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/T0285/ # command:# Making conformation for sequence T0285 numbered 1 through 125 Created new target T0285 from T0285.a2m # command:# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/T0285/ # command:Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0285//projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0285/manyalignments-good-all.under or /projects/compbio/experiments/protein-predict/casp7/T0285//projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0285/manyalignments-good-all.under.gz for input Trying /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0285/manyalignments-good-all.under # reading script from file /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0285/manyalignments-good-all.under # Reading fragments from alignment file # Attempting to read fragment alignments from file 1bx0A/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/T0285/1bx0A/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0285/1bx0A/merged-good-all-a2m.gz for input Trying 1bx0A/merged-good-all-a2m Error: Couldn't open file 1bx0A/merged-good-all-a2m or 1bx0A/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ifrA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0285 read from 1ifrA/merged-good-all-a2m # 1ifrA read from 1ifrA/merged-good-all-a2m # found chain 1ifrA in training set T0285 34 :AMPNWSLR 1ifrA 463 :SMGNWQIK # choosing archetypes in rotamer library T0285 46 :VDRNNQDLLKRPLPPG 1ifrA 471 :RQNGDDPLLTYRFPPK T0285 62 :IMVLAPRLTAKHPYDK 1ifrA 495 :VTIWAAGAGATHSPPT T0285 78 :VQDRN 1ifrA 514 :WKAQN T0285 91 :TLNDGNSVKVVTISAGRD 1ifrA 519 :TWGCGNSLRTALINSTGE Number of specific fragments extracted= 5 number of extra gaps= 0 total=5 Number of alignments=1 # 1ifrA read from 1ifrA/merged-good-all-a2m # found chain 1ifrA in training set T0285 34 :AMPNWSLR 1ifrA 463 :SMGNWQIK T0285 46 :VDRNNQDLLKRPLPPGI 1ifrA 471 :RQNGDDPLLTYRFPPKF T0285 91 :TLNDGNSVKVVTISAGRDEGPDR 1ifrA 488 :TLKAGQVVTIWAAGAGATHSPPT Number of specific fragments extracted= 3 number of extra gaps= 0 total=8 Number of alignments=2 # 1ifrA read from 1ifrA/merged-good-all-a2m # found chain 1ifrA in training set T0285 34 :AMPNWSLR 1ifrA 463 :SMGNWQIK T0285 46 :VDRNNQDLLKRPLPPG 1ifrA 471 :RQNGDDPLLTYRFPPK T0285 62 :IMVLAPRLTAKHPYDK 1ifrA 495 :VTIWAAGAGATHSPPT T0285 78 :VQDRN 1ifrA 514 :WKAQN T0285 91 :TLNDGNSVKVVTISAGRD 1ifrA 519 :TWGCGNSLRTALINSTGE Number of specific fragments extracted= 5 number of extra gaps= 0 total=13 Number of alignments=3 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1kz9A/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/T0285/1kz9A/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0285/1kz9A/merged-good-all-a2m.gz for input Trying 1kz9A/merged-good-all-a2m Error: Couldn't open file 1kz9A/merged-good-all-a2m or 1kz9A/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1iq3A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1iq3A expands to /projects/compbio/data/pdb/1iq3.pdb.gz 1iq3A:# T0285 read from 1iq3A/merged-good-all-a2m # 1iq3A read from 1iq3A/merged-good-all-a2m # adding 1iq3A to template set # found chain 1iq3A in template set T0285 72 :KHPYDKVQDRNRKLY 1iq3A 18 :EEQREYYVNQFRSLQ T0285 93 :NDGNSVK 1iq3A 33 :PDPSSFI T0285 102 :T 1iq3A 40 :S T0285 103 :ISAGRDEGPDRDIIWEMF 1iq3A 48 :FTKSKLSIPELSYIWELS Number of specific fragments extracted= 4 number of extra gaps= 0 total=17 Number of alignments=4 # 1iq3A read from 1iq3A/merged-good-all-a2m # found chain 1iq3A in template set T0285 58 :LPPG 1iq3A 9 :YPDE T0285 67 :PRLTAKHPYDKVQDRNRKLY 1iq3A 13 :PWRITEEQREYYVNQFRSLQ T0285 93 :NDGNSVK 1iq3A 33 :PDPSSFI T0285 102 :T 1iq3A 40 :S T0285 103 :ISAGRDEGPDRDIIWEMF 1iq3A 48 :FTKSKLSIPELSYIWELS Number of specific fragments extracted= 5 number of extra gaps= 0 total=22 Number of alignments=5 # 1iq3A read from 1iq3A/merged-good-all-a2m # found chain 1iq3A in template set T0285 72 :KHPYDKVQDRNRKLY 1iq3A 18 :EEQREYYVNQFRSLQ T0285 93 :NDGNSVK 1iq3A 33 :PDPSSFI T0285 102 :T 1iq3A 40 :S T0285 103 :ISAGRDEGPDRDIIWEMF 1iq3A 48 :FTKSKLSIPELSYIWELS Number of specific fragments extracted= 4 number of extra gaps= 0 total=26 Number of alignments=6 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1b65A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1b65A expands to /projects/compbio/data/pdb/1b65.pdb.gz 1b65A:# T0285 read from 1b65A/merged-good-all-a2m # 1b65A read from 1b65A/merged-good-all-a2m # adding 1b65A to template set # found chain 1b65A in template set T0285 32 :LRAMPNWSLRFVYIVDRNNQDLLKRPLPPGIMVLAPRLTAKHPY 1b65A 29 :ITDVDGVGVGFQTIIENEPRPGRKRPARSGVTAILPHMQSETPV T0285 84 :KLYG 1b65A 73 :PVYA T0285 99 :KVVTISAGR 1b65A 77 :GVHRFNGNG Number of specific fragments extracted= 3 number of extra gaps= 0 total=29 Number of alignments=7 # 1b65A read from 1b65A/merged-good-all-a2m # found chain 1b65A in template set T0285 32 :LRAMPNWSLRFVYIVDRNNQDLLKRPLPPGIMVLAPRLTAKHPY 1b65A 29 :ITDVDGVGVGFQTIIENEPRPGRKRPARSGVTAILPHMQSETPV T0285 84 :KLYG 1b65A 73 :PVYA T0285 99 :KVVTISAGR 1b65A 77 :GVHRFNGNG Number of specific fragments extracted= 3 number of extra gaps= 0 total=32 Number of alignments=8 # 1b65A read from 1b65A/merged-good-all-a2m # found chain 1b65A in template set T0285 32 :LRAMPNWSLRFVYIVDRNNQDLLKRPLPPGIMVLAPRLTAKHPY 1b65A 29 :ITDVDGVGVGFQTIIENEPRPGRKRPARSGVTAILPHMQSETPV T0285 84 :KLYG 1b65A 73 :PVYA T0285 99 :KVVTISAGR 1b65A 77 :GVHRFNGNG Number of specific fragments extracted= 3 number of extra gaps= 0 total=35 Number of alignments=9 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1frn/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/T0285/1frn/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0285/1frn/merged-good-all-a2m.gz for input Trying 1frn/merged-good-all-a2m Error: Couldn't open file 1frn/merged-good-all-a2m or 1frn/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1qfzA/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/T0285/1qfzA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0285/1qfzA/merged-good-all-a2m.gz for input Trying 1qfzA/merged-good-all-a2m Error: Couldn't open file 1qfzA/merged-good-all-a2m or 1qfzA/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1qgaA/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/T0285/1qgaA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0285/1qgaA/merged-good-all-a2m.gz for input Trying 1qgaA/merged-good-all-a2m Error: Couldn't open file 1qgaA/merged-good-all-a2m or 1qgaA/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1fjrA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1fjrA expands to /projects/compbio/data/pdb/1fjr.pdb.gz 1fjrA:# T0285 read from 1fjrA/merged-good-all-a2m # 1fjrA read from 1fjrA/merged-good-all-a2m # adding 1fjrA to template set # found chain 1fjrA in template set T0285 25 :TQQLTQDLRA 1fjrA 87 :SDEELAELDP T0285 43 :VYIVDRNNQDLLKRPLPPGIMVLAP 1fjrA 97 :FLNVTLDDGSVSRRHFKNELIVQWD T0285 68 :R 1fjrA 135 :R T0285 69 :LTAKH 1fjrA 143 :LFENG T0285 74 :PYDKVQDRNRKLYGRHITLNDGNS 1fjrA 152 :HFDRVTLRKREYCLQHLTFADGNA T0285 98 :VKVVTISA 1fjrA 178 :IRIAPHNC Number of specific fragments extracted= 6 number of extra gaps= 0 total=41 Number of alignments=10 # 1fjrA read from 1fjrA/merged-good-all-a2m # found chain 1fjrA in template set T0285 25 :TQQLTQDLRA 1fjrA 87 :SDEELAELDP T0285 43 :VYIVDRNNQDLLKRPLPPGIMVLAP 1fjrA 97 :FLNVTLDDGSVSRRHFKNELIVQWD T0285 68 :RLTAKH 1fjrA 135 :REEQDK T0285 74 :PYDKVQDRNRKLYGRHITLNDGNSVKVVTI 1fjrA 152 :HFDRVTLRKREYCLQHLTFADGNATSIRIA Number of specific fragments extracted= 4 number of extra gaps= 0 total=45 Number of alignments=11 # 1fjrA read from 1fjrA/merged-good-all-a2m # found chain 1fjrA in template set T0285 25 :TQQLTQDLRA 1fjrA 87 :SDEELAELDP T0285 43 :VYIVDRNNQDLLKRPLPPGIMVLAP 1fjrA 97 :FLNVTLDDGSVSRRHFKNELIVQWD T0285 68 :R 1fjrA 135 :R T0285 69 :LTAKH 1fjrA 143 :LFENG T0285 74 :PYDKVQDRNRKLYGRHITLNDGNS 1fjrA 152 :HFDRVTLRKREYCLQHLTFADGNA T0285 98 :VKVVTISA 1fjrA 178 :IRIAPHNC Number of specific fragments extracted= 6 number of extra gaps= 0 total=51 Number of alignments=12 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2a59A/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/T0285/2a59A/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0285/2a59A/merged-good-all-a2m.gz for input Trying 2a59A/merged-good-all-a2m Error: Couldn't open file 2a59A/merged-good-all-a2m or 2a59A/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1bawA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1bawA expands to /projects/compbio/data/pdb/1baw.pdb.gz 1bawA:# T0285 read from 1bawA/merged-good-all-a2m # 1bawA read from 1bawA/merged-good-all-a2m # adding 1bawA to template set # found chain 1bawA in template set Warning: unaligning (T0285)S104 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1bawA)C89 Warning: unaligning (T0285)A105 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1bawA)C89 T0285 35 :MPNWSLRFVY 1bawA 24 :HPGDTVKWVN T0285 55 :KRPLPPGIM 1bawA 34 :NKLPPHNIL T0285 69 :LTAKHPYDKVQDRNRKLY 1bawA 43 :FDDKQVPGASKELADKLS T0285 87 :GRHITLNDGNSVKVVTI 1bawA 71 :SYEITFSSDFPAGTYTY T0285 106 :GRDEGPD 1bawA 90 :APHRGAG Number of specific fragments extracted= 5 number of extra gaps= 1 total=56 Number of alignments=13 # 1bawA read from 1bawA/merged-good-all-a2m # found chain 1bawA in template set T0285 35 :MPNWSLRFVY 1bawA 24 :HPGDTVKWVN T0285 55 :KRPLPPGIMVLAPRL 1bawA 34 :NKLPPHNILFDDKQV T0285 75 :YDKVQDRNRKLY 1bawA 49 :PGASKELADKLS Number of specific fragments extracted= 3 number of extra gaps= 0 total=59 Number of alignments=14 # 1bawA read from 1bawA/merged-good-all-a2m # found chain 1bawA in template set Warning: unaligning (T0285)S104 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1bawA)C89 Warning: unaligning (T0285)A105 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1bawA)C89 T0285 35 :MPNWSLRFVY 1bawA 24 :HPGDTVKWVN T0285 55 :KRPLPPGIM 1bawA 34 :NKLPPHNIL T0285 69 :LTAKHPYDKVQDRNRKLY 1bawA 43 :FDDKQVPGASKELADKLS T0285 87 :GRHITLNDGNSVKVVTI 1bawA 71 :SYEITFSSDFPAGTYTY T0285 106 :GRDEGPD 1bawA 90 :APHRGAG Number of specific fragments extracted= 5 number of extra gaps= 1 total=64 Number of alignments=15 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1c41A/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/T0285/1c41A/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0285/1c41A/merged-good-all-a2m.gz for input Trying 1c41A/merged-good-all-a2m Error: Couldn't open file 1c41A/merged-good-all-a2m or 1c41A/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1qg0A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1qg0A expands to /projects/compbio/data/pdb/1qg0.pdb.gz 1qg0A:# T0285 read from 1qg0A/merged-good-all-a2m # 1qg0A read from 1qg0A/merged-good-all-a2m # adding 1qg0A to template set # found chain 1qg0A in template set T0285 37 :NWSLRFV 1qg0A 49 :GETWHMV T0285 45 :IVDRN 1qg0A 56 :FSTEG T0285 55 :KRPLPPG 1qg0A 61 :EVPYREG T0285 62 :IMVLAPRLTAKHPYD 1qg0A 70 :IGIVPDGIDKNGKPH T0285 84 :KL 1qg0A 85 :KL T0285 88 :RHITL 1qg0A 87 :RLYSI T0285 93 :NDGNSVKVVTI 1qg0A 100 :GDSKTVSLCVK T0285 104 :SAGRDEGPDRDIIWEMFLENLE 1qg0A 113 :VYTNDAGEVVKGVCSNFLCDLK Number of specific fragments extracted= 8 number of extra gaps= 0 total=72 Number of alignments=16 # 1qg0A read from 1qg0A/merged-good-all-a2m # found chain 1qg0A in template set T0285 64 :VLAPR 1qg0A 72 :IVPDG T0285 79 :QDRNRKLYG 1qg0A 77 :IDKNGKPHK T0285 88 :RHITL 1qg0A 87 :RLYSI T0285 93 :NDGNSVKVVTI 1qg0A 100 :GDSKTVSLCVK T0285 104 :SAGRDEGPDR 1qg0A 113 :VYTNDAGEVV T0285 114 :DIIWEMFLE 1qg0A 124 :GVCSNFLCD T0285 124 :L 1qg0A 133 :L Number of specific fragments extracted= 7 number of extra gaps= 0 total=79 Number of alignments=17 # 1qg0A read from 1qg0A/merged-good-all-a2m # found chain 1qg0A in template set T0285 37 :NWSLRFV 1qg0A 49 :GETWHMV T0285 45 :IVDRN 1qg0A 56 :FSTEG T0285 55 :KRPLPPG 1qg0A 61 :EVPYREG T0285 62 :IMVLAPRLTAKHPYD 1qg0A 70 :IGIVPDGIDKNGKPH T0285 84 :KL 1qg0A 85 :KL T0285 88 :RHITL 1qg0A 87 :RLYSI T0285 93 :NDGNSVKVVTI 1qg0A 100 :GDSKTVSLCVK T0285 104 :SAGRDEGPDRDIIWEMFLENLE 1qg0A 113 :VYTNDAGEVVKGVCSNFLCDLK Number of specific fragments extracted= 8 number of extra gaps= 0 total=87 Number of alignments=18 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1kz4A/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/T0285/1kz4A/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0285/1kz4A/merged-good-all-a2m.gz for input Trying 1kz4A/merged-good-all-a2m Error: Couldn't open file 1kz4A/merged-good-all-a2m or 1kz4A/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1b2rA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1b2rA expands to /projects/compbio/data/pdb/1b2r.pdb.gz 1b2rA:# T0285 read from 1b2rA/merged-good-all-a2m # 1b2rA read from 1b2rA/merged-good-all-a2m # adding 1b2rA to template set # found chain 1b2rA in template set Warning: unaligning (T0285)K72 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1b2rA)H106 Warning: unaligning (T0285)H73 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1b2rA)H106 Warning: unaligning (T0285)P74 because of BadResidue code BAD_PEPTIDE in next template residue (1b2rA)E108 Warning: unaligning (T0285)Y75 because of BadResidue code BAD_PEPTIDE at template residue (1b2rA)E108 Warning: unaligning (T0285)N82 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1b2rA)E111 Warning: unaligning (T0285)R83 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1b2rA)E111 T0285 33 :RAMPNWSLRFVYIV 1b2rA 69 :KNGKPEKLRLYSIA T0285 47 :DRNNQDLLK 1b2rA 84 :TRHGDDVDD T0285 60 :PGIMVLAPRLTA 1b2rA 93 :KTISLCVRQLEY T0285 76 :D 1b2rA 109 :S T0285 84 :KLYG 1b2rA 112 :TVYG T0285 92 :LNDGNSVKVVTISAGRDEGPD 1b2rA 124 :IEPGSEVKITGPVGKEMLLPD Number of specific fragments extracted= 6 number of extra gaps= 2 total=93 Number of alignments=19 # 1b2rA read from 1b2rA/merged-good-all-a2m # found chain 1b2rA in template set Warning: unaligning (T0285)K72 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1b2rA)H106 Warning: unaligning (T0285)H73 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1b2rA)H106 Warning: unaligning (T0285)P74 because of BadResidue code BAD_PEPTIDE in next template residue (1b2rA)E108 Warning: unaligning (T0285)Y75 because of BadResidue code BAD_PEPTIDE at template residue (1b2rA)E108 Warning: unaligning (T0285)N82 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1b2rA)E111 Warning: unaligning (T0285)R83 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1b2rA)E111 T0285 23 :R 1b2rA 69 :K T0285 34 :AMPNWSLRFVYIV 1b2rA 70 :NGKPEKLRLYSIA T0285 47 :DRNNQDLLKR 1b2rA 84 :TRHGDDVDDK T0285 61 :GIMVLAPRLTA 1b2rA 94 :TISLCVRQLEY T0285 81 :R 1b2rA 109 :S T0285 84 :KLYG 1b2rA 112 :TVYG T0285 92 :LNDGNSVKVVTISAGRDEGPD 1b2rA 124 :IEPGSEVKITGPVGKEMLLPD Number of specific fragments extracted= 7 number of extra gaps= 2 total=100 Number of alignments=20 # 1b2rA read from 1b2rA/merged-good-all-a2m # found chain 1b2rA in template set Warning: unaligning (T0285)K72 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1b2rA)H106 Warning: unaligning (T0285)H73 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1b2rA)H106 Warning: unaligning (T0285)P74 because of BadResidue code BAD_PEPTIDE in next template residue (1b2rA)E108 Warning: unaligning (T0285)Y75 because of BadResidue code BAD_PEPTIDE at template residue (1b2rA)E108 Warning: unaligning (T0285)N82 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1b2rA)E111 Warning: unaligning (T0285)R83 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1b2rA)E111 T0285 33 :RAMPNWSLRFVYIV 1b2rA 69 :KNGKPEKLRLYSIA T0285 47 :DRNNQDLLK 1b2rA 84 :TRHGDDVDD T0285 60 :PGIMVLAPRLTA 1b2rA 93 :KTISLCVRQLEY T0285 76 :D 1b2rA 109 :S T0285 84 :KLYG 1b2rA 112 :TVYG T0285 92 :LNDGNSVKVVTISAGRDEGPD 1b2rA 124 :IEPGSEVKITGPVGKEMLLPD Number of specific fragments extracted= 6 number of extra gaps= 2 total=106 Number of alignments=21 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2lao/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/T0285/2lao/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0285/2lao/merged-good-all-a2m.gz for input Trying 2lao/merged-good-all-a2m Error: Couldn't open file 2lao/merged-good-all-a2m or 2lao/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1frqA/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/T0285/1frqA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0285/1frqA/merged-good-all-a2m.gz for input Trying 1frqA/merged-good-all-a2m Error: Couldn't open file 1frqA/merged-good-all-a2m or 1frqA/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1kz6A/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/T0285/1kz6A/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0285/1kz6A/merged-good-all-a2m.gz for input Trying 1kz6A/merged-good-all-a2m Error: Couldn't open file 1kz6A/merged-good-all-a2m or 1kz6A/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1sm4A/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/T0285/1sm4A/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0285/1sm4A/merged-good-all-a2m.gz for input Trying 1sm4A/merged-good-all-a2m Error: Couldn't open file 1sm4A/merged-good-all-a2m or 1sm4A/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1t8cA/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/T0285/1t8cA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0285/1t8cA/merged-good-all-a2m.gz for input Trying 1t8cA/merged-good-all-a2m Error: Couldn't open file 1t8cA/merged-good-all-a2m or 1t8cA/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ivtA/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/T0285/1ivtA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0285/1ivtA/merged-good-all-a2m.gz for input Trying 1ivtA/merged-good-all-a2m Error: Couldn't open file 1ivtA/merged-good-all-a2m or 1ivtA/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 2etlA/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/T0285/2etlA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0285/2etlA/merged-good-all-a2m.gz for input Trying 2etlA/merged-good-all-a2m Error: Couldn't open file 2etlA/merged-good-all-a2m or 2etlA/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1qh0A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1qh0A expands to /projects/compbio/data/pdb/1qh0.pdb.gz 1qh0A:# T0285 read from 1qh0A/merged-good-all-a2m # 1qh0A read from 1qh0A/merged-good-all-a2m # adding 1qh0A to template set # found chain 1qh0A in template set Warning: unaligning (T0285)A105 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1qh0A)K105 Warning: unaligning (T0285)G106 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1qh0A)K105 Warning: unaligning (T0285)R107 because of BadResidue code BAD_PEPTIDE in next template residue (1qh0A)P107 Warning: unaligning (T0285)D108 because of BadResidue code BAD_PEPTIDE at template residue (1qh0A)P107 Warning: unaligning (T0285)E109 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1qh0A)E108 T0285 39 :SLRFVYIVDRNNQ 1qh0A 39 :IVQHIKFDLTGGN T0285 54 :LKRPLPPGIMVLAPRLTAKHPYDKVQD 1qh0A 52 :LKYIEGQSIGIIPPGVDKNGKPEKDRD T0285 81 :RNRKLYGRHITL 1qh0A 86 :HGDDVDDKTISL T0285 100 :VVT 1qh0A 98 :CVR T0285 103 :IS 1qh0A 102 :LE T0285 110 :GPDR 1qh0A 109 :SGET T0285 116 :IWEMFLENLE 1qh0A 116 :VCSTYLTHIE Number of specific fragments extracted= 7 number of extra gaps= 1 total=113 Number of alignments=22 # 1qh0A read from 1qh0A/merged-good-all-a2m # found chain 1qh0A in template set Warning: unaligning (T0285)A105 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1qh0A)K105 Warning: unaligning (T0285)G106 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1qh0A)K105 Warning: unaligning (T0285)R107 because of BadResidue code BAD_PEPTIDE in next template residue (1qh0A)P107 Warning: unaligning (T0285)D108 because of BadResidue code BAD_PEPTIDE at template residue (1qh0A)P107 Warning: unaligning (T0285)E109 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1qh0A)E108 T0285 57 :PLPPG 1qh0A 53 :KYIEG T0285 62 :IMVLAPRLTAKHPYDKVQD 1qh0A 60 :IGIIPPGVDKNGKPEKDRD T0285 81 :RNRKLYGRHITL 1qh0A 86 :HGDDVDDKTISL T0285 100 :VVTI 1qh0A 98 :CVRQ T0285 104 :S 1qh0A 103 :E T0285 110 :GPDR 1qh0A 109 :SGET T0285 114 :D 1qh0A 115 :G T0285 116 :IWEMFLENLE 1qh0A 116 :VCSTYLTHIE Number of specific fragments extracted= 8 number of extra gaps= 1 total=121 Number of alignments=23 # 1qh0A read from 1qh0A/merged-good-all-a2m # found chain 1qh0A in template set Warning: unaligning (T0285)A105 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1qh0A)K105 Warning: unaligning (T0285)G106 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1qh0A)K105 Warning: unaligning (T0285)R107 because of BadResidue code BAD_PEPTIDE in next template residue (1qh0A)P107 Warning: unaligning (T0285)D108 because of BadResidue code BAD_PEPTIDE at template residue (1qh0A)P107 Warning: unaligning (T0285)E109 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1qh0A)E108 T0285 39 :SLRFVYIVDRNNQ 1qh0A 39 :IVQHIKFDLTGGN T0285 54 :LKRPLPPGIMVLAPRLTAKHPYDKVQD 1qh0A 52 :LKYIEGQSIGIIPPGVDKNGKPEKDRD T0285 81 :RNRKLYGRHITL 1qh0A 86 :HGDDVDDKTISL T0285 100 :VVT 1qh0A 98 :CVR T0285 103 :IS 1qh0A 102 :LE T0285 110 :GPDR 1qh0A 109 :SGET T0285 116 :IWEMFLENLE 1qh0A 116 :VCSTYLTHIE Number of specific fragments extracted= 7 number of extra gaps= 1 total=128 Number of alignments=24 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1kyyA/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/T0285/1kyyA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0285/1kyyA/merged-good-all-a2m.gz for input Trying 1kyyA/merged-good-all-a2m Error: Couldn't open file 1kyyA/merged-good-all-a2m or 1kyyA/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1wuzA/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/T0285/1wuzA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0285/1wuzA/merged-good-all-a2m.gz for input Trying 1wuzA/merged-good-all-a2m Error: Couldn't open file 1wuzA/merged-good-all-a2m or 1wuzA/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1gawA/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/T0285/1gawA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0285/1gawA/merged-good-all-a2m.gz for input Trying 1gawA/merged-good-all-a2m Error: Couldn't open file 1gawA/merged-good-all-a2m or 1gawA/merged-good-all-a2m.gz for input # command:# PrintAlignmentsContacts allconstraints.under Using radius: 8.0000 NUMB_ALIGNS: 24 Done printing distance constraints # command: