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/T0306/ # command:# Making conformation for sequence T0306 numbered 1 through 95 Created new target T0306 from T0306.a2m # command:# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/T0306/ # command:Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0306//projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0306/manyalignments-good-all.under or /projects/compbio/experiments/protein-predict/casp7/T0306//projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0306/manyalignments-good-all.under.gz for input Trying /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0306/manyalignments-good-all.under # reading script from file /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0306/manyalignments-good-all.under # Reading fragments from alignment file # Attempting to read fragment alignments from file 1g0uI/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1g0uI expands to /projects/compbio/data/pdb/1g0u.pdb.gz 1g0uI:# T0306 read from 1g0uI/merged-good-all-a2m # 1g0uI read from 1g0uI/merged-good-all-a2m # adding 1g0uI to template set # found chain 1g0uI in template set T0306 21 :HDKLLMVEM 1g0uI -2 :NGGIVVAMT # choosing archetypes in rotamer library T0306 36 :PDGQCAVAIDNIGAGT 1g0uI 8 :GKDCVAIACDLRLGSQ T0306 52 :GEWVLLVSG 1g0uI 39 :GHVFLGITG T0306 62 :SARQA 1g0uI 58 :MFRYK T0306 67 :HKSETSPVDLCVIGI 1g0uI 90 :RRFGPYFVGPVVAGI T0306 82 :V 1g0uI 110 :I Number of specific fragments extracted= 6 number of extra gaps= 0 total=6 Number of alignments=1 # 1g0uI read from 1g0uI/merged-good-all-a2m # found chain 1g0uI in template set T0306 21 :HDKLLMVEM 1g0uI -2 :NGGIVVAMT T0306 36 :PDGQCAVAIDNIGAGT 1g0uI 8 :GKDCVAIACDLRLGSQ T0306 52 :GEWVLLVSG 1g0uI 39 :GHVFLGITG T0306 61 :SSARQA 1g0uI 57 :EMFRYK T0306 68 :KSETSPVDLCVIGI 1g0uI 91 :RFGPYFVGPVVAGI T0306 82 :V 1g0uI 110 :I Number of specific fragments extracted= 6 number of extra gaps= 0 total=12 Number of alignments=2 # 1g0uI read from 1g0uI/merged-good-all-a2m # found chain 1g0uI in template set T0306 21 :HDKLLMVEM 1g0uI -2 :NGGIVVAMT T0306 36 :PDGQCAVAIDNIGAGT 1g0uI 8 :GKDCVAIACDLRLGSQ T0306 52 :GEWVLLVSG 1g0uI 39 :GHVFLGITG Number of specific fragments extracted= 3 number of extra gaps= 0 total=15 Number of alignments=3 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1pgl1/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1pgl1 expands to /projects/compbio/data/pdb/1pgl.pdb.gz 1pgl1:# T0306 read from 1pgl1/merged-good-all-a2m # 1pgl1 read from 1pgl1/merged-good-all-a2m # adding 1pgl1 to template set # found chain 1pgl1 in template set T0306 17 :HGLAHDKLLMVE 1pgl1 4 :QQTVWNQMATVR T0306 30 :IDPQGNPD 1pgl1 16 :TPLNFDSS T0306 38 :GQCAVAIDNIGAG 1pgl1 26 :SFCQFSVDLLGGG T0306 51 :TGEWVLLVSGSSARQAH 1pgl1 44 :TGDWITLVQNSPISNLL Number of specific fragments extracted= 4 number of extra gaps= 0 total=19 Number of alignments=4 # 1pgl1 read from 1pgl1/merged-good-all-a2m # found chain 1pgl1 in template set T0306 17 :HGLAHDKLLMVE 1pgl1 4 :QQTVWNQMATVR T0306 30 :IDPQGNPD 1pgl1 16 :TPLNFDSS T0306 38 :GQCAVAIDNIGAG 1pgl1 26 :SFCQFSVDLLGGG T0306 51 :TGEWVLLVSGSSARQAH 1pgl1 44 :TGDWITLVQNSPISNLL Number of specific fragments extracted= 4 number of extra gaps= 0 total=23 Number of alignments=5 # 1pgl1 read from 1pgl1/merged-good-all-a2m # found chain 1pgl1 in template set T0306 21 :HDKLLMVE 1pgl1 8 :WNQMATVR T0306 30 :IDPQGN 1pgl1 16 :TPLNFD T0306 36 :PDGQCAVAIDNIGAG 1pgl1 24 :KQSFCQFSVDLLGGG T0306 51 :TGEWVLLVSGSSARQAHKS 1pgl1 44 :TGDWITLVQNSPISNLLRV T0306 74 :VDLCVIGIVDEVVSG 1pgl1 67 :KGCLMVKVVMSGNAA Number of specific fragments extracted= 5 number of extra gaps= 0 total=28 Number of alignments=6 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2ae0X/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2ae0X expands to /projects/compbio/data/pdb/2ae0.pdb.gz 2ae0X:# T0306 read from 2ae0X/merged-good-all-a2m # 2ae0X read from 2ae0X/merged-good-all-a2m # adding 2ae0X to template set # found chain 2ae0X in template set T0306 12 :CTVRHHGLAHDKLLMVEMI 2ae0X 258 :VASDRSIIPPGTTLLAEVP T0306 31 :DPQGNPDG 2ae0X 279 :DNNGKFNG T0306 39 :QCAVAIDNIGAGTGEWVLLV 2ae0X 291 :RLMVALDVGGAIKGQHFDIY T0306 60 :GSSARQAHKSETSPVDLCVI 2ae0X 314 :GPEAGHRAGWYNHYGRVWVL Number of specific fragments extracted= 4 number of extra gaps= 0 total=32 Number of alignments=7 # 2ae0X read from 2ae0X/merged-good-all-a2m # found chain 2ae0X in template set T0306 12 :CTVRHHGLAHDKLLMVEMI 2ae0X 258 :VASDRSIIPPGTTLLAEVP T0306 31 :DPQGNPDG 2ae0X 279 :DNNGKFNG T0306 39 :QCAVAIDNIGAGTGEWVLLVS 2ae0X 291 :RLMVALDVGGAIKGQHFDIYQ T0306 60 :GSSARQAHKSETSPVDLCVI 2ae0X 314 :GPEAGHRAGWYNHYGRVWVL Number of specific fragments extracted= 4 number of extra gaps= 0 total=36 Number of alignments=8 # 2ae0X read from 2ae0X/merged-good-all-a2m # found chain 2ae0X in template set T0306 11 :VCTVRHHGLAHDKLLMVEMI 2ae0X 257 :SVASDRSIIPPGTTLLAEVP T0306 31 :DPQGNPDGQC 2ae0X 279 :DNNGKFNGQY T0306 41 :AVAIDNIGAGTGEWVLLV 2ae0X 293 :MVALDVGGAIKGQHFDIY T0306 59 :SGSSARQAHKSETSPVDLCVI 2ae0X 313 :IGPEAGHRAGWYNHYGRVWVL Number of specific fragments extracted= 4 number of extra gaps= 0 total=40 Number of alignments=9 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1mrg/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1mrg expands to /projects/compbio/data/pdb/1mrg.pdb.gz 1mrg:Warning: there is no chain 1mrg will retry with 1mrgA Skipped atom 678, because occupancy 0.5 <= existing 0.500 in 1mrg Skipped atom 680, because occupancy 0.500 <= existing 0.500 in 1mrg Skipped atom 682, because occupancy 0.500 <= existing 0.500 in 1mrg Skipped atom 684, because occupancy 0.500 <= existing 0.500 in 1mrg Skipped atom 686, because occupancy 0.500 <= existing 0.500 in 1mrg Skipped atom 688, because occupancy 0.500 <= existing 0.500 in 1mrg Skipped atom 690, because occupancy 0.500 <= existing 0.500 in 1mrg Skipped atom 692, because occupancy 0.500 <= existing 0.500 in 1mrg # T0306 read from 1mrg/merged-good-all-a2m # 1mrg read from 1mrg/merged-good-all-a2m # adding 1mrg to template set # found chain 1mrg in template set Warning: unaligning (T0306)Q39 because of BadResidue code BAD_PEPTIDE in next template residue (1mrg)I60 Warning: unaligning (T0306)C40 because of BadResidue code BAD_PEPTIDE at template residue (1mrg)I60 Warning: unaligning (T0306)T51 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1mrg)D77 Warning: unaligning (T0306)G52 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1mrg)D77 T0306 12 :CTVRHHGLAHD 1mrg 34 :IPLLLPSVSGA T0306 23 :KLLMVEMIDPQGN 1mrg 46 :RYLLMHLFNRDGK T0306 41 :AVAID 1mrg 61 :TVAVD T0306 46 :NIGAG 1mrg 71 :IMGYL T0306 53 :EWVLLVSGSSARQAHKS 1mrg 78 :TTSYFFNEPAAELASQY Number of specific fragments extracted= 5 number of extra gaps= 2 total=45 Number of alignments=10 # 1mrg read from 1mrg/merged-good-all-a2m # found chain 1mrg in template set Warning: unaligning (T0306)Q39 because of BadResidue code BAD_PEPTIDE in next template residue (1mrg)I60 Warning: unaligning (T0306)C40 because of BadResidue code BAD_PEPTIDE at template residue (1mrg)I60 Warning: unaligning (T0306)T51 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1mrg)D77 Warning: unaligning (T0306)G52 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1mrg)D77 T0306 12 :CTVRHHGLAHD 1mrg 34 :IPLLLPSVSGA T0306 23 :KLLMVEMIDPQGN 1mrg 46 :RYLLMHLFNRDGK T0306 41 :AVAID 1mrg 61 :TVAVD T0306 46 :NIGAG 1mrg 71 :IMGYL T0306 53 :EWVLLVSGSSARQAHKS 1mrg 78 :TTSYFFNEPAAELASQY Number of specific fragments extracted= 5 number of extra gaps= 2 total=50 Number of alignments=11 # 1mrg read from 1mrg/merged-good-all-a2m # found chain 1mrg in template set Warning: unaligning (T0306)Q39 because of BadResidue code BAD_PEPTIDE in next template residue (1mrg)I60 Warning: unaligning (T0306)C40 because of BadResidue code BAD_PEPTIDE at template residue (1mrg)I60 Warning: unaligning (T0306)T51 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1mrg)D77 Warning: unaligning (T0306)G52 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1mrg)D77 T0306 12 :CTVRHHGLAHD 1mrg 34 :IPLLLPSVSGA T0306 23 :KLLMVEMIDPQGN 1mrg 46 :RYLLMHLFNRDGK T0306 41 :AVAID 1mrg 61 :TVAVD T0306 46 :NIGAG 1mrg 71 :IMGYL T0306 53 :EWVLLVSGSSARQAHKS 1mrg 78 :TTSYFFNEPAAELASQY Number of specific fragments extracted= 5 number of extra gaps= 2 total=55 Number of alignments=12 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2c3mA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2c3mA expands to /projects/compbio/data/pdb/2c3m.pdb.gz 2c3mA:# T0306 read from 2c3mA/merged-good-all-a2m # 2c3mA read from 2c3mA/merged-good-all-a2m # adding 2c3mA to template set # found chain 2c3mA in template set T0306 44 :IDNIGAGTGEWVLLVSG 2c3mA 261 :FDYVGAPDAERVIVSMG T0306 61 :SSARQAHKSETSPVDLCVIGIV 2c3mA 284 :EEVINHLAAKGEKIGLIKVRLY Number of specific fragments extracted= 2 number of extra gaps= 0 total=57 Number of alignments=13 # 2c3mA read from 2c3mA/merged-good-all-a2m # found chain 2c3mA in template set T0306 44 :IDNIGAGTGEWVLLVSG 2c3mA 261 :FDYVGAPDAERVIVSMG T0306 61 :SSARQAHKSETSPVDLCVIGIV 2c3mA 284 :EEVINHLAAKGEKIGLIKVRLY Number of specific fragments extracted= 2 number of extra gaps= 0 total=59 Number of alignments=14 # 2c3mA read from 2c3mA/merged-good-all-a2m # found chain 2c3mA in template set T0306 44 :IDNIGAGTGEWVLLVSGSS 2c3mA 261 :FDYVGAPDAERVIVSMGSS T0306 63 :ARQAHKSETSPVDLCVIGIVD 2c3mA 286 :VINHLAAKGEKIGLIKVRLYR Number of specific fragments extracted= 2 number of extra gaps= 0 total=61 Number of alignments=15 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1mrj/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0306 read from 1mrj/merged-good-all-a2m # 1mrj read from 1mrj/merged-good-all-a2m # found chain 1mrj in training set Warning: unaligning (T0306)K23 because of BadResidue code BAD_PEPTIDE at template residue (1mrj)R46 T0306 12 :CTVRHHGLAH 1mrj 34 :IPLLRSSLPG T0306 24 :LLMVEMIDPQGN 1mrj 47 :YALIHLTNYADE T0306 39 :QCAVAID 1mrj 59 :TISVAID T0306 46 :NIGAGTGEWVLLVSGSSARQAHKS 1mrj 71 :IMGYRAGDTSYFFNEASATEAAKY Number of specific fragments extracted= 4 number of extra gaps= 1 total=65 Number of alignments=16 # 1mrj read from 1mrj/merged-good-all-a2m # found chain 1mrj in training set Warning: unaligning (T0306)K23 because of BadResidue code BAD_PEPTIDE at template residue (1mrj)R46 T0306 12 :CTVRHHGLAH 1mrj 34 :IPLLRSSLPG T0306 24 :LLMVEMIDPQGN 1mrj 47 :YALIHLTNYADE T0306 39 :QCAVAID 1mrj 59 :TISVAID T0306 46 :NIGAGTGEWVLLVSGSSARQAHKS 1mrj 71 :IMGYRAGDTSYFFNEASATEAAKY Number of specific fragments extracted= 4 number of extra gaps= 1 total=69 Number of alignments=17 # 1mrj read from 1mrj/merged-good-all-a2m # found chain 1mrj in training set T0306 23 :KLLMVE 1mrj 48 :ALIHLT T0306 31 :DPQG 1mrj 54 :NYAD T0306 38 :GQCAVAID 1mrj 58 :ETISVAID T0306 46 :NIGAGTGEWVLLVSGSSARQAHKS 1mrj 71 :IMGYRAGDTSYFFNEASATEAAKY Number of specific fragments extracted= 4 number of extra gaps= 0 total=73 Number of alignments=18 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1wi1A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1wi1A expands to /projects/compbio/data/pdb/1wi1.pdb.gz 1wi1A:# T0306 read from 1wi1A/merged-good-all-a2m # 1wi1A read from 1wi1A/merged-good-all-a2m # adding 1wi1A to template set # found chain 1wi1A in template set T0306 3 :LAVVT 1wi1A 32 :LVQVS T0306 8 :GQIVCTVRHHGLAHDKLL 1wi1A 39 :TFAMCSYREKKAEPQELL T0306 27 :VEMIDPQGNPDG 1wi1A 63 :VDYTDPQPGLEG T0306 39 :QCAVAI 1wi1A 77 :AFFNAV T0306 50 :GTGEWVLLVSG 1wi1A 83 :KEGDTVIFASD T0306 61 :SSARQAHKSETSP 1wi1A 103 :QAMYRATGQSHKP Number of specific fragments extracted= 6 number of extra gaps= 0 total=79 Number of alignments=19 # 1wi1A read from 1wi1A/merged-good-all-a2m # found chain 1wi1A in template set T0306 3 :LAVVT 1wi1A 32 :LVQVS T0306 8 :GQIVCTVRHHGLAHDKLL 1wi1A 39 :TFAMCSYREKKAEPQELL T0306 27 :VEMIDPQGNPDG 1wi1A 63 :VDYTDPQPGLEG T0306 39 :QCAVAI 1wi1A 77 :AFFNAV T0306 50 :GTGEWVLLVSG 1wi1A 83 :KEGDTVIFASD T0306 61 :SSARQAHKSETSP 1wi1A 103 :QAMYRATGQSHKP Number of specific fragments extracted= 6 number of extra gaps= 0 total=85 Number of alignments=20 # 1wi1A read from 1wi1A/merged-good-all-a2m # found chain 1wi1A in template set T0306 2 :KLAVVTG 1wi1A 31 :VLVQVSQ T0306 9 :QIVCTVRHHGLAHDKLL 1wi1A 40 :FAMCSYREKKAEPQELL T0306 27 :VEMIDPQGN 1wi1A 63 :VDYTDPQPG T0306 36 :PDGQCAVAI 1wi1A 74 :GGRAFFNAV T0306 50 :GTGEWVLLVSG 1wi1A 83 :KEGDTVIFASD T0306 61 :SSARQAHKSETSPV 1wi1A 103 :QAMYRATGQSHKPV Number of specific fragments extracted= 6 number of extra gaps= 0 total=91 Number of alignments=21 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1s5uA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0306 read from 1s5uA/merged-good-all-a2m # 1s5uA read from 1s5uA/merged-good-all-a2m # found chain 1s5uA in training set T0306 9 :QIVCTVRHHGLAHDKLLMVEMI 1s5uA 75 :MLEIQTEITSMRGTSLVFTQRI T0306 31 :DPQGNPDGQCAVAIDNI 1s5uA 98 :NAENTLLNEAEVLVVCV Number of specific fragments extracted= 2 number of extra gaps= 0 total=93 Number of alignments=22 # 1s5uA read from 1s5uA/merged-good-all-a2m # found chain 1s5uA in training set T0306 9 :QIVCTVRHHGLAHDKLLMVEMI 1s5uA 75 :MLEIQTEITSMRGTSLVFTQRI T0306 31 :DPQGNPDGQCAVAIDNI 1s5uA 98 :NAENTLLNEAEVLVVCV Number of specific fragments extracted= 2 number of extra gaps= 0 total=95 Number of alignments=23 # 1s5uA read from 1s5uA/merged-good-all-a2m # found chain 1s5uA in training set T0306 8 :GQIVCTVRHHGLAHDKLLMVEMI 1s5uA 74 :DMLEIQTEITSMRGTSLVFTQRI T0306 31 :DPQGNPDGQCAVAIDNIGAGTGEW 1s5uA 98 :NAENTLLNEAEVLVVCVDPLKMKP Number of specific fragments extracted= 2 number of extra gaps= 0 total=97 Number of alignments=24 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1b0pA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1b0pA expands to /projects/compbio/data/pdb/1b0p.pdb.gz 1b0pA:# T0306 read from 1b0pA/merged-good-all-a2m # 1b0pA read from 1b0pA/merged-good-all-a2m # adding 1b0pA to template set # found chain 1b0pA in template set T0306 44 :IDNIGAGTGEWVLLVSG 1b0pA 261 :FDYVGAPDAERVIVSMG T0306 61 :SSARQAHKSETSPVDLCVI 1b0pA 284 :EEVINHLAAKGEKIGLIKV Number of specific fragments extracted= 2 number of extra gaps= 0 total=99 Number of alignments=25 # 1b0pA read from 1b0pA/merged-good-all-a2m # found chain 1b0pA in template set T0306 44 :IDNIGAGTGEWVLLVSG 1b0pA 261 :FDYVGAPDAERVIVSMG T0306 61 :SSARQAHKSETSPVDLCVI 1b0pA 284 :EEVINHLAAKGEKIGLIKV Number of specific fragments extracted= 2 number of extra gaps= 0 total=101 Number of alignments=26 # 1b0pA read from 1b0pA/merged-good-all-a2m # found chain 1b0pA in template set T0306 44 :IDNIGAGTGEWVLLVSGSS 1b0pA 261 :FDYVGAPDAERVIVSMGSS T0306 63 :ARQAHKSETSPVDLCVIGIV 1b0pA 286 :VINHLAAKGEKIGLIKVRLY Number of specific fragments extracted= 2 number of extra gaps= 0 total=103 Number of alignments=27 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1q5rH/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/T0306/1q5rH/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0306/1q5rH/merged-good-all-a2m.gz for input Trying 1q5rH/merged-good-all-a2m Error: Couldn't open file 1q5rH/merged-good-all-a2m or 1q5rH/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1sq9A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1sq9A expands to /projects/compbio/data/pdb/1sq9.pdb.gz 1sq9A:# T0306 read from 1sq9A/merged-good-all-a2m # 1sq9A read from 1sq9A/merged-good-all-a2m # adding 1sq9A to template set # found chain 1sq9A in template set Number of specific fragments extracted= 0 number of extra gaps= 0 total=103 # 1sq9A read from 1sq9A/merged-good-all-a2m # found chain 1sq9A in template set Number of specific fragments extracted= 0 number of extra gaps= 0 total=103 # 1sq9A read from 1sq9A/merged-good-all-a2m # found chain 1sq9A in template set Warning: unaligning (T0306)S61 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1sq9A)G286 T0306 21 :HDKLLMVEMI 1sq9A 233 :SNSIRSVKFS T0306 35 :NPDGQCAVAID 1sq9A 243 :PQGSLLAIAHD T0306 46 :NIGAGTGEWVLLVSG 1sq9A 262 :LYETEFGERIGSLSV Number of specific fragments extracted= 3 number of extra gaps= 0 total=106 Number of alignments=28 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1bmv1/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1bmv1 expands to /projects/compbio/data/pdb/1bmv.pdb.gz 1bmv1:# T0306 read from 1bmv1/merged-good-all-a2m # 1bmv1 read from 1bmv1/merged-good-all-a2m # adding 1bmv1 to template set # found chain 1bmv1 in template set Warning: unaligning (T0306)G8 because of BadResidue code BAD_PEPTIDE in next template residue (1bmv1)Q1010 Warning: unaligning (T0306)Q9 because of BadResidue code BAD_PEPTIDE at template residue (1bmv1)Q1010 Warning: unaligning (T0306)N35 because of BadResidue code BAD_PEPTIDE in next template residue (1bmv1)K1024 Warning: unaligning (T0306)P36 because of BadResidue code BAD_PEPTIDE at template residue (1bmv1)K1024 Warning: unaligning (T0306)D37 because of BadResidue code BAD_PEPTIDE at template residue (1bmv1)Q1025 Warning: unaligning (T0306)G38 because of BadResidue code BAD_PEPTIDE at template residue (1bmv1)S1026 T0306 10 :IVCTVRHHGLA 1bmv1 1011 :MATVRTPLNFD T0306 34 :G 1bmv1 1022 :S T0306 39 :QCAVAIDNIGAG 1bmv1 1027 :FCQFSVDLLGGG T0306 51 :TGEWVLLVSGSSARQAHKSETSPVDLCVIGIVDEVVS 1bmv1 1044 :TGDWITLVQNSPISNLLRVAAWKKGCLMVKVVMSGNA Number of specific fragments extracted= 4 number of extra gaps= 2 total=110 Number of alignments=29 # 1bmv1 read from 1bmv1/merged-good-all-a2m # found chain 1bmv1 in template set Warning: unaligning (T0306)G8 because of BadResidue code BAD_PEPTIDE in next template residue (1bmv1)Q1010 Warning: unaligning (T0306)Q9 because of BadResidue code BAD_PEPTIDE at template residue (1bmv1)Q1010 Warning: unaligning (T0306)N35 because of BadResidue code BAD_PEPTIDE in next template residue (1bmv1)K1024 Warning: unaligning (T0306)P36 because of BadResidue code BAD_PEPTIDE at template residue (1bmv1)K1024 Warning: unaligning (T0306)D37 because of BadResidue code BAD_PEPTIDE at template residue (1bmv1)Q1025 Warning: unaligning (T0306)G38 because of BadResidue code BAD_PEPTIDE at template residue (1bmv1)S1026 T0306 10 :IVCTVRHHGLA 1bmv1 1011 :MATVRTPLNFD T0306 34 :G 1bmv1 1022 :S T0306 39 :QCAVAIDNIGAG 1bmv1 1027 :FCQFSVDLLGGG T0306 51 :TGEWVLLVSGSSARQAHKSETSPVDLCVIGIVDEVVS 1bmv1 1044 :TGDWITLVQNSPISNLLRVAAWKKGCLMVKVVMSGNA Number of specific fragments extracted= 4 number of extra gaps= 2 total=114 Number of alignments=30 # 1bmv1 read from 1bmv1/merged-good-all-a2m # found chain 1bmv1 in template set Warning: unaligning (T0306)Q9 because of BadResidue code BAD_PEPTIDE at template residue (1bmv1)Q1010 Warning: unaligning (T0306)N35 because of BadResidue code BAD_PEPTIDE in next template residue (1bmv1)K1024 Warning: unaligning (T0306)P36 because of BadResidue code BAD_PEPTIDE at template residue (1bmv1)K1024 Warning: unaligning (T0306)D37 because of BadResidue code BAD_PEPTIDE at template residue (1bmv1)Q1025 Warning: unaligning (T0306)G38 because of BadResidue code BAD_PEPTIDE at template residue (1bmv1)S1026 T0306 10 :IVCTVRHHGLA 1bmv1 1011 :MATVRTPLNFD T0306 34 :G 1bmv1 1022 :S T0306 39 :QCAVAIDNIGAG 1bmv1 1027 :FCQFSVDLLGGG T0306 51 :TGEWVLLVSGSSARQAHKSETSPVDLCVIGIVDEVV 1bmv1 1044 :TGDWITLVQNSPISNLLRVAAWKKGCLMVKVVMSGN Number of specific fragments extracted= 4 number of extra gaps= 2 total=118 Number of alignments=31 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1sqrA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1sqrA expands to /projects/compbio/data/pdb/1sqr.pdb.gz 1sqrA:# T0306 read from 1sqrA/merged-good-all-a2m # 1sqrA read from 1sqrA/merged-good-all-a2m # adding 1sqrA to template set # found chain 1sqrA in template set T0306 30 :IDPQGNPDGQCAVAIDNIGAG 1sqrA 10 :YRRSKENQHNNVMIIKPLDVN T0306 59 :SGSSARQAHKS 1sqrA 31 :SREEASKLIGR Number of specific fragments extracted= 2 number of extra gaps= 0 total=120 Number of alignments=32 # 1sqrA read from 1sqrA/merged-good-all-a2m # found chain 1sqrA in template set T0306 30 :IDPQGNPDGQCAVAIDNIGAG 1sqrA 10 :YRRSKENQHNNVMIIKPLDVN T0306 59 :SGSSARQAHKS 1sqrA 31 :SREEASKLIGR Number of specific fragments extracted= 2 number of extra gaps= 0 total=122 Number of alignments=33 # 1sqrA read from 1sqrA/merged-good-all-a2m # found chain 1sqrA in template set T0306 29 :MIDP 1sqrA 10 :YRRS T0306 34 :GNPDGQCAVAIDNIGAG 1sqrA 14 :KENQHNNVMIIKPLDVN T0306 59 :SGSSARQAHK 1sqrA 31 :SREEASKLIG T0306 69 :SETSPVDLCV 1sqrA 48 :PSGKILKGKI Number of specific fragments extracted= 4 number of extra gaps= 0 total=126 Number of alignments=34 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1xpkA/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/T0306/1xpkA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0306/1xpkA/merged-good-all-a2m.gz for input Trying 1xpkA/merged-good-all-a2m Error: Couldn't open file 1xpkA/merged-good-all-a2m or 1xpkA/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1kmvA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0306 read from 1kmvA/merged-good-all-a2m # 1kmvA read from 1kmvA/merged-good-all-a2m # found chain 1kmvA in training set Warning: unaligning (T0306)S59 because of BadResidue code BAD_PEPTIDE in next template residue (1kmvA)G117 Warning: unaligning (T0306)G60 because of BadResidue code BAD_PEPTIDE at template residue (1kmvA)G117 T0306 19 :LAHD 1kmvA 67 :LKGR T0306 24 :LLMVEMIDPQGNPDGQCAVA 1kmvA 71 :INLVLSRELKEPPQGAHFLS T0306 49 :AGTGEWVLLV 1kmvA 106 :ANKVDMVWIV T0306 61 :SSARQAHKSETSPVDLCVIGI 1kmvA 118 :SSVYKEAMNHPGHLKLFVTRI Number of specific fragments extracted= 4 number of extra gaps= 1 total=130 Number of alignments=35 # 1kmvA read from 1kmvA/merged-good-all-a2m # found chain 1kmvA in training set Warning: unaligning (T0306)S59 because of BadResidue code BAD_PEPTIDE in next template residue (1kmvA)G117 Warning: unaligning (T0306)G60 because of BadResidue code BAD_PEPTIDE at template residue (1kmvA)G117 T0306 19 :LAHD 1kmvA 67 :LKGR T0306 24 :LLMVEMIDPQGNPDGQCAVA 1kmvA 71 :INLVLSRELKEPPQGAHFLS T0306 49 :AGTGEWVLLV 1kmvA 106 :ANKVDMVWIV T0306 61 :SSARQAHKSETSPVDLCVIGI 1kmvA 118 :SSVYKEAMNHPGHLKLFVTRI Number of specific fragments extracted= 4 number of extra gaps= 1 total=134 Number of alignments=36 # 1kmvA read from 1kmvA/merged-good-all-a2m # found chain 1kmvA in training set Warning: unaligning (T0306)S59 because of BadResidue code BAD_PEPTIDE in next template residue (1kmvA)G117 Warning: unaligning (T0306)G60 because of BadResidue code BAD_PEPTIDE at template residue (1kmvA)G117 T0306 19 :LAHD 1kmvA 67 :LKGR T0306 24 :LLMVEMIDPQGNPDGQCAVA 1kmvA 71 :INLVLSRELKEPPQGAHFLS T0306 49 :AGTGEWVLLV 1kmvA 106 :ANKVDMVWIV T0306 61 :SSARQAHKSETSPVDLCVIGI 1kmvA 118 :SSVYKEAMNHPGHLKLFVTRI Number of specific fragments extracted= 4 number of extra gaps= 1 total=138 Number of alignments=37 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2gw6A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2gw6A expands to /projects/compbio/data/pdb/2gw6.pdb.gz 2gw6A:# T0306 read from 2gw6A/merged-good-all-a2m # 2gw6A read from 2gw6A/merged-good-all-a2m # adding 2gw6A to template set # found chain 2gw6A in template set T0306 13 :TVRHHGLA 2gw6A 47 :CVGLPELQ T0306 23 :KLLMVEMIDPQGNP 2gw6A 55 :LICLVGTEIEGEGL T0306 53 :EWVLLVSG 2gw6A 69 :QTVVPTPI T0306 61 :SSARQAHKSETSPVDLCVIG 2gw6A 90 :KASRKLQGDPDLPMSFTLAI T0306 85 :VVSGGQVIFHK 2gw6A 110 :VESDSTIVYYK Number of specific fragments extracted= 5 number of extra gaps= 0 total=143 Number of alignments=38 # 2gw6A read from 2gw6A/merged-good-all-a2m # found chain 2gw6A in template set T0306 13 :TVRHHGLA 2gw6A 47 :CVGLPELQ T0306 23 :KLLMVEMIDPQGNP 2gw6A 55 :LICLVGTEIEGEGL T0306 53 :EWVLLVSG 2gw6A 69 :QTVVPTPI T0306 61 :SSARQAHKSETSPVDLCVIG 2gw6A 90 :KASRKLQGDPDLPMSFTLAI T0306 85 :VVSGGQVIFHK 2gw6A 110 :VESDSTIVYYK Number of specific fragments extracted= 5 number of extra gaps= 0 total=148 Number of alignments=39 # 2gw6A read from 2gw6A/merged-good-all-a2m # found chain 2gw6A in template set T0306 13 :TVRHHGLA 2gw6A 47 :CVGLPELQ T0306 23 :KLLMVEMIDPQGNP 2gw6A 55 :LICLVGTEIEGEGL T0306 53 :EWVLLVSG 2gw6A 69 :QTVVPTPI T0306 61 :SSARQAHKSETSPVDLCVI 2gw6A 90 :KASRKLQGDPDLPMSFTLA T0306 84 :EVVSGGQVIFHK 2gw6A 109 :IVESDSTIVYYK Number of specific fragments extracted= 5 number of extra gaps= 0 total=153 Number of alignments=40 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1zd0A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1zd0A expands to /projects/compbio/data/pdb/1zd0.pdb.gz 1zd0A:Skipped atom 93, because occupancy 0.500 <= existing 0.500 in 1zd0A Skipped atom 95, because occupancy 0.500 <= existing 0.500 in 1zd0A Skipped atom 97, because occupancy 0.500 <= existing 0.500 in 1zd0A Skipped atom 99, because occupancy 0.500 <= existing 0.500 in 1zd0A Skipped atom 101, because occupancy 0.500 <= existing 0.500 in 1zd0A Skipped atom 320, because occupancy 0.350 <= existing 0.650 in 1zd0A Skipped atom 322, because occupancy 0.350 <= existing 0.650 in 1zd0A Skipped atom 324, because occupancy 0.350 <= existing 0.650 in 1zd0A Skipped atom 351, because occupancy 0.350 <= existing 0.650 in 1zd0A Skipped atom 353, because occupancy 0.350 <= existing 0.650 in 1zd0A Skipped atom 355, because occupancy 0.350 <= existing 0.650 in 1zd0A Skipped atom 357, because occupancy 0.350 <= existing 0.650 in 1zd0A Skipped atom 458, because occupancy 0.350 <= existing 0.650 in 1zd0A Skipped atom 460, because occupancy 0.350 <= existing 0.650 in 1zd0A Skipped atom 481, because occupancy 0.350 <= existing 0.650 in 1zd0A Skipped atom 483, because occupancy 0.350 <= existing 0.650 in 1zd0A Skipped atom 485, because occupancy 0.350 <= existing 0.650 in 1zd0A Skipped atom 487, because occupancy 0.350 <= existing 0.650 in 1zd0A Skipped atom 489, because occupancy 0.350 <= existing 0.650 in 1zd0A Skipped atom 496, because occupancy 0.350 <= existing 0.650 in 1zd0A Skipped atom 498, because occupancy 0.350 <= existing 0.650 in 1zd0A Skipped atom 500, because occupancy 0.350 <= existing 0.650 in 1zd0A Skipped atom 502, because occupancy 0.350 <= existing 0.650 in 1zd0A Skipped atom 525, because occupancy 0.350 <= existing 0.650 in 1zd0A Skipped atom 528, because occupancy 0.350 <= existing 0.650 in 1zd0A Skipped atom 634, because occupancy 0.350 <= existing 0.650 in 1zd0A Skipped atom 636, because occupancy 0.350 <= existing 0.650 in 1zd0A Skipped atom 638, because occupancy 0.350 <= existing 0.650 in 1zd0A Skipped atom 640, because occupancy 0.350 <= existing 0.650 in 1zd0A Skipped atom 789, because occupancy 0.250 <= existing 0.750 in 1zd0A Skipped atom 791, because occupancy 0.250 <= existing 0.750 in 1zd0A Skipped atom 793, because occupancy 0.250 <= existing 0.750 in 1zd0A Skipped atom 838, because occupancy 0.350 <= existing 0.650 in 1zd0A Skipped atom 840, because occupancy 0.350 <= existing 0.650 in 1zd0A Skipped atom 901, because occupancy 0.350 <= existing 0.650 in 1zd0A Skipped atom 903, because occupancy 0.350 <= existing 0.650 in 1zd0A Skipped atom 909, because occupancy 0.350 <= existing 0.650 in 1zd0A Skipped atom 911, because occupancy 0.350 <= existing 0.650 in 1zd0A Skipped atom 913, because occupancy 0.350 <= existing 0.650 in 1zd0A Skipped atom 928, because occupancy 0.350 <= existing 0.650 in 1zd0A Skipped atom 930, because occupancy 0.350 <= existing 0.650 in 1zd0A Skipped atom 932, because occupancy 0.350 <= existing 0.650 in 1zd0A Skipped atom 934, because occupancy 0.350 <= existing 0.650 in 1zd0A Skipped atom 966, because occupancy 0.350 <= existing 0.650 in 1zd0A Skipped atom 968, because occupancy 0.350 <= existing 0.650 in 1zd0A Skipped atom 970, because occupancy 0.350 <= existing 0.650 in 1zd0A Skipped atom 972, because occupancy 0.350 <= existing 0.650 in 1zd0A Skipped atom 995, because occupancy 0.350 <= existing 0.650 in 1zd0A Skipped atom 997, because occupancy 0.350 <= existing 0.650 in 1zd0A Skipped atom 999, because occupancy 0.350 <= existing 0.650 in 1zd0A Skipped atom 1001, because occupancy 0.350 <= existing 0.650 in 1zd0A Skipped atom 1003, because occupancy 0.350 <= existing 0.650 in 1zd0A Skipped atom 1026, because occupancy 0.350 <= existing 0.650 in 1zd0A Skipped atom 1028, because occupancy 0.350 <= existing 0.650 in 1zd0A Skipped atom 1030, because occupancy 0.350 <= existing 0.650 in 1zd0A Skipped atom 1032, because occupancy 0.350 <= existing 0.650 in 1zd0A Skipped atom 1081, because occupancy 0.350 <= existing 0.650 in 1zd0A Skipped atom 1083, because occupancy 0.350 <= existing 0.650 in 1zd0A Skipped atom 1085, because occupancy 0.350 <= existing 0.650 in 1zd0A Skipped atom 1087, because occupancy 0.350 <= existing 0.650 in 1zd0A Skipped atom 1089, because occupancy 0.350 <= existing 0.650 in 1zd0A Skipped atom 1128, because occupancy 0.250 <= existing 0.750 in 1zd0A Skipped atom 1130, because occupancy 0.250 <= existing 0.750 in 1zd0A Skipped atom 1132, because occupancy 0.250 <= existing 0.750 in 1zd0A Skipped atom 1134, because occupancy 0.250 <= existing 0.750 in 1zd0A # T0306 read from 1zd0A/merged-good-all-a2m # 1zd0A read from 1zd0A/merged-good-all-a2m # adding 1zd0A to template set # found chain 1zd0A in template set T0306 48 :GAGTGEWVLLVSGSSARQAH 1zd0A 95 :GAKEGENYIVTFGENASALL Number of specific fragments extracted= 1 number of extra gaps= 0 total=154 Number of alignments=41 # 1zd0A read from 1zd0A/merged-good-all-a2m # found chain 1zd0A in template set T0306 48 :GAGTGEWVLLVSGSSARQAH 1zd0A 95 :GAKEGENYIVTFGENASALL Number of specific fragments extracted= 1 number of extra gaps= 0 total=155 Number of alignments=42 # 1zd0A read from 1zd0A/merged-good-all-a2m # found chain 1zd0A in template set T0306 48 :GAGTGEWVLLVSGSSARQAH 1zd0A 95 :GAKEGENYIVTFGENASALL Number of specific fragments extracted= 1 number of extra gaps= 0 total=156 Number of alignments=43 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1i0lA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1i0lA expands to /projects/compbio/data/pdb/1i0l.pdb.gz 1i0lA:# T0306 read from 1i0lA/merged-good-all-a2m # 1i0lA read from 1i0lA/merged-good-all-a2m # adding 1i0lA to template set # found chain 1i0lA in template set T0306 22 :DKLLMVEMIDPQGNPDGQCAVAIDNIGAGTGEWVLLVSG 1i0lA 74 :MEFICVSSYGEGLTSSGQVRMLLDTRHSIEGHHVLIVED T0306 61 :SSARQAHKSETSPVDLCVI 1i0lA 121 :NYLYHMYFTRRPASLKTVV T0306 81 :IVDE 1i0lA 140 :LLDK Number of specific fragments extracted= 3 number of extra gaps= 0 total=159 Number of alignments=44 # 1i0lA read from 1i0lA/merged-good-all-a2m # found chain 1i0lA in template set T0306 22 :DKLLMVEMIDPQGNPDGQCAVAIDNIGAGTGEWVLLVSG 1i0lA 74 :MEFICVSSYGEGLTSSGQVRMLLDTRHSIEGHHVLIVED T0306 61 :SSARQAHKSETSPVDLCVI 1i0lA 121 :NYLYHMYFTRRPASLKTVV T0306 81 :IVDE 1i0lA 140 :LLDK Number of specific fragments extracted= 3 number of extra gaps= 0 total=162 Number of alignments=45 # 1i0lA read from 1i0lA/merged-good-all-a2m # found chain 1i0lA in template set T0306 22 :DKLLMVEMIDPQGNPDGQCAVAIDNIGAGTGEWVLLVSG 1i0lA 74 :MEFICVSSYGEGLTSSGQVRMLLDTRHSIEGHHVLIVED T0306 61 :SSARQAHKS 1i0lA 121 :NYLYHMYFT T0306 71 :TSPVDLCVIGIVD 1i0lA 130 :RRPASLKTVVLLD Number of specific fragments extracted= 3 number of extra gaps= 0 total=165 Number of alignments=46 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2gaeA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2gaeA expands to /projects/compbio/data/pdb/2gae.pdb.gz 2gaeA:# T0306 read from 2gaeA/merged-good-all-a2m # 2gaeA read from 2gaeA/merged-good-all-a2m # adding 2gaeA to template set # found chain 2gaeA in template set Warning: unaligning (T0306)V27 because of BadResidue code BAD_PEPTIDE in next template residue (2gaeA)E294 Warning: unaligning (T0306)E28 because of BadResidue code BAD_PEPTIDE at template residue (2gaeA)E294 T0306 12 :CTVRHHGLAHDKLLM 2gaeA 278 :VASDRSIIPPGTTLL T0306 29 :MI 2gaeA 295 :VP T0306 31 :DPQGNPDG 2gaeA 299 :DNNGKFNG T0306 39 :QCAVAIDNIGAGTGEWVLLV 2gaeA 311 :RLMVALDVGGAIKGQHFDIY T0306 59 :SGSSARQAHKSETSPVDLCVI 2gaeA 333 :IGPEAGHRAGWYNHYGRVWVL Number of specific fragments extracted= 5 number of extra gaps= 1 total=170 Number of alignments=47 # 2gaeA read from 2gaeA/merged-good-all-a2m # found chain 2gaeA in template set Warning: unaligning (T0306)V27 because of BadResidue code BAD_PEPTIDE in next template residue (2gaeA)E294 Warning: unaligning (T0306)E28 because of BadResidue code BAD_PEPTIDE at template residue (2gaeA)E294 T0306 12 :CTVRHHGLAHDKLLM 2gaeA 278 :VASDRSIIPPGTTLL T0306 29 :MI 2gaeA 295 :VP T0306 31 :DPQGNPDG 2gaeA 299 :DNNGKFNG T0306 39 :QCAVAIDNIGAGTGEWVLLVS 2gaeA 311 :RLMVALDVGGAIKGQHFDIYQ T0306 60 :GSSARQAHKSETSPVDLCVI 2gaeA 334 :GPEAGHRAGWYNHYGRVWVL Number of specific fragments extracted= 5 number of extra gaps= 1 total=175 Number of alignments=48 # 2gaeA read from 2gaeA/merged-good-all-a2m # found chain 2gaeA in template set Warning: unaligning (T0306)V27 because of BadResidue code BAD_PEPTIDE in next template residue (2gaeA)E294 Warning: unaligning (T0306)E28 because of BadResidue code BAD_PEPTIDE at template residue (2gaeA)E294 T0306 11 :VCTVRHHGLAHDKLLM 2gaeA 277 :SVASDRSIIPPGTTLL T0306 29 :MI 2gaeA 295 :VP T0306 31 :DPQGNPDGQC 2gaeA 299 :DNNGKFNGQY T0306 41 :AVAIDNIGAGTGEWVLLV 2gaeA 313 :MVALDVGGAIKGQHFDIY T0306 59 :SGSSARQAHKSETSPVDLCVI 2gaeA 333 :IGPEAGHRAGWYNHYGRVWVL Number of specific fragments extracted= 5 number of extra gaps= 1 total=180 Number of alignments=49 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1q5qH/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/T0306/1q5qH/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0306/1q5qH/merged-good-all-a2m.gz for input Trying 1q5qH/merged-good-all-a2m Error: Couldn't open file 1q5qH/merged-good-all-a2m or 1q5qH/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1wucA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1wucA expands to /projects/compbio/data/pdb/1wuc.pdb.gz 1wucA:Skipped atom 479, because occupancy 0.500 <= existing 0.500 in 1wucA Skipped atom 481, because occupancy 0.500 <= existing 0.500 in 1wucA Skipped atom 483, because occupancy 0.500 <= existing 0.500 in 1wucA Skipped atom 1669, because occupancy 0.500 <= existing 0.500 in 1wucA Skipped atom 1671, because occupancy 0.500 <= existing 0.500 in 1wucA Skipped atom 1787, because occupancy 0.500 <= existing 0.500 in 1wucA Skipped atom 1789, because occupancy 0.500 <= existing 0.500 in 1wucA Skipped atom 1893, because occupancy 0.500 <= existing 0.500 in 1wucA Skipped atom 1895, because occupancy 0.500 <= existing 0.500 in 1wucA # T0306 read from 1wucA/merged-good-all-a2m # 1wucA read from 1wucA/merged-good-all-a2m # adding 1wucA to template set # found chain 1wucA in template set T0306 20 :AHDKLLMVEMIDPQGN 1wucA 45 :DDKRFVLVDITTTSKK T0306 39 :QCAVAIDNIG 1wucA 61 :TVKVAIDVTD T0306 76 :LCVIGIVDEVVS 1wucA 71 :VYVVGYQDKWDG T0306 90 :QVI 1wucA 83 :KDR Number of specific fragments extracted= 4 number of extra gaps= 0 total=184 Number of alignments=50 # 1wucA read from 1wucA/merged-good-all-a2m # found chain 1wucA in template set T0306 20 :AHDKLLMVEMIDPQGN 1wucA 45 :DDKRFVLVDITTTSKK T0306 39 :QCAVAIDNIG 1wucA 61 :TVKVAIDVTD T0306 76 :LCVIGIVDEVVS 1wucA 71 :VYVVGYQDKWDG T0306 90 :QVI 1wucA 83 :KDR Number of specific fragments extracted= 4 number of extra gaps= 0 total=188 Number of alignments=51 # 1wucA read from 1wucA/merged-good-all-a2m # found chain 1wucA in template set T0306 21 :HDKLLMVEMIDPQGN 1wucA 46 :DKRFVLVDITTTSKK T0306 39 :QCAVAIDN 1wucA 61 :TVKVAIDV T0306 74 :VDLCVIGIVDEV 1wucA 69 :TDVYVVGYQDKW T0306 88 :GGQVIF 1wucA 81 :DGKDRA Number of specific fragments extracted= 4 number of extra gaps= 0 total=192 Number of alignments=52 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ryp2/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1ryp2 expands to /projects/compbio/data/pdb/1ryp.pdb.gz 1ryp2:# T0306 read from 1ryp2/merged-good-all-a2m # 1ryp2 read from 1ryp2/merged-good-all-a2m # adding 1ryp2 to template set # found chain 1ryp2 in template set T0306 9 :QIVCTVRH 1ryp2 1 :TSVISMKY T0306 37 :DGQCAVAIDNIG 1ryp2 9 :DNGVIIAADNLG T0306 49 :AGTGEWVLLV 1ryp2 37 :VGDNTVVGIS T0306 83 :DE 1ryp2 47 :GD Number of specific fragments extracted= 4 number of extra gaps= 0 total=196 Number of alignments=53 # 1ryp2 read from 1ryp2/merged-good-all-a2m # found chain 1ryp2 in template set T0306 9 :QIVCTVRH 1ryp2 1 :TSVISMKY T0306 37 :DGQCAVAIDNIG 1ryp2 9 :DNGVIIAADNLG T0306 49 :AGTGEWVLLV 1ryp2 37 :VGDNTVVGIS T0306 83 :DE 1ryp2 47 :GD Number of specific fragments extracted= 4 number of extra gaps= 0 total=200 Number of alignments=54 # 1ryp2 read from 1ryp2/merged-good-all-a2m # found chain 1ryp2 in template set T0306 9 :QIVCTVRHH 1ryp2 1 :TSVISMKYD T0306 38 :GQCAVAIDNIG 1ryp2 10 :NGVIIAADNLG T0306 49 :AGTGEWVLLVSG 1ryp2 37 :VGDNTVVGISGD T0306 61 :SSARQA 1ryp2 53 :QHIERL T0306 67 :HKSETSPV 1ryp2 73 :ADAEEALE T0306 75 :DLCVIGIVDEVVSGGQVIF 1ryp2 101 :PLWNAIIVAGVQSNGDQFL Number of specific fragments extracted= 6 number of extra gaps= 0 total=206 Number of alignments=55 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1v04A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1v04A expands to /projects/compbio/data/pdb/1v04.pdb.gz 1v04A:# T0306 read from 1v04A/merged-good-all-a2m # 1v04A read from 1v04A/merged-good-all-a2m # adding 1v04A to template set # found chain 1v04A in template set Warning: unaligning (T0306)I47 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1v04A)S272 Warning: unaligning (T0306)G48 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1v04A)S272 Warning: unaligning (T0306)K68 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1v04A)D295 Warning: unaligning (T0306)S69 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1v04A)D295 T0306 9 :QIVCTV 1v04A 234 :YVYIAE T0306 19 :LAHDKLLMVE 1v04A 240 :LLAHKIHVYE T0306 30 :IDPQGNPDGQCAV 1v04A 250 :KHANWTLTPLRVL T0306 43 :AIDN 1v04A 267 :LVDN T0306 49 :AGT 1v04A 273 :VDP T0306 52 :GEWVLLVSGSSARQAH 1v04A 278 :GDLWVGCHPNGMRIFF T0306 70 :ETSPVDLCVIGIVDEVVSGGQV 1v04A 296 :AENPPGSEVLRIQDILSEEPKV Number of specific fragments extracted= 7 number of extra gaps= 2 total=213 Number of alignments=56 # 1v04A read from 1v04A/merged-good-all-a2m # found chain 1v04A in template set Warning: unaligning (T0306)I47 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1v04A)S272 Warning: unaligning (T0306)G48 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1v04A)S272 Warning: unaligning (T0306)K68 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1v04A)D295 Warning: unaligning (T0306)S69 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1v04A)D295 T0306 9 :QIVCTV 1v04A 234 :YVYIAE T0306 19 :LAHDKLLMVE 1v04A 240 :LLAHKIHVYE T0306 30 :IDPQGNPDGQCAV 1v04A 250 :KHANWTLTPLRVL T0306 43 :AIDN 1v04A 267 :LVDN T0306 49 :AGT 1v04A 273 :VDP T0306 52 :GEWVLLVSGSSARQAH 1v04A 278 :GDLWVGCHPNGMRIFF T0306 70 :ETSPVDLCVIGIVDEVVSGGQV 1v04A 296 :AENPPGSEVLRIQDILSEEPKV Number of specific fragments extracted= 7 number of extra gaps= 2 total=220 Number of alignments=57 # 1v04A read from 1v04A/merged-good-all-a2m # found chain 1v04A in template set Warning: unaligning (T0306)I47 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1v04A)S272 Warning: unaligning (T0306)G48 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1v04A)S272 Warning: unaligning (T0306)K68 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1v04A)D295 Warning: unaligning (T0306)S69 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1v04A)D295 T0306 8 :GQIVCTV 1v04A 233 :KYVYIAE T0306 19 :LAHDKLLMVE 1v04A 240 :LLAHKIHVYE T0306 30 :IDPQGNPDGQCAV 1v04A 250 :KHANWTLTPLRVL T0306 43 :AIDN 1v04A 267 :LVDN T0306 49 :A 1v04A 273 :V T0306 50 :GTGEWVLLVSGSSARQAH 1v04A 276 :VTGDLWVGCHPNGMRIFF T0306 70 :ETSPVDLCVIGI 1v04A 296 :AENPPGSEVLRI T0306 83 :DEVVSGGQ 1v04A 308 :QDILSEEP Number of specific fragments extracted= 8 number of extra gaps= 2 total=228 Number of alignments=58 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1kekA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1kekA expands to /projects/compbio/data/pdb/1kek.pdb.gz 1kekA:# T0306 read from 1kekA/merged-good-all-a2m # 1kekA read from 1kekA/merged-good-all-a2m # adding 1kekA to template set # found chain 1kekA in template set T0306 44 :IDNIGAGTGEWVLLVSGSSAR 1kekA 261 :FDYVGAPDAERVIVSMGSSCE T0306 65 :QAHKSETSPVDLCVI 1kekA 288 :NHLAAKGEKIGLIKV Number of specific fragments extracted= 2 number of extra gaps= 0 total=230 Number of alignments=59 # 1kekA read from 1kekA/merged-good-all-a2m # found chain 1kekA in template set T0306 44 :IDNIGAGTGEWVLLVSGSSAR 1kekA 261 :FDYVGAPDAERVIVSMGSSCE T0306 65 :QAHKSETSPVDLCVIG 1kekA 288 :NHLAAKGEKIGLIKVR Number of specific fragments extracted= 2 number of extra gaps= 0 total=232 Number of alignments=60 # 1kekA read from 1kekA/merged-good-all-a2m # found chain 1kekA in template set T0306 44 :IDNIGAGTGEWVLLVSGSS 1kekA 261 :FDYVGAPDAERVIVSMGSS T0306 63 :ARQAH 1kekA 287 :INHLA T0306 69 :SETSPVDLCVIGIV 1kekA 292 :AKGEKIGLIKVRLY Number of specific fragments extracted= 3 number of extra gaps= 0 total=235 Number of alignments=61 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1hxmA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1hxmA expands to /projects/compbio/data/pdb/1hxm.pdb.gz 1hxmA:# T0306 read from 1hxmA/merged-good-all-a2m # 1hxmA read from 1hxmA/merged-good-all-a2m # adding 1hxmA to template set # found chain 1hxmA in template set T0306 8 :GQIVCTVRHHGLAHDKLLMVEMI 1hxmA 19 :ATLRCSMKGEAIGNYYINWYRKT T0306 34 :GNPDGQCAVAID 1hxmA 58 :PGFKDNFQGDID T0306 49 :AGTGEWVLLVSG 1hxmA 70 :IAKNLAVLKILA T0306 72 :SPVDLCVIGIVDEVVSGGQV 1hxmA 84 :ERDEGSYYCACDTLGMGGEY Number of specific fragments extracted= 4 number of extra gaps= 0 total=239 Number of alignments=62 # 1hxmA read from 1hxmA/merged-good-all-a2m # found chain 1hxmA in template set T0306 8 :GQIVCTVRHHGLAHDKLLMVEMI 1hxmA 19 :ATLRCSMKGEAIGNYYINWYRKT T0306 34 :GNPDGQCAVAID 1hxmA 58 :PGFKDNFQGDID T0306 49 :AGTGEWVLLVSG 1hxmA 70 :IAKNLAVLKILA T0306 73 :PVDLCVIGIVDEVVSGGQV 1hxmA 85 :RDEGSYYCACDTLGMGGEY Number of specific fragments extracted= 4 number of extra gaps= 0 total=243 Number of alignments=63 # 1hxmA read from 1hxmA/merged-good-all-a2m # found chain 1hxmA in template set T0306 8 :GQIVCTVRHHGLAHDKLLMVEMIDPQGN 1hxmA 19 :ATLRCSMKGEAIGNYYINWYRKTQGNTM T0306 36 :PDGQCAVAID 1hxmA 60 :FKDNFQGDID T0306 49 :AGTGEWVLLV 1hxmA 70 :IAKNLAVLKI Number of specific fragments extracted= 3 number of extra gaps= 0 total=246 Number of alignments=64 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1y2tA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1y2tA expands to /projects/compbio/data/pdb/1y2t.pdb.gz 1y2tA:# T0306 read from 1y2tA/merged-good-all-a2m # 1y2tA read from 1y2tA/merged-good-all-a2m # adding 1y2tA to template set # found chain 1y2tA in template set T0306 2 :KLAVVTGQIVCTVRH 1y2tA 33 :TWDEVRGEYVLTMGG T0306 21 :HDKLLMVEMIDPQ 1y2tA 48 :SGTSGSLRFVSSD T0306 37 :DGQCAVAI 1y2tA 61 :TDESFVAT T0306 47 :IGAGTGEWVL 1y2tA 69 :FGVHNYKRWC T0306 80 :GIVDEV 1y2tA 79 :DIVTNL Number of specific fragments extracted= 5 number of extra gaps= 0 total=251 Number of alignments=65 # 1y2tA read from 1y2tA/merged-good-all-a2m # found chain 1y2tA in template set T0306 2 :KLAVVTGQIVCTVRH 1y2tA 33 :TWDEVRGEYVLTMGG T0306 21 :HDKLLMVEMIDPQ 1y2tA 48 :SGTSGSLRFVSSD T0306 37 :DGQCAVAI 1y2tA 61 :TDESFVAT T0306 47 :IGAGTGEWVL 1y2tA 69 :FGVHNYKRWC T0306 80 :GIVDEV 1y2tA 79 :DIVTNL Number of specific fragments extracted= 5 number of extra gaps= 0 total=256 Number of alignments=66 # 1y2tA read from 1y2tA/merged-good-all-a2m # found chain 1y2tA in template set T0306 2 :KLAVVTGQIVCTVRHH 1y2tA 33 :TWDEVRGEYVLTMGGS T0306 22 :DKLLMVEMIDPQ 1y2tA 49 :GTSGSLRFVSSD T0306 37 :DGQCAVAI 1y2tA 61 :TDESFVAT T0306 47 :IGAGTGEWVLL 1y2tA 69 :FGVHNYKRWCD Number of specific fragments extracted= 4 number of extra gaps= 0 total=260 Number of alignments=67 # command:# PrintAlignmentsContacts allconstraints.under Using radius: 8.0000 NUMB_ALIGNS: 67 Done printing distance constraints # command: