# 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/T0346/ # command:# Making conformation for sequence T0346 numbered 1 through 172 Created new target T0346 from T0346.a2m # command:# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/T0346/ # command:Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0346//projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0346/manyalignments-good-all.under or /projects/compbio/experiments/protein-predict/casp7/T0346//projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0346/manyalignments-good-all.under.gz for input Trying /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0346/manyalignments-good-all.under # reading script from file /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0346/manyalignments-good-all.under # Reading fragments from alignment file # Attempting to read fragment alignments from file 1xyhA/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/T0346/1xyhA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0346/1xyhA/merged-good-all-a2m.gz for input Trying 1xyhA/merged-good-all-a2m Error: Couldn't open file 1xyhA/merged-good-all-a2m or 1xyhA/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 2rmcA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2rmcA expands to /projects/compbio/data/pdb/2rmc.pdb.gz 2rmcA:# T0346 read from 2rmcA/merged-good-all-a2m # 2rmcA read from 2rmcA/merged-good-all-a2m # adding 2rmcA to template set # found chain 2rmcA in template set T0346 4 :CHFDIEINREPVGRIMFQLFSDICPKTCKNFLCLCSGEKGLG 2rmcA 40 :VFFDVRIGDKDVGRIVIGLFGNVVPKTVENFVALATGEKGYG # choosing archetypes in rotamer library T0346 54 :YKGSTFHRVVKNFMIQGGDFSEGNGKGGESIYGGYFKDENFILKHDRAFLLSMANRGKHTNGSQFFITTKPAPHLDGVHVVFGLVISGFEVIEQIENLKTDAASRPYADVRVIDCGVLA 2rmcA 82 :YKGSIFHRVIKDFMIQGGDFTARDGTGGMSIYGETFPDENFKLKHYGIGWVSMANAGPDTNGSQFFITLTKPTWLDGKHVVFGKVLDGMTVVHSIELQATDGHDRPLTDCTIVNSGKID Number of specific fragments extracted= 2 number of extra gaps= 0 total=2 Number of alignments=1 # 2rmcA read from 2rmcA/merged-good-all-a2m # found chain 2rmcA in template set T0346 4 :CHFDIEINREPVGRIMFQLFSDICPKTCKNFLCLCSGEKGLG 2rmcA 40 :VFFDVRIGDKDVGRIVIGLFGNVVPKTVENFVALATGEKGYG T0346 54 :YKGSTFHRVVKNFMIQGGDFSEGNGKGGESIYGGYFKDENFILKHDRAFLLSMANRGKHTNGSQFFITTKPAPHLDGVHVVFGLVISGFEVIEQIENLKTDAASRPYADVRVIDCGVL 2rmcA 82 :YKGSIFHRVIKDFMIQGGDFTARDGTGGMSIYGETFPDENFKLKHYGIGWVSMANAGPDTNGSQFFITLTKPTWLDGKHVVFGKVLDGMTVVHSIELQATDGHDRPLTDCTIVNSGKI Number of specific fragments extracted= 2 number of extra gaps= 0 total=4 Number of alignments=2 # 2rmcA read from 2rmcA/merged-good-all-a2m # found chain 2rmcA in template set T0346 3 :QCHFDIEINREPVGRIMFQLFSDICPKTCKNFLCLCSGEKG 2rmcA 39 :KVFFDVRIGDKDVGRIVIGLFGNVVPKTVENFVALATGEKG T0346 52 :LCYKGSTFHRVVKNFMIQGGDFSEGNGKGGESIYGGYFKDENFILKHDRAFLLSMANRGKHTNGSQFFITTKPAPHLDGVHVVFGLVISGFEVIEQIENLKTDAASRPYADVRVIDCGVLA 2rmcA 80 :YGYKGSIFHRVIKDFMIQGGDFTARDGTGGMSIYGETFPDENFKLKHYGIGWVSMANAGPDTNGSQFFITLTKPTWLDGKHVVFGKVLDGMTVVHSIELQATDGHDRPLTDCTIVNSGKID 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 1awqA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1awqA expands to /projects/compbio/data/pdb/1awq.pdb.gz 1awqA:# T0346 read from 1awqA/merged-good-all-a2m # 1awqA read from 1awqA/merged-good-all-a2m # adding 1awqA to template set # found chain 1awqA in template set T0346 1 :SPQCHFDIEINREPVGRIMFQLFSDICPKTCKNFLCLCSGEKGLG 1awqA 1003 :NPTVFFDIAVDGEPLGRVSFELFADKVPKTAENFRALSTGEKGFG T0346 54 :YKGSTFHRVVKNFMIQGGDFSEGNGKGGESIYGGYFKDENFILKHDRAFLLSMANRGKHTNGSQFFITTKPAPHLDGVHVVFGLVISGFEVIEQIENL 1awqA 1048 :YKGSCFHRIIPGFMCQGGDFTRHNGTGGKSIYGEKFEDENFILKHTGPGILSMANAGPNTNGSQFFICTAKTEWLDGKHVVFGKVKEGMNIVEAMERF T0346 153 :TDAASRPYADVRVIDCGVL 1awqA 1146 :GSRNGKTSKKITIADCGQL Number of specific fragments extracted= 3 number of extra gaps= 0 total=9 Number of alignments=4 # 1awqA read from 1awqA/merged-good-all-a2m # found chain 1awqA in template set T0346 1 :SPQCHFDIEINREPVGRIMFQLFSDICPKTCKNFLCLCSGEKGLG 1awqA 1003 :NPTVFFDIAVDGEPLGRVSFELFADKVPKTAENFRALSTGEKGFG T0346 54 :YKGSTFHRVVKNFMIQGGDFSEGNGKGGESIYGGYFKDENFILKHDRAFLLSMANRGKHTNGSQFFITTKPAPHLDGVHVVFGLVISGFEVIEQIENL 1awqA 1048 :YKGSCFHRIIPGFMCQGGDFTRHNGTGGKSIYGEKFEDENFILKHTGPGILSMANAGPNTNGSQFFICTAKTEWLDGKHVVFGKVKEGMNIVEAMERF T0346 153 :TDAASRPYADVRVIDCGVL 1awqA 1146 :GSRNGKTSKKITIADCGQL Number of specific fragments extracted= 3 number of extra gaps= 0 total=12 Number of alignments=5 # 1awqA read from 1awqA/merged-good-all-a2m # found chain 1awqA in template set T0346 1 :SPQCHFDIEINREPVGRIMFQLFSDICPKTCKNFLCLCSGE 1awqA 1003 :NPTVFFDIAVDGEPLGRVSFELFADKVPKTAENFRALSTGE T0346 50 :KKLCYKGSTFHRVVKNFMIQGGDFSEGNGKGGESIYGGYFKDENFILKHDRAFLLSMANRGKHTNGSQFFITTKPAPHLDGVHVVFGLVISGFEVIEQIENL 1awqA 1044 :KGFGYKGSCFHRIIPGFMCQGGDFTRHNGTGGKSIYGEKFEDENFILKHTGPGILSMANAGPNTNGSQFFICTAKTEWLDGKHVVFGKVKEGMNIVEAMERF T0346 153 :TDAASRPYADVRVIDCGVLA 1awqA 1146 :GSRNGKTSKKITIADCGQLE Number of specific fragments extracted= 3 number of extra gaps= 0 total=15 Number of alignments=6 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1qngA/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/T0346/1qngA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0346/1qngA/merged-good-all-a2m.gz for input Trying 1qngA/merged-good-all-a2m Error: Couldn't open file 1qngA/merged-good-all-a2m or 1qngA/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1lopA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1lopA expands to /projects/compbio/data/pdb/1lop.pdb.gz 1lopA:# T0346 read from 1lopA/merged-good-all-a2m # 1lopA read from 1lopA/merged-good-all-a2m # adding 1lopA to template set # found chain 1lopA in template set T0346 9 :EINREPVGRIMFQLFSDICPKTCKNFLCLC 1lopA 2 :VTFHTNHGDIVIKTFDDKAPETVKNFLDYC T0346 41 :EKGL 1lopA 32 :REGF T0346 54 :YKGSTFHRVVKNFMIQGGDFSEGNGKGGE 1lopA 36 :YNNTIFHRVINGFMIQGGGFEPGMKQKAT T0346 86 :GGYFKDENFILKHDRAFLLSMANRG 1lopA 65 :KEPIKNEANNGLKNTRGTLAMARTQ T0346 111 :KHTNGSQFFITTKPAPHLD 1lopA 91 :PHSATAQFFINVVDNDFLN T0346 130 :GVHVVFGLVISGFEVIEQIENLKT 1lopA 118 :WGYCVFAEVVDGMDEVDKIKGVAT T0346 154 :DA 1lopA 145 :GM T0346 156 :ASRPYADVRVIDCGVLA 1lopA 148 :QDVPKEDVIIESVTVSE Number of specific fragments extracted= 8 number of extra gaps= 0 total=23 Number of alignments=7 # 1lopA read from 1lopA/merged-good-all-a2m # found chain 1lopA in template set T0346 9 :EINREPVGRIMFQLFSDICPKTCKNFLCLCSGEK 1lopA 2 :VTFHTNHGDIVIKTFDDKAPETVKNFLDYCREGF T0346 54 :YKGSTFHRVVKNFMIQGGDFS 1lopA 36 :YNNTIFHRVINGFMIQGGGFE T0346 77 :NGKGGESI 1lopA 57 :PGMKQKAT T0346 86 :GGYFKDENFILKHDRAFLLSMANRG 1lopA 65 :KEPIKNEANNGLKNTRGTLAMARTQ T0346 111 :KHTNGSQFFITTKPAPHLDGV 1lopA 91 :PHSATAQFFINVVDNDFLNFS T0346 132 :HVVFGLVISGFEVIEQIENLKT 1lopA 120 :YCVFAEVVDGMDEVDKIKGVAT T0346 154 :DA 1lopA 145 :GM T0346 157 :SRPYADVRVIDCGVLA 1lopA 149 :DVPKEDVIIESVTVSE Number of specific fragments extracted= 8 number of extra gaps= 0 total=31 Number of alignments=8 # 1lopA read from 1lopA/merged-good-all-a2m # found chain 1lopA in template set T0346 4 :CHFD 1lopA 2 :VTFH T0346 13 :EPVGRIMFQLFSDICPKTCKNFLCLCSGE 1lopA 6 :TNHGDIVIKTFDDKAPETVKNFLDYCREG T0346 53 :CYKGSTFHRVVKNFMIQGGDFSEGNGKGGES 1lopA 35 :FYNNTIFHRVINGFMIQGGGFEPGMKQKATK T0346 86 :GGYFKDENFILKHDRAFLLSMANRGKHTNGSQFFITTKPAPHLD 1lopA 66 :EPIKNEANNGLKNTRGTLAMARTQAPHSATAQFFINVVDNDFLN T0346 130 :GVHVVFGLVISGFEVIEQIENLKTD 1lopA 118 :WGYCVFAEVVDGMDEVDKIKGVATG T0346 157 :SRPYADVRVIDCGVLA 1lopA 149 :DVPKEDVIIESVTVSE Number of specific fragments extracted= 6 number of extra gaps= 0 total=37 Number of alignments=9 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1zmfA/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/T0346/1zmfA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0346/1zmfA/merged-good-all-a2m.gz for input Trying 1zmfA/merged-good-all-a2m Error: Couldn't open file 1zmfA/merged-good-all-a2m or 1zmfA/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1awsA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1awsA expands to /projects/compbio/data/pdb/1aws.pdb.gz 1awsA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0346 read from 1awsA/merged-good-all-a2m # 1awsA read from 1awsA/merged-good-all-a2m # adding 1awsA to template set # found chain 1awsA in template set T0346 1 :SPQCHFDIEINREPVGRIMFQLFSDICPKTCKNFLCLCSGEKGLG 1awsA 1003 :NPTVFFDIAVDGEPLGRVSFELFADKVPKTAENFRALSTGEKGFG T0346 54 :YKGSTFHRVVKNFMIQGGDFSEGNGKGGESIYGGYFKDENFILKHDRAFLLSMANRGKHTNGSQFFITTKPAPHLDGVHVVFGLVISGFEVIEQIENL 1awsA 1048 :YKGSCFHRIIPGFMCQGGDFTRHNGTGGKSIYGEKFEDENFILKHTGPGILSMANAGPNTNGSQFFICTAKTEWLDGKHVVFGKVKEGMNIVEAMERF T0346 153 :TDAASRPYADVRVIDCGVL 1awsA 1146 :GSRNGKTSKKITIADCGQL Number of specific fragments extracted= 3 number of extra gaps= 0 total=40 Number of alignments=10 # 1awsA read from 1awsA/merged-good-all-a2m # found chain 1awsA in template set T0346 1 :SPQCHFDIEINREPVGRIMFQLFSDICPKTCKNFLCLCSGEKGLG 1awsA 1003 :NPTVFFDIAVDGEPLGRVSFELFADKVPKTAENFRALSTGEKGFG T0346 54 :YKGSTFHRVVKNFMIQGGDFSEGNGKGGESIYGGYFKDENFILKHDRAFLLSMANRGKHTNGSQFFITTKPAPHLDGVHVVFGLVISGFEVIEQIENL 1awsA 1048 :YKGSCFHRIIPGFMCQGGDFTRHNGTGGKSIYGEKFEDENFILKHTGPGILSMANAGPNTNGSQFFICTAKTEWLDGKHVVFGKVKEGMNIVEAMERF T0346 153 :TDAASRPYADVRVIDCGVL 1awsA 1146 :GSRNGKTSKKITIADCGQL Number of specific fragments extracted= 3 number of extra gaps= 0 total=43 Number of alignments=11 # 1awsA read from 1awsA/merged-good-all-a2m # found chain 1awsA in template set T0346 1 :SPQCHFDIEINREPVGRIMFQLFSDICPKTCKNFLCLCSGE 1awsA 1003 :NPTVFFDIAVDGEPLGRVSFELFADKVPKTAENFRALSTGE T0346 50 :KKLCYKGSTFHRVVKNFMIQGGDFSEGNGKGGESIYGGYFKDENFILKHDRAFLLSMANRGKHTNGSQFFITTKPAPHLDGVHVVFGLVISGFEVIEQIENL 1awsA 1044 :KGFGYKGSCFHRIIPGFMCQGGDFTRHNGTGGKSIYGEKFEDENFILKHTGPGILSMANAGPNTNGSQFFICTAKTEWLDGKHVVFGKVKEGMNIVEAMERF T0346 153 :TDAASRPYADVRVIDCGVLA 1awsA 1146 :GSRNGKTSKKITIADCGQLE Number of specific fragments extracted= 3 number of extra gaps= 0 total=46 Number of alignments=12 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2eslA/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/T0346/2eslA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0346/2eslA/merged-good-all-a2m.gz for input Trying 2eslA/merged-good-all-a2m Error: Couldn't open file 2eslA/merged-good-all-a2m or 2eslA/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1zcxA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1zcxA expands to Error: no filename for 1zcxA 1zcxA expands to Error: no filename for 1zcxA 1zcxA expands to Error: no filename for 1zcxA # T0346 read from 1zcxA/merged-good-all-a2m # 1zcxA read from 1zcxA/merged-good-all-a2m # adding 1zcxA to template set Error: can't find template for 1zcxA or 1zcxA, so skipping it. # 1zcxA read from 1zcxA/merged-good-all-a2m # adding 1zcxA to template set Error: can't find template for 1zcxA or 1zcxA, so skipping it. # 1zcxA read from 1zcxA/merged-good-all-a2m # adding 1zcxA to template set Error: can't find template for 1zcxA or 1zcxA, so skipping it. # Reading fragments from alignment file # Attempting to read fragment alignments from file 1yndA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1yndA expands to /projects/compbio/data/pdb/1ynd.pdb.gz 1yndA:# T0346 read from 1yndA/merged-good-all-a2m # 1yndA read from 1yndA/merged-good-all-a2m # adding 1yndA to template set # found chain 1yndA in template set T0346 1 :SPQCHFDIEINREPVGRIMFQLFSDICPKTCKNFLCLCSGEKGLG 1yndA 3 :NPTVFFDIAVDGEPLGRVSFELFADKVPKTAENFRALSTGEKGFG T0346 54 :YKGSTFHRVVKNFMIQGGDFSEGNGKGGESIYGGYFKDENFILKHDRAFLLSMANRGKHTNGSQFFITTKPAPHLDGVHVVFGLVISGFEVIEQIENL 1yndA 48 :YKGSCFHRIIPGFMCQGGDFTRHNGTGGKSIYGEKFEDENFILKHTGPGILSMANAGPNTNGSQFFICTAKTEWLDGKHVVFGKVKEGMNIVEAMERF T0346 153 :TDAASRPYADVRVIDCGVL 1yndA 146 :GSRNGKTSKKITIADCGQL Number of specific fragments extracted= 3 number of extra gaps= 0 total=49 Number of alignments=13 # 1yndA read from 1yndA/merged-good-all-a2m # found chain 1yndA in template set T0346 1 :SPQCHFDIEINREPVGRIMFQLFSDICPKTCKNFLCLCSGEKGLG 1yndA 3 :NPTVFFDIAVDGEPLGRVSFELFADKVPKTAENFRALSTGEKGFG T0346 54 :YKGSTFHRVVKNFMIQGGDFSEGNGKGGESIYGGYFKDENFILKHDRAFLLSMANRGKHTNGSQFFITTKPAPHLDGVHVVFGLVISGFEVIEQIENLK 1yndA 48 :YKGSCFHRIIPGFMCQGGDFTRHNGTGGKSIYGEKFEDENFILKHTGPGILSMANAGPNTNGSQFFICTAKTEWLDGKHVVFGKVKEGMNIVEAMERFG T0346 154 :DAASRPYADVRVIDCGVL 1yndA 147 :SRNGKTSKKITIADCGQL Number of specific fragments extracted= 3 number of extra gaps= 0 total=52 Number of alignments=14 # 1yndA read from 1yndA/merged-good-all-a2m # found chain 1yndA in template set T0346 1 :SPQCHFDIEINREPVGRIMFQLFSDICPKTCKNFLCLCSGE 1yndA 3 :NPTVFFDIAVDGEPLGRVSFELFADKVPKTAENFRALSTGE T0346 50 :KKLCYKGSTFHRVVKNFMIQGGDFSEGNGKGGESIYGGYFKDENFILKHDRAFLLSMANRGKHTNGSQFFITTKPAPHLDGVHVVFGLVISGFEVIEQIENL 1yndA 44 :KGFGYKGSCFHRIIPGFMCQGGDFTRHNGTGGKSIYGEKFEDENFILKHTGPGILSMANAGPNTNGSQFFICTAKTEWLDGKHVVFGKVKEGMNIVEAMERF T0346 153 :TDAASRPYADVRVIDCGVLA 1yndA 146 :GSRNGKTSKKITIADCGQLE Number of specific fragments extracted= 3 number of extra gaps= 0 total=55 Number of alignments=15 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2nul/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/T0346/2nul/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0346/2nul/merged-good-all-a2m.gz for input Trying 2nul/merged-good-all-a2m Error: Couldn't open file 2nul/merged-good-all-a2m or 2nul/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 2c3bA/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/T0346/2c3bA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0346/2c3bA/merged-good-all-a2m.gz for input Trying 2c3bA/merged-good-all-a2m Error: Couldn't open file 2c3bA/merged-good-all-a2m or 2c3bA/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ihgA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1ihgA expands to /projects/compbio/data/pdb/1ihg.pdb.gz 1ihgA:# T0346 read from 1ihgA/merged-good-all-a2m # 1ihgA read from 1ihgA/merged-good-all-a2m # adding 1ihgA to template set # found chain 1ihgA in template set T0346 2 :PQCHFDIEINREPVGRIMFQLFSDICPKTCKNFLCLCSGEKGLGKTTGKKLCYKGSTFHRVVKNFMIQGGDFSEGNGKGGESIYGGYFKDENFILKHDRAFLLSMANRGKHTNGSQFFITTKPAPHLDGVHVVFGLVISGFEVIEQIENLKTD 1ihgA 16 :PRVFFDVDIGGERVGRIVLELFADIVPKTAENFRALCTGEKGIGPTTGKPLHFKGCPFHRIIKKFMIQGGDFSNQNGTGGESIYGEKFEDENFHYKHDKEGLLSMANAGSNTNGSQFFITTVPTPHLDGKHVVFGQVIKGMGVAKILENVEVK T0346 156 :ASRPYADVRVIDCGVLA 1ihgA 169 :GEKPAKLCVIAECGELK Number of specific fragments extracted= 2 number of extra gaps= 0 total=57 Number of alignments=16 # 1ihgA read from 1ihgA/merged-good-all-a2m # found chain 1ihgA in template set T0346 4 :CHFDIEINREPVGRIMFQLFSDICPKTCKNFLCLCSGEKGLGKTTGKKLCYKGSTFHRVVKNFMIQGGDFSEGNGKGGESIYGGYFKDENFILKHDRAFLLSMANRGKHTNGSQFFITTKPAPHLDGVHVVFGLVISGFEVIEQIENLKT 1ihgA 18 :VFFDVDIGGERVGRIVLELFADIVPKTAENFRALCTGEKGIGPTTGKPLHFKGCPFHRIIKKFMIQGGDFSNQNGTGGESIYGEKFEDENFHYKHDKEGLLSMANAGSNTNGSQFFITTVPTPHLDGKHVVFGQVIKGMGVAKILENVEV T0346 155 :AASRPYADVRVIDCGVLA 1ihgA 168 :KGEKPAKLCVIAECGELK Number of specific fragments extracted= 2 number of extra gaps= 0 total=59 Number of alignments=17 # 1ihgA read from 1ihgA/merged-good-all-a2m # found chain 1ihgA in template set T0346 2 :PQCHFDIEINREPVGRIMFQLFSDICPKTCKNFLCLCSGEKGLGKTTGKKLCYKGSTFHRVVKNFMIQGGDFSEGNGKGGESIYGGYFKDENFILKHDRAFLLSMANRGKHTNGSQFFITTKPAPHLDGVHVVFGLVISGFEVIEQIENLKTDAA 1ihgA 16 :PRVFFDVDIGGERVGRIVLELFADIVPKTAENFRALCTGEKGIGPTTGKPLHFKGCPFHRIIKKFMIQGGDFSNQNGTGGESIYGEKFEDENFHYKHDKEGLLSMANAGSNTNGSQFFITTVPTPHLDGKHVVFGQVIKGMGVAKILENVEVKGE T0346 158 :RPYADVRVIDCGVLA 1ihgA 171 :KPAKLCVIAECGELK Number of specific fragments extracted= 2 number of extra gaps= 0 total=61 Number of alignments=18 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1a58/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1a58 expands to /projects/compbio/data/pdb/1a58.pdb.gz 1a58:Warning: there is no chain 1a58 will retry with 1a58A # T0346 read from 1a58/merged-good-all-a2m # 1a58 read from 1a58/merged-good-all-a2m # adding 1a58 to template set # found chain 1a58 in template set T0346 3 :QCHFDIEINREPVGRIMFQLFSDICPKTCKNFLCLCSGEKGLGKTTGKKLCYKGSTFHRVVKNFMIQGGDFSEGNGKGGESIYGGYFKDENFILKHDRAFLLSMANRGKHTNGSQFFITTKPAPHLDGVHVVFGLVISGFEVIEQIENLKTDAASRPYADVRVIDCGVL 1a58 8 :RVFLDVTIDGNLAGRIVMELYNDIAPRTCNNFLMLCTGMAGTGKISGKPLHYKGSTFHRVIKNFMIQGGDFTKGDGTGGESIYGGMFDDEEFVMKHDEPFVVSMANKGPNTNGSQFFITTTPAPHLNNIHVVFGKVVSGQEVVTKIEYLKTNSKNRPLADVVILNCGEL Number of specific fragments extracted= 1 number of extra gaps= 0 total=62 Number of alignments=19 # 1a58 read from 1a58/merged-good-all-a2m # found chain 1a58 in template set T0346 4 :CHFDIEINREPVGRIMFQLFSDICPKTCKNFLCLCSGEKGLGKTTGKKLCYKGSTFHRVVKNFMIQGGDFSEGNGKGGESIYGGYFKDENFILKHDRAFLLSMANRGKHTNGSQFFITTKPAPHLDGVHVVFGLVISGFEVIEQIENLKTDAASRPYADVRVIDCGVL 1a58 9 :VFLDVTIDGNLAGRIVMELYNDIAPRTCNNFLMLCTGMAGTGKISGKPLHYKGSTFHRVIKNFMIQGGDFTKGDGTGGESIYGGMFDDEEFVMKHDEPFVVSMANKGPNTNGSQFFITTTPAPHLNNIHVVFGKVVSGQEVVTKIEYLKTNSKNRPLADVVILNCGEL Number of specific fragments extracted= 1 number of extra gaps= 0 total=63 Number of alignments=20 # 1a58 read from 1a58/merged-good-all-a2m # found chain 1a58 in template set T0346 2 :PQCHFDIEINREPVGRIMFQLFSDICPKTCKNFLCLCSGEKGLGKTTGKKLCYKGSTFHRVVKNFMIQGGDFSEGNGKGGESIYGGYFKDENFILKHDRAFLLSMANRGKHTNGSQFFITTKPAPHLDGVHVVFGLVISGFEVIEQIENLKTDAASRPYADVRVIDCGVLA 1a58 7 :RRVFLDVTIDGNLAGRIVMELYNDIAPRTCNNFLMLCTGMAGTGKISGKPLHYKGSTFHRVIKNFMIQGGDFTKGDGTGGESIYGGMFDDEEFVMKHDEPFVVSMANKGPNTNGSQFFITTTPAPHLNNIHVVFGKVVSGQEVVTKIEYLKTNSKNRPLADVVILNCGELV Number of specific fragments extracted= 1 number of extra gaps= 0 total=64 Number of alignments=21 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2gw2A/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/T0346/2gw2A/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0346/2gw2A/merged-good-all-a2m.gz for input Trying 2gw2A/merged-good-all-a2m Error: Couldn't open file 2gw2A/merged-good-all-a2m or 2gw2A/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1vdnA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1vdnA expands to /projects/compbio/data/pdb/1vdn.pdb.gz 1vdnA:# T0346 read from 1vdnA/merged-good-all-a2m # 1vdnA read from 1vdnA/merged-good-all-a2m # adding 1vdnA to template set # found chain 1vdnA in template set Warning: unaligning (T0346)P2 because first residue in template chain is (1vdnA)S2 Warning: unaligning (T0346)L171 because last residue in template chain is (1vdnA)L162 T0346 3 :QCHFDIEINREPVGRIMFQLFSDICPKTCKNFLCLCSGEKGLG 1vdnA 3 :QVYFDVEADGQPIGRVVFKLYNDIVPKTAENFRALCTGEKGFG T0346 54 :YKGSTFHRVVKNFMIQGGDFSEGNGKGGESIYGGYFKDENFILKHDRAFLLSMANRGKHTNGSQFFITTKPAPHLDGVHVVFGLVISGFEVIEQIENL 1vdnA 46 :YAGSPFHRVIPDFMLQGGDFTAGNGTGGKSIYGGKFPDENFKKHHDRPGLLSMANAGPNTNGSQFFITTVPCPWLDGKHVVFGEVVDGYDIVKKVESL T0346 153 :TDAASRPYADVRVIDCGV 1vdnA 144 :GSPSGATKARIVVAKSGE Number of specific fragments extracted= 3 number of extra gaps= 0 total=67 Number of alignments=22 # 1vdnA read from 1vdnA/merged-good-all-a2m # found chain 1vdnA in template set Warning: unaligning (T0346)L171 because last residue in template chain is (1vdnA)L162 T0346 3 :QCHFDIEINREPVGRIMFQLFSDICPKTCKNFLCLCSGEKGLG 1vdnA 3 :QVYFDVEADGQPIGRVVFKLYNDIVPKTAENFRALCTGEKGFG T0346 54 :YKGSTFHRVVKNFMIQGGDFSEGNGKGGESIYGGYFKDENFILKHDRAFLLSMANRGKHTNGSQFFITTKPAPHLDGVHVVFGLVISGFEVIEQIENLK 1vdnA 46 :YAGSPFHRVIPDFMLQGGDFTAGNGTGGKSIYGGKFPDENFKKHHDRPGLLSMANAGPNTNGSQFFITTVPCPWLDGKHVVFGEVVDGYDIVKKVESLG T0346 154 :DAASRPYADVRVIDCGV 1vdnA 145 :SPSGATKARIVVAKSGE Number of specific fragments extracted= 3 number of extra gaps= 0 total=70 Number of alignments=23 # 1vdnA read from 1vdnA/merged-good-all-a2m # found chain 1vdnA in template set Warning: unaligning (T0346)P2 because first residue in template chain is (1vdnA)S2 Warning: unaligning (T0346)L171 because last residue in template chain is (1vdnA)L162 T0346 3 :QCHFDIEINREPVGRIMFQLFSDICPKTCKNFLCLCSGE 1vdnA 3 :QVYFDVEADGQPIGRVVFKLYNDIVPKTAENFRALCTGE T0346 50 :KKLCYKGSTFHRVVKNFMIQGGDFSEGNGKGGESIYGGYFKDENFILKHDRAFLLSMANRGKHTNGSQFFITTKPAPHLDGVHVVFGLVISGFEVIEQIENL 1vdnA 42 :KGFGYAGSPFHRVIPDFMLQGGDFTAGNGTGGKSIYGGKFPDENFKKHHDRPGLLSMANAGPNTNGSQFFITTVPCPWLDGKHVVFGEVVDGYDIVKKVESL T0346 153 :TDAASRPYADVRVIDCGV 1vdnA 144 :GSPSGATKARIVVAKSGE Number of specific fragments extracted= 3 number of extra gaps= 0 total=73 Number of alignments=24 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2fu0A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2fu0A expands to /projects/compbio/data/pdb/2fu0.pdb.gz 2fu0A:# T0346 read from 2fu0A/merged-good-all-a2m # 2fu0A read from 2fu0A/merged-good-all-a2m # adding 2fu0A to template set # found chain 2fu0A in template set Warning: unaligning (T0346)L171 because last residue in template chain is (2fu0A)N159 T0346 7 :DIEINREPVGRIMFQLFSDICPKTCKNFLCLC 2fu0A 6 :KSAIIYTTMGDIHISLFYKECKKTVQNFSVHS T0346 41 :EKGL 2fu0A 38 :INGY T0346 54 :YKGSTFHRVVKNFMIQGGD 2fu0A 42 :YNNCIFHRVIKHFMVQTGD T0346 74 :SEGNGKGGESIYGGYFKDEN 2fu0A 61 :PSGDGTGGESIWGNEFEDEF T0346 94 :FILKHDRAFLLSMANRGKHTNGSQFFITTKPAPHLDGVHVVFGLVISGFEVIEQIENLKTDAASRPYADVRVIDCGV 2fu0A 82 :DHLNHSKPFMVSMANCGPNTNGSQFFITTVPCPWLDFKHTVFGKVTQGSKIVLDIEKVRTDKRDKPLEDIKILNIKI Number of specific fragments extracted= 5 number of extra gaps= 0 total=78 Number of alignments=25 # 2fu0A read from 2fu0A/merged-good-all-a2m # found chain 2fu0A in template set Warning: unaligning (T0346)L171 because last residue in template chain is (2fu0A)N159 T0346 7 :DIEINREPVGRIMFQLFSDICPKTCKNFLCLCSGEK 2fu0A 6 :KSAIIYTTMGDIHISLFYKECKKTVQNFSVHSINGY T0346 54 :YKGSTFHRVVKNFMIQGGDFS 2fu0A 42 :YNNCIFHRVIKHFMVQTGDPS T0346 76 :GNGKGGESIYGGYFKDEN 2fu0A 63 :GDGTGGESIWGNEFEDEF T0346 94 :FILKHDRAFLLSMANRGKHTNGSQFFITTKPAPHLDGVHVVFGLVISGFEVIEQIENLKTDAASRPYADVRVIDCGV 2fu0A 82 :DHLNHSKPFMVSMANCGPNTNGSQFFITTVPCPWLDFKHTVFGKVTQGSKIVLDIEKVRTDKRDKPLEDIKILNIKI Number of specific fragments extracted= 4 number of extra gaps= 0 total=82 Number of alignments=26 # 2fu0A read from 2fu0A/merged-good-all-a2m # found chain 2fu0A in template set T0346 9 :EINREPVGRIMFQLFSDICPKTCKNFLCLCSGE 2fu0A 8 :AIIYTTMGDIHISLFYKECKKTVQNFSVHSING T0346 53 :CYKGSTFHRVVKNFMIQGGDFSEGNGKGGESIYGGYFKDENFILKHDRAFLLSMANRGKHTNGSQFFITTKPAPHLDGVHVVFGLVISGFEVIEQIENLKTDAASRPYADVRVIDCGV 2fu0A 41 :YYNNCIFHRVIKHFMVQTGDPSGDGTGGESIWGNEFEDEFFDHLNHSKPFMVSMANCGPNTNGSQFFITTVPCPWLDFKHTVFGKVTQGSKIVLDIEKVRTDKRDKPLEDIKILNIKI Number of specific fragments extracted= 2 number of extra gaps= 0 total=84 Number of alignments=27 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1xwnA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1xwnA expands to /projects/compbio/data/pdb/1xwn.pdb.gz 1xwnA:# T0346 read from 1xwnA/merged-good-all-a2m # 1xwnA read from 1xwnA/merged-good-all-a2m # adding 1xwnA to template set # found chain 1xwnA in template set T0346 1 :SPQCHFDIEINREPVGRIMFQLFSDICPKTCKNFLCLC 1xwnA 6 :PDSWQPPNVYLETSMGIIVLELYWKHAPKTCKNFAELA T0346 41 :EKGL 1xwnA 44 :RRGY T0346 54 :YKGSTFHRVVKNFMIQGGD 1xwnA 48 :YNGTKFHRIIKDFMIQGGD T0346 74 :SEGNGKGGESIYGGYFKDEN 1xwnA 67 :PTGTGRGGASIYGKQFEDEL T0346 94 :FILKHDRAFLLSMANRGKHTNGSQFFITTKPAPHLDGVHVVFGLVISGFEVIEQIENLKTDAASRPYADVRVIDCGVLA 1xwnA 88 :PDLKFTGAGILAMANAGPDTNGSQFFVTLAPTQWLDGKHTIFGRVCQGIGMVNRVGMVETNSQDRPVDDVKIIKAYPSG Number of specific fragments extracted= 5 number of extra gaps= 0 total=89 Number of alignments=28 # 1xwnA read from 1xwnA/merged-good-all-a2m # found chain 1xwnA in template set T0346 2 :PQCHFDIEINREPVGRIMFQLFSDICPKTCKNFLCLCSGEK 1xwnA 7 :DSWQPPNVYLETSMGIIVLELYWKHAPKTCKNFAELARRGY T0346 54 :YKGSTFHRVVKNFMIQGGDFS 1xwnA 48 :YNGTKFHRIIKDFMIQGGDPT T0346 76 :GNGKGGESIYGGYFKDEN 1xwnA 69 :GTGRGGASIYGKQFEDEL T0346 94 :FILKHDRAFLLSMANRGKHTNGSQFFITTKPAPHLDGVHVVFGLVISGFEVIEQIENLKTDAASRPYADVRVIDCGVLA 1xwnA 88 :PDLKFTGAGILAMANAGPDTNGSQFFVTLAPTQWLDGKHTIFGRVCQGIGMVNRVGMVETNSQDRPVDDVKIIKAYPSG Number of specific fragments extracted= 4 number of extra gaps= 0 total=93 Number of alignments=29 # 1xwnA read from 1xwnA/merged-good-all-a2m # found chain 1xwnA in template set T0346 1 :SPQCHFDI 1xwnA 11 :PPNVYLET T0346 14 :PVGRIMFQLFSDICPKTCKNFLCLCSGE 1xwnA 19 :SMGIIVLELYWKHAPKTCKNFAELARRG T0346 53 :CYKGSTFHRVVKNFMIQGGDFSEGNGKGGESIYGGYFKDENFILKHDRAFLLSMANRGKHTNGSQFFITTKPAPHLDGVHVVFGLVISGFEVIEQIENLKTDAASRPYADVRVIDCGVLA 1xwnA 47 :YYNGTKFHRIIKDFMIQGGDPTGTGRGGASIYGKQFEDELHPDLKFTGAGILAMANAGPDTNGSQFFVTLAPTQWLDGKHTIFGRVCQGIGMVNRVGMVETNSQDRPVDDVKIIKAYPSG Number of specific fragments extracted= 3 number of extra gaps= 0 total=96 Number of alignments=30 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1w74A/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/T0346/1w74A/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0346/1w74A/merged-good-all-a2m.gz for input Trying 1w74A/merged-good-all-a2m Error: Couldn't open file 1w74A/merged-good-all-a2m or 1w74A/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1clh/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1clh expands to /projects/compbio/data/pdb/1clh.pdb.gz 1clh:Warning: there is no chain 1clh will retry with 1clhA # T0346 read from 1clh/merged-good-all-a2m # 1clh read from 1clh/merged-good-all-a2m # adding 1clh to template set # found chain 1clh in template set Warning: unaligning (T0346)V62 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (1clh)I50 Warning: unaligning (T0346)V63 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (1clh)I50 Warning: unaligning (T0346)Q69 because of BadResidue code BAD_PEPTIDE in next template residue (1clh)G57 Warning: unaligning (T0346)G70 because of BadResidue code BAD_PEPTIDE at template residue (1clh)G57 T0346 2 :P 1clh 5 :P T0346 8 :IEINREPVGRIMFQLFSDICPKTCKNFLCLC 1clh 6 :HVLLTTSAGNIELELDKQKAPVSVQNFVDYV T0346 41 :EKGL 1clh 37 :NSGF T0346 54 :YKGSTFHR 1clh 41 :YNNTTFHR T0346 64 :KNFMI 1clh 51 :PGFMI T0346 71 :GDFSEGNGKGGE 1clh 58 :GGFTEQMQQKKP T0346 86 :GGYFKDENFILKHDRAFLLSMANRG 1clh 70 :NPPIKNEADNGLRNTRGTIAMARTA T0346 111 :KHTNGSQFFITTKPAPHLD 1clh 96 :KDSATSQFFINVADNAFLD T0346 130 :GVHVVFGLVISGFEVIEQIENLKT 1clh 120 :FGYAVFGKVVKGMDVADKISQVPT T0346 154 :DAASRPYADVRVIDCGVL 1clh 148 :PYQNVPSKPVVILSAKVL Number of specific fragments extracted= 10 number of extra gaps= 2 total=106 Number of alignments=31 # 1clh read from 1clh/merged-good-all-a2m # found chain 1clh in template set Warning: unaligning (T0346)V62 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (1clh)I50 Warning: unaligning (T0346)V63 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (1clh)I50 Warning: unaligning (T0346)Q69 because of BadResidue code BAD_PEPTIDE in next template residue (1clh)G57 Warning: unaligning (T0346)G70 because of BadResidue code BAD_PEPTIDE at template residue (1clh)G57 T0346 2 :PQC 1clh 3 :GDP T0346 8 :IEINREPVGRIMFQLFSDICPKTCKNFLCLCSGEK 1clh 6 :HVLLTTSAGNIELELDKQKAPVSVQNFVDYVNSGF T0346 54 :YKGSTFHR 1clh 41 :YNNTTFHR T0346 64 :KNFMI 1clh 51 :PGFMI T0346 71 :GDFS 1clh 58 :GGFT T0346 76 :GNGKGGES 1clh 62 :EQMQQKKP T0346 86 :GGYFKDENFILKHDRAFLLSMANR 1clh 70 :NPPIKNEADNGLRNTRGTIAMART T0346 110 :GKHTNGSQFFITTKPAPHLDGV 1clh 95 :DKDSATSQFFINVADNAFLDHG T0346 132 :HVVFGLVISGFEVIEQIENLKT 1clh 122 :YAVFGKVVKGMDVADKISQVPT T0346 154 :DAASRPYADVRVIDCGVLA 1clh 148 :PYQNVPSKPVVILSAKVLP Number of specific fragments extracted= 10 number of extra gaps= 2 total=116 Number of alignments=32 # 1clh read from 1clh/merged-good-all-a2m # found chain 1clh in template set Warning: unaligning (T0346)V62 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (1clh)I50 Warning: unaligning (T0346)V63 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (1clh)I50 Warning: unaligning (T0346)Q69 because of BadResidue code BAD_PEPTIDE in next template residue (1clh)G57 Warning: unaligning (T0346)G70 because of BadResidue code BAD_PEPTIDE at template residue (1clh)G57 T0346 1 :SPQCHFDI 1clh 4 :DPHVLLTT T0346 14 :PVGRIMFQLFSDICPKTCKNFLCLCSGE 1clh 12 :SAGNIELELDKQKAPVSVQNFVDYVNSG T0346 53 :CYKGSTFHR 1clh 40 :FYNNTTFHR T0346 64 :KNFMI 1clh 51 :PGFMI T0346 71 :GDFSEGNGKGGES 1clh 58 :GGFTEQMQQKKPN T0346 86 :GGYFKDENFILKHDRAFLLSMANRGKHTNGSQFFITTKPAPHLD 1clh 71 :PPIKNEADNGLRNTRGTIAMARTADKDSATSQFFINVADNAFLD T0346 131 :VHVVFGLVISGFEVIEQIENLKTDA 1clh 121 :GYAVFGKVVKGMDVADKISQVPTHD T0346 156 :ASRPYADVRVIDCGVLA 1clh 150 :QNVPSKPVVILSAKVLP Number of specific fragments extracted= 8 number of extra gaps= 2 total=124 Number of alignments=33 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2bitX/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2bitX expands to /projects/compbio/data/pdb/2bit.pdb.gz 2bitX:# T0346 read from 2bitX/merged-good-all-a2m # 2bitX read from 2bitX/merged-good-all-a2m # adding 2bitX to template set # found chain 2bitX in template set Warning: unaligning (T0346)T58 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2bitX)F53 Warning: unaligning (T0346)F59 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2bitX)F53 T0346 1 :SPQCHFDIEINREPVGRIMFQLFSDICPKTCKNFLCLCSGEKGLG 2bitX 3 :NPLVYLDVDANGKPLGRVVLELKADVVPKTAENFRALCTGEKGFG T0346 54 :YKGS 2bitX 48 :YKGS T0346 60 :HRVVKNFMIQGGDFSEGNGKGGESIYGGYFKDENFILKHDRAFLLSMANRGKHTNGSQFFITTKPAPHLDGVHVVFGLVISGFEVIEQIENL 2bitX 54 :HRVIPSFMCQAGDFTNHNGTGGKSIYGSRFPDENFTLKHVGPGVLSMANAGPNTNGSQFFICTIKTDWLDGKHVVFGHVIEGMDVVKKIESF T0346 153 :TDAASRPYADVRVIDCGVLA 2bitX 146 :GSKSGRTSKKIVITDCGQLS Number of specific fragments extracted= 4 number of extra gaps= 1 total=128 Number of alignments=34 # 2bitX read from 2bitX/merged-good-all-a2m # found chain 2bitX in template set Warning: unaligning (T0346)T58 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2bitX)F53 Warning: unaligning (T0346)F59 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2bitX)F53 T0346 1 :SPQCHFDIEINREPVGRIMFQLFSDICPKTCKNFLCLCSGEKGLG 2bitX 3 :NPLVYLDVDANGKPLGRVVLELKADVVPKTAENFRALCTGEKGFG T0346 54 :YKGS 2bitX 48 :YKGS T0346 60 :HRVVKNFMIQGGDFSEGNGKGGESIYGGYFKDENFILKHDRAFLLSMANRGKHTNGSQFFITTKPAPHLDGVHVVFGLVISGFEVIEQIENLK 2bitX 54 :HRVIPSFMCQAGDFTNHNGTGGKSIYGSRFPDENFTLKHVGPGVLSMANAGPNTNGSQFFICTIKTDWLDGKHVVFGHVIEGMDVVKKIESFG T0346 154 :DAASRPYADVRVIDCGVLA 2bitX 147 :SKSGRTSKKIVITDCGQLS Number of specific fragments extracted= 4 number of extra gaps= 1 total=132 Number of alignments=35 # 2bitX read from 2bitX/merged-good-all-a2m # found chain 2bitX in template set Warning: unaligning (T0346)T58 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2bitX)F53 Warning: unaligning (T0346)F59 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2bitX)F53 T0346 2 :PQCHFDIEINREPVGRIMFQLFSDICPKTCKNFLCLCSGE 2bitX 4 :PLVYLDVDANGKPLGRVVLELKADVVPKTAENFRALCTGE T0346 50 :KKLCYKGS 2bitX 44 :KGFGYKGS T0346 60 :HRVVKNFMIQGGDFSEGNGKGGESIYGGYFKDENFILKHDRAFLLSMANRGKHTNGSQFFITTKPAPHLDGVHVVFGLVISGFEVIEQIENL 2bitX 54 :HRVIPSFMCQAGDFTNHNGTGGKSIYGSRFPDENFTLKHVGPGVLSMANAGPNTNGSQFFICTIKTDWLDGKHVVFGHVIEGMDVVKKIESF T0346 153 :TDAASRPYADVRVIDCGVLA 2bitX 146 :GSKSGRTSKKIVITDCGQLS Number of specific fragments extracted= 4 number of extra gaps= 1 total=136 Number of alignments=36 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1h0pA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1h0pA expands to /projects/compbio/data/pdb/1h0p.pdb.gz 1h0pA:Skipped atom 983, because occupancy 0.46 <= existing 0.540 in 1h0pA Skipped atom 985, because occupancy 0.460 <= existing 0.540 in 1h0pA Skipped atom 987, because occupancy 0.460 <= existing 0.540 in 1h0pA Skipped atom 989, because occupancy 0.460 <= existing 0.540 in 1h0pA Skipped atom 991, because occupancy 0.460 <= existing 0.540 in 1h0pA Skipped atom 1106, because occupancy 0.460 <= existing 0.540 in 1h0pA Skipped atom 1108, because occupancy 0.460 <= existing 0.540 in 1h0pA Skipped atom 1110, because occupancy 0.460 <= existing 0.540 in 1h0pA Skipped atom 1112, because occupancy 0.460 <= existing 0.540 in 1h0pA Skipped atom 1114, because occupancy 0.460 <= existing 0.540 in 1h0pA # T0346 read from 1h0pA/merged-good-all-a2m # 1h0pA read from 1h0pA/merged-good-all-a2m # adding 1h0pA to template set # found chain 1h0pA in template set Warning: unaligning (T0346)T153 because of BadResidue code BAD_PEPTIDE in next template residue (1h0pA)L172 Warning: unaligning (T0346)D154 because of BadResidue code BAD_PEPTIDE at template residue (1h0pA)L172 T0346 4 :CHFDIEINREPVGRIMFQLFSDICPKTCKNFLCLCSGEKGLG 1h0pA 30 :VYFDMEIGGKPIGRIVIGLFGKTVPKTATNFIELAKKPKGEG T0346 54 :YKGSTFHRVVKNFMIQGGDFSEGNGKGGESIYGGYFKDENFILKHDRAFLLSMANRGKHTNGSQFFITTKPAPHLDGVHVVFGLVISGFEVIEQIENLK 1h0pA 72 :YPGSKFHRVIADFMIQGGDFTRGDGTGGRSIYGEKFADENFKLKHYGAGWLSMANAGADTNGSQFFITTVKTPWLDGRHVVFGKILEGMDVVRKIEQTE T0346 155 :AASRPYADVRVIDCGVLA 1h0pA 173 :PGDRPKQDVIIAASGHIA Number of specific fragments extracted= 3 number of extra gaps= 1 total=139 Number of alignments=37 # 1h0pA read from 1h0pA/merged-good-all-a2m # found chain 1h0pA in template set Warning: unaligning (T0346)T153 because of BadResidue code BAD_PEPTIDE in next template residue (1h0pA)L172 Warning: unaligning (T0346)D154 because of BadResidue code BAD_PEPTIDE at template residue (1h0pA)L172 T0346 4 :CHFDIEINREPVGRIMFQLFSDICPKTCKNFLCLCSGEKGLG 1h0pA 30 :VYFDMEIGGKPIGRIVIGLFGKTVPKTATNFIELAKKPKGEG T0346 54 :YKGSTFHRVVKNFMIQGGDFSEGNGKGGESIYGGYFKDENFILKHDRAFLLSMANRGKHTNGSQFFITTKPAPHLDGVHVVFGLVISGFEVIEQIENLK 1h0pA 72 :YPGSKFHRVIADFMIQGGDFTRGDGTGGRSIYGEKFADENFKLKHYGAGWLSMANAGADTNGSQFFITTVKTPWLDGRHVVFGKILEGMDVVRKIEQTE T0346 155 :AASRPYADVRVIDCGVLA 1h0pA 173 :PGDRPKQDVIIAASGHIA Number of specific fragments extracted= 3 number of extra gaps= 1 total=142 Number of alignments=38 # 1h0pA read from 1h0pA/merged-good-all-a2m # found chain 1h0pA in template set Warning: unaligning (T0346)T153 because of BadResidue code BAD_PEPTIDE in next template residue (1h0pA)L172 Warning: unaligning (T0346)D154 because of BadResidue code BAD_PEPTIDE at template residue (1h0pA)L172 T0346 3 :QCHFDIEINREPVGRIMFQLFSDICPKTCKNFLCLCSGEKGL 1h0pA 29 :RVYFDMEIGGKPIGRIVIGLFGKTVPKTATNFIELAKKPKGE T0346 53 :CYKGSTFHRVVKNFMIQGGDFSEGNGKGGESIYGGYFKDENFILKHDRAFLLSMANRGKHTNGSQFFITTKPAPHLDGVHVVFGLVISGFEVIEQIENLK 1h0pA 71 :GYPGSKFHRVIADFMIQGGDFTRGDGTGGRSIYGEKFADENFKLKHYGAGWLSMANAGADTNGSQFFITTVKTPWLDGRHVVFGKILEGMDVVRKIEQTE T0346 155 :AASRPYADVRVIDCGVL 1h0pA 173 :PGDRPKQDVIIAASGHI Number of specific fragments extracted= 3 number of extra gaps= 1 total=145 Number of alignments=39 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1cwoA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1cwoA expands to /projects/compbio/data/pdb/1cwo.pdb.gz 1cwoA:# T0346 read from 1cwoA/merged-good-all-a2m # 1cwoA read from 1cwoA/merged-good-all-a2m # adding 1cwoA to template set # found chain 1cwoA in template set T0346 1 :SPQCHFDIEINREPVGRIMFQLFSDICPKTCKNFLCLCSGEKGLG 1cwoA 3 :NPTVFFDIAVDGEPLGRVSFELFADKVPKTAENFRALSTGEKGFG T0346 54 :YKGSTFHRVVKNFMIQGGDFSEGNGKGGESIYGGYFKDENFILKHDRAFLLSMANRGKHTNGSQFFITTKPAPHLDGVHVVFGLVISGFEVIEQIENL 1cwoA 48 :YKGSCFHRIIPGFMCQGGDFTRHNGTGGKSIYGEKFEDENFILKHTGPGILSMANAGPNTNGSQFFICTAKTEWLDGKHVVFGKVKEGMNIVEAMERF T0346 153 :TDAASRPYADVRVIDCGVL 1cwoA 146 :GSRNGKTSKKITIADCGQL Number of specific fragments extracted= 3 number of extra gaps= 0 total=148 Number of alignments=40 # 1cwoA read from 1cwoA/merged-good-all-a2m # found chain 1cwoA in template set T0346 1 :SPQCHFDIEINREPVGRIMFQLFSDICPKTCKNFLCLCSGEKGLG 1cwoA 3 :NPTVFFDIAVDGEPLGRVSFELFADKVPKTAENFRALSTGEKGFG T0346 54 :YKGSTFHRVVKNFMIQGGDFSEGNGKGGESIYGGYFKDENFILKHDRAFLLSMANRGKHTNGSQFFITTKPAPHLDGVHVVFGLVISGFEVIEQIENLK 1cwoA 48 :YKGSCFHRIIPGFMCQGGDFTRHNGTGGKSIYGEKFEDENFILKHTGPGILSMANAGPNTNGSQFFICTAKTEWLDGKHVVFGKVKEGMNIVEAMERFG T0346 154 :DAASRPYADVRVIDCGVL 1cwoA 147 :SRNGKTSKKITIADCGQL Number of specific fragments extracted= 3 number of extra gaps= 0 total=151 Number of alignments=41 # 1cwoA read from 1cwoA/merged-good-all-a2m # found chain 1cwoA in template set T0346 1 :SPQCHFDIEINREPVGRIMFQLFSDICPKTCKNFLCLCSGE 1cwoA 3 :NPTVFFDIAVDGEPLGRVSFELFADKVPKTAENFRALSTGE T0346 50 :KKLCYKGSTFHRVVKNFMIQGGDFSEGNGKGGESIYGGYFKDENFILKHDRAFLLSMANRGKHTNGSQFFITTKPAPHLDGVHVVFGLVISGFEVIEQIENL 1cwoA 44 :KGFGYKGSCFHRIIPGFMCQGGDFTRHNGTGGKSIYGEKFEDENFILKHTGPGILSMANAGPNTNGSQFFICTAKTEWLDGKHVVFGKVKEGMNIVEAMERF T0346 153 :TDAASRPYADVRVIDCGVLA 1cwoA 146 :GSRNGKTSKKITIADCGQLE Number of specific fragments extracted= 3 number of extra gaps= 0 total=154 Number of alignments=42 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1qoiA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1qoiA expands to /projects/compbio/data/pdb/1qoi.pdb.gz 1qoiA:# T0346 read from 1qoiA/merged-good-all-a2m # 1qoiA read from 1qoiA/merged-good-all-a2m # adding 1qoiA to template set # found chain 1qoiA in template set Warning: unaligning (T0346)L171 because last residue in template chain is (1qoiA)M177 T0346 1 :SPQCHFDIEINREPVGRIMFQLFSDICPKTCKNFLCLCSGEKG 1qoiA 10 :NPVVFFDVSIGGQEVGRMKIELFADVVPKTAENFRQFCTGEFR T0346 47 :TTGKKLCYKGSTFHRVVKNFMIQGGDFSEGNGKGGESIYGGYFKDENFILKHDRAFLLSMANRGKHTNGSQFFITTKPAPHLDGVHVVFGLVISGFEVIEQIENLKTDAASRPYADVRVIDCGV 1qoiA 53 :KDGVPIGYKGSTFHRVIKDFMIQGGDFVNGDGTGVASIYRGPFADENFKLRHSAPGLLSMANSGPSTNGCQFFITCSKCDWLDGKHVVFGKIIDGLLVMRKIENVPTGPNNKPKLPVVISQCGE Number of specific fragments extracted= 2 number of extra gaps= 0 total=156 Number of alignments=43 # 1qoiA read from 1qoiA/merged-good-all-a2m # found chain 1qoiA in template set Warning: unaligning (T0346)L171 because last residue in template chain is (1qoiA)M177 T0346 1 :SPQCHFDIEINREPVGRIMFQLFSDICPKTCKNFLCLCSGEK 1qoiA 10 :NPVVFFDVSIGGQEVGRMKIELFADVVPKTAENFRQFCTGEF T0346 46 :KTTGKKLCYKGSTFHRVVKNFMIQGGDFSEGNGKGGESIYGGYFKDENFILKHDRAFLLSMANRGKHTNGSQFFITTKPAPHLDGVHVVFGLVISGFEVIEQIENLKTDAASRPYADVRVIDCGV 1qoiA 52 :RKDGVPIGYKGSTFHRVIKDFMIQGGDFVNGDGTGVASIYRGPFADENFKLRHSAPGLLSMANSGPSTNGCQFFITCSKCDWLDGKHVVFGKIIDGLLVMRKIENVPTGPNNKPKLPVVISQCGE Number of specific fragments extracted= 2 number of extra gaps= 0 total=158 Number of alignments=44 # 1qoiA read from 1qoiA/merged-good-all-a2m # found chain 1qoiA in template set Warning: unaligning (T0346)L171 because last residue in template chain is (1qoiA)M177 T0346 2 :PQCHFDIEINREPVGRIMFQLFSDICPKTCKNFLCLCSGE 1qoiA 11 :PVVFFDVSIGGQEVGRMKIELFADVVPKTAENFRQFCTGE T0346 45 :GKTTGKKLCYKGSTFHRVVKNFMIQGGDFSEGNGKGGESIYGGYFKDENFILKHDRAFLLSMANRGKHTNGSQFFITTKPAPHLDGVHVVFGLVISGFEVIEQIENLKTDAASRPYADVRVIDCGV 1qoiA 51 :FRKDGVPIGYKGSTFHRVIKDFMIQGGDFVNGDGTGVASIYRGPFADENFKLRHSAPGLLSMANSGPSTNGCQFFITCSKCDWLDGKHVVFGKIIDGLLVMRKIENVPTGPNNKPKLPVVISQCGE Number of specific fragments extracted= 2 number of extra gaps= 0 total=160 Number of alignments=45 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2cfeA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2cfeA expands to /projects/compbio/data/pdb/2cfe.pdb.gz 2cfeA:Skipped atom 658, because occupancy 0.500 <= existing 0.500 in 2cfeA Skipped atom 660, because occupancy 0.500 <= existing 0.500 in 2cfeA Skipped atom 662, because occupancy 0.500 <= existing 0.500 in 2cfeA Skipped atom 664, because occupancy 0.500 <= existing 0.500 in 2cfeA Skipped atom 666, because occupancy 0.500 <= existing 0.500 in 2cfeA # T0346 read from 2cfeA/merged-good-all-a2m # 2cfeA read from 2cfeA/merged-good-all-a2m # adding 2cfeA to template set # found chain 2cfeA in template set Warning: unaligning (T0346)L171 because last residue in template chain is (2cfeA)C162 T0346 2 :PQCHFDIEINREPVGRIMFQLFSDICPKTCKNFLCLCSGEKGLG 2cfeA 2 :SNVFFDITKNGAPLGTIKFKLFDDVVPKTAANFRALCTGEKGFG T0346 54 :YKGSTFHRVVKNFMIQGGDFSEGNGKGGESIYGGYFKDENFILKHDRAFLLSMANRGKHTNGSQFFITTKPAPHLDGVHVVFGLVISGFEVIEQIENL 2cfeA 46 :YAGSHFHRVIPDFMLQGGDFTAGNGTGGKSIYGAKFADENFQLKHNKPGLLSMANAGPNTNGSQFFITTVVTSWLDGKHVVFGEVIDGMNVVKAIEAE T0346 153 :TDAASRPYADVRVIDCGV 2cfeA 144 :GSGSGKPRSRIEIAKCGV Number of specific fragments extracted= 3 number of extra gaps= 0 total=163 Number of alignments=46 # 2cfeA read from 2cfeA/merged-good-all-a2m # found chain 2cfeA in template set Warning: unaligning (T0346)L171 because last residue in template chain is (2cfeA)C162 T0346 2 :PQCHFDIEINREPVGRIMFQLFSDICPKTCKNFLCLCSGEKGLG 2cfeA 2 :SNVFFDITKNGAPLGTIKFKLFDDVVPKTAANFRALCTGEKGFG T0346 54 :YKGSTFHRVVKNFMIQGGDFSEGNGKGGESIYGGYFKDENFILKHDRAFLLSMANRGKHTNGSQFFITTKPAPHLDGVHVVFGLVISGFEVIEQIENLK 2cfeA 46 :YAGSHFHRVIPDFMLQGGDFTAGNGTGGKSIYGAKFADENFQLKHNKPGLLSMANAGPNTNGSQFFITTVVTSWLDGKHVVFGEVIDGMNVVKAIEAEG T0346 154 :DAASRPYADVRVIDCGV 2cfeA 145 :SGSGKPRSRIEIAKCGV Number of specific fragments extracted= 3 number of extra gaps= 0 total=166 Number of alignments=47 # 2cfeA read from 2cfeA/merged-good-all-a2m # found chain 2cfeA in template set Warning: unaligning (T0346)L171 because last residue in template chain is (2cfeA)C162 T0346 2 :PQCHFDIEINREPVGRIMFQLFSDICPKTCKNFLCLCSGE 2cfeA 2 :SNVFFDITKNGAPLGTIKFKLFDDVVPKTAANFRALCTGE T0346 50 :KKLCYKGSTFHRVVKNFMIQGGDFSEGNGKGGESIYGGYFKDENFILKHDRAFLLSMANRGKHTNGSQFFITTKPAPHLDGVHVVFGLVISGFEVIEQIENL 2cfeA 42 :KGFGYAGSHFHRVIPDFMLQGGDFTAGNGTGGKSIYGAKFADENFQLKHNKPGLLSMANAGPNTNGSQFFITTVVTSWLDGKHVVFGEVIDGMNVVKAIEAE T0346 153 :TDAASRPYADVRVIDCGV 2cfeA 144 :GSGSGKPRSRIEIAKCGV Number of specific fragments extracted= 3 number of extra gaps= 0 total=169 Number of alignments=48 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1dywA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1dywA expands to /projects/compbio/data/pdb/1dyw.pdb.gz 1dywA:# T0346 read from 1dywA/merged-good-all-a2m # 1dywA read from 1dywA/merged-good-all-a2m # adding 1dywA to template set # found chain 1dywA in template set Warning: unaligning (T0346)Y85 because of BadResidue code BAD_PEPTIDE in next template residue (1dywA)G87 Warning: unaligning (T0346)G86 because of BadResidue code BAD_PEPTIDE at template residue (1dywA)G87 Warning: unaligning (T0346)V163 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (1dywA)M164 Warning: unaligning (T0346)R164 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (1dywA)M164 T0346 2 :PQCHFDIEINREPVGRIMFQLFSDICPKTCKNFLCLCSGEKGLG 1dywA 4 :SKVFFDITIGGKASGRIVMELYDDVVPKTAGNFRALCTGENGIG T0346 47 :TTGKKLCYKGSTFHRVVKNFMIQGGDFSEGNGKGGESI 1dywA 48 :KSGKPLHFKGSKFHRIIPNFMIQGGDFTRGNGTGGESI T0346 87 :GYFKDENFILKHDRAFLLSMANRGKHTNGSQFFITTKPAPHLDGVHVVFGLVISGFEVIEQIENL 1dywA 88 :EKFPDENFKEKHTGPGVLSMANAGPNTNGSQFFLCTVKTEWLDGKHVVFGRVVEGLDVVKAVESN T0346 153 :TDAASRPYAD 1dywA 153 :GSQSGKPVKD T0346 165 :VIDCGVL 1dywA 165 :IADCGQL Number of specific fragments extracted= 5 number of extra gaps= 2 total=174 Number of alignments=49 # 1dywA read from 1dywA/merged-good-all-a2m # found chain 1dywA in template set Warning: unaligning (T0346)Y85 because of BadResidue code BAD_PEPTIDE in next template residue (1dywA)G87 Warning: unaligning (T0346)G86 because of BadResidue code BAD_PEPTIDE at template residue (1dywA)G87 Warning: unaligning (T0346)V163 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (1dywA)M164 Warning: unaligning (T0346)R164 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (1dywA)M164 T0346 2 :PQCHFDIEINREPVGRIMFQLFSDICPKTCKNFLCLCSGEKGLG 1dywA 4 :SKVFFDITIGGKASGRIVMELYDDVVPKTAGNFRALCTGENGIG T0346 47 :TTGKKLCYKGSTFHRVVKNFMIQGGDFSEGNGKGGESI 1dywA 48 :KSGKPLHFKGSKFHRIIPNFMIQGGDFTRGNGTGGESI T0346 87 :GYFKDENFILKHDRAFLLSMANRGKHTNGSQFFITTKPAPHLDGVHVVFGLVISGFEVIEQIENLK 1dywA 88 :EKFPDENFKEKHTGPGVLSMANAGPNTNGSQFFLCTVKTEWLDGKHVVFGRVVEGLDVVKAVESNG T0346 154 :DAASRPYAD 1dywA 154 :SQSGKPVKD T0346 165 :VIDCGVL 1dywA 165 :IADCGQL Number of specific fragments extracted= 5 number of extra gaps= 2 total=179 Number of alignments=50 # 1dywA read from 1dywA/merged-good-all-a2m # found chain 1dywA in template set Warning: unaligning (T0346)Y85 because of BadResidue code BAD_PEPTIDE in next template residue (1dywA)G87 Warning: unaligning (T0346)G86 because of BadResidue code BAD_PEPTIDE at template residue (1dywA)G87 Warning: unaligning (T0346)V163 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (1dywA)M164 Warning: unaligning (T0346)R164 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (1dywA)M164 T0346 2 :PQCHFDIEINREPVGRIMFQLFSDICPKTCKNFLCLCSGE 1dywA 4 :SKVFFDITIGGKASGRIVMELYDDVVPKTAGNFRALCTGE T0346 43 :GLGKTTGKKLCYKGSTFHRVVKNFMIQGGDFSEGNGKGGESI 1dywA 44 :NGIGKSGKPLHFKGSKFHRIIPNFMIQGGDFTRGNGTGGESI T0346 87 :GYFKDENFILKHDRAFLLSMANRGKHTNGSQFFITTKPAPHLDGVHVVFGLVISGFEVIEQIENL 1dywA 88 :EKFPDENFKEKHTGPGVLSMANAGPNTNGSQFFLCTVKTEWLDGKHVVFGRVVEGLDVVKAVESN T0346 153 :TDAASRPYAD 1dywA 153 :GSQSGKPVKD T0346 165 :VIDCGVLA 1dywA 165 :IADCGQLK Number of specific fragments extracted= 5 number of extra gaps= 2 total=184 Number of alignments=51 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2b71A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2b71A expands to /projects/compbio/data/pdb/2b71.pdb.gz 2b71A:# T0346 read from 2b71A/merged-good-all-a2m # 2b71A read from 2b71A/merged-good-all-a2m # adding 2b71A to template set # found chain 2b71A in template set Warning: unaligning (T0346)M67 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2b71A)I89 Warning: unaligning (T0346)I68 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2b71A)I89 Warning: unaligning (T0346)G86 because of BadResidue code BAD_PEPTIDE in next template residue (2b71A)E107 Warning: unaligning (T0346)G87 because of BadResidue code BAD_PEPTIDE at template residue (2b71A)E107 Warning: unaligning (T0346)F119 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2b71A)I141 Warning: unaligning (T0346)I120 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2b71A)I141 Warning: unaligning (T0346)V170 because last residue in template chain is (2b71A)T191 T0346 8 :IEINREPVGRIMFQLFSDICPKTCKNFLCLC 2b71A 40 :YITIYTNLGDFEVELYWYHSPKTCLNFYTLC T0346 41 :EKGL 2b71A 71 :EMGF T0346 54 :YKGSTFHRVVKNF 2b71A 75 :YDNTIFHRVIPNF T0346 69 :QGGD 2b71A 90 :QGGD T0346 74 :SEGNGKGGESIY 2b71A 94 :PTGTGKGGKSIY T0346 88 :YFKDEN 2b71A 108 :YFEDEI T0346 94 :FILKHDRAFLLSMANRGKHTNGSQF 2b71A 115 :KELKHTGAGILSMSNNGPNTNSSQF T0346 121 :TTKPAPHLDGVHVVFGLVISGFEVIEQIENLKTDAASRPYADVRVIDCG 2b71A 142 :TLAPLPHLDGKHTIFARVSKNMTCIENIASVQTTATNKPIFDLKILRTS Number of specific fragments extracted= 8 number of extra gaps= 3 total=192 Number of alignments=52 # 2b71A read from 2b71A/merged-good-all-a2m # found chain 2b71A in template set Warning: unaligning (T0346)M67 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2b71A)I89 Warning: unaligning (T0346)I68 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2b71A)I89 Warning: unaligning (T0346)G86 because of BadResidue code BAD_PEPTIDE in next template residue (2b71A)E107 Warning: unaligning (T0346)G87 because of BadResidue code BAD_PEPTIDE at template residue (2b71A)E107 Warning: unaligning (T0346)F119 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2b71A)I141 Warning: unaligning (T0346)I120 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2b71A)I141 Warning: unaligning (T0346)V170 because last residue in template chain is (2b71A)T191 T0346 7 :DIEINREPVGRIMFQLFSDICPKTCKNFLCLCSGEK 2b71A 39 :GYITIYTNLGDFEVELYWYHSPKTCLNFYTLCEMGF T0346 54 :YKGSTFHRVVKNF 2b71A 75 :YDNTIFHRVIPNF T0346 69 :QGGDFS 2b71A 90 :QGGDPT T0346 76 :GNGKGGESIY 2b71A 96 :GTGKGGKSIY T0346 88 :YFKDEN 2b71A 108 :YFEDEI T0346 94 :FILKHDRAFLLSMANRGKHTNGSQF 2b71A 115 :KELKHTGAGILSMSNNGPNTNSSQF T0346 121 :TTKPAPHLDGVHVVFGLVISGFEVIEQIENLKTDAASRPYADVRVIDCG 2b71A 142 :TLAPLPHLDGKHTIFARVSKNMTCIENIASVQTTATNKPIFDLKILRTS Number of specific fragments extracted= 7 number of extra gaps= 3 total=199 Number of alignments=53 # 2b71A read from 2b71A/merged-good-all-a2m # found chain 2b71A in template set Warning: unaligning (T0346)M67 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2b71A)I89 Warning: unaligning (T0346)I68 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2b71A)I89 Warning: unaligning (T0346)Y85 because of BadResidue code BAD_PEPTIDE in next template residue (2b71A)E107 Warning: unaligning (T0346)G86 because of BadResidue code BAD_PEPTIDE at template residue (2b71A)E107 Warning: unaligning (T0346)F119 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2b71A)I141 Warning: unaligning (T0346)I120 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2b71A)I141 T0346 5 :HFDIEI 2b71A 40 :YITIYT T0346 14 :PVGRIMFQLFSDICPKTCKNFLCLCSGE 2b71A 46 :NLGDFEVELYWYHSPKTCLNFYTLCEMG T0346 53 :CYKGSTFHRVVKNF 2b71A 74 :FYDNTIFHRVIPNF T0346 69 :QGGDFSEGNGKGGESI 2b71A 90 :QGGDPTGTGKGGKSIY T0346 87 :GYFKDENFILKHDRAFLLSMANRGKHTNGSQF 2b71A 108 :YFEDEINKELKHTGAGILSMSNNGPNTNSSQF T0346 121 :TTKPAPHLDGVHVVFGLVISGFEVIEQIENLKTDAASRPYADVRVIDCG 2b71A 142 :TLAPLPHLDGKHTIFARVSKNMTCIENIASVQTTATNKPIFDLKILRTS Number of specific fragments extracted= 6 number of extra gaps= 3 total=205 Number of alignments=54 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1xo7A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0346 read from 1xo7A/merged-good-all-a2m # 1xo7A read from 1xo7A/merged-good-all-a2m # found chain 1xo7A in training set Warning: unaligning (T0346)G40 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1xo7A)E45 Warning: unaligning (T0346)E41 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1xo7A)E45 Warning: unaligning (T0346)K42 because of BadResidue code BAD_PEPTIDE at template residue (1xo7A)N46 Warning: unaligning (T0346)S105 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1xo7A)M101 Warning: unaligning (T0346)M106 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1xo7A)M101 Warning: unaligning (T0346)A107 because of BadResidue code BAD_PEPTIDE at template residue (1xo7A)A102 Warning: unaligning (T0346)L171 because last residue in template chain is (1xo7A)L166 T0346 3 :QCHFDIEINREPVGRIMFQLFSDICPKTCKNFLCLCS 1xo7A 7 :KVYFDITIGDEPVGRVVIGLFGNDVPKTVENFKQLAS T0346 43 :GLG 1xo7A 47 :GFG T0346 54 :YKGSTFHRVVKNFMIQGGDFSEGNGKGGESIYGGYFKDENFILKH 1xo7A 50 :YKGSIFHRVIRNFMIQGGDFTNFDGTGGKSIYGTRFDDENLKIKH T0346 100 :RAFLL 1xo7A 95 :FVGAV T0346 108 :NRGKHTNGSQFFITTKPAPHLDGVHVVFGLVISGFEVIEQIENLKTDAASRPYADVRVIDCGV 1xo7A 103 :NAGPNSNGSQFFVTTAPTPWLDGRHVVFGKVVEGMDVVKKVENTKTGLNDKPKKAVKINDCGV Number of specific fragments extracted= 5 number of extra gaps= 2 total=210 Number of alignments=55 # 1xo7A read from 1xo7A/merged-good-all-a2m # found chain 1xo7A in training set Warning: unaligning (T0346)G40 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1xo7A)E45 Warning: unaligning (T0346)E41 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1xo7A)E45 Warning: unaligning (T0346)K42 because of BadResidue code BAD_PEPTIDE at template residue (1xo7A)N46 Warning: unaligning (T0346)S105 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1xo7A)M101 Warning: unaligning (T0346)M106 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1xo7A)M101 Warning: unaligning (T0346)A107 because of BadResidue code BAD_PEPTIDE at template residue (1xo7A)A102 Warning: unaligning (T0346)L171 because last residue in template chain is (1xo7A)L166 T0346 3 :QCHFDIEINREPVGRIMFQLFSDICPKTCKNFLCLCS 1xo7A 7 :KVYFDITIGDEPVGRVVIGLFGNDVPKTVENFKQLAS T0346 43 :GLG 1xo7A 47 :GFG T0346 54 :YKGSTFHRVVKNFMIQGGDFSEGNGKGGESIYGGYFKDENFILKH 1xo7A 50 :YKGSIFHRVIRNFMIQGGDFTNFDGTGGKSIYGTRFDDENLKIKH T0346 100 :RAFLL 1xo7A 95 :FVGAV T0346 108 :NRGKHTNGSQFFITTKPAPHLDGVHVVFGLVISGFEVIEQIENLKTDAASRPYADVRVIDCGV 1xo7A 103 :NAGPNSNGSQFFVTTAPTPWLDGRHVVFGKVVEGMDVVKKVENTKTGLNDKPKKAVKINDCGV Number of specific fragments extracted= 5 number of extra gaps= 2 total=215 Number of alignments=56 # 1xo7A read from 1xo7A/merged-good-all-a2m # found chain 1xo7A in training set Warning: unaligning (T0346)G40 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1xo7A)E45 Warning: unaligning (T0346)E41 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1xo7A)E45 Warning: unaligning (T0346)K42 because of BadResidue code BAD_PEPTIDE at template residue (1xo7A)N46 Warning: unaligning (T0346)S105 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1xo7A)M101 Warning: unaligning (T0346)M106 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1xo7A)M101 Warning: unaligning (T0346)A107 because of BadResidue code BAD_PEPTIDE at template residue (1xo7A)A102 Warning: unaligning (T0346)L171 because last residue in template chain is (1xo7A)L166 T0346 2 :PQCHFDIEINREPVGRIMFQLFSDICPKTCKNFLCLCS 1xo7A 6 :DKVYFDITIGDEPVGRVVIGLFGNDVPKTVENFKQLAS T0346 51 :KLCYKGSTFHRVVKNFMIQGGDFSEGNGKGGESIYGGYFKDENFILKHDR 1xo7A 47 :GFGYKGSIFHRVIRNFMIQGGDFTNFDGTGGKSIYGTRFDDENLKIKHFV T0346 102 :FLL 1xo7A 97 :GAV T0346 108 :NRGKHTNGSQFFITTKPAPHLDGVHVVFGLVISGFEVIEQIENLKTDAASRPYADVRVIDCGV 1xo7A 103 :NAGPNSNGSQFFVTTAPTPWLDGRHVVFGKVVEGMDVVKKVENTKTGLNDKPKKAVKINDCGV Number of specific fragments extracted= 4 number of extra gaps= 2 total=219 Number of alignments=57 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1cynA/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/T0346/1cynA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0346/1cynA/merged-good-all-a2m.gz for input Trying 1cynA/merged-good-all-a2m Error: Couldn't open file 1cynA/merged-good-all-a2m or 1cynA/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1qnhA/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/T0346/1qnhA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0346/1qnhA/merged-good-all-a2m.gz for input Trying 1qnhA/merged-good-all-a2m Error: Couldn't open file 1qnhA/merged-good-all-a2m or 1qnhA/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1j2aA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1j2aA expands to /projects/compbio/data/pdb/1j2a.pdb.gz 1j2aA:# T0346 read from 1j2aA/merged-good-all-a2m # 1j2aA read from 1j2aA/merged-good-all-a2m # adding 1j2aA to template set # found chain 1j2aA in template set Warning: unaligning (T0346)V170 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1j2aA)L165 Warning: unaligning (T0346)L171 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1j2aA)L165 T0346 2 :P 1j2aA 5 :P T0346 8 :IEINREPVGRIMFQLFSDICPKTCKNFLCLC 1j2aA 6 :HVLLTTSAGNIELELDKQKAPVSVQNFVDYV T0346 41 :EKGL 1j2aA 37 :NSGF T0346 54 :YKGSTFHRVVKNFMIQGGDFSEGNGKGGE 1j2aA 41 :YNNTTFHRVIPGFMIQGGGFTEQMQQKKP T0346 86 :GGYFKDENFILKHDRAFLLSMANR 1j2aA 70 :NPPIKNEADNGLRNTRGTIAMART T0346 110 :GKHTNGSQFFITTKPAPHLD 1j2aA 95 :DKDSATSQFFINVADNAFLD T0346 130 :GVHVVFGLVISGFEVIEQIENLKT 1j2aA 120 :FGYAVFGKVVKGMDVADKISQVPT T0346 154 :DAASRPYADVRVIDCG 1j2aA 148 :PYQNVPSKPVVILSAT Number of specific fragments extracted= 8 number of extra gaps= 1 total=227 Number of alignments=58 # 1j2aA read from 1j2aA/merged-good-all-a2m # found chain 1j2aA in template set Warning: unaligning (T0346)V170 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1j2aA)L165 Warning: unaligning (T0346)L171 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1j2aA)L165 T0346 8 :IEINREPVGRIMFQLFSDICPKTCKNFLCLCSGEK 1j2aA 6 :HVLLTTSAGNIELELDKQKAPVSVQNFVDYVNSGF T0346 54 :YKGSTFHRVVKNFMIQGGDFS 1j2aA 41 :YNNTTFHRVIPGFMIQGGGFT T0346 76 :GNGKGGES 1j2aA 62 :EQMQQKKP T0346 86 :GGYFKDENFILKHDRAFLLSMANR 1j2aA 70 :NPPIKNEADNGLRNTRGTIAMART T0346 110 :GKHTNGSQFFITTKPAPHLDGV 1j2aA 95 :DKDSATSQFFINVADNAFLDHG T0346 132 :HVVFGLVISGFEVIEQIENLKT 1j2aA 122 :YAVFGKVVKGMDVADKISQVPT T0346 154 :DAASRPYADVRVIDCG 1j2aA 148 :PYQNVPSKPVVILSAT Number of specific fragments extracted= 7 number of extra gaps= 1 total=234 Number of alignments=59 # 1j2aA read from 1j2aA/merged-good-all-a2m # found chain 1j2aA in template set Warning: unaligning (T0346)V170 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1j2aA)L165 Warning: unaligning (T0346)L171 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1j2aA)L165 T0346 1 :SPQCHFDI 1j2aA 4 :DPHVLLTT T0346 14 :PVGRIMFQLFSDICPKTCKNFLCLCSGE 1j2aA 12 :SAGNIELELDKQKAPVSVQNFVDYVNSG T0346 53 :CYKGSTFHRVVKNFMIQGGDFSEGNGKGGES 1j2aA 40 :FYNNTTFHRVIPGFMIQGGGFTEQMQQKKPN T0346 86 :GGYFKDENFILKHDRAFLLSMANRGKHTNGSQFFITTKPAPHLD 1j2aA 71 :PPIKNEADNGLRNTRGTIAMARTADKDSATSQFFINVADNAFLD T0346 131 :VHVVFGLVISGFEVIEQIENLKTDAAS 1j2aA 121 :GYAVFGKVVKGMDVADKISQVPTHDVG T0346 158 :RPYADVRVIDCG 1j2aA 152 :VPSKPVVILSAT Number of specific fragments extracted= 6 number of extra gaps= 1 total=240 Number of alignments=60 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1v9tA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0346 read from 1v9tA/merged-good-all-a2m # 1v9tA read from 1v9tA/merged-good-all-a2m # found chain 1v9tA in training set Warning: unaligning (T0346)T58 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1v9tA)F46 Warning: unaligning (T0346)F59 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1v9tA)F46 T0346 2 :P 1v9tA 5 :P T0346 8 :IEINREPVGRIMFQLFSDICPKTCKNFLCLC 1v9tA 6 :HVLLTTSAGNIELELDKQKAPVSVQNFVDYV T0346 41 :EKGL 1v9tA 37 :NSGF T0346 54 :YKGS 1v9tA 41 :YNNT T0346 60 :HRVVKNFMIQGGDFSEGNGKGGE 1v9tA 47 :HRVIPGFMIQGGGFTEQMQQKKP T0346 86 :GGYFKDENFILKHDRAFLLSMANR 1v9tA 70 :NPPIKNEADNGLRNTRGTIAMART T0346 110 :GKHTNGSQFFITTKPAPHLD 1v9tA 95 :DKDSATSQFFINVADNAFLD T0346 130 :GVHVVFGLVISGFEVIEQIENLKT 1v9tA 120 :FGYAVFGKVVKGMDVADKISQVPT T0346 154 :DA 1v9tA 147 :GP T0346 156 :ASRPYADVRVIDCGVL 1v9tA 150 :QNVPSKPVVILSATVL Number of specific fragments extracted= 10 number of extra gaps= 1 total=250 Number of alignments=61 # 1v9tA read from 1v9tA/merged-good-all-a2m # found chain 1v9tA in training set Warning: unaligning (T0346)T58 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1v9tA)F46 Warning: unaligning (T0346)F59 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1v9tA)F46 T0346 7 :DIEINREPVGRIMFQLFSDICPKTCKNFLCLCSGEK 1v9tA 5 :PHVLLTTSAGNIELELDKQKAPVSVQNFVDYVNSGF T0346 54 :YKGS 1v9tA 41 :YNNT T0346 60 :HRVVKNFMIQGGDFSEGN 1v9tA 47 :HRVIPGFMIQGGGFTEQM T0346 79 :KGGES 1v9tA 65 :QQKKP T0346 86 :GGYFKDENFILKHDRAFLLSMANR 1v9tA 70 :NPPIKNEADNGLRNTRGTIAMART T0346 110 :GKHTNGSQFFITTKPAPHLDGV 1v9tA 95 :DKDSATSQFFINVADNAFLDHG T0346 132 :HVVFGLVISGFEVIEQIENLKT 1v9tA 122 :YAVFGKVVKGMDVADKISQVPT T0346 155 :AA 1v9tA 147 :GP T0346 157 :SRPYADVRVIDCGVLA 1v9tA 151 :NVPSKPVVILSATVLP Number of specific fragments extracted= 9 number of extra gaps= 1 total=259 Number of alignments=62 # 1v9tA read from 1v9tA/merged-good-all-a2m # found chain 1v9tA in training set Warning: unaligning (T0346)T58 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1v9tA)F46 Warning: unaligning (T0346)F59 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1v9tA)F46 T0346 1 :SPQCHFDI 1v9tA 4 :DPHVLLTT T0346 14 :PVGRIMFQLFSDICPKTCKNFLCLCSGE 1v9tA 12 :SAGNIELELDKQKAPVSVQNFVDYVNSG T0346 53 :CYKGS 1v9tA 40 :FYNNT T0346 60 :HRVVKNFMIQGGDFSEGNGKGGES 1v9tA 47 :HRVIPGFMIQGGGFTEQMQQKKPN T0346 86 :GGYFKDENFILKHDRAFLLSMANRGKHTNGSQFFITTKPAPHLD 1v9tA 71 :PPIKNEADNGLRNTRGTIAMARTADKDSATSQFFINVADNAFLD T0346 131 :VHVVFGLVISGFEVIEQIENLKTD 1v9tA 121 :GYAVFGKVVKGMDVADKISQVPTH T0346 155 :A 1v9tA 147 :G T0346 156 :ASRPYADVRVIDCGVLA 1v9tA 150 :QNVPSKPVVILSATVLP Number of specific fragments extracted= 8 number of extra gaps= 1 total=267 Number of alignments=63 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2alfA/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/T0346/2alfA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0346/2alfA/merged-good-all-a2m.gz for input Trying 2alfA/merged-good-all-a2m Error: Couldn't open file 2alfA/merged-good-all-a2m or 2alfA/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 2cpl/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2cpl expands to /projects/compbio/data/pdb/2cpl.pdb.gz 2cpl:Warning: there is no chain 2cpl will retry with 2cplA # T0346 read from 2cpl/merged-good-all-a2m # 2cpl read from 2cpl/merged-good-all-a2m # adding 2cpl to template set # found chain 2cpl in template set T0346 1 :SPQCHFDIEINREPVGRIMFQLFSDICPKTCKNFLCLCSGEKGLG 2cpl 3 :NPTVFFDIAVDGEPLGRVSFELFADKVPKTAENFRALSTGEKGFG T0346 54 :YKGSTFHRVVKNFMIQGGDFSEGNGKGGESIYGGYFKDENFILKHDRAFLLSMANRGKHTNGSQFFITTKPAPHLDGVHVVFGLVISGFEVIEQIENL 2cpl 48 :YKGSCFHRIIPGFMCQGGDFTRHNGTGGKSIYGEKFEDENFILKHTGPGILSMANAGPNTNGSQFFICTAKTEWLDGKHVVFGKVKEGMNIVEAMERF T0346 153 :TDAASRPYADVRVIDCGVL 2cpl 146 :GSRNGKTSKKITIADCGQL Number of specific fragments extracted= 3 number of extra gaps= 0 total=270 Number of alignments=64 # 2cpl read from 2cpl/merged-good-all-a2m # found chain 2cpl in template set T0346 1 :SPQCHFDIEINREPVGRIMFQLFSDICPKTCKNFLCLCSGEKGLG 2cpl 3 :NPTVFFDIAVDGEPLGRVSFELFADKVPKTAENFRALSTGEKGFG T0346 54 :YKGSTFHRVVKNFMIQGGDFSEGNGKGGESIYGGYFKDENFILKHDRAFLLSMANRGKHTNGSQFFITTKPAPHLDGVHVVFGLVISGFEVIEQIENLK 2cpl 48 :YKGSCFHRIIPGFMCQGGDFTRHNGTGGKSIYGEKFEDENFILKHTGPGILSMANAGPNTNGSQFFICTAKTEWLDGKHVVFGKVKEGMNIVEAMERFG T0346 154 :DAASRPYADVRVIDCGVL 2cpl 147 :SRNGKTSKKITIADCGQL Number of specific fragments extracted= 3 number of extra gaps= 0 total=273 Number of alignments=65 # 2cpl read from 2cpl/merged-good-all-a2m # found chain 2cpl in template set T0346 1 :SPQCHFDIEINREPVGRIMFQLFSDICPKTCKNFLCLCSGE 2cpl 3 :NPTVFFDIAVDGEPLGRVSFELFADKVPKTAENFRALSTGE T0346 50 :KKLCYKGSTFHRVVKNFMIQGGDFSEGNGKGGESIYGGYFKDENFILKHDRAFLLSMANRGKHTNGSQFFITTKPAPHLDGVHVVFGLVISGFEVIEQIENL 2cpl 44 :KGFGYKGSCFHRIIPGFMCQGGDFTRHNGTGGKSIYGEKFEDENFILKHTGPGILSMANAGPNTNGSQFFICTAKTEWLDGKHVVFGKVKEGMNIVEAMERF T0346 153 :TDAASRPYADVRVIDCGVLA 2cpl 146 :GSRNGKTSKKITIADCGQLE Number of specific fragments extracted= 3 number of extra gaps= 0 total=276 Number of alignments=66 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1z81A/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/T0346/1z81A/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0346/1z81A/merged-good-all-a2m.gz for input Trying 1z81A/merged-good-all-a2m Error: Couldn't open file 1z81A/merged-good-all-a2m or 1z81A/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 2a2nA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2a2nA expands to /projects/compbio/data/pdb/2a2n.pdb.gz 2a2nA:# T0346 read from 2a2nA/merged-good-all-a2m # 2a2nA read from 2a2nA/merged-good-all-a2m # adding 2a2nA to template set # found chain 2a2nA in template set Warning: unaligning (T0346)L171 because last residue in template chain is (2a2nA)K646 T0346 1 :SPQCHFDIEINREPVGRIMFQLFSDICPKTCKNFLCLC 2a2nA 486 :GPKRVSDSAIIHTSMGDIHTKLFPVECPKTVENFCVHS T0346 41 :EKGL 2a2nA 524 :RNGY T0346 54 :YKGSTFHRVVKNFMIQGGD 2a2nA 528 :YNGHTFHRIIKGFMIQTGD T0346 74 :SEGNGKGGESIYGGYFKDEN 2a2nA 547 :PTGTGMGGESIWGGEFEDEF T0346 94 :FILKHDRAFLLSMANRGKHTNGSQFFITTKPAPHLDGVHVVFGLVISGFEVIEQIENLKTDAA 2a2nA 568 :STLRHDRPYTLSMANAGSNTNGSQFFITVVPTPWLDNKHTVFGRVTKGMEVVQRISNVKVNPK T0346 157 :SRPYADVRVIDCGV 2a2nA 632 :DKPYEDVSIINITV Number of specific fragments extracted= 6 number of extra gaps= 0 total=282 Number of alignments=67 # 2a2nA read from 2a2nA/merged-good-all-a2m # found chain 2a2nA in template set Warning: unaligning (T0346)L171 because last residue in template chain is (2a2nA)K646 T0346 1 :SPQCHFDIEINREPVGRIMFQLFSDICPKTCKNFLCLCSGEK 2a2nA 486 :GPKRVSDSAIIHTSMGDIHTKLFPVECPKTVENFCVHSRNGY T0346 54 :YKGSTFHRVVKNFMIQGGDFS 2a2nA 528 :YNGHTFHRIIKGFMIQTGDPT T0346 76 :GNGKGGESIYGGYFKDEN 2a2nA 549 :GTGMGGESIWGGEFEDEF T0346 94 :FILKHDRAFLLSMANRGKHTNGSQFFITTKPAPHLDGVHVVFGLVISGFEVIEQIENLKTDAA 2a2nA 568 :STLRHDRPYTLSMANAGSNTNGSQFFITVVPTPWLDNKHTVFGRVTKGMEVVQRISNVKVNPK T0346 157 :SRPYADVRVIDCGV 2a2nA 632 :DKPYEDVSIINITV Number of specific fragments extracted= 5 number of extra gaps= 0 total=287 Number of alignments=68 # 2a2nA read from 2a2nA/merged-good-all-a2m # found chain 2a2nA in template set T0346 7 :DIEINREPVGRIMFQLFSDICPKTCKNFLCLCSGE 2a2nA 492 :DSAIIHTSMGDIHTKLFPVECPKTVENFCVHSRNG T0346 53 :CYKGSTFHRVVKNFMIQGGDFSEGNGKGGESIYGGYFKDENFILKHDRAFLLSMANRGKHTNGSQFFITTKPAPHLDGVHVVFGLVISGFEVIEQIENLKTDAA 2a2nA 527 :YYNGHTFHRIIKGFMIQTGDPTGTGMGGESIWGGEFEDEFHSTLRHDRPYTLSMANAGSNTNGSQFFITVVPTPWLDNKHTVFGRVTKGMEVVQRISNVKVNPK T0346 157 :SRPYADVRVIDCGV 2a2nA 632 :DKPYEDVSIINITV Number of specific fragments extracted= 3 number of extra gaps= 0 total=290 Number of alignments=69 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1m9eA/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/T0346/1m9eA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0346/1m9eA/merged-good-all-a2m.gz for input Trying 1m9eA/merged-good-all-a2m Error: Couldn't open file 1m9eA/merged-good-all-a2m or 1m9eA/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1zkcA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1zkcA expands to /projects/compbio/data/pdb/1zkc.pdb.gz 1zkcA:# T0346 read from 1zkcA/merged-good-all-a2m # 1zkcA read from 1zkcA/merged-good-all-a2m # adding 1zkcA to template set # found chain 1zkcA in template set T0346 7 :DIEINREPVGRIMFQLFSDICPKTCKNFLCLC 1zkcA 280 :GYVRLHTNKGDLNLELHCDLTPKTCENFIRLC T0346 41 :EKGL 1zkcA 312 :KKHY T0346 54 :YKGSTFHRVVKNFMIQGGD 1zkcA 316 :YDGTIFHRSIRNFVIQGGD T0346 74 :SEGNGKGGESIYGGYFKDEN 1zkcA 335 :PTGTGTGGESYWGKPFKDEF T0346 94 :FILKHDRAFLLSMANRGKHTNGSQFFITTKPAPHLDGVHVVFGLVISGFEVIEQIENLKTDAA 1zkcA 356 :PNLSHTGRGILSMANSGPNSNRSQFFITFRSCAYLDKKHTIFGRVVGGFDVLTAMENVESDPK T0346 157 :SRPYADVRVIDCGVL 1zkcA 420 :DRPKEEIRIDATTVF Number of specific fragments extracted= 6 number of extra gaps= 0 total=296 Number of alignments=70 # 1zkcA read from 1zkcA/merged-good-all-a2m # found chain 1zkcA in template set T0346 8 :IEINREPVGRIMFQLFSDICPKTCKNFLCLCSGEK 1zkcA 281 :YVRLHTNKGDLNLELHCDLTPKTCENFIRLCKKHY T0346 54 :YKGSTFHRVVKNFMIQGGDFS 1zkcA 316 :YDGTIFHRSIRNFVIQGGDPT T0346 76 :GNGKGGESIYGGYFKDEN 1zkcA 337 :GTGTGGESYWGKPFKDEF T0346 94 :FILKHDRAFLLSMANRGKHTNGSQFFITTKPAPHLDGVHVVFGLVISGFEVIEQIENLKTDAA 1zkcA 356 :PNLSHTGRGILSMANSGPNSNRSQFFITFRSCAYLDKKHTIFGRVVGGFDVLTAMENVESDPK T0346 157 :SRPYADVRVIDCGVL 1zkcA 420 :DRPKEEIRIDATTVF Number of specific fragments extracted= 5 number of extra gaps= 0 total=301 Number of alignments=71 # 1zkcA read from 1zkcA/merged-good-all-a2m # found chain 1zkcA in template set T0346 5 :HFDIEI 1zkcA 281 :YVRLHT T0346 14 :PVGRIMFQLFSDICPKTCKNFLCLCSGE 1zkcA 287 :NKGDLNLELHCDLTPKTCENFIRLCKKH T0346 53 :CYKGSTFHRVVKNFMIQGGDFSEGNGKGGESIYGGYFKDENFILKHDRAFLLSMANRGKHTNGSQFFITTKPAPHLDGVHVVFGLVISGFEVIEQIENLKTDAA 1zkcA 315 :YYDGTIFHRSIRNFVIQGGDPTGTGTGGESYWGKPFKDEFRPNLSHTGRGILSMANSGPNSNRSQFFITFRSCAYLDKKHTIFGRVVGGFDVLTAMENVESDPK T0346 157 :SRPYADVRVIDCGV 1zkcA 420 :DRPKEEIRIDATTV Number of specific fragments extracted= 4 number of extra gaps= 0 total=305 Number of alignments=72 # command:Using radius: 8.0000 Alignment mode NUMB_ALIGNS: 72 Adding 925 constraints to all.constraints Done adding distance constraints # command:Reading probabilities from probabilities.dat Reading constraints from ConstraintSet all.constraints maxweight: 1.0000 Optimizing... Probability sum: -330.4926, CN propb: -330.4926 weights: 0.6433 constraints: 420 # command:Found ConstraintSet # PrintContacts align.constraints_v3 Number of constraints in align.constraints 420 # command:Found ConstraintSet # PrintContacts align_bonus.constraints_v3 Number of constraints in align.constraints.bonus 420 # command:Found ConstraintSet # PrintContacts rejected.constraints_v3 Number of constraints in rejected.constraints 505 # command:Found ConstraintSet # PrintContacts rejected_bonus.constraints_v3 Number of constraints in rejected.constraints.bonus 505 # command:Found ConstraintSet # PrintContacts non_contacts.constraints_v3 Number of constraints in noncontact.constraints 0 # command:Found ConstraintSet # PrintContacts non_contacts_bonus.constraints_v3 Number of constraints in noncontact.constraints.bonus 0 # command:Found ConstraintSet # PrintContacts all.constraints_v3 Number of constraints in all.constraints 925 # command: