parameters: 0.6 1.3 0.5 200 50 # command:# Prefix for input files set to /projects/compbio/experiments/undertaker/atoms-inputs/ # command:# reading dunbrack-2191.atoms # #computed average backbone with maximum peptide_sq_deviance = 0.002 # computed average trans backbone unit from 53157 examples # computed average trans backbone unit before proline from 2010 examples # computed average cis backbone unit from 97 examples # trans (non-proline) backbone unit: # CA= -2.2087 1.0126 -0.0030 # O= -0.1499 2.2440 0.0016 # C= -0.6889 1.1368 -0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4581 -0.0000 0.0000 # cis backbone unit: # CA= -0.1436 2.4534 -0.0002 # O= -2.0284 0.9742 0.0015 # C= -0.8018 1.0771 -0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4668 0.0000 0.0000 # trans backbone unit before proline: # CA= -2.2100 1.0631 -0.0014 # O= -0.1236 2.2458 0.0075 # C= -0.6872 1.1517 -0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4660 0.0000 0.0000 # After reading dunbrack-2191.atoms have 2191 chains in training database # Count of chains,residues,atoms: 2191,500310,3902258 # 493341 residues have no bad marker # 3226 residues lack atoms needed to compute omega # 1453 residues have cis peptide # number of each bad type: # NON_STANDARD_RESIDUE 4 # HAS_OXT 1167 # TOO_MANY_ATOMS 1 # TOO_FEW_ATOMS 3052 # HAS_UNKNOWN_ATOMS 9 # HAS_DUPLICATE_ATOMS 0 # CHAIN_BREAK_BEFORE 979 # NON_PLANAR_PEPTIDE 888 # BAD_PEPTIDE 2680 # Note: may sum to more than number of residues, # because one residue may have multiple problems # command:# Reading rotamer library from dunbrack-2191.rot # command:# Prefix for input files set to /projects/compbio/experiments/undertaker/spots/ # command:# ReadAtomType exp-pdb.types Read AtomType exp-pdb with 49 types. # command:# ReadClashTable exp-pdb-2191-2symm.clash # Read ClashTable exp-pdb-2191-2symm checking bonds symmetric at MaxSep 2 # command:# command:# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/T0302/ # command:# Making conformation for sequence T0302 numbered 1 through 132 Created new target T0302 from T0302.a2m # command:# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/T0302/ # command:Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0302//projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0302/manyalignments-good-all.under or /projects/compbio/experiments/protein-predict/casp7/T0302//projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0302/manyalignments-good-all.under.gz for input Trying /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0302/manyalignments-good-all.under # reading script from file /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0302/manyalignments-good-all.under # Reading fragments from alignment file # Attempting to read fragment alignments from file 1fqiA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1fqiA expands to /projects/compbio/data/pdb/1fqi.pdb.gz 1fqiA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0302 read from 1fqiA/merged-good-all-a2m # 1fqiA read from 1fqiA/merged-good-all-a2m # adding 1fqiA to template set # found chain 1fqiA in template set T0302 1 :SMVSPEEAVKWGESFDKLLSHRDGLEAFTRFLKTEFSEENIEFWIACEDFK 1fqiA 286 :DIPTKMRVERWAFNFSELIRDPKGRQSFQHFLRKEFSGENLGFWEACEDLK # choosing archetypes in rotamer library T0302 53 :SKGPQQIHLKAKAIYEKFIQTDAPKEVNLDFHTKEVITNSITQPTLHSFDAAQSRVYQLMEQDSYTRFLKSDIYLDLMEG 1fqiA 337 :YGDQSKVKEKAEEIYKLFLAPGARRWINIDGKTMDITVKGLKHPHRYVLDAAQTHIYMLMKKDSYARYLKSPIYKEMLAK Number of specific fragments extracted= 2 number of extra gaps= 0 total=2 Number of alignments=1 # 1fqiA read from 1fqiA/merged-good-all-a2m # found chain 1fqiA in template set T0302 1 :SMVSPEEAVKWGESFDKLLSHRDGLEAFTRFLKTEFSEENIEFWIACEDFK 1fqiA 286 :DIPTKMRVERWAFNFSELIRDPKGRQSFQHFLRKEFSGENLGFWEACEDLK T0302 53 :SKGPQQIHLKAKAIYEKFIQTDAPKEVNLDFHTKEVITNSITQPTLHSFDAAQSRVYQLMEQDSYTRFLKSDIYLDLMEG 1fqiA 337 :YGDQSKVKEKAEEIYKLFLAPGARRWINIDGKTMDITVKGLKHPHRYVLDAAQTHIYMLMKKDSYARYLKSPIYKEMLAK Number of specific fragments extracted= 2 number of extra gaps= 0 total=4 Number of alignments=2 # 1fqiA read from 1fqiA/merged-good-all-a2m # found chain 1fqiA in template set T0302 1 :SMVSPEEAVKWGESFDKLLSHRDGLEAFTRFLKTEFSEENIEFWIACEDFKK 1fqiA 286 :DIPTKMRVERWAFNFSELIRDPKGRQSFQHFLRKEFSGENLGFWEACEDLKY T0302 54 :KGPQQIHLKAKAIYEKFIQTDAPKEVNLDFHTKEVITNSITQPTLHSFDAAQSRVYQLMEQDSYTRFLKSDIYLDLMEG 1fqiA 338 :GDQSKVKEKAEEIYKLFLAPGARRWINIDGKTMDITVKGLKHPHRYVLDAAQTHIYMLMKKDSYARYLKSPIYKEMLAK Number of specific fragments extracted= 2 number of extra gaps= 0 total=6 Number of alignments=3 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1y3nA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1y3nA expands to /projects/compbio/data/pdb/1y3n.pdb.gz 1y3nA:# T0302 read from 1y3nA/merged-good-all-a2m # 1y3nA read from 1y3nA/merged-good-all-a2m # adding 1y3nA to template set # found chain 1y3nA in template set T0302 27 :AFTRF 1y3nA 79 :KFIRY T0302 32 :LKTEFSEENIEFWIACEDF 1y3nA 95 :LIDQNAPNLKAFFKTHPEV T0302 51 :KKSKGPQ 1y3nA 396 :ERQWTND T0302 62 :KAKAIYEKFIQTDAP 1y3nA 403 :VALQGIDMYIKNKYV T0302 77 :KEVNLDFHTKEVITNSITQPTLHSFDAAQSRVY 1y3nA 422 :TGVNLTVEEREIYDKYWPDVKTYMFEMGQSWVM T0302 121 :LKSDIYLDLMEG 1y3nA 461 :KTWNDYQQQLKN Number of specific fragments extracted= 6 number of extra gaps= 0 total=12 Number of alignments=4 # 1y3nA read from 1y3nA/merged-good-all-a2m # found chain 1y3nA in template set T0302 2 :MVSPEEAVKWGESFDKLLS 1y3nA 90 :IPLNKLIDQNAPNLKAFFK T0302 21 :HRDGLEAF 1y3nA 110 :HPEVQRAI T0302 52 :KSKGPQ 1y3nA 397 :RQWTND T0302 62 :KAKAIYEKFIQTDA 1y3nA 403 :VALQGIDMYIKNKY T0302 76 :PKEVNLDFHTKEVITNSI 1y3nA 421 :FTGVNLTVEEREIYDKYW T0302 98 :LHSFDAAQSRVYQLMEQD 1y3nA 439 :PDVKTYMFEMGQSWVMGT T0302 117 :YTRFLKSDIYLDLMEG 1y3nA 457 :KDPEKTWNDYQQQLKN Number of specific fragments extracted= 7 number of extra gaps= 0 total=19 Number of alignments=5 # 1y3nA read from 1y3nA/merged-good-all-a2m # found chain 1y3nA in template set T0302 2 :MVSPEEAVKWGESFDKLLS 1y3nA 90 :IPLNKLIDQNAPNLKAFFK T0302 54 :KGPQ 1y3nA 109 :THPE T0302 58 :QIHL 1y3nA 394 :EYER T0302 62 :KAKAIYEKFIQTDA 1y3nA 403 :VALQGIDMYIKNKY T0302 76 :PKEVNLDFHTKEVITNSI 1y3nA 421 :FTGVNLTVEEREIYDKYW T0302 98 :LHSFDAAQSRVYQLM 1y3nA 439 :PDVKTYMFEMGQSWV T0302 113 :E 1y3nA 460 :E T0302 121 :LKSDIYLDLME 1y3nA 461 :KTWNDYQQQLK Number of specific fragments extracted= 8 number of extra gaps= 0 total=27 Number of alignments=6 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1agrH/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1agrH expands to /projects/compbio/data/pdb/1agr.pdb.gz 1agrH:# T0302 read from 1agrH/merged-good-all-a2m # 1agrH read from 1agrH/merged-good-all-a2m # adding 1agrH to template set # found chain 1agrH in template set Warning: unaligning (T0302)G12 because first residue in template chain is (1agrH)A60 T0302 13 :ESFDKLLSHRDGLEAFTRFLKTEFSEENIEFWIACEDFKKSKGPQQIHLKAKAIYEKFIQTDAPKEVNLDFHTKEVITNSITQPTLHSFDAAQSRVYQLMEQDSYTRFLKS 1agrH 61 :ESLENLINHECGLAAFKAFLKSEYSEENIDFWISCEEYKKIKSPSKLSPKAKKIYNEFISVQATKEVNLDSCTREETSRNMLEPTITCFDEAQKKIFNLMEKDSYRRFLKS Number of specific fragments extracted= 1 number of extra gaps= 0 total=28 Number of alignments=7 # 1agrH read from 1agrH/merged-good-all-a2m # found chain 1agrH in template set Warning: unaligning (T0302)G12 because first residue in template chain is (1agrH)A60 T0302 13 :ESFDKLLSHRDGLEAFTRFLKTEFSEENIEFWIACEDFKKSKGPQQIHLKAKAIYEKFIQTDAPKEVNLDFHTKEVITNSITQPTLHSFDAAQSRVYQLMEQDSYTRFLKS 1agrH 61 :ESLENLINHECGLAAFKAFLKSEYSEENIDFWISCEEYKKIKSPSKLSPKAKKIYNEFISVQATKEVNLDSCTREETSRNMLEPTITCFDEAQKKIFNLMEKDSYRRFLKS Number of specific fragments extracted= 1 number of extra gaps= 0 total=29 Number of alignments=8 # 1agrH read from 1agrH/merged-good-all-a2m # found chain 1agrH in template set Warning: unaligning (T0302)G12 because first residue in template chain is (1agrH)A60 T0302 13 :ESFDKLLSHRDGLEAFTRFLKTEFSEENIEFWIACEDFKKSKGPQQIHLKAKAIYEKFIQTDAPKEVNLDFHTKEVITNSITQPTLHSFDAAQSRVYQLMEQDSYTRFLKS 1agrH 61 :ESLENLINHECGLAAFKAFLKSEYSEENIDFWISCEEYKKIKSPSKLSPKAKKIYNEFISVQATKEVNLDSCTREETSRNMLEPTITCFDEAQKKIFNLMEKDSYRRFLKS Number of specific fragments extracted= 1 number of extra gaps= 0 total=30 Number of alignments=9 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2crpA/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/T0302/2crpA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0302/2crpA/merged-good-all-a2m.gz for input Trying 2crpA/merged-good-all-a2m Error: Couldn't open file 2crpA/merged-good-all-a2m or 2crpA/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 2af0A/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/T0302/2af0A/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0302/2af0A/merged-good-all-a2m.gz for input Trying 2af0A/merged-good-all-a2m Error: Couldn't open file 2af0A/merged-good-all-a2m or 2af0A/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ngnA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1ngnA expands to /projects/compbio/data/pdb/1ngn.pdb.gz 1ngnA:Skipped atom 495, because occupancy 0.5 <= existing 0.500 in 1ngnA Skipped atom 497, because occupancy 0.500 <= existing 0.500 in 1ngnA Skipped atom 499, because occupancy 0.500 <= existing 0.500 in 1ngnA Skipped atom 501, because occupancy 0.500 <= existing 0.500 in 1ngnA # T0302 read from 1ngnA/merged-good-all-a2m # 1ngnA read from 1ngnA/merged-good-all-a2m # adding 1ngnA to template set # found chain 1ngnA in template set T0302 22 :RDGLEAFTRFLKTEFSEENI 1ngnA 446 :KMAIPVLWEFLEKYPSAEVA T0302 44 :WIACEDFKKS 1ngnA 470 :WRDVSELLKP T0302 54 :KGPQQIHLKAKAIYEKFIQTDAPKEVN 1ngnA 481 :GLYDLRAKTIIKFSDEYLTKQWRYPIE T0302 81 :LDFHTKEVITNSIT 1ngnA 511 :IGKYGNDSYRIFCV T0302 95 :QPTLHSFDAAQSRVYQL 1ngnA 531 :HPEDHKLNKYHDWLWEN Number of specific fragments extracted= 5 number of extra gaps= 0 total=35 Number of alignments=10 # 1ngnA read from 1ngnA/merged-good-all-a2m # found chain 1ngnA in template set T0302 22 :RDGLEAFTRFLKTEFSEENIE 1ngnA 446 :KMAIPVLWEFLEKYPSAEVAR T0302 44 :WIACEDF 1ngnA 470 :WRDVSEL T0302 51 :KKSKGPQQIHLKAKAIYEKFIQTDAPKEVN 1ngnA 478 :KPLGLYDLRAKTIIKFSDEYLTKQWRYPIE T0302 81 :LDFHTKEVITNS 1ngnA 511 :IGKYGNDSYRIF T0302 95 :QPTLHSFDAAQSRVYQL 1ngnA 531 :HPEDHKLNKYHDWLWEN Number of specific fragments extracted= 5 number of extra gaps= 0 total=40 Number of alignments=11 # 1ngnA read from 1ngnA/merged-good-all-a2m # found chain 1ngnA in template set T0302 21 :HRDGLEAFTRFLKTEFSEEN 1ngnA 445 :GKMAIPVLWEFLEKYPSAEV T0302 44 :WIACEDFKKS 1ngnA 470 :WRDVSELLKP T0302 54 :KGPQQIHLKAKAIYEKFIQTDAPKEVN 1ngnA 481 :GLYDLRAKTIIKFSDEYLTKQWRYPIE T0302 81 :LDFHTKEVITNSITQ 1ngnA 511 :IGKYGNDSYRIFCVN T0302 96 :PTLHSFDAAQSRVYQLMEQ 1ngnA 532 :PEDHKLNKYHDWLWENHEK Number of specific fragments extracted= 5 number of extra gaps= 0 total=45 Number of alignments=12 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1eh2/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1eh2 expands to /projects/compbio/data/pdb/1eh2.pdb.gz 1eh2:Warning: there is no chain 1eh2 will retry with 1eh2A # T0302 read from 1eh2/merged-good-all-a2m # 1eh2 read from 1eh2/merged-good-all-a2m # adding 1eh2 to template set # found chain 1eh2 in template set T0302 46 :ACEDFKKS 1eh2 13 :DKAKYDAI T0302 54 :KGPQQIHLKAK 1eh2 31 :LSGDKVKPVLL T0302 72 :QT 1eh2 42 :NS T0302 80 :NLDFHTKEVITNSI 1eh2 44 :KLPVDILGRVWELS T0302 94 :TQ 1eh2 62 :DG T0302 96 :PTLHSFDAAQSRVYQLMEQDSYT 1eh2 65 :LDRDEFAVAMFLVYCALEKEPVP Number of specific fragments extracted= 6 number of extra gaps= 0 total=51 Number of alignments=13 # 1eh2 read from 1eh2/merged-good-all-a2m # found chain 1eh2 in template set T0302 56 :PQQIHLKAKAIY 1eh2 10 :KPEDKAKYDAIF T0302 68 :EKFIQTD 1eh2 37 :KPVLLNS T0302 80 :NLDFHTKEVITNSI 1eh2 44 :KLPVDILGRVWELS T0302 94 :TQPTLHSFDAAQSRVYQLMEQDSYT 1eh2 63 :GMLDRDEFAVAMFLVYCALEKEPVP Number of specific fragments extracted= 4 number of extra gaps= 0 total=55 Number of alignments=14 # 1eh2 read from 1eh2/merged-good-all-a2m # found chain 1eh2 in template set T0302 56 :PQQIHLKAKAIY 1eh2 10 :KPEDKAKYDAIF T0302 68 :EKFIQTDA 1eh2 37 :KPVLLNSK T0302 81 :LDFHTKEVITNSI 1eh2 45 :LPVDILGRVWELS T0302 96 :PTLHSFDAAQSRVYQLMEQDSYT 1eh2 65 :LDRDEFAVAMFLVYCALEKEPVP Number of specific fragments extracted= 4 number of extra gaps= 0 total=59 Number of alignments=15 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1b64/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1b64 expands to /projects/compbio/data/pdb/1b64.pdb.gz 1b64:Warning: there is no chain 1b64 will retry with 1b64A # T0302 read from 1b64/merged-good-all-a2m # 1b64 read from 1b64/merged-good-all-a2m # adding 1b64 to template set # found chain 1b64 in template set T0302 86 :KEVITNSITQPTLH 1b64 21 :MAKLEECVRSIQAD T0302 101 :FDAAQSRV 1b64 66 :TDMLEEQI Number of specific fragments extracted= 2 number of extra gaps= 0 total=61 Number of alignments=16 # 1b64 read from 1b64/merged-good-all-a2m # found chain 1b64 in template set T0302 55 :GP 1b64 20 :DM T0302 83 :FHTKEVITNSI 1b64 22 :AKLEECVRSIQ T0302 94 :T 1b64 34 :D T0302 95 :QPTLHS 1b64 63 :KVGTDM T0302 104 :AQSRV 1b64 69 :LEEQI Number of specific fragments extracted= 5 number of extra gaps= 0 total=66 Number of alignments=17 # 1b64 read from 1b64/merged-good-all-a2m # found chain 1b64 in template set T0302 55 :GPQQIHLKAKA 1b64 20 :DMAKLEECVRS Number of specific fragments extracted= 1 number of extra gaps= 0 total=67 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1omwA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1omwA expands to /projects/compbio/data/pdb/1omw.pdb.gz 1omwA:# T0302 read from 1omwA/merged-good-all-a2m # 1omwA read from 1omwA/merged-good-all-a2m # adding 1omwA to template set # found chain 1omwA in template set Warning: unaligning (T0302)L81 because of BadResidue code BAD_PEPTIDE in next template residue (1omwA)S125 Warning: unaligning (T0302)D82 because of BadResidue code BAD_PEPTIDE at template residue (1omwA)S125 T0302 9 :VKWGESFDKLLSHRDGLEAFTRFLKT 1omwA 49 :DRGEVTFEKIFSQKLGYLLFRDFCLK T0302 35 :EFSEENIEFWIACEDFKKSKGPQQIHLKAKAIYEKFIQ 1omwA 77 :EEAKPLVEFYEEIKKYEKLETEEERLVCSREIFDTYIM T0302 76 :PKEVN 1omwA 119 :ACSHP T0302 83 :FHTKEVITNSI 1omwA 126 :KSAIEHVQGHL T0302 94 :TQPTLHSFDAAQSRVYQLMEQDSYTRFLKSDIYLDLM 1omwA 139 :KQVPPDLFQPYIEEICQNLRGDVFQKFIESDKFTRFC Number of specific fragments extracted= 5 number of extra gaps= 1 total=72 Number of alignments=18 # 1omwA read from 1omwA/merged-good-all-a2m # found chain 1omwA in template set Warning: unaligning (T0302)L81 because of BadResidue code BAD_PEPTIDE in next template residue (1omwA)S125 Warning: unaligning (T0302)D82 because of BadResidue code BAD_PEPTIDE at template residue (1omwA)S125 T0302 9 :VKWGESFDKLLSHRDGLEAFTRFLKT 1omwA 49 :DRGEVTFEKIFSQKLGYLLFRDFCLK T0302 35 :EFSEENIEFWIACEDFKKSKGPQQIHLKAKAIYEKFIQTDA 1omwA 77 :EEAKPLVEFYEEIKKYEKLETEEERLVCSREIFDTYIMKEL T0302 76 :PKEVN 1omwA 119 :ACSHP T0302 83 :FHTKEVITNSI 1omwA 126 :KSAIEHVQGHL T0302 94 :TQPTLHSFDAAQSRVYQLMEQDSYTRFLKSDIYLDLM 1omwA 139 :KQVPPDLFQPYIEEICQNLRGDVFQKFIESDKFTRFC Number of specific fragments extracted= 5 number of extra gaps= 1 total=77 Number of alignments=19 # 1omwA read from 1omwA/merged-good-all-a2m # found chain 1omwA in template set Warning: unaligning (T0302)L81 because of BadResidue code BAD_PEPTIDE in next template residue (1omwA)S125 Warning: unaligning (T0302)D82 because of BadResidue code BAD_PEPTIDE at template residue (1omwA)S125 T0302 10 :KWGESFDKLLSHRDGLEAFTRFLKTEFS 1omwA 50 :RGEVTFEKIFSQKLGYLLFRDFCLKHLE T0302 38 :EENIEFWIACEDFKKSKGPQQIHLKAKAIYEKFIQT 1omwA 80 :KPLVEFYEEIKKYEKLETEEERLVCSREIFDTYIMK T0302 76 :PKEVN 1omwA 119 :ACSHP T0302 83 :FHTKEVITNSITQ 1omwA 126 :KSAIEHVQGHLVK T0302 96 :PTLHSFDAAQSRVYQLMEQDSYTRFLKSDIYLDLM 1omwA 141 :VPPDLFQPYIEEICQNLRGDVFQKFIESDKFTRFC Number of specific fragments extracted= 5 number of extra gaps= 1 total=82 Number of alignments=20 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1eztA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1eztA expands to /projects/compbio/data/pdb/1ezt.pdb.gz 1eztA:# T0302 read from 1eztA/merged-good-all-a2m # 1eztA read from 1eztA/merged-good-all-a2m # adding 1eztA to template set # found chain 1eztA in template set Warning: unaligning (T0302)V3 because first residue in template chain is (1eztA)V5 Warning: unaligning (T0302)E131 because last residue in template chain is (1eztA)N133 T0302 4 :SPEEAVKWGESFDKLLSHRDGLEAFTRFLKTEFSEENIEFWIACEDFKKSKGPQQIHLKAKAIYEKFIQTDAPKEVNLDFHTKEVITNSITQPTLHSFDAAQSRVYQLMEQDSYTRFLKSDIYLDLM 1eztA 6 :SQEEVKKWAESLENLINHECGLAAFKAFLKSEYSEENIDFWISCEEYKKIKSPSKLSPKAKKIYNEFISVQATKEVNLDSCTREETSRNMLEPTITCFDEAQKKIFNLMEKDSYRRFLKSRFYLDLT Number of specific fragments extracted= 1 number of extra gaps= 0 total=83 Number of alignments=21 # 1eztA read from 1eztA/merged-good-all-a2m # found chain 1eztA in template set Warning: unaligning (T0302)V3 because first residue in template chain is (1eztA)V5 Warning: unaligning (T0302)E131 because last residue in template chain is (1eztA)N133 T0302 4 :SPEEAVKWGESFDKLLSHRDGLEAFTRFLKTEFSEENIEFWIACEDFKKSKGPQQIHLKAKAIYEKFIQTDAPKEVNLDFHTKEVITNSITQPTLHSFDAAQSRVYQLMEQDSYTRFLKSDIYLDLM 1eztA 6 :SQEEVKKWAESLENLINHECGLAAFKAFLKSEYSEENIDFWISCEEYKKIKSPSKLSPKAKKIYNEFISVQATKEVNLDSCTREETSRNMLEPTITCFDEAQKKIFNLMEKDSYRRFLKSRFYLDLT Number of specific fragments extracted= 1 number of extra gaps= 0 total=84 Number of alignments=22 # 1eztA read from 1eztA/merged-good-all-a2m # found chain 1eztA in template set Warning: unaligning (T0302)V3 because first residue in template chain is (1eztA)V5 T0302 4 :SPEEAVKWGESFDKLLSHRDGLEAFTRFLKTEFSEENIEFWIACEDFKKSKGPQQIHLKAKAIYEKFIQTDAPKEVNLDFHTKEVITNSITQPTLHSFDAAQSRVYQLMEQDSYTRFLKSDIYLDL 1eztA 6 :SQEEVKKWAESLENLINHECGLAAFKAFLKSEYSEENIDFWISCEEYKKIKSPSKLSPKAKKIYNEFISVQATKEVNLDSCTREETSRNMLEPTITCFDEAQKKIFNLMEKDSYRRFLKSRFYLDL Number of specific fragments extracted= 1 number of extra gaps= 0 total=85 Number of alignments=23 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2es0A/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/T0302/2es0A/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0302/2es0A/merged-good-all-a2m.gz for input Trying 2es0A/merged-good-all-a2m Error: Couldn't open file 2es0A/merged-good-all-a2m or 2es0A/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 2bt2A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2bt2A expands to /projects/compbio/data/pdb/2bt2.pdb.gz 2bt2A:Skipped atom 45, because occupancy 0.300 <= existing 0.700 in 2bt2A Skipped atom 49, because occupancy 0.300 <= existing 0.700 in 2bt2A Skipped atom 51, because occupancy 0.300 <= existing 0.700 in 2bt2A Skipped atom 477, because occupancy 0.500 <= existing 0.500 in 2bt2A Skipped atom 481, because occupancy 0.500 <= existing 0.500 in 2bt2A Skipped atom 483, because occupancy 0.500 <= existing 0.500 in 2bt2A Skipped atom 485, because occupancy 0.500 <= existing 0.500 in 2bt2A Skipped atom 487, because occupancy 0.500 <= existing 0.500 in 2bt2A Skipped atom 489, because occupancy 0.500 <= existing 0.500 in 2bt2A Skipped atom 491, because occupancy 0.500 <= existing 0.500 in 2bt2A Skipped atom 493, because occupancy 0.500 <= existing 0.500 in 2bt2A Skipped atom 542, because occupancy 0.400 <= existing 0.600 in 2bt2A Skipped atom 546, because occupancy 0.400 <= existing 0.600 in 2bt2A Skipped atom 548, because occupancy 0.400 <= existing 0.600 in 2bt2A Skipped atom 550, because occupancy 0.400 <= existing 0.600 in 2bt2A Skipped atom 552, because occupancy 0.400 <= existing 0.600 in 2bt2A Skipped atom 554, because occupancy 0.400 <= existing 0.600 in 2bt2A Skipped atom 556, because occupancy 0.400 <= existing 0.600 in 2bt2A Skipped atom 558, because occupancy 0.400 <= existing 0.600 in 2bt2A Skipped atom 641, because occupancy 0.400 <= existing 0.600 in 2bt2A Skipped atom 645, because occupancy 0.400 <= existing 0.600 in 2bt2A Skipped atom 647, because occupancy 0.400 <= existing 0.600 in 2bt2A # T0302 read from 2bt2A/merged-good-all-a2m # 2bt2A read from 2bt2A/merged-good-all-a2m # adding 2bt2A to template set # found chain 2bt2A in template set T0302 5 :PEEAVKWGESFDKLLSHRDGLEAFTRFLKTEFSEENIEFWIACEDFKKSKGPQQIHLKAKAIYEKFIQTDAPKEVNLDFHTKEVITNSITQPTLHSFDAAQSRVYQLMEQDSYTRFLKSDIYLDLMEG 2bt2A 56 :SEDVLGWRESFDLLLSSKNGVAAFHAFLKTEFSEENLEFWLACEEFKKIRSATKLASRAHQIFEEFICSEAPKEVNIDHETRELTRMNLQTATATCFDAAQGKTRTLMEKDSYPRFLKSPAYRDLAAQ Number of specific fragments extracted= 1 number of extra gaps= 0 total=86 Number of alignments=24 # 2bt2A read from 2bt2A/merged-good-all-a2m # found chain 2bt2A in template set T0302 5 :PEEAVKWGESFDKLLSHRDGLEAFTRFLKTEFSEENIEFWIACEDFKKSKGPQQIHLKAKAIYEKFIQTDAPKEVNLDFHTKEVITNSITQPTLHSFDAAQSRVYQLMEQDSYTRFLKSDIYLDLMEG 2bt2A 56 :SEDVLGWRESFDLLLSSKNGVAAFHAFLKTEFSEENLEFWLACEEFKKIRSATKLASRAHQIFEEFICSEAPKEVNIDHETRELTRMNLQTATATCFDAAQGKTRTLMEKDSYPRFLKSPAYRDLAAQ Number of specific fragments extracted= 1 number of extra gaps= 0 total=87 Number of alignments=25 # 2bt2A read from 2bt2A/merged-good-all-a2m # found chain 2bt2A in template set T0302 5 :PEEAVKWGESFDKLLSHRDGLEAFTRFLKTEFSEENIEFWIACEDFKKSKGPQQIHLKAKAIYEKFIQTDAPKEVNLDFHTKEVITNSITQPTLHSFDAAQSRVYQLMEQDSYTRFLKSDIYLDLMEG 2bt2A 56 :SEDVLGWRESFDLLLSSKNGVAAFHAFLKTEFSEENLEFWLACEEFKKIRSATKLASRAHQIFEEFICSEAPKEVNIDHETRELTRMNLQTATATCFDAAQGKTRTLMEKDSYPRFLKSPAYRDLAAQ Number of specific fragments extracted= 1 number of extra gaps= 0 total=88 Number of alignments=26 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2acxA/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/T0302/2acxA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0302/2acxA/merged-good-all-a2m.gz for input Trying 2acxA/merged-good-all-a2m Error: Couldn't open file 2acxA/merged-good-all-a2m or 2acxA/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1iapA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1iapA expands to /projects/compbio/data/pdb/1iap.pdb.gz 1iapA:# T0302 read from 1iapA/merged-good-all-a2m # 1iapA read from 1iapA/merged-good-all-a2m # adding 1iapA to template set # found chain 1iapA in template set T0302 13 :ESFDKLLSHRDGLEAFTRFLKTEFSEENIEFWIACEDFKK 1iapA 47 :QSLEQVKRRPAHLMALLQHVALQFEPGPLLCCLHADMLGS T0302 54 :KGPQQIHLKAKAIYEKFIQTDAPKEVNLDFHTKEVITNSITQ 1iapA 87 :LGPKEAKKAFLDFYHSFLEKTAVLRVPVPPNVAFELDRTRAD T0302 96 :PTLHSFDAAQSRVYQLME 1iapA 130 :ISEDVQRRFVQEVVQSQQ T0302 114 :QDSYTRFLK 1iapA 151 :GRQLEDFRS Number of specific fragments extracted= 4 number of extra gaps= 0 total=92 Number of alignments=27 # 1iapA read from 1iapA/merged-good-all-a2m # found chain 1iapA in template set T0302 13 :ESFDKLLSHRDGLEAFTRFLKTEFSEENIEFWIACEDFKK 1iapA 47 :QSLEQVKRRPAHLMALLQHVALQFEPGPLLCCLHADMLGS T0302 54 :KGPQQIHLKAKAIYEKFIQTDAPKEVNLDFHTKEVITNSI 1iapA 87 :LGPKEAKKAFLDFYHSFLEKTAVLRVPVPPNVAFELDRTR T0302 94 :TQPTLHSFDAAQSRVYQLME 1iapA 128 :DLISEDVQRRFVQEVVQSQQ T0302 114 :QDSYTRFLK 1iapA 151 :GRQLEDFRS Number of specific fragments extracted= 4 number of extra gaps= 0 total=96 Number of alignments=28 # 1iapA read from 1iapA/merged-good-all-a2m # found chain 1iapA in template set T0302 13 :ESFDKLLSHRDGLEAFTRFLKTEFSEENIEFWIACEDFKK 1iapA 47 :QSLEQVKRRPAHLMALLQHVALQFEPGPLLCCLHADMLGS T0302 54 :KGPQQIHLKAKAIYEKFIQTDAPKEVNLDFHTKEVITNSITQ 1iapA 87 :LGPKEAKKAFLDFYHSFLEKTAVLRVPVPPNVAFELDRTRAD T0302 96 :PTLHSFDAAQSRVYQLME 1iapA 130 :ISEDVQRRFVQEVVQSQQ Number of specific fragments extracted= 3 number of extra gaps= 0 total=99 Number of alignments=29 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1emuA/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/T0302/1emuA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0302/1emuA/merged-good-all-a2m.gz for input Trying 1emuA/merged-good-all-a2m Error: Couldn't open file 1emuA/merged-good-all-a2m or 1emuA/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1eca/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0302 read from 1eca/merged-good-all-a2m # 1eca read from 1eca/merged-good-all-a2m # found chain 1eca in training set Warning: unaligning (T0302)Y117 because of BadResidue code TOO_FEW_ATOMS+NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1eca)A115 Warning: unaligning (T0302)T118 because of BadResidue code TOO_FEW_ATOMS+NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1eca)A115 T0302 21 :HRDGLEAFTRFLKT 1eca 2 :SADQISTVQASFDK T0302 36 :FSEENIEFWIACEDF 1eca 16 :VKGDPVGILYAVFKA T0302 51 :KKSKGPQQIHLKAKAIYEKF 1eca 47 :ESIKGTAPFETHANRIVGFF T0302 71 :IQTDAP 1eca 69 :IIGELP T0302 80 :NLDFHTKEVITNSI 1eca 75 :NIEADVNTFVASHK T0302 94 :TQPTLHSFDAAQSRVYQLMEQD 1eca 90 :RGVTHDQLNNFRAGFVSYMKAH T0302 116 :S 1eca 113 :D T0302 119 :RFL 1eca 116 :GAE T0302 124 :DIYLDLME 1eca 119 :AAWGATLD Number of specific fragments extracted= 9 number of extra gaps= 1 total=108 Number of alignments=30 # 1eca read from 1eca/merged-good-all-a2m # found chain 1eca in training set Warning: unaligning (T0302)Y117 because of BadResidue code TOO_FEW_ATOMS+NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1eca)A115 Warning: unaligning (T0302)T118 because of BadResidue code TOO_FEW_ATOMS+NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1eca)A115 T0302 4 :S 1eca 2 :S T0302 22 :RDGLEAFTRFLKT 1eca 3 :ADQISTVQASFDK T0302 36 :FSEENIEFWIAC 1eca 16 :VKGDPVGILYAV T0302 50 :FK 1eca 28 :FK T0302 52 :KSKGPQQIHLKAKAIYEKF 1eca 48 :SIKGTAPFETHANRIVGFF T0302 71 :IQTDAP 1eca 69 :IIGELP T0302 80 :NLDFHTKEVITNSI 1eca 75 :NIEADVNTFVASHK T0302 94 :TQPTLHSFDAAQSRVYQLMEQD 1eca 90 :RGVTHDQLNNFRAGFVSYMKAH T0302 116 :S 1eca 113 :D T0302 119 :RFL 1eca 116 :GAE T0302 124 :DIYLDLME 1eca 119 :AAWGATLD Number of specific fragments extracted= 11 number of extra gaps= 1 total=119 Number of alignments=31 # 1eca read from 1eca/merged-good-all-a2m # found chain 1eca in training set Warning: unaligning (T0302)V3 because first residue in template chain is (1eca)L1 T0302 4 :SPEEAVKWGESFDKLLSHRDGLEA 1eca 2 :SADQISTVQASFDKVKGDPVGILY T0302 46 :AC 1eca 26 :AV T0302 50 :FK 1eca 28 :FK T0302 54 :KGPQ 1eca 30 :ADPS T0302 58 :QIHLKAKAIYEKFIQ 1eca 54 :PFETHANRIVGFFSK T0302 73 :TDAP 1eca 71 :GELP T0302 80 :NL 1eca 75 :NI T0302 83 :FHTKEVITNSITQ 1eca 77 :EADVNTFVASHKP T0302 96 :PTLHSFDAAQSRVYQLMEQDSY 1eca 92 :VTHDQLNNFRAGFVSYMKAHTD Number of specific fragments extracted= 9 number of extra gaps= 0 total=128 Number of alignments=32 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2bv1A/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/T0302/2bv1A/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0302/2bv1A/merged-good-all-a2m.gz for input Trying 2bv1A/merged-good-all-a2m Error: Couldn't open file 2bv1A/merged-good-all-a2m or 2bv1A/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1zv4X/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/T0302/1zv4X/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0302/1zv4X/merged-good-all-a2m.gz for input Trying 1zv4X/merged-good-all-a2m Error: Couldn't open file 1zv4X/merged-good-all-a2m or 1zv4X/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1dk8A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0302 read from 1dk8A/merged-good-all-a2m # 1dk8A read from 1dk8A/merged-good-all-a2m # found chain 1dk8A in training set T0302 1 :SMVSPEEAVKWGESFDKLLSHRDGLEAFTRFLKTEFSEENIEFWIACEDFKKS 1dk8A 112 :SASPTPPYLKWAESLHSLLDDQDGISLFRTFLKQEGCADLLDFWFACTGFRKL T0302 54 :KGPQQIHLKAKAIYEKFIQTDA 1dk8A 169 :SNEEKRLKLARAIYRKYILDNN T0302 81 :LDFHTKEVITNSI 1dk8A 197 :TKPATKSFIKGCI T0302 94 :TQPTLHSFDAAQSRVYQLMEQDSYTRFLKSDIYLDLMEG 1dk8A 212 :QLIDPAMFDQAQTEIQATMEENTYPSFLKSDIYLEYTRT Number of specific fragments extracted= 4 number of extra gaps= 0 total=132 Number of alignments=33 # 1dk8A read from 1dk8A/merged-good-all-a2m # found chain 1dk8A in training set T0302 1 :SMVSPEEAVKWGESFDKLLSHRDGLEAFTRFLKTEFSEENIEFWIACEDFKKSK 1dk8A 112 :SASPTPPYLKWAESLHSLLDDQDGISLFRTFLKQEGCADLLDFWFACTGFRKLE T0302 55 :GPQQIHLKAKAIYEKFIQTDA 1dk8A 170 :NEEKRLKLARAIYRKYILDNN T0302 81 :LDFHTKEVITNSI 1dk8A 197 :TKPATKSFIKGCI T0302 94 :TQPTLHSFDAAQSRVYQLMEQDSYTRFLKSDIYLDLME 1dk8A 212 :QLIDPAMFDQAQTEIQATMEENTYPSFLKSDIYLEYTR Number of specific fragments extracted= 4 number of extra gaps= 0 total=136 Number of alignments=34 # 1dk8A read from 1dk8A/merged-good-all-a2m # found chain 1dk8A in training set T0302 2 :MVSPEEAVKWGESFDKLLSHRDGLEAFTRFLKTEFSEENIEFWIACEDFKKS 1dk8A 113 :ASPTPPYLKWAESLHSLLDDQDGISLFRTFLKQEGCADLLDFWFACTGFRKL T0302 54 :KGPQQIHLKAKAIYEKFIQTDA 1dk8A 169 :SNEEKRLKLARAIYRKYILDNN T0302 81 :LDFHTKEVITNSITQ 1dk8A 197 :TKPATKSFIKGCIMK T0302 96 :PTLHSFDAAQSRVYQLMEQDSYTRFLKSDIYL 1dk8A 214 :IDPAMFDQAQTEIQATMEENTYPSFLKSDIYL Number of specific fragments extracted= 4 number of extra gaps= 0 total=140 Number of alignments=35 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2a72A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2a72A expands to /projects/compbio/data/pdb/2a72.pdb.gz 2a72A:# T0302 read from 2a72A/merged-good-all-a2m # 2a72A read from 2a72A/merged-good-all-a2m # adding 2a72A to template set # found chain 2a72A in template set T0302 1 :SMVSPEEAVKWGESFDKLLSHRDGLEAFTRFLKTEFSEENIEFWIACEDFKK 2a72A 320 :KEPSQQRVKRWGFGMDEALKDPVGREQFLKFLESEFSSENLRFWLAVEDLKK T0302 54 :KGPQQIHLKAKAIYEKFIQTDAPKEVNLDFHTKEVITNSITQPTLHSFDAAQSRVYQLMEQDSYTRFLKSDIYLDLMEG 2a72A 372 :RPIKEVPSRVQEIWQEFLAPGAPSAINLDSKSYDKTTHNVKEPGRYTFEDAQEHIYKLMKSDSYPRFIRSSAYQELLQA Number of specific fragments extracted= 2 number of extra gaps= 0 total=142 Number of alignments=36 # 2a72A read from 2a72A/merged-good-all-a2m # found chain 2a72A in template set T0302 1 :SMVSPEEAVKWGESFDKLLSHRDGLEAFTRFLKTEFSEENIEFWIACEDFKK 2a72A 320 :KEPSQQRVKRWGFGMDEALKDPVGREQFLKFLESEFSSENLRFWLAVEDLKK T0302 54 :KGPQQIHLKAKAIYEKFIQTDAPKEVNLDFHTKEVITNSITQPTLHSFDAAQSRVYQLMEQDSYTRFLKSDIYLDLMEG 2a72A 372 :RPIKEVPSRVQEIWQEFLAPGAPSAINLDSKSYDKTTHNVKEPGRYTFEDAQEHIYKLMKSDSYPRFIRSSAYQELLQA Number of specific fragments extracted= 2 number of extra gaps= 0 total=144 Number of alignments=37 # 2a72A read from 2a72A/merged-good-all-a2m # found chain 2a72A in template set T0302 1 :SMVSPEEAVKWGESFDKLLSHRDGLEAFTRFLKTEFSEENIEFWIACEDFKK 2a72A 320 :KEPSQQRVKRWGFGMDEALKDPVGREQFLKFLESEFSSENLRFWLAVEDLKK T0302 54 :KGPQQIHLKAKAIYEKFIQTDAPKEVNLDFHTKEVITNSITQPTLHSFDAAQSRVYQLMEQDSYTRFLKSDIYLDLMEG 2a72A 372 :RPIKEVPSRVQEIWQEFLAPGAPSAINLDSKSYDKTTHNVKEPGRYTFEDAQEHIYKLMKSDSYPRFIRSSAYQELLQA Number of specific fragments extracted= 2 number of extra gaps= 0 total=146 Number of alignments=38 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1x3kA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1x3kA expands to /projects/compbio/data/pdb/1x3k.pdb.gz 1x3kA:# T0302 read from 1x3kA/merged-good-all-a2m # 1x3kA read from 1x3kA/merged-good-all-a2m # adding 1x3kA to template set # found chain 1x3kA in template set T0302 2 :MVSPEEAVKWGESFDKLLSH 1x3kA 4 :GLSDSEEKLVRDAWAPIHGD T0302 22 :RDGLEAFTRFLKT 1x3kA 26 :GTANTVFYNYLKK T0302 35 :EFSEE 1x3kA 41 :SNQDK T0302 51 :KKSKGPQQIHLKAKAIYEKF 1x3kA 55 :DEVKDTANFKLIAGRIFTIF T0302 73 :TD 1x3kA 79 :KN T0302 79 :VNLDFHTKEVITNSI 1x3kA 81 :VGNDKGFQKVIADMS T0302 94 :TQPTLHSFDAAQSRVYQLM 1x3kA 101 :RPITHGSYNDLRGVIYDSM T0302 113 :EQDSYTRFLKS 1x3kA 125 :HGAAWNKMMDN T0302 124 :DIYLDLMEG 1x3kA 138 :YVFYECLDG Number of specific fragments extracted= 9 number of extra gaps= 0 total=155 Number of alignments=39 # 1x3kA read from 1x3kA/merged-good-all-a2m # found chain 1x3kA in template set T0302 2 :MVSPEEAVKWGESFDKLLSH 1x3kA 4 :GLSDSEEKLVRDAWAPIHGD T0302 22 :RDGLEAFTRFLKT 1x3kA 26 :GTANTVFYNYLKK T0302 35 :EFSEE 1x3kA 41 :SNQDK T0302 52 :KSKGPQQIHLKAKAIYEKF 1x3kA 56 :EVKDTANFKLIAGRIFTIF T0302 73 :TD 1x3kA 79 :KN T0302 79 :VNLDFHTKEVITNSI 1x3kA 81 :VGNDKGFQKVIADMS T0302 94 :TQPTLHSFDAAQSRVYQLM 1x3kA 101 :RPITHGSYNDLRGVIYDSM T0302 113 :EQDSYTRFLKS 1x3kA 125 :HGAAWNKMMDN T0302 124 :DIYLDLMEG 1x3kA 138 :YVFYECLDG Number of specific fragments extracted= 9 number of extra gaps= 0 total=164 Number of alignments=40 # 1x3kA read from 1x3kA/merged-good-all-a2m # found chain 1x3kA in template set T0302 1 :SMVSPEEAVKWGESFDKLLSH 1x3kA 3 :VGLSDSEEKLVRDAWAPIHGD T0302 22 :RDGLEAFTRFLKTEFS 1x3kA 26 :GTANTVFYNYLKKYPS T0302 50 :FKKSKGPQQIHLKAKAIYEKFIQ 1x3kA 54 :LDEVKDTANFKLIAGRIFTIFDN T0302 80 :NLDFHTKEVITNSITQ 1x3kA 82 :GNDKGFQKVIADMSGP T0302 96 :PTLHSFDAAQSRVYQLM 1x3kA 103 :ITHGSYNDLRGVIYDSM T0302 113 :EQDSYTRFL 1x3kA 129 :WNKMMDNFF T0302 124 :DIYLDLMEG 1x3kA 138 :YVFYECLDG Number of specific fragments extracted= 7 number of extra gaps= 0 total=171 Number of alignments=41 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1cmzA/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/T0302/1cmzA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0302/1cmzA/merged-good-all-a2m.gz for input Trying 1cmzA/merged-good-all-a2m Error: Couldn't open file 1cmzA/merged-good-all-a2m or 1cmzA/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1r89A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0302 read from 1r89A/merged-good-all-a2m # 1r89A read from 1r89A/merged-good-all-a2m # found chain 1r89A in training set T0302 4 :SPEEAVK 1r89A 2 :KVEEILE T0302 14 :SFDKLLSH 1r89A 9 :KALELVIP T0302 22 :RDGLEAFTRFLKT 1r89A 18 :EEEVRKGREAEEE T0302 43 :FWIACEDF 1r89A 31 :LRRRLDEL T0302 57 :QQIHLKAKAIYEKFIQ 1r89A 232 :LDNLARFVHLCREFME T0302 73 :TDAPKEVN 1r89A 256 :PKHPLEIE T0302 82 :DFHTKEVITNSI 1r89A 264 :PERLRKIVEERG T0302 95 :QPTLH 1r89A 287 :DIVDD T0302 100 :SFDAAQSRVYQLMEQDSY 1r89A 296 :QLERASRKIFEFLERENF Number of specific fragments extracted= 9 number of extra gaps= 0 total=180 Number of alignments=42 # 1r89A read from 1r89A/merged-good-all-a2m # found chain 1r89A in training set T0302 5 :PEEA 1r89A 3 :VEEI T0302 12 :GESFDKLLSH 1r89A 7 :LEKALELVIP T0302 22 :RDGLEAFTRFLKT 1r89A 18 :EEEVRKGREAEEE T0302 43 :FWIACEDFK 1r89A 31 :LRRRLDELG T0302 56 :PQQIHLKAKAIYEKFIQ 1r89A 231 :SLDNLARFVHLCREFME T0302 73 :T 1r89A 256 :P T0302 76 :PKEVNLD 1r89A 257 :KHPLEIE T0302 83 :FHTKEVITNS 1r89A 265 :ERLRKIVEER T0302 94 :T 1r89A 275 :G T0302 95 :QPT 1r89A 287 :DIV T0302 98 :LHSFDAAQSRVYQLMEQDSY 1r89A 294 :YPQLERASRKIFEFLERENF Number of specific fragments extracted= 11 number of extra gaps= 0 total=191 Number of alignments=43 # 1r89A read from 1r89A/merged-good-all-a2m # found chain 1r89A in training set T0302 5 :PEEAV 1r89A 3 :VEEIL T0302 13 :ESFDKLLS 1r89A 8 :EKALELVI T0302 21 :HRDGLEAFTR 1r89A 17 :DEEEVRKGRE T0302 46 :ACEDFKKSKGPQ 1r89A 27 :AEEELRRRLDEL T0302 58 :QIHLKAKAIYEKFIQT 1r89A 233 :DNLARFVHLCREFMEA T0302 74 :DAPKEVNLDFHTKEVITNSITQ 1r89A 255 :KPKHPLEIEPERLRKIVEERGT T0302 96 :PTLHSFDAAQSRVYQLMEQDSY 1r89A 292 :NLYPQLERASRKIFEFLERENF Number of specific fragments extracted= 7 number of extra gaps= 0 total=198 Number of alignments=44 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1htjF/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1htjF expands to /projects/compbio/data/pdb/1htj.pdb.gz 1htjF:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0302 read from 1htjF/merged-good-all-a2m # 1htjF read from 1htjF/merged-good-all-a2m # adding 1htjF to template set # found chain 1htjF in template set T0302 11 :WGESFDKLLSHRDGLEAFTRFLKTEFSEENIEFWIACEDFKK 1htjF 310 :IFQDLEKLKSRPAHLGVFLRYIFSQADPSPLLFYLCAEVYQQ T0302 54 :KGPQQIHLKAKAIYEKFIQTDAPKEVNLDFHTKEVITNSI 1htjF 352 :ASPKDSRSLGKDIWNIFLEKNAPLRVKIPEMLQAEIDSRL T0302 94 :TQPTLHSFDAAQSRVYQLMEQDS 1htjF 394 :SEDARGVLCEAQEAAMPEIQEQI T0302 124 :DIYLDLMEG 1htjF 417 :HDYRTKRTL Number of specific fragments extracted= 4 number of extra gaps= 0 total=202 Number of alignments=45 # 1htjF read from 1htjF/merged-good-all-a2m # found chain 1htjF in template set T0302 8 :AVKWGESFDKLLSHRDGLEAFTRFLKTEFSEENIEFWIACEDFKKS 1htjF 307 :SDIIFQDLEKLKSRPAHLGVFLRYIFSQADPSPLLFYLCAEVYQQA T0302 55 :GPQQIHLKAKAIYEKFIQTDAPKEVNLDFHTKEVITNSI 1htjF 353 :SPKDSRSLGKDIWNIFLEKNAPLRVKIPEMLQAEIDSRL T0302 94 :TQPTLHSFDAAQSRVYQLMEQDS 1htjF 394 :SEDARGVLCEAQEAAMPEIQEQI T0302 124 :DIYLDLME 1htjF 417 :HDYRTKRT Number of specific fragments extracted= 4 number of extra gaps= 0 total=206 Number of alignments=46 # 1htjF read from 1htjF/merged-good-all-a2m # found chain 1htjF in template set T0302 11 :WGESFDKLLSHRDGLEAFTRFLKTEFSEENIEFWIACEDFKK 1htjF 310 :IFQDLEKLKSRPAHLGVFLRYIFSQADPSPLLFYLCAEVYQQ T0302 54 :KGPQQIHLKAKAIYEKFIQTDAPKEVNLDFHTKEVITNSITQ 1htjF 352 :ASPKDSRSLGKDIWNIFLEKNAPLRVKIPEMLQAEIDSRLRN T0302 96 :PTLHSFDAAQSRVYQLMEQDSY 1htjF 396 :DARGVLCEAQEAAMPEIQEQIH T0302 125 :IYLDLME 1htjF 418 :DYRTKRT Number of specific fragments extracted= 4 number of extra gaps= 0 total=210 Number of alignments=47 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1agrE/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1agrE expands to /projects/compbio/data/pdb/1agr.pdb.gz 1agrE:# T0302 read from 1agrE/merged-good-all-a2m # 1agrE read from 1agrE/merged-good-all-a2m # adding 1agrE to template set # found chain 1agrE in template set Warning: unaligning (T0302)V3 because first residue in template chain is (1agrE)V51 T0302 4 :SPEEAVKWGESFDKLLSHRDGLEAFTRFLKTEFSEENIEFWIACEDFKKSKGPQQIHLKAKAIYEKFIQTDAPKEVNLDFHTKEVITNSITQPTLHSFDAAQSRVYQLMEQDSYTRFLKSDIYLD 1agrE 52 :SQEEVKKWAESLENLINHECGLAAFKAFLKSEYSEENIDFWISCEEYKKIKSPSKLSPKAKKIYNEFISVQATKEVNLDSCTREETSRNMLEPTITCFDEAQKKIFNLMEKDSYRRFLKSRFYLD Number of specific fragments extracted= 1 number of extra gaps= 0 total=211 Number of alignments=48 # 1agrE read from 1agrE/merged-good-all-a2m # found chain 1agrE in template set Warning: unaligning (T0302)V3 because first residue in template chain is (1agrE)V51 T0302 4 :SPEEAVKWGESFDKLLSHRDGLEAFTRFLKTEFSEENIEFWIACEDFKKSKGPQQIHLKAKAIYEKFIQTDAPKEVNLDFHTKEVITNSITQPTLHSFDAAQSRVYQLMEQDSYTRFLKSDIYLD 1agrE 52 :SQEEVKKWAESLENLINHECGLAAFKAFLKSEYSEENIDFWISCEEYKKIKSPSKLSPKAKKIYNEFISVQATKEVNLDSCTREETSRNMLEPTITCFDEAQKKIFNLMEKDSYRRFLKSRFYLD Number of specific fragments extracted= 1 number of extra gaps= 0 total=212 Number of alignments=49 # 1agrE read from 1agrE/merged-good-all-a2m # found chain 1agrE in template set Warning: unaligning (T0302)V3 because first residue in template chain is (1agrE)V51 T0302 4 :SPEEAVKWGESFDKLLSHRDGLEAFTRFLKTEFSEENIEFWIACEDFKKSKGPQQIHLKAKAIYEKFIQTDAPKEVNLDFHTKEVITNSITQPTLHSFDAAQSRVYQLMEQDSYTRFLKSDIYLD 1agrE 52 :SQEEVKKWAESLENLINHECGLAAFKAFLKSEYSEENIDFWISCEEYKKIKSPSKLSPKAKKIYNEFISVQATKEVNLDSCTREETSRNMLEPTITCFDEAQKKIFNLMEKDSYRRFLKSRFYLD Number of specific fragments extracted= 1 number of extra gaps= 0 total=213 Number of alignments=50 # command:# PrintAlignmentsContacts allconstraints.under Using radius: 8.0000 NUMB_ALIGNS: 50 Done printing distance constraints # command: