parameters: 0.6 1.3 0.5 200 50 # command:# Prefix for input files set to /projects/compbio/experiments/undertaker/atoms-inputs/ # command:# reading dunbrack-2191.atoms # #computed average backbone with maximum peptide_sq_deviance = 0.002 # computed average trans backbone unit from 53157 examples # computed average trans backbone unit before proline from 2010 examples # computed average cis backbone unit from 97 examples # trans (non-proline) backbone unit: # CA= -2.2087 1.0126 -0.0030 # O= -0.1499 2.2440 0.0016 # C= -0.6889 1.1368 -0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4581 -0.0000 0.0000 # cis backbone unit: # CA= -0.1436 2.4534 -0.0002 # O= -2.0284 0.9742 0.0015 # C= -0.8018 1.0771 -0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4668 0.0000 0.0000 # trans backbone unit before proline: # CA= -2.2100 1.0631 -0.0014 # O= -0.1236 2.2458 0.0075 # C= -0.6872 1.1517 -0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4660 0.0000 0.0000 # After reading dunbrack-2191.atoms have 2191 chains in training database # Count of chains,residues,atoms: 2191,500310,3902258 # 493341 residues have no bad marker # 3226 residues lack atoms needed to compute omega # 1453 residues have cis peptide # number of each bad type: # NON_STANDARD_RESIDUE 4 # HAS_OXT 1167 # TOO_MANY_ATOMS 1 # TOO_FEW_ATOMS 3052 # HAS_UNKNOWN_ATOMS 9 # HAS_DUPLICATE_ATOMS 0 # CHAIN_BREAK_BEFORE 979 # NON_PLANAR_PEPTIDE 888 # BAD_PEPTIDE 2680 # Note: may sum to more than number of residues, # because one residue may have multiple problems # command:# Reading rotamer library from dunbrack-2191.rot # command:# Prefix for input files set to /projects/compbio/experiments/undertaker/spots/ # command:# ReadAtomType exp-pdb.types Read AtomType exp-pdb with 49 types. # command:# ReadClashTable exp-pdb-2191-2symm.clash # Read ClashTable exp-pdb-2191-2symm checking bonds symmetric at MaxSep 2 # command:# command:# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/T0290/ # command:# Making conformation for sequence T0290 numbered 1 through 173 Created new target T0290 from T0290.a2m # command:# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/T0290/ # command:Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0290//projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0290/manyalignments-good-all.under or /projects/compbio/experiments/protein-predict/casp7/T0290//projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0290/manyalignments-good-all.under.gz for input Trying /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0290/manyalignments-good-all.under # reading script from file /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0290/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/T0290/1xyhA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0290/1xyhA/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:# T0290 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 T0290 6 :FDIAINNQPAGRVVFELFSDVCPKTCENFRCLCTGEKGTG 2rmcA 42 :FDVRIGDKDVGRIVIGLFGNVVPKTVENFVALATGEKGYG # choosing archetypes in rotamer library T0290 54 :YKSCLFHRVVKDFMVQGGDFSEGNGRGGESIYGGFFEDESFAVKHNAAFLLSMANRGKDTNGSQFFITTKPTPHLDGHHVVFGQVISGQEVVREIENQKTDAASKPFAEVRILSCGELI 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 T0290 5 :FFDIAINNQPAGRVVFELFSDVCPKTCENFRCLCTGEKGTG 2rmcA 41 :FFDVRIGDKDVGRIVIGLFGNVVPKTVENFVALATGEKGYG T0290 54 :YKSCLFHRVVKDFMVQGGDFSEGNGRGGESIYGGFFEDESFAVKHNAAFLLSMANRGKDTNGSQFFITTKPTPHLDGHHVVFGQVISGQEVVREIENQKTDAASKPFAEVRILSCGELI 2rmcA 82 :YKGSIFHRVIKDFMIQGGDFTARDGTGGMSIYGETFPDENFKLKHYGIGWVSMANAGPDTNGSQFFITLTKPTWLDGKHVVFGKVLDGMTVVHSIELQATDGHDRPLTDCTIVNSGKID 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 T0290 4 :CFFDIAINNQPAGRVVFELFSDVCPKTCENFRCLCTGE 2rmcA 40 :VFFDVRIGDKDVGRIVIGLFGNVVPKTVENFVALATGE T0290 50 :KPLHYKSCLFHRVVKDFMVQGGDFSEGNGRGGESIYGGFFEDESFAVKHNAAFLLSMANRGKDTNGSQFFITTKPTPHLDGHHVVFGQVISGQEVVREIENQKTDAASKPFAEVRILSCGELI 2rmcA 78 :KGYGYKGSIFHRVIKDFMIQGGDFTARDGTGGMSIYGETFPDENFKLKHYGIGWVSMANAGPDTNGSQFFITLTKPTWLDGKHVVFGKVLDGMTVVHSIELQATDGHDRPLTDCTIVNSGKID 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:# T0290 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 Warning: unaligning (T0290)I172 because last residue in template chain is (1awqA)E1165 T0290 1 :RPRCFFDIAINNQPAGRVVFELFSDVCPKTCENFRCLCTGEKGTG 1awqA 1003 :NPTVFFDIAVDGEPLGRVSFELFADKVPKTAENFRALSTGEKGFG T0290 54 :YKSCLFHRVVKDFMVQGGDFSEGNGRGGESIYGGFFEDESFAVKHNAAFLLSMANRGKDTNGSQFFITTKPTPHLDGHHVVFGQVISGQEVVREIENQK 1awqA 1048 :YKGSCFHRIIPGFMCQGGDFTRHNGTGGKSIYGEKFEDENFILKHTGPGILSMANAGPNTNGSQFFICTAKTEWLDGKHVVFGKVKEGMNIVEAMERFG T0290 154 :DAASKPFAEVRILSCGEL 1awqA 1147 :SRNGKTSKKITIADCGQL 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 Warning: unaligning (T0290)I172 because last residue in template chain is (1awqA)E1165 T0290 1 :RPRCFFDIAINNQPAGRVVFELFSDVCPKTCENFRCLCTGEKGTG 1awqA 1003 :NPTVFFDIAVDGEPLGRVSFELFADKVPKTAENFRALSTGEKGFG T0290 54 :YKSCLFHRVVKDFMVQGGDFSEGNGRGGESIYGGFFEDESFAVKHNAAFLLSMANRGKDTNGSQFFITTKPTPHLDGHHVVFGQVISGQEVVREIENQK 1awqA 1048 :YKGSCFHRIIPGFMCQGGDFTRHNGTGGKSIYGEKFEDENFILKHTGPGILSMANAGPNTNGSQFFICTAKTEWLDGKHVVFGKVKEGMNIVEAMERFG T0290 154 :DAASKPFAEVRILSCGEL 1awqA 1147 :SRNGKTSKKITIADCGQL 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 Warning: unaligning (T0290)I172 because last residue in template chain is (1awqA)E1165 T0290 1 :RPRCFFDIAINNQPAGRVVFELFSDVCPKTCENFRCLCTGE 1awqA 1003 :NPTVFFDIAVDGEPLGRVSFELFADKVPKTAENFRALSTGE T0290 50 :KPLHYKSCLFHRVVKDFMVQGGDFSEGNGRGGESIYGGFFEDESFAVKHNAAFLLSMANRGKDTNGSQFFITTKPTPHLDGHHVVFGQVISGQEVVREIENQ 1awqA 1044 :KGFGYKGSCFHRIIPGFMCQGGDFTRHNGTGGKSIYGEKFEDENFILKHTGPGILSMANAGPNTNGSQFFICTAKTEWLDGKHVVFGKVKEGMNIVEAMERF T0290 153 :TDAASKPFAEVRILSCGEL 1awqA 1146 :GSRNGKTSKKITIADCGQL 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/T0290/1qngA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0290/1qngA/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:# T0290 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 Warning: unaligning (T0290)I172 because last residue in template chain is (1lopA)E164 T0290 9 :AINNQPAGRVVFELFSDVCPKTCENFRCLC 1lopA 2 :VTFHTNHGDIVIKTFDDKAPETVKNFLDYC T0290 41 :EKG 1lopA 32 :REG T0290 53 :HYKSCLFHRVVKDFMVQGGDFSEGNGRGGE 1lopA 35 :FYNNTIFHRVINGFMIQGGGFEPGMKQKAT T0290 86 :GGFFEDESFAVKHNAAFLLSMANRG 1lopA 65 :KEPIKNEANNGLKNTRGTLAMARTQ T0290 111 :KDTNGSQFFITTKPTPHLD 1lopA 91 :PHSATAQFFINVVDNDFLN T0290 130 :GHHVVFGQVISGQEVVREIENQKT 1lopA 118 :WGYCVFAEVVDGMDEVDKIKGVAT T0290 155 :A 1lopA 146 :M T0290 156 :ASKPFAEVRILSCGEL 1lopA 148 :QDVPKEDVIIESVTVS 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 Warning: unaligning (T0290)I172 because last residue in template chain is (1lopA)E164 T0290 9 :AINNQPAGRVVFELFSDVCPKTCENFRCLCTGEK 1lopA 2 :VTFHTNHGDIVIKTFDDKAPETVKNFLDYCREGF T0290 54 :YKSCLFHRVVKDFMVQGGDF 1lopA 36 :YNNTIFHRVINGFMIQGGGF T0290 76 :GNGRGGESI 1lopA 56 :EPGMKQKAT T0290 86 :GGFFEDESFAVKHNAAFLLSMANRG 1lopA 65 :KEPIKNEANNGLKNTRGTLAMARTQ T0290 111 :KDTNGSQFFITTKPTPHLDGH 1lopA 91 :PHSATAQFFINVVDNDFLNFS T0290 132 :HVVFGQVISGQEVVREIENQKTDA 1lopA 120 :YCVFAEVVDGMDEVDKIKGVATGR T0290 156 :ASKPFAEVRILSCGEL 1lopA 148 :QDVPKEDVIIESVTVS Number of specific fragments extracted= 7 number of extra gaps= 0 total=30 Number of alignments=8 # 1lopA read from 1lopA/merged-good-all-a2m # found chain 1lopA in template set T0290 9 :AINNQPAGRVVFELFSDVCPKTCENFRCLCTGE 1lopA 2 :VTFHTNHGDIVIKTFDDKAPETVKNFLDYCREG T0290 53 :HYKSCLFHRVVKDFMVQGGDFSEGNGRGGES 1lopA 35 :FYNNTIFHRVINGFMIQGGGFEPGMKQKATK T0290 86 :GGFFEDESFAVKHNAAFLLSMANRGKDTNGSQFFITTKPTPHLD 1lopA 66 :EPIKNEANNGLKNTRGTLAMARTQAPHSATAQFFINVVDNDFLN T0290 130 :GHHVVFGQVISGQEVVREIENQKTDA 1lopA 118 :WGYCVFAEVVDGMDEVDKIKGVATGR T0290 156 :ASKPFAEVRILSCGEL 1lopA 148 :QDVPKEDVIIESVTVS Number of specific fragments extracted= 5 number of extra gaps= 0 total=35 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/T0290/1zmfA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0290/1zmfA/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 # T0290 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 Warning: unaligning (T0290)I172 because last residue in template chain is (1awsA)E1165 T0290 1 :RPRCFFDIAINNQPAGRVVFELFSDVCPKTCENFRCLCTGEKGTG 1awsA 1003 :NPTVFFDIAVDGEPLGRVSFELFADKVPKTAENFRALSTGEKGFG T0290 54 :YKSCLFHRVVKDFMVQGGDFSEGNGRGGESIYGGFFEDESFAVKHNAAFLLSMANRGKDTNGSQFFITTKPTPHLDGHHVVFGQVISGQEVVREIENQK 1awsA 1048 :YKGSCFHRIIPGFMCQGGDFTRHNGTGGKSIYGEKFEDENFILKHTGPGILSMANAGPNTNGSQFFICTAKTEWLDGKHVVFGKVKEGMNIVEAMERFG T0290 154 :DAASKPFAEVRILSCGEL 1awsA 1147 :SRNGKTSKKITIADCGQL Number of specific fragments extracted= 3 number of extra gaps= 0 total=38 Number of alignments=10 # 1awsA read from 1awsA/merged-good-all-a2m # found chain 1awsA in template set Warning: unaligning (T0290)I172 because last residue in template chain is (1awsA)E1165 T0290 1 :RPRCFFDIAINNQPAGRVVFELFSDVCPKTCENFRCLCTGEKGTG 1awsA 1003 :NPTVFFDIAVDGEPLGRVSFELFADKVPKTAENFRALSTGEKGFG T0290 54 :YKSCLFHRVVKDFMVQGGDFSEGNGRGGESIYGGFFEDESFAVKHNAAFLLSMANRGKDTNGSQFFITTKPTPHLDGHHVVFGQVISGQEVVREIENQK 1awsA 1048 :YKGSCFHRIIPGFMCQGGDFTRHNGTGGKSIYGEKFEDENFILKHTGPGILSMANAGPNTNGSQFFICTAKTEWLDGKHVVFGKVKEGMNIVEAMERFG T0290 154 :DAASKPFAEVRILSCGEL 1awsA 1147 :SRNGKTSKKITIADCGQL Number of specific fragments extracted= 3 number of extra gaps= 0 total=41 Number of alignments=11 # 1awsA read from 1awsA/merged-good-all-a2m # found chain 1awsA in template set Warning: unaligning (T0290)I172 because last residue in template chain is (1awsA)E1165 T0290 1 :RPRCFFDIAINNQPAGRVVFELFSDVCPKTCENFRCLCTGE 1awsA 1003 :NPTVFFDIAVDGEPLGRVSFELFADKVPKTAENFRALSTGE T0290 50 :KPLHYKSCLFHRVVKDFMVQGGDFSEGNGRGGESIYGGFFEDESFAVKHNAAFLLSMANRGKDTNGSQFFITTKPTPHLDGHHVVFGQVISGQEVVREIENQ 1awsA 1044 :KGFGYKGSCFHRIIPGFMCQGGDFTRHNGTGGKSIYGEKFEDENFILKHTGPGILSMANAGPNTNGSQFFICTAKTEWLDGKHVVFGKVKEGMNIVEAMERF T0290 153 :TDAASKPFAEVRILSCGEL 1awsA 1146 :GSRNGKTSKKITIADCGQL Number of specific fragments extracted= 3 number of extra gaps= 0 total=44 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/T0290/2eslA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0290/2eslA/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 /projects/compbio/data/pdb/1zcx.pdb.gz 1zcxA:# T0290 read from 1zcxA/merged-good-all-a2m # 1zcxA read from 1zcxA/merged-good-all-a2m # adding 1zcxA to template set # found chain 1zcxA in template set T0290 1 :RPRCFFDIAINNQPAGRVVFELFSDVCPKTCENFRCLCTGEKGT 1zcxA 139 :NPQVYMDIKIGNKPAGRIQMLLRSDVVPMTAENFRCLCTHEKGF T0290 53 :HYKSCLFHRVVKDFMVQGGDFSEGNGRGGESIYGGFFEDESFAVKHNAAFLLSMANRGKDTNGSQFFITTKPTPHLDGHHVVFGQVISGQEVVREIENQK 1zcxA 183 :GFKGSSFHRIIPQFMCQGGDFTNHNGTGGKSIYGKKFDDENFILKHTGPGLLSMANSGPNTNGSQFFLTCDKTDWLDGKHVVFGEVTEGLDVLRQIEAQG T0290 154 :DAASKPFAEVRILSCGEL 1zcxA 283 :SKDGKPKQKVIIADCGEY Number of specific fragments extracted= 3 number of extra gaps= 0 total=47 Number of alignments=13 # 1zcxA read from 1zcxA/merged-good-all-a2m # found chain 1zcxA in template set T0290 1 :RPRCFFDIAINNQPAGRVVFELFSDVCPKTCENFRCLCTGEKGTG 1zcxA 139 :NPQVYMDIKIGNKPAGRIQMLLRSDVVPMTAENFRCLCTHEKGFG T0290 54 :YKSCLFHRVVKDFMVQGGDFSEGNGRGGESIYGGFFEDESFAVKHNAAFLLSMANRGKDTNGSQFFITTKPTPHLDGHHVVFGQVISGQEVVREIENQK 1zcxA 184 :FKGSSFHRIIPQFMCQGGDFTNHNGTGGKSIYGKKFDDENFILKHTGPGLLSMANSGPNTNGSQFFLTCDKTDWLDGKHVVFGEVTEGLDVLRQIEAQG T0290 154 :DAASKPFAEVRILSCGEL 1zcxA 283 :SKDGKPKQKVIIADCGEY Number of specific fragments extracted= 3 number of extra gaps= 0 total=50 Number of alignments=14 # 1zcxA read from 1zcxA/merged-good-all-a2m # found chain 1zcxA in template set T0290 1 :RPRCFFDIAINNQPAGRVVFELFSDVCPKTCENFRCLCTGE 1zcxA 139 :NPQVYMDIKIGNKPAGRIQMLLRSDVVPMTAENFRCLCTHE T0290 50 :KPLHYKSCLFHRVVKDFMVQGGDFSEGNGRGGESIYGGFFEDESFAVKHNAAFLLSMANRGKDTNGSQFFITTKPTPHLDGHHVVFGQVISGQEVVREIENQ 1zcxA 180 :KGFGFKGSSFHRIIPQFMCQGGDFTNHNGTGGKSIYGKKFDDENFILKHTGPGLLSMANSGPNTNGSQFFLTCDKTDWLDGKHVVFGEVTEGLDVLRQIEAQ T0290 153 :TDAASKPFAEVRILSCGE 1zcxA 282 :GSKDGKPKQKVIIADCGE Number of specific fragments extracted= 3 number of extra gaps= 0 total=53 Number of alignments=15 # 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:# T0290 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 Warning: unaligning (T0290)I172 because last residue in template chain is (1yndA)E165 T0290 1 :RPRCFFDIAINNQPAGRVVFELFSDVCPKTCENFRCLCTGEKGT 1yndA 3 :NPTVFFDIAVDGEPLGRVSFELFADKVPKTAENFRALSTGEKGF T0290 53 :HYKSCLFHRVVKDFMVQGGDFSEGNGRGGESIYGGFFEDESFAVKHNAAFLLSMANRGKDTNGSQFFITTKPTPHLDGHHVVFGQVISGQEVVREIENQK 1yndA 47 :GYKGSCFHRIIPGFMCQGGDFTRHNGTGGKSIYGEKFEDENFILKHTGPGILSMANAGPNTNGSQFFICTAKTEWLDGKHVVFGKVKEGMNIVEAMERFG T0290 154 :DAASKPFAEVRILSCGEL 1yndA 147 :SRNGKTSKKITIADCGQL Number of specific fragments extracted= 3 number of extra gaps= 0 total=56 Number of alignments=16 # 1yndA read from 1yndA/merged-good-all-a2m # found chain 1yndA in template set Warning: unaligning (T0290)I172 because last residue in template chain is (1yndA)E165 T0290 1 :RPRCFFDIAINNQPAGRVVFELFSDVCPKTCENFRCLCTGEKGTG 1yndA 3 :NPTVFFDIAVDGEPLGRVSFELFADKVPKTAENFRALSTGEKGFG T0290 54 :YKSCLFHRVVKDFMVQGGDFSEGNGRGGESIYGGFFEDESFAVKHNAAFLLSMANRGKDTNGSQFFITTKPTPHLDGHHVVFGQVISGQEVVREIENQK 1yndA 48 :YKGSCFHRIIPGFMCQGGDFTRHNGTGGKSIYGEKFEDENFILKHTGPGILSMANAGPNTNGSQFFICTAKTEWLDGKHVVFGKVKEGMNIVEAMERFG T0290 154 :DAASKPFAEVRILSCGEL 1yndA 147 :SRNGKTSKKITIADCGQL Number of specific fragments extracted= 3 number of extra gaps= 0 total=59 Number of alignments=17 # 1yndA read from 1yndA/merged-good-all-a2m # found chain 1yndA in template set Warning: unaligning (T0290)I172 because last residue in template chain is (1yndA)E165 T0290 1 :RPRCFFDIAINNQPAGRVVFELFSDVCPKTCENFRCLCTGE 1yndA 3 :NPTVFFDIAVDGEPLGRVSFELFADKVPKTAENFRALSTGE T0290 50 :KPLHYKSCLFHRVVKDFMVQGGDFSEGNGRGGESIYGGFFEDESFAVKHNAAFLLSMANRGKDTNGSQFFITTKPTPHLDGHHVVFGQVISGQEVVREIENQ 1yndA 44 :KGFGYKGSCFHRIIPGFMCQGGDFTRHNGTGGKSIYGEKFEDENFILKHTGPGILSMANAGPNTNGSQFFICTAKTEWLDGKHVVFGKVKEGMNIVEAMERF T0290 153 :TDAASKPFAEVRILSCGEL 1yndA 146 :GSRNGKTSKKITIADCGQL Number of specific fragments extracted= 3 number of extra gaps= 0 total=62 Number of alignments=18 # 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/T0290/2nul/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0290/2nul/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/T0290/2c3bA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0290/2c3bA/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:# T0290 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 T0290 4 :CFFDIAINNQPAGRVVFELFSDVCPKTCENFRCLCTGEKGTGKSTQKPLHYKSCLFHRVVKDFMVQGGDFSEGNGRGGESIYGGFFEDESFAVKHNAAFLLSMANRGKDTNGSQFFITTKPTPHLDGHHVVFGQVISGQEVVREIENQKTD 1ihgA 18 :VFFDVDIGGERVGRIVLELFADIVPKTAENFRALCTGEKGIGPTTGKPLHFKGCPFHRIIKKFMIQGGDFSNQNGTGGESIYGEKFEDENFHYKHDKEGLLSMANAGSNTNGSQFFITTVPTPHLDGKHVVFGQVIKGMGVAKILENVEVK T0290 156 :ASKPFAEVRILSCGELI 1ihgA 169 :GEKPAKLCVIAECGELK Number of specific fragments extracted= 2 number of extra gaps= 0 total=64 Number of alignments=19 # 1ihgA read from 1ihgA/merged-good-all-a2m # found chain 1ihgA in template set T0290 2 :PRCFFDIAINNQPAGRVVFELFSDVCPKTCENFRCLCTGEKGTGKSTQKPLHYKSCLFHRVVKDFMVQGGDFSEGNGRGGESIYGGFFEDESFAVKHNAAFLLSMANRGKDTNGSQFFITTKPTPHLDGHHVVFGQVISGQEVVREIENQKT 1ihgA 16 :PRVFFDVDIGGERVGRIVLELFADIVPKTAENFRALCTGEKGIGPTTGKPLHFKGCPFHRIIKKFMIQGGDFSNQNGTGGESIYGEKFEDENFHYKHDKEGLLSMANAGSNTNGSQFFITTVPTPHLDGKHVVFGQVIKGMGVAKILENVEV T0290 155 :AASKPFAEVRILSCGELI 1ihgA 168 :KGEKPAKLCVIAECGELK Number of specific fragments extracted= 2 number of extra gaps= 0 total=66 Number of alignments=20 # 1ihgA read from 1ihgA/merged-good-all-a2m # found chain 1ihgA in template set T0290 2 :PRCFFDIAINNQPAGRVVFELFSDVCPKTCENFRCLCTGEKGTGKSTQKPLHYKSCLFHRVVKDFMVQGGDFSEGNGRGGESIYGGFFEDESFAVKHNAAFLLSMANRGKDTNGSQFFITTKPTPHLDGHHVVFGQVISGQEVVREIENQKTDAA 1ihgA 16 :PRVFFDVDIGGERVGRIVLELFADIVPKTAENFRALCTGEKGIGPTTGKPLHFKGCPFHRIIKKFMIQGGDFSNQNGTGGESIYGEKFEDENFHYKHDKEGLLSMANAGSNTNGSQFFITTVPTPHLDGKHVVFGQVIKGMGVAKILENVEVKGE T0290 158 :KPFAEVRILSCGELI 1ihgA 171 :KPAKLCVIAECGELK Number of specific fragments extracted= 2 number of extra gaps= 0 total=68 Number of alignments=21 # 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 # T0290 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 Warning: unaligning (T0290)I172 because last residue in template chain is (1a58)V177 T0290 6 :FDIAINNQPAGRVVFELFSDVCPKTCENFRCLCTGEKGTGKSTQKPLHYKSCLFHRVVKDFMVQGGDFSEGNGRGGESIYGGFFEDESFAVKHNAAFLLSMANRGKDTNGSQFFITTKPTPHLDGHHVVFGQVISGQEVVREIENQKTDAASKPFAEVRILSCGEL 1a58 11 :LDVTIDGNLAGRIVMELYNDIAPRTCNNFLMLCTGMAGTGKISGKPLHYKGSTFHRVIKNFMIQGGDFTKGDGTGGESIYGGMFDDEEFVMKHDEPFVVSMANKGPNTNGSQFFITTTPAPHLNNIHVVFGKVVSGQEVVTKIEYLKTNSKNRPLADVVILNCGEL Number of specific fragments extracted= 1 number of extra gaps= 0 total=69 Number of alignments=22 # 1a58 read from 1a58/merged-good-all-a2m # found chain 1a58 in template set Warning: unaligning (T0290)I172 because last residue in template chain is (1a58)V177 T0290 4 :CFFDIAINNQPAGRVVFELFSDVCPKTCENFRCLCTGEKGTGKSTQKPLHYKSCLFHRVVKDFMVQGGDFSEGNGRGGESIYGGFFEDESFAVKHNAAFLLSMANRGKDTNGSQFFITTKPTPHLDGHHVVFGQVISGQEVVREIENQKTDAASKPFAEVRILSCGEL 1a58 9 :VFLDVTIDGNLAGRIVMELYNDIAPRTCNNFLMLCTGMAGTGKISGKPLHYKGSTFHRVIKNFMIQGGDFTKGDGTGGESIYGGMFDDEEFVMKHDEPFVVSMANKGPNTNGSQFFITTTPAPHLNNIHVVFGKVVSGQEVVTKIEYLKTNSKNRPLADVVILNCGEL Number of specific fragments extracted= 1 number of extra gaps= 0 total=70 Number of alignments=23 # 1a58 read from 1a58/merged-good-all-a2m # found chain 1a58 in template set T0290 3 :RCFFDIAINNQPAGRVVFELFSDVCPKTCENFRCLCTGEKGTGKSTQKPLHYKSCLFHRVVKDFMVQGGDFSEGNGRGGESIYGGFFEDESFAVKHNAAFLLSMANRGKDTNGSQFFITTKPTPHLDGHHVVFGQVISGQEVVREIENQKTDAASKPFAEVRILSCGEL 1a58 8 :RVFLDVTIDGNLAGRIVMELYNDIAPRTCNNFLMLCTGMAGTGKISGKPLHYKGSTFHRVIKNFMIQGGDFTKGDGTGGESIYGGMFDDEEFVMKHDEPFVVSMANKGPNTNGSQFFITTTPAPHLNNIHVVFGKVVSGQEVVTKIEYLKTNSKNRPLADVVILNCGEL Number of specific fragments extracted= 1 number of extra gaps= 0 total=71 Number of alignments=24 # 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:# T0290 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 (T0290)L171 because last residue in template chain is (1vdnA)L162 T0290 5 :FFDIAINNQPAGRVVFELFSDVCPKTCENFRCLCTGEKGT 1vdnA 5 :YFDVEADGQPIGRVVFKLYNDIVPKTAENFRALCTGEKGF T0290 53 :HYKSCLFHRVVKDFMVQGGDFSEGNGRGGESIYGGFFEDESFAVKHNAAFLLSMANRGKDTNGSQFFITTKPTPHLDGHHVVFGQVISGQEVVREIENQK 1vdnA 45 :GYAGSPFHRVIPDFMLQGGDFTAGNGTGGKSIYGGKFPDENFKKHHDRPGLLSMANAGPNTNGSQFFITTVPCPWLDGKHVVFGEVVDGYDIVKKVESLG T0290 154 :DAASKPFAEVRILSCGE 1vdnA 145 :SPSGATKARIVVAKSGE Number of specific fragments extracted= 3 number of extra gaps= 0 total=74 Number of alignments=25 # 1vdnA read from 1vdnA/merged-good-all-a2m # found chain 1vdnA in template set Warning: unaligning (T0290)L171 because last residue in template chain is (1vdnA)L162 T0290 3 :RCFFDIAINNQPAGRVVFELFSDVCPKTCENFRCLCTGEKGTG 1vdnA 3 :QVYFDVEADGQPIGRVVFKLYNDIVPKTAENFRALCTGEKGFG T0290 54 :YKSCLFHRVVKDFMVQGGDFSEGNGRGGESIYGGFFEDESFAVKHNAAFLLSMANRGKDTNGSQFFITTKPTPHLDGHHVVFGQVISGQEVVREIENQK 1vdnA 46 :YAGSPFHRVIPDFMLQGGDFTAGNGTGGKSIYGGKFPDENFKKHHDRPGLLSMANAGPNTNGSQFFITTVPCPWLDGKHVVFGEVVDGYDIVKKVESLG T0290 154 :DAASKPFAEVRILSCGE 1vdnA 145 :SPSGATKARIVVAKSGE Number of specific fragments extracted= 3 number of extra gaps= 0 total=77 Number of alignments=26 # 1vdnA read from 1vdnA/merged-good-all-a2m # found chain 1vdnA in template set Warning: unaligning (T0290)P2 because first residue in template chain is (1vdnA)S2 Warning: unaligning (T0290)L171 because last residue in template chain is (1vdnA)L162 T0290 3 :RCFFDIAINNQPAGRVVFELFSDVCPKTCENFRCLCTGE 1vdnA 3 :QVYFDVEADGQPIGRVVFKLYNDIVPKTAENFRALCTGE T0290 50 :KPLHYKSCLFHRVVKDFMVQGGDFSEGNGRGGESIYGGFFEDESFAVKHNAAFLLSMANRGKDTNGSQFFITTKPTPHLDGHHVVFGQVISGQEVVREIENQ 1vdnA 42 :KGFGYAGSPFHRVIPDFMLQGGDFTAGNGTGGKSIYGGKFPDENFKKHHDRPGLLSMANAGPNTNGSQFFITTVPCPWLDGKHVVFGEVVDGYDIVKKVESL T0290 153 :TDAASKPFAEVRILSCGE 1vdnA 144 :GSPSGATKARIVVAKSGE Number of specific fragments extracted= 3 number of extra gaps= 0 total=80 Number of alignments=27 # 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:# T0290 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 (T0290)F6 because first residue in template chain is (2fu0A)P5 T0290 7 :DIAINNQPAGRVVFELFSDVCPKTCENFRCLC 2fu0A 6 :KSAIIYTTMGDIHISLFYKECKKTVQNFSVHS T0290 41 :EKG 2fu0A 38 :ING T0290 53 :HYKSCLFHRVVKDFMVQGGD 2fu0A 41 :YYNNCIFHRVIKHFMVQTGD T0290 74 :SEGNGRGGESIYGGFFEDESFA 2fu0A 61 :PSGDGTGGESIWGNEFEDEFFD T0290 96 :VKHNAAFLLSMANRGKDTNGSQFFITTKPTPHLDGHHVVFGQVISGQEVVREIENQKTDAASKPFAEVRILSCGE 2fu0A 84 :LNHSKPFMVSMANCGPNTNGSQFFITTVPCPWLDFKHTVFGKVTQGSKIVLDIEKVRTDKRDKPLEDIKILNIKI Number of specific fragments extracted= 5 number of extra gaps= 0 total=85 Number of alignments=28 # 2fu0A read from 2fu0A/merged-good-all-a2m # found chain 2fu0A in template set Warning: unaligning (T0290)F6 because first residue in template chain is (2fu0A)P5 T0290 7 :DIAINNQPAGRVVFELFSDVCPKTCENFRCLCTGEK 2fu0A 6 :KSAIIYTTMGDIHISLFYKECKKTVQNFSVHSINGY T0290 54 :YKSCLFHRVVKDFMVQGGDFS 2fu0A 42 :YNNCIFHRVIKHFMVQTGDPS T0290 76 :GNGRGGESIYGGFFEDES 2fu0A 63 :GDGTGGESIWGNEFEDEF T0290 94 :FAVKHNAAFLLSMANRGKDTNGSQFFITTKPTPHLDGHHVVFGQVISGQEVVREIENQKTDAASKPFAEVRILSCGE 2fu0A 82 :DHLNHSKPFMVSMANCGPNTNGSQFFITTVPCPWLDFKHTVFGKVTQGSKIVLDIEKVRTDKRDKPLEDIKILNIKI Number of specific fragments extracted= 4 number of extra gaps= 0 total=89 Number of alignments=29 # 2fu0A read from 2fu0A/merged-good-all-a2m # found chain 2fu0A in template set T0290 8 :IAINNQPAGRVVFELFSDVCPKTCENFRCLCTGE 2fu0A 7 :SAIIYTTMGDIHISLFYKECKKTVQNFSVHSING T0290 53 :HYKSCLFHRVVKDFMVQGGDFSEGNGRGGESIYGGFFEDESFAVKHNAAFLLSMANRGKDTNGSQFFITTKPTPHLDGHHVVFGQVISGQEVVREIENQKTDAASKPFAEVRILSCGE 2fu0A 41 :YYNNCIFHRVIKHFMVQTGDPSGDGTGGESIWGNEFEDEFFDHLNHSKPFMVSMANCGPNTNGSQFFITTVPCPWLDFKHTVFGKVTQGSKIVLDIEKVRTDKRDKPLEDIKILNIKI Number of specific fragments extracted= 2 number of extra gaps= 0 total=91 Number of alignments=30 # 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:# T0290 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 T0290 2 :PRCFFDIAINNQPAGRVVFELFSDVCPKTCENFRCLC 1xwnA 7 :DSWQPPNVYLETSMGIIVLELYWKHAPKTCKNFAELA T0290 41 :EKG 1xwnA 44 :RRG T0290 53 :HYKSCLFHRVVKDFMVQGGD 1xwnA 47 :YYNGTKFHRIIKDFMIQGGD T0290 74 :SEGNGRGGESIYGGFFEDESFA 1xwnA 67 :PTGTGRGGASIYGKQFEDELHP T0290 96 :VKHNAAFLLSMANRGKDTNGSQFFITTKPTPHLDGHHVVFGQVISGQEVVREIENQKTDAASKPFAEVRILSCGEL 1xwnA 90 :LKFTGAGILAMANAGPDTNGSQFFVTLAPTQWLDGKHTIFGRVCQGIGMVNRVGMVETNSQDRPVDDVKIIKAYPS Number of specific fragments extracted= 5 number of extra gaps= 0 total=96 Number of alignments=31 # 1xwnA read from 1xwnA/merged-good-all-a2m # found chain 1xwnA in template set T0290 2 :PRCFFDIAINNQPAGRVVFELFSDVCPKTCENFRCLCTGEK 1xwnA 7 :DSWQPPNVYLETSMGIIVLELYWKHAPKTCKNFAELARRGY T0290 54 :YKSCLFHRVVKDFMVQGGDFS 1xwnA 48 :YNGTKFHRIIKDFMIQGGDPT T0290 76 :GNGRGGESIYGGFFEDES 1xwnA 69 :GTGRGGASIYGKQFEDEL T0290 94 :FAVKHNAAFLLSMANRGKDTNGSQFFITTKPTPHLDGHHVVFGQVISGQEVVREIENQKTDAASKPFAEVRILSCGEL 1xwnA 88 :PDLKFTGAGILAMANAGPDTNGSQFFVTLAPTQWLDGKHTIFGRVCQGIGMVNRVGMVETNSQDRPVDDVKIIKAYPS Number of specific fragments extracted= 4 number of extra gaps= 0 total=100 Number of alignments=32 # 1xwnA read from 1xwnA/merged-good-all-a2m # found chain 1xwnA in template set T0290 8 :IAINNQPAGRVVFELFSDVCPKTCENFRCLCTGE 1xwnA 13 :NVYLETSMGIIVLELYWKHAPKTCKNFAELARRG T0290 53 :HYKSCLFHRVVKDFMVQGGDFSEGNGRGGESIYGGFFEDESFAVKHNAAFLLSMANRGKDTNGSQFFITTKPTPHLDGHHVVFGQVISGQEVVREIENQKTDAASKPFAEVRILSCGE 1xwnA 47 :YYNGTKFHRIIKDFMIQGGDPTGTGRGGASIYGKQFEDELHPDLKFTGAGILAMANAGPDTNGSQFFVTLAPTQWLDGKHTIFGRVCQGIGMVNRVGMVETNSQDRPVDDVKIIKAYP Number of specific fragments extracted= 2 number of extra gaps= 0 total=102 Number of alignments=33 # 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/T0290/1w74A/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0290/1w74A/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 # T0290 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 (T0290)V62 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (1clh)I50 Warning: unaligning (T0290)V63 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (1clh)I50 Warning: unaligning (T0290)Q69 because of BadResidue code BAD_PEPTIDE in next template residue (1clh)G57 Warning: unaligning (T0290)G70 because of BadResidue code BAD_PEPTIDE at template residue (1clh)G57 Warning: unaligning (T0290)I172 because last residue in template chain is (1clh)P166 T0290 7 :DIAINNQPAGRVVFELFSDVCPKTCENFRCLC 1clh 5 :PHVLLTTSAGNIELELDKQKAPVSVQNFVDYV T0290 41 :EKG 1clh 37 :NSG T0290 53 :HYKSCLFHR 1clh 40 :FYNNTTFHR T0290 64 :KDFMV 1clh 51 :PGFMI T0290 71 :GDFSEGNGRGGE 1clh 58 :GGFTEQMQQKKP T0290 86 :GGFFEDESFAVKHNAAFLLSMANRG 1clh 70 :NPPIKNEADNGLRNTRGTIAMARTA T0290 111 :KDTNGSQFFITTKPTPHLD 1clh 96 :KDSATSQFFINVADNAFLD T0290 130 :GHHVVFGQVISGQEVVREIENQKT 1clh 120 :FGYAVFGKVVKGMDVADKISQVPT T0290 154 :DAASKPFAEVRILSCGEL 1clh 148 :PYQNVPSKPVVILSAKVL Number of specific fragments extracted= 9 number of extra gaps= 2 total=111 Number of alignments=34 # 1clh read from 1clh/merged-good-all-a2m # found chain 1clh in template set Warning: unaligning (T0290)V62 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (1clh)I50 Warning: unaligning (T0290)V63 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (1clh)I50 Warning: unaligning (T0290)Q69 because of BadResidue code BAD_PEPTIDE in next template residue (1clh)G57 Warning: unaligning (T0290)G70 because of BadResidue code BAD_PEPTIDE at template residue (1clh)G57 Warning: unaligning (T0290)I172 because last residue in template chain is (1clh)P166 T0290 7 :DIAINNQPAGRVVFELFSDVCPKTCENFRCLCTGEK 1clh 5 :PHVLLTTSAGNIELELDKQKAPVSVQNFVDYVNSGF T0290 54 :YKSCLFHR 1clh 41 :YNNTTFHR T0290 64 :KDFMV 1clh 51 :PGFMI T0290 71 :GDFS 1clh 58 :GGFT T0290 76 :GNGRGGES 1clh 62 :EQMQQKKP T0290 86 :GGFFEDESFAVKHNAAFLLSMANR 1clh 70 :NPPIKNEADNGLRNTRGTIAMART T0290 110 :GKDTNGSQFFITTKPTPHLDGH 1clh 95 :DKDSATSQFFINVADNAFLDHG T0290 132 :HVVFGQVISGQEVVREIENQKT 1clh 122 :YAVFGKVVKGMDVADKISQVPT T0290 154 :D 1clh 148 :P T0290 156 :ASKPFAEVRILSCGEL 1clh 150 :QNVPSKPVVILSAKVL Number of specific fragments extracted= 10 number of extra gaps= 2 total=121 Number of alignments=35 # 1clh read from 1clh/merged-good-all-a2m # found chain 1clh in template set Warning: unaligning (T0290)V62 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (1clh)I50 Warning: unaligning (T0290)V63 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (1clh)I50 Warning: unaligning (T0290)Q69 because of BadResidue code BAD_PEPTIDE in next template residue (1clh)G57 Warning: unaligning (T0290)G70 because of BadResidue code BAD_PEPTIDE at template residue (1clh)G57 Warning: unaligning (T0290)I172 because last residue in template chain is (1clh)P166 T0290 8 :IAINNQPAGRVVFELFSDVCPKTCENFRCLCTGE 1clh 6 :HVLLTTSAGNIELELDKQKAPVSVQNFVDYVNSG T0290 53 :HYKSCLFHR 1clh 40 :FYNNTTFHR T0290 64 :KDFMV 1clh 51 :PGFMI T0290 71 :GDFSEGNGRGGES 1clh 58 :GGFTEQMQQKKPN T0290 86 :GGFFEDESFAVKHNAAFLLSMANRGKDTNGSQFFITTKPTPHLD 1clh 71 :PPIKNEADNGLRNTRGTIAMARTADKDSATSQFFINVADNAFLD T0290 130 :GHHVVFGQVISGQEVVREIENQKTDA 1clh 120 :FGYAVFGKVVKGMDVADKISQVPTHD T0290 156 :ASKPFAEVRILSCGEL 1clh 150 :QNVPSKPVVILSAKVL Number of specific fragments extracted= 7 number of extra gaps= 2 total=128 Number of alignments=36 # 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:# T0290 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 (T0290)L58 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2bitX)F53 Warning: unaligning (T0290)F59 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2bitX)F53 T0290 2 :PRCFFDIAINNQPAGRVVFELFSDVCPKTCENFRCLCTGEKGT 2bitX 4 :PLVYLDVDANGKPLGRVVLELKADVVPKTAENFRALCTGEKGF T0290 53 :HYKSC 2bitX 47 :GYKGS T0290 60 :HRVVKDFMVQGGDFSEGNGRGGESIYGGFFEDESFAVKHNAAFLLSMANRGKDTNGSQFFITTKPTPHLDGHHVVFGQVISGQEVVREIENQK 2bitX 54 :HRVIPSFMCQAGDFTNHNGTGGKSIYGSRFPDENFTLKHVGPGVLSMANAGPNTNGSQFFICTIKTDWLDGKHVVFGHVIEGMDVVKKIESFG T0290 154 :DAASKPFAEVRILSCGEL 2bitX 147 :SKSGRTSKKIVITDCGQL Number of specific fragments extracted= 4 number of extra gaps= 1 total=132 Number of alignments=37 # 2bitX read from 2bitX/merged-good-all-a2m # found chain 2bitX in template set Warning: unaligning (T0290)L58 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2bitX)F53 Warning: unaligning (T0290)F59 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2bitX)F53 T0290 1 :RPRCFFDIAINNQPAGRVVFELFSDVCPKTCENFRCLCTGEKGTG 2bitX 3 :NPLVYLDVDANGKPLGRVVLELKADVVPKTAENFRALCTGEKGFG T0290 54 :YKSC 2bitX 48 :YKGS T0290 60 :HRVVKDFMVQGGDFSEGNGRGGESIYGGFFEDESFAVKHNAAFLLSMANRGKDTNGSQFFITTKPTPHLDGHHVVFGQVISGQEVVREIENQK 2bitX 54 :HRVIPSFMCQAGDFTNHNGTGGKSIYGSRFPDENFTLKHVGPGVLSMANAGPNTNGSQFFICTIKTDWLDGKHVVFGHVIEGMDVVKKIESFG T0290 154 :DAASKPFAEVRILSCGEL 2bitX 147 :SKSGRTSKKIVITDCGQL Number of specific fragments extracted= 4 number of extra gaps= 1 total=136 Number of alignments=38 # 2bitX read from 2bitX/merged-good-all-a2m # found chain 2bitX in template set Warning: unaligning (T0290)L58 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2bitX)F53 Warning: unaligning (T0290)F59 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2bitX)F53 T0290 1 :RPRCFFDIAINNQPAGRVVFELFSDVCPKTCENFRCLCTGE 2bitX 3 :NPLVYLDVDANGKPLGRVVLELKADVVPKTAENFRALCTGE T0290 50 :KPLHYKSC 2bitX 44 :KGFGYKGS T0290 60 :HRVVKDFMVQGGDFSEGNGRGGESIYGGFFEDESFAVKHNAAFLLSMANRGKDTNGSQFFITTKPTPHLDGHHVVFGQVISGQEVVREIENQ 2bitX 54 :HRVIPSFMCQAGDFTNHNGTGGKSIYGSRFPDENFTLKHVGPGVLSMANAGPNTNGSQFFICTIKTDWLDGKHVVFGHVIEGMDVVKKIESF T0290 153 :TDAASKPFAEVRILSCGEL 2bitX 146 :GSKSGRTSKKIVITDCGQL Number of specific fragments extracted= 4 number of extra gaps= 1 total=140 Number of alignments=39 # 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 # T0290 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 (T0290)T153 because of BadResidue code BAD_PEPTIDE in next template residue (1h0pA)L172 Warning: unaligning (T0290)D154 because of BadResidue code BAD_PEPTIDE at template residue (1h0pA)L172 T0290 6 :FDIAINNQPAGRVVFELFSDVCPKTCENFRCLCTGEKGT 1h0pA 32 :FDMEIGGKPIGRIVIGLFGKTVPKTATNFIELAKKPKGE T0290 53 :HYKSCLFHRVVKDFMVQGGDFSEGNGRGGESIYGGFFEDESFAVKHNAAFLLSMANRGKDTNGSQFFITTKPTPHLDGHHVVFGQVISGQEVVREIENQK 1h0pA 71 :GYPGSKFHRVIADFMIQGGDFTRGDGTGGRSIYGEKFADENFKLKHYGAGWLSMANAGADTNGSQFFITTVKTPWLDGRHVVFGKILEGMDVVRKIEQTE T0290 155 :AASKPFAEVRILSCGEL 1h0pA 173 :PGDRPKQDVIIAASGHI Number of specific fragments extracted= 3 number of extra gaps= 1 total=143 Number of alignments=40 # 1h0pA read from 1h0pA/merged-good-all-a2m # found chain 1h0pA in template set Warning: unaligning (T0290)T153 because of BadResidue code BAD_PEPTIDE in next template residue (1h0pA)L172 Warning: unaligning (T0290)D154 because of BadResidue code BAD_PEPTIDE at template residue (1h0pA)L172 T0290 5 :FFDIAINNQPAGRVVFELFSDVCPKTCENFRCLCTGEKGTG 1h0pA 31 :YFDMEIGGKPIGRIVIGLFGKTVPKTATNFIELAKKPKGEG T0290 54 :YKSCLFHRVVKDFMVQGGDFSEGNGRGGESIYGGFFEDESFAVKHNAAFLLSMANRGKDTNGSQFFITTKPTPHLDGHHVVFGQVISGQEVVREIENQK 1h0pA 72 :YPGSKFHRVIADFMIQGGDFTRGDGTGGRSIYGEKFADENFKLKHYGAGWLSMANAGADTNGSQFFITTVKTPWLDGRHVVFGKILEGMDVVRKIEQTE T0290 155 :AASKPFAEVRILSCGEL 1h0pA 173 :PGDRPKQDVIIAASGHI Number of specific fragments extracted= 3 number of extra gaps= 1 total=146 Number of alignments=41 # 1h0pA read from 1h0pA/merged-good-all-a2m # found chain 1h0pA in template set Warning: unaligning (T0290)T153 because of BadResidue code BAD_PEPTIDE in next template residue (1h0pA)L172 Warning: unaligning (T0290)D154 because of BadResidue code BAD_PEPTIDE at template residue (1h0pA)L172 T0290 3 :RCFFDIAINNQPAGRVVFELFSDVCPKTCENFRCLCTGEKGT 1h0pA 29 :RVYFDMEIGGKPIGRIVIGLFGKTVPKTATNFIELAKKPKGE T0290 53 :HYKSCLFHRVVKDFMVQGGDFSEGNGRGGESIYGGFFEDESFAVKHNAAFLLSMANRGKDTNGSQFFITTKPTPHLDGHHVVFGQVISGQEVVREIENQK 1h0pA 71 :GYPGSKFHRVIADFMIQGGDFTRGDGTGGRSIYGEKFADENFKLKHYGAGWLSMANAGADTNGSQFFITTVKTPWLDGRHVVFGKILEGMDVVRKIEQTE T0290 155 :AASKPFAEVRILSCGEL 1h0pA 173 :PGDRPKQDVIIAASGHI Number of specific fragments extracted= 3 number of extra gaps= 1 total=149 Number of alignments=42 # 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:# T0290 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 Warning: unaligning (T0290)I172 because last residue in template chain is (1cwoA)E165 T0290 1 :RPRCFFDIAINNQPAGRVVFELFSDVCPKTCENFRCLCTGEKGT 1cwoA 3 :NPTVFFDIAVDGEPLGRVSFELFADKVPKTAENFRALSTGEKGF T0290 53 :HYKSCLFHRVVKDFMVQGGDFSEGNGRGGESIYGGFFEDESFAVKHNAAFLLSMANRGKDTNGSQFFITTKPTPHLDGHHVVFGQVISGQEVVREIENQK 1cwoA 47 :GYKGSCFHRIIPGFMCQGGDFTRHNGTGGKSIYGEKFEDENFILKHTGPGILSMANAGPNTNGSQFFICTAKTEWLDGKHVVFGKVKEGMNIVEAMERFG T0290 154 :DAASKPFAEVRILSCGEL 1cwoA 147 :SRNGKTSKKITIADCGQL Number of specific fragments extracted= 3 number of extra gaps= 0 total=152 Number of alignments=43 # 1cwoA read from 1cwoA/merged-good-all-a2m # found chain 1cwoA in template set Warning: unaligning (T0290)I172 because last residue in template chain is (1cwoA)E165 T0290 1 :RPRCFFDIAINNQPAGRVVFELFSDVCPKTCENFRCLCTGEKGTG 1cwoA 3 :NPTVFFDIAVDGEPLGRVSFELFADKVPKTAENFRALSTGEKGFG T0290 54 :YKSCLFHRVVKDFMVQGGDFSEGNGRGGESIYGGFFEDESFAVKHNAAFLLSMANRGKDTNGSQFFITTKPTPHLDGHHVVFGQVISGQEVVREIENQK 1cwoA 48 :YKGSCFHRIIPGFMCQGGDFTRHNGTGGKSIYGEKFEDENFILKHTGPGILSMANAGPNTNGSQFFICTAKTEWLDGKHVVFGKVKEGMNIVEAMERFG T0290 154 :DAASKPFAEVRILSCGEL 1cwoA 147 :SRNGKTSKKITIADCGQL Number of specific fragments extracted= 3 number of extra gaps= 0 total=155 Number of alignments=44 # 1cwoA read from 1cwoA/merged-good-all-a2m # found chain 1cwoA in template set Warning: unaligning (T0290)I172 because last residue in template chain is (1cwoA)E165 T0290 1 :RPRCFFDIAINNQPAGRVVFELFSDVCPKTCENFRCLCTGE 1cwoA 3 :NPTVFFDIAVDGEPLGRVSFELFADKVPKTAENFRALSTGE T0290 50 :KPLHYKSCLFHRVVKDFMVQGGDFSEGNGRGGESIYGGFFEDESFAVKHNAAFLLSMANRGKDTNGSQFFITTKPTPHLDGHHVVFGQVISGQEVVREIENQ 1cwoA 44 :KGFGYKGSCFHRIIPGFMCQGGDFTRHNGTGGKSIYGEKFEDENFILKHTGPGILSMANAGPNTNGSQFFICTAKTEWLDGKHVVFGKVKEGMNIVEAMERF T0290 153 :TDAASKPFAEVRILSCGEL 1cwoA 146 :GSRNGKTSKKITIADCGQL Number of specific fragments extracted= 3 number of extra gaps= 0 total=158 Number of alignments=45 # 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:# T0290 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 (T0290)L171 because last residue in template chain is (1qoiA)M177 T0290 1 :RPRCFFDIAINNQPAGRVVFELFSDVCPKTCENFRCLCTGEKG 1qoiA 10 :NPVVFFDVSIGGQEVGRMKIELFADVVPKTAENFRQFCTGEFR T0290 47 :STQKPLHYKSCLFHRVVKDFMVQGGDFSEGNGRGGESIYGGFFEDESFAVKHNAAFLLSMANRGKDTNGSQFFITTKPTPHLDGHHVVFGQVISGQEVVREIENQKTDAASKPFAEVRILSCGE 1qoiA 53 :KDGVPIGYKGSTFHRVIKDFMIQGGDFVNGDGTGVASIYRGPFADENFKLRHSAPGLLSMANSGPSTNGCQFFITCSKCDWLDGKHVVFGKIIDGLLVMRKIENVPTGPNNKPKLPVVISQCGE Number of specific fragments extracted= 2 number of extra gaps= 0 total=160 Number of alignments=46 # 1qoiA read from 1qoiA/merged-good-all-a2m # found chain 1qoiA in template set Warning: unaligning (T0290)L171 because last residue in template chain is (1qoiA)M177 T0290 1 :RPRCFFDIAINNQPAGRVVFELFSDVCPKTCENFRCLCTGEK 1qoiA 10 :NPVVFFDVSIGGQEVGRMKIELFADVVPKTAENFRQFCTGEF T0290 46 :KSTQKPLHYKSCLFHRVVKDFMVQGGDFSEGNGRGGESIYGGFFEDESFAVKHNAAFLLSMANRGKDTNGSQFFITTKPTPHLDGHHVVFGQVISGQEVVREIENQKTDAASKPFAEVRILSCGE 1qoiA 52 :RKDGVPIGYKGSTFHRVIKDFMIQGGDFVNGDGTGVASIYRGPFADENFKLRHSAPGLLSMANSGPSTNGCQFFITCSKCDWLDGKHVVFGKIIDGLLVMRKIENVPTGPNNKPKLPVVISQCGE Number of specific fragments extracted= 2 number of extra gaps= 0 total=162 Number of alignments=47 # 1qoiA read from 1qoiA/merged-good-all-a2m # found chain 1qoiA in template set Warning: unaligning (T0290)L171 because last residue in template chain is (1qoiA)M177 T0290 1 :RPRCFFDIAINNQPAGRVVFELFSDVCPKTCENFRCLCTGE 1qoiA 10 :NPVVFFDVSIGGQEVGRMKIELFADVVPKTAENFRQFCTGE T0290 45 :GKSTQKPLHYKSCLFHRVVKDFMVQGGDFSEGNGRGGESIYGGFFEDESFAVKHNAAFLLSMANRGKDTNGSQFFITTKPTPHLDGHHVVFGQVISGQEVVREIENQKTDAASKPFAEVRILSCGE 1qoiA 51 :FRKDGVPIGYKGSTFHRVIKDFMIQGGDFVNGDGTGVASIYRGPFADENFKLRHSAPGLLSMANSGPSTNGCQFFITCSKCDWLDGKHVVFGKIIDGLLVMRKIENVPTGPNNKPKLPVVISQCGE Number of specific fragments extracted= 2 number of extra gaps= 0 total=164 Number of alignments=48 # 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 # T0290 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 (T0290)L171 because last residue in template chain is (2cfeA)C162 T0290 2 :PRCFFDIAINNQPAGRVVFELFSDVCPKTCENFRCLCTGEKGT 2cfeA 2 :SNVFFDITKNGAPLGTIKFKLFDDVVPKTAANFRALCTGEKGF T0290 53 :HYKSCLFHRVVKDFMVQGGDFSEGNGRGGESIYGGFFEDESFAVKHNAAFLLSMANRGKDTNGSQFFITTKPTPHLDGHHVVFGQVISGQEVVREIENQK 2cfeA 45 :GYAGSHFHRVIPDFMLQGGDFTAGNGTGGKSIYGAKFADENFQLKHNKPGLLSMANAGPNTNGSQFFITTVVTSWLDGKHVVFGEVIDGMNVVKAIEAEG T0290 154 :DAASKPFAEVRILSCGE 2cfeA 145 :SGSGKPRSRIEIAKCGV Number of specific fragments extracted= 3 number of extra gaps= 0 total=167 Number of alignments=49 # 2cfeA read from 2cfeA/merged-good-all-a2m # found chain 2cfeA in template set Warning: unaligning (T0290)L171 because last residue in template chain is (2cfeA)C162 T0290 2 :PRCFFDIAINNQPAGRVVFELFSDVCPKTCENFRCLCTGEKGTG 2cfeA 2 :SNVFFDITKNGAPLGTIKFKLFDDVVPKTAANFRALCTGEKGFG T0290 54 :YKSCLFHRVVKDFMVQGGDFSEGNGRGGESIYGGFFEDESFAVKHNAAFLLSMANRGKDTNGSQFFITTKPTPHLDGHHVVFGQVISGQEVVREIENQK 2cfeA 46 :YAGSHFHRVIPDFMLQGGDFTAGNGTGGKSIYGAKFADENFQLKHNKPGLLSMANAGPNTNGSQFFITTVVTSWLDGKHVVFGEVIDGMNVVKAIEAEG T0290 154 :DAASKPFAEVRILSCGE 2cfeA 145 :SGSGKPRSRIEIAKCGV Number of specific fragments extracted= 3 number of extra gaps= 0 total=170 Number of alignments=50 # 2cfeA read from 2cfeA/merged-good-all-a2m # found chain 2cfeA in template set T0290 2 :PRCFFDIAINNQPAGRVVFELFSDVCPKTCENFRCLCTGE 2cfeA 2 :SNVFFDITKNGAPLGTIKFKLFDDVVPKTAANFRALCTGE T0290 50 :KPLHYKSCLFHRVVKDFMVQGGDFSEGNGRGGESIYGGFFEDESFAVKHNAAFLLSMANRGKDTNGSQFFITTKPTPHLDGHHVVFGQVISGQEVVREIENQ 2cfeA 42 :KGFGYAGSHFHRVIPDFMLQGGDFTAGNGTGGKSIYGAKFADENFQLKHNKPGLLSMANAGPNTNGSQFFITTVVTSWLDGKHVVFGEVIDGMNVVKAIEAE T0290 153 :TDAASKPFAEVRILSCGE 2cfeA 144 :GSGSGKPRSRIEIAKCGV Number of specific fragments extracted= 3 number of extra gaps= 0 total=173 Number of alignments=51 # 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:# T0290 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 (T0290)Y85 because of BadResidue code BAD_PEPTIDE in next template residue (1dywA)G87 Warning: unaligning (T0290)G86 because of BadResidue code BAD_PEPTIDE at template residue (1dywA)G87 Warning: unaligning (T0290)V163 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (1dywA)M164 Warning: unaligning (T0290)R164 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (1dywA)M164 Warning: unaligning (T0290)I172 because last residue in template chain is (1dywA)K172 T0290 4 :CFFDIAINNQPAGRVVFELFSDVCPKTCENFRCLCTGEKGT 1dywA 6 :VFFDITIGGKASGRIVMELYDDVVPKTAGNFRALCTGENGI T0290 46 :KSTQKPLHYKSCLFHRVVKDFMVQGGDFSEGNGRGGESI 1dywA 47 :GKSGKPLHFKGSKFHRIIPNFMIQGGDFTRGNGTGGESI T0290 87 :GFFEDESFAVKHNAAFLLSMANRGKDTNGSQFFITTKPTPHLDGHHVVFGQVISGQEVVREIENQK 1dywA 88 :EKFPDENFKEKHTGPGVLSMANAGPNTNGSQFFLCTVKTEWLDGKHVVFGRVVEGLDVVKAVESNG T0290 154 :DAASKPFAE 1dywA 154 :SQSGKPVKD T0290 165 :ILSCGEL 1dywA 165 :IADCGQL Number of specific fragments extracted= 5 number of extra gaps= 2 total=178 Number of alignments=52 # 1dywA read from 1dywA/merged-good-all-a2m # found chain 1dywA in template set Warning: unaligning (T0290)Y85 because of BadResidue code BAD_PEPTIDE in next template residue (1dywA)G87 Warning: unaligning (T0290)G86 because of BadResidue code BAD_PEPTIDE at template residue (1dywA)G87 Warning: unaligning (T0290)V163 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (1dywA)M164 Warning: unaligning (T0290)R164 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (1dywA)M164 Warning: unaligning (T0290)I172 because last residue in template chain is (1dywA)K172 T0290 1 :RPRCFFDIAINNQPAGRVVFELFSDVCPKTCENFRCLCTGEKGTG 1dywA 3 :RSKVFFDITIGGKASGRIVMELYDDVVPKTAGNFRALCTGENGIG T0290 47 :STQKPLHYKSCLFHRVVKDFMVQGGDFSEGNGRGGESI 1dywA 48 :KSGKPLHFKGSKFHRIIPNFMIQGGDFTRGNGTGGESI T0290 87 :GFFEDESFAVKHNAAFLLSMANRGKDTNGSQFFITTKPTPHLDGHHVVFGQVISGQEVVREIENQK 1dywA 88 :EKFPDENFKEKHTGPGVLSMANAGPNTNGSQFFLCTVKTEWLDGKHVVFGRVVEGLDVVKAVESNG T0290 154 :DAASKPFAE 1dywA 154 :SQSGKPVKD T0290 165 :ILSCGEL 1dywA 165 :IADCGQL Number of specific fragments extracted= 5 number of extra gaps= 2 total=183 Number of alignments=53 # 1dywA read from 1dywA/merged-good-all-a2m # found chain 1dywA in template set Warning: unaligning (T0290)Y85 because of BadResidue code BAD_PEPTIDE in next template residue (1dywA)G87 Warning: unaligning (T0290)G86 because of BadResidue code BAD_PEPTIDE at template residue (1dywA)G87 Warning: unaligning (T0290)V163 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (1dywA)M164 Warning: unaligning (T0290)R164 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (1dywA)M164 Warning: unaligning (T0290)I172 because last residue in template chain is (1dywA)K172 T0290 1 :RPRCFFDIAINNQPAGRVVFELFSDVCPKTCENFRCLCTGE 1dywA 3 :RSKVFFDITIGGKASGRIVMELYDDVVPKTAGNFRALCTGE T0290 43 :GTGKSTQKPLHYKSCLFHRVVKDFMVQGGDFSEGNGRGGESI 1dywA 44 :NGIGKSGKPLHFKGSKFHRIIPNFMIQGGDFTRGNGTGGESI T0290 87 :GFFEDESFAVKHNAAFLLSMANRGKDTNGSQFFITTKPTPHLDGHHVVFGQVISGQEVVREIENQ 1dywA 88 :EKFPDENFKEKHTGPGVLSMANAGPNTNGSQFFLCTVKTEWLDGKHVVFGRVVEGLDVVKAVESN T0290 153 :TDAASKPFAE 1dywA 153 :GSQSGKPVKD T0290 165 :ILSCGEL 1dywA 165 :IADCGQL Number of specific fragments extracted= 5 number of extra gaps= 2 total=188 Number of alignments=54 # 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:# T0290 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 (T0290)M67 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2b71A)I89 Warning: unaligning (T0290)V68 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2b71A)I89 Warning: unaligning (T0290)G86 because of BadResidue code BAD_PEPTIDE in next template residue (2b71A)E107 Warning: unaligning (T0290)G87 because of BadResidue code BAD_PEPTIDE at template residue (2b71A)E107 Warning: unaligning (T0290)F119 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2b71A)I141 Warning: unaligning (T0290)I120 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2b71A)I141 Warning: unaligning (T0290)E170 because last residue in template chain is (2b71A)T191 T0290 7 :DIAINNQPAGRVVFELFSDVCPKTCENFRCLC 2b71A 39 :GYITIYTNLGDFEVELYWYHSPKTCLNFYTLC T0290 41 :EKG 2b71A 71 :EMG T0290 53 :HYKSCLFHRVVKDF 2b71A 74 :FYDNTIFHRVIPNF T0290 69 :QGGD 2b71A 90 :QGGD T0290 74 :SEGNGRGGESIY 2b71A 94 :PTGTGKGGKSIY T0290 88 :FFEDESFA 2b71A 108 :YFEDEINK T0290 96 :VKHNAAFLLSMANRGKDTNGSQF 2b71A 117 :LKHTGAGILSMSNNGPNTNSSQF T0290 121 :TTKPTPHLDGHHVVFGQVISGQEVVREIENQKTDAASKPFAEVRILSCG 2b71A 142 :TLAPLPHLDGKHTIFARVSKNMTCIENIASVQTTATNKPIFDLKILRTS Number of specific fragments extracted= 8 number of extra gaps= 3 total=196 Number of alignments=55 # 2b71A read from 2b71A/merged-good-all-a2m # found chain 2b71A in template set Warning: unaligning (T0290)M67 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2b71A)I89 Warning: unaligning (T0290)V68 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2b71A)I89 Warning: unaligning (T0290)G86 because of BadResidue code BAD_PEPTIDE in next template residue (2b71A)E107 Warning: unaligning (T0290)G87 because of BadResidue code BAD_PEPTIDE at template residue (2b71A)E107 Warning: unaligning (T0290)F119 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2b71A)I141 Warning: unaligning (T0290)I120 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2b71A)I141 Warning: unaligning (T0290)E170 because last residue in template chain is (2b71A)T191 T0290 7 :DIAINNQPAGRVVFELFSDVCPKTCENFRCLCTGEK 2b71A 39 :GYITIYTNLGDFEVELYWYHSPKTCLNFYTLCEMGF T0290 54 :YKSCLFHRVVKDF 2b71A 75 :YDNTIFHRVIPNF T0290 69 :QGGDFS 2b71A 90 :QGGDPT T0290 76 :GNGRGGESIY 2b71A 96 :GTGKGGKSIY T0290 88 :FFEDES 2b71A 108 :YFEDEI T0290 94 :FAVKHNAAFLLSMANRGKDTNGSQF 2b71A 115 :KELKHTGAGILSMSNNGPNTNSSQF T0290 121 :TTKPTPHLDGHHVVFGQVISGQEVVREIENQKTDAASKPFAEVRILSCG 2b71A 142 :TLAPLPHLDGKHTIFARVSKNMTCIENIASVQTTATNKPIFDLKILRTS Number of specific fragments extracted= 7 number of extra gaps= 3 total=203 Number of alignments=56 # 2b71A read from 2b71A/merged-good-all-a2m # found chain 2b71A in template set Warning: unaligning (T0290)M67 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2b71A)I89 Warning: unaligning (T0290)V68 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2b71A)I89 Warning: unaligning (T0290)Y85 because of BadResidue code BAD_PEPTIDE in next template residue (2b71A)E107 Warning: unaligning (T0290)G86 because of BadResidue code BAD_PEPTIDE at template residue (2b71A)E107 Warning: unaligning (T0290)F119 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2b71A)I141 Warning: unaligning (T0290)I120 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2b71A)I141 T0290 8 :IAINNQPAGRVVFELFSDVCPKTCENFRCLCTGE 2b71A 40 :YITIYTNLGDFEVELYWYHSPKTCLNFYTLCEMG T0290 53 :HYKSCLFHRVVKDF 2b71A 74 :FYDNTIFHRVIPNF T0290 69 :QGGDFSEGNGRGGESI 2b71A 90 :QGGDPTGTGKGGKSIY T0290 87 :GFFEDESFAVKHNAAFLLSMANRGKDTNGSQF 2b71A 108 :YFEDEINKELKHTGAGILSMSNNGPNTNSSQF T0290 121 :TTKPTPHLDGHHVVFGQVISGQEVVREIENQKTDAASKPFAEVRILSCG 2b71A 142 :TLAPLPHLDGKHTIFARVSKNMTCIENIASVQTTATNKPIFDLKILRTS Number of specific fragments extracted= 5 number of extra gaps= 3 total=208 Number of alignments=57 # 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 # T0290 read from 1xo7A/merged-good-all-a2m # 1xo7A read from 1xo7A/merged-good-all-a2m # found chain 1xo7A in training set Warning: unaligning (T0290)G40 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1xo7A)E45 Warning: unaligning (T0290)E41 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1xo7A)E45 Warning: unaligning (T0290)K42 because of BadResidue code BAD_PEPTIDE at template residue (1xo7A)N46 Warning: unaligning (T0290)S105 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1xo7A)M101 Warning: unaligning (T0290)M106 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1xo7A)M101 Warning: unaligning (T0290)A107 because of BadResidue code BAD_PEPTIDE at template residue (1xo7A)A102 Warning: unaligning (T0290)L171 because last residue in template chain is (1xo7A)L166 T0290 5 :FFDIAINNQPAGRVVFELFSDVCPKTCENFRCLCT 1xo7A 9 :YFDITIGDEPVGRVVIGLFGNDVPKTVENFKQLAS T0290 43 :GT 1xo7A 47 :GF T0290 53 :HYKSCLFHRVVKDFMVQGGDFSEGNGRGGESIYGGFFEDESFAVKH 1xo7A 49 :GYKGSIFHRVIRNFMIQGGDFTNFDGTGGKSIYGTRFDDENLKIKH T0290 100 :AAFLL 1xo7A 95 :FVGAV T0290 108 :NRGKDTNGSQFFITTKPTPHLDGHHVVFGQVISGQEVVREIENQKTDAASKPFAEVRILSCGE 1xo7A 103 :NAGPNSNGSQFFVTTAPTPWLDGRHVVFGKVVEGMDVVKKVENTKTGLNDKPKKAVKINDCGV Number of specific fragments extracted= 5 number of extra gaps= 2 total=213 Number of alignments=58 # 1xo7A read from 1xo7A/merged-good-all-a2m # found chain 1xo7A in training set Warning: unaligning (T0290)G40 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1xo7A)E45 Warning: unaligning (T0290)E41 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1xo7A)E45 Warning: unaligning (T0290)K42 because of BadResidue code BAD_PEPTIDE at template residue (1xo7A)N46 Warning: unaligning (T0290)S105 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1xo7A)M101 Warning: unaligning (T0290)M106 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1xo7A)M101 Warning: unaligning (T0290)A107 because of BadResidue code BAD_PEPTIDE at template residue (1xo7A)A102 Warning: unaligning (T0290)L171 because last residue in template chain is (1xo7A)L166 T0290 2 :PRCFFDIAINNQPAGRVVFELFSDVCPKTCENFRCLCT 1xo7A 6 :DKVYFDITIGDEPVGRVVIGLFGNDVPKTVENFKQLAS T0290 43 :GTG 1xo7A 47 :GFG T0290 54 :YKSCLFHRVVKDFMVQGGDFSEGNGRGGESIYGGFFEDESFAVKH 1xo7A 50 :YKGSIFHRVIRNFMIQGGDFTNFDGTGGKSIYGTRFDDENLKIKH T0290 100 :AAFLL 1xo7A 95 :FVGAV T0290 108 :NRGKDTNGSQFFITTKPTPHLDGHHVVFGQVISGQEVVREIENQKTDAASKPFAEVRILSCGE 1xo7A 103 :NAGPNSNGSQFFVTTAPTPWLDGRHVVFGKVVEGMDVVKKVENTKTGLNDKPKKAVKINDCGV Number of specific fragments extracted= 5 number of extra gaps= 2 total=218 Number of alignments=59 # 1xo7A read from 1xo7A/merged-good-all-a2m # found chain 1xo7A in training set Warning: unaligning (T0290)G40 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1xo7A)E45 Warning: unaligning (T0290)E41 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1xo7A)E45 Warning: unaligning (T0290)K50 because of BadResidue code BAD_PEPTIDE at template residue (1xo7A)N46 Warning: unaligning (T0290)S105 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1xo7A)M101 Warning: unaligning (T0290)M106 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1xo7A)M101 Warning: unaligning (T0290)A107 because of BadResidue code BAD_PEPTIDE at template residue (1xo7A)A102 Warning: unaligning (T0290)L171 because last residue in template chain is (1xo7A)L166 T0290 2 :PRCFFDIAINNQPAGRVVFELFSDVCPKTCENFRCLCT 1xo7A 6 :DKVYFDITIGDEPVGRVVIGLFGNDVPKTVENFKQLAS T0290 51 :PLHYKSCLFHRVVKDFMVQGGDFSEGNGRGGESIYGGFFEDESFAVKHNAA 1xo7A 47 :GFGYKGSIFHRVIRNFMIQGGDFTNFDGTGGKSIYGTRFDDENLKIKHFVG T0290 103 :LL 1xo7A 98 :AV T0290 108 :NRGKDTNGSQFFITTKPTPHLDGHHVVFGQVISGQEVVREIENQKTDAASKPFAEVRILSCGE 1xo7A 103 :NAGPNSNGSQFFVTTAPTPWLDGRHVVFGKVVEGMDVVKKVENTKTGLNDKPKKAVKINDCGV Number of specific fragments extracted= 4 number of extra gaps= 2 total=222 Number of alignments=60 # 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/T0290/1cynA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0290/1cynA/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/T0290/1qnhA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0290/1qnhA/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:# T0290 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 (T0290)E170 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1j2aA)L165 Warning: unaligning (T0290)L171 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1j2aA)L165 Warning: unaligning (T0290)I172 because last residue in template chain is (1j2aA)P166 T0290 7 :DIAINNQPAGRVVFELFSDVCPKTCENFRCLC 1j2aA 5 :PHVLLTTSAGNIELELDKQKAPVSVQNFVDYV T0290 41 :EKG 1j2aA 37 :NSG T0290 53 :HYKSCLFHRVVKDFMVQGGDFSEGNGRGGE 1j2aA 40 :FYNNTTFHRVIPGFMIQGGGFTEQMQQKKP T0290 86 :GGFFEDESFAVKHNAAFLLSMANRG 1j2aA 70 :NPPIKNEADNGLRNTRGTIAMARTA T0290 111 :KDTNGSQFFITTKPTPHLD 1j2aA 96 :KDSATSQFFINVADNAFLD T0290 130 :GHHVVFGQVISGQEVVREIENQKT 1j2aA 120 :FGYAVFGKVVKGMDVADKISQVPT T0290 154 :DAASKPFAEVRILSCG 1j2aA 148 :PYQNVPSKPVVILSAT Number of specific fragments extracted= 7 number of extra gaps= 1 total=229 Number of alignments=61 # 1j2aA read from 1j2aA/merged-good-all-a2m # found chain 1j2aA in template set Warning: unaligning (T0290)E170 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1j2aA)L165 Warning: unaligning (T0290)L171 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1j2aA)L165 Warning: unaligning (T0290)I172 because last residue in template chain is (1j2aA)P166 T0290 8 :IAINNQPAGRVVFELFSDVCPKTCENFRCLCTGEK 1j2aA 6 :HVLLTTSAGNIELELDKQKAPVSVQNFVDYVNSGF T0290 54 :YKSCLFHRVVKDFMVQGGDFS 1j2aA 41 :YNNTTFHRVIPGFMIQGGGFT T0290 76 :GNGRGGES 1j2aA 62 :EQMQQKKP T0290 86 :GGFFEDESFAVKHNAAFLLSMANR 1j2aA 70 :NPPIKNEADNGLRNTRGTIAMART T0290 110 :GKDTNGSQFFITTKPTPHLDGH 1j2aA 95 :DKDSATSQFFINVADNAFLDHG T0290 132 :HVVFGQVISGQEVVREIENQKT 1j2aA 122 :YAVFGKVVKGMDVADKISQVPT T0290 154 :DAASKPFAEVRILSCG 1j2aA 148 :PYQNVPSKPVVILSAT Number of specific fragments extracted= 7 number of extra gaps= 1 total=236 Number of alignments=62 # 1j2aA read from 1j2aA/merged-good-all-a2m # found chain 1j2aA in template set Warning: unaligning (T0290)E170 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1j2aA)L165 Warning: unaligning (T0290)L171 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1j2aA)L165 T0290 8 :IAINNQPAGRVVFELFSDVCPKTCENFRCLCTGE 1j2aA 6 :HVLLTTSAGNIELELDKQKAPVSVQNFVDYVNSG T0290 53 :HYKSCLFHRVVKDFMVQGGDFSEGNGRGGES 1j2aA 40 :FYNNTTFHRVIPGFMIQGGGFTEQMQQKKPN T0290 86 :GGFFEDESFAVKHNAAFLLSMANRGKDTNGSQFFITTKPTPHLD 1j2aA 71 :PPIKNEADNGLRNTRGTIAMARTADKDSATSQFFINVADNAFLD T0290 130 :GHHVVFGQVISGQEVVREIENQKTDAAS 1j2aA 120 :FGYAVFGKVVKGMDVADKISQVPTHDVG T0290 158 :KPFAEVRILSCG 1j2aA 152 :VPSKPVVILSAT Number of specific fragments extracted= 5 number of extra gaps= 1 total=241 Number of alignments=63 # 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 # T0290 read from 1v9tA/merged-good-all-a2m # 1v9tA read from 1v9tA/merged-good-all-a2m # found chain 1v9tA in training set Warning: unaligning (T0290)L58 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1v9tA)F46 Warning: unaligning (T0290)F59 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1v9tA)F46 Warning: unaligning (T0290)I172 because last residue in template chain is (1v9tA)P166 T0290 7 :DIAINNQPAGRVVFELFSDVCPKTCENFRCLC 1v9tA 5 :PHVLLTTSAGNIELELDKQKAPVSVQNFVDYV T0290 41 :EKG 1v9tA 37 :NSG T0290 53 :HYKSC 1v9tA 40 :FYNNT T0290 60 :HRVVKDFMVQGGDFSEGNGRGGE 1v9tA 47 :HRVIPGFMIQGGGFTEQMQQKKP T0290 86 :GGFFEDESFAVKHNAAFLLSMANRG 1v9tA 70 :NPPIKNEADNGLRNTRGTIAMARTA T0290 111 :KDTNGSQFFITTKPTPHLD 1v9tA 96 :KDSATSQFFINVADNAFLD T0290 130 :GHHVVFGQVISGQEVVREIENQKT 1v9tA 120 :FGYAVFGKVVKGMDVADKISQVPT T0290 154 :DAASKPFAEVRILSCGEL 1v9tA 148 :PYQNVPSKPVVILSATVL Number of specific fragments extracted= 8 number of extra gaps= 1 total=249 Number of alignments=64 # 1v9tA read from 1v9tA/merged-good-all-a2m # found chain 1v9tA in training set Warning: unaligning (T0290)L58 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1v9tA)F46 Warning: unaligning (T0290)F59 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1v9tA)F46 Warning: unaligning (T0290)I172 because last residue in template chain is (1v9tA)P166 T0290 7 :DIAINNQPAGRVVFELFSDVCPKTCENFRCLCTGEK 1v9tA 5 :PHVLLTTSAGNIELELDKQKAPVSVQNFVDYVNSGF T0290 54 :YKSC 1v9tA 41 :YNNT T0290 60 :HRVVKDFMVQGGDFS 1v9tA 47 :HRVIPGFMIQGGGFT T0290 77 :NGRGGESI 1v9tA 62 :EQMQQKKP T0290 86 :GGFFEDESFAVKHNAAFLLSMANR 1v9tA 70 :NPPIKNEADNGLRNTRGTIAMART T0290 110 :GKDTNGSQFFITTKPTPHLDGH 1v9tA 95 :DKDSATSQFFINVADNAFLDHG T0290 132 :HVVFGQVISGQEVVREIENQKT 1v9tA 122 :YAVFGKVVKGMDVADKISQVPT T0290 154 :DA 1v9tA 147 :GP T0290 156 :ASKPFAEVRILSCGEL 1v9tA 150 :QNVPSKPVVILSATVL Number of specific fragments extracted= 9 number of extra gaps= 1 total=258 Number of alignments=65 # 1v9tA read from 1v9tA/merged-good-all-a2m # found chain 1v9tA in training set Warning: unaligning (T0290)L58 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1v9tA)F46 Warning: unaligning (T0290)F59 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1v9tA)F46 T0290 8 :IAINNQPAGRVVFELFSDVCPKTCENFRCLCTGE 1v9tA 6 :HVLLTTSAGNIELELDKQKAPVSVQNFVDYVNSG T0290 53 :HYKSC 1v9tA 40 :FYNNT T0290 60 :HRVVKDFMVQGGDFSEGNGRGGES 1v9tA 47 :HRVIPGFMIQGGGFTEQMQQKKPN T0290 86 :GGFFEDESFAVKHNAAFLLSMANRGKDTNGSQFFITTKPTPHLD 1v9tA 71 :PPIKNEADNGLRNTRGTIAMARTADKDSATSQFFINVADNAFLD T0290 130 :GHHVVFGQVISGQEVVREIENQKTDA 1v9tA 120 :FGYAVFGKVVKGMDVADKISQVPTHD T0290 156 :ASKPFAEVRILSCGEL 1v9tA 150 :QNVPSKPVVILSATVL Number of specific fragments extracted= 6 number of extra gaps= 1 total=264 Number of alignments=66 # 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/T0290/2alfA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0290/2alfA/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 # T0290 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 Warning: unaligning (T0290)I172 because last residue in template chain is (2cpl)E165 T0290 1 :RPRCFFDIAINNQPAGRVVFELFSDVCPKTCENFRCLCTGEKGT 2cpl 3 :NPTVFFDIAVDGEPLGRVSFELFADKVPKTAENFRALSTGEKGF T0290 53 :HYKSCLFHRVVKDFMVQGGDFSEGNGRGGESIYGGFFEDESFAVKHNAAFLLSMANRGKDTNGSQFFITTKPTPHLDGHHVVFGQVISGQEVVREIENQK 2cpl 47 :GYKGSCFHRIIPGFMCQGGDFTRHNGTGGKSIYGEKFEDENFILKHTGPGILSMANAGPNTNGSQFFICTAKTEWLDGKHVVFGKVKEGMNIVEAMERFG T0290 154 :DAASKPFAEVRILSCGEL 2cpl 147 :SRNGKTSKKITIADCGQL Number of specific fragments extracted= 3 number of extra gaps= 0 total=267 Number of alignments=67 # 2cpl read from 2cpl/merged-good-all-a2m # found chain 2cpl in template set Warning: unaligning (T0290)I172 because last residue in template chain is (2cpl)E165 T0290 1 :RPRCFFDIAINNQPAGRVVFELFSDVCPKTCENFRCLCTGEKGTG 2cpl 3 :NPTVFFDIAVDGEPLGRVSFELFADKVPKTAENFRALSTGEKGFG T0290 54 :YKSCLFHRVVKDFMVQGGDFSEGNGRGGESIYGGFFEDESFAVKHNAAFLLSMANRGKDTNGSQFFITTKPTPHLDGHHVVFGQVISGQEVVREIENQK 2cpl 48 :YKGSCFHRIIPGFMCQGGDFTRHNGTGGKSIYGEKFEDENFILKHTGPGILSMANAGPNTNGSQFFICTAKTEWLDGKHVVFGKVKEGMNIVEAMERFG T0290 154 :DAASKPFAEVRILSCGEL 2cpl 147 :SRNGKTSKKITIADCGQL Number of specific fragments extracted= 3 number of extra gaps= 0 total=270 Number of alignments=68 # 2cpl read from 2cpl/merged-good-all-a2m # found chain 2cpl in template set Warning: unaligning (T0290)I172 because last residue in template chain is (2cpl)E165 T0290 1 :RPRCFFDIAINNQPAGRVVFELFSDVCPKTCENFRCLCTGE 2cpl 3 :NPTVFFDIAVDGEPLGRVSFELFADKVPKTAENFRALSTGE T0290 50 :KPLHYKSCLFHRVVKDFMVQGGDFSEGNGRGGESIYGGFFEDESFAVKHNAAFLLSMANRGKDTNGSQFFITTKPTPHLDGHHVVFGQVISGQEVVREIENQ 2cpl 44 :KGFGYKGSCFHRIIPGFMCQGGDFTRHNGTGGKSIYGEKFEDENFILKHTGPGILSMANAGPNTNGSQFFICTAKTEWLDGKHVVFGKVKEGMNIVEAMERF T0290 153 :TDAASKPFAEVRILSCGEL 2cpl 146 :GSRNGKTSKKITIADCGQL Number of specific fragments extracted= 3 number of extra gaps= 0 total=273 Number of alignments=69 # 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/T0290/1z81A/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0290/1z81A/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:# T0290 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 T0290 1 :RPRCFFDIAINNQPAGRVVFELFSDVCPKTCENFRCLC 2a2nA 486 :GPKRVSDSAIIHTSMGDIHTKLFPVECPKTVENFCVHS T0290 41 :EKG 2a2nA 524 :RNG T0290 53 :HYKSCLFHRVVKDFMVQGGD 2a2nA 527 :YYNGHTFHRIIKGFMIQTGD T0290 74 :SEGNGRGGESIYGGFFEDESFA 2a2nA 547 :PTGTGMGGESIWGGEFEDEFHS T0290 96 :VKHNAAFLLSMANRGKDTNGSQFFITTKPTPHLDGHHVVFGQVISGQEVVREIENQKTDAA 2a2nA 570 :LRHDRPYTLSMANAGSNTNGSQFFITVVPTPWLDNKHTVFGRVTKGMEVVQRISNVKVNPK T0290 157 :SKPFAEVRILSCGE 2a2nA 632 :DKPYEDVSIINITV Number of specific fragments extracted= 6 number of extra gaps= 0 total=279 Number of alignments=70 # 2a2nA read from 2a2nA/merged-good-all-a2m # found chain 2a2nA in template set T0290 1 :RPRCFFDIAINNQPAGRVVFELFSDVCPKTCENFRCLCTGEK 2a2nA 486 :GPKRVSDSAIIHTSMGDIHTKLFPVECPKTVENFCVHSRNGY T0290 54 :YKSCLFHRVVKDFMVQGGDFS 2a2nA 528 :YNGHTFHRIIKGFMIQTGDPT T0290 76 :GNGRGGESIYGGFFEDES 2a2nA 549 :GTGMGGESIWGGEFEDEF T0290 94 :FAVKHNAAFLLSMANRGKDTNGSQFFITTKPTPHLDGHHVVFGQVISGQEVVREIENQKTDA 2a2nA 568 :STLRHDRPYTLSMANAGSNTNGSQFFITVVPTPWLDNKHTVFGRVTKGMEVVQRISNVKVNP T0290 156 :ASKPFAEVRILSCGE 2a2nA 631 :TDKPYEDVSIINITV Number of specific fragments extracted= 5 number of extra gaps= 0 total=284 Number of alignments=71 # 2a2nA read from 2a2nA/merged-good-all-a2m # found chain 2a2nA in template set T0290 7 :DIAINNQPAGRVVFELFSDVCPKTCENFRCLCTGE 2a2nA 492 :DSAIIHTSMGDIHTKLFPVECPKTVENFCVHSRNG T0290 53 :HYKSCLFHRVVKDFMVQGGDFSEGNGRGGESIYGGFFEDESFAVKHNAAFLLSMANRGKDTNGSQFFITTKPTPHLDGHHVVFGQVISGQEVVREIENQKTDAA 2a2nA 527 :YYNGHTFHRIIKGFMIQTGDPTGTGMGGESIWGGEFEDEFHSTLRHDRPYTLSMANAGSNTNGSQFFITVVPTPWLDNKHTVFGRVTKGMEVVQRISNVKVNPK T0290 157 :SKPFAEVRILSCGE 2a2nA 632 :DKPYEDVSIINITV Number of specific fragments extracted= 3 number of extra gaps= 0 total=287 Number of alignments=72 # 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/T0290/1m9eA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0290/1m9eA/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:# T0290 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 T0290 8 :IAINNQPAGRVVFELFSDVCPKTCENFRCLC 1zkcA 281 :YVRLHTNKGDLNLELHCDLTPKTCENFIRLC T0290 41 :EKG 1zkcA 312 :KKH T0290 53 :HYKSCLFHRVVKDFMVQGGD 1zkcA 315 :YYDGTIFHRSIRNFVIQGGD T0290 74 :SEGNGRGGESIYGGFFEDESFA 1zkcA 335 :PTGTGTGGESYWGKPFKDEFRP T0290 96 :VKHNAAFLLSMANRGKDTNGSQFFITTKPTPHLDGHHVVFGQVISGQEVVREIENQKTDAA 1zkcA 358 :LSHTGRGILSMANSGPNSNRSQFFITFRSCAYLDKKHTIFGRVVGGFDVLTAMENVESDPK T0290 157 :SKPFAEVRILSCGELIP 1zkcA 420 :DRPKEEIRIDATTVFVD Number of specific fragments extracted= 6 number of extra gaps= 0 total=293 Number of alignments=73 # 1zkcA read from 1zkcA/merged-good-all-a2m # found chain 1zkcA in template set T0290 7 :DIAINNQPAGRVVFELFSDVCPKTCENFRCLCTGEK 1zkcA 280 :GYVRLHTNKGDLNLELHCDLTPKTCENFIRLCKKHY T0290 54 :YKSCLFHRVVKDFMVQGGDFS 1zkcA 316 :YDGTIFHRSIRNFVIQGGDPT T0290 76 :GNGRGGESIYGGFFEDES 1zkcA 337 :GTGTGGESYWGKPFKDEF T0290 94 :FAVKHNAAFLLSMANRGKDTNGSQFFITTKPTPHLDGHHVVFGQVISGQEVVREIENQKTDAA 1zkcA 356 :PNLSHTGRGILSMANSGPNSNRSQFFITFRSCAYLDKKHTIFGRVVGGFDVLTAMENVESDPK T0290 157 :SKPFAEVRILSCGELI 1zkcA 420 :DRPKEEIRIDATTVFV Number of specific fragments extracted= 5 number of extra gaps= 0 total=298 Number of alignments=74 # 1zkcA read from 1zkcA/merged-good-all-a2m # found chain 1zkcA in template set T0290 7 :DIAINNQPAGRVVFELFSDVCPKTCENFRCLCTGE 1zkcA 280 :GYVRLHTNKGDLNLELHCDLTPKTCENFIRLCKKH T0290 53 :HYKSCLFHRVVKDFMVQGGDFSEGNGRGGESIYGGFFEDESFAVKHNAAFLLSMANRGKDTNGSQFFITTKPTPHLDGHHVVFGQVISGQEVVREIENQKTDAA 1zkcA 315 :YYDGTIFHRSIRNFVIQGGDPTGTGTGGESYWGKPFKDEFRPNLSHTGRGILSMANSGPNSNRSQFFITFRSCAYLDKKHTIFGRVVGGFDVLTAMENVESDPK T0290 157 :SKPFAEVRILSCGELI 1zkcA 420 :DRPKEEIRIDATTVFV Number of specific fragments extracted= 3 number of extra gaps= 0 total=301 Number of alignments=75 # command:# PrintAlignmentsContacts allconstraints.under Using radius: 8.0000 NUMB_ALIGNS: 75 Done printing distance constraints # command: