# 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/T0365/ # command:# Making conformation for sequence T0365 numbered 1 through 226 Created new target T0365 from T0365.a2m # command:# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/T0365/ # command:Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0365//projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0365/manyalignments-good-all.under or /projects/compbio/experiments/protein-predict/casp7/T0365//projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0365/manyalignments-good-all.under.gz for input Trying /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0365/manyalignments-good-all.under # reading script from file /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0365/manyalignments-good-all.under # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ofcX/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1ofcX expands to /projects/compbio/data/pdb/1ofc.pdb.gz 1ofcX:Skipped atom 744, because occupancy 0.5 <= existing 0.500 in 1ofcX Skipped atom 746, because occupancy 0.500 <= existing 0.500 in 1ofcX Skipped atom 748, because occupancy 0.500 <= existing 0.500 in 1ofcX Skipped atom 750, because occupancy 0.500 <= existing 0.500 in 1ofcX Skipped atom 752, because occupancy 0.500 <= existing 0.500 in 1ofcX Skipped atom 754, because occupancy 0.500 <= existing 0.500 in 1ofcX Skipped atom 756, because occupancy 0.500 <= existing 0.500 in 1ofcX Skipped atom 934, because occupancy 0.500 <= existing 0.500 in 1ofcX Skipped atom 936, because occupancy 0.500 <= existing 0.500 in 1ofcX Skipped atom 938, because occupancy 0.500 <= existing 0.500 in 1ofcX Skipped atom 940, because occupancy 0.500 <= existing 0.500 in 1ofcX Skipped atom 942, because occupancy 0.500 <= existing 0.500 in 1ofcX Skipped atom 1428, because occupancy 0.500 <= existing 0.500 in 1ofcX Skipped atom 1430, because occupancy 0.500 <= existing 0.500 in 1ofcX Skipped atom 1432, because occupancy 0.500 <= existing 0.500 in 1ofcX Skipped atom 1434, because occupancy 0.500 <= existing 0.500 in 1ofcX Skipped atom 1436, because occupancy 0.500 <= existing 0.500 in 1ofcX Skipped atom 1438, because occupancy 0.500 <= existing 0.500 in 1ofcX Skipped atom 1440, because occupancy 0.500 <= existing 0.500 in 1ofcX Skipped atom 1729, because occupancy 0.500 <= existing 0.500 in 1ofcX Skipped atom 1731, because occupancy 0.500 <= existing 0.500 in 1ofcX Skipped atom 1733, because occupancy 0.500 <= existing 0.500 in 1ofcX Skipped atom 1735, because occupancy 0.500 <= existing 0.500 in 1ofcX Skipped atom 1812, because occupancy 0.500 <= existing 0.500 in 1ofcX Skipped atom 1814, because occupancy 0.500 <= existing 0.500 in 1ofcX Skipped atom 1816, because occupancy 0.500 <= existing 0.500 in 1ofcX Skipped atom 1818, because occupancy 0.500 <= existing 0.500 in 1ofcX Skipped atom 1820, because occupancy 0.500 <= existing 0.500 in 1ofcX Skipped atom 1822, because occupancy 0.500 <= existing 0.500 in 1ofcX Skipped atom 1824, because occupancy 0.500 <= existing 0.500 in 1ofcX Skipped atom 1849, because occupancy 0.500 <= existing 0.500 in 1ofcX Skipped atom 1851, because occupancy 0.500 <= existing 0.500 in 1ofcX Skipped atom 1853, because occupancy 0.500 <= existing 0.500 in 1ofcX Skipped atom 1855, because occupancy 0.500 <= existing 0.500 in 1ofcX Skipped atom 1857, because occupancy 0.500 <= existing 0.500 in 1ofcX Skipped atom 1859, because occupancy 0.500 <= existing 0.500 in 1ofcX # T0365 read from 1ofcX/merged-good-all-a2m # 1ofcX read from 1ofcX/merged-good-all-a2m # adding 1ofcX to template set # found chain 1ofcX in template set Warning: unaligning (T0365)Q115 because of BadResidue code BAD_PEPTIDE in next template residue (1ofcX)N901 Warning: unaligning (T0365)A116 because of BadResidue code BAD_PEPTIDE at template residue (1ofcX)N901 T0365 3 :VNSILGVFAKSPIKPLQEHMDKVYD 1ofcX 820 :IDNIAKDVEGKTPEEVIEYNAVFWE # choosing archetypes in rotamer library T0365 42 :GNWDDA 1ofcX 850 :QDIERI T0365 51 :RKQISLAEKQGDSLKR 1ofcX 856 :MGQIERGEGKIQRRLS T0365 92 :QDKIANKAKD 1ofcX 872 :IKKALDQKMS T0365 109 :R 1ofcX 882 :R T0365 110 :QLLIP 1ofcX 889 :QLRLQ T0365 117 :LQV 1ofcX 902 :YTE T0365 120 :PFIAYLQRCIDA 1ofcX 906 :EDRFLVCMLHKL T0365 132 :VGLAQQVINE 1ofcX 925 :YEELRAAIRA T0365 149 :G 1ofcX 935 :S T0365 150 :FRGR 1ofcX 938 :FRFD T0365 154 :EVDFVAKMINELDII 1ofcX 948 :TALELQRRCNTLITL T0365 169 :EEDTDDLQIQ 1ofcX 964 :ERENIELEEK Number of specific fragments extracted= 13 number of extra gaps= 1 total=13 Number of alignments=1 # 1ofcX read from 1ofcX/merged-good-all-a2m # found chain 1ofcX in template set Warning: unaligning (T0365)L7 because of BadResidue code BAD_PEPTIDE at template residue (1ofcX)A716 Warning: unaligning (T0365)L72 because of BadResidue code BAD_PEPTIDE in next template residue (1ofcX)S794 Warning: unaligning (T0365)P73 because of BadResidue code BAD_PEPTIDE at template residue (1ofcX)S794 Warning: unaligning (T0365)S188 because of BadResidue code BAD_PEPTIDE in next template residue (1ofcX)N901 Warning: unaligning (T0365)E189 because of BadResidue code BAD_PEPTIDE at template residue (1ofcX)N901 T0365 8 :GVFAKS 1ofcX 717 :PRPPKQ T0365 14 :PIKP 1ofcX 730 :FFPP T0365 28 :CASLLVPFFEATI 1ofcX 735 :LFELLDQEIYYFR T0365 45 :DDAVQIRKQIS 1ofcX 766 :KVQREEQRKID T0365 62 :DSLKREIRLT 1ofcX 783 :EEEIQEKENL T0365 74 :SGL 1ofcX 795 :QGF T0365 78 :MPVERTDLLELLTQQDK 1ofcX 798 :TAWTKRDFNQFIKANEK T0365 109 :RQLLIPQAL 1ofcX 815 :YGRDDIDNI T0365 118 :QVPFIAYLQRCIDAV 1ofcX 832 :PEEVIEYNAVFWERC T0365 150 :F 1ofcX 849 :L T0365 153 :REVDFVA 1ofcX 850 :QDIERIM T0365 163 :NELDIIEEDTDDLQI 1ofcX 857 :GQIERGEGKIQRRLS T0365 178 :QLRRQLFAL 1ofcX 874 :KALDQKMSR T0365 190 :LNPVDVMFLYKT 1ofcX 902 :YTEIEDRFLVCM T0365 202 :IEWVGGLAD 1ofcX 925 :YEELRAAIR T0365 211 :LAERVGSRLELMLA 1ofcX 951 :ELQRRCNTLITLIE Number of specific fragments extracted= 16 number of extra gaps= 3 total=29 Number of alignments=2 # 1ofcX read from 1ofcX/merged-good-all-a2m # found chain 1ofcX in template set Warning: unaligning (T0365)G42 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1ofcX)Y752 Warning: unaligning (T0365)L72 because of BadResidue code BAD_PEPTIDE in next template residue (1ofcX)S794 Warning: unaligning (T0365)P73 because of BadResidue code BAD_PEPTIDE at template residue (1ofcX)S794 Warning: unaligning (T0365)S188 because of BadResidue code BAD_PEPTIDE in next template residue (1ofcX)N901 Warning: unaligning (T0365)E189 because of BadResidue code BAD_PEPTIDE at template residue (1ofcX)N901 T0365 2 :PVNSILGVFAKSPIKPLQEHMDK 1ofcX 723 :PIVQDFQFFPPRLFELLDQEIYY T0365 37 :EATIT 1ofcX 746 :FRKTV T0365 45 :DDAVQIRKQIS 1ofcX 766 :KVQREEQRKID T0365 62 :DSLKREIRLT 1ofcX 783 :EEEIQEKENL T0365 74 :SGL 1ofcX 795 :QGF T0365 78 :MPVERTDLLELLTQQDK 1ofcX 798 :TAWTKRDFNQFIKANEK T0365 100 :KDISG 1ofcX 821 :DNIAK T0365 110 :QLL 1ofcX 826 :DVE T0365 113 :IPQA 1ofcX 830 :KTPE T0365 120 :PFIAYLQRCIDA 1ofcX 834 :EVIEYNAVFWER T0365 153 :REVDFVA 1ofcX 850 :QDIERIM T0365 163 :NELDIIEEDTDDL 1ofcX 857 :GQIERGEGKIQRR T0365 176 :QIQLRRQLFALE 1ofcX 872 :IKKALDQKMSRY T0365 190 :LNPVDVMFLYKT 1ofcX 902 :YTEIEDRFLVCM T0365 202 :IEWVGGLADL 1ofcX 925 :YEELRAAIRA T0365 212 :AERVGSRLELMLAR 1ofcX 952 :LQRRCNTLITLIER Number of specific fragments extracted= 16 number of extra gaps= 3 total=45 Number of alignments=3 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ohuA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1ohuA expands to /projects/compbio/data/pdb/1ohu.pdb.gz 1ohuA: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 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 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 # T0365 read from 1ohuA/merged-good-all-a2m # 1ohuA read from 1ohuA/merged-good-all-a2m # adding 1ohuA to template set # found chain 1ohuA in template set Warning: unaligning (T0365)S74 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ohuA)P165 Warning: unaligning (T0365)P79 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ohuA)P165 T0365 10 :FAKSPIK 1ohuA 105 :LPSGVQP T0365 28 :CASLLVPFFEATITGNWDDAVQIRKQI 1ohuA 112 :EHEMMRVMGTIFEKKHAENFETFSEQL T0365 61 :GDSLKREIRLTLP 1ohuA 145 :SFSLYQDVVRTVG T0365 80 :VERTDLLELLT 1ohuA 166 :MSYGRLIGLIS T0365 102 :ISGRVIGRQLL 1ohuA 177 :FGGFVAAKMME T0365 114 :PQALQVPFIAYLQRCI 1ohuA 188 :SVELQGQVRNLFVYTS T0365 133 :GLAQQVIN 1ohuA 204 :LFIKTRIR T0365 142 :LDDL 1ohuA 214 :WKEH T0365 152 :GREVDFVAKMINELDIIEEDTD 1ohuA 218 :NRSWDDFMTLGKQMKEDYERAE Number of specific fragments extracted= 9 number of extra gaps= 0 total=54 Number of alignments=4 # 1ohuA read from 1ohuA/merged-good-all-a2m # found chain 1ohuA in template set Warning: unaligning (T0365)S74 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ohuA)P165 Warning: unaligning (T0365)P79 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ohuA)P165 T0365 8 :GVFAKSPIK 1ohuA 103 :PGLPSGVQP T0365 28 :CASLLVPFFEATITGNWDDAVQIRKQI 1ohuA 112 :EHEMMRVMGTIFEKKHAENFETFSEQL T0365 62 :DSLKREIRLTLP 1ohuA 146 :FSLYQDVVRTVG T0365 80 :VERTDLLELLTQQDKIANKA 1ohuA 166 :MSYGRLIGLISFGGFVAAKM T0365 109 :RQL 1ohuA 186 :MES T0365 115 :QALQVPFIAYLQRCID 1ohuA 189 :VELQGQVRNLFVYTSL T0365 134 :LAQQVIN 1ohuA 205 :FIKTRIR T0365 142 :LDDL 1ohuA 214 :WKEH T0365 152 :GREVDFVAKMINELDIIEEDTD 1ohuA 218 :NRSWDDFMTLGKQMKEDYERAE Number of specific fragments extracted= 9 number of extra gaps= 0 total=63 Number of alignments=5 # 1ohuA read from 1ohuA/merged-good-all-a2m # found chain 1ohuA in template set Warning: unaligning (T0365)S74 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ohuA)P165 Warning: unaligning (T0365)P79 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ohuA)P165 T0365 11 :AKSPIKP 1ohuA 106 :PSGVQPE T0365 29 :ASLLVPFFEATITGNWDDAVQIRKQI 1ohuA 113 :HEMMRVMGTIFEKKHAENFETFSEQL T0365 62 :DSLKREIRLTLP 1ohuA 146 :FSLYQDVVRTVG T0365 80 :VERTDLLELLTQQD 1ohuA 166 :MSYGRLIGLISFGG T0365 101 :DISGRVIGR 1ohuA 180 :FVAAKMMES T0365 113 :IPQALQVPFIAYLQR 1ohuA 190 :ELQGQVRNLFVYTSL T0365 134 :LAQQVIN 1ohuA 205 :FIKTRIR T0365 141 :EL 1ohuA 216 :EH T0365 152 :GREVDFVAKMINELDIIEEDTD 1ohuA 218 :NRSWDDFMTLGKQMKEDYERAE Number of specific fragments extracted= 9 number of extra gaps= 0 total=72 Number of alignments=6 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1z72A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1z72A expands to /projects/compbio/data/pdb/1z72.pdb.gz 1z72A:Skipped atom 11, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 13, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 15, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 17, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 19, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 21, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 23, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 25, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 55, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 57, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 59, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 61, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 63, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 65, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 67, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 69, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 71, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 84, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 86, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 88, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 90, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 92, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 94, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 96, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 98, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 143, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 145, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 147, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 149, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 151, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 153, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 155, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 157, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 159, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 161, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 163, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 165, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 167, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 169, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 171, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 188, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 190, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 192, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 194, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 196, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 198, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 200, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 202, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 204, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 302, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 304, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 306, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 308, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 310, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 312, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 314, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 316, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 318, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 372, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 374, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 376, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 378, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 380, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 382, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 384, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 386, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 388, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 398, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 400, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 402, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 404, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 406, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 408, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 410, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 412, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 414, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 431, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 433, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 435, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 437, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 439, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 441, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 443, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 445, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 447, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 559, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 561, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 563, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 565, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 567, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 569, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 571, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 573, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 575, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 577, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 579, because occupancy 0.500 <= existing 0.500 in 1z72A 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 Skipped atom 661, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 663, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 665, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 667, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 669, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 671, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 673, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 675, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 677, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 746, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 748, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 750, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 752, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 754, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 756, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 758, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 760, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 762, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 951, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 953, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 955, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 957, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 959, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 961, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 963, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 965, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 967, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 1067, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 1069, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 1071, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 1073, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 1075, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 1077, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 1079, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 1081, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 1083, because occupancy 0.500 <= existing 0.500 in 1z72A 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 Skipped atom 1342, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 1344, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 1346, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 1348, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 1350, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 1352, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 1384, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 1386, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 1388, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 1390, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 1392, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 1394, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 1396, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 1398, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 1407, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 1409, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 1411, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 1413, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 1415, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 1417, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 1419, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 1421, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 1423, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 1432, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 1434, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 1436, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 1438, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 1440, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 1442, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 1444, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 1446, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 1448, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 1450, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 1452, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 1454, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 1511, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 1513, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 1515, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 1517, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 1519, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 1521, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 1523, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 1525, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 1723, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 1725, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 1727, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 1729, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 1731, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 1733, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 1735, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 1737, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 1739, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 1741, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 1743, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 1745, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 1747, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 1749, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 1751, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 1753, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 1755, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 1757, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 1759, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 1761, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 1763, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 1765, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 1767, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 1769, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 1771, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 1773, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 1775, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 1777, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 1779, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 1781, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 1783, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 1785, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 1787, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 1789, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 1791, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 1793, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 1802, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 1804, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 1806, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 1808, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 1810, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 1812, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 1814, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 1816, because occupancy 0.500 <= existing 0.500 in 1z72A Skipped atom 1818, because occupancy 0.500 <= existing 0.500 in 1z72A # T0365 read from 1z72A/merged-good-all-a2m # 1z72A read from 1z72A/merged-good-all-a2m # adding 1z72A to template set # found chain 1z72A in template set Warning: unaligning (T0365)E147 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1z72A)R195 Warning: unaligning (T0365)G149 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1z72A)R195 T0365 10 :FAKS 1z72A 38 :FAGT T0365 14 :PIKPLQEH 1z72A 43 :ENKVLKDY T0365 22 :MDKVYDCASLLVPFF 1z72A 58 :FDAFLSMLGACVAHA T0365 42 :GNWDDAVQIRKQISLAEKQGDSLKREIRLTLP 1z72A 73 :DKLESKLRFAKQLGFLEADEDGYFQKAFKELK T0365 80 :VERTDLLELLTQQDKIAN 1z72A 114 :TLHPVTKAFQDLMYSAVA T0365 98 :KAKDISGRVIG 1z72A 135 :YAHLLVMLVIA T0365 110 :QLLIPQ 1z72A 156 :DLALPE T0365 118 :QVPFIAYLQ 1z72A 162 :VYIHSEWIN T0365 131 :AVGLAQQVINELDDLL 1z72A 177 :FAEWVQFLVDELNRVG T0365 153 :REVDFVAKMINELDIIE 1z72A 196 :EDLTELQQRWNQAVALE Number of specific fragments extracted= 10 number of extra gaps= 0 total=82 Number of alignments=7 # 1z72A read from 1z72A/merged-good-all-a2m # found chain 1z72A in template set Warning: unaligning (T0365)E147 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1z72A)R195 Warning: unaligning (T0365)G149 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1z72A)R195 T0365 14 :PIKPLQEHMDKVYDCASLLVPFFEATIT 1z72A 43 :ENKVLKDYLIQDYHFFDAFLSMLGACVA T0365 42 :GNWDDAVQIRKQISLAEKQGDSLKREIRLTLP 1z72A 73 :DKLESKLRFAKQLGFLEADEDGYFQKAFKELK T0365 80 :VERTDLLELLTQQDKIAN 1z72A 114 :TLHPVTKAFQDLMYSAVA T0365 101 :DISGRVIG 1z72A 138 :LLVMLVIA T0365 110 :QLLIPQ 1z72A 156 :DLALPE T0365 119 :VPFIAYLQ 1z72A 163 :YIHSEWIN T0365 131 :AVGLAQQVINELDDLL 1z72A 177 :FAEWVQFLVDELNRVG T0365 153 :REVDFVAKMINELDIIE 1z72A 196 :EDLTELQQRWNQAVALE Number of specific fragments extracted= 8 number of extra gaps= 0 total=90 Number of alignments=8 # 1z72A read from 1z72A/merged-good-all-a2m # found chain 1z72A in template set T0365 35 :FFEATITGNWDDAVQIR 1z72A 13 :TVGELLKSSQKDWQAAI T0365 63 :SLKREIRLT 1z72A 32 :RFVKELFAG T0365 79 :PVERTDLLELLTQQDKIANKAKDISGRVIGRQ 1z72A 41 :TIENKVLKDYLIQDYHFFDAFLSMLGACVAHA T0365 113 :IPQALQVPFIAYLQRCIDAVGLAQ 1z72A 73 :DKLESKLRFAKQLGFLEADEDGYF T0365 137 :QVINE 1z72A 98 :KAFKE T0365 148 :AGFRGREV 1z72A 103 :LKVAENDY T0365 156 :DF 1z72A 117 :PV T0365 169 :EEDTDDLQIQLRRQ 1z72A 119 :TKAFQDLMYSAVAS T0365 188 :S 1z72A 133 :S T0365 191 :NPVDVMFLYKTI 1z72A 134 :DYAHLLVMLVIA T0365 203 :EWVG 1z72A 167 :EWIN T0365 207 :GLADLAERVGSRLELM 1z72A 176 :FFAEWVQFLVDELNRV Number of specific fragments extracted= 12 number of extra gaps= 0 total=102 Number of alignments=9 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ouvA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1ouvA expands to /projects/compbio/data/pdb/1ouv.pdb.gz 1ouvA:# T0365 read from 1ouvA/merged-good-all-a2m # 1ouvA read from 1ouvA/merged-good-all-a2m # adding 1ouvA to template set # found chain 1ouvA in template set T0365 11 :AKSPIKPLQEHMDKVYDCASL 1ouvA 74 :GQGVEKNLKKAASFYAKACDL T0365 32 :LVPFFEATITG 1ouvA 100 :CHLLGNLYYSG T0365 76 :LFMPVERTDLLELLTQQDKI 1ouvA 111 :QGVSQNTNKALQYYSKACDL T0365 100 :KDISGRVIGR 1ouvA 134 :EGCASLGGIY T0365 110 :QLLIPQALQVPFIA 1ouvA 145 :DGKVVTRDFKKAVE T0365 179 :LRRQLFAL 1ouvA 159 :YFTKACDL T0365 188 :S 1ouvA 167 :N T0365 191 :NPVDVMFLYKTI 1ouvA 168 :DGDGCTILGSLY T0365 205 :VGGLADLAERVGS 1ouvA 189 :LKKALASYDKACD Number of specific fragments extracted= 9 number of extra gaps= 0 total=111 Number of alignments=10 # 1ouvA read from 1ouvA/merged-good-all-a2m # found chain 1ouvA in template set T0365 11 :AKSPIKPLQEHMDKVYDCASL 1ouvA 74 :GQGVEKNLKKAASFYAKACDL T0365 32 :LVPFFEATI 1ouvA 100 :CHLLGNLYY T0365 74 :SGLFMPVERTDLLELLTQQDKI 1ouvA 109 :SGQGVSQNTNKALQYYSKACDL T0365 100 :KDISGRVIGR 1ouvA 134 :EGCASLGGIY T0365 110 :QLLIPQALQVPFIAYLQRCI 1ouvA 145 :DGKVVTRDFKKAVEYFTKAC T0365 130 :DAVGLAQQVINE 1ouvA 191 :KALASYDKACDL T0365 142 :LDDL 1ouvA 211 :AGNM T0365 146 :LEAGFRGREVDFVAKMINELDIIE 1ouvA 216 :HHGEGATKNFKEALARYSKACELE Number of specific fragments extracted= 8 number of extra gaps= 0 total=119 Number of alignments=11 # 1ouvA read from 1ouvA/merged-good-all-a2m # found chain 1ouvA in template set Warning: unaligning (T0365)S13 because first residue in template chain is (1ouvA)D28 T0365 14 :PIKPLQEHMD 1ouvA 29 :PKELVGLGAK T0365 38 :ATITGNWDDAVQIRKQISL 1ouvA 39 :SYKEKDFTQAKKYFEKACD T0365 81 :ERTDLLELLTQ 1ouvA 60 :ENSGCFNLGVL T0365 105 :RVIG 1ouvA 71 :YYQG T0365 112 :LIPQALQVPFIAYLQRCID 1ouvA 75 :QGVEKNLKKAASFYAKACD T0365 131 :AV 1ouvA 100 :CH T0365 138 :VINEL 1ouvA 102 :LLGNL T0365 145 :LLEAGFRGREVDFVAKMINELDI 1ouvA 107 :YYSGQGVSQNTNKALQYYSKACD T0365 173 :DDLQIQLRRQLFALE 1ouvA 153 :FKKAVEYFTKACDLN T0365 191 :NPVDVMFLYKTI 1ouvA 168 :DGDGCTILGSLY T0365 205 :VGGLADLAERVGS 1ouvA 189 :LKKALASYDKACD Number of specific fragments extracted= 11 number of extra gaps= 0 total=130 Number of alignments=12 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1vljA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0365 read from 1vljA/merged-good-all-a2m # 1vljA read from 1vljA/merged-good-all-a2m # found chain 1vljA in training set T0365 11 :AKSPIKP 1vljA 206 :DGSSPEI T0365 21 :HMDKVYDCASLLVPFFEATI 1vljA 213 :SNEIAEGTIRTIMKMTERLI T0365 41 :TGNWDDAVQIR 1vljA 235 :PDDYEARANLA T0365 66 :REIRLTLPS 1vljA 246 :WSATIALNG T0365 75 :GLFMPVE 1vljA 259 :GRRGGEW T0365 84 :DLLELLTQQDKIAN 1vljA 266 :ACHRIEHSLSALYD T0365 100 :KDISGRVIGRQLL 1vljA 283 :GAGLAIVFPAWMK T0365 113 :IPQALQVPFIAYLQRCI 1vljA 297 :VYRKNPAQFERFAKKIF T0365 133 :GLAQQVINELDDLLEA 1vljA 321 :ELILKGIEAFKNWLKK T0365 149 :GFRGREVDFVAKM 1vljA 347 :GIPEEDIDKIVDN T0365 176 :QIQLRRQLFALESEL 1vljA 360 :VMLLVEKNLKPKGAS T0365 191 :NP 1vljA 382 :ER T0365 203 :EWVGGLADL 1vljA 384 :EDVREILKL Number of specific fragments extracted= 13 number of extra gaps= 0 total=143 Number of alignments=13 # 1vljA read from 1vljA/merged-good-all-a2m # found chain 1vljA in training set T0365 21 :HMDKVYDCASLLVPFFEATI 1vljA 213 :SNEIAEGTIRTIMKMTERLI T0365 41 :TGNWDDAVQIRK 1vljA 235 :PDDYEARANLAW T0365 67 :EIRL 1vljA 247 :SATI T0365 71 :TLPSGLFMPVE 1vljA 255 :TMAVGRRGGEW T0365 84 :DLLELLTQQDKIAN 1vljA 266 :ACHRIEHSLSALYD T0365 98 :KAKDISGRVIGRQL 1vljA 285 :GLAIVFPAWMKYVY T0365 115 :QALQVPFIAYLQRCI 1vljA 299 :RKNPAQFERFAKKIF T0365 133 :GLAQQVINELDDLLEA 1vljA 321 :ELILKGIEAFKNWLKK T0365 149 :GFRGREVDFVAKMI 1vljA 347 :GIPEEDIDKIVDNV T0365 177 :IQLRRQLFALESE 1vljA 361 :MLLVEKNLKPKGA T0365 190 :LNPVDV 1vljA 381 :LEREDV T0365 199 :YKTIEW 1vljA 387 :REILKL Number of specific fragments extracted= 12 number of extra gaps= 0 total=155 Number of alignments=14 # 1vljA read from 1vljA/merged-good-all-a2m # found chain 1vljA in training set T0365 21 :HMDKVYDCASLLVPFFEATI 1vljA 213 :SNEIAEGTIRTIMKMTERLI T0365 41 :TGNWDDAVQIRKQ 1vljA 235 :PDDYEARANLAWS T0365 68 :IRLTLPSGL 1vljA 248 :ATIALNGTM T0365 84 :DLLELLTQQDKIA 1vljA 266 :ACHRIEHSLSALY T0365 97 :NKAKDISGRVIGRQLLIPQALQVPFIAYLQ 1vljA 284 :AGLAIVFPAWMKYVYRKNPAQFERFAKKIF T0365 127 :RCIDAVGLAQQVINEL 1vljA 322 :LILKGIEAFKNWLKKV T0365 148 :AGFRGREVDFVAKM 1vljA 346 :AGIPEEDIDKIVDN T0365 176 :QIQLRRQLFALES 1vljA 360 :VMLLVEKNLKPKG T0365 189 :ELNPVD 1vljA 380 :VLERED T0365 198 :LYKTIE 1vljA 386 :VREILK Number of specific fragments extracted= 10 number of extra gaps= 0 total=165 Number of alignments=15 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1kgnA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1kgnA expands to /projects/compbio/data/pdb/1kgn.pdb.gz 1kgnA:# T0365 read from 1kgnA/merged-good-all-a2m # 1kgnA read from 1kgnA/merged-good-all-a2m # adding 1kgnA to template set # found chain 1kgnA in template set T0365 9 :VFAKSPIKPLQEHMDKVYDCASLLVPFFEATIT 1kgnA 88 :LLPDAETMHEEAVYTNIAFMESVHAKSYSNIFM T0365 42 :GNWD 1kgnA 123 :ASTP T0365 50 :IRKQISLAEKQG 1kgnA 127 :QINEAFRWSEEN T0365 83 :TDLLELLTQQDKIAN 1kgnA 139 :ENLQRKAKIIMSYYN T0365 99 :A 1kgnA 167 :L T0365 102 :ISGRVIGRQLLIP 1kgnA 173 :YSGFYLPMYLSSR T0365 116 :ALQVPFIAYLQRCIDAVGLAQQVINE 1kgnA 186 :AKLTNTADIIRLIIRDESVHGYYIGY T0365 145 :LLEAGFRGREVDFVAKMINELDIIEEDTDDLQIQLRRQLFALES 1kgnA 212 :KYQQGVKKLSEAEQEEYKAYTFDLMYDLYENEIEYTEDIYDDLG T0365 191 :NPVDVMFLYKTI 1kgnA 256 :WTEDVKRFLRYN T0365 209 :A 1kgnA 268 :A Number of specific fragments extracted= 10 number of extra gaps= 0 total=175 Number of alignments=16 # 1kgnA read from 1kgnA/merged-good-all-a2m # found chain 1kgnA in template set T0365 8 :GVFAKSPIKPLQEHMDKVYDCASLLVPFFEATIT 1kgnA 87 :SLLPDAETMHEEAVYTNIAFMESVHAKSYSNIFM T0365 42 :GNWD 1kgnA 123 :ASTP T0365 50 :IRKQISLAEKQGDSLKREI 1kgnA 127 :QINEAFRWSEENENLQRKA T0365 83 :TDLLELLT 1kgnA 146 :KIIMSYYN T0365 96 :ANKAKDISGRVIGR 1kgnA 158 :LKKKVASTLLESFL T0365 110 :QL 1kgnA 183 :SS T0365 115 :QALQVPFIAYLQRCIDAVGLAQQVI 1kgnA 185 :RAKLTNTADIIRLIIRDESVHGYYI T0365 143 :DDLLEAGFRGREVDFVAKMINELDIIEEDTDDLQIQLRRQLFALES 1kgnA 210 :GYKYQQGVKKLSEAEQEEYKAYTFDLMYDLYENEIEYTEDIYDDLG T0365 191 :NPVDVMFLYKT 1kgnA 256 :WTEDVKRFLRY T0365 208 :LADLA 1kgnA 267 :NANKA Number of specific fragments extracted= 10 number of extra gaps= 0 total=185 Number of alignments=17 # 1kgnA read from 1kgnA/merged-good-all-a2m # found chain 1kgnA in template set T0365 16 :KPLQEHMDKVYDCASLLVPFFEATIT 1kgnA 95 :MHEEAVYTNIAFMESVHAKSYSNIFM T0365 43 :NWD 1kgnA 124 :STP T0365 50 :IRKQISLAEKQ 1kgnA 127 :QINEAFRWSEE T0365 82 :RTDLLELLTQQDKIAN 1kgnA 138 :NENLQRKAKIIMSYYN T0365 98 :KAKDISGRVIG 1kgnA 157 :PLKKKVASTLL T0365 119 :VPFIAYLQRCIDAVGLAQQVINE 1kgnA 189 :TNTADIIRLIIRDESVHGYYIGY T0365 145 :LLEAGFRGREVDFVAKMINELDIIEEDTDDLQIQLRRQLFALES 1kgnA 212 :KYQQGVKKLSEAEQEEYKAYTFDLMYDLYENEIEYTEDIYDDLG T0365 191 :NPVDVMFLYKTI 1kgnA 256 :WTEDVKRFLRYN T0365 209 :ADL 1kgnA 268 :ANK Number of specific fragments extracted= 9 number of extra gaps= 0 total=194 Number of alignments=18 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1sumB/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1sumB expands to /projects/compbio/data/pdb/1sum.pdb.gz 1sumB:# T0365 read from 1sumB/merged-good-all-a2m # 1sumB read from 1sumB/merged-good-all-a2m # adding 1sumB to template set # found chain 1sumB in template set T0365 16 :KPLQEHMDKVYDCASLLVPFFEATI 1sumB 7 :EKVEEFKKGVLKAGWFIEKMFRNSI T0365 41 :TGNWDDAVQIRKQ 1sumB 36 :ERNESLAREVIAD T0365 54 :ISLAEKQGDSLKREIRLTLP 1sumB 52 :VDQMEVEIQEKAMEVLGLFS T0365 79 :PVER 1sumB 72 :PIGK T0365 83 :TDLLELLTQQDKIANKAKDISGRVI 1sumB 81 :TAGIRVAELIENIADKCHDIAKNVL T0365 108 :GRQLLIPQAL 1sumB 107 :LMEEPPLKPL T0365 119 :VPFIAYLQRCIDAVGLAQQVIN 1sumB 117 :EDIPAMANQTSEMLKFALRMFA T0365 152 :GREVDFVAK 1sumB 139 :DVNVEKSFE T0365 165 :LDIIEEDTDDLQIQLRRQLFAL 1sumB 148 :VCRMDSKVDDLYEKVREELLLY T0365 187 :ESELNPVDVMFLYKTIEWVGGLADLAERVGSRLELMLAR 1sumB 172 :ESPKYVKRALLLLEIAGNIEIIADYATNIVEVSVYMVQG Number of specific fragments extracted= 10 number of extra gaps= 0 total=204 Number of alignments=19 # 1sumB read from 1sumB/merged-good-all-a2m # found chain 1sumB in template set T0365 15 :IKPLQEHMDKVYDCASLLVPFFEATI 1sumB 6 :NEKVEEFKKGVLKAGWFIEKMFRNSI T0365 41 :TGNWDDAVQIRK 1sumB 36 :ERNESLAREVIA T0365 53 :QISLAEKQGDSLKREIRLTLP 1sumB 51 :VVDQMEVEIQEKAMEVLGLFS T0365 79 :PVERT 1sumB 72 :PIGKP T0365 86 :LELLTQQDKIANKAKDISGRVI 1sumB 84 :IRVAELIENIADKCHDIAKNVL T0365 108 :GRQLLIPQALQ 1sumB 107 :LMEEPPLKPLE T0365 120 :PFIAYLQRCIDAVGLAQQVI 1sumB 118 :DIPAMANQTSEMLKFALRMF T0365 151 :RGREVDFVAKMINELDIIEEDTDDLQIQLRRQLFALES 1sumB 138 :ADVNVEKSFEVCRMDSKVDDLYEKVREELLLYMMESPK T0365 191 :NPVDVMFLYKTIEWVGGLADLAERVGSRLELMLAR 1sumB 176 :YVKRALLLLEIAGNIEIIADYATNIVEVSVYMVQG Number of specific fragments extracted= 9 number of extra gaps= 0 total=213 Number of alignments=20 # 1sumB read from 1sumB/merged-good-all-a2m # found chain 1sumB in template set Warning: unaligning (T0365)P14 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1sumB)L5 T0365 15 :IKPLQEHMDKVYDCASLLVPFFEATI 1sumB 6 :NEKVEEFKKGVLKAGWFIEKMFRNSI T0365 41 :TGNWDDAVQIRKQ 1sumB 36 :ERNESLAREVIAD T0365 54 :ISLAEKQGDSLKREIRLTLP 1sumB 52 :VDQMEVEIQEKAMEVLGLFS T0365 83 :TDLLELLTQQDKIANKAKDISGRVI 1sumB 81 :TAGIRVAELIENIADKCHDIAKNVL T0365 108 :GRQLLIPQAL 1sumB 107 :LMEEPPLKPL T0365 120 :PFIAYLQRCIDAVGLAQQVIN 1sumB 118 :DIPAMANQTSEMLKFALRMFA T0365 152 :GREVDFVAKMI 1sumB 139 :DVNVEKSFEVC T0365 167 :IIEEDTDDLQIQLRRQLFALESE 1sumB 150 :RMDSKVDDLYEKVREELLLYMME T0365 191 :N 1sumB 173 :S T0365 192 :PVDVMFLYKTIEWVGGLADLAERVGSRLELML 1sumB 177 :VKRALLLLEIAGNIEIIADYATNIVEVSVYMV Number of specific fragments extracted= 10 number of extra gaps= 1 total=223 Number of alignments=21 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1vctA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1vctA expands to /projects/compbio/data/pdb/1vct.pdb.gz 1vctA:Skipped atom 136, because occupancy 0.500 <= existing 0.500 in 1vctA Skipped atom 138, because occupancy 0.500 <= existing 0.500 in 1vctA Skipped atom 555, because occupancy 0.500 <= existing 0.500 in 1vctA Skipped atom 557, because occupancy 0.500 <= existing 0.500 in 1vctA Skipped atom 559, because occupancy 0.500 <= existing 0.500 in 1vctA Skipped atom 858, because occupancy 0.500 <= existing 0.500 in 1vctA Skipped atom 860, because occupancy 0.500 <= existing 0.500 in 1vctA Skipped atom 862, because occupancy 0.500 <= existing 0.500 in 1vctA Skipped atom 864, because occupancy 0.500 <= existing 0.500 in 1vctA Skipped atom 866, because occupancy 0.500 <= existing 0.500 in 1vctA Skipped atom 868, because occupancy 0.500 <= existing 0.500 in 1vctA Skipped atom 870, because occupancy 0.500 <= existing 0.500 in 1vctA Skipped atom 872, because occupancy 0.500 <= existing 0.500 in 1vctA Skipped atom 874, because occupancy 0.500 <= existing 0.500 in 1vctA Skipped atom 876, because occupancy 0.500 <= existing 0.500 in 1vctA Skipped atom 878, because occupancy 0.500 <= existing 0.500 in 1vctA Skipped atom 880, because occupancy 0.500 <= existing 0.500 in 1vctA Skipped atom 882, because occupancy 0.500 <= existing 0.500 in 1vctA Skipped atom 884, because occupancy 0.500 <= existing 0.500 in 1vctA Skipped atom 886, because occupancy 0.500 <= existing 0.500 in 1vctA Skipped atom 888, because occupancy 0.500 <= existing 0.500 in 1vctA Skipped atom 890, because occupancy 0.500 <= existing 0.500 in 1vctA Skipped atom 892, because occupancy 0.500 <= existing 0.500 in 1vctA Skipped atom 894, because occupancy 0.500 <= existing 0.500 in 1vctA Skipped atom 896, because occupancy 0.500 <= existing 0.500 in 1vctA Skipped atom 898, because occupancy 0.500 <= existing 0.500 in 1vctA Skipped atom 900, because occupancy 0.500 <= existing 0.500 in 1vctA Skipped atom 1027, because occupancy 0.500 <= existing 0.500 in 1vctA Skipped atom 1034, because occupancy 0.500 <= existing 0.500 in 1vctA Skipped atom 1036, because occupancy 0.500 <= existing 0.500 in 1vctA Skipped atom 1038, because occupancy 0.500 <= existing 0.500 in 1vctA Skipped atom 1040, because occupancy 0.500 <= existing 0.500 in 1vctA Skipped atom 1042, because occupancy 0.500 <= existing 0.500 in 1vctA Skipped atom 1044, because occupancy 0.500 <= existing 0.500 in 1vctA Skipped atom 1046, because occupancy 0.500 <= existing 0.500 in 1vctA Skipped atom 1048, because occupancy 0.500 <= existing 0.500 in 1vctA Skipped atom 1050, because occupancy 0.500 <= existing 0.500 in 1vctA Skipped atom 1052, because occupancy 0.500 <= existing 0.500 in 1vctA Skipped atom 1054, because occupancy 0.500 <= existing 0.500 in 1vctA Skipped atom 1056, because occupancy 0.500 <= existing 0.500 in 1vctA Skipped atom 1058, because occupancy 0.500 <= existing 0.500 in 1vctA Skipped atom 1060, because occupancy 0.500 <= existing 0.500 in 1vctA Skipped atom 1062, because occupancy 0.500 <= existing 0.500 in 1vctA Skipped atom 1064, because occupancy 0.500 <= existing 0.500 in 1vctA Skipped atom 1066, because occupancy 0.500 <= existing 0.500 in 1vctA Skipped atom 1068, because occupancy 0.500 <= existing 0.500 in 1vctA Skipped atom 1070, because occupancy 0.500 <= existing 0.500 in 1vctA Skipped atom 1072, because occupancy 0.500 <= existing 0.500 in 1vctA Skipped atom 1074, because occupancy 0.500 <= existing 0.500 in 1vctA Skipped atom 1076, because occupancy 0.500 <= existing 0.500 in 1vctA Skipped atom 1078, because occupancy 0.500 <= existing 0.500 in 1vctA Skipped atom 1080, because occupancy 0.500 <= existing 0.500 in 1vctA Skipped atom 1082, because occupancy 0.500 <= existing 0.500 in 1vctA Skipped atom 1084, because occupancy 0.500 <= existing 0.500 in 1vctA Skipped atom 1086, because occupancy 0.500 <= existing 0.500 in 1vctA Skipped atom 1088, because occupancy 0.500 <= existing 0.500 in 1vctA Skipped atom 1090, because occupancy 0.500 <= existing 0.500 in 1vctA Skipped atom 1092, because occupancy 0.500 <= existing 0.500 in 1vctA Skipped atom 1094, because occupancy 0.500 <= existing 0.500 in 1vctA Skipped atom 1096, because occupancy 0.500 <= existing 0.500 in 1vctA Skipped atom 1098, because occupancy 0.500 <= existing 0.500 in 1vctA Skipped atom 1100, because occupancy 0.500 <= existing 0.500 in 1vctA Skipped atom 1102, because occupancy 0.500 <= existing 0.500 in 1vctA Skipped atom 1104, because occupancy 0.500 <= existing 0.500 in 1vctA Skipped atom 1106, because occupancy 0.500 <= existing 0.500 in 1vctA Skipped atom 1108, because occupancy 0.500 <= existing 0.500 in 1vctA Skipped atom 1110, because occupancy 0.500 <= existing 0.500 in 1vctA Skipped atom 1112, because occupancy 0.500 <= existing 0.500 in 1vctA Skipped atom 1114, because occupancy 0.500 <= existing 0.500 in 1vctA Skipped atom 1116, because occupancy 0.500 <= existing 0.500 in 1vctA Skipped atom 1118, because occupancy 0.500 <= existing 0.500 in 1vctA Skipped atom 1120, because occupancy 0.500 <= existing 0.500 in 1vctA Skipped atom 1122, because occupancy 0.500 <= existing 0.500 in 1vctA Skipped atom 1124, because occupancy 0.500 <= existing 0.500 in 1vctA Skipped atom 1126, because occupancy 0.500 <= existing 0.500 in 1vctA Skipped atom 1128, because occupancy 0.500 <= existing 0.500 in 1vctA Skipped atom 1130, because occupancy 0.500 <= existing 0.500 in 1vctA Skipped atom 1132, because occupancy 0.500 <= existing 0.500 in 1vctA Skipped atom 1134, because occupancy 0.500 <= existing 0.500 in 1vctA Skipped atom 1136, because occupancy 0.500 <= existing 0.500 in 1vctA Skipped atom 1138, because occupancy 0.500 <= existing 0.500 in 1vctA Skipped atom 1140, because occupancy 0.500 <= existing 0.500 in 1vctA Skipped atom 1142, because occupancy 0.500 <= existing 0.500 in 1vctA Skipped atom 1144, because occupancy 0.500 <= existing 0.500 in 1vctA Skipped atom 1146, because occupancy 0.500 <= existing 0.500 in 1vctA Skipped atom 1148, because occupancy 0.500 <= existing 0.500 in 1vctA Skipped atom 1150, because occupancy 0.500 <= existing 0.500 in 1vctA Skipped atom 1152, because occupancy 0.500 <= existing 0.500 in 1vctA Skipped atom 1154, because occupancy 0.500 <= existing 0.500 in 1vctA Skipped atom 1156, because occupancy 0.500 <= existing 0.500 in 1vctA Skipped atom 1158, because occupancy 0.500 <= existing 0.500 in 1vctA Skipped atom 1160, because occupancy 0.500 <= existing 0.500 in 1vctA Skipped atom 1162, because occupancy 0.500 <= existing 0.500 in 1vctA Skipped atom 1164, because occupancy 0.500 <= existing 0.500 in 1vctA Skipped atom 1166, because occupancy 0.500 <= existing 0.500 in 1vctA Skipped atom 1168, because occupancy 0.500 <= existing 0.500 in 1vctA Skipped atom 1170, because occupancy 0.500 <= existing 0.500 in 1vctA Skipped atom 1172, because occupancy 0.500 <= existing 0.500 in 1vctA Skipped atom 1174, because occupancy 0.500 <= existing 0.500 in 1vctA Skipped atom 1176, because occupancy 0.500 <= existing 0.500 in 1vctA Skipped atom 1178, because occupancy 0.500 <= existing 0.500 in 1vctA Skipped atom 1180, because occupancy 0.500 <= existing 0.500 in 1vctA Skipped atom 1182, because occupancy 0.500 <= existing 0.500 in 1vctA Skipped atom 1184, because occupancy 0.500 <= existing 0.500 in 1vctA Skipped atom 1186, because occupancy 0.500 <= existing 0.500 in 1vctA Skipped atom 1188, because occupancy 0.500 <= existing 0.500 in 1vctA Skipped atom 1190, because occupancy 0.500 <= existing 0.500 in 1vctA Skipped atom 1192, because occupancy 0.500 <= existing 0.500 in 1vctA Skipped atom 1194, because occupancy 0.500 <= existing 0.500 in 1vctA Skipped atom 1196, because occupancy 0.500 <= existing 0.500 in 1vctA Skipped atom 1198, because occupancy 0.500 <= existing 0.500 in 1vctA Skipped atom 1200, because occupancy 0.500 <= existing 0.500 in 1vctA Skipped atom 1202, because occupancy 0.500 <= existing 0.500 in 1vctA Skipped atom 1204, because occupancy 0.500 <= existing 0.500 in 1vctA Skipped atom 1206, because occupancy 0.500 <= existing 0.500 in 1vctA Skipped atom 1208, because occupancy 0.500 <= existing 0.500 in 1vctA Skipped atom 1210, because occupancy 0.500 <= existing 0.500 in 1vctA Skipped atom 1212, because occupancy 0.500 <= existing 0.500 in 1vctA Skipped atom 1346, because occupancy 0.500 <= existing 0.500 in 1vctA Skipped atom 1348, because occupancy 0.500 <= existing 0.500 in 1vctA Skipped atom 1350, because occupancy 0.500 <= existing 0.500 in 1vctA Skipped atom 1352, because occupancy 0.500 <= existing 0.500 in 1vctA Skipped atom 1354, because occupancy 0.500 <= existing 0.500 in 1vctA Skipped atom 1356, because occupancy 0.500 <= existing 0.500 in 1vctA Skipped atom 1358, because occupancy 0.500 <= existing 0.500 in 1vctA Skipped atom 1360, because occupancy 0.500 <= existing 0.500 in 1vctA Skipped atom 1362, because occupancy 0.500 <= existing 0.500 in 1vctA Skipped atom 1364, because occupancy 0.500 <= existing 0.500 in 1vctA Skipped atom 1366, because occupancy 0.500 <= existing 0.500 in 1vctA Skipped atom 1368, because occupancy 0.500 <= existing 0.500 in 1vctA Skipped atom 1370, because occupancy 0.500 <= existing 0.500 in 1vctA Skipped atom 1372, because occupancy 0.500 <= existing 0.500 in 1vctA Skipped atom 1374, because occupancy 0.500 <= existing 0.500 in 1vctA Skipped atom 1376, because occupancy 0.500 <= existing 0.500 in 1vctA Skipped atom 1378, because occupancy 0.500 <= existing 0.500 in 1vctA Skipped atom 1380, because occupancy 0.500 <= existing 0.500 in 1vctA Skipped atom 1382, because occupancy 0.500 <= existing 0.500 in 1vctA Skipped atom 1384, because occupancy 0.500 <= existing 0.500 in 1vctA Skipped atom 1386, because occupancy 0.500 <= existing 0.500 in 1vctA Skipped atom 1388, because occupancy 0.500 <= existing 0.500 in 1vctA Skipped atom 1390, because occupancy 0.500 <= existing 0.500 in 1vctA Skipped atom 1392, because occupancy 0.500 <= existing 0.500 in 1vctA Skipped atom 1394, because occupancy 0.500 <= existing 0.500 in 1vctA # T0365 read from 1vctA/merged-good-all-a2m # 1vctA read from 1vctA/merged-good-all-a2m # adding 1vctA to template set # found chain 1vctA in template set T0365 13 :SPIK 1vctA 10 :EPKS T0365 18 :LQEHMDKVYDCASLLVPFFEATI 1vctA 14 :VKEIFIEMKDTVELMVDLAYASL T0365 41 :TGN 1vctA 38 :FGD T0365 48 :VQIRKQISLAEKQGDSLKREIRLT 1vctA 41 :KEIAEEVLELEERIDLLNYQLMMH T0365 83 :T 1vctA 73 :K T0365 84 :DLLELLTQQDKIANKAKDISGRVIG 1vctA 80 :TILQIANAIEDISNAAGDLAKMVLE T0365 110 :QLLIPQALQVPFIA 1vctA 105 :GVELHPVIKETILE Number of specific fragments extracted= 7 number of extra gaps= 0 total=230 Number of alignments=22 # 1vctA read from 1vctA/merged-good-all-a2m # found chain 1vctA in template set T0365 114 :PQALQVPFIAYLQRCIDAVGLAQ 1vctA 14 :VKEIFIEMKDTVELMVDLAYASL T0365 142 :LDD 1vctA 37 :LFG T0365 159 :AKMINELDIIEEDTDDLQIQLRRQLFALES 1vctA 41 :KEIAEEVLELEERIDLLNYQLMMHSVLAAR T0365 191 :NPVDVMFLYKTIEWVGGLADLAERVGSRLELMLAR 1vctA 71 :NVKEAEQVITILQIANAIEDISNAAGDLAKMVLEG Number of specific fragments extracted= 4 number of extra gaps= 0 total=234 Number of alignments=23 # 1vctA read from 1vctA/merged-good-all-a2m # found chain 1vctA in template set T0365 87 :ELLTQQDKIANKAKDISGRVIGRQL 1vctA 16 :EIFIEMKDTVELMVDLAYASLLFGD T0365 115 :QALQVPFIAYLQRCIDAVGLAQQVINE 1vctA 41 :KEIAEEVLELEERIDLLNYQLMMHSVL T0365 148 :AGFRGREVDFVAKMINELDIIEEDTDDLQ 1vctA 68 :AARNVKEAEQVITILQIANAIEDISNAAG T0365 178 :QLRRQLFALES 1vctA 97 :DLAKMVLEGVE T0365 190 :LNPVDVMFLYK 1vctA 108 :LHPVIKETILE Number of specific fragments extracted= 5 number of extra gaps= 0 total=239 Number of alignments=24 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1urvA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1urvA expands to /projects/compbio/data/pdb/1urv.pdb.gz 1urvA:# T0365 read from 1urvA/merged-good-all-a2m # 1urvA read from 1urvA/merged-good-all-a2m # adding 1urvA to template set # found chain 1urvA in template set Warning: unaligning (T0365)S103 because of BadResidue code BAD_PEPTIDE in next template residue (1urvA)L115 Warning: unaligning (T0365)G104 because of BadResidue code BAD_PEPTIDE at template residue (1urvA)L115 T0365 21 :HMDKVYDCASLLV 1urvA 23 :ERKAVQAMWARLY T0365 34 :PFFEATI 1urvA 44 :AILVRFF T0365 41 :TGNWDDAVQ 1urvA 66 :MEDPLEMER T0365 53 :QISLAEKQGDSLKREIRLTLP 1urvA 77 :QLRKHASRVMGALNTVVENLH T0365 81 :ERTDLLELLTQQDKI 1urvA 98 :DPDKVSSVLALVGKA T0365 102 :I 1urvA 113 :H T0365 110 :QLLI 1urvA 116 :KHKV T0365 116 :AL 1urvA 120 :EP T0365 119 :VPFIAYLQRCID 1urvA 122 :VYFKILSGVILE T0365 145 :LLEAGFRGREVDFVAKMINELDII 1urvA 134 :VVAEEFASDFPPETQRAWAKLRGL T0365 172 :TDDLQIQLRRQ 1urvA 158 :IYSHVTAAYKE Number of specific fragments extracted= 11 number of extra gaps= 1 total=250 Number of alignments=25 # 1urvA read from 1urvA/merged-good-all-a2m # found chain 1urvA in template set T0365 21 :HMDKVYDCASLLV 1urvA 23 :ERKAVQAMWARLY T0365 42 :GNWDDA 1urvA 36 :ANSEDV T0365 61 :GDSLKREIRLTLPSGLFM 1urvA 42 :GVAILVRFFVNFPSAKQY T0365 108 :GRQLLIPQALQV 1urvA 63 :FKHMEDPLEMER T0365 130 :DAVGLAQQVINELDDLLEAG 1urvA 77 :QLRKHASRVMGALNTVVENL T0365 153 :REVDFVAKMINELDIIE 1urvA 97 :HDPDKVSSVLALVGKAH T0365 172 :TDDLQIQLRRQLFAL 1urvA 124 :FKILSGVILEVVAEE T0365 187 :ESELNPVDVMFLYKTIEWVGGLADLAER 1urvA 140 :ASDFPPETQRAWAKLRGLIYSHVTAAYK Number of specific fragments extracted= 8 number of extra gaps= 0 total=258 Number of alignments=26 # 1urvA read from 1urvA/merged-good-all-a2m # found chain 1urvA in template set Warning: unaligning (T0365)S103 because of BadResidue code BAD_PEPTIDE in next template residue (1urvA)L115 Warning: unaligning (T0365)R109 because of BadResidue code BAD_PEPTIDE at template residue (1urvA)L115 T0365 12 :KSPIKPLQEHMDKVYD 1urvA 21 :EAERKAVQAMWARLYA T0365 28 :CASLLVPFFEA 1urvA 42 :GVAILVRFFVN T0365 42 :GNWDDAVQ 1urvA 67 :EDPLEMER T0365 53 :QISLAEKQGDSLKREIRLTLP 1urvA 77 :QLRKHASRVMGALNTVVENLH T0365 81 :ERTDLLELLTQQDKIA 1urvA 98 :DPDKVSSVLALVGKAH T0365 110 :QLLIPQALQVPFIAYL 1urvA 116 :KHKVEPVYFKILSGVI T0365 143 :DDLLEAGFRGREVDFVAKMINELDII 1urvA 132 :LEVVAEEFASDFPPETQRAWAKLRGL T0365 172 :TDDLQIQLRRQ 1urvA 158 :IYSHVTAAYKE Number of specific fragments extracted= 8 number of extra gaps= 1 total=266 Number of alignments=27 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1n81A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1n81A expands to /projects/compbio/data/pdb/1n81.pdb.gz 1n81A:# T0365 read from 1n81A/merged-good-all-a2m # 1n81A read from 1n81A/merged-good-all-a2m # adding 1n81A to template set # found chain 1n81A in template set T0365 14 :PIKPLQEHMDKVYDCASLLVPFF 1n81A 31 :LSPRIRKVGDIEFHACSDYIYLL T0365 38 :ATITGNWDDAVQIR 1n81A 54 :MTLSKDPEKFNYAL T0365 81 :ERTDLLELLTQ 1n81A 69 :DRVSIRRYVRK T0365 92 :QDKIANKAKDISGRVI 1n81A 94 :QDNIVNRISDRLISYC T0365 109 :RQLLIPQALQVPFIAYLQRCIDAVGLAQQVINE 1n81A 110 :TDKEVTEDYIKKIDDYLWVEQRVIEEVSINVDH T0365 152 :GREVDFVAKMIN 1n81A 143 :AREVKEKKRIMN T0365 164 :ELDIIEEDTDDLQ 1n81A 158 :LIRMLFDTYEYVK T0365 210 :DLAERVGSRLELMLA 1n81A 177 :DQYKDAAARISQFLI Number of specific fragments extracted= 8 number of extra gaps= 0 total=274 Number of alignments=28 # 1n81A read from 1n81A/merged-good-all-a2m # found chain 1n81A in template set T0365 8 :GVFAKSPIKPLQEHMDKVYDCASLLVPFFEA 1n81A 25 :HETHAPLSPRIRKVGDIEFHACSDYIYLLMT T0365 40 :ITGNWDDAVQIR 1n81A 56 :LSKDPEKFNYAL T0365 59 :KQGDSLKREIRLTLPS 1n81A 71 :VSIRRYVRKNQNRYNY T0365 78 :MPVERT 1n81A 87 :FLIEER T0365 91 :QQDKIANKAKDISGRVI 1n81A 93 :VQDNIVNRISDRLISYC T0365 109 :RQLLIPQALQVPFIAYLQRCIDAVGLAQQVINE 1n81A 110 :TDKEVTEDYIKKIDDYLWVEQRVIEEVSINVDH T0365 152 :GREVDFVAKMIN 1n81A 143 :AREVKEKKRIMN T0365 173 :DDLQIQLRRQLFALESE 1n81A 156 :KKLIRMLFDTYEYVKDV T0365 191 :N 1n81A 173 :K T0365 210 :DLAERVGSRLELMLA 1n81A 177 :DQYKDAAARISQFLI Number of specific fragments extracted= 10 number of extra gaps= 0 total=284 Number of alignments=29 # 1n81A read from 1n81A/merged-good-all-a2m # found chain 1n81A in template set T0365 8 :GVFAKSPIKPLQEHMDKVYDCASLLVPFFEATI 1n81A 25 :HETHAPLSPRIRKVGDIEFHACSDYIYLLMTLS T0365 42 :GNWDDAVQIR 1n81A 58 :KDPEKFNYAL T0365 53 :QISLAEK 1n81A 72 :SIRRYVR T0365 67 :EIRLTLPSGL 1n81A 79 :KNQNRYNYFL T0365 80 :VERT 1n81A 89 :IEER T0365 91 :QQDKIANKAKDISGRV 1n81A 93 :VQDNIVNRISDRLISY T0365 108 :GRQLLIPQALQVPFIAYLQRCIDAVGLAQQVINE 1n81A 109 :CTDKEVTEDYIKKIDDYLWVEQRVIEEVSINVDH T0365 152 :GREVDFVAKMIN 1n81A 143 :AREVKEKKRIMN T0365 173 :DDLQIQLRRQLFALES 1n81A 156 :KKLIRMLFDTYEYVKD T0365 190 :LN 1n81A 172 :VK T0365 210 :DLAERVGSRLELMLA 1n81A 177 :DQYKDAAARISQFLI Number of specific fragments extracted= 11 number of extra gaps= 0 total=295 Number of alignments=30 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2f6hX/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2f6hX expands to /projects/compbio/data/pdb/2f6h.pdb.gz 2f6hX:# T0365 read from 2f6hX/merged-good-all-a2m # 2f6hX read from 2f6hX/merged-good-all-a2m # adding 2f6hX to template set # found chain 2f6hX in template set Warning: unaligning (T0365)N43 because first residue in template chain is (2f6hX)N22 Warning: unaligning (T0365)R153 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2f6hX)M149 T0365 44 :WDDA 2f6hX 23 :ATQI T0365 51 :RKQISLAEKQGDSLKREIRLTLPSGLFMP 2f6hX 27 :NEELYRLLEDTEILNQEITEGLLKGFEVP T0365 80 :VERTDL 2f6hX 63 :LSKRDV T0365 86 :LELLTQQ 2f6hX 92 :ESFLAQV T0365 96 :ANKAKDISG 2f6hX 99 :LTTIQKVVT T0365 110 :QLL 2f6hX 108 :QLK T0365 114 :PQALQVPFIAYLQRCIDAVGLAQQVINELDD 2f6hX 111 :GNDLIPSGVFWLANVRELYSFVVFALNSILT T0365 154 :EVDFVAKMINELDIIEEDTDDLQIQLRRQ 2f6hX 150 :TDEEYKEYVSLVTELKDDFEALSYNIYNI T0365 197 :FLYKTIEWVGGLA 2f6hX 179 :WLKKLQKQLQKKA Number of specific fragments extracted= 9 number of extra gaps= 0 total=304 Number of alignments=31 # 2f6hX read from 2f6hX/merged-good-all-a2m # found chain 2f6hX in template set Warning: unaligning (T0365)R153 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2f6hX)M149 Warning: unaligning (T0365)E189 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2f6hX)E222 T0365 44 :WD 2f6hX 23 :AT T0365 49 :QIRKQISLAEKQGDSLKREIRLTLPSGLFMP 2f6hX 25 :QINEELYRLLEDTEILNQEITEGLLKGFEVP T0365 80 :VERTDL 2f6hX 63 :LSKRDV T0365 87 :ELLTQQDKIANKA 2f6hX 70 :YPARILIIVLSEM T0365 100 :KDISGRVIGR 2f6hX 92 :ESFLAQVLTT T0365 110 :QLLI 2f6hX 108 :QLKG T0365 115 :QALQVPFIAYLQRCIDAVGLAQQVINELDD 2f6hX 112 :NDLIPSGVFWLANVRELYSFVVFALNSILT T0365 154 :EVDFVAKMINELDIIEEDTDDLQIQLR 2f6hX 150 :TDEEYKEYVSLVTELKDDFEALSYNIY T0365 181 :RQLFAL 2f6hX 181 :KKLQKQ T0365 190 :LNPVD 2f6hX 223 :YTMDD T0365 198 :LYKTIEWVGGLADLA 2f6hX 228 :ILTFFNSIYWCMKSF T0365 213 :ERVGSRLELML 2f6hX 246 :NEVFHAVVTTL Number of specific fragments extracted= 12 number of extra gaps= 0 total=316 Number of alignments=32 # 2f6hX read from 2f6hX/merged-good-all-a2m # found chain 2f6hX in template set Warning: unaligning (T0365)F10 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2f6hX)M149 T0365 11 :AKSPIKPLQEHMDKVYDCAS 2f6hX 150 :TDEEYKEYVSLVTELKDDFE T0365 31 :LLVPFFEAT 2f6hX 171 :LSYNIYNIW T0365 47 :AVQIRKQISLA 2f6hX 180 :LKKLQKQLQKK T0365 68 :IRLTLPSG 2f6hX 191 :AINAVVIS T0365 80 :VERTDLLELLTQQDK 2f6hX 223 :YTMDDILTFFNSIYW T0365 95 :IANKAKDIS 2f6hX 256 :LLNYVDAIC T0365 104 :GRVIGRQLLIPQALQVPFIAYLQRCIDAVGL 2f6hX 266 :NELIMKRNFLSWKRGLQLNYNVTRLEEWCKT T0365 137 :QVINELDDLLEAGFR 2f6hX 307 :QHLIQTAKLLQVRKY T0365 154 :EVDFV 2f6hX 322 :TIEDI T0365 181 :RQLFALESELNPVDVMFLYK 2f6hX 327 :DILRGICYSLTPAQLQKLIS T0365 201 :TIEWVGGLADLAER 2f6hX 361 :ILRYVADIVKKEAA Number of specific fragments extracted= 11 number of extra gaps= 0 total=327 Number of alignments=33 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1j1vA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1j1vA expands to /projects/compbio/data/pdb/1j1v.pdb.gz 1j1vA: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 # T0365 read from 1j1vA/merged-good-all-a2m # 1j1vA read from 1j1vA/merged-good-all-a2m # adding 1j1vA to template set # found chain 1j1vA in template set T0365 47 :AVQIRKQISLAEK 1j1vA 376 :IDNIQKTVAEYYK T0365 80 :VERTDLL 1j1vA 389 :IKVADLL T0365 115 :QALQVPFIAYLQRCIDAVGLA 1j1vA 397 :KRRSRSVARPRQMAMALAKEL T0365 139 :INELDDL 1j1vA 422 :LPEIGDA T0365 150 :FRGREVDFVAKMINELDIIEED 1j1vA 429 :FGGRDHTTVLHACRKIEQLREE T0365 172 :TDDLQIQLRRQL 1j1vA 454 :IKEDFSNLIRTL Number of specific fragments extracted= 6 number of extra gaps= 0 total=333 Number of alignments=34 # 1j1vA read from 1j1vA/merged-good-all-a2m # found chain 1j1vA in template set T0365 100 :KDISGRVIGR 1j1vA 377 :DNIQKTVAEY T0365 110 :QLLIPQALQVPFIAYLQRCIDA 1j1vA 396 :SKRRSRSVARPRQMAMALAKEL T0365 139 :INELDDL 1j1vA 422 :LPEIGDA T0365 150 :FRGREVDFVAKMINELDIIEED 1j1vA 429 :FGGRDHTTVLHACRKIEQLREE T0365 172 :TDDLQIQLRRQL 1j1vA 454 :IKEDFSNLIRTL Number of specific fragments extracted= 5 number of extra gaps= 0 total=338 Number of alignments=35 # 1j1vA read from 1j1vA/merged-good-all-a2m # found chain 1j1vA in template set T0365 47 :AVQIRKQISLA 1j1vA 376 :IDNIQKTVAEY T0365 80 :VERTDLL 1j1vA 389 :IKVADLL T0365 111 :LLIPQALQVPFIAYLQ 1j1vA 397 :KRRSRSVARPRQMAMA T0365 128 :CIDAV 1j1vA 413 :LAKEL T0365 139 :INELDDL 1j1vA 422 :LPEIGDA T0365 150 :FRGREVDFVAKMINELDIIEED 1j1vA 429 :FGGRDHTTVLHACRKIEQLREE T0365 172 :TDDLQIQLRRQL 1j1vA 454 :IKEDFSNLIRTL Number of specific fragments extracted= 7 number of extra gaps= 0 total=345 Number of alignments=36 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1oq9A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1oq9A expands to /projects/compbio/data/pdb/1oq9.pdb.gz 1oq9A:# T0365 read from 1oq9A/merged-good-all-a2m # 1oq9A read from 1oq9A/merged-good-all-a2m # adding 1oq9A to template set # found chain 1oq9A in template set T0365 42 :GNWDD 1oq9A 74 :DGFDE T0365 50 :IRKQISLAEKQ 1oq9A 79 :QVRELRERAKE T0365 61 :GDSLKREIRLTLPSGLFM 1oq9A 107 :ALPTYQTMLNTLDGVRDE T0365 79 :PV 1oq9A 129 :PT T0365 84 :DLLELLTQQDKIANKAKDISGRVIGR 1oq9A 131 :SWAIWTRAWTAEENRHGDLLNKYLYL T0365 110 :QLL 1oq9A 159 :RVD T0365 118 :QVPFIAYLQRCID 1oq9A 162 :MRQIEKTIQYLIG T0365 131 :AVGLAQQVINELDDLLEAG 1oq9A 195 :QERATFISHGNTARQAKEH T0365 154 :EVDFVAKMINELDIIEEDTDDLQIQLRRQLFALES 1oq9A 214 :GDIKLAQICGTIAADEKRHETAYTKIVEKLFEIDP T0365 192 :PVDVMFLYKTIEW 1oq9A 249 :DGTVLAFADMMRK T0365 207 :GLADLAERVGSR 1oq9A 277 :NLFDHFSAVAQR Number of specific fragments extracted= 11 number of extra gaps= 0 total=356 Number of alignments=37 # 1oq9A read from 1oq9A/merged-good-all-a2m # found chain 1oq9A in template set T0365 2 :PVNSILGVFAKSPIKPLQEHMDKVYD 1oq9A 24 :VHVQVTHSMPPQKIEIFKSLDNWAEE T0365 42 :GNWDDAVQIRKQISLAEKQ 1oq9A 71 :PASDGFDEQVRELRERAKE T0365 61 :GDSLKREIRLTLPS 1oq9A 107 :ALPTYQTMLNTLDG T0365 75 :GLFMPVE 1oq9A 125 :TGASPTS T0365 82 :RTDLLELLTQQDKIAN 1oq9A 136 :TRAWTAEENRHGDLLN T0365 98 :KAKDISGRVIGRQLL 1oq9A 164 :QIEKTIQYLIGSGMD T0365 113 :IPQALQVPFIAYLQRCIDAVGLAQQVINELDD 1oq9A 181 :TENSPYLGFIYTSFQERATFISHGNTARQAKE T0365 153 :REVDFVAKMINELDIIEEDTDDLQIQLRRQLFALE 1oq9A 213 :HGDIKLAQICGTIAADEKRHETAYTKIVEKLFEID T0365 191 :NPVDVMFLYKTIEW 1oq9A 248 :PDGTVLAFADMMRK T0365 206 :GGLADLAERVGSR 1oq9A 276 :DNLFDHFSAVAQR Number of specific fragments extracted= 10 number of extra gaps= 0 total=366 Number of alignments=38 # 1oq9A read from 1oq9A/merged-good-all-a2m # found chain 1oq9A in template set T0365 63 :SLKREIRLTLPSGL 1oq9A 109 :PTYQTMLNTLDGVR T0365 84 :DLLELLTQQDKIANKAKDISGRVIGRQLLIPQALQVPFIAYLQRC 1oq9A 131 :SWAIWTRAWTAEENRHGDLLNKYLYLSGRVDMRQIEKTIQYLIGS T0365 129 :IDAVGLAQQVIN 1oq9A 200 :FISHGNTARQAK T0365 152 :GREVDFVAKMINELDIIEEDTDDLQIQLRRQLFALE 1oq9A 212 :EHGDIKLAQICGTIAADEKRHETAYTKIVEKLFEID T0365 191 :NPVDVMFLYKTIEW 1oq9A 248 :PDGTVLAFADMMRK T0365 207 :GLADLAERVG 1oq9A 277 :NLFDHFSAVA T0365 217 :SRLELML 1oq9A 299 :DILEFLV Number of specific fragments extracted= 7 number of extra gaps= 0 total=373 Number of alignments=39 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1o5hA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1o5hA expands to /projects/compbio/data/pdb/1o5h.pdb.gz 1o5hA: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 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 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 # T0365 read from 1o5hA/merged-good-all-a2m # 1o5hA read from 1o5hA/merged-good-all-a2m # adding 1o5hA to template set # found chain 1o5hA in template set T0365 10 :FAKSPIKPLQEHMD 1o5hA 3 :VERLSLKEFCDMVA T0365 24 :KVYDCASLLVPFFEATITGN 1o5hA 31 :VGAMACALAEMVANFTRKKK T0365 44 :WDDAVQIRKQISLAEKQGDSLKREIRLT 1o5hA 56 :EPEMERIVEAMEEARLKLFDLAKKDMEA T0365 72 :LPSG 1o5hA 87 :VMKA T0365 81 :ERTDLLELLTQQDKIANKAKDISGRVIGRQLLIPQALQVPFIAYLQRCIDAVGLAQQVINELDD 1o5hA 98 :LQNALKEAASVPMDVIRVMKDLAHELEKLAEFGNKNLASDTLNAADLCHAVFQVEKVNVLINLK T0365 149 :GF 1o5hA 162 :EI T0365 153 :REVDFVAKMINELDIIEEDTDDLQIQLRRQLFAL 1o5hA 164 :SDETFRKNMLEELEEQEAQIEGCYQRVKKMLEGI Number of specific fragments extracted= 7 number of extra gaps= 0 total=380 Number of alignments=40 # 1o5hA read from 1o5hA/merged-good-all-a2m # found chain 1o5hA in template set T0365 10 :FAKSPIKPLQEHMD 1o5hA 3 :VERLSLKEFCDMVA T0365 24 :KVYDCASLLVPFFEATITGN 1o5hA 31 :VGAMACALAEMVANFTRKKK T0365 44 :WDDAVQIRKQISLAEKQGDSLKR 1o5hA 56 :EPEMERIVEAMEEARLKLFDLAK T0365 67 :EIRLTLPSGLFM 1o5hA 82 :EAFEKVMKAYKS T0365 81 :E 1o5hA 94 :S T0365 82 :RTDLLELLTQQDKIANKAKDISGRVIGRQLLIPQALQVPFIAYLQRCIDAVGLAQQVINELDD 1o5hA 99 :QNALKEAASVPMDVIRVMKDLAHELEKLAEFGNKNLASDTLNAADLCHAVFQVEKVNVLINLK T0365 152 :G 1o5hA 162 :E T0365 153 :REVDFVAKMINELDIIEEDTDDLQIQLRRQLFALESE 1o5hA 164 :SDETFRKNMLEELEEQEAQIEGCYQRVKKMLEGIVWS Number of specific fragments extracted= 8 number of extra gaps= 0 total=388 Number of alignments=41 # 1o5hA read from 1o5hA/merged-good-all-a2m # found chain 1o5hA in template set Warning: unaligning (T0365)V9 because first residue in template chain is (1o5hA)E2 T0365 10 :FAKSPIKPLQEHMD 1o5hA 3 :VERLSLKEFCDMVA T0365 24 :KVYDCASLLVPFFEATITGN 1o5hA 31 :VGAMACALAEMVANFTRKKK T0365 44 :WDDAVQIRKQISLAEKQGDSLKREIRLT 1o5hA 56 :EPEMERIVEAMEEARLKLFDLAKKDMEA T0365 72 :LPSG 1o5hA 87 :VMKA T0365 82 :RTDLLELLTQQDKIANKAKDISGRVIGRQLLIPQALQVPFIAYLQRCIDAVGLAQQVINELDD 1o5hA 99 :QNALKEAASVPMDVIRVMKDLAHELEKLAEFGNKNLASDTLNAADLCHAVFQVEKVNVLINLK T0365 150 :F 1o5hA 163 :I T0365 153 :REVDFVAKMINELDIIEEDTDDLQIQLRRQL 1o5hA 164 :SDETFRKNMLEELEEQEAQIEGCYQRVKKML Number of specific fragments extracted= 7 number of extra gaps= 0 total=395 Number of alignments=42 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1h6pA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1h6pA expands to /projects/compbio/data/pdb/1h6p.pdb.gz 1h6pA:# T0365 read from 1h6pA/merged-good-all-a2m # 1h6pA read from 1h6pA/merged-good-all-a2m # adding 1h6pA to template set # found chain 1h6pA in template set Warning: unaligning (T0365)E81 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1h6pA)V97 Warning: unaligning (T0365)D166 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1h6pA)R192 T0365 19 :QEHMDKVYDCASLLVPFFEATITGNWDDAVQIRKQISLA 1h6pA 48 :LEEAVNRWVLKFYFHEALRAFRGSRYGDFRQIRDIMQAL T0365 78 :MPV 1h6pA 89 :RPL T0365 83 :TDLLELLTQQDKIAN 1h6pA 98 :SRLLRVMQCLSRIEE T0365 98 :KAKDISGRVIGRQLLI 1h6pA 128 :PLESAINVLEMIKTEF T0365 116 :ALQVPFIA 1h6pA 144 :TLTEAVVE T0365 124 :YLQRCIDAVGLAQ 1h6pA 153 :SRKLVKEAAVIIC T0365 142 :LD 1h6pA 166 :IK T0365 152 :GREVDFVAKMINEL 1h6pA 168 :NKEFEKASKILKKH T0365 180 :RRQLFALESE 1h6pA 195 :LLNIIREKNL T0365 190 :LNPVDVM 1h6pA 212 :FSYETFQ T0365 199 :YKTIEWVGG 1h6pA 219 :QKMLRFLES Number of specific fragments extracted= 11 number of extra gaps= 0 total=406 Number of alignments=43 # 1h6pA read from 1h6pA/merged-good-all-a2m # found chain 1h6pA in template set Warning: unaligning (T0365)E81 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1h6pA)V97 Warning: unaligning (T0365)D166 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1h6pA)R192 T0365 19 :QEHMDKVYDCASLLVPFFEATITGNWDDAVQIRKQISLA 1h6pA 48 :LEEAVNRWVLKFYFHEALRAFRGSRYGDFRQIRDIMQAL T0365 76 :LFMPV 1h6pA 87 :LVRPL T0365 84 :DLLELLTQQDKIAN 1h6pA 99 :RLLRVMQCLSRIEE T0365 98 :KAKDISGRVIGR 1h6pA 128 :PLESAINVLEMI T0365 110 :QLLIPQALQVPFIAYL 1h6pA 142 :EFTLTEAVVESSRKLV T0365 129 :IDAVGLAQ 1h6pA 158 :KEAAVIIC T0365 142 :LD 1h6pA 166 :IK T0365 152 :GREVDFVAKMINEL 1h6pA 168 :NKEFEKASKILKKH T0365 180 :RRQLFALESE 1h6pA 195 :LLNIIREKNL T0365 190 :LNPVDV 1h6pA 212 :FSYETF T0365 198 :LYKTIEWVGG 1h6pA 218 :QQKMLRFLES Number of specific fragments extracted= 11 number of extra gaps= 0 total=417 Number of alignments=44 # 1h6pA read from 1h6pA/merged-good-all-a2m # found chain 1h6pA in template set Warning: unaligning (T0365)F77 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1h6pA)V97 Warning: unaligning (T0365)R82 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1h6pA)V97 T0365 19 :QEHMDKVYDCASLLVPFFEATITGNWDDAVQIRKQISLA 1h6pA 48 :LEEAVNRWVLKFYFHEALRAFRGSRYGDFRQIRDIMQAL T0365 72 :LPSGL 1h6pA 87 :LVRPL T0365 83 :TDLLELLT 1h6pA 98 :SRLLRVMQ T0365 91 :QQDKIANKAKDISGR 1h6pA 128 :PLESAINVLEMIKTE T0365 111 :LLIPQALQVPFIAYLQRCIDAV 1h6pA 143 :FTLTEAVVESSRKLVKEAAVII T0365 138 :VINE 1h6pA 165 :CIKN T0365 153 :REVDFVAKMINEL 1h6pA 169 :KEFEKASKILKKH T0365 180 :RRQLFALESE 1h6pA 195 :LLNIIREKNL T0365 190 :LNPVDVM 1h6pA 212 :FSYETFQ T0365 199 :YKTIEWVGG 1h6pA 219 :QKMLRFLES Number of specific fragments extracted= 10 number of extra gaps= 0 total=427 Number of alignments=45 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1wkbA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1wkbA expands to /projects/compbio/data/pdb/1wkb.pdb.gz 1wkbA:# T0365 read from 1wkbA/merged-good-all-a2m # 1wkbA read from 1wkbA/merged-good-all-a2m # adding 1wkbA to template set # found chain 1wkbA in template set T0365 80 :VERTDLLELLTQQDKIANKAKDIS 1wkbA 689 :WRRKEVGKLRKQIERFYELISQFA T0365 108 :GRQLL 1wkbA 713 :EYEVK T0365 115 :Q 1wkbA 718 :G T0365 116 :ALQVPFIAYLQRCIDAVGLAQQVINEL 1wkbA 721 :ELKDIDRWMLHRLNKAIKETTNALEEF T0365 143 :DDLLEAGF 1wkbA 750 :RTAVQWAF T0365 170 :EDTDDLQIQLRRQL 1wkbA 758 :YSIMNDLRWYLRRT T0365 185 :A 1wkbA 772 :E T0365 188 :SELNPVDVMFLYKTIEWVGGLA 1wkbA 773 :GRDDEAKRYVLRTLADVWVRLM Number of specific fragments extracted= 8 number of extra gaps= 0 total=435 Number of alignments=46 # 1wkbA read from 1wkbA/merged-good-all-a2m # found chain 1wkbA in template set T0365 80 :VERTDLLELLTQQDKIANKAKDIS 1wkbA 689 :WRRKEVGKLRKQIERFYELISQFA T0365 108 :GRQLLIPQALQVPFIAYLQRCIDAVGLAQQVINELD 1wkbA 713 :EYEVKGNVELKDIDRWMLHRLNKAIKETTNALEEFR T0365 161 :MINELDIIEEDTDDLQIQLRRQ 1wkbA 749 :TRTAVQWAFYSIMNDLRWYLRR T0365 186 :LESELNPVDVMFLYKTIEWVGGLA 1wkbA 771 :TEGRDDEAKRYVLRTLADVWVRLM Number of specific fragments extracted= 4 number of extra gaps= 0 total=439 Number of alignments=47 # 1wkbA read from 1wkbA/merged-good-all-a2m # found chain 1wkbA in template set T0365 78 :MPVERTDLLELLTQQDKIANKAKDISG 1wkbA 687 :FDWRRKEVGKLRKQIERFYELISQFAE T0365 109 :RQLL 1wkbA 714 :YEVK T0365 113 :IPQALQVPFIAYLQRC 1wkbA 721 :ELKDIDRWMLHRLNKA T0365 132 :VGLAQQVINEL 1wkbA 737 :IKETTNALEEF T0365 153 :R 1wkbA 748 :R T0365 165 :LDIIEEDTDDLQIQLRRQLFALESELN 1wkbA 749 :TRTAVQWAFYSIMNDLRWYLRRTEGRD T0365 192 :PVDVMFLYKTIEWVGGLA 1wkbA 777 :EAKRYVLRTLADVWVRLM Number of specific fragments extracted= 7 number of extra gaps= 0 total=446 Number of alignments=48 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1t72A/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/T0365/1t72A/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0365/1t72A/merged-good-all-a2m.gz for input Trying 1t72A/merged-good-all-a2m Error: Couldn't open file 1t72A/merged-good-all-a2m or 1t72A/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ku1A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1ku1A expands to /projects/compbio/data/pdb/1ku1.pdb.gz 1ku1A:# T0365 read from 1ku1A/merged-good-all-a2m # 1ku1A read from 1ku1A/merged-good-all-a2m # adding 1ku1A to template set # found chain 1ku1A in template set T0365 9 :VFAKS 1ku1A -8 :LVPRG T0365 14 :PIK 1ku1A -2 :HMD T0365 17 :PLQEHMDKVYD 1ku1A 562 :EFIECTNAFNE T0365 28 :CASLLVP 1ku1A 577 :GIPMLIE T0365 42 :GNWDDAVQIR 1ku1A 590 :DSDKDIAEFL T0365 58 :EKQGDSLK 1ku1A 608 :KKTIGLLL T0365 66 :R 1ku1A 629 :R T0365 67 :EIRLTLPSGLFMPVERTDLLELLTQQDK 1ku1A 640 :EAIRILLTKFRLPGESQQIERIIEAFSS T0365 98 :KAKD 1ku1A 668 :AYCE T0365 110 :QLLIPQALQ 1ku1A 672 :NQDYDPSKI T0365 119 :VPFIAYLQRCIDAVGLA 1ku1A 696 :DSVFILSYSIIMLNTDL T0365 149 :GFRGR 1ku1A 716 :QVKEH T0365 154 :EVDFVAK 1ku1A 722 :SFEDYSG T0365 174 :DLQIQLRRQLFA 1ku1A 742 :WYLDRVYCSIRD Number of specific fragments extracted= 14 number of extra gaps= 0 total=460 Number of alignments=49 # 1ku1A read from 1ku1A/merged-good-all-a2m # found chain 1ku1A in template set Warning: unaligning (T0365)G8 because first residue in template chain is (1ku1A)G-9 T0365 9 :VFAKS 1ku1A -8 :LVPRG T0365 14 :PIKP 1ku1A -2 :HMDR T0365 18 :LQEHMDKVYD 1ku1A 563 :FIECTNAFNE T0365 28 :CASLLVP 1ku1A 577 :GIPMLIE T0365 42 :GNWDDAVQI 1ku1A 590 :DSDKDIAEF T0365 51 :RKQISLA 1ku1A 608 :KKTIGLL T0365 59 :KQGDSLKR 1ku1A 622 :SLLNEYIR T0365 67 :EIRLTLPSGLFMPVERTDLLELLTQQDKIA 1ku1A 640 :EAIRILLTKFRLPGESQQIERIIEAFSSAY T0365 108 :GRQLLIPQA 1ku1A 670 :CENQDYDPS T0365 118 :QVPFIAYLQRCIDAVGLAQ 1ku1A 695 :ADSVFILSYSIIMLNTDLH T0365 152 :G 1ku1A 716 :Q T0365 153 :REVDFVAK 1ku1A 721 :MSFEDYSG T0365 174 :DLQIQLRRQLFA 1ku1A 742 :WYLDRVYCSIRD T0365 188 :SE 1ku1A 754 :KE Number of specific fragments extracted= 14 number of extra gaps= 0 total=474 Number of alignments=50 # 1ku1A read from 1ku1A/merged-good-all-a2m # found chain 1ku1A in template set T0365 8 :GVFAKSPIK 1ku1A -8 :LVPRGSHMD T0365 17 :PLQEHMDKVYD 1ku1A 562 :EFIECTNAFNE T0365 28 :CASLLVP 1ku1A 577 :GIPMLIE T0365 42 :GNWDDAVQIR 1ku1A 590 :DSDKDIAEFL T0365 70 :LTLPSG 1ku1A 600 :FNNNNR T0365 80 :VERTDLLELL 1ku1A 606 :MNKKTIGLLL T0365 94 :KIANKAKDI 1ku1A 622 :SLLNEYIRL T0365 103 :SGRVIGRQLLIP 1ku1A 641 :AIRILLTKFRLP T0365 115 :QALQVPFIAYL 1ku1A 655 :SQQIERIIEAF T0365 132 :VGLAQQ 1ku1A 666 :SSAYCE T0365 147 :EAGFRGR 1ku1A 672 :NQDYDPS T0365 154 :EVDFVAKMINELDIIEEDT 1ku1A 694 :DADSVFILSYSIIMLNTDL T0365 178 :QLRRQLFALESELN 1ku1A 725 :DYSGNLKGCCNHKD T0365 196 :MFLYKTIEWVGG 1ku1A 742 :WYLDRVYCSIRD Number of specific fragments extracted= 14 number of extra gaps= 0 total=488 Number of alignments=51 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1hw1A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0365 read from 1hw1A/merged-good-all-a2m # 1hw1A read from 1hw1A/merged-good-all-a2m # found chain 1hw1A in training set T0365 5 :SILGVFAKSPIKPLQEHMDKVYDCA 1hw1A 85 :TLARLDHESVPQLIDNLLSVRTNIS T0365 33 :VPFFEATITGNWDDAVQIRK 1hw1A 110 :TIFIRTAFRQHPDKAQEVLA T0365 71 :TLPS 1hw1A 130 :TANE T0365 78 :MPVERTDL 1hw1A 134 :VADHADAF T0365 96 :ANKAKDISGRVIGRQLL 1hw1A 142 :AELDYNIFRGLAFASGN T0365 115 :QAL 1hw1A 159 :PIY T0365 119 :VPFIAYLQRCID 1hw1A 166 :NGMKGLYTRIGR T0365 131 :AVGLAQQVINELDDLLEAGFR 1hw1A 185 :ARSLALGFYHKLSALCSEGAH T0365 156 :DFVAKM 1hw1A 206 :DQVYET T0365 165 :LDIIEEDTDDLQIQLRR 1hw1A 212 :VRRYGHESGEIWHRMQK Number of specific fragments extracted= 10 number of extra gaps= 0 total=498 Number of alignments=52 # 1hw1A read from 1hw1A/merged-good-all-a2m # found chain 1hw1A in training set T0365 7 :LGVFAKSPIKPLQEHMDKVYDC 1hw1A 87 :ARLDHESVPQLIDNLLSVRTNI T0365 32 :LVPFFEATITGNWDDAVQIR 1hw1A 109 :STIFIRTAFRQHPDKAQEVL T0365 70 :LTLPS 1hw1A 129 :ATANE T0365 78 :MPVERTDL 1hw1A 134 :VADHADAF T0365 96 :ANKAKDISGRVIGRQLL 1hw1A 142 :AELDYNIFRGLAFASGN T0365 115 :QA 1hw1A 159 :PI T0365 117 :LQVPFIAYLQRCI 1hw1A 164 :ILNGMKGLYTRIG T0365 130 :DAVGLAQQVINELDDLLEAGFR 1hw1A 184 :EARSLALGFYHKLSALCSEGAH T0365 156 :DFVAKM 1hw1A 206 :DQVYET T0365 165 :LDIIEEDTDDLQIQLRR 1hw1A 212 :VRRYGHESGEIWHRMQK Number of specific fragments extracted= 10 number of extra gaps= 0 total=508 Number of alignments=53 # 1hw1A read from 1hw1A/merged-good-all-a2m # found chain 1hw1A in training set T0365 7 :LGVFAKSPIKPLQEHMDKVYD 1hw1A 87 :ARLDHESVPQLIDNLLSVRTN T0365 31 :LLVPFFEATITGNWDDAVQIRKQ 1hw1A 108 :ISTIFIRTAFRQHPDKAQEVLAT T0365 72 :LPS 1hw1A 131 :ANE T0365 78 :MPVERT 1hw1A 134 :VADHAD T0365 87 :ELLTQQDKIANKAKDISG 1hw1A 140 :AFAELDYNIFRGLAFASG T0365 114 :PQALQVPF 1hw1A 158 :NPIYGLIL T0365 122 :IAYLQRCID 1hw1A 169 :KGLYTRIGR T0365 131 :AVGLAQQVINELDDLLEAGFR 1hw1A 185 :ARSLALGFYHKLSALCSEGAH T0365 156 :DFVAKM 1hw1A 206 :DQVYET T0365 165 :LDIIEEDTDDLQIQLRR 1hw1A 212 :VRRYGHESGEIWHRMQK Number of specific fragments extracted= 10 number of extra gaps= 0 total=518 Number of alignments=54 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2c6cA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2c6cA expands to /projects/compbio/data/pdb/2c6c.pdb.gz 2c6cA:# T0365 read from 2c6cA/merged-good-all-a2m # 2c6cA read from 2c6cA/merged-good-all-a2m # adding 2c6cA to template set # found chain 2c6cA in template set Warning: unaligning (T0365)R151 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2c6cA)N657 Warning: unaligning (T0365)E154 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2c6cA)N657 T0365 75 :GLFMPVERTDLLELLTQQ 2c6cA 590 :SIVLPFDCRDYAVVLRKY T0365 96 :ANKAKDISG 2c6cA 608 :ADKIYSISM T0365 105 :RVIGRQLL 2c6cA 621 :EMKTYSVS T0365 118 :QVPFIAYLQRCIDAVGLAQQVIN 2c6cA 629 :FDSLFSAVKNFTEIASKFSERLQ T0365 149 :GF 2c6cA 652 :DF T0365 155 :VDFVAKMINELDIIE 2c6cA 658 :PIVLRMMNDQLMFLE T0365 179 :LRRQLFALESELNPVD 2c6cA 708 :IYDALFDIESKVDPSK T0365 197 :FLYKTIEWVGGLADLAERVGSR 2c6cA 724 :AWGEVKRQIYVAAFTVQAAAET Number of specific fragments extracted= 8 number of extra gaps= 0 total=526 Number of alignments=55 # 2c6cA read from 2c6cA/merged-good-all-a2m # found chain 2c6cA in template set Warning: unaligning (T0365)R151 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2c6cA)N657 Warning: unaligning (T0365)E154 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2c6cA)N657 T0365 76 :LFMPVERTDLL 2c6cA 591 :IVLPFDCRDYA T0365 90 :TQQDKIANKAKDISG 2c6cA 602 :VVLRKYADKIYSISM T0365 105 :RVIGRQLLI 2c6cA 621 :EMKTYSVSF T0365 119 :VPFIAYLQRCIDAVGLAQQVI 2c6cA 630 :DSLFSAVKNFTEIASKFSERL T0365 148 :AGF 2c6cA 651 :QDF T0365 155 :VDFVAKMINELDIIE 2c6cA 658 :PIVLRMMNDQLMFLE T0365 179 :LRRQLFALESELNPVDV 2c6cA 708 :IYDALFDIESKVDPSKA T0365 198 :LYKTIEWVGGLADLAERVGSR 2c6cA 725 :WGEVKRQIYVAAFTVQAAAET Number of specific fragments extracted= 8 number of extra gaps= 0 total=534 Number of alignments=56 # 2c6cA read from 2c6cA/merged-good-all-a2m # found chain 2c6cA in template set Warning: unaligning (T0365)R151 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2c6cA)N657 Warning: unaligning (T0365)E154 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2c6cA)N657 T0365 77 :FMPVERTDLLELLT 2c6cA 592 :VLPFDCRDYAVVLR T0365 94 :KIANKAKDISG 2c6cA 606 :KYADKIYSISM T0365 113 :IPQALQVP 2c6cA 617 :KHPQEMKT T0365 127 :RCIDAVGLAQQVINELDDLL 2c6cA 631 :SLFSAVKNFTEIASKFSERL T0365 148 :AGF 2c6cA 651 :QDF T0365 155 :VDFVAKMINELDIIE 2c6cA 658 :PIVLRMMNDQLMFLE T0365 179 :LRRQLFALESELNPVD 2c6cA 708 :IYDALFDIESKVDPSK T0365 197 :FLYKTIEWVGGLADLAERVGSRL 2c6cA 724 :AWGEVKRQIYVAAFTVQAAAETL Number of specific fragments extracted= 8 number of extra gaps= 0 total=542 Number of alignments=57 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1xwmA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1xwmA expands to /projects/compbio/data/pdb/1xwm.pdb.gz 1xwmA:# T0365 read from 1xwmA/merged-good-all-a2m # 1xwmA read from 1xwmA/merged-good-all-a2m # adding 1xwmA to template set # found chain 1xwmA in template set Warning: unaligning (T0365)S13 because first residue in template chain is (1xwmA)T4 T0365 14 :PIKPLQEHMDKVYDCASLLVPFFEATI 1xwmA 5 :FADDLASLHNKLIEMGRLTEVALQQAI T0365 41 :TGNWDDAVQIRK 1xwmA 36 :TQNANLAMAVID T0365 53 :QISLAEKQGDSLKREIRLT 1xwmA 51 :SIDALEEEVNDFALWLIAA T0365 80 :VERTDL 1xwmA 72 :PVATDL T0365 86 :LELLTQQDKIANKAKDISGRVIGRQLL 1xwmA 84 :IKIASDIERIADFAVNIAKACIRIGGQ T0365 116 :ALQ 1xwmA 111 :PFV T0365 119 :VPFIAYLQRCIDAVGL 1xwmA 117 :GPLVLMYRLATDMVST T0365 138 :VINELDD 1xwmA 133 :AIAAYDR T0365 153 :REVD 1xwmA 140 :EDAS T0365 161 :MINELDIIEEDTDDLQIQLRRQL 1xwmA 144 :LAAQIADMDHRVDEQYGEMMASL T0365 188 :SELNPVDVMFLYKTIEWVGGLADLAERVGSRLELMLA 1xwmA 173 :DAATLAQMNVLALVARYIERTADHATNIAEHLVYLVK Number of specific fragments extracted= 11 number of extra gaps= 0 total=553 Number of alignments=58 # 1xwmA read from 1xwmA/merged-good-all-a2m # found chain 1xwmA in template set Warning: unaligning (T0365)S13 because first residue in template chain is (1xwmA)T4 T0365 14 :PIKPLQEHMDKVYDCASLLVPFFEATI 1xwmA 5 :FADDLASLHNKLIEMGRLTEVALQQAI T0365 41 :TGNWDDAVQIRK 1xwmA 36 :TQNANLAMAVID T0365 53 :QISLAEKQGDSLKREIRLT 1xwmA 51 :SIDALEEEVNDFALWLIAA T0365 76 :L 1xwmA 71 :Q T0365 80 :VERT 1xwmA 72 :PVAT T0365 84 :DL 1xwmA 79 :RI T0365 86 :LELLTQQDKIANKAKDISGRVIGRQL 1xwmA 84 :IKIASDIERIADFAVNIAKACIRIGG T0365 112 :LIPQAL 1xwmA 111 :PFVMDI T0365 119 :VPFIAYLQRCID 1xwmA 117 :GPLVLMYRLATD T0365 134 :LAQQVINELDD 1xwmA 129 :MVSTAIAAYDR T0365 153 :REVD 1xwmA 140 :EDAS T0365 161 :MINELDIIEEDTDDLQIQLRRQLFALESE 1xwmA 144 :LAAQIADMDHRVDEQYGEMMASLLAVAKT T0365 191 :N 1xwmA 173 :D T0365 192 :PVDVMFLYKTIEWVGGLADLAERVGSRLELMLAR 1xwmA 177 :LAQMNVLALVARYIERTADHATNIAEHLVYLVKG Number of specific fragments extracted= 14 number of extra gaps= 0 total=567 Number of alignments=59 # 1xwmA read from 1xwmA/merged-good-all-a2m # found chain 1xwmA in template set T0365 14 :PIKPLQEHMDKVYDCASLLVPFFE 1xwmA 12 :LHNKLIEMGRLTEVALQQAIEAFQ T0365 41 :TGNWDDAVQIRK 1xwmA 36 :TQNANLAMAVID T0365 53 :QISLAEKQGDSLKREIRLT 1xwmA 51 :SIDALEEEVNDFALWLIAA T0365 80 :VERTD 1xwmA 72 :PVATD T0365 85 :LLELLTQQDKIANKAKDISGRVIGRQLLIP 1xwmA 83 :AIKIASDIERIADFAVNIAKACIRIGGQPF T0365 119 :VPFIAYLQRCIDAVGLAQQVINE 1xwmA 117 :GPLVLMYRLATDMVSTAIAAYDR T0365 153 :REVD 1xwmA 140 :EDAS T0365 161 :MINELDIIEEDTDDLQIQLRRQLFALES 1xwmA 144 :LAAQIADMDHRVDEQYGEMMASLLAVAK T0365 190 :LN 1xwmA 172 :TD T0365 192 :PVDVMFLYKTIEWVGGLADLAERVGSRLELML 1xwmA 177 :LAQMNVLALVARYIERTADHATNIAEHLVYLV Number of specific fragments extracted= 10 number of extra gaps= 0 total=577 Number of alignments=60 # command:Using radius: 8.0000 Alignment mode NUMB_ALIGNS: 60 Adding 4095 constraints to all.constraints Done adding distance constraints # command:Reading probabilities from probabilities.dat Reading constraints from ConstraintSet all.constraints maxweight: 1.0000 Optimizing... Probability sum: -381.4659, CN propb: -381.4659 weights: 0.2949 constraints: 444 # command:Found ConstraintSet # PrintContacts align.constraints_v3 Number of constraints in align.constraints 444 # command:Found ConstraintSet # PrintContacts align_bonus.constraints_v3 Number of constraints in align.constraints.bonus 444 # command:Found ConstraintSet # PrintContacts rejected.constraints_v3 Number of constraints in rejected.constraints 3651 # command:Found ConstraintSet # PrintContacts rejected_bonus.constraints_v3 Number of constraints in rejected.constraints.bonus 3651 # command:Found ConstraintSet # PrintContacts non_contacts.constraints_v3 Number of constraints in noncontact.constraints 0 # command:Found ConstraintSet # PrintContacts non_contacts_bonus.constraints_v3 Number of constraints in noncontact.constraints.bonus 0 # command:Found ConstraintSet # PrintContacts all.constraints_v3 Number of constraints in all.constraints 4095 # command: