 < 8.7777] w=0.5209 to align # Constraint # added constraint: constraint((T0288)I33.CB, (T0288)Y85.CB) [> 4.4915 = 7.4858 < 9.7316] w=0.4996 to align # Constraint # added constraint: constraint((T0288)I19.CB, (T0288)V34.CB) [> 4.6437 = 7.7394 < 10.0613] w=0.4820 to align # Constraint # added constraint: constraint((T0288)V7.CB, (T0288)Y85.CB) [> 3.7926 = 6.3210 < 8.2173] w=0.4810 to align # Constraint # added constraint: constraint((T0288)A49.CB, (T0288)K87.CB) [> 4.2155 = 7.0259 < 9.1336] w=0.4709 to align # Constraint # added constraint: constraint((T0288)S20.CB, (T0288)F37.CB) [> 4.4790 = 7.4651 < 9.7046] w=0.4582 to align # Constraint # added constraint: constraint((T0288)C30.CB, (T0288)I54.CB) [> 4.1449 = 6.9081 < 8.9805] w=0.4411 to align # Constraint # added constraint: constraint((T0288)V7.CB, (T0288)T47.CB) [> 3.0142 = 5.0236 < 6.5307] w=0.4411 to align # Constraint # added constraint: constraint((T0288)K11.CB, (T0288)V77.CB) [> 4.0043 = 6.6738 < 8.6759] w=0.4391 to align # Constraint # added constraint: constraint((T0288)A25.CB, (T0288)T66.CB) [> 3.4975 = 5.8292 < 7.5779] w=0.4121 to align # Constraint # added constraint: constraint((T0288)G51.CA, (T0288)L88.CB) [> 3.5502 = 5.9170 < 7.6920] w=0.4011 to align # Constraint # added constraint: constraint((T0288)S20.CB, (T0288)V36.CB) [> 4.5861 = 7.6434 < 9.9364] w=0.3991 to align # Constraint # added constraint: constraint((T0288)A25.CB, (T0288)K67.CB) [> 4.1126 = 6.8544 < 8.9107] w=0.3822 to align # Constraint # added constraint: constraint((T0288)G24.CA, (T0288)V70.CB) [> 4.0081 = 6.6801 < 8.6841] w=0.3722 to align # Constraint # added constraint: constraint((T0288)C30.CB, (T0288)I62.CB) [> 4.0708 = 6.7847 < 8.8201] w=0.3713 to align # Constraint # added constraint: constraint((T0288)K6.CB, (T0288)Y85.CB) [> 4.2195 = 7.0326 < 9.1423] w=0.3712 to align # Constraint # added constraint: constraint((T0288)P4.CB, (T0288)Y85.CB) [> 4.1645 = 6.9409 < 9.0231] w=0.3602 to align # Constraint # added constraint: constraint((T0288)G5.CA, (T0288)K87.CB) [> 4.2531 = 7.0885 < 9.2150] w=0.3512 to align # Constraint # added constraint: constraint((T0288)A13.CB, (T0288)G79.CA) [> 4.1089 = 6.8482 < 8.9027] w=0.3493 to align # Constraint # added constraint: constraint((T0288)K11.CB, (T0288)K78.CB) [> 4.1237 = 6.8729 < 8.9348] w=0.3393 to align # Constraint # added constraint: constraint((T0288)L16.CB, (T0288)F37.CB) [> 4.3507 = 7.2511 < 9.4265] w=0.3363 to align # Constraint # added constraint: constraint((T0288)I17.CB, (T0288)V77.CB) [> 4.5209 = 7.5347 < 9.7952] w=0.3293 to align # Constraint # added constraint: constraint((T0288)C30.CB, (T0288)T55.CB) [> 3.8695 = 6.4492 < 8.3839] w=0.3283 to align # Constraint # added constraint: constraint((T0288)P29.CB, (T0288)K63.CB) [> 3.7088 = 6.1813 < 8.0357] w=0.2903 to align # Constraint # added constraint: constraint((T0288)N58.CB, (T0288)K78.CB) [> 4.4085 = 7.3474 < 9.5516] w=0.2893 to align # Constraint # added constraint: constraint((T0288)N58.CB, (T0288)I83.CB) [> 4.1994 = 6.9990 < 9.0986] w=0.2661 to align # Constraint # added constraint: constraint((T0288)L9.CB, (T0288)G18.CA) [> 4.6170 = 7.6949 < 10.0034] w=0.2628 to align # Constraint # added constraint: constraint((T0288)I54.CB, (T0288)I74.CB) [> 4.6813 = 7.8021 < 10.1427] w=0.2425 to align # Constraint # added constraint: constraint((T0288)G23.CA, (T0288)V70.CB) [> 4.6255 = 7.7091 < 10.0219] w=0.2195 to align # Constraint # added constraint: constraint((T0288)A25.CB, (T0288)K65.CB) [> 4.0054 = 6.6758 < 8.6785] w=0.2125 to align # Constraint # added constraint: constraint((T0288)N58.CB, (T0288)E80.CB) [> 4.4143 = 7.3572 < 9.5643] w=0.1796 to align # Constraint # added constraint: constraint((T0288)G56.CA, (T0288)T82.CB) [> 4.7732 = 7.9553 < 10.3419] w=0.1644 to align # Constraint # added constraint: constraint((T0288)V7.CB, (T0288)A42.CB) [> 4.5254 = 7.5423 < 9.8050] w=0.1617 to align # Constraint # added constraint: constraint((T0288)T8.CB, (T0288)T47.CB) [> 3.5313 = 5.8855 < 7.6512] w=0.1607 to align # Constraint # added constraint: constraint((T0288)Q26.CB, (T0288)K67.CB) [> 3.8157 = 6.3595 < 8.2674] w=0.1597 to align # Constraint # added constraint: constraint((T0288)L31.CB, (T0288)T55.CB) [> 4.3511 = 7.2519 < 9.4274] w=0.1518 to align # Constraint # added constraint: constraint((T0288)Q14.CB, (T0288)T40.CB) [> 3.9937 = 6.6561 < 8.6530] w=0.1517 to align # Constraint # added constraint: constraint((T0288)Y32.CB, (T0288)L88.CB) [> 4.3461 = 7.2435 < 9.4165] w=0.1497 to align # Constraint # added constraint: constraint((T0288)N15.CB, (T0288)V77.CB) [> 4.0070 = 6.6783 < 8.6818] w=0.1497 to align # Constraint # added constraint: constraint((T0288)G24.CA, (T0288)E53.CB) [> 4.1398 = 6.8996 < 8.9695] w=0.1466 to align # Constraint # added constraint: constraint((T0288)G56.CA, (T0288)M73.CB) [> 4.6367 = 7.7278 < 10.0461] w=0.1459 to align # Constraint # added constraint: constraint((T0288)Y27.CB, (T0288)K67.CB) [> 3.5934 = 5.9891 < 7.7858] w=0.1307 to align # Constraint # added constraint: constraint((T0288)G56.CA, (T0288)Y85.CB) [> 4.5352 = 7.5586 < 9.8262] w=0.1305 to align # Constraint # added constraint: constraint((T0288)G5.CA, (T0288)T47.CB) [> 4.5720 = 7.6200 < 9.9059] w=0.1217 to align # Constraint # added constraint: constraint((T0288)Q10.CB, (T0288)I83.CB) [> 4.1212 = 6.8686 < 8.9292] w=0.1207 to align # Constraint # added constraint: constraint((T0288)Y32.CB, (T0288)A50.CB) [> 4.5779 = 7.6298 < 9.9187] w=0.1197 to align # Constraint # added constraint: constraint((T0288)G18.CA, (T0288)V48.CB) [> 4.6589 = 7.7649 < 10.0944] w=0.1197 to align # Constraint # added constraint: constraint((T0288)P29.CB, (T0288)T66.CB) [> 4.3060 = 7.1768 < 9.3298] w=0.1196 to align # Constraint # added constraint: constraint((T0288)L31.CB, (T0288)E69.CB) [> 4.3237 = 7.2062 < 9.3681] w=0.1189 to align # Constraint # added constraint: constraint((T0288)L31.CB, (T0288)A71.CB) [> 4.4606 = 7.4343 < 9.6645] w=0.1160 to align # Constraint # added constraint: constraint((T0288)L9.CB, (T0288)I19.CB) [> 4.4614 = 7.4356 < 9.6663] w=0.1131 to align # Constraint # added constraint: constraint((T0288)T55.CB, (T0288)I83.CB) [> 4.6751 = 7.7918 < 10.1294] w=0.1128 to align # Constraint # added constraint: constraint((T0288)D12.CB, (T0288)V81.CB) [> 3.9664 = 6.6107 < 8.5939] w=0.1108 to align # Constraint # added constraint: constraint((T0288)Q10.CB, (T0288)L44.CB) [> 4.4091 = 7.3486 < 9.5531] w=0.1098 to align # Constraint # added constraint: constraint((T0288)L16.CB, (T0288)I74.CB) [> 4.0238 = 6.7063 < 8.7182] w=0.1060 to align # Constraint # added constraint: constraint((T0288)C30.CB, (T0288)G56.CA) [> 4.6379 = 7.7298 < 10.0488] w=0.0968 to align # Constraint # added constraint: constraint((T0288)K6.CB, (T0288)K87.CB) [> 4.3654 = 7.2757 < 9.4583] w=0.0908 to align # Constraint # added constraint: constraint((T0288)P29.CB, (T0288)T55.CB) [> 3.7202 = 6.2003 < 8.0604] w=0.0907 to align # Constraint # added constraint: constraint((T0288)G23.CA, (T0288)V34.CB) [> 4.6910 = 7.8183 < 10.1638] w=0.0898 to align # Constraint # added constraint: constraint((T0288)I19.CB, (T0288)I54.CB) [> 4.6436 = 7.7393 < 10.0611] w=0.0898 to align # Constraint # added constraint: constraint((T0288)I19.CB, (T0288)I74.CB) [> 4.2842 = 7.1403 < 9.2824] w=0.0898 to align # Constraint # added constraint: constraint((T0288)A50.CB, (T0288)L88.CB) [> 4.3870 = 7.3116 < 9.5051] w=0.0898 to align # Constraint # added constraint: constraint((T0288)G5.CA, (T0288)T55.CB) [> 4.4355 = 7.3924 < 9.6102] w=0.0808 to align # Constraint # added constraint: constraint((T0288)L16.CB, (T0288)Q75.CB) [> 4.1000 = 6.8333 < 8.8833] w=0.0808 to align # Constraint # added constraint: constraint((T0288)V7.CB, (T0288)V81.CB) [> 4.6704 = 7.7840 < 10.1193] w=0.0798 to align # Constraint # added constraint: constraint((T0288)G59.CA, (T0288)I83.CB) [> 4.5227 = 7.5379 < 9.7993] w=0.0738 to align # Constraint # added constraint: constraint((T0288)P29.CB, (T0288)K67.CB) [> 4.4629 = 7.4382 < 9.6697] w=0.0699 to align # Constraint # added constraint: constraint((T0288)D52.CB, (T0288)I83.CB) [> 4.7153 = 7.8589 < 10.2165] w=0.0699 to align # Constraint # added constraint: constraint((T0288)G5.CA, (T0288)I83.CB) [> 4.5930 = 7.6550 < 9.9515] w=0.0599 to align # Constraint # added constraint: constraint((T0288)C30.CB, (T0288)K67.CB) [> 2.4408 = 4.0681 < 5.2885] w=0.0599 to align # Constraint # added constraint: constraint((T0288)I17.CB, (T0288)F37.CB) [> 4.7197 = 7.8661 < 10.2260] w=0.0599 to align # Constraint # added constraint: constraint((T0288)S20.CB, (T0288)A50.CB) [> 4.2790 = 7.1317 < 9.2712] w=0.0599 to align # Constraint # added constraint: constraint((T0288)V7.CB, (T0288)D52.CB) [> 4.5234 = 7.5390 < 9.8007] w=0.0599 to align # Constraint # added constraint: constraint((T0288)I17.CB, (T0288)V57.CB) [> 4.6003 = 7.6672 < 9.9674] w=0.0599 to align # Constraint # added constraint: constraint((T0288)G18.CA, (T0288)N39.CB) [> 3.8599 = 6.4331 < 8.3630] w=0.0599 to align # Constraint # added constraint: constraint((T0288)I21.CB, (T0288)I62.CB) [> 3.9722 = 6.6204 < 8.6065] w=0.0599 to align # Constraint # added constraint: constraint((T0288)G23.CA, (T0288)I62.CB) [> 4.1864 = 6.9773 < 9.0705] w=0.0599 to align # Constraint # added constraint: constraint((T0288)R60.CB, (T0288)V70.CB) [> 2.8969 = 4.8282 < 6.2766] w=0.0599 to align # Constraint # added constraint: constraint((T0288)G18.CA, (T0288)Q35.CB) [> 4.6122 = 7.6869 < 9.9930] w=0.0599 to align # Constraint # added constraint: constraint((T0288)S20.CB, (T0288)A71.CB) [> 4.0937 = 6.8229 < 8.8697] w=0.0599 to align # Constraint # added constraint: constraint((T0288)L31.CB, (T0288)G56.CA) [> 4.5277 = 7.5462 < 9.8100] w=0.0599 to align # Constraint # added constraint: constraint((T0288)P29.CB, (T0288)E53.CB) [> 3.1425 = 5.2375 < 6.8088] w=0.0569 to align # Constraint # added constraint: constraint((T0288)P29.CB, (T0288)I54.CB) [> 4.0448 = 6.7414 < 8.7638] w=0.0499 to align # Constraint # added constraint: constraint((T0288)C28.CB, (T0288)T55.CB) [> 3.8687 = 6.4478 < 8.3822] w=0.0498 to align # Constraint # added constraint: constraint((T0288)G59.CA, (T0288)V81.CB) [> 4.5105 = 7.5176 < 9.7728] w=0.0498 to align # Constraint # added constraint: constraint((T0288)Y32.CB, (T0288)K67.CB) [> 4.4175 = 7.3625 < 9.5713] w=0.0471 to align # Constraint # added constraint: constraint((T0288)Y27.CB, (T0288)E53.CB) [> 3.6946 = 6.1577 < 8.0050] w=0.0468 to align # Constraint # added constraint: constraint((T0288)K6.CB, (T0288)D52.CB) [> 4.6575 = 7.7626 < 10.0913] w=0.0409 to align # Constraint # added constraint: constraint((T0288)V3.CB, (T0288)L88.CB) [> 4.1926 = 6.9876 < 9.0840] w=0.0409 to align # Constraint # added constraint: constraint((T0288)C28.CB, (T0288)K67.CB) [> 3.8401 = 6.4001 < 8.3201] w=0.0399 to align # Constraint # added constraint: constraint((T0288)G56.CA, (T0288)N86.CB) [> 3.3268 = 5.5447 < 7.2081] w=0.0360 to align # Constraint # added constraint: constraint((T0288)M2.CB, (T0288)Y90.CB) [> 4.0301 = 6.7169 < 8.7319] w=0.0299 to align # Constraint # added constraint: constraint((T0288)P4.CB, (T0288)G56.CA) [> 4.6163 = 7.6938 < 10.0019] w=0.0299 to align # Constraint # added constraint: constraint((T0288)R60.CB, (T0288)E76.CB) [> 4.7754 = 7.9589 < 10.3466] w=0.0299 to align # Constraint # added constraint: constraint((T0288)I17.CB, (T0288)V48.CB) [> 4.7232 = 7.8720 < 10.2336] w=0.0299 to align # Constraint # added constraint: constraint((T0288)V36.CB, (T0288)D45.CB) [> 3.8158 = 6.3597 < 8.2676] w=0.0299 to align # Constraint # added constraint: constraint((T0288)V3.CB, (T0288)Y85.CB) [> 3.8538 = 6.4230 < 8.3499] w=0.0299 to align # Constraint # added constraint: constraint((T0288)V7.CB, (T0288)K87.CB) [> 3.9022 = 6.5037 < 8.4548] w=0.0299 to align # Constraint # added constraint: constraint((T0288)T8.CB, (T0288)L44.CB) [> 4.7275 = 7.8792 < 10.2430] w=0.0299 to align # Constraint # added constraint: constraint((T0288)G22.CA, (T0288)A71.CB) [> 4.3424 = 7.2373 < 9.4085] w=0.0299 to align # Constraint # added constraint: constraint((T0288)V3.CB, (T0288)Y91.CB) [> 4.1335 = 6.8891 < 8.9559] w=0.0299 to align # Constraint # added constraint: constraint((T0288)V7.CB, (T0288)V57.CB) [> 4.7243 = 7.8738 < 10.2360] w=0.0299 to align # Constraint # added constraint: constraint((T0288)L16.CB, (T0288)D38.CB) [> 3.5772 = 5.9621 < 7.7507] w=0.0299 to align # Constraint # added constraint: constraint((T0288)G18.CA, (T0288)D38.CB) [> 2.8072 = 4.6787 < 6.0823] w=0.0299 to align # Constraint # added constraint: constraint((T0288)I21.CB, (T0288)V57.CB) [> 4.6724 = 7.7873 < 10.1234] w=0.0299 to align # Constraint # added constraint: constraint((T0288)G23.CA, (T0288)K63.CB) [> 4.4962 = 7.4937 < 9.7418] w=0.0299 to align # Constraint # added constraint: constraint((T0288)M2.CB, (T0288)G51.CA) [> 4.7913 = 7.9856 < 10.3812] w=0.0299 to align # Constraint # added constraint: constraint((T0288)G5.CA, (T0288)D52.CB) [> 4.6835 = 7.8058 < 10.1476] w=0.0299 to align # Constraint # added constraint: constraint((T0288)G51.CA, (T0288)Y90.CB) [> 4.5985 = 7.6641 < 9.9634] w=0.0299 to align # Constraint # added constraint: constraint((T0288)C30.CB, (T0288)S61.CB) [> 4.7319 = 7.8866 < 10.2526] w=0.0298 to align # Constraint # added constraint: constraint((T0288)C28.CB, (T0288)V68.CB) [> 4.7429 = 7.9049 < 10.2763] w=0.0200 to align # Constraint # added constraint: constraint((T0288)C28.CB, (T0288)I62.CB) [> 3.8085 = 6.3476 < 8.2519] w=0.0200 to align # Constraint # added constraint: constraint((T0288)G5.CA, (T0288)L88.CB) [> 4.4202 = 7.3670 < 9.5771] w=0.0200 to align # Constraint # added constraint: constraint((T0288)P4.CB, (T0288)Y91.CB) [> 4.4012 = 7.3353 < 9.5359] w=0.0200 to align # Constraint # added constraint: constraint((T0288)G24.CA, (T0288)G51.CA) [> 4.3755 = 7.2925 < 9.4803] w=0.0199 to align # Constraint # added constraint: constraint((T0288)Y32.CB, (T0288)K65.CB) [> 3.7141 = 6.1901 < 8.0471] w=0.0120 to align # Constraint # added constraint: constraint((T0288)D52.CB, (T0288)Y90.CB) [> 3.8507 = 6.4178 < 8.3432] w=0.0110 to align # Constraint # added constraint: constraint((T0288)K6.CB, (T0288)T55.CB) [> 4.6409 = 7.7348 < 10.0552] w=0.0100 to align # Constraint # added constraint: constraint((T0288)M2.CB, (T0288)Y91.CB) [> 3.7420 = 6.2366 < 8.1076] w=0.0100 to align # Constraint # added constraint: constraint((T0288)T8.CB, (T0288)I17.CB) [> 3.8699 = 6.4499 < 8.3848] w=0.0100 to align # Constraint # added constraint: constraint((T0288)C30.CB, (T0288)Y90.CB) [> 4.6677 = 7.7795 < 10.1133] w=0.0100 to align # Constraint # added constraint: constraint((T0288)C30.CB, (T0288)Y91.CB) [> 4.5453 = 7.5754 < 9.8481] w=0.0100 to align # Constraint # added constraint: constraint((T0288)N15.CB, (T0288)G51.CA) [> 4.6856 = 7.8094 < 10.1522] w=0.0099 to align # Constraint # added constraint: constraint((T0288)L9.CB, (T0288)Y32.CB) [> 3.2762 = 5.4603 < 7.0984] w=0.0099 to align # Constraint # added constraint: constraint((T0288)L9.CB, (T0288)K67.CB) [> 3.8822 = 6.4704 < 8.4115] w=0.0099 to align # Constraint # added constraint: constraint((T0288)Q10.CB, (T0288)L31.CB) [> 4.2718 = 7.1197 < 9.2556] w=0.0099 to align # Constraint # added constraint: constraint((T0288)Q10.CB, (T0288)Y32.CB) [> 3.4423 = 5.7372 < 7.4584] w=0.0099 to align # Constraint # added constraint: constraint((T0288)L9.CB, (T0288)S20.CB) [> 3.3396 = 5.5660 < 7.2358] w=0.0034 to align # SetCost created cost = # ( 1.0000 * align ) # command:# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0288/ # command:# reading script from file servers-clean.under # Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/T0288/decoys/ # ReadConformPDB reading from PDB file refine-chimera1.pdb.gz looking for model 1 # Found a chain break before 86 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file robetta-model1.pdb.gz looking for model 1 # Found a chain break before 28 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file robetta-model2.pdb.gz looking for model 1 # ReadConformPDB reading from PDB file robetta-model3.pdb.gz looking for model 1 # Found a chain break before 27 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file robetta-model4.pdb.gz looking for model 1 # Found a chain break before 25 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file robetta-model5.pdb.gz looking for model 1 # Found a chain break before 27 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file tr288.pdb.gz looking for model 1 # WARNING: incomplete conformation T0288 can't currently be optimized by undertaker # ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0288 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_POPULUS_TS1 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0288 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_POPULUS_TS2 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0288 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_POPULUS_TS3 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0288 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_POPULUS_TS4 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0288 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_POPULUS_TS5 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_RECOM_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0288 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_RECOM_TS1 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_RECOM_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0288 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_RECOM_TS2 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_RECOM_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0288 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_RECOM_TS3 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_RECOM_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0288 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_RECOM_TS4 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_RECOM_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0288 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_RECOM_TS5 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0288 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_TS1 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0288 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_TS2 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0288 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_TS3 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0288 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_TS4 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0288 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_TS5 # ReadConformPDB reading from PDB file servers/3Dpro_TS1.pdb.gz looking for model 1 # naming current conformation 3Dpro_TS1 # ReadConformPDB reading from PDB file servers/3Dpro_TS2.pdb.gz looking for model 1 # Found a chain break before 30 # copying to AlignedFragments data structure # naming current conformation 3Dpro_TS2 # ReadConformPDB reading from PDB file servers/3Dpro_TS3.pdb.gz looking for model 1 # Found a chain break before 88 # copying to AlignedFragments data structure # naming current conformation 3Dpro_TS3 # ReadConformPDB reading from PDB file servers/3Dpro_TS4.pdb.gz looking for model 1 # Found a chain break before 68 # copying to AlignedFragments data structure # naming current conformation 3Dpro_TS4 # ReadConformPDB reading from PDB file servers/3Dpro_TS5.pdb.gz looking for model 1 # naming current conformation 3Dpro_TS5 # ReadConformPDB reading from PDB file servers/ABIpro_TS1.pdb.gz looking for model 1 # Found a chain break before 90 # copying to AlignedFragments data structure # naming current conformation ABIpro_TS1 # ReadConformPDB reading from PDB file servers/ABIpro_TS2.pdb.gz looking for model 1 # Found a chain break before 76 # copying to AlignedFragments data structure # naming current conformation ABIpro_TS2 # ReadConformPDB reading from PDB file servers/ABIpro_TS3.pdb.gz looking for model 1 # Found a chain break before 90 # copying to AlignedFragments data structure # naming current conformation ABIpro_TS3 # ReadConformPDB reading from PDB file servers/ABIpro_TS4.pdb.gz looking for model 1 # Found a chain break before 86 # copying to AlignedFragments data structure # naming current conformation ABIpro_TS4 # ReadConformPDB reading from PDB file servers/ABIpro_TS5.pdb.gz looking for model 1 # Found a chain break before 81 # copying to AlignedFragments data structure # naming current conformation ABIpro_TS5 # ReadConformPDB reading from PDB file servers/BayesHH_TS1.pdb.gz looking for model 1 # naming current conformation BayesHH_TS1 # ReadConformPDB reading from PDB file servers/Bilab-ENABLE_TS1.pdb.gz looking for model 1 # Found a chain break before 46 # copying to AlignedFragments data structure # naming current conformation Bilab-ENABLE_TS1 # ReadConformPDB reading from PDB file servers/Bilab-ENABLE_TS2.pdb.gz looking for model 1 # Found a chain break before 86 # copying to AlignedFragments data structure # naming current conformation Bilab-ENABLE_TS2 # ReadConformPDB reading from PDB file servers/Bilab-ENABLE_TS3.pdb.gz looking for model 1 # Found a chain break before 88 # copying to AlignedFragments data structure # naming current conformation Bilab-ENABLE_TS3 # ReadConformPDB reading from PDB file servers/Bilab-ENABLE_TS4.pdb.gz looking for model 1 # Found a chain break before 46 # copying to AlignedFragments data structure # naming current conformation Bilab-ENABLE_TS4 # ReadConformPDB reading from PDB file servers/Bilab-ENABLE_TS5.pdb.gz looking for model 1 # Found a chain break before 63 # copying to AlignedFragments data structure # naming current conformation Bilab-ENABLE_TS5 # ReadConformPDB reading from PDB file servers/CIRCLE_TS1.pdb.gz looking for model 1 # Found a chain break before 88 # copying to AlignedFragments data structure # naming current conformation CIRCLE_TS1 # ReadConformPDB reading from PDB file servers/CIRCLE_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0288 can't currently be optimized by undertaker # naming current conformation CIRCLE_TS2 # ReadConformPDB reading from PDB file servers/CIRCLE_TS3.pdb.gz looking for model 1 # Found a chain break before 58 # copying to AlignedFragments data structure # naming current conformation CIRCLE_TS3 # ReadConformPDB reading from PDB file servers/CIRCLE_TS4.pdb.gz looking for model 1 # Found a chain break before 85 # copying to AlignedFragments data structure # naming current conformation CIRCLE_TS4 # ReadConformPDB reading from PDB file servers/CIRCLE_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0288 can't currently be optimized by undertaker # naming current conformation CIRCLE_TS5 # ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0288 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation CaspIta-FOX_TS1 # ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS2.pdb.gz looking for model 1 # Found a chain break before 29 # copying to AlignedFragments data structure # naming current conformation CaspIta-FOX_TS2 # ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0288 can't currently be optimized by undertaker # naming current conformation CaspIta-FOX_TS3 # ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS4.pdb.gz looking for model 1 # Found a chain break before 48 # copying to AlignedFragments data structure # naming current conformation CaspIta-FOX_TS4 # ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS5.pdb.gz looking for model 1 # Found a chain break before 30 # copying to AlignedFragments data structure # naming current conformation CaspIta-FOX_TS5 # ReadConformPDB reading from PDB file servers/Distill_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0288 can't currently be optimized by undertaker # naming current conformation Distill_TS1 # ReadConformPDB reading from PDB file servers/Distill_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0288 can't currently be optimized by undertaker # naming current conformation Distill_TS2 # ReadConformPDB reading from PDB file servers/Distill_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0288 can't currently be optimized by undertaker # naming current conformation Distill_TS3 # ReadConformPDB reading from PDB file servers/Distill_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0288 can't currently be optimized by undertaker # naming current conformation Distill_TS4 # ReadConformPDB reading from PDB file servers/Distill_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0288 can't currently be optimized by undertaker # naming current conformation Distill_TS5 # ReadConformPDB reading from PDB file servers/FAMSD_TS1.pdb.gz looking for model 1 # Found a chain break before 37 # copying to AlignedFragments data structure # naming current conformation FAMSD_TS1 # ReadConformPDB reading from PDB file servers/FAMSD_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0288 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation FAMSD_TS2 # ReadConformPDB reading from PDB file servers/FAMSD_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0288 can't currently be optimized by undertaker # naming current conformation FAMSD_TS3 # ReadConformPDB reading from PDB file servers/FAMSD_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0288 can't currently be optimized by undertaker # naming current conformation FAMSD_TS4 # ReadConformPDB reading from PDB file servers/FAMSD_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0288 can't currently be optimized by undertaker # naming current conformation FAMSD_TS5 # ReadConformPDB reading from PDB file servers/FAMS_TS1.pdb.gz looking for model 1 # Found a chain break before 62 # copying to AlignedFragments data structure # naming current conformation FAMS_TS1 # ReadConformPDB reading from PDB file servers/FAMS_TS2.pdb.gz looking for model 1 # Found a chain break before 92 # copying to AlignedFragments data structure # naming current conformation FAMS_TS2 # ReadConformPDB reading from PDB file servers/FAMS_TS3.pdb.gz looking for model 1 # Found a chain break before 91 # copying to AlignedFragments data structure # naming current conformation FAMS_TS3 # ReadConformPDB reading from PDB file servers/FAMS_TS4.pdb.gz looking for model 1 # Found a chain break before 79 # copying to AlignedFragments data structure # naming current conformation FAMS_TS4 # ReadConformPDB reading from PDB file servers/FAMS_TS5.pdb.gz looking for model 1 # Found a chain break before 90 # copying to AlignedFragments data structure # naming current conformation FAMS_TS5 # ReadConformPDB reading from PDB file servers/FOLDpro_TS1.pdb.gz looking for model 1 # Found a chain break before 28 # copying to AlignedFragments data structure # naming current conformation FOLDpro_TS1 # ReadConformPDB reading from PDB file servers/FOLDpro_TS2.pdb.gz looking for model 1 # Found a chain break before 73 # copying to AlignedFragments data structure # naming current conformation FOLDpro_TS2 # ReadConformPDB reading from PDB file servers/FOLDpro_TS3.pdb.gz looking for model 1 # Found a chain break before 30 # copying to AlignedFragments data structure # naming current conformation FOLDpro_TS3 # ReadConformPDB reading from PDB file servers/FOLDpro_TS4.pdb.gz looking for model 1 # Found a chain break before 59 # copying to AlignedFragments data structure # naming current conformation FOLDpro_TS4 # ReadConformPDB reading from PDB file servers/FOLDpro_TS5.pdb.gz looking for model 1 # Found a chain break before 45 # copying to AlignedFragments data structure # naming current conformation FOLDpro_TS5 # ReadConformPDB reading from PDB file servers/FORTE1_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0288 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation FORTE1_AL1 # ReadConformPDB reading from PDB file servers/FORTE1_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0288 can't currently be optimized by undertaker # naming current conformation FORTE1_AL2 # ReadConformPDB reading from PDB file servers/FORTE1_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0288 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation FORTE1_AL3 # ReadConformPDB reading from PDB file servers/FORTE1_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0288 can't currently be optimized by undertaker # naming current conformation FORTE1_AL4 # ReadConformPDB reading from PDB file servers/FORTE1_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0288 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation FORTE1_AL5 # ReadConformPDB reading from PDB file servers/FORTE2_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0288 can't currently be optimized by undertaker # naming current conformation FORTE2_AL1 # ReadConformPDB reading from PDB file servers/FORTE2_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0288 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation FORTE2_AL2 # ReadConformPDB reading from PDB file servers/FORTE2_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0288 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation FORTE2_AL3 # ReadConformPDB reading from PDB file servers/FORTE2_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0288 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation FORTE2_AL4 # ReadConformPDB reading from PDB file servers/FORTE2_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0288 can't currently be optimized by undertaker # naming current conformation FORTE2_AL5 # ReadConformPDB reading from PDB file servers/FPSOLVER-SERVER_TS1.pdb.gz looking for model 1 # Found a chain break before 92 # copying to AlignedFragments data structure # naming current conformation FPSOLVER-SERVER_TS1 # ReadConformPDB reading from PDB file servers/FUGMOD_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0288 can't currently be optimized by undertaker # naming current conformation FUGMOD_TS1 # ReadConformPDB reading from PDB file servers/FUGMOD_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0288 can't currently be optimized by undertaker # naming current conformation FUGMOD_TS2 # ReadConformPDB reading from PDB file servers/FUGMOD_TS3.pdb.gz looking for model 1 # naming current conformation FUGMOD_TS3 # ReadConformPDB reading from PDB file servers/FUGMOD_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0288 can't currently be optimized by undertaker # naming current conformation FUGMOD_TS4 # ReadConformPDB reading from PDB file servers/FUGMOD_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0288 can't currently be optimized by undertaker # naming current conformation FUGMOD_TS5 # ReadConformPDB reading from PDB file servers/FUGUE_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0288 can't currently be optimized by undertaker # naming current conformation FUGUE_AL1 # ReadConformPDB reading from PDB file servers/FUGUE_AL2.pdb.gz looking for model 1 Skipped atom 211, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL2.pdb.gz # WARNING: incomplete conformation T0288 can't currently be optimized by undertaker # naming current conformation FUGUE_AL2 # ReadConformPDB reading from PDB file servers/FUGUE_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0288 can't currently be optimized by undertaker # naming current conformation FUGUE_AL3 # ReadConformPDB reading from PDB file servers/FUGUE_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0288 can't currently be optimized by undertaker # naming current conformation FUGUE_AL4 # ReadConformPDB reading from PDB file servers/FUGUE_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0288 can't currently be optimized by undertaker # naming current conformation FUGUE_AL5 # ReadConformPDB reading from PDB file servers/FUNCTION_TS1.pdb.gz looking for model 1 # Found a chain break before 62 # copying to AlignedFragments data structure # naming current conformation FUNCTION_TS1 # ReadConformPDB reading from PDB file servers/FUNCTION_TS2.pdb.gz looking for model 1 # Found a chain break before 92 # copying to AlignedFragments data structure # naming current conformation FUNCTION_TS2 # ReadConformPDB reading from PDB file servers/FUNCTION_TS3.pdb.gz looking for model 1 # Found a chain break before 91 # copying to AlignedFragments data structure # naming current conformation FUNCTION_TS3 # ReadConformPDB reading from PDB file servers/FUNCTION_TS4.pdb.gz looking for model 1 # Found a chain break before 79 # copying to AlignedFragments data structure # naming current conformation FUNCTION_TS4 # ReadConformPDB reading from PDB file servers/FUNCTION_TS5.pdb.gz looking for model 1 # Found a chain break before 90 # copying to AlignedFragments data structure # naming current conformation FUNCTION_TS5 # ReadConformPDB reading from PDB file servers/Frankenstein_TS1.pdb.gz looking for model 1 # naming current conformation Frankenstein_TS1 # ReadConformPDB reading from PDB file servers/Frankenstein_TS2.pdb.gz looking for model 1 # Found a chain break before 23 # copying to AlignedFragments data structure # naming current conformation Frankenstein_TS2 # ReadConformPDB reading from PDB file servers/Frankenstein_TS3.pdb.gz looking for model 1 # naming current conformation Frankenstein_TS3 # ReadConformPDB reading from PDB file servers/Frankenstein_TS4.pdb.gz looking for model 1 # naming current conformation Frankenstein_TS4 # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0288 can't currently be optimized by undertaker # naming current conformation GeneSilicoMetaServer_TS1 # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS2.pdb.gz looking for model 1 # Found a chain break before 78 # copying to AlignedFragments data structure # naming current conformation GeneSilicoMetaServer_TS2 # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS3.pdb.gz looking for model 1 # naming current conformation GeneSilicoMetaServer_TS3 # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS4.pdb.gz looking for model 1 # naming current conformation GeneSilicoMetaServer_TS4 # ReadConformPDB reading from PDB file servers/HHpred1_TS1.pdb.gz looking for model 1 # Found a chain break before 63 # copying to AlignedFragments data structure # naming current conformation HHpred1_TS1 # ReadConformPDB reading from PDB file servers/HHpred2_TS1.pdb.gz looking for model 1 # Found a chain break before 40 # copying to AlignedFragments data structure # naming current conformation HHpred2_TS1 # ReadConformPDB reading from PDB file servers/HHpred3_TS1.pdb.gz looking for model 1 # Found a chain break before 40 # copying to AlignedFragments data structure # naming current conformation HHpred3_TS1 # ReadConformPDB reading from PDB file servers/Huber-Torda-Server_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0288 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation Huber-Torda-Server_TS1 # ReadConformPDB reading from PDB file servers/Huber-Torda-Server_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0288 can't currently be optimized by undertaker # naming current conformation Huber-Torda-Server_TS2 # ReadConformPDB reading from PDB file servers/Huber-Torda-Server_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0288 can't currently be optimized by undertaker # naming current conformation Huber-Torda-Server_TS3 # ReadConformPDB reading from PDB file servers/Huber-Torda-Server_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0288 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation Huber-Torda-Server_TS4 # ReadConformPDB reading from PDB file servers/Huber-Torda-Server_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0288 can't currently be optimized by undertaker # naming current conformation Huber-Torda-Server_TS5 # ReadConformPDB reading from PDB file servers/LOOPP_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0288 can't currently be optimized by undertaker # naming current conformation LOOPP_TS1 # ReadConformPDB reading from PDB file servers/LOOPP_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0288 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation LOOPP_TS2 # ReadConformPDB reading from PDB file servers/LOOPP_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0288 can't currently be optimized by undertaker # naming current conformation LOOPP_TS3 # ReadConformPDB reading from PDB file servers/LOOPP_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0288 can't currently be optimized by undertaker # naming current conformation LOOPP_TS4 # ReadConformPDB reading from PDB file servers/LOOPP_TS5.pdb.gz looking for model 1 # Found a chain break before 79 # copying to AlignedFragments data structure # naming current conformation LOOPP_TS5 # ReadConformPDB reading from PDB file servers/MIG_FROST_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0288 can't currently be optimized by undertaker # naming current conformation MIG_FROST_AL1 # ReadConformPDB reading from PDB file servers/MIG_FROST_FLEX_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0288 can't currently be optimized by undertaker # naming current conformation MIG_FROST_FLEX_AL1 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS1.pdb.gz looking for model 1 # Found a chain break before 78 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server_TS1 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS2.pdb.gz looking for model 1 # Found a chain break before 28 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server_TS2 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS3.pdb.gz looking for model 1 # naming current conformation Ma-OPUS-server_TS3 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS4.pdb.gz looking for model 1 # Found a chain break before 88 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server_TS4 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS5.pdb.gz looking for model 1 # Found a chain break before 29 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server_TS5 # ReadConformPDB reading from PDB file servers/MetaTasser_TS1.pdb.gz looking for model 1 # Found a chain break before 92 # copying to AlignedFragments data structure # naming current conformation MetaTasser_TS1 # ReadConformPDB reading from PDB file servers/MetaTasser_TS2.pdb.gz looking for model 1 # Found a chain break before 92 # copying to AlignedFragments data structure # naming current conformation MetaTasser_TS2 # ReadConformPDB reading from PDB file servers/MetaTasser_TS3.pdb.gz looking for model 1 # Found a chain break before 92 # copying to AlignedFragments data structure # naming current conformation MetaTasser_TS3 # ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS1.pdb.gz looking for model 1 # naming current conformation PROTINFO-AB_TS1 # ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS2.pdb.gz looking for model 1 # naming current conformation PROTINFO-AB_TS2 # ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS3.pdb.gz looking for model 1 # naming current conformation PROTINFO-AB_TS3 # ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS4.pdb.gz looking for model 1 # naming current conformation PROTINFO-AB_TS4 # ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS5.pdb.gz looking for model 1 # naming current conformation PROTINFO-AB_TS5 # ReadConformPDB reading from PDB file servers/PROTINFO_TS1.pdb.gz looking for model 1 # Found a chain break before 38 # copying to AlignedFragments data structure # naming current conformation PROTINFO_TS1 # ReadConformPDB reading from PDB file servers/PROTINFO_TS2.pdb.gz looking for model 1 # Found a chain break before 38 # copying to AlignedFragments data structure # naming current conformation PROTINFO_TS2 # ReadConformPDB reading from PDB file servers/PROTINFO_TS3.pdb.gz looking for model 1 # Found a chain break before 38 # copying to AlignedFragments data structure # naming current conformation PROTINFO_TS3 # ReadConformPDB reading from PDB file servers/PROTINFO_TS4.pdb.gz looking for model 1 # naming current conformation PROTINFO_TS4 # ReadConformPDB reading from PDB file servers/PROTINFO_TS5.pdb.gz looking for model 1 # Found a chain break before 77 # copying to AlignedFragments data structure # naming current conformation PROTINFO_TS5 # ReadConformPDB reading from PDB file servers/Pcons6_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0288 can't currently be optimized by undertaker # naming current conformation Pcons6_TS1 # ReadConformPDB reading from PDB file servers/Pcons6_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0288 can't currently be optimized by undertaker # naming current conformation Pcons6_TS2 # ReadConformPDB reading from PDB file servers/Pcons6_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0288 can't currently be optimized by undertaker # naming current conformation Pcons6_TS3 # ReadConformPDB reading from PDB file servers/Pcons6_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0288 can't currently be optimized by undertaker # naming current conformation Pcons6_TS4 # ReadConformPDB reading from PDB file servers/Pcons6_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0288 can't currently be optimized by undertaker # naming current conformation Pcons6_TS5 # ReadConformPDB reading from PDB file servers/Phyre-1_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0288 can't currently be optimized by undertaker # naming current conformation Phyre-1_TS1 # ReadConformPDB reading from PDB file servers/Phyre-2_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0288 can't currently be optimized by undertaker # naming current conformation Phyre-2_TS1 # ReadConformPDB reading from PDB file servers/Phyre-2_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0288 can't currently be optimized by undertaker # naming current conformation Phyre-2_TS2 # ReadConformPDB reading from PDB file servers/Phyre-2_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0288 can't currently be optimized by undertaker # naming current conformation Phyre-2_TS3 # ReadConformPDB reading from PDB file servers/Phyre-2_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0288 can't currently be optimized by undertaker # naming current conformation Phyre-2_TS4 # ReadConformPDB reading from PDB file servers/Phyre-2_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0288 can't currently be optimized by undertaker # naming current conformation Phyre-2_TS5 # ReadConformPDB reading from PDB file servers/Pmodeller6_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0288 can't currently be optimized by undertaker # naming current conformation Pmodeller6_TS1 # ReadConformPDB reading from PDB file servers/Pmodeller6_TS2.pdb.gz looking for model 1 # Found a chain break before 28 # copying to AlignedFragments data structure # naming current conformation Pmodeller6_TS2 # ReadConformPDB reading from PDB file servers/Pmodeller6_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0288 can't currently be optimized by undertaker # naming current conformation Pmodeller6_TS3 # ReadConformPDB reading from PDB file servers/Pmodeller6_TS4.pdb.gz looking for model 1 # Found a chain break before 25 # copying to AlignedFragments data structure # naming current conformation Pmodeller6_TS4 # ReadConformPDB reading from PDB file servers/Pmodeller6_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0288 can't currently be optimized by undertaker # naming current conformation Pmodeller6_TS5 # ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS1.pdb.gz looking for model 1 # Found a chain break before 78 # copying to AlignedFragments data structure # naming current conformation RAPTOR-ACE_TS1 # ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS2.pdb.gz looking for model 1 # Found a chain break before 78 # copying to AlignedFragments data structure # naming current conformation RAPTOR-ACE_TS2 # ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS3.pdb.gz looking for model 1 # naming current conformation RAPTOR-ACE_TS3 # ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS4.pdb.gz looking for model 1 # naming current conformation RAPTOR-ACE_TS4 # ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS5.pdb.gz looking for model 1 # naming current conformation RAPTOR-ACE_TS5 # ReadConformPDB reading from PDB file servers/RAPTORESS_TS1.pdb.gz looking for model 1 # Found a chain break before 62 # copying to AlignedFragments data structure # naming current conformation RAPTORESS_TS1 # ReadConformPDB reading from PDB file servers/RAPTORESS_TS2.pdb.gz looking for model 1 # Found a chain break before 28 # copying to AlignedFragments data structure # naming current conformation RAPTORESS_TS2 # ReadConformPDB reading from PDB file servers/RAPTORESS_TS3.pdb.gz looking for model 1 # Found a chain break before 40 # copying to AlignedFragments data structure # naming current conformation RAPTORESS_TS3 # ReadConformPDB reading from PDB file servers/RAPTORESS_TS4.pdb.gz looking for model 1 # Found a chain break before 28 # copying to AlignedFragments data structure # naming current conformation RAPTORESS_TS4 # ReadConformPDB reading from PDB file servers/RAPTORESS_TS5.pdb.gz looking for model 1 # Found a chain break before 28 # copying to AlignedFragments data structure # naming current conformation RAPTORESS_TS5 # ReadConformPDB reading from PDB file servers/RAPTOR_TS1.pdb.gz looking for model 1 # Found a chain break before 78 # copying to AlignedFragments data structure # naming current conformation RAPTOR_TS1 # ReadConformPDB reading from PDB file servers/RAPTOR_TS2.pdb.gz looking for model 1 # Found a chain break before 78 # copying to AlignedFragments data structure # naming current conformation RAPTOR_TS2 # ReadConformPDB reading from PDB file servers/RAPTOR_TS3.pdb.gz looking for model 1 # naming current conformation RAPTOR_TS3 # ReadConformPDB reading from PDB file servers/RAPTOR_TS4.pdb.gz looking for model 1 # Found a chain break before 27 # copying to AlignedFragments data structure # naming current conformation RAPTOR_TS4 # ReadConformPDB reading from PDB file servers/RAPTOR_TS5.pdb.gz looking for model 1 # naming current conformation RAPTOR_TS5 # ReadConformPDB reading from PDB file servers/ROBETTA_TS1.pdb.gz looking for model 1 # Found a chain break before 28 # copying to AlignedFragments data structure # naming current conformation ROBETTA_TS1 # ReadConformPDB reading from PDB file servers/ROBETTA_TS2.pdb.gz looking for model 1 # naming current conformation ROBETTA_TS2 # ReadConformPDB reading from PDB file servers/ROBETTA_TS3.pdb.gz looking for model 1 # Found a chain break before 27 # copying to AlignedFragments data structure # naming current conformation ROBETTA_TS3 # ReadConformPDB reading from PDB file servers/ROBETTA_TS4.pdb.gz looking for model 1 # Found a chain break before 25 # copying to AlignedFragments data structure # naming current conformation ROBETTA_TS4 # ReadConformPDB reading from PDB file servers/ROBETTA_TS5.pdb.gz looking for model 1 # Found a chain break before 27 # copying to AlignedFragments data structure # naming current conformation ROBETTA_TS5 # ReadConformPDB reading from PDB file servers/ROKKY_TS1.pdb.gz looking for model 1 # Found a chain break before 15 # copying to AlignedFragments data structure # naming current conformation ROKKY_TS1 # ReadConformPDB reading from PDB file servers/ROKKY_TS2.pdb.gz looking for model 1 # Found a chain break before 16 # copying to AlignedFragments data structure # naming current conformation ROKKY_TS2 # ReadConformPDB reading from PDB file servers/ROKKY_TS3.pdb.gz looking for model 1 # naming current conformation ROKKY_TS3 # ReadConformPDB reading from PDB file servers/ROKKY_TS4.pdb.gz looking for model 1 # Found a chain break before 16 # copying to AlignedFragments data structure # naming current conformation ROKKY_TS4 # ReadConformPDB reading from PDB file servers/ROKKY_TS5.pdb.gz looking for model 1 # Found a chain break before 63 # copying to AlignedFragments data structure # naming current conformation ROKKY_TS5 # ReadConformPDB reading from PDB file servers/SAM-T02_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0288 can't currently be optimized by undertaker # naming current conformation SAM-T02_AL1 # ReadConformPDB reading from PDB file servers/SAM-T02_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0288 can't currently be optimized by undertaker # naming current conformation SAM-T02_AL2 # ReadConformPDB reading from PDB file servers/SAM-T02_AL3.pdb.gz looking for model 1 Skipped atom 15, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL3.pdb.gz Skipped atom 280, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL3.pdb.gz Skipped atom 292, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL3.pdb.gz Skipped atom 294, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL3.pdb.gz Skipped atom 296, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL3.pdb.gz Skipped atom 298, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL3.pdb.gz Skipped atom 300, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL3.pdb.gz Skipped atom 302, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL3.pdb.gz Skipped atom 304, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL3.pdb.gz Skipped atom 306, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL3.pdb.gz Skipped atom 308, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL3.pdb.gz Skipped atom 310, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL3.pdb.gz Skipped atom 312, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL3.pdb.gz Skipped atom 314, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL3.pdb.gz Skipped atom 316, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL3.pdb.gz Skipped atom 318, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL3.pdb.gz # WARNING: incomplete conformation T0288 can't currently be optimized by undertaker # naming current conformation SAM-T02_AL3 # ReadConformPDB reading from PDB file servers/SAM-T02_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0288 can't currently be optimized by undertaker # naming current conformation SAM-T02_AL4 # ReadConformPDB reading from PDB file servers/SAM-T02_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0288 can't currently be optimized by undertaker # naming current conformation SAM-T02_AL5 # ReadConformPDB reading from PDB file servers/SAM-T99_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0288 can't currently be optimized by undertaker # naming current conformation SAM-T99_AL1 # ReadConformPDB reading from PDB file servers/SAM-T99_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0288 can't currently be optimized by undertaker # naming current conformation SAM-T99_AL2 # ReadConformPDB reading from PDB file servers/SAM-T99_AL3.pdb.gz looking for model 1 Skipped atom 291, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz # WARNING: incomplete conformation T0288 can't currently be optimized by undertaker # naming current conformation SAM-T99_AL3 # ReadConformPDB reading from PDB file servers/SAM-T99_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0288 can't currently be optimized by undertaker # naming current conformation SAM-T99_AL4 # ReadConformPDB reading from PDB file servers/SAM-T99_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0288 can't currently be optimized by undertaker # naming current conformation SAM-T99_AL5 # ReadConformPDB reading from PDB file servers/SAM_T06_server_TS1.pdb.gz looking for model 1 # Found a chain break before 78 # copying to AlignedFragments data structure # naming current conformation SAM_T06_server_TS1 # ReadConformPDB reading from PDB file servers/SAM_T06_server_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0288 can't currently be optimized by undertaker # naming current conformation SAM_T06_server_TS2 # ReadConformPDB reading from PDB file servers/SAM_T06_server_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0288 can't currently be optimized by undertaker # naming current conformation SAM_T06_server_TS3 # ReadConformPDB reading from PDB file servers/SAM_T06_server_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0288 can't currently be optimized by undertaker # naming current conformation SAM_T06_server_TS4 # ReadConformPDB reading from PDB file servers/SAM_T06_server_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0288 can't currently be optimized by undertaker # naming current conformation SAM_T06_server_TS5 # ReadConformPDB reading from PDB file servers/SP3_TS1.pdb.gz looking for model 1 # Found a chain break before 61 # copying to AlignedFragments data structure # naming current conformation SP3_TS1 # ReadConformPDB reading from PDB file servers/SP3_TS2.pdb.gz looking for model 1 # Found a chain break before 63 # copying to AlignedFragments data structure # naming current conformation SP3_TS2 # ReadConformPDB reading from PDB file servers/SP3_TS3.pdb.gz looking for model 1 # Found a chain break before 79 # copying to AlignedFragments data structure # naming current conformation SP3_TS3 # ReadConformPDB reading from PDB file servers/SP3_TS4.pdb.gz looking for model 1 # naming current conformation SP3_TS4 # ReadConformPDB reading from PDB file servers/SP3_TS5.pdb.gz looking for model 1 # Found a chain break before 77 # copying to AlignedFragments data structure # naming current conformation SP3_TS5 # ReadConformPDB reading from PDB file servers/SP4_TS1.pdb.gz looking for model 1 # Found a chain break before 63 # copying to AlignedFragments data structure # naming current conformation SP4_TS1 # ReadConformPDB reading from PDB file servers/SP4_TS2.pdb.gz looking for model 1 # naming current conformation SP4_TS2 # ReadConformPDB reading from PDB file servers/SP4_TS3.pdb.gz looking for model 1 # Found a chain break before 87 # copying to AlignedFragments data structure # naming current conformation SP4_TS3 # ReadConformPDB reading from PDB file servers/SP4_TS4.pdb.gz looking for model 1 # Found a chain break before 27 # copying to AlignedFragments data structure # naming current conformation SP4_TS4 # ReadConformPDB reading from PDB file servers/SP4_TS5.pdb.gz looking for model 1 # Found a chain break before 22 # copying to AlignedFragments data structure # naming current conformation SP4_TS5 # ReadConformPDB reading from PDB file servers/SPARKS2_TS1.pdb.gz looking for model 1 # Found a chain break before 61 # copying to AlignedFragments data structure # naming current conformation SPARKS2_TS1 # ReadConformPDB reading from PDB file servers/SPARKS2_TS2.pdb.gz looking for model 1 # Found a chain break before 63 # copying to AlignedFragments data structure # naming current conformation SPARKS2_TS2 # ReadConformPDB reading from PDB file servers/SPARKS2_TS3.pdb.gz looking for model 1 # Found a chain break before 79 # copying to AlignedFragments data structure # naming current conformation SPARKS2_TS3 # ReadConformPDB reading from PDB file servers/SPARKS2_TS4.pdb.gz looking for model 1 # naming current conformation SPARKS2_TS4 # ReadConformPDB reading from PDB file servers/SPARKS2_TS5.pdb.gz looking for model 1 # naming current conformation SPARKS2_TS5 # ReadConformPDB reading from PDB file servers/UNI-EID_bnmx_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0288 can't currently be optimized by undertaker # naming current conformation UNI-EID_bnmx_TS1 # ReadConformPDB reading from PDB file servers/UNI-EID_bnmx_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0288 can't currently be optimized by undertaker # naming current conformation UNI-EID_bnmx_TS2 # ReadConformPDB reading from PDB file servers/UNI-EID_bnmx_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0288 can't currently be optimized by undertaker # naming current conformation UNI-EID_bnmx_TS3 # ReadConformPDB reading from PDB file servers/UNI-EID_bnmx_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0288 can't currently be optimized by undertaker # naming current conformation UNI-EID_bnmx_TS4 # ReadConformPDB reading from PDB file servers/UNI-EID_bnmx_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0288 can't currently be optimized by undertaker # naming current conformation UNI-EID_bnmx_TS5 # ReadConformPDB reading from PDB file servers/UNI-EID_expm_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0288 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation UNI-EID_expm_TS1 # ReadConformPDB reading from PDB file servers/UNI-EID_sfst_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0288 can't currently be optimized by undertaker # naming current conformation UNI-EID_sfst_AL1 # ReadConformPDB reading from PDB file servers/UNI-EID_sfst_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0288 can't currently be optimized by undertaker # naming current conformation UNI-EID_sfst_AL2 # ReadConformPDB reading from PDB file servers/UNI-EID_sfst_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0288 can't currently be optimized by undertaker # naming current conformation UNI-EID_sfst_AL3 # ReadConformPDB reading from PDB file servers/UNI-EID_sfst_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0288 can't currently be optimized by undertaker # naming current conformation UNI-EID_sfst_AL4 # ReadConformPDB reading from PDB file servers/UNI-EID_sfst_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0288 can't currently be optimized by undertaker # naming current conformation UNI-EID_sfst_AL5 # ReadConformPDB reading from PDB file servers/Zhang-Server_TS1.pdb.gz looking for model 1 # Found a chain break before 62 # copying to AlignedFragments data structure # naming current conformation Zhang-Server_TS1 # ReadConformPDB reading from PDB file servers/Zhang-Server_TS2.pdb.gz looking for model 1 # Found a chain break before 25 # copying to AlignedFragments data structure # naming current conformation Zhang-Server_TS2 # ReadConformPDB reading from PDB file servers/Zhang-Server_TS3.pdb.gz looking for model 1 # naming current conformation Zhang-Server_TS3 # ReadConformPDB reading from PDB file servers/Zhang-Server_TS4.pdb.gz looking for model 1 # naming current conformation Zhang-Server_TS4 # ReadConformPDB reading from PDB file servers/Zhang-Server_TS5.pdb.gz looking for model 1 # Found a chain break before 27 # copying to AlignedFragments data structure # naming current conformation Zhang-Server_TS5 # ReadConformPDB reading from PDB file servers/beautshot_TS1.pdb.gz looking for model 1 # Found a chain break before 90 # copying to AlignedFragments data structure # naming current conformation beautshot_TS1 # ReadConformPDB reading from PDB file servers/beautshotbase_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0288 can't currently be optimized by undertaker # naming current conformation beautshotbase_TS1 # ReadConformPDB reading from PDB file servers/forecast-s_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0288 can't currently be optimized by undertaker # naming current conformation forecast-s_AL1 # ReadConformPDB reading from PDB file servers/forecast-s_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0288 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation forecast-s_AL2 # ReadConformPDB reading from PDB file servers/forecast-s_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0288 can't currently be optimized by undertaker # naming current conformation forecast-s_AL3 # ReadConformPDB reading from PDB file servers/forecast-s_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0288 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation forecast-s_AL4 # ReadConformPDB reading from PDB file servers/forecast-s_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0288 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation forecast-s_AL5 # ReadConformPDB reading from PDB file servers/gtg_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0288 can't currently be optimized by undertaker # naming current conformation gtg_AL1 # ReadConformPDB reading from PDB file servers/gtg_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0288 can't currently be optimized by undertaker # naming current conformation gtg_AL2 # ReadConformPDB reading from PDB file servers/gtg_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0288 can't currently be optimized by undertaker # naming current conformation gtg_AL3 # ReadConformPDB reading from PDB file servers/gtg_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0288 can't currently be optimized by undertaker # naming current conformation gtg_AL4 # ReadConformPDB reading from PDB file servers/gtg_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0288 can't currently be optimized by undertaker # naming current conformation gtg_AL5 # ReadConformPDB reading from PDB file servers/karypis.srv.2_TS1.pdb.gz looking for model 1 # Found a chain break before 15 # copying to AlignedFragments data structure # naming current conformation karypis.srv.2_TS1 # ReadConformPDB reading from PDB file servers/karypis.srv.2_TS2.pdb.gz looking for model 1 # naming current conformation karypis.srv.2_TS2 # ReadConformPDB reading from PDB file servers/karypis.srv.2_TS3.pdb.gz looking for model 1 # Found a chain break before 78 # copying to AlignedFragments data structure # naming current conformation karypis.srv.2_TS3 # ReadConformPDB reading from PDB file servers/karypis.srv.2_TS4.pdb.gz looking for model 1 # Found a chain break before 78 # copying to AlignedFragments data structure # naming current conformation karypis.srv.2_TS4 # ReadConformPDB reading from PDB file servers/karypis.srv.2_TS5.pdb.gz looking for model 1 # Found a chain break before 86 # copying to AlignedFragments data structure # naming current conformation karypis.srv.2_TS5 # ReadConformPDB reading from PDB file servers/karypis.srv.4_TS1.pdb.gz looking for model 1 WARNING: atoms too close: (T0288)G59.O and (T0288)R60.N only 0.000 apart, marking (T0288)R60.N as missing # WARNING: incomplete conformation T0288 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation karypis.srv.4_TS1 # ReadConformPDB reading from PDB file servers/karypis.srv_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0288 can't currently be optimized by undertaker # naming current conformation karypis.srv_TS1 # ReadConformPDB reading from PDB file servers/karypis.srv_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0288 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation karypis.srv_TS2 # ReadConformPDB reading from PDB file servers/karypis.srv_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0288 can't currently be optimized by undertaker # naming current conformation karypis.srv_TS3 # ReadConformPDB reading from PDB file servers/karypis.srv_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0288 can't currently be optimized by undertaker # naming current conformation karypis.srv_TS4 # ReadConformPDB reading from PDB file servers/karypis.srv_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0288 can't currently be optimized by undertaker # naming current conformation karypis.srv_TS5 # ReadConformPDB reading from PDB file servers/keasar-server_TS1.pdb.gz looking for model 1 # Found a chain break before 16 # copying to AlignedFragments data structure # naming current conformation keasar-server_TS1 # ReadConformPDB reading from PDB file servers/keasar-server_TS2.pdb.gz looking for model 1 # naming current conformation keasar-server_TS2 # ReadConformPDB reading from PDB file servers/keasar-server_TS3.pdb.gz looking for model 1 # Found a chain break before 92 # copying to AlignedFragments data structure # naming current conformation keasar-server_TS3 # ReadConformPDB reading from PDB file servers/keasar-server_TS4.pdb.gz looking for model 1 # Found a chain break before 5 # copying to AlignedFragments data structure # naming current conformation keasar-server_TS4 # ReadConformPDB reading from PDB file servers/keasar-server_TS5.pdb.gz looking for model 1 # Found a chain break before 81 # copying to AlignedFragments data structure # naming current conformation keasar-server_TS5 # ReadConformPDB reading from PDB file servers/mGen-3D_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0288 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation mGen-3D_TS1 # ReadConformPDB reading from PDB file servers/nFOLD_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0288 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation nFOLD_TS1 # ReadConformPDB reading from PDB file servers/nFOLD_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0288 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation nFOLD_TS2 # ReadConformPDB reading from PDB file servers/nFOLD_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0288 can't currently be optimized by undertaker # naming current conformation nFOLD_TS3 # ReadConformPDB reading from PDB file servers/nFOLD_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0288 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation nFOLD_TS4 # ReadConformPDB reading from PDB file servers/nFOLD_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0288 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation nFOLD_TS5 # ReadConformPDB reading from PDB file servers/shub_TS1.pdb.gz looking for model 1 # Found a chain break before 92 # copying to AlignedFragments data structure # naming current conformation shub_TS1 # command:Using radius: 8.0000 Using models AND alignments for constraints model score -0.7309 model score -0.6760 model score -0.5580 model score -0.7217 model score -0.6557 model score -0.6633 model score -0.7315 model score -0.4159 model score -0.4262 model score -0.1573 model score -0.4294 model score 0.1443 model score -0.4961 model score -0.4977 model score -0.4554 model score -0.4673 model score -0.4678 model score -0.3674 model score -0.3807 model score -0.2358 model score -0.2173 model score -0.0354 model score -0.7577 model score -0.6124 model score 0.8758 model score 1.6618 model score 1.4251 model score 1.1779 model score 1.2297 model score 1.2342 model score 1.2279 model score 1.3920 model score -0.5638 model score -0.6282 model score -0.6241 model score -0.6373 model score -0.6035 model score -0.6791 model score -0.6885 model score -0.6745 model score -0.5793 model score -0.6863 model score -0.6776 model score -0.3834 model score -0.7275 model score -0.7276 model score -0.6350 model score -0.1482 model score 1.2770 model score 1.2770 model score 1.2769 model score 1.2770 model score 1.2770 model score -0.6748 model score -0.6575 model score -0.7029 model score -0.6527 model score -0.7054 model score -0.5576 model score -0.5112 model score -0.5259 model score -0.6553 model score -0.5834 model score -0.7402 model score 1.2160 model score 1.6057 model score 1.3753 model score 0.4277 model score 1.2770 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 2.1443 model score -0.6690 model score -0.6890 model score -0.7627 model score -0.5983 model score -0.4638 model score 1.2769 model score 1.2770 model score 1.2770 model score 1.2771 model score 1.2769 model score -0.5576 model score -0.5112 model score -0.5259 model score -0.6553 model score -0.5834 model score -0.6882 model score -0.6984 model score -0.6882 model score -0.6882 model score -0.6807 model score -0.7273 model score -0.6558 model score -0.6798 model score -0.7424 model score -0.5364 model score -0.5364 model score -0.5264 model score -0.3061 model score -0.3261 model score -0.0802 model score -0.6074 model score -0.2536 model score -0.5583 model score -0.7357 model score -0.3599 model score -0.2080 model score 1.2768 model score 1.2768 model score -0.7184 model score -0.4564 model score -0.6502 model score -0.6048 model score -0.7076 model score -0.6024 model score -0.6143 model score -0.6387 model score -0.7049 model score -0.7063 model score -0.7101 model score -0.7141 model score -0.7009 model score -0.7033 model score -0.7044 model score -0.6853 model score -0.6739 model score -0.6885 model score -0.6445 model score -0.6596 model score -0.7190 model score -0.7312 model score -0.6445 model score -0.5557 model score -0.7490 model score -0.7490 model score -0.7490 model score -0.7490 model score -0.7490 model score -0.5818 model score -0.6760 model score -0.5840 model score -0.6557 model score -0.7067 model score -0.7281 model score -0.7238 model score -0.6622 model score -0.6540 model score -0.7397 model score -0.6755 model score -0.6452 model score -0.6429 model score -0.6165 model score -0.5648 model score -0.7048 model score -0.7048 model score -0.6728 model score -0.6821 model score -0.6911 model score -0.6760 model score -0.5580 model score -0.7217 model score -0.6557 model score -0.6633 model score -0.5558 model score -0.7113 model score -0.6463 model score -0.6752 model score -0.7363 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2770 model score 1.2770 model score 1.2770 model score 1.2770 model score 1.2771 model score -0.7470 model score -0.6346 model score -0.4619 model score -0.3798 model score -0.6236 model score -0.6719 model score -0.7390 model score -0.7008 model score -0.5936 model score -0.7113 model score -0.7390 model score -0.6630 model score -0.7233 model score -0.5994 model score -0.5067 model score -0.7044 model score -0.7390 model score -0.7008 model score -0.3101 model score -0.6573 model score 1.2768 model score 1.2770 model score 1.2770 model score 1.2770 model score 1.2771 model score -0.6929 model score 1.2768 model score 1.2770 model score 1.2770 model score 1.2770 model score 1.2771 model score -0.7226 model score -0.7300 model score -0.7222 model score -0.7066 model score -0.7289 model score -0.7164 model score -0.7258 model score 1.2769 model score 1.2771 model score 1.2771 model score 1.2770 model score 1.2769 model score 1.2771 model score 1.2768 model score 1.2773 model score 1.2771 model score 1.2767 model score -0.7436 model score -0.6681 model score -0.7358 model score -0.7358 model score -0.6678 model score 1.4768 model score -0.7534 model score -0.6726 model score -0.4444 model score -0.5879 model score -0.6079 model score -0.5935 model score -0.6155 model score -0.6283 model score -0.5470 model score -0.6386 model score -0.5779 model score -0.6657 model score -0.5336 model score -0.6553 model score -0.5013 model score -0.5000 model score -0.6840 USE_META, weight: 0.9902 cost: -0.7309 min: -0.7627 max: 2.1443 USE_META, weight: 0.9732 cost: -0.6760 min: -0.7627 max: 2.1443 USE_META, weight: 0.9366 cost: -0.5580 min: -0.7627 max: 2.1443 USE_META, weight: 0.9873 cost: -0.7217 min: -0.7627 max: 2.1443 USE_META, weight: 0.9669 cost: -0.6557 min: -0.7627 max: 2.1443 USE_META, weight: 0.9692 cost: -0.6633 min: -0.7627 max: 2.1443 USE_META, weight: 0.9904 cost: -0.7315 min: -0.7627 max: 2.1443 USE_META, 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1.0000 eval: 0.0000 min: 0.0000 max: 0.5265 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.5265 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.5265 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.5265 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.5265 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.5265 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.5265 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.5265 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.5265 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.5265 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.5265 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.5265 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.5265 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.5265 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.5265 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.5265 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.5265 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.5265 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.5265 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.5265 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.5265 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.5265 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.5265 USE_EVALUE, weight: 0.4012 eval: 0.3503 min: 0.0000 max: 0.5265 USE_EVALUE, weight: 0.4012 eval: 0.3503 min: 0.0000 max: 0.5265 USE_EVALUE, weight: 0.4012 eval: 0.3503 min: 0.0000 max: 0.5265 USE_EVALUE, weight: 0.7001 eval: 0.1754 min: 0.0000 max: 0.5265 USE_EVALUE, weight: 0.7001 eval: 0.1754 min: 0.0000 max: 0.5265 USE_EVALUE, weight: 0.7001 eval: 0.1754 min: 0.0000 max: 0.5265 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.5265 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.5265 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.5265 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.5265 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.5265 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.5265 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.5265 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.5265 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.5265 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.5265 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.5265 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.5265 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.5265 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.5265 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.5265 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.5265 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.5265 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.5265 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.5265 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.5265 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.5265 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.5265 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.5265 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.5265 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.5265 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.5265 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.5265 USE_EVALUE, weight: 0.9940 eval: 0.0035 min: 0.0000 max: 0.5265 USE_EVALUE, weight: 0.9940 eval: 0.0035 min: 0.0000 max: 0.5265 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.5265 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.5265 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.5265 USE_EVALUE, weight: 0.9965 eval: 0.0021 min: 0.0000 max: 0.5265 USE_EVALUE, weight: 0.9965 eval: 0.0021 min: 0.0000 max: 0.5265 USE_EVALUE, weight: 0.9965 eval: 0.0021 min: 0.0000 max: 0.5265 USE_EVALUE, weight: 0.3370 eval: 0.3878 min: 0.0000 max: 0.5265 USE_EVALUE, weight: 0.3370 eval: 0.3878 min: 0.0000 max: 0.5265 USE_EVALUE, weight: 0.3370 eval: 0.3878 min: 0.0000 max: 0.5265 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.5265 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.5265 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.5265 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.5265 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.5265 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.5265 USE_EVALUE, weight: 0.9999 eval: 0.0001 min: 0.0000 max: 0.5265 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.5265 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.5265 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.5265 USE_EVALUE, weight: 0.9999 eval: 0.0000 min: 0.0000 max: 0.5265 USE_EVALUE, weight: 0.9999 eval: 0.0000 min: 0.0000 max: 0.5265 USE_EVALUE, weight: 0.9999 eval: 0.0000 min: 0.0000 max: 0.5265 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.5265 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.5265 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.5265 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.5265 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.5265 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.5265 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.5265 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.5265 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.5265 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.5265 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.5265 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.5265 Number of contacts in models: 257 Number of contacts in alignments: 108 NUMB_ALIGNS: 108 Adding 1591 constraints to all3.constraints Done adding distance constraints # command:Reading probabilities from probabilities.dat Reading constraints from ConstraintSet all3.constraints maxweight: 1.0000 Optimizing... Probability sum: -167.9884, CN propb: -167.9884 weights: 0.4521 constraints: 268 # command:Found ConstraintSet # PrintContacts align.constraints_meta03 Number of constraints in align3.constraints 268 # command:Found ConstraintSet # PrintContacts align_bonus.constraints_meta03 Number of constraints in align3.constraints.bonus 268 # command:Found ConstraintSet # PrintContacts rejected.constraints_meta03 Number of constraints in rejected3.constraints 1323 # command:Found ConstraintSet # PrintContacts rejected_bonus.constraints_meta03 Number of constraints in rejected3.constraints.bonus 1323 # command:Found ConstraintSet # PrintContacts non_contacts.constraints_meta03 Number of constraints in noncontact3.constraints 0 # command:Found ConstraintSet # PrintContacts non_contacts_bonus.constraints_meta03 Number of constraints in noncontact3.constraints.bonus 0 # command:Found ConstraintSet # PrintContacts all.constraints_meta03 Number of constraints in all3.constraints 1591 # command: