# 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:Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0346//projects/compbio/experiments/protein-predict/casp7/T0346/align.constraints_v3.costfcn or /projects/compbio/experiments/protein-predict/casp7/T0346//projects/compbio/experiments/protein-predict/casp7/T0346/align.constraints_v3.costfcn.gz for input Trying /projects/compbio/experiments/protein-predict/casp7/T0346/align.constraints_v3.costfcn # reading script from file /projects/compbio/experiments/protein-predict/casp7/T0346/align.constraints_v3.costfcn # future Constraint commands -> align # future HelixConstraint commands -> align # future StrandConstraint commands -> align # future SheetConstraint commands -> align # future Hbond commands -> align # future SSbond commands -> align # Constraint # added constraint: constraint((T0346)L22.CB, (T0346)C31.CB) [> 2.5501 = 4.2501 < 5.5251] w=1.0000 to align # Constraint # added constraint: constraint((T0346)L22.CB, (T0346)F135.CB) [> 3.7902 = 6.3170 < 8.2121] w=1.0000 to align # Constraint # added constraint: constraint((T0346)L22.CB, (T0346)G136.CA) [> 3.1536 = 5.2561 < 6.8329] w=1.0000 to align # Constraint # added constraint: constraint((T0346)F23.CB, (T0346)F135.CB) [> 3.4587 = 5.7645 < 7.4938] w=1.0000 to align # Constraint # added constraint: constraint((T0346)F23.CB, (T0346)G136.CA) [> 3.0673 = 5.1121 < 6.6458] w=1.0000 to align # Constraint # added constraint: constraint((T0346)C27.CB, (T0346)F135.CB) [> 2.5913 = 4.3188 < 5.6144] w=1.0000 to align # Constraint # added constraint: constraint((T0346)T30.CB, (T0346)V133.CB) [> 3.3026 = 5.5044 < 7.1557] w=1.0000 to align # Constraint # added constraint: constraint((T0346)T30.CB, (T0346)F135.CB) [> 2.5257 = 4.2095 < 5.4724] w=1.0000 to align # Constraint # added constraint: constraint((T0346)C31.CB, (T0346)F135.CB) [> 3.2586 = 5.4310 < 7.0602] w=1.0000 to align # Constraint # added constraint: constraint((T0346)F34.CB, (T0346)F118.CB) [> 4.1765 = 6.9608 < 9.0491] w=1.0000 to align # Constraint # added constraint: constraint((T0346)L37.CB, (T0346)S116.CB) [> 3.4157 = 5.6929 < 7.4008] w=1.0000 to align # Constraint # added constraint: constraint((T0346)C38.CB, (T0346)Y54.CB) [> 3.4283 = 5.7139 < 7.4281] w=1.0000 to align # Constraint # added constraint: constraint((T0346)C38.CB, (T0346)C168.CB) [> 2.6756 = 4.4593 < 5.7971] w=1.0000 to align # Constraint # added constraint: constraint((T0346)C38.CB, (T0346)G169.CA) [> 3.0399 = 5.0665 < 6.5864] w=1.0000 to align # Constraint # added constraint: constraint((T0346)Y54.CB, (T0346)C168.CB) [> 3.0241 = 5.0402 < 6.5523] w=1.0000 to align # Constraint # added constraint: constraint((T0346)K55.CB, (T0346)V165.CB) [> 3.7693 = 6.2821 < 8.1668] w=1.0000 to align # Constraint # added constraint: constraint((T0346)P14.CB, (T0346)I166.CB) [> 3.9481 = 6.5802 < 8.5543] w=1.0000 to align # Constraint # added constraint: constraint((T0346)V15.CB, (T0346)V144.CB) [> 3.4428 = 5.7381 < 7.4595] w=1.0000 to align # Constraint # added constraint: constraint((T0346)G16.CA, (T0346)V144.CB) [> 2.8905 = 4.8175 < 6.2628] w=1.0000 to align # Constraint # added constraint: constraint((T0346)R17.CB, (T0346)V144.CB) [> 4.0533 = 6.7556 < 8.7823] w=1.0000 to align # Constraint # added constraint: constraint((T0346)I18.CB, (T0346)V138.CB) [> 3.6353 = 6.0588 < 7.8764] w=1.0000 to align # Constraint # added constraint: constraint((T0346)I18.CB, (T0346)S140.CB) [> 4.1961 = 6.9935 < 9.0916] w=1.0000 to align # Constraint # added constraint: constraint((T0346)I18.CB, (T0346)G141.CA) [> 2.9782 = 4.9637 < 6.4528] w=1.0000 to align # Constraint # added constraint: constraint((T0346)I18.CB, (T0346)V144.CB) [> 3.0687 = 5.1145 < 6.6489] w=1.0000 to align # Constraint # added constraint: constraint((T0346)I18.CB, (T0346)I145.CB) [> 3.7007 = 6.1679 < 8.0183] w=1.0000 to align # Constraint # added constraint: constraint((T0346)M19.CB, (T0346)V138.CB) [> 4.2455 = 7.0759 < 9.1986] w=1.0000 to align # Constraint # added constraint: constraint((T0346)M19.CB, (T0346)I139.CB) [> 2.9819 = 4.9698 < 6.4607] w=1.0000 to align # Constraint # added constraint: constraint((T0346)M19.CB, (T0346)S140.CB) [> 2.2826 = 3.8044 < 4.9457] w=1.0000 to align # Constraint # added constraint: constraint((T0346)M19.CB, (T0346)G141.CA) [> 3.8655 = 6.4426 < 8.3753] w=1.0000 to align # Constraint # added constraint: constraint((T0346)F20.CB, (T0346)G136.CA) [> 3.5431 = 5.9051 < 7.6767] w=1.0000 to align # Constraint # added constraint: constraint((T0346)F20.CB, (T0346)L137.CB) [> 3.9711 = 6.6186 < 8.6042] w=1.0000 to align # Constraint # added constraint: constraint((T0346)F20.CB, (T0346)V138.CB) [> 3.4965 = 5.8275 < 7.5758] w=1.0000 to align # Constraint # added constraint: constraint((T0346)Q21.CB, (T0346)G136.CA) [> 3.5438 = 5.9063 < 7.6782] w=1.0000 to align # Constraint # added constraint: constraint((T0346)Q21.CB, (T0346)L137.CB) [> 3.1721 = 5.2869 < 6.8729] w=1.0000 to align # Constraint # added constraint: constraint((T0346)Q21.CB, (T0346)I139.CB) [> 2.8284 = 4.7140 < 6.1283] w=1.0000 to align # Constraint # added constraint: constraint((T0346)F89.CB, (T0346)H112.CB) [> 4.2836 = 7.1394 < 9.2812] w=1.0000 to align # Constraint # added constraint: constraint((T0346)E92.CB, (T0346)V133.CB) [> 3.2350 = 5.3917 < 7.0093] w=1.0000 to align # Constraint # added constraint: constraint((T0346)R100.CB, (T0346)P124.CB) [> 3.3612 = 5.6021 < 7.2827] w=1.0000 to align # Constraint # added constraint: constraint((T0346)F102.CB, (T0346)T121.CB) [> 4.0099 = 6.6832 < 8.6882] w=1.0000 to align # Constraint # added constraint: constraint((T0346)F102.CB, (T0346)L137.CB) [> 3.3856 = 5.6427 < 7.3355] w=1.0000 to align # Constraint # added constraint: constraint((T0346)F102.CB, (T0346)V138.CB) [> 2.3165 = 3.8609 < 5.0191] w=1.0000 to align # Constraint # added constraint: constraint((T0346)L103.CB, (T0346)T121.CB) [> 2.8664 = 4.7773 < 6.2105] w=1.0000 to align # Constraint # added constraint: constraint((T0346)L103.CB, (T0346)V134.CB) [> 3.4661 = 5.7768 < 7.5098] w=1.0000 to align # Constraint # added constraint: constraint((T0346)L103.CB, (T0346)G136.CA) [> 3.9433 = 6.5722 < 8.5438] w=1.0000 to align # Constraint # added constraint: constraint((T0346)L103.CB, (T0346)L137.CB) [> 3.4079 = 5.6798 < 7.3838] w=1.0000 to align # Constraint # added constraint: constraint((T0346)L104.CB, (T0346)F118.CB) [> 3.6921 = 6.1535 < 7.9995] w=1.0000 to align # Constraint # added constraint: constraint((T0346)L104.CB, (T0346)V134.CB) [> 4.2018 = 7.0031 < 9.1040] w=1.0000 to align # Constraint # added constraint: constraint((T0346)N114.CB, (T0346)V133.CB) [> 4.0179 = 6.6965 < 8.7054] w=1.0000 to align # Constraint # added constraint: constraint((T0346)T122.CB, (T0346)I145.CB) [> 3.8719 = 6.4531 < 8.3890] w=1.0000 to align # Constraint # added constraint: constraint((T0346)L151.CB, (T0346)A161.CB) [> 3.4355 = 5.7259 < 7.4437] w=1.0000 to align # Constraint # added constraint: constraint((T0346)K55.CB, (T0346)D167.CB) [> 3.6850 = 6.1416 < 7.9841] w=1.0000 to align # Constraint # added constraint: constraint((T0346)K55.CB, (T0346)C168.CB) [> 3.5216 = 5.8693 < 7.6301] w=1.0000 to align # Constraint # added constraint: constraint((T0346)G56.CA, (T0346)V165.CB) [> 3.2910 = 5.4850 < 7.1305] w=1.0000 to align # Constraint # added constraint: constraint((T0346)G56.CA, (T0346)I166.CB) [> 4.0518 = 6.7530 < 8.7789] w=1.0000 to align # Constraint # added constraint: constraint((T0346)S57.CB, (T0346)G71.CA) [> 3.0359 = 5.0598 < 6.5778] w=1.0000 to align # Constraint # added constraint: constraint((T0346)S57.CB, (T0346)D72.CB) [> 3.9637 = 6.6062 < 8.5881] w=1.0000 to align # Constraint # added constraint: constraint((T0346)S57.CB, (T0346)V165.CB) [> 3.1949 = 5.3249 < 6.9223] w=1.0000 to align # Constraint # added constraint: constraint((T0346)N65.CB, (T0346)T122.CB) [> 3.8898 = 6.4830 < 8.4279] w=1.0000 to align # Constraint # added constraint: constraint((T0346)N65.CB, (T0346)K123.CB) [> 3.4118 = 5.6863 < 7.3922] w=1.0000 to align # Constraint # added constraint: constraint((T0346)F66.CB, (T0346)T122.CB) [> 3.8573 = 6.4289 < 8.3576] w=1.0000 to align # Constraint # added constraint: constraint((T0346)F66.CB, (T0346)K123.CB) [> 3.6556 = 6.0927 < 7.9205] w=1.0000 to align # Constraint # added constraint: constraint((T0346)G71.CA, (T0346)S116.CB) [> 3.1462 = 5.2437 < 6.8168] w=1.0000 to align # Constraint # added constraint: constraint((T0346)G71.CA, (T0346)Q117.CB) [> 2.9334 = 4.8891 < 6.3558] w=1.0000 to align # Constraint # added constraint: constraint((T0346)G71.CA, (T0346)F118.CB) [> 3.6327 = 6.0546 < 7.8709] w=1.0000 to align # Constraint # added constraint: constraint((T0346)D72.CB, (T0346)S116.CB) [> 4.0061 = 6.6769 < 8.6799] w=1.0000 to align # Constraint # added constraint: constraint((T0346)D72.CB, (T0346)Q117.CB) [> 3.1807 = 5.3012 < 6.8916] w=1.0000 to align # Constraint # added constraint: constraint((T0346)Y88.CB, (T0346)H112.CB) [> 4.1083 = 6.8471 < 8.9012] w=1.0000 to align # Constraint # added constraint: constraint((T0346)H98.CB, (T0346)D129.CB) [> 3.4022 = 5.6703 < 7.3714] w=0.9986 to align # Constraint # added constraint: constraint((T0346)H98.CB, (T0346)V134.CB) [> 3.7558 = 6.2596 < 8.1375] w=0.9971 to align # Constraint # added constraint: constraint((T0346)D91.CB, (T0346)V133.CB) [> 3.1675 = 5.2791 < 6.8628] w=0.9971 to align # Constraint # added constraint: constraint((T0346)F20.CB, (T0346)I139.CB) [> 3.8851 = 6.4751 < 8.4177] w=0.9957 to align # Constraint # added constraint: constraint((T0346)L22.CB, (T0346)F34.CB) [> 3.8237 = 6.3729 < 8.2847] w=0.9957 to align # Constraint # added constraint: constraint((T0346)L22.CB, (T0346)L35.CB) [> 3.8683 = 6.4471 < 8.3813] w=0.9957 to align # Constraint # added constraint: constraint((T0346)C27.CB, (T0346)V134.CB) [> 4.4996 = 7.4993 < 9.7491] w=0.9957 to align # Constraint # added constraint: constraint((T0346)F34.CB, (T0346)F135.CB) [> 3.9288 = 6.5480 < 8.5124] w=0.9957 to align # Constraint # added constraint: constraint((T0346)S57.CB, (T0346)G70.CA) [> 3.9744 = 6.6239 < 8.6111] w=0.9957 to align # Constraint # added constraint: constraint((T0346)H60.CB, (T0346)Q69.CB) [> 4.0219 = 6.7032 < 8.7142] w=0.9957 to align # Constraint # added constraint: constraint((T0346)H60.CB, (T0346)G70.CA) [> 3.5161 = 5.8601 < 7.6182] w=0.9957 to align # Constraint # added constraint: constraint((T0346)R61.CB, (T0346)G70.CA) [> 4.1501 = 6.9169 < 8.9920] w=0.9957 to align # Constraint # added constraint: constraint((T0346)V62.CB, (T0346)I148.CB) [> 3.7965 = 6.3274 < 8.2257] w=0.9957 to align # Constraint # added constraint: constraint((T0346)V62.CB, (T0346)E149.CB) [> 3.6943 = 6.1572 < 8.0043] w=0.9957 to align # Constraint # added constraint: constraint((T0346)V62.CB, (T0346)L151.CB) [> 3.8072 = 6.3454 < 8.2490] w=0.9957 to align # Constraint # added constraint: constraint((T0346)V62.CB, (T0346)P159.CB) [> 3.2344 = 5.3907 < 7.0079] w=0.9957 to align # Constraint # added constraint: constraint((T0346)F66.CB, (T0346)A125.CB) [> 4.2006 = 7.0010 < 9.1013] w=0.9957 to align # Constraint # added constraint: constraint((T0346)Q69.CB, (T0346)Q117.CB) [> 3.8987 = 6.4978 < 8.4471] w=0.9957 to align # Constraint # added constraint: constraint((T0346)Q69.CB, (T0346)F118.CB) [> 4.2981 = 7.1635 < 9.3126] w=0.9957 to align # Constraint # added constraint: constraint((T0346)G70.CA, (T0346)Q117.CB) [> 3.4580 = 5.7633 < 7.4923] w=0.9957 to align # Constraint # added constraint: constraint((T0346)K97.CB, (T0346)V134.CB) [> 3.8572 = 6.4286 < 8.3572] w=0.9957 to align # Constraint # added constraint: constraint((T0346)L151.CB, (T0346)Y160.CB) [> 3.9688 = 6.6146 < 8.5990] w=0.9957 to align # Constraint # added constraint: constraint((T0346)A101.CB, (T0346)T121.CB) [> 3.5368 = 5.8947 < 7.6631] w=0.9855 to align # Constraint # added constraint: constraint((T0346)K29.CB, (T0346)F89.CB) [> 3.9934 = 6.6556 < 8.6523] w=0.9855 to align # Constraint # added constraint: constraint((T0346)L104.CB, (T0346)G136.CA) [> 2.4282 = 4.0470 < 5.2611] w=0.9568 to align # Constraint # added constraint: constraint((T0346)M67.CB, (T0346)F119.CB) [> 2.6493 = 4.4156 < 5.7402] w=0.9566 to align # Constraint # added constraint: constraint((T0346)M67.CB, (T0346)I120.CB) [> 3.7019 = 6.1698 < 8.0208] w=0.9566 to align # Constraint # added constraint: constraint((T0346)M67.CB, (T0346)T121.CB) [> 3.0024 = 5.0039 < 6.5051] w=0.9566 to align # Constraint # added constraint: constraint((T0346)M67.CB, (T0346)T122.CB) [> 3.5766 = 5.9610 < 7.7493] w=0.9566 to align # Constraint # added constraint: constraint((T0346)I68.CB, (T0346)F119.CB) [> 3.7583 = 6.2639 < 8.1431] w=0.9566 to align # Constraint # added constraint: constraint((T0346)I68.CB, (T0346)I120.CB) [> 3.0403 = 5.0672 < 6.5874] w=0.9566 to align # Constraint # added constraint: constraint((T0346)I68.CB, (T0346)T122.CB) [> 4.1517 = 6.9195 < 8.9953] w=0.9566 to align # Constraint # added constraint: constraint((T0346)I68.CB, (T0346)I148.CB) [> 3.2463 = 5.4105 < 7.0337] w=0.9566 to align # Constraint # added constraint: constraint((T0346)I120.CB, (T0346)V138.CB) [> 3.8908 = 6.4846 < 8.4300] w=0.9566 to align # Constraint # added constraint: constraint((T0346)V15.CB, (T0346)Q147.CB) [> 3.2941 = 5.4902 < 7.1373] w=0.9566 to align # Constraint # added constraint: constraint((T0346)I26.CB, (T0346)L96.CB) [> 3.6964 = 6.1607 < 8.0089] w=0.9566 to align # Constraint # added constraint: constraint((T0346)T30.CB, (T0346)N114.CB) [> 4.1838 = 6.9731 < 9.0650] w=0.9566 to align # Constraint # added constraint: constraint((T0346)Y54.CB, (T0346)G71.CA) [> 3.4817 = 5.8028 < 7.5437] w=0.9566 to align # Constraint # added constraint: constraint((T0346)H60.CB, (T0346)D72.CB) [> 3.6440 = 6.0733 < 7.8953] w=0.9566 to align # Constraint # added constraint: constraint((T0346)H98.CB, (T0346)P126.CB) [> 3.7220 = 6.2033 < 8.0643] w=0.9566 to align # Constraint # added constraint: constraint((T0346)V15.CB, (T0346)I148.CB) [> 3.9457 = 6.5762 < 8.5491] w=0.9566 to align # Constraint # added constraint: constraint((T0346)G56.CA, (T0346)R164.CB) [> 3.2976 = 5.4960 < 7.1448] w=0.9566 to align # Constraint # added constraint: constraint((T0346)S57.CB, (T0346)R164.CB) [> 4.3040 = 7.1734 < 9.3254] w=0.9566 to align # Constraint # added constraint: constraint((T0346)S105.CB, (T0346)F118.CB) [> 3.9820 = 6.6366 < 8.6276] w=0.9566 to align # Constraint # added constraint: constraint((T0346)S105.CB, (T0346)H132.CB) [> 2.7990 = 4.6650 < 6.0645] w=0.9566 to align # Constraint # added constraint: constraint((T0346)S105.CB, (T0346)V133.CB) [> 3.8193 = 6.3655 < 8.2752] w=0.9566 to align # Constraint # added constraint: constraint((T0346)S105.CB, (T0346)F135.CB) [> 4.1143 = 6.8573 < 8.9144] w=0.9566 to align # Constraint # added constraint: constraint((T0346)M106.CB, (T0346)F118.CB) [> 3.4592 = 5.7653 < 7.4949] w=0.9566 to align # Constraint # added constraint: constraint((T0346)M106.CB, (T0346)H132.CB) [> 3.5163 = 5.8605 < 7.6187] w=0.9566 to align # Constraint # added constraint: constraint((T0346)A107.CB, (T0346)H132.CB) [> 4.2498 = 7.0830 < 9.2078] w=0.9566 to align # Constraint # added constraint: constraint((T0346)F66.CB, (T0346)T121.CB) [> 4.5229 = 7.5382 < 9.7997] w=0.9566 to align # Constraint # added constraint: constraint((T0346)F20.CB, (T0346)L104.CB) [> 3.4059 = 5.6765 < 7.3794] w=0.9553 to align # Constraint # added constraint: constraint((T0346)F89.CB, (T0346)N114.CB) [> 3.2271 = 5.3785 < 6.9921] w=0.9553 to align # Constraint # added constraint: constraint((T0346)F102.CB, (T0346)F142.CB) [> 3.1802 = 5.3003 < 6.8903] w=0.9553 to align # Constraint # added constraint: constraint((T0346)L104.CB, (T0346)L137.CB) [> 3.6558 = 6.0931 < 7.9210] w=0.9553 to align # Constraint # added constraint: constraint((T0346)L104.CB, (T0346)V138.CB) [> 4.2081 = 7.0134 < 9.1174] w=0.9553 to align # Constraint # added constraint: constraint((T0346)A107.CB, (T0346)Q117.CB) [> 2.4256 = 4.0426 < 5.2554] w=0.9552 to align # Constraint # added constraint: constraint((T0346)L103.CB, (T0346)I120.CB) [> 4.2729 = 7.1215 < 9.2579] w=0.9537 to align # Constraint # added constraint: constraint((T0346)F102.CB, (T0346)I145.CB) [> 4.1138 = 6.8564 < 8.9133] w=0.9524 to align # Constraint # added constraint: constraint((T0346)F102.CB, (T0346)I120.CB) [> 4.0595 = 6.7658 < 8.7955] w=0.9523 to align # Constraint # added constraint: constraint((T0346)G70.CA, (T0346)F119.CB) [> 4.1219 = 6.8698 < 8.9307] w=0.9523 to align # Constraint # added constraint: constraint((T0346)Q69.CB, (T0346)F119.CB) [> 2.4611 = 4.1018 < 5.3323] w=0.9523 to align # Constraint # added constraint: constraint((T0346)F23.CB, (T0346)L137.CB) [> 4.6322 = 7.7203 < 10.0364] w=0.9523 to align # Constraint # added constraint: constraint((T0346)A101.CB, (T0346)T122.CB) [> 3.3012 = 5.5021 < 7.1527] w=0.9423 to align # Constraint # added constraint: constraint((T0346)E82.CB, (T0346)S116.CB) [> 3.4390 = 5.7316 < 7.4511] w=0.9409 to align # Constraint # added constraint: constraint((T0346)A101.CB, (T0346)P124.CB) [> 4.1325 = 6.8875 < 8.9537] w=0.9409 to align # Constraint # added constraint: constraint((T0346)A101.CB, (T0346)K123.CB) [> 3.4720 = 5.7867 < 7.5227] w=0.9409 to align # Constraint # added constraint: constraint((T0346)L104.CB, (T0346)I120.CB) [> 3.4637 = 5.7729 < 7.5047] w=0.9407 to align # Constraint # added constraint: constraint((T0346)A101.CB, (T0346)F142.CB) [> 4.3028 = 7.1714 < 9.3229] w=0.9248 to align # Constraint # added constraint: constraint((T0346)L35.CB, (T0346)V170.CB) [> 3.5939 = 5.9898 < 7.7867] w=0.9137 to align # Constraint # added constraint: constraint((T0346)M106.CB, (T0346)V133.CB) [> 2.7996 = 4.6660 < 6.0658] w=0.9134 to align # Constraint # added constraint: constraint((T0346)S105.CB, (T0346)V134.CB) [> 2.8493 = 4.7489 < 6.1736] w=0.9134 to align # Constraint # added constraint: constraint((T0346)L104.CB, (T0346)F119.CB) [> 4.5470 = 7.5783 < 9.8518] w=0.9133 to align # Constraint # added constraint: constraint((T0346)R17.CB, (T0346)G141.CA) [> 3.9543 = 6.5904 < 8.5676] w=0.9133 to align # Constraint # added constraint: constraint((T0346)G16.CA, (T0346)G141.CA) [> 4.4461 = 7.4101 < 9.6332] w=0.9133 to align # Constraint # added constraint: constraint((T0346)M106.CB, (T0346)Q117.CB) [> 4.2526 = 7.0876 < 9.2139] w=0.9133 to align # Constraint # added constraint: constraint((T0346)I68.CB, (T0346)I145.CB) [> 3.7115 = 6.1859 < 8.0416] w=0.9133 to align # Constraint # added constraint: constraint((T0346)S105.CB, (T0346)F119.CB) [> 3.5810 = 5.9683 < 7.7588] w=0.9133 to align # Constraint # added constraint: constraint((T0346)M67.CB, (T0346)A125.CB) [> 4.1648 = 6.9413 < 9.0237] w=0.9133 to align # Constraint # added constraint: constraint((T0346)F59.CB, (T0346)P159.CB) [> 3.9546 = 6.5910 < 8.5683] w=0.9133 to align # Constraint # added constraint: constraint((T0346)F59.CB, (T0346)I148.CB) [> 3.7785 = 6.2975 < 8.1868] w=0.9133 to align # Constraint # added constraint: constraint((T0346)T58.CB, (T0346)V165.CB) [> 4.4616 = 7.4360 < 9.6669] w=0.9133 to align # Constraint # added constraint: constraint((T0346)L96.CB, (T0346)V134.CB) [> 2.3174 = 3.8623 < 5.0210] w=0.9121 to align # Constraint # added constraint: constraint((T0346)T30.CB, (T0346)M106.CB) [> 3.7823 = 6.3039 < 8.1951] w=0.9120 to align # Constraint # added constraint: constraint((T0346)S105.CB, (T0346)T121.CB) [> 4.1156 = 6.8593 < 8.9171] w=0.9120 to align # Constraint # added constraint: constraint((T0346)M106.CB, (T0346)F135.CB) [> 3.9338 = 6.5563 < 8.5232] w=0.9120 to align # Constraint # added constraint: constraint((T0346)A107.CB, (T0346)F118.CB) [> 3.5191 = 5.8651 < 7.6246] w=0.9120 to align # Constraint # added constraint: constraint((T0346)H98.CB, (T0346)T121.CB) [> 3.4927 = 5.8211 < 7.5674] w=0.9107 to align # Constraint # added constraint: constraint((T0346)V62.CB, (T0346)V163.CB) [> 4.2958 = 7.1596 < 9.3075] w=0.9094 to align # Constraint # added constraint: constraint((T0346)N33.CB, (T0346)S83.CB) [> 3.1662 = 5.2771 < 6.8602] w=0.9092 to align # Constraint # added constraint: constraint((T0346)H98.CB, (T0346)L128.CB) [> 2.9840 = 4.9733 < 6.4653] w=0.9092 to align # Constraint # added constraint: constraint((T0346)Q69.CB, (T0346)A107.CB) [> 3.4832 = 5.8054 < 7.5470] w=0.9091 to align # Constraint # added constraint: constraint((T0346)L151.CB, (T0346)V163.CB) [> 3.7571 = 6.2618 < 8.1403] w=0.9089 to align # Constraint # added constraint: constraint((T0346)F59.CB, (T0346)G70.CA) [> 2.8989 = 4.8316 < 6.2810] w=0.9089 to align # Constraint # added constraint: constraint((T0346)F59.CB, (T0346)Q69.CB) [> 3.9063 = 6.5105 < 8.4636] w=0.9089 to align # Constraint # added constraint: constraint((T0346)T58.CB, (T0346)G70.CA) [> 4.1006 = 6.8343 < 8.8845] w=0.9089 to align # Constraint # added constraint: constraint((T0346)C38.CB, (T0346)V170.CB) [> 3.6609 = 6.1016 < 7.9321] w=0.8992 to align # Constraint # added constraint: constraint((T0346)S57.CB, (T0346)F73.CB) [> 2.8042 = 4.6736 < 6.0757] w=0.8945 to align # Constraint # added constraint: constraint((T0346)C27.CB, (T0346)E92.CB) [> 2.9294 = 4.8823 < 6.3470] w=0.8830 to align # Constraint # added constraint: constraint((T0346)T30.CB, (T0346)E92.CB) [> 2.9890 = 4.9817 < 6.4763] w=0.8830 to align # Constraint # added constraint: constraint((T0346)M106.CB, (T0346)G115.CA) [> 4.3817 = 7.3028 < 9.4936] w=0.8815 to align # Constraint # added constraint: constraint((T0346)D91.CB, (T0346)N108.CB) [> 4.5691 = 7.6152 < 9.8998] w=0.8802 to align # Constraint # added constraint: constraint((T0346)K29.CB, (T0346)E92.CB) [> 3.2645 = 5.4407 < 7.0730] w=0.8802 to align # Constraint # added constraint: constraint((T0346)F59.CB, (T0346)I68.CB) [> 3.1328 = 5.2214 < 6.7878] w=0.8699 to align # Constraint # added constraint: constraint((T0346)T58.CB, (T0346)D162.CB) [> 3.4635 = 5.7725 < 7.5042] w=0.8699 to align # Constraint # added constraint: constraint((T0346)F59.CB, (T0346)V163.CB) [> 2.6410 = 4.4017 < 5.7223] w=0.8699 to align # Constraint # added constraint: constraint((T0346)T58.CB, (T0346)R164.CB) [> 3.1726 = 5.2877 < 6.8740] w=0.8699 to align # Constraint # added constraint: constraint((T0346)T58.CB, (T0346)V163.CB) [> 3.6039 = 6.0065 < 7.8085] w=0.8699 to align # Constraint # added constraint: constraint((T0346)F23.CB, (T0346)L96.CB) [> 3.9459 = 6.5765 < 8.5495] w=0.8687 to align # Constraint # added constraint: constraint((T0346)A107.CB, (T0346)F119.CB) [> 3.2773 = 5.4622 < 7.1008] w=0.8686 to align # Constraint # added constraint: constraint((T0346)S105.CB, (T0346)L128.CB) [> 4.0822 = 6.8037 < 8.8448] w=0.8686 to align # Constraint # added constraint: constraint((T0346)N33.CB, (T0346)I84.CB) [> 3.2633 = 5.4388 < 7.0705] w=0.8660 to align # Constraint # added constraint: constraint((T0346)N108.CB, (T0346)Q117.CB) [> 4.6243 = 7.7071 < 10.0193] w=0.8657 to align # Constraint # added constraint: constraint((T0346)G70.CA, (T0346)A107.CB) [> 4.4973 = 7.4954 < 9.7440] w=0.8657 to align # Constraint # added constraint: constraint((T0346)F89.CB, (T0346)G115.CA) [> 4.0098 = 6.6830 < 8.6879] w=0.8541 to align # Constraint # added constraint: constraint((T0346)N33.CB, (T0346)F89.CB) [> 4.1703 = 6.9506 < 9.0357] w=0.8541 to align # Constraint # added constraint: constraint((T0346)N93.CB, (T0346)V133.CB) [> 3.9290 = 6.5483 < 8.5128] w=0.8541 to align # Constraint # added constraint: constraint((T0346)V62.CB, (T0346)T153.CB) [> 2.9458 = 4.9097 < 6.3826] w=0.8516 to align # Constraint # added constraint: constraint((T0346)H60.CB, (T0346)G76.CA) [> 3.2204 = 5.3673 < 6.9775] w=0.8515 to align # Constraint # added constraint: constraint((T0346)P28.CB, (T0346)E92.CB) [> 4.5603 = 7.6005 < 9.8806] w=0.8512 to align # Constraint # added constraint: constraint((T0346)S105.CB, (T0346)G136.CA) [> 4.6753 = 7.7922 < 10.1298] w=0.8397 to align # Constraint # added constraint: constraint((T0346)D72.CB, (T0346)G81.CA) [> 3.2239 = 5.3733 < 6.9852] w=0.8384 to align # Constraint # added constraint: constraint((T0346)L103.CB, (T0346)V138.CB) [> 4.6150 = 7.6916 < 9.9991] w=0.8279 to align # Constraint # added constraint: constraint((T0346)M67.CB, (T0346)K123.CB) [> 4.5034 = 7.5058 < 9.7575] w=0.8265 to align # Constraint # added constraint: constraint((T0346)H60.CB, (T0346)P159.CB) [> 4.4361 = 7.3935 < 9.6115] w=0.8265 to align # Constraint # added constraint: constraint((T0346)R100.CB, (T0346)T121.CB) [> 4.1936 = 6.9893 < 9.0862] w=0.8265 to align # Constraint # added constraint: constraint((T0346)S39.CB, (T0346)V170.CB) [> 3.3504 = 5.5840 < 7.2592] w=0.8226 to align # Constraint # added constraint: constraint((T0346)G80.CA, (T0346)Q117.CB) [> 4.3553 = 7.2589 < 9.4366] w=0.8226 to align # Constraint # added constraint: constraint((T0346)C31.CB, (T0346)G136.CA) [> 4.4196 = 7.3660 < 9.5759] w=0.8222 to align # Constraint # added constraint: constraint((T0346)S57.CB, (T0346)G76.CA) [> 4.0825 = 6.8042 < 8.8454] w=0.8095 to align # Constraint # added constraint: constraint((T0346)G78.CA, (T0346)Q117.CB) [> 3.9031 = 6.5052 < 8.4567] w=0.8082 to align # Constraint # added constraint: constraint((T0346)K32.CB, (T0346)I84.CB) [> 4.4209 = 7.3682 < 9.5786] w=0.7937 to align # Constraint # added constraint: constraint((T0346)C36.CB, (T0346)I84.CB) [> 2.8772 = 4.7954 < 6.2340] w=0.7937 to align # Constraint # added constraint: constraint((T0346)L37.CB, (T0346)I84.CB) [> 4.0161 = 6.6936 < 8.7017] w=0.7937 to align # Constraint # added constraint: constraint((T0346)F73.CB, (T0346)S116.CB) [> 3.8667 = 6.4444 < 8.3778] w=0.7937 to align # Constraint # added constraint: constraint((T0346)S39.CB, (T0346)G169.CA) [> 3.3037 = 5.5062 < 7.1581] w=0.7934 to align # Constraint # added constraint: constraint((T0346)E92.CB, (T0346)F135.CB) [> 4.5457 = 7.5762 < 9.8490] w=0.7934 to align # Constraint # added constraint: constraint((T0346)F23.CB, (T0346)V134.CB) [> 4.5347 = 7.5578 < 9.8252] w=0.7836 to align # Constraint # added constraint: constraint((T0346)R61.CB, (T0346)R158.CB) [> 4.1123 = 6.8539 < 8.9101] w=0.7832 to align # Constraint # added constraint: constraint((T0346)C27.CB, (T0346)L96.CB) [> 4.3416 = 7.2360 < 9.4068] w=0.7820 to align # Constraint # added constraint: constraint((T0346)K55.CB, (T0346)I166.CB) [> 4.3835 = 7.3058 < 9.4976] w=0.7802 to align # Constraint # added constraint: constraint((T0346)T58.CB, (T0346)P159.CB) [> 4.5565 = 7.5941 < 9.8724] w=0.7788 to align # Constraint # added constraint: constraint((T0346)G81.CA, (T0346)Q117.CB) [> 3.8425 = 6.4041 < 8.3254] w=0.7648 to align # Constraint # added constraint: constraint((T0346)R61.CB, (T0346)G78.CA) [> 4.2484 = 7.0807 < 9.2049] w=0.7648 to align # Constraint # added constraint: constraint((T0346)N33.CB, (T0346)Y85.CB) [> 4.2422 = 7.0703 < 9.1913] w=0.7503 to align # Constraint # added constraint: constraint((T0346)D7.CB, (T0346)C168.CB) [> 4.1059 = 6.8432 < 8.8962] w=0.7372 to align # Constraint # added constraint: constraint((T0346)D7.CB, (T0346)R17.CB) [> 3.1663 = 5.2772 < 6.8603] w=0.7372 to align # Constraint # added constraint: constraint((T0346)F6.CB, (T0346)C168.CB) [> 3.0137 = 5.0228 < 6.5296] w=0.7372 to align # Constraint # added constraint: constraint((T0346)H5.CB, (T0346)M19.CB) [> 3.0062 = 5.0104 < 6.5135] w=0.7372 to align # Constraint # added constraint: constraint((T0346)F94.CB, (T0346)G130.CA) [> 2.6094 = 4.3491 < 5.6538] w=0.7370 to align # Constraint # added constraint: constraint((T0346)C4.CB, (T0346)L35.CB) [> 3.6103 = 6.0171 < 7.8222] w=0.7357 to align # Constraint # added constraint: constraint((T0346)D7.CB, (T0346)D167.CB) [> 2.4247 = 4.0412 < 5.2535] w=0.7227 to align # Constraint # added constraint: constraint((T0346)I8.CB, (T0346)R17.CB) [> 4.3918 = 7.3196 < 9.5155] w=0.7227 to align # Constraint # added constraint: constraint((T0346)I8.CB, (T0346)I18.CB) [> 3.8230 = 6.3716 < 8.2831] w=0.7227 to align # Constraint # added constraint: constraint((T0346)I8.CB, (T0346)V165.CB) [> 3.7924 = 6.3208 < 8.2170] w=0.7227 to align # Constraint # added constraint: constraint((T0346)C4.CB, (T0346)L22.CB) [> 3.8836 = 6.4727 < 8.4145] w=0.7097 to align # Constraint # added constraint: constraint((T0346)C4.CB, (T0346)M19.CB) [> 4.3800 = 7.3000 < 9.4900] w=0.7083 to align # Constraint # added constraint: constraint((T0346)C4.CB, (T0346)F20.CB) [> 3.1302 = 5.2170 < 6.7821] w=0.7083 to align # Constraint # added constraint: constraint((T0346)C4.CB, (T0346)C38.CB) [> 2.6925 = 4.4875 < 5.8338] w=0.7083 to align # Constraint # added constraint: constraint((T0346)C4.CB, (T0346)C168.CB) [> 4.0825 = 6.8042 < 8.8454] w=0.7083 to align # Constraint # added constraint: constraint((T0346)C4.CB, (T0346)G169.CA) [> 3.3644 = 5.6074 < 7.2896] w=0.7083 to align # Constraint # added constraint: constraint((T0346)H5.CB, (T0346)R17.CB) [> 3.3024 = 5.5040 < 7.1551] w=0.7083 to align # Constraint # added constraint: constraint((T0346)H5.CB, (T0346)I18.CB) [> 4.0252 = 6.7087 < 8.7213] w=0.7083 to align # Constraint # added constraint: constraint((T0346)H5.CB, (T0346)C168.CB) [> 3.8185 = 6.3642 < 8.2734] w=0.7083 to align # Constraint # added constraint: constraint((T0346)F6.CB, (T0346)R17.CB) [> 4.1013 = 6.8356 < 8.8862] w=0.7083 to align # Constraint # added constraint: constraint((T0346)F6.CB, (T0346)I18.CB) [> 2.8551 = 4.7584 < 6.1859] w=0.7083 to align # Constraint # added constraint: constraint((T0346)F6.CB, (T0346)Y54.CB) [> 4.3409 = 7.2349 < 9.4054] w=0.7083 to align # Constraint # added constraint: constraint((T0346)F6.CB, (T0346)V165.CB) [> 3.0313 = 5.0522 < 6.5679] w=0.7083 to align # Constraint # added constraint: constraint((T0346)D7.CB, (T0346)G16.CA) [> 3.8100 = 6.3499 < 8.2549] w=0.7083 to align # Constraint # added constraint: constraint((T0346)D7.CB, (T0346)V165.CB) [> 4.2629 = 7.1048 < 9.2362] w=0.7083 to align # Constraint # added constraint: constraint((T0346)D7.CB, (T0346)I166.CB) [> 2.8492 = 4.7486 < 6.1732] w=0.7083 to align # Constraint # added constraint: constraint((T0346)Y54.CB, (T0346)F73.CB) [> 3.7640 = 6.2733 < 8.1552] w=0.7070 to align # Constraint # added constraint: constraint((T0346)F119.CB, (T0346)H132.CB) [> 4.7121 = 7.8534 < 10.2095] w=0.6964 to align # Constraint # added constraint: constraint((T0346)C4.CB, (T0346)V170.CB) [> 3.2597 = 5.4328 < 7.0626] w=0.6954 to align # Constraint # added constraint: constraint((T0346)I8.CB, (T0346)I166.CB) [> 3.9635 = 6.6059 < 8.5876] w=0.6938 to align # Constraint # added constraint: constraint((T0346)I8.CB, (T0346)V144.CB) [> 3.4677 = 5.7796 < 7.5134] w=0.6938 to align # Constraint # added constraint: constraint((T0346)F6.CB, (T0346)D167.CB) [> 4.4983 = 7.4971 < 9.7462] w=0.6938 to align # Constraint # added constraint: constraint((T0346)I18.CB, (T0346)I120.CB) [> 4.5992 = 7.6653 < 9.9649] w=0.6935 to align # Constraint # added constraint: constraint((T0346)F94.CB, (T0346)V133.CB) [> 3.9363 = 6.5605 < 8.5286] w=0.6924 to align # Constraint # added constraint: constraint((T0346)C4.CB, (T0346)F34.CB) [> 4.2130 = 7.0216 < 9.1280] w=0.6924 to align # Constraint # added constraint: constraint((T0346)I8.CB, (T0346)I148.CB) [> 3.8878 = 6.4796 < 8.4235] w=0.6794 to align # Constraint # added constraint: constraint((T0346)H5.CB, (T0346)F20.CB) [> 4.4262 = 7.3770 < 9.5901] w=0.6794 to align # Constraint # added constraint: constraint((T0346)V63.CB, (T0346)T153.CB) [> 4.0844 = 6.8073 < 8.8495] w=0.6785 to align # Constraint # added constraint: constraint((T0346)G56.CA, (T0346)F73.CB) [> 4.3770 = 7.2951 < 9.4836] w=0.6781 to align # Constraint # added constraint: constraint((T0346)E9.CB, (T0346)I166.CB) [> 2.6103 = 4.3505 < 5.6557] w=0.6781 to align # Constraint # added constraint: constraint((T0346)I26.CB, (T0346)N93.CB) [> 4.2579 = 7.0965 < 9.2254] w=0.6781 to align # Constraint # added constraint: constraint((T0346)L22.CB, (T0346)L104.CB) [> 4.6029 = 7.6716 < 9.9730] w=0.6662 to align # Constraint # added constraint: constraint((T0346)Q69.CB, (T0346)G78.CA) [> 4.6470 = 7.7451 < 10.0686] w=0.6636 to align # Constraint # added constraint: constraint((T0346)K29.CB, (T0346)Y85.CB) [> 4.6397 = 7.7329 < 10.0527] w=0.6636 to align # Constraint # added constraint: constraint((T0346)Q21.CB, (T0346)V138.CB) [> 4.7038 = 7.8397 < 10.1917] w=0.6544 to align # Constraint # added constraint: constraint((T0346)I18.CB, (T0346)F142.CB) [> 4.6269 = 7.7116 < 10.0250] w=0.6535 to align # Constraint # added constraint: constraint((T0346)F94.CB, (T0346)V134.CB) [> 4.5909 = 7.6515 < 9.9469] w=0.6504 to align # Constraint # added constraint: constraint((T0346)I8.CB, (T0346)R164.CB) [> 4.2212 = 7.0354 < 9.1460] w=0.6504 to align # Constraint # added constraint: constraint((T0346)I8.CB, (T0346)V163.CB) [> 3.9035 = 6.5058 < 8.4575] w=0.6504 to align # Constraint # added constraint: constraint((T0346)F6.CB, (T0346)F20.CB) [> 4.5274 = 7.5457 < 9.8094] w=0.6504 to align # Constraint # added constraint: constraint((T0346)R61.CB, (T0346)F119.CB) [> 4.6492 = 7.7487 < 10.0732] w=0.6501 to align # Constraint # added constraint: constraint((T0346)N11.CB, (T0346)A161.CB) [> 2.6925 = 4.4875 < 5.8337] w=0.6491 to align # Constraint # added constraint: constraint((T0346)I10.CB, (T0346)A161.CB) [> 2.9923 = 4.9871 < 6.4833] w=0.6491 to align # Constraint # added constraint: constraint((T0346)H5.CB, (T0346)C38.CB) [> 4.5751 = 7.6251 < 9.9127] w=0.6491 to align # Constraint # added constraint: constraint((T0346)I10.CB, (T0346)V163.CB) [> 3.1002 = 5.1670 < 6.7171] w=0.6347 to align # Constraint # added constraint: constraint((T0346)H60.CB, (T0346)R158.CB) [> 3.5793 = 5.9654 < 7.7551] w=0.6111 to align # Constraint # added constraint: constraint((T0346)F59.CB, (T0346)V165.CB) [> 4.6642 = 7.7737 < 10.1058] w=0.6097 to align # Constraint # added constraint: constraint((T0346)Q3.CB, (T0346)Q21.CB) [> 3.4059 = 5.6766 < 7.3795] w=0.6085 to align # Constraint # added constraint: constraint((T0346)Q3.CB, (T0346)L22.CB) [> 4.3710 = 7.2849 < 9.4704] w=0.6071 to align # Constraint # added constraint: constraint((T0346)Q3.CB, (T0346)M19.CB) [> 3.5522 = 5.9203 < 7.6964] w=0.6071 to align # Constraint # added constraint: constraint((T0346)L37.CB, (T0346)G71.CA) [> 4.6327 = 7.7212 < 10.0376] w=0.6058 to align # Constraint # added constraint: constraint((T0346)E9.CB, (T0346)R164.CB) [> 2.8823 = 4.8038 < 6.2450] w=0.6058 to align # Constraint # added constraint: constraint((T0346)G110.CA, (T0346)V131.CB) [> 4.6181 = 7.6968 < 10.0058] w=0.6058 to align # Constraint # added constraint: constraint((T0346)S39.CB, (T0346)C168.CB) [> 4.5354 = 7.5590 < 9.8267] w=0.5769 to align # Constraint # added constraint: constraint((T0346)L37.CB, (T0346)S83.CB) [> 4.5520 = 7.5866 < 9.8626] w=0.5637 to align # Constraint # added constraint: constraint((T0346)L37.CB, (T0346)F73.CB) [> 4.6175 = 7.6959 < 10.0047] w=0.5624 to align # Constraint # added constraint: constraint((T0346)M19.CB, (T0346)L171.CB) [> 4.1880 = 6.9800 < 9.0740] w=0.5624 to align # Constraint # added constraint: constraint((T0346)T58.CB, (T0346)D72.CB) [> 4.5887 = 7.6478 < 9.9422] w=0.5624 to align # Constraint # added constraint: constraint((T0346)F34.CB, (T0346)L104.CB) [> 4.5680 = 7.6133 < 9.8973] w=0.5624 to align # Constraint # added constraint: constraint((T0346)L104.CB, (T0346)T121.CB) [> 4.6107 = 7.6844 < 9.9897] w=0.5229 to align # Constraint # added constraint: constraint((T0346)L103.CB, (T0346)A125.CB) [> 4.5889 = 7.6482 < 9.9426] w=0.5219 to align # Constraint # added constraint: constraint((T0346)Q69.CB, (T0346)I120.CB) [> 4.7495 = 7.9158 < 10.2906] w=0.5200 to align # Constraint # added constraint: constraint((T0346)F59.CB, (T0346)R164.CB) [> 4.5310 = 7.5516 < 9.8171] w=0.5190 to align # Constraint # added constraint: constraint((T0346)K64.CB, (T0346)T153.CB) [> 3.4807 = 5.8012 < 7.5415] w=0.5050 to align # Constraint # added constraint: constraint((T0346)R100.CB, (T0346)K123.CB) [> 4.4090 = 7.3484 < 9.5529] w=0.4914 to align # Constraint # added constraint: constraint((T0346)G71.CA, (T0346)V165.CB) [> 4.5348 = 7.5580 < 9.8254] w=0.4810 to align # Constraint # added constraint: constraint((T0346)H60.CB, (T0346)G71.CA) [> 4.5952 = 7.6586 < 9.9562] w=0.4810 to align # Constraint # added constraint: constraint((T0346)V15.CB, (T0346)V163.CB) [> 3.5872 = 5.9787 < 7.7723] w=0.4810 to align # Constraint # added constraint: constraint((T0346)F102.CB, (T0346)T122.CB) [> 4.4011 = 7.3351 < 9.5356] w=0.4800 to align # Constraint # added constraint: constraint((T0346)I95.CB, (T0346)V134.CB) [> 4.6138 = 7.6897 < 9.9966] w=0.4797 to align # Constraint # added constraint: constraint((T0346)G71.CA, (T0346)A107.CB) [> 4.7267 = 7.8778 < 10.2412] w=0.4771 to align # Constraint # added constraint: constraint((T0346)I68.CB, (T0346)V163.CB) [> 4.7020 = 7.8367 < 10.1877] w=0.4752 to align # Constraint # added constraint: constraint((T0346)P2.CB, (T0346)C31.CB) [> 3.8810 = 6.4683 < 8.4088] w=0.4609 to align # Constraint # added constraint: constraint((T0346)L37.CB, (T0346)C53.CB) [> 2.8799 = 4.7998 < 6.2398] w=0.4490 to align # Constraint # added constraint: constraint((T0346)G86.CA, (T0346)G115.CA) [> 4.4386 = 7.3976 < 9.6170] w=0.4376 to align # Constraint # added constraint: constraint((T0346)R61.CB, (T0346)P159.CB) [> 4.6344 = 7.7241 < 10.0413] w=0.4366 to align # Constraint # added constraint: constraint((T0346)S105.CB, (T0346)I120.CB) [> 4.7315 = 7.8859 < 10.2516] w=0.4337 to align # Constraint # added constraint: constraint((T0346)K64.CB, (T0346)T122.CB) [> 4.4539 = 7.4231 < 9.6500] w=0.4337 to align # Constraint # added constraint: constraint((T0346)F94.CB, (T0346)V131.CB) [> 4.6414 = 7.7357 < 10.0565] w=0.4336 to align # Constraint # added constraint: constraint((T0346)F59.CB, (T0346)G71.CA) [> 4.6698 = 7.7830 < 10.1179] w=0.3928 to align # Constraint # added constraint: constraint((T0346)N108.CB, (T0346)V131.CB) [> 4.7241 = 7.8735 < 10.2356] w=0.3918 to align # Constraint # added constraint: constraint((T0346)C53.CB, (T0346)F73.CB) [> 3.9459 = 6.5766 < 8.5495] w=0.3899 to align # Constraint # added constraint: constraint((T0346)S24.CB, (T0346)L35.CB) [> 4.6248 = 7.7079 < 10.0203] w=0.3889 to align # Constraint # added constraint: constraint((T0346)D91.CB, (T0346)M106.CB) [> 4.6777 = 7.7961 < 10.1350] w=0.3756 to align # Constraint # added constraint: constraint((T0346)N108.CB, (T0346)V133.CB) [> 4.5492 = 7.5820 < 9.8567] w=0.3498 to align # Constraint # added constraint: constraint((T0346)R12.CB, (T0346)I166.CB) [> 3.3977 = 5.6628 < 7.3617] w=0.3496 to align # Constraint # added constraint: constraint((T0346)G70.CA, (T0346)V165.CB) [> 4.6896 = 7.8159 < 10.1607] w=0.3465 to align # Constraint # added constraint: constraint((T0346)G16.CA, (T0346)Q147.CB) [> 4.6874 = 7.8123 < 10.1560] w=0.3465 to align # Constraint # added constraint: constraint((T0346)C53.CB, (T0346)C168.CB) [> 4.4545 = 7.4242 < 9.6515] w=0.3463 to align # Constraint # added constraint: constraint((T0346)G78.CA, (T0346)A107.CB) [> 4.7232 = 7.8721 < 10.2337] w=0.3325 to align # Constraint # added constraint: constraint((T0346)L52.CB, (T0346)F73.CB) [> 4.1347 = 6.8912 < 8.9585] w=0.3176 to align # Constraint # added constraint: constraint((T0346)E41.CB, (T0346)C53.CB) [> 4.1877 = 6.9794 < 9.0733] w=0.3044 to align # Constraint # added constraint: constraint((T0346)L52.CB, (T0346)E82.CB) [> 4.2532 = 7.0886 < 9.2152] w=0.3036 to align # Constraint # added constraint: constraint((T0346)S1.CB, (T0346)D25.CB) [> 3.7305 = 6.2175 < 8.0827] w=0.3020 to align # Constraint # added constraint: constraint((T0346)F6.CB, (T0346)M19.CB) [> 4.6865 = 7.8109 < 10.1542] w=0.2890 to align # Constraint # added constraint: constraint((T0346)E13.CB, (T0346)V163.CB) [> 3.8528 = 6.4213 < 8.3477] w=0.2773 to align # Constraint # added constraint: constraint((T0346)E9.CB, (T0346)M19.CB) [> 4.4003 = 7.3338 < 9.5339] w=0.2628 to align # Constraint # added constraint: constraint((T0346)I10.CB, (T0346)M19.CB) [> 3.1909 = 5.3182 < 6.9137] w=0.2628 to align # Constraint # added constraint: constraint((T0346)N11.CB, (T0346)F20.CB) [> 4.0495 = 6.7492 < 8.7740] w=0.2628 to align # Constraint # added constraint: constraint((T0346)N11.CB, (T0346)V165.CB) [> 3.5622 = 5.9371 < 7.7182] w=0.2628 to align # Constraint # added constraint: constraint((T0346)M106.CB, (T0346)V134.CB) [> 4.6336 = 7.7227 < 10.0395] w=0.2617 to align # Constraint # added constraint: constraint((T0346)F20.CB, (T0346)F34.CB) [> 4.7269 = 7.8781 < 10.2416] w=0.2602 to align # Constraint # added constraint: constraint((T0346)M106.CB, (T0346)F119.CB) [> 4.4935 = 7.4891 < 9.7358] w=0.2210 to align # Constraint # added constraint: constraint((T0346)I8.CB, (T0346)Q21.CB) [> 3.5968 = 5.9947 < 7.7931] w=0.2194 to align # Constraint # added constraint: constraint((T0346)C36.CB, (T0346)C53.CB) [> 4.5566 = 7.5943 < 9.8726] w=0.2162 to align # Constraint # added constraint: constraint((T0346)L44.CB, (T0346)S74.CB) [> 4.5179 = 7.5298 < 9.7888] w=0.2015 to align # Constraint # added constraint: constraint((T0346)S57.CB, (T0346)S74.CB) [> 3.7882 = 6.3136 < 8.2077] w=0.1918 to align # Constraint # added constraint: constraint((T0346)D99.CB, (T0346)T121.CB) [> 3.7062 = 6.1770 < 8.0301] w=0.1918 to align # Constraint # added constraint: constraint((T0346)Y88.CB, (T0346)R109.CB) [> 4.6701 = 7.7835 < 10.1186] w=0.1908 to align # Constraint # added constraint: constraint((T0346)L52.CB, (T0346)S116.CB) [> 4.5651 = 7.6085 < 9.8911] w=0.1735 to align # Constraint # added constraint: constraint((T0346)F34.CB, (T0346)G136.CA) [> 4.6919 = 7.8198 < 10.1658] w=0.1735 to align # Constraint # added constraint: constraint((T0346)F102.CB, (T0346)I139.CB) [> 4.6582 = 7.7638 < 10.0929] w=0.1735 to align # Constraint # added constraint: constraint((T0346)K42.CB, (T0346)L52.CB) [> 3.0157 = 5.0261 < 6.5340] w=0.1590 to align # Constraint # added constraint: constraint((T0346)Q3.CB, (T0346)A172.CB) [> 3.0478 = 5.0797 < 6.6037] w=0.1586 to align # Constraint # added constraint: constraint((T0346)G56.CA, (T0346)S74.CB) [> 3.8719 = 6.4532 < 8.3892] w=0.1485 to align # Constraint # added constraint: constraint((T0346)D7.CB, (T0346)L22.CB) [> 3.3123 = 5.5204 < 7.1766] w=0.1446 to align # Constraint # added constraint: constraint((T0346)D7.CB, (T0346)S24.CB) [> 3.4476 = 5.7459 < 7.4697] w=0.1446 to align # Constraint # added constraint: constraint((T0346)T58.CB, (T0346)E75.CB) [> 3.4302 = 5.7169 < 7.4320] w=0.1327 to align # Constraint # added constraint: constraint((T0346)K50.CB, (T0346)S74.CB) [> 2.9126 = 4.8544 < 6.3107] w=0.1301 to align # Constraint # added constraint: constraint((T0346)K51.CB, (T0346)F73.CB) [> 4.2762 = 7.1270 < 9.2650] w=0.1301 to align # Constraint # added constraint: constraint((T0346)L52.CB, (T0346)I84.CB) [> 3.3776 = 5.6294 < 7.3182] w=0.1301 to align # Constraint # added constraint: constraint((T0346)V63.CB, (T0346)T122.CB) [> 4.5647 = 7.6078 < 9.8902] w=0.1301 to align # Constraint # added constraint: constraint((T0346)Y88.CB, (T0346)N108.CB) [> 4.7500 = 7.9167 < 10.2917] w=0.1298 to align # Constraint # added constraint: constraint((T0346)G87.CA, (T0346)T113.CB) [> 3.7361 = 6.2268 < 8.0948] w=0.1198 to align # Constraint # added constraint: constraint((T0346)I10.CB, (T0346)L171.CB) [> 3.7668 = 6.2781 < 8.1615] w=0.1185 to align # Constraint # added constraint: constraint((T0346)G87.CA, (T0346)N114.CB) [> 3.5357 = 5.8928 < 7.6607] w=0.1170 to align # Constraint # added constraint: constraint((T0346)S74.CB, (T0346)S116.CB) [> 4.1782 = 6.9637 < 9.0529] w=0.1157 to align # Constraint # added constraint: constraint((T0346)I10.CB, (T0346)D167.CB) [> 4.6217 = 7.7028 < 10.0137] w=0.1038 to align # Constraint # added constraint: constraint((T0346)G56.CA, (T0346)E75.CB) [> 4.1888 = 6.9813 < 9.0757] w=0.1038 to align # Constraint # added constraint: constraint((T0346)C53.CB, (T0346)S116.CB) [> 3.9312 = 6.5520 < 8.5176] w=0.1025 to align # Constraint # added constraint: constraint((T0346)P28.CB, (T0346)D91.CB) [> 4.4934 = 7.4890 < 9.7357] w=0.1010 to align # Constraint # added constraint: constraint((T0346)V63.CB, (T0346)K152.CB) [> 3.2774 = 5.4623 < 7.1010] w=0.1007 to align # Constraint # added constraint: constraint((T0346)R17.CB, (T0346)D167.CB) [> 4.7208 = 7.8680 < 10.2284] w=0.0911 to align # Constraint # added constraint: constraint((T0346)G86.CA, (T0346)S116.CB) [> 4.3912 = 7.3187 < 9.5143] w=0.0908 to align # Constraint # added constraint: constraint((T0346)T58.CB, (T0346)F73.CB) [> 3.4122 = 5.6871 < 7.3932] w=0.0906 to align # Constraint # added constraint: constraint((T0346)T58.CB, (T0346)S74.CB) [> 4.2268 = 7.0447 < 9.1581] w=0.0906 to align # Constraint # added constraint: constraint((T0346)N93.CB, (T0346)H132.CB) [> 3.5668 = 5.9446 < 7.7280] w=0.0893 to align # Constraint # added constraint: constraint((T0346)L44.CB, (T0346)S57.CB) [> 4.5925 = 7.6541 < 9.9504] w=0.0880 to align # Constraint # added constraint: constraint((T0346)I95.CB, (T0346)V133.CB) [> 3.9170 = 6.5284 < 8.4869] w=0.0879 to align # Constraint # added constraint: constraint((T0346)F94.CB, (T0346)H132.CB) [> 4.7796 = 7.9660 < 10.3559] w=0.0867 to align # Constraint # added constraint: constraint((T0346)Y54.CB, (T0346)G70.CA) [> 4.6609 = 7.7682 < 10.0987] w=0.0867 to align # Constraint # added constraint: constraint((T0346)G56.CA, (T0346)D167.CB) [> 4.7676 = 7.9460 < 10.3299] w=0.0867 to align # Constraint # added constraint: constraint((T0346)F23.CB, (T0346)K97.CB) [> 4.1135 = 6.8559 < 8.9127] w=0.0864 to align # Constraint # added constraint: constraint((T0346)N93.CB, (T0346)K111.CB) [> 4.4416 = 7.4026 < 9.6234] w=0.0864 to align # Constraint # added constraint: constraint((T0346)D99.CB, (T0346)L128.CB) [> 2.6285 = 4.3808 < 5.6951] w=0.0864 to align # Constraint # added constraint: constraint((T0346)F59.CB, (T0346)D162.CB) [> 4.0330 = 6.7216 < 8.7381] w=0.0863 to align # Constraint # added constraint: constraint((T0346)D7.CB, (T0346)I18.CB) [> 4.6549 = 7.7582 < 10.0856] w=0.0737 to align # Constraint # added constraint: constraint((T0346)F6.CB, (T0346)V170.CB) [> 3.1376 = 5.2293 < 6.7981] w=0.0723 to align # Constraint # added constraint: constraint((T0346)K90.CB, (T0346)N108.CB) [> 4.3440 = 7.2400 < 9.4120] w=0.0723 to align # Constraint # added constraint: constraint((T0346)H60.CB, (T0346)E75.CB) [> 3.1608 = 5.2680 < 6.8484] w=0.0723 to align # Constraint # added constraint: constraint((T0346)I95.CB, (T0346)F135.CB) [> 4.6971 = 7.8285 < 10.1771] w=0.0619 to align # Constraint # added constraint: constraint((T0346)R100.CB, (T0346)T122.CB) [> 3.7458 = 6.2429 < 8.1158] w=0.0591 to align # Constraint # added constraint: constraint((T0346)R61.CB, (T0346)N77.CB) [> 3.7083 = 6.1805 < 8.0347] w=0.0578 to align # Constraint # added constraint: constraint((T0346)F20.CB, (T0346)I120.CB) [> 4.4769 = 7.4614 < 9.6998] w=0.0477 to align # Constraint # added constraint: constraint((T0346)Y54.CB, (T0346)D167.CB) [> 4.4517 = 7.4195 < 9.6453] w=0.0477 to align # Constraint # added constraint: constraint((T0346)A107.CB, (T0346)V133.CB) [> 4.5842 = 7.6403 < 9.9324] w=0.0477 to align # Constraint # added constraint: constraint((T0346)L96.CB, (T0346)S105.CB) [> 4.6694 = 7.7824 < 10.1172] w=0.0463 to align # Constraint # added constraint: constraint((T0346)K42.CB, (T0346)G56.CA) [> 2.8518 = 4.7530 < 6.1789] w=0.0448 to align # Constraint # added constraint: constraint((T0346)F20.CB, (T0346)L103.CB) [> 3.5802 = 5.9669 < 7.7570] w=0.0447 to align # Constraint # added constraint: constraint((T0346)T30.CB, (T0346)S105.CB) [> 3.5761 = 5.9602 < 7.7482] w=0.0447 to align # Constraint # added constraint: constraint((T0346)E92.CB, (T0346)V131.CB) [> 2.8007 = 4.6679 < 6.0682] w=0.0447 to align # Constraint # added constraint: constraint((T0346)F102.CB, (T0346)V134.CB) [> 3.0128 = 5.0213 < 6.5277] w=0.0447 to align # Constraint # added constraint: constraint((T0346)F102.CB, (T0346)G136.CA) [> 3.7157 = 6.1928 < 8.0506] w=0.0447 to align # Constraint # added constraint: constraint((T0346)L103.CB, (T0346)F118.CB) [> 3.3765 = 5.6274 < 7.3157] w=0.0447 to align # Constraint # added constraint: constraint((T0346)L103.CB, (T0346)F119.CB) [> 4.3750 = 7.2916 < 9.4791] w=0.0447 to align # Constraint # added constraint: constraint((T0346)L103.CB, (T0346)F135.CB) [> 3.7833 = 6.3054 < 8.1971] w=0.0447 to align # Constraint # added constraint: constraint((T0346)D7.CB, (T0346)F23.CB) [> 4.5875 = 7.6459 < 9.9396] w=0.0434 to align # Constraint # added constraint: constraint((T0346)H60.CB, (T0346)V163.CB) [> 4.7964 = 7.9939 < 10.3921] w=0.0434 to align # Constraint # added constraint: constraint((T0346)I120.CB, (T0346)I148.CB) [> 4.7760 = 7.9600 < 10.3480] w=0.0434 to align # Constraint # added constraint: constraint((T0346)L103.CB, (T0346)P124.CB) [> 4.7917 = 7.9861 < 10.3820] w=0.0434 to align # Constraint # added constraint: constraint((T0346)I95.CB, (T0346)G130.CA) [> 4.7359 = 7.8932 < 10.2612] w=0.0434 to align # Constraint # added constraint: constraint((T0346)R61.CB, (T0346)G71.CA) [> 4.7057 = 7.8428 < 10.1957] w=0.0434 to align # Constraint # added constraint: constraint((T0346)D72.CB, (T0346)G115.CA) [> 4.6371 = 7.7285 < 10.0471] w=0.0434 to align # Constraint # added constraint: constraint((T0346)D72.CB, (T0346)F118.CB) [> 4.4150 = 7.3583 < 9.5658] w=0.0434 to align # Constraint # added constraint: constraint((T0346)Q69.CB, (T0346)M106.CB) [> 3.5001 = 5.8336 < 7.5837] w=0.0432 to align # Constraint # added constraint: constraint((T0346)G70.CA, (T0346)M106.CB) [> 4.6106 = 7.6843 < 9.9896] w=0.0432 to align # Constraint # added constraint: constraint((T0346)K90.CB, (T0346)A107.CB) [> 4.2655 = 7.1091 < 9.2419] w=0.0432 to align # Constraint # added constraint: constraint((T0346)V62.CB, (T0346)D162.CB) [> 4.7064 = 7.8440 < 10.1972] w=0.0429 to align # Constraint # added constraint: constraint((T0346)H60.CB, (T0346)D162.CB) [> 3.0951 = 5.1585 < 6.7061] w=0.0429 to align # Constraint # added constraint: constraint((T0346)N93.CB, (T0346)S105.CB) [> 4.7666 = 7.9443 < 10.3276] w=0.0318 to align # Constraint # added constraint: constraint((T0346)N33.CB, (T0346)G87.CA) [> 4.7053 = 7.8422 < 10.1948] w=0.0317 to align # Constraint # added constraint: constraint((T0346)A101.CB, (T0346)I120.CB) [> 4.6560 = 7.7599 < 10.0879] w=0.0289 to align # Constraint # added constraint: constraint((T0346)D7.CB, (T0346)C31.CB) [> 3.6708 = 6.1180 < 7.9534] w=0.0289 to align # Constraint # added constraint: constraint((T0346)L44.CB, (T0346)C53.CB) [> 3.7423 = 6.2372 < 8.1083] w=0.0289 to align # Constraint # added constraint: constraint((T0346)F6.CB, (T0346)A172.CB) [> 3.5978 = 5.9964 < 7.7953] w=0.0289 to align # Constraint # added constraint: constraint((T0346)E9.CB, (T0346)D167.CB) [> 2.5926 = 4.3211 < 5.6174] w=0.0289 to align # Constraint # added constraint: constraint((T0346)K79.CB, (T0346)R158.CB) [> 4.0848 = 6.8079 < 8.8503] w=0.0145 to align # Constraint # added constraint: constraint((T0346)D72.CB, (T0346)I84.CB) [> 4.6565 = 7.7608 < 10.0891] w=0.0145 to align # Constraint # added constraint: constraint((T0346)F66.CB, (T0346)K152.CB) [> 4.7974 = 7.9957 < 10.3944] w=0.0145 to align # Constraint # added constraint: constraint((T0346)G78.CA, (T0346)R109.CB) [> 4.5234 = 7.5390 < 9.8008] w=0.0145 to align # Constraint # added constraint: constraint((T0346)F23.CB, (T0346)N93.CB) [> 4.5942 = 7.6569 < 9.9540] w=0.0145 to align # Constraint # added constraint: constraint((T0346)I68.CB, (T0346)T121.CB) [> 4.7060 = 7.8433 < 10.1962] w=0.0043 to align # Constraint # added constraint: constraint((T0346)G71.CA, (T0346)F119.CB) [> 4.6826 = 7.8043 < 10.1456] w=0.0043 to align # Constraint # added constraint: constraint((T0346)F118.CB, (T0346)V133.CB) [> 3.9195 = 6.5325 < 8.4923] w=0.0043 to align # Constraint # added constraint: constraint((T0346)F119.CB, (T0346)V133.CB) [> 4.7792 = 7.9653 < 10.3549] w=0.0043 to align # Constraint # added constraint: constraint((T0346)Q21.CB, (T0346)L104.CB) [> 4.5536 = 7.5894 < 9.8662] w=0.0029 to align # Constraint # added constraint: constraint((T0346)N93.CB, (T0346)M106.CB) [> 4.7829 = 7.9714 < 10.3629] w=0.0029 to align # Constraint # added constraint: constraint((T0346)D99.CB, (T0346)K123.CB) [> 4.7983 = 7.9972 < 10.3963] w=0.0014 to align # SetCost created cost = # ( 1.0000 * align ) # command:# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0346/ # command:# reading script from file servers-clean.under # Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/T0346/decoys/ # ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0346 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation 3D-JIGSAW_POPULUS_TS1 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0346 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation 3D-JIGSAW_POPULUS_TS2 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0346 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation 3D-JIGSAW_POPULUS_TS3 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0346 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation 3D-JIGSAW_POPULUS_TS4 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0346 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation 3D-JIGSAW_POPULUS_TS5 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_RECOM_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0346 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation 3D-JIGSAW_RECOM_TS1 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_RECOM_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0346 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation 3D-JIGSAW_RECOM_TS2 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_RECOM_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0346 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation 3D-JIGSAW_RECOM_TS3 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_RECOM_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0346 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation 3D-JIGSAW_RECOM_TS4 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_RECOM_TS5.pdb.gz looking for model 1 # Found a chain break before 163 # copying to AlignedFragments data structure # naming current conformation 3D-JIGSAW_RECOM_TS5 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0346 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation 3D-JIGSAW_TS1 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0346 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation 3D-JIGSAW_TS2 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0346 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation 3D-JIGSAW_TS3 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_TS4.pdb.gz looking for model 1 # Found a chain break before 163 # copying to AlignedFragments data structure # naming current conformation 3D-JIGSAW_TS4 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_TS5.pdb.gz looking for model 1 # Found a chain break before 163 # copying to AlignedFragments data structure # naming current conformation 3D-JIGSAW_TS5 # ReadConformPDB reading from PDB file servers/3Dpro_TS1.pdb.gz looking for model 1 # Found a chain break before 155 # copying to AlignedFragments data structure # naming current conformation 3Dpro_TS1 # ReadConformPDB reading from PDB file servers/3Dpro_TS2.pdb.gz looking for model 1 # Found a chain break before 110 # copying to AlignedFragments data structure # naming current conformation 3Dpro_TS2 # ReadConformPDB reading from PDB file servers/3Dpro_TS3.pdb.gz looking for model 1 # Found a chain break before 124 # copying to AlignedFragments data structure # naming current conformation 3Dpro_TS3 # ReadConformPDB reading from PDB file servers/3Dpro_TS4.pdb.gz looking for model 1 # Found a chain break before 124 # copying to AlignedFragments data structure # naming current conformation 3Dpro_TS4 # ReadConformPDB reading from PDB file servers/3Dpro_TS5.pdb.gz looking for model 1 # Found a chain break before 124 # copying to AlignedFragments data structure # naming current conformation 3Dpro_TS5 # ReadConformPDB reading from PDB file servers/ABIpro_TS1.pdb.gz looking for model 1 # Found a chain break before 167 # copying to AlignedFragments data structure # naming current conformation ABIpro_TS1 # ReadConformPDB reading from PDB file servers/ABIpro_TS2.pdb.gz looking for model 1 # Found a chain break before 167 # copying to AlignedFragments data structure # naming current conformation ABIpro_TS2 # ReadConformPDB reading from PDB file servers/ABIpro_TS3.pdb.gz looking for model 1 # Found a chain break before 165 # copying to AlignedFragments data structure # naming current conformation ABIpro_TS3 # ReadConformPDB reading from PDB file servers/ABIpro_TS4.pdb.gz looking for model 1 # Found a chain break before 118 # copying to AlignedFragments data structure # naming current conformation ABIpro_TS4 # ReadConformPDB reading from PDB file servers/ABIpro_TS5.pdb.gz looking for model 1 # Found a chain break before 133 # copying to AlignedFragments data structure # naming current conformation ABIpro_TS5 # ReadConformPDB reading from PDB file servers/BayesHH_TS1.pdb.gz looking for model 1 # Found a chain break before 93 # copying to AlignedFragments data structure # naming current conformation BayesHH_TS1 # ReadConformPDB reading from PDB file servers/Bilab-ENABLE_TS1.pdb.gz looking for model 1 # Found a chain break before 97 # copying to AlignedFragments data structure # naming current conformation Bilab-ENABLE_TS1 # ReadConformPDB reading from PDB file servers/Bilab-ENABLE_TS2.pdb.gz looking for model 1 # Found a chain break before 155 # copying to AlignedFragments data structure # naming current conformation Bilab-ENABLE_TS2 # ReadConformPDB reading from PDB file servers/Bilab-ENABLE_TS3.pdb.gz looking for model 1 # Found a chain break before 93 # copying to AlignedFragments data structure # naming current conformation Bilab-ENABLE_TS3 # ReadConformPDB reading from PDB file servers/Bilab-ENABLE_TS4.pdb.gz looking for model 1 # Found a chain break before 97 # copying to AlignedFragments data structure # naming current conformation Bilab-ENABLE_TS4 # ReadConformPDB reading from PDB file servers/Bilab-ENABLE_TS5.pdb.gz looking for model 1 # Found a chain break before 155 # copying to AlignedFragments data structure # naming current conformation Bilab-ENABLE_TS5 # ReadConformPDB reading from PDB file servers/CIRCLE_TS1.pdb.gz looking for model 1 # Found a chain break before 158 # copying to AlignedFragments data structure # naming current conformation CIRCLE_TS1 # ReadConformPDB reading from PDB file servers/CIRCLE_TS2.pdb.gz looking for model 1 # Found a chain break before 169 # copying to AlignedFragments data structure # naming current conformation CIRCLE_TS2 # ReadConformPDB reading from PDB file servers/CIRCLE_TS3.pdb.gz looking for model 1 # Found a chain break before 154 # copying to AlignedFragments data structure # naming current conformation CIRCLE_TS3 # ReadConformPDB reading from PDB file servers/CIRCLE_TS4.pdb.gz looking for model 1 # Found a chain break before 114 # copying to AlignedFragments data structure # naming current conformation CIRCLE_TS4 # ReadConformPDB reading from PDB file servers/CIRCLE_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0346 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation CIRCLE_TS5 # ReadConformPDB reading from PDB file servers/CPHmodels_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0346 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation CPHmodels_TS1 # ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS1.pdb.gz looking for model 1 # naming current conformation CaspIta-FOX_TS1 # ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0346 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation CaspIta-FOX_TS2 # ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS3.pdb.gz looking for model 1 # Found a chain break before 163 # copying to AlignedFragments data structure # naming current conformation CaspIta-FOX_TS3 # ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0346 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation CaspIta-FOX_TS4 # ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0346 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation CaspIta-FOX_TS5 # ReadConformPDB reading from PDB file servers/Distill_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0346 can't currently be optimized by undertaker # naming current conformation Distill_TS1 # ReadConformPDB reading from PDB file servers/Distill_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0346 can't currently be optimized by undertaker # naming current conformation Distill_TS2 # ReadConformPDB reading from PDB file servers/Distill_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0346 can't currently be optimized by undertaker # naming current conformation Distill_TS3 # ReadConformPDB reading from PDB file servers/Distill_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0346 can't currently be optimized by undertaker # naming current conformation Distill_TS4 # ReadConformPDB reading from PDB file servers/Distill_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0346 can't currently be optimized by undertaker # naming current conformation Distill_TS5 # ReadConformPDB reading from PDB file servers/FAMSD_TS1.pdb.gz looking for model 1 # naming current conformation FAMSD_TS1 # ReadConformPDB reading from PDB file servers/FAMSD_TS2.pdb.gz looking for model 1 # Found a chain break before 168 # copying to AlignedFragments data structure # naming current conformation FAMSD_TS2 # ReadConformPDB reading from PDB file servers/FAMSD_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0346 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation FAMSD_TS3 # ReadConformPDB reading from PDB file servers/FAMSD_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0346 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation FAMSD_TS4 # ReadConformPDB reading from PDB file servers/FAMSD_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0346 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation FAMSD_TS5 # ReadConformPDB reading from PDB file servers/FAMS_TS1.pdb.gz looking for model 1 # Found a chain break before 169 # copying to AlignedFragments data structure # naming current conformation FAMS_TS1 # ReadConformPDB reading from PDB file servers/FAMS_TS2.pdb.gz looking for model 1 # Found a chain break before 154 # copying to AlignedFragments data structure # naming current conformation FAMS_TS2 # ReadConformPDB reading from PDB file servers/FAMS_TS3.pdb.gz looking for model 1 # Found a chain break before 158 # copying to AlignedFragments data structure # naming current conformation FAMS_TS3 # ReadConformPDB reading from PDB file servers/FAMS_TS4.pdb.gz looking for model 1 # Found a chain break before 114 # copying to AlignedFragments data structure # naming current conformation FAMS_TS4 # ReadConformPDB reading from PDB file servers/FAMS_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0346 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation FAMS_TS5 # ReadConformPDB reading from PDB file servers/FOLDpro_TS1.pdb.gz looking for model 1 # Found a chain break before 154 # copying to AlignedFragments data structure # naming current conformation FOLDpro_TS1 # ReadConformPDB reading from PDB file servers/FOLDpro_TS2.pdb.gz looking for model 1 # Found a chain break before 163 # copying to AlignedFragments data structure # naming current conformation FOLDpro_TS2 # ReadConformPDB reading from PDB file servers/FOLDpro_TS3.pdb.gz looking for model 1 # Found a chain break before 155 # copying to AlignedFragments data structure # naming current conformation FOLDpro_TS3 # ReadConformPDB reading from PDB file servers/FOLDpro_TS4.pdb.gz looking for model 1 # Found a chain break before 124 # copying to AlignedFragments data structure # naming current conformation FOLDpro_TS4 # ReadConformPDB reading from PDB file servers/FOLDpro_TS5.pdb.gz looking for model 1 # Found a chain break before 124 # copying to AlignedFragments data structure # naming current conformation FOLDpro_TS5 # ReadConformPDB reading from PDB file servers/FORTE1_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0346 can't currently be optimized by undertaker # naming current conformation FORTE1_AL1 # ReadConformPDB reading from PDB file servers/FORTE1_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0346 can't currently be optimized by undertaker # naming current conformation FORTE1_AL2 # ReadConformPDB reading from PDB file servers/FORTE1_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0346 can't currently be optimized by undertaker # naming current conformation FORTE1_AL3 # ReadConformPDB reading from PDB file servers/FORTE1_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0346 can't currently be optimized by undertaker # naming current conformation FORTE1_AL4 # ReadConformPDB reading from PDB file servers/FORTE1_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0346 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation FORTE1_AL5 # ReadConformPDB reading from PDB file servers/FORTE2_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0346 can't currently be optimized by undertaker # naming current conformation FORTE2_AL1 # ReadConformPDB reading from PDB file servers/FORTE2_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0346 can't currently be optimized by undertaker # naming current conformation FORTE2_AL2 # ReadConformPDB reading from PDB file servers/FORTE2_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0346 can't currently be optimized by undertaker # naming current conformation FORTE2_AL3 # ReadConformPDB reading from PDB file servers/FORTE2_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0346 can't currently be optimized by undertaker # naming current conformation FORTE2_AL4 # ReadConformPDB reading from PDB file servers/FORTE2_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0346 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation FORTE2_AL5 # ReadConformPDB reading from PDB file servers/FPSOLVER-SERVER_TS1.pdb.gz looking for model 1 # Found a chain break before 36 # copying to AlignedFragments data structure # naming current conformation FPSOLVER-SERVER_TS1 # ReadConformPDB reading from PDB file servers/FPSOLVER-SERVER_TS2.pdb.gz looking for model 1 # Found a chain break before 107 # copying to AlignedFragments data structure # naming current conformation FPSOLVER-SERVER_TS2 # ReadConformPDB reading from PDB file servers/FPSOLVER-SERVER_TS3.pdb.gz looking for model 1 # Found a chain break before 36 # copying to AlignedFragments data structure # naming current conformation FPSOLVER-SERVER_TS3 # ReadConformPDB reading from PDB file servers/FPSOLVER-SERVER_TS4.pdb.gz looking for model 1 # Found a chain break before 31 # copying to AlignedFragments data structure # naming current conformation FPSOLVER-SERVER_TS4 # ReadConformPDB reading from PDB file servers/FPSOLVER-SERVER_TS5.pdb.gz looking for model 1 # Found a chain break before 31 # copying to AlignedFragments data structure # naming current conformation FPSOLVER-SERVER_TS5 # ReadConformPDB reading from PDB file servers/FUGMOD_TS1.pdb.gz looking for model 1 # Found a chain break before 93 # copying to AlignedFragments data structure # naming current conformation FUGMOD_TS1 # ReadConformPDB reading from PDB file servers/FUGMOD_TS2.pdb.gz looking for model 1 # naming current conformation FUGMOD_TS2 # ReadConformPDB reading from PDB file servers/FUGMOD_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0346 can't currently be optimized by undertaker # naming current conformation FUGMOD_TS3 # ReadConformPDB reading from PDB file servers/FUGMOD_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0346 can't currently be optimized by undertaker # naming current conformation FUGMOD_TS4 # ReadConformPDB reading from PDB file servers/FUGMOD_TS5.pdb.gz looking for model 1 # Found a chain break before 170 # copying to AlignedFragments data structure # naming current conformation FUGMOD_TS5 # ReadConformPDB reading from PDB file servers/FUGUE_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0346 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation FUGUE_AL1 # ReadConformPDB reading from PDB file servers/FUGUE_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0346 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation FUGUE_AL2 # ReadConformPDB reading from PDB file servers/FUGUE_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0346 can't currently be optimized by undertaker # naming current conformation FUGUE_AL3 # ReadConformPDB reading from PDB file servers/FUGUE_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0346 can't currently be optimized by undertaker # naming current conformation FUGUE_AL4 # ReadConformPDB reading from PDB file servers/FUGUE_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0346 can't currently be optimized by undertaker # naming current conformation FUGUE_AL5 # ReadConformPDB reading from PDB file servers/FUNCTION_TS1.pdb.gz looking for model 1 # Found a chain break before 169 # copying to AlignedFragments data structure # naming current conformation FUNCTION_TS1 # ReadConformPDB reading from PDB file servers/FUNCTION_TS2.pdb.gz looking for model 1 # Found a chain break before 154 # copying to AlignedFragments data structure # naming current conformation FUNCTION_TS2 # ReadConformPDB reading from PDB file servers/FUNCTION_TS3.pdb.gz looking for model 1 # Found a chain break before 158 # copying to AlignedFragments data structure # naming current conformation FUNCTION_TS3 # ReadConformPDB reading from PDB file servers/FUNCTION_TS4.pdb.gz looking for model 1 # Found a chain break before 153 # copying to AlignedFragments data structure # naming current conformation FUNCTION_TS4 # ReadConformPDB reading from PDB file servers/FUNCTION_TS5.pdb.gz looking for model 1 # Found a chain break before 159 # copying to AlignedFragments data structure # naming current conformation FUNCTION_TS5 # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS1.pdb.gz looking for model 1 # Found a chain break before 93 # copying to AlignedFragments data structure # naming current conformation GeneSilicoMetaServer_TS1 # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS2.pdb.gz looking for model 1 # Found a chain break before 70 # copying to AlignedFragments data structure # naming current conformation GeneSilicoMetaServer_TS2 # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS3.pdb.gz looking for model 1 # Found a chain break before 164 # copying to AlignedFragments data structure # naming current conformation GeneSilicoMetaServer_TS3 # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS4.pdb.gz looking for model 1 # Found a chain break before 124 # copying to AlignedFragments data structure # naming current conformation GeneSilicoMetaServer_TS4 # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS5.pdb.gz looking for model 1 # Found a chain break before 124 # copying to AlignedFragments data structure # naming current conformation GeneSilicoMetaServer_TS5 # ReadConformPDB reading from PDB file servers/HHpred1_TS1.pdb.gz looking for model 1 # Found a chain break before 93 # copying to AlignedFragments data structure # naming current conformation HHpred1_TS1 # ReadConformPDB reading from PDB file servers/HHpred2_TS1.pdb.gz looking for model 1 # Found a chain break before 153 # copying to AlignedFragments data structure # naming current conformation HHpred2_TS1 # ReadConformPDB reading from PDB file servers/HHpred3_TS1.pdb.gz looking for model 1 # Found a chain break before 153 # copying to AlignedFragments data structure # naming current conformation HHpred3_TS1 # ReadConformPDB reading from PDB file servers/Huber-Torda-Server_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0346 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation Huber-Torda-Server_TS1 # ReadConformPDB reading from PDB file servers/Huber-Torda-Server_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0346 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation Huber-Torda-Server_TS2 # ReadConformPDB reading from PDB file servers/Huber-Torda-Server_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0346 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation Huber-Torda-Server_TS3 # ReadConformPDB reading from PDB file servers/Huber-Torda-Server_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0346 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation Huber-Torda-Server_TS4 # ReadConformPDB reading from PDB file servers/Huber-Torda-Server_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0346 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation Huber-Torda-Server_TS5 # ReadConformPDB reading from PDB file servers/LOOPP_TS1.pdb.gz looking for model 1 # Found a chain break before 69 # copying to AlignedFragments data structure # naming current conformation LOOPP_TS1 # ReadConformPDB reading from PDB file servers/LOOPP_TS2.pdb.gz looking for model 1 # Found a chain break before 64 # copying to AlignedFragments data structure # naming current conformation LOOPP_TS2 # ReadConformPDB reading from PDB file servers/LOOPP_TS3.pdb.gz looking for model 1 # Found a chain break before 115 # copying to AlignedFragments data structure # naming current conformation LOOPP_TS3 # ReadConformPDB reading from PDB file servers/LOOPP_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0346 can't currently be optimized by undertaker # naming current conformation LOOPP_TS4 # ReadConformPDB reading from PDB file servers/LOOPP_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0346 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation LOOPP_TS5 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server2_TS1.pdb.gz looking for model 1 # Found a chain break before 124 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server2_TS1 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server2_TS2.pdb.gz looking for model 1 # Found a chain break before 93 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server2_TS2 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server2_TS3.pdb.gz looking for model 1 # Found a chain break before 13 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server2_TS3 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server2_TS4.pdb.gz looking for model 1 # Found a chain break before 164 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server2_TS4 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server2_TS5.pdb.gz looking for model 1 # Found a chain break before 27 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server2_TS5 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS1.pdb.gz looking for model 1 # Found a chain break before 124 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server_TS1 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS2.pdb.gz looking for model 1 # Found a chain break before 54 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server_TS2 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS3.pdb.gz looking for model 1 # Found a chain break before 93 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server_TS3 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS4.pdb.gz looking for model 1 # Found a chain break before 157 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server_TS4 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS5.pdb.gz looking for model 1 # Found a chain break before 164 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server_TS5 # ReadConformPDB reading from PDB file servers/MetaTasser_TS1.pdb.gz looking for model 1 # Found a chain break before 171 # copying to AlignedFragments data structure # naming current conformation MetaTasser_TS1 # ReadConformPDB reading from PDB file servers/MetaTasser_TS2.pdb.gz looking for model 1 # Found a chain break before 171 # copying to AlignedFragments data structure # naming current conformation MetaTasser_TS2 # ReadConformPDB reading from PDB file servers/MetaTasser_TS3.pdb.gz looking for model 1 # Found a chain break before 170 # copying to AlignedFragments data structure # naming current conformation MetaTasser_TS3 # ReadConformPDB reading from PDB file servers/NN_PUT_lab_TS1.pdb.gz looking for model 1 # Found a chain break before 69 # copying to AlignedFragments data structure # naming current conformation NN_PUT_lab_TS1 # ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS1.pdb.gz looking for model 1 # naming current conformation PROTINFO-AB_TS1 # ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS2.pdb.gz looking for model 1 # naming current conformation PROTINFO-AB_TS2 # ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS3.pdb.gz looking for model 1 # naming current conformation PROTINFO-AB_TS3 # ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS4.pdb.gz looking for model 1 # naming current conformation PROTINFO-AB_TS4 # ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS5.pdb.gz looking for model 1 # naming current conformation PROTINFO-AB_TS5 # ReadConformPDB reading from PDB file servers/PROTINFO_TS1.pdb.gz looking for model 1 # naming current conformation PROTINFO_TS1 # ReadConformPDB reading from PDB file servers/PROTINFO_TS2.pdb.gz looking for model 1 # Found a chain break before 58 # copying to AlignedFragments data structure # naming current conformation PROTINFO_TS2 # ReadConformPDB reading from PDB file servers/PROTINFO_TS3.pdb.gz looking for model 1 # naming current conformation PROTINFO_TS3 # ReadConformPDB reading from PDB file servers/PROTINFO_TS4.pdb.gz looking for model 1 # naming current conformation PROTINFO_TS4 # ReadConformPDB reading from PDB file servers/PROTINFO_TS5.pdb.gz looking for model 1 # Found a chain break before 101 # copying to AlignedFragments data structure # naming current conformation PROTINFO_TS5 # ReadConformPDB reading from PDB file servers/Pcons6_TS1.pdb.gz looking for model 1 # Found a chain break before 100 # copying to AlignedFragments data structure # naming current conformation Pcons6_TS1 # ReadConformPDB reading from PDB file servers/Pcons6_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0346 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation Pcons6_TS2 # ReadConformPDB reading from PDB file servers/Pcons6_TS3.pdb.gz looking for model 1 # Found a chain break before 64 # copying to AlignedFragments data structure # naming current conformation Pcons6_TS3 # ReadConformPDB reading from PDB file servers/Pcons6_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0346 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation Pcons6_TS4 # ReadConformPDB reading from PDB file servers/Pcons6_TS5.pdb.gz looking for model 1 # Found a chain break before 101 # copying to AlignedFragments data structure # naming current conformation Pcons6_TS5 # ReadConformPDB reading from PDB file servers/Phyre-1_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0346 can't currently be optimized by undertaker # naming current conformation Phyre-1_TS1 # ReadConformPDB reading from PDB file servers/Phyre-2_TS1.pdb.gz looking for model 1 # naming current conformation Phyre-2_TS1 # ReadConformPDB reading from PDB file servers/Phyre-2_TS2.pdb.gz looking for model 1 # Found a chain break before 171 # copying to AlignedFragments data structure # naming current conformation Phyre-2_TS2 # ReadConformPDB reading from PDB file servers/Phyre-2_TS3.pdb.gz looking for model 1 # Found a chain break before 171 # copying to AlignedFragments data structure # naming current conformation Phyre-2_TS3 # ReadConformPDB reading from PDB file servers/Phyre-2_TS4.pdb.gz looking for model 1 # naming current conformation Phyre-2_TS4 # ReadConformPDB reading from PDB file servers/Phyre-2_TS5.pdb.gz looking for model 1 # naming current conformation Phyre-2_TS5 # ReadConformPDB reading from PDB file servers/Pmodeller6_TS1.pdb.gz looking for model 1 # Found a chain break before 100 # copying to AlignedFragments data structure # naming current conformation Pmodeller6_TS1 # ReadConformPDB reading from PDB file servers/Pmodeller6_TS2.pdb.gz looking for model 1 # Found a chain break before 100 # copying to AlignedFragments data structure # naming current conformation Pmodeller6_TS2 # ReadConformPDB reading from PDB file servers/Pmodeller6_TS3.pdb.gz looking for model 1 # Found a chain break before 100 # copying to AlignedFragments data structure # naming current conformation Pmodeller6_TS3 # ReadConformPDB reading from PDB file servers/Pmodeller6_TS4.pdb.gz looking for model 1 # Found a chain break before 100 # copying to AlignedFragments data structure # naming current conformation Pmodeller6_TS4 # ReadConformPDB reading from PDB file servers/Pmodeller6_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0346 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation Pmodeller6_TS5 # ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS1.pdb.gz looking for model 1 # Found a chain break before 64 # copying to AlignedFragments data structure # naming current conformation RAPTOR-ACE_TS1 # ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS2.pdb.gz looking for model 1 # Found a chain break before 154 # copying to AlignedFragments data structure # naming current conformation RAPTOR-ACE_TS2 # ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS3.pdb.gz looking for model 1 # Found a chain break before 164 # copying to AlignedFragments data structure # naming current conformation RAPTOR-ACE_TS3 # ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS4.pdb.gz looking for model 1 # Found a chain break before 140 # copying to AlignedFragments data structure # naming current conformation RAPTOR-ACE_TS4 # ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS5.pdb.gz looking for model 1 # Found a chain break before 156 # copying to AlignedFragments data structure # naming current conformation RAPTOR-ACE_TS5 # ReadConformPDB reading from PDB file servers/RAPTORESS_TS1.pdb.gz looking for model 1 # Found a chain break before 58 # copying to AlignedFragments data structure # naming current conformation RAPTORESS_TS1 # ReadConformPDB reading from PDB file servers/RAPTORESS_TS2.pdb.gz looking for model 1 # Found a chain break before 123 # copying to AlignedFragments data structure # naming current conformation RAPTORESS_TS2 # ReadConformPDB reading from PDB file servers/RAPTORESS_TS3.pdb.gz looking for model 1 # Found a chain break before 123 # copying to AlignedFragments data structure # naming current conformation RAPTORESS_TS3 # ReadConformPDB reading from PDB file servers/RAPTORESS_TS4.pdb.gz looking for model 1 # Found a chain break before 53 # copying to AlignedFragments data structure # naming current conformation RAPTORESS_TS4 # ReadConformPDB reading from PDB file servers/RAPTORESS_TS5.pdb.gz looking for model 1 # Found a chain break before 56 # copying to AlignedFragments data structure # naming current conformation RAPTORESS_TS5 # ReadConformPDB reading from PDB file servers/RAPTOR_TS1.pdb.gz looking for model 1 # naming current conformation RAPTOR_TS1 # ReadConformPDB reading from PDB file servers/RAPTOR_TS2.pdb.gz looking for model 1 # Found a chain break before 124 # copying to AlignedFragments data structure # naming current conformation RAPTOR_TS2 # ReadConformPDB reading from PDB file servers/RAPTOR_TS3.pdb.gz looking for model 1 # Found a chain break before 164 # copying to AlignedFragments data structure # naming current conformation RAPTOR_TS3 # ReadConformPDB reading from PDB file servers/RAPTOR_TS4.pdb.gz looking for model 1 # Found a chain break before 124 # copying to AlignedFragments data structure # naming current conformation RAPTOR_TS4 # ReadConformPDB reading from PDB file servers/RAPTOR_TS5.pdb.gz looking for model 1 # Found a chain break before 64 # copying to AlignedFragments data structure # naming current conformation RAPTOR_TS5 # ReadConformPDB reading from PDB file servers/ROBETTA_TS1.pdb.gz looking for model 1 # Found a chain break before 100 # copying to AlignedFragments data structure # naming current conformation ROBETTA_TS1 # ReadConformPDB reading from PDB file servers/ROBETTA_TS2.pdb.gz looking for model 1 # Found a chain break before 100 # copying to AlignedFragments data structure # naming current conformation ROBETTA_TS2 # ReadConformPDB reading from PDB file servers/ROBETTA_TS3.pdb.gz looking for model 1 # Found a chain break before 100 # copying to AlignedFragments data structure # naming current conformation ROBETTA_TS3 # ReadConformPDB reading from PDB file servers/ROBETTA_TS4.pdb.gz looking for model 1 # Found a chain break before 100 # copying to AlignedFragments data structure # naming current conformation ROBETTA_TS4 # ReadConformPDB reading from PDB file servers/ROBETTA_TS5.pdb.gz looking for model 1 # Found a chain break before 100 # copying to AlignedFragments data structure # naming current conformation ROBETTA_TS5 # ReadConformPDB reading from PDB file servers/ROKKY_TS1.pdb.gz looking for model 1 # Found a chain break before 101 # copying to AlignedFragments data structure # naming current conformation ROKKY_TS1 # ReadConformPDB reading from PDB file servers/ROKKY_TS2.pdb.gz looking for model 1 # Found a chain break before 101 # copying to AlignedFragments data structure # naming current conformation ROKKY_TS2 # ReadConformPDB reading from PDB file servers/ROKKY_TS3.pdb.gz looking for model 1 # Found a chain break before 101 # copying to AlignedFragments data structure # naming current conformation ROKKY_TS3 # ReadConformPDB reading from PDB file servers/ROKKY_TS4.pdb.gz looking for model 1 # Found a chain break before 124 # copying to AlignedFragments data structure # naming current conformation ROKKY_TS4 # ReadConformPDB reading from PDB file servers/ROKKY_TS5.pdb.gz looking for model 1 # Found a chain break before 101 # copying to AlignedFragments data structure # naming current conformation ROKKY_TS5 # ReadConformPDB reading from PDB file servers/SAM-T02_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0346 can't currently be optimized by undertaker # naming current conformation SAM-T02_AL1 # ReadConformPDB reading from PDB file servers/SAM-T02_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0346 can't currently be optimized by undertaker # naming current conformation SAM-T02_AL2 # ReadConformPDB reading from PDB file servers/SAM-T02_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0346 can't currently be optimized by undertaker # naming current conformation SAM-T02_AL3 # ReadConformPDB reading from PDB file servers/SAM-T02_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0346 can't currently be optimized by undertaker # naming current conformation SAM-T02_AL4 # ReadConformPDB reading from PDB file servers/SAM-T02_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0346 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation SAM-T02_AL5 # ReadConformPDB reading from PDB file servers/SAM-T99_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0346 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation SAM-T99_AL1 # ReadConformPDB reading from PDB file servers/SAM-T99_AL2.pdb.gz looking for model 1 Skipped atom 103, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL2.pdb.gz # WARNING: incomplete conformation T0346 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation SAM-T99_AL2 # ReadConformPDB reading from PDB file servers/SAM-T99_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0346 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation SAM-T99_AL3 # ReadConformPDB reading from PDB file servers/SAM-T99_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0346 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation SAM-T99_AL4 # ReadConformPDB reading from PDB file servers/SAM-T99_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0346 can't currently be optimized by undertaker # naming current conformation SAM-T99_AL5 # ReadConformPDB reading from PDB file servers/SAM_T06_server_TS1.pdb.gz looking for model 1 # Found a chain break before 164 # copying to AlignedFragments data structure # naming current conformation SAM_T06_server_TS1 # ReadConformPDB reading from PDB file servers/SAM_T06_server_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0346 can't currently be optimized by undertaker # naming current conformation SAM_T06_server_TS2 # ReadConformPDB reading from PDB file servers/SAM_T06_server_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0346 can't currently be optimized by undertaker # naming current conformation SAM_T06_server_TS3 # ReadConformPDB reading from PDB file servers/SAM_T06_server_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0346 can't currently be optimized by undertaker # naming current conformation SAM_T06_server_TS4 # ReadConformPDB reading from PDB file servers/SAM_T06_server_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0346 can't currently be optimized by undertaker # naming current conformation SAM_T06_server_TS5 # ReadConformPDB reading from PDB file servers/SP3_TS1.pdb.gz looking for model 1 # Found a chain break before 140 # copying to AlignedFragments data structure # naming current conformation SP3_TS1 # ReadConformPDB reading from PDB file servers/SP3_TS2.pdb.gz looking for model 1 # Found a chain break before 92 # copying to AlignedFragments data structure # naming current conformation SP3_TS2 # ReadConformPDB reading from PDB file servers/SP3_TS3.pdb.gz looking for model 1 # Found a chain break before 97 # copying to AlignedFragments data structure # naming current conformation SP3_TS3 # ReadConformPDB reading from PDB file servers/SP3_TS4.pdb.gz looking for model 1 # Found a chain break before 154 # copying to AlignedFragments data structure # naming current conformation SP3_TS4 # ReadConformPDB reading from PDB file servers/SP3_TS5.pdb.gz looking for model 1 # Found a chain break before 92 # copying to AlignedFragments data structure # naming current conformation SP3_TS5 # ReadConformPDB reading from PDB file servers/SP4_TS1.pdb.gz looking for model 1 # Found a chain break before 140 # copying to AlignedFragments data structure # naming current conformation SP4_TS1 # ReadConformPDB reading from PDB file servers/SP4_TS2.pdb.gz looking for model 1 # Found a chain break before 92 # copying to AlignedFragments data structure # naming current conformation SP4_TS2 # ReadConformPDB reading from PDB file servers/SP4_TS3.pdb.gz looking for model 1 # Found a chain break before 154 # copying to AlignedFragments data structure # naming current conformation SP4_TS3 # ReadConformPDB reading from PDB file servers/SP4_TS4.pdb.gz looking for model 1 # Found a chain break before 97 # copying to AlignedFragments data structure # naming current conformation SP4_TS4 # ReadConformPDB reading from PDB file servers/SP4_TS5.pdb.gz looking for model 1 # Found a chain break before 112 # copying to AlignedFragments data structure # naming current conformation SP4_TS5 # ReadConformPDB reading from PDB file servers/SPARKS2_TS1.pdb.gz looking for model 1 # Found a chain break before 97 # copying to AlignedFragments data structure # naming current conformation SPARKS2_TS1 # ReadConformPDB reading from PDB file servers/SPARKS2_TS2.pdb.gz looking for model 1 # Found a chain break before 92 # copying to AlignedFragments data structure # naming current conformation SPARKS2_TS2 # ReadConformPDB reading from PDB file servers/SPARKS2_TS3.pdb.gz looking for model 1 # Found a chain break before 97 # copying to AlignedFragments data structure # naming current conformation SPARKS2_TS3 # ReadConformPDB reading from PDB file servers/SPARKS2_TS4.pdb.gz looking for model 1 # Found a chain break before 92 # copying to AlignedFragments data structure # naming current conformation SPARKS2_TS4 # ReadConformPDB reading from PDB file servers/SPARKS2_TS5.pdb.gz looking for model 1 # Found a chain break before 124 # copying to AlignedFragments data structure # naming current conformation SPARKS2_TS5 # ReadConformPDB reading from PDB file servers/UNI-EID_bnmx_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0346 can't currently be optimized by undertaker # naming current conformation UNI-EID_bnmx_TS1 # ReadConformPDB reading from PDB file servers/UNI-EID_bnmx_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0346 can't currently be optimized by undertaker # naming current conformation UNI-EID_bnmx_TS2 # ReadConformPDB reading from PDB file servers/UNI-EID_bnmx_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0346 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation UNI-EID_bnmx_TS3 # ReadConformPDB reading from PDB file servers/UNI-EID_bnmx_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0346 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation UNI-EID_bnmx_TS4 # ReadConformPDB reading from PDB file servers/UNI-EID_bnmx_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0346 can't currently be optimized by undertaker # naming current conformation UNI-EID_bnmx_TS5 # ReadConformPDB reading from PDB file servers/UNI-EID_expm_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0346 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation UNI-EID_expm_TS1 # ReadConformPDB reading from PDB file servers/UNI-EID_sfst_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0346 can't currently be optimized by undertaker # naming current conformation UNI-EID_sfst_AL1 # ReadConformPDB reading from PDB file servers/UNI-EID_sfst_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0346 can't currently be optimized by undertaker # naming current conformation UNI-EID_sfst_AL2 # ReadConformPDB reading from PDB file servers/UNI-EID_sfst_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0346 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation UNI-EID_sfst_AL3 # ReadConformPDB reading from PDB file servers/UNI-EID_sfst_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0346 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation UNI-EID_sfst_AL4 # ReadConformPDB reading from PDB file servers/UNI-EID_sfst_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0346 can't currently be optimized by undertaker # naming current conformation UNI-EID_sfst_AL5 # ReadConformPDB reading from PDB file servers/Zhang-Server_TS1.pdb.gz looking for model 1 # naming current conformation Zhang-Server_TS1 # ReadConformPDB reading from PDB file servers/Zhang-Server_TS2.pdb.gz looking for model 1 # naming current conformation Zhang-Server_TS2 # ReadConformPDB reading from PDB file servers/Zhang-Server_TS3.pdb.gz looking for model 1 # Found a chain break before 44 # copying to AlignedFragments data structure # naming current conformation Zhang-Server_TS3 # ReadConformPDB reading from PDB file servers/Zhang-Server_TS4.pdb.gz looking for model 1 # Found a chain break before 77 # copying to AlignedFragments data structure # naming current conformation Zhang-Server_TS4 # ReadConformPDB reading from PDB file servers/Zhang-Server_TS5.pdb.gz looking for model 1 # Found a chain break before 115 # copying to AlignedFragments data structure # naming current conformation Zhang-Server_TS5 # ReadConformPDB reading from PDB file servers/beautshot_TS1.pdb.gz looking for model 1 # Found a chain break before 171 # copying to AlignedFragments data structure # naming current conformation beautshot_TS1 # ReadConformPDB reading from PDB file servers/beautshotbase_TS1.pdb.gz looking for model 1 # Found a chain break before 166 # copying to AlignedFragments data structure # naming current conformation beautshotbase_TS1 # ReadConformPDB reading from PDB file servers/forecast-s_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0346 can't currently be optimized by undertaker # naming current conformation forecast-s_AL1 # ReadConformPDB reading from PDB file servers/forecast-s_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0346 can't currently be optimized by undertaker # naming current conformation forecast-s_AL2 # ReadConformPDB reading from PDB file servers/forecast-s_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0346 can't currently be optimized by undertaker # naming current conformation forecast-s_AL3 # ReadConformPDB reading from PDB file servers/forecast-s_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0346 can't currently be optimized by undertaker # naming current conformation forecast-s_AL4 # ReadConformPDB reading from PDB file servers/forecast-s_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0346 can't currently be optimized by undertaker # naming current conformation forecast-s_AL5 # ReadConformPDB reading from PDB file servers/gtg_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0346 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation gtg_AL1 # ReadConformPDB reading from PDB file servers/gtg_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0346 can't currently be optimized by undertaker # naming current conformation gtg_AL2 # ReadConformPDB reading from PDB file servers/gtg_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0346 can't currently be optimized by undertaker # naming current conformation gtg_AL3 # ReadConformPDB reading from PDB file servers/gtg_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0346 can't currently be optimized by undertaker # naming current conformation gtg_AL4 # ReadConformPDB reading from PDB file servers/gtg_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0346 can't currently be optimized by undertaker # naming current conformation gtg_AL5 # ReadConformPDB reading from PDB file servers/karypis.srv.2_TS1.pdb.gz looking for model 1 # Found a chain break before 124 # copying to AlignedFragments data structure # naming current conformation karypis.srv.2_TS1 # ReadConformPDB reading from PDB file servers/karypis.srv.2_TS2.pdb.gz looking for model 1 # Found a chain break before 124 # copying to AlignedFragments data structure # naming current conformation karypis.srv.2_TS2 # ReadConformPDB reading from PDB file servers/karypis.srv.2_TS3.pdb.gz looking for model 1 # Found a chain break before 124 # copying to AlignedFragments data structure # naming current conformation karypis.srv.2_TS3 # ReadConformPDB reading from PDB file servers/karypis.srv.2_TS4.pdb.gz looking for model 1 # Found a chain break before 124 # copying to AlignedFragments data structure # naming current conformation karypis.srv.2_TS4 # ReadConformPDB reading from PDB file servers/karypis.srv.2_TS5.pdb.gz looking for model 1 # Found a chain break before 155 # copying to AlignedFragments data structure # naming current conformation karypis.srv.2_TS5 # ReadConformPDB reading from PDB file servers/karypis.srv.4_TS1.pdb.gz looking for model 1 # Found a chain break before 169 # copying to AlignedFragments data structure # naming current conformation karypis.srv.4_TS1 # ReadConformPDB reading from PDB file servers/karypis.srv.4_TS2.pdb.gz looking for model 1 # Found a chain break before 169 # copying to AlignedFragments data structure # naming current conformation karypis.srv.4_TS2 # ReadConformPDB reading from PDB file servers/karypis.srv.4_TS4.pdb.gz looking for model 1 # Found a chain break before 169 # copying to AlignedFragments data structure # naming current conformation karypis.srv.4_TS4 # ReadConformPDB reading from PDB file servers/karypis.srv.4_TS5.pdb.gz looking for model 1 WARNING: atoms too close: (T0346)Y160.O and (T0346)A161.N only 0.000 apart, marking (T0346)A161.N as missing WARNING: atoms too close: (T0346)C168.O and (T0346)G169.N only 0.000 apart, marking (T0346)G169.N as missing # WARNING: incomplete conformation T0346 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation karypis.srv.4_TS5 # ReadConformPDB reading from PDB file servers/karypis.srv_TS1.pdb.gz looking for model 1 # Found a chain break before 112 # copying to AlignedFragments data structure # naming current conformation karypis.srv_TS1 # ReadConformPDB reading from PDB file servers/karypis.srv_TS2.pdb.gz looking for model 1 # Found a chain break before 124 # copying to AlignedFragments data structure # naming current conformation karypis.srv_TS2 # ReadConformPDB reading from PDB file servers/karypis.srv_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0346 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation karypis.srv_TS3 # ReadConformPDB reading from PDB file servers/karypis.srv_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0346 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation karypis.srv_TS4 # ReadConformPDB reading from PDB file servers/karypis.srv_TS5.pdb.gz looking for model 1 # Found a chain break before 54 # copying to AlignedFragments data structure # naming current conformation karypis.srv_TS5 # ReadConformPDB reading from PDB file servers/keasar-server_TS1.pdb.gz looking for model 1 # naming current conformation keasar-server_TS1 # ReadConformPDB reading from PDB file servers/keasar-server_TS2.pdb.gz looking for model 1 # naming current conformation keasar-server_TS2 # ReadConformPDB reading from PDB file servers/keasar-server_TS3.pdb.gz looking for model 1 # naming current conformation keasar-server_TS3 # ReadConformPDB reading from PDB file servers/keasar-server_TS4.pdb.gz looking for model 1 # naming current conformation keasar-server_TS4 # ReadConformPDB reading from PDB file servers/keasar-server_TS5.pdb.gz looking for model 1 # naming current conformation keasar-server_TS5 # ReadConformPDB reading from PDB file servers/mGen-3D_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0346 can't currently be optimized by undertaker # naming current conformation mGen-3D_TS1 # ReadConformPDB reading from PDB file servers/nFOLD_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0346 can't currently be optimized by undertaker # naming current conformation nFOLD_TS1 # ReadConformPDB reading from PDB file servers/nFOLD_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0346 can't currently be optimized by undertaker # naming current conformation nFOLD_TS2 # ReadConformPDB reading from PDB file servers/nFOLD_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0346 can't currently be optimized by undertaker # naming current conformation nFOLD_TS3 # ReadConformPDB reading from PDB file servers/nFOLD_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0346 can't currently be optimized by undertaker # naming current conformation nFOLD_TS4 # ReadConformPDB reading from PDB file servers/nFOLD_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0346 can't currently be optimized by undertaker # naming current conformation nFOLD_TS5 # ReadConformPDB reading from PDB file servers/shub_TS1.pdb.gz looking for model 1 # Found a chain break before 166 # copying to AlignedFragments data structure # naming current conformation shub_TS1 # command:Using radius: 8.0000 Using models AND alignments for constraints model score -0.7722 model score -0.7734 model score -0.7871 model score -0.7886 model score -0.7433 model score -0.8232 model score -0.8046 model score -0.8255 model score -0.8003 model score -0.7899 model score -0.7981 model score -0.8232 model score -0.8076 model score -0.7957 model score -0.7426 model score -0.8285 model score -0.8269 model score -0.7483 model score -0.7387 model score -0.7566 model score 1.6317 model score 1.8308 model score 1.6449 model score 1.7448 model score 1.9208 model score -0.8216 model score -0.7773 model score -0.7760 model score -0.8038 model score -0.7919 model score -0.7779 model score -0.7447 model score -0.7596 model score -0.7732 model score -0.7509 model score -0.7791 model score -0.7019 model score -0.7998 model score -0.6759 model score -0.8128 model score -0.7075 model score -0.7319 model score 1.2697 model score 1.2693 model score 1.2679 model score 1.2695 model score 1.2683 model score -0.7829 model score -0.7565 model score -0.7488 model score -0.7369 model score -0.7618 model score -0.7770 model score -0.7732 model score -0.7447 model score -0.7509 model score -0.7791 model score -0.8097 model score -0.5210 model score -0.8226 model score -0.7483 model score -0.7387 model score 1.2665 model score 1.2668 model score 1.2801 model score 1.2790 model score 1.2786 model score 1.2665 model score 1.2668 model score 1.2794 model score 1.2780 model score 1.2807 model score 2.1473 model score 2.2271 model score 2.1473 model score 2.2431 model score 2.1791 model score -0.8048 model score -0.8060 model score 1.2705 model score 2.0787 model score 1.9671 model score 1.2665 model score 1.2672 model score 1.2771 model score 1.2830 model score 1.2812 model score -0.7169 model score -0.7079 model score -0.7825 model score -0.7534 model score -0.7690 model score -0.8047 model score -0.7652 model score -0.7590 model score -0.8004 model score -0.8005 model score -0.7962 model score -0.8165 model score -0.8165 model score -0.8068 model score -0.7954 model score -0.8205 model score -0.7888 model score -0.7706 model score -0.6604 model score -0.7691 model score -0.7205 model score -0.6382 model score -0.7052 model score -0.8062 model score -0.3551 model score -0.3187 model score -0.7523 model score 2.3937 model score -0.8062 model score -0.7641 model score -0.3551 model score -0.3643 model score -0.7523 model score -0.7554 model score -0.6003 model score -0.6151 model score -0.6604 model score -0.7342 model score -0.7320 model score -0.7353 model score -0.7331 model score -0.7304 model score -0.7353 model score -0.7615 model score -0.8099 model score -0.7850 model score -0.7550 model score -0.7495 model score -0.8072 model score -0.7856 model score -0.7830 model score -0.7740 model score -0.7836 model score -0.7954 model score -0.7951 model score -0.7951 model score -0.7954 model score -0.7954 model score -0.8092 model score -0.8002 model score -0.8008 model score -0.8055 model score -0.7830 model score -0.7461 model score -0.8136 model score -0.7640 model score -0.7189 model score -0.8104 model score -0.7074 model score -0.7414 model score -0.5571 model score -0.6045 model score -0.6402 model score -0.7797 model score -0.8036 model score -0.7307 model score -0.7590 model score -0.7569 model score -0.8055 model score -0.8059 model score -0.8008 model score -0.8092 model score -0.8002 model score -0.7724 model score -0.7527 model score -0.7470 model score -0.7190 model score -0.7661 model score 1.2663 model score 1.2664 model score 1.2662 model score 1.2670 model score 1.2662 model score 1.2672 model score 1.2672 model score 1.2667 model score 1.2669 model score 1.2670 model score -0.7794 model score -0.5635 model score -0.8012 model score -0.6622 model score -0.5077 model score -0.7189 model score -0.5616 model score -0.4345 model score -0.8136 model score -0.5884 model score -0.7141 model score -0.5375 model score -0.8136 model score -0.4334 model score -0.5598 model score -0.7253 model score -0.5385 model score -0.4345 model score -0.5884 model score -0.8029 model score 1.2662 model score 1.2670 model score 1.2673 model score 1.2662 model score 1.2669 model score -0.7843 model score 1.2662 model score 1.2670 model score 1.2673 model score 1.2662 model score 1.2669 model score -0.8125 model score -0.7940 model score -0.8073 model score -0.8050 model score -0.8001 model score -0.7639 model score -0.7593 model score 1.2665 model score 1.2667 model score 1.2806 model score 1.2818 model score 1.2771 model score 1.2672 model score 1.2663 model score 1.2665 model score 1.2662 model score 1.2663 model score -0.7778 model score -0.7778 model score -0.7734 model score -0.7710 model score -0.7901 model score 1.8260 model score 2.0335 model score 1.7700 model score 2.0479 model score -0.7912 model score -0.8000 model score -0.7615 model score -0.7842 model score -0.7772 model score -0.7204 model score -0.7270 model score -0.7196 model score -0.7223 model score -0.7407 model score -0.8005 model score -0.8005 model score -0.4251 model score -0.5252 model score 2.0699 model score 2.0303 model score -0.7378 USE_META, weight: 0.9843 cost: -0.7722 min: -0.8285 max: 2.3937 USE_META, weight: 0.9846 cost: -0.7734 min: -0.8285 max: 2.3937 USE_META, weight: 0.9884 cost: -0.7871 min: -0.8285 max: 2.3937 USE_META, weight: 0.9888 cost: -0.7886 min: -0.8285 max: 2.3937 USE_META, weight: 0.9762 cost: -0.7433 min: -0.8285 max: 2.3937 USE_META, weight: 0.9985 cost: -0.8232 min: -0.8285 max: 2.3937 USE_META, weight: 0.9933 cost: -0.8046 min: -0.8285 max: 2.3937 USE_META, weight: 0.9992 cost: -0.8255 min: -0.8285 max: 2.3937 USE_META, weight: 0.9921 cost: -0.8003 min: -0.8285 max: 2.3937 USE_META, weight: 0.9892 cost: -0.7899 min: -0.8285 max: 2.3937 USE_META, weight: 0.9915 cost: -0.7981 min: -0.8285 max: 2.3937 USE_META, weight: 0.9985 cost: -0.8232 min: -0.8285 max: 2.3937 USE_META, weight: 0.9941 cost: -0.8076 min: -0.8285 max: 2.3937 USE_META, weight: 0.9908 cost: -0.7957 min: -0.8285 max: 2.3937 USE_META, weight: 0.9760 cost: -0.7426 min: -0.8285 max: 2.3937 USE_META, weight: 1.0000 cost: -0.8285 min: -0.8285 max: 2.3937 USE_META, weight: 0.9995 cost: -0.8269 min: -0.8285 max: 2.3937 USE_META, weight: 0.9776 cost: -0.7483 min: -0.8285 max: 2.3937 USE_META, weight: 0.9749 cost: -0.7387 min: -0.8285 max: 2.3937 USE_META, weight: 0.9799 cost: -0.7566 min: -0.8285 max: 2.3937 USE_META, weight: 0.3129 cost: 1.6317 min: -0.8285 max: 2.3937 USE_META, weight: 0.2572 cost: 1.8308 min: -0.8285 max: 2.3937 USE_META, weight: 0.3092 cost: 1.6449 min: -0.8285 max: 2.3937 USE_META, weight: 0.2812 cost: 1.7448 min: -0.8285 max: 2.3937 USE_META, weight: 0.2321 cost: 1.9208 min: -0.8285 max: 2.3937 USE_META, weight: 0.9981 cost: -0.8216 min: -0.8285 max: 2.3937 USE_META, weight: 0.9857 cost: -0.7773 min: -0.8285 max: 2.3937 USE_META, weight: 0.9853 cost: -0.7760 min: 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min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0000 Number of contacts in models: 259 Number of contacts in alignments: 72 NUMB_ALIGNS: 72 Adding 4596 constraints to all3.constraints Done adding distance constraints # command:Reading probabilities from probabilities.dat Reading constraints from ConstraintSet all3.constraints maxweight: 1.0000 Optimizing... Probability sum: -322.6639, CN propb: -322.6639 weights: 0.5837 constraints: 445 # command:Found ConstraintSet # PrintContacts align.constraints_meta03 Number of constraints in align3.constraints 445 # command:Found ConstraintSet # PrintContacts align_bonus.constraints_meta03 Number of constraints in align3.constraints.bonus 445 # command:Found ConstraintSet # PrintContacts rejected.constraints_meta03 Number of constraints in rejected3.constraints 4151 # command:Found ConstraintSet # PrintContacts rejected_bonus.constraints_meta03 Number of constraints in rejected3.constraints.bonus 4151 # command:Found ConstraintSet # PrintContacts non_contacts.constraints_meta03 Number of constraints in noncontact3.constraints 0 # command:Found ConstraintSet # PrintContacts non_contacts_bonus.constraints_meta03 Number of constraints in noncontact3.constraints.bonus 0 # command:Found ConstraintSet # PrintContacts all.constraints_meta03 Number of constraints in all3.constraints 4596 # command: