# command:# Prefix for input files set to /projects/compbio/experiments/undertaker/atoms-inputs/ # command:# reading cullpdb_pc80_res1.2_R0.2_d070810_chains408.atoms.gz # #computed average backbone with maximum peptide_sq_deviance = 0.002 # computed average trans backbone unit from 1600 examples # computed average trans backbone unit before proline from 52 examples # trans (non-proline) backbone unit: # CA= -2.2097 1.0151 -0.0046 # O= -0.1488 2.2425 0.0020 # C= -0.6903 1.1357 0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4580 -0.0000 -0.0000 # cis backbone unit: # CA= -0.1462 2.4515 0.0018 # O= -2.0272 0.9713 0.0022 # C= -0.8006 1.0755 0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4659 0.0000 0.0000 # trans backbone unit before proline: # CA= -2.2063 1.0654 0.0002 # O= -0.1193 2.2442 0.0054 # C= -0.6842 1.1479 -0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4661 -0.0000 0.0000 # After reading cullpdb_pc80_res1.2_R0.2_d070810_chains408.atoms.gz have 408 chains in training database # Count of chains,residues,atoms: 408,82795,639989 # 81291 residues have no bad marker # 565 residues lack atoms needed to compute omega # 313 residues have cis peptide # number of each bad type: # NON_STANDARD_RESIDUE 1 # HAS_OXT 265 # TOO_MANY_ATOMS 0 # TOO_FEW_ATOMS 378 # HAS_UNKNOWN_ATOMS 0 # HAS_DUPLICATE_ATOMS 0 # CHAIN_BREAK_BEFORE 139 # NON_PLANAR_PEPTIDE 424 # BAD_PEPTIDE 803 # Note: may sum to more than number of residues, # because one residue may have multiple problems # command:# Reading rotamer library from dunbrack-40pc-3157.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 # command:# Making conformation for sequence T0315 numbered 1 through 257 Created new target T0315 from T0315.a2m # command:CPU_time= 6.368 sec, elapsed time= 6.590 sec. # command:# reading script from file all-templates.under # Reading fragments from alignment file # Attempting to read fragment alignments from file 1j6oA/T0315-1j6oA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1j6oA expands to /projects/compbio/data/pdb/1j6o.pdb.gz 1j6oA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0315 read from 1j6oA/T0315-1j6oA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1j6oA read from 1j6oA/T0315-1j6oA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1j6oA to template set # found chain 1j6oA in template set Warning: unaligning (T0315)G91 because of BadResidue code BAD_PEPTIDE in next template residue (1j6oA)E90 Warning: unaligning (T0315)E92 because of BadResidue code BAD_PEPTIDE at template residue (1j6oA)E90 T0315 1 :MLIDTHVHLNDEQYDDDLSEVITRAREAGVDRMFVVGFNKSTIERAMKLIDEYDFLYGIIGWHPVDAIDFTEEHLEWIESLAQHPKVIGI 1j6oA -1 :HMVDTHAHLHFHQFDDDRNAVISSFEENNIEFVVNVGVNLEDSKKSLDLSKTSDRIFCSVGVHPHDAKEVPEDFIEHLEKFAKDEKVVAI # choosing archetypes in rotamer library T0315 93 :MGLDYHWDKSPADVQKEVFRKQIALAKRLKLPIIIHNREATQDCIDILLEEHAEEVGGIMHSFSGSPEIADIVTN 1j6oA 91 :TGLDFFRNISPAEVQKRVFVEQIELAGKLNLPLVVHIRDAYSEAYEILRTESLPEKRGVIHAFSSDYEWAKKFID T0315 169 :LNFYISLGGPVTFKNAKQPKEVAKHVSMERLLVETDAPYLSPHPYRGKRNEPARVTLVAEQIAELKGLSYEEVCEQTTKNAEKLF 1j6oA 166 :LGFLLGIGGPVTYPKNEALREVVKRVGLEYIVLETDCPFLPPQPFRGKRNEPKYLKYVVETISQVLGVPEAKVDEATTENARRIF Number of specific fragments extracted= 3 number of extra gaps= 1 total=3 Will force an alignment to be made, even if fragment is small Number of alignments=1 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1j6oA/T0315-1j6oA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0315 read from 1j6oA/T0315-1j6oA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1j6oA read from 1j6oA/T0315-1j6oA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1j6oA in template set Warning: unaligning (T0315)G91 because of BadResidue code BAD_PEPTIDE in next template residue (1j6oA)E90 Warning: unaligning (T0315)E92 because of BadResidue code BAD_PEPTIDE at template residue (1j6oA)E90 T0315 2 :LIDTHVHLNDEQYDDDLSEVITRAREAGVDRMFVVGFNKSTIERAMKLIDEYDFLYGIIGWHPVDAIDFTEEHLEWIESLAQHPKVIGI 1j6oA 0 :MVDTHAHLHFHQFDDDRNAVISSFEENNIEFVVNVGVNLEDSKKSLDLSKTSDRIFCSVGVHPHDAKEVPEDFIEHLEKFAKDEKVVAI T0315 93 :MGLDYHWDKSPADVQKEVFRKQIALAKRLKLPIIIHNREATQDCIDILLEEHAEEVGGIMHSFSGSPEIADIVTN 1j6oA 91 :TGLDFFRNISPAEVQKRVFVEQIELAGKLNLPLVVHIRDAYSEAYEILRTESLPEKRGVIHAFSSDYEWAKKFID T0315 169 :LNFYISLGGPVTFKNAKQPKEVAKHVSMERLLVETDAPYLSPHPYRGKRNEPARVTLVAEQIAELKGLSYEEVCEQTTKNAEKLF 1j6oA 166 :LGFLLGIGGPVTYPKNEALREVVKRVGLEYIVLETDCPFLPPQPFRGKRNEPKYLKYVVETISQVLGVPEAKVDEATTENARRIF Number of specific fragments extracted= 3 number of extra gaps= 1 total=6 Will force an alignment to be made, even if fragment is small Number of alignments=2 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1j6oA/T0315-1j6oA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0315 read from 1j6oA/T0315-1j6oA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1j6oA read from 1j6oA/T0315-1j6oA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1j6oA in template set Warning: unaligning (T0315)G91 because of BadResidue code BAD_PEPTIDE in next template residue (1j6oA)E90 Warning: unaligning (T0315)E92 because of BadResidue code BAD_PEPTIDE at template residue (1j6oA)E90 T0315 2 :LIDTHVHLNDEQYDDDLSEVITRAREAGVDRMFVVGFNKSTIERAMKLIDEYDFLYGIIGWHPVDAIDFTEEHLEWIESLAQHPKVIGI 1j6oA 0 :MVDTHAHLHFHQFDDDRNAVISSFEENNIEFVVNVGVNLEDSKKSLDLSKTSDRIFCSVGVHPHDAKEVPEDFIEHLEKFAKDEKVVAI T0315 93 :MGLDYHWDKSPADVQKEVFRKQIALAKRLKLPIIIHNREATQDCIDILLEEHAEEVGGIMHSFSGSPEIADI 1j6oA 91 :TGLDFFRNISPAEVQKRVFVEQIELAGKLNLPLVVHIRDAYSEAYEILRTESLPEKRGVIHAFSSDYEWAKK T0315 166 :TNKLNFYISLGGPVTFKNAKQPKEVAKHVSMERLLVETDAPYLSPHPYRGKRNEPARVTLVAEQIAELKGLSYEEVCEQTTKNAEKLF 1j6oA 163 :FIDLGFLLGIGGPVTYPKNEALREVVKRVGLEYIVLETDCPFLPPQPFRGKRNEPKYLKYVVETISQVLGVPEAKVDEATTENARRIF Number of specific fragments extracted= 3 number of extra gaps= 1 total=9 Will force an alignment to be made, even if fragment is small Number of alignments=3 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1yixA/T0315-1yixA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1yixA expands to /projects/compbio/data/pdb/1yix.pdb.gz 1yixA:# T0315 read from 1yixA/T0315-1yixA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1yixA read from 1yixA/T0315-1yixA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1yixA to template set # found chain 1yixA in template set Warning: unaligning (T0315)G91 because of BadResidue code BAD_PEPTIDE in next template residue (1yixA)E94 Warning: unaligning (T0315)E92 because of BadResidue code BAD_PEPTIDE at template residue (1yixA)E94 T0315 2 :LIDTHVHLNDEQYDD 1yixA 3 :LVDSHCHLDGLDYES T0315 17 :DLSEVITRAREAGVDRMFVVGFNKSTIERAMKLIDEYDFLYGIIGWHPVDAIDFTE 1yixA 21 :DVDDVLAKAAARDVKFCLAVATTLPSYLHMRDLVGERDNVVFSCGVHPLNQNDPYD T0315 75 :LEWIESLAQHPKVIGI 1yixA 77 :VEDLRRLAAEEGVVAL T0315 93 :MGLDYHWDKSPADVQKEVFRKQIALAKRLKLPIIIHNREATQDCIDILLEEHAEEVGGIMHSFSGSPEIADIVTN 1yixA 95 :TGLDYYYTPETKVRQQESFIHHIQIGRELNKPVIVHTRDARADTLAILREEKVTDCGGVLHCFTEDRETAGKLLD T0315 169 :LNFYISLGGPVTFKNAKQPKEVAKHVSMERLLVETDAPYLSPHPYRGKRNEPARVTLVAEQIAELKGLSYEEVCEQTTKNAEKLFNLN 1yixA 170 :LGFYISFSGIVTFRNAEQLRDAARYVPLDRLLVETDSPYLAPVPHRGKENQPAMVRDVAEYMAVLKGVAVEELAQVTTDNFARLFHID Number of specific fragments extracted= 5 number of extra gaps= 1 total=14 Will force an alignment to be made, even if fragment is small Number of alignments=4 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1yixA/T0315-1yixA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0315 read from 1yixA/T0315-1yixA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1yixA read from 1yixA/T0315-1yixA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1yixA in template set Warning: unaligning (T0315)G91 because of BadResidue code BAD_PEPTIDE in next template residue (1yixA)E94 Warning: unaligning (T0315)E92 because of BadResidue code BAD_PEPTIDE at template residue (1yixA)E94 T0315 2 :LIDTHVHLNDEQY 1yixA 3 :LVDSHCHLDGLDY T0315 15 :DDDLSEVITRAREAGVDRMFVVGFNKSTIERAMKLIDEYDFLYGIIGWHPVDAIDFTE 1yixA 19 :HKDVDDVLAKAAARDVKFCLAVATTLPSYLHMRDLVGERDNVVFSCGVHPLNQNDPYD T0315 75 :LEWIESLAQHPKVIGI 1yixA 77 :VEDLRRLAAEEGVVAL T0315 93 :MGLDYHWDKSPADVQKEVFRKQIALAKRLKLPIIIHNREATQDCIDILLEEHAEEVGGIMHSFSGSPEIADIVTN 1yixA 95 :TGLDYYYTPETKVRQQESFIHHIQIGRELNKPVIVHTRDARADTLAILREEKVTDCGGVLHCFTEDRETAGKLLD T0315 169 :LNFYISLGGPVTFKNAKQPKEVAKHVSMERLLVETDAPYLSPHPYRGKRNEPARVTLVAEQIAELKGLSYEEVCEQTTKNAEKLFNLN 1yixA 170 :LGFYISFSGIVTFRNAEQLRDAARYVPLDRLLVETDSPYLAPVPHRGKENQPAMVRDVAEYMAVLKGVAVEELAQVTTDNFARLFHID Number of specific fragments extracted= 5 number of extra gaps= 1 total=19 Will force an alignment to be made, even if fragment is small Number of alignments=5 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1yixA/T0315-1yixA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0315 read from 1yixA/T0315-1yixA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1yixA read from 1yixA/T0315-1yixA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1yixA in template set Warning: unaligning (T0315)G91 because of BadResidue code BAD_PEPTIDE in next template residue (1yixA)E94 Warning: unaligning (T0315)E92 because of BadResidue code BAD_PEPTIDE at template residue (1yixA)E94 T0315 2 :LIDTHVHLNDEQYDD 1yixA 3 :LVDSHCHLDGLDYES T0315 17 :DLSEVITRAREAGVDRMFVVGFNKSTIERAMKLIDEYDFLYGIIGWHPVDAIDFTE 1yixA 21 :DVDDVLAKAAARDVKFCLAVATTLPSYLHMRDLVGERDNVVFSCGVHPLNQNDPYD T0315 75 :LEWIESLAQHPKVIGI 1yixA 77 :VEDLRRLAAEEGVVAL T0315 93 :MGLDYHWDKSPADVQKEVFRKQIALAKRLKLPIIIHNREATQDCIDILLEEHAEEVGGIMHSFSGSPEIADI 1yixA 95 :TGLDYYYTPETKVRQQESFIHHIQIGRELNKPVIVHTRDARADTLAILREEKVTDCGGVLHCFTEDRETAGK T0315 166 :TNKLNFYISLGGPVTFKNAKQPKEVAKHVSMERLLVETDAPYLSPHPYRGKRNEPARVTLVAEQIAELKGLSYEEVCEQTTKNAEKLFNLNS 1yixA 167 :LLDLGFYISFSGIVTFRNAEQLRDAARYVPLDRLLVETDSPYLAPVPHRGKENQPAMVRDVAEYMAVLKGVAVEELAQVTTDNFARLFHIDA Number of specific fragments extracted= 5 number of extra gaps= 1 total=24 Will force an alignment to be made, even if fragment is small Number of alignments=6 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1xwyA/T0315-1xwyA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1xwyA expands to /projects/compbio/data/pdb/1xwy.pdb.gz 1xwyA:# T0315 read from 1xwyA/T0315-1xwyA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1xwyA read from 1xwyA/T0315-1xwyA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1xwyA to template set # found chain 1xwyA in template set Warning: unaligning (T0315)L2 because first residue in template chain is (1xwyA)M1 Warning: unaligning (T0315)G91 because of BadResidue code BAD_PEPTIDE in next template residue (1xwyA)E91 Warning: unaligning (T0315)E92 because of BadResidue code BAD_PEPTIDE at template residue (1xwyA)E91 T0315 3 :IDTHVHLNDEQYDDDLSEVITRAREAGVDRMFVVGFNKSTIERAMKLIDEYDFLYGIIGWHPVDAIDFTEEHLEWIESLAQHPKVIGI 1xwyA 2 :FDIGVNLTSSQFAKDRDDVVACAFDAGVNGLLITGTNLRESQQAQKLARQYSSCWSTAGVHPHDSSQWQAATEEAIIELAAQPEVVAI T0315 93 :MGLDYHWDKSPADVQKEVFRKQIALAKRLKLPIIIHNREATQDCIDIL 1xwyA 92 :CGLDFNRNFSTPEEQERAFVAQLRIAADLNMPVFMHCRDAHERFMTLL T0315 144 :HAEEVG 1xwyA 142 :WLDKLP T0315 150 :GIMHSFSGSPEIADIVTN 1xwyA 149 :AVLHCFTGTREEMQACVA T0315 169 :LNFYISLGGPVTF 1xwyA 167 :HGIYIGITGWVCD T0315 182 :KNAKQPKEVAKHVSMERLLVETDAPYLSPHPYRGK 1xwyA 181 :RRGLELRELLPLIPAEKLLIETDAPYLLPRDLTPK T0315 217 :RNEPARVTLVAEQIAELKGLSYEEVCEQTTKNAEKLFNLN 1xwyA 220 :RNEPAHLPHILQRIAHWRGEDAAWLAATTDANVKTLFGIA Number of specific fragments extracted= 7 number of extra gaps= 1 total=31 Will force an alignment to be made, even if fragment is small Number of alignments=7 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1xwyA/T0315-1xwyA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0315 read from 1xwyA/T0315-1xwyA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1xwyA read from 1xwyA/T0315-1xwyA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1xwyA in template set Warning: unaligning (T0315)L2 because first residue in template chain is (1xwyA)M1 Warning: unaligning (T0315)G91 because of BadResidue code BAD_PEPTIDE in next template residue (1xwyA)E91 Warning: unaligning (T0315)E92 because of BadResidue code BAD_PEPTIDE at template residue (1xwyA)E91 T0315 3 :IDTHVHLNDEQYDDDLSEVITRAREAGVDRMFVVGFNKSTIERAMKLIDEYDFLYGIIGWHPVDAIDFTEEHLEWIESLAQHPKVIGI 1xwyA 2 :FDIGVNLTSSQFAKDRDDVVACAFDAGVNGLLITGTNLRESQQAQKLARQYSSCWSTAGVHPHDSSQWQAATEEAIIELAAQPEVVAI T0315 93 :MGLDYHWDKSPADVQKEVFRKQIALAKRLKLPIIIHNREATQDCIDILLEEHAEEVGGIMHSFSGSPEIADIVTN 1xwyA 92 :CGLDFNRNFSTPEEQERAFVAQLRIAADLNMPVFMHCRDAHERFMTLLEPWLDKLPGAVLHCFTGTREEMQACVA T0315 169 :LNFYISLGGPVT 1xwyA 167 :HGIYIGITGWVC T0315 181 :FKNAKQPKEVAKHVSMERLLVETDAPYLSPHPYRGK 1xwyA 180 :ERRGLELRELLPLIPAEKLLIETDAPYLLPRDLTPK T0315 217 :RNEPARVTLVAEQIAELKGLSYEEVCEQTTKNAEKLFNLN 1xwyA 220 :RNEPAHLPHILQRIAHWRGEDAAWLAATTDANVKTLFGIA Number of specific fragments extracted= 5 number of extra gaps= 1 total=36 Will force an alignment to be made, even if fragment is small Number of alignments=8 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1xwyA/T0315-1xwyA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0315 read from 1xwyA/T0315-1xwyA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1xwyA read from 1xwyA/T0315-1xwyA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1xwyA in template set Warning: unaligning (T0315)L2 because first residue in template chain is (1xwyA)M1 Warning: unaligning (T0315)G91 because of BadResidue code BAD_PEPTIDE in next template residue (1xwyA)E91 Warning: unaligning (T0315)E92 because of BadResidue code BAD_PEPTIDE at template residue (1xwyA)E91 T0315 3 :IDTHVHLNDEQYDDDLSEVITRAREAGVDRMFVVGFNKSTIERAMKLIDEYDFLYGIIGWHPVDAIDFTEEHLEWIESLAQHPKVIGI 1xwyA 2 :FDIGVNLTSSQFAKDRDDVVACAFDAGVNGLLITGTNLRESQQAQKLARQYSSCWSTAGVHPHDSSQWQAATEEAIIELAAQPEVVAI T0315 93 :MGLDYHWDKSPADVQKEVFRKQIALAKRLKLPIIIHNREATQDCIDILLEEHAEEVGGIMHSFSGSPEIADI 1xwyA 92 :CGLDFNRNFSTPEEQERAFVAQLRIAADLNMPVFMHCRDAHERFMTLLEPWLDKLPGAVLHCFTGTREEMQA T0315 166 :TNKLNFYISLGGPVTFK 1xwyA 164 :CVAHGIYIGITGWVCDE T0315 183 :NAKQPKEVAKHVSMERLLVETDAPYLSPHP 1xwyA 182 :RGLELRELLPLIPAEKLLIETDAPYLLPRD T0315 213 :YRGKRNEPARVTLVAEQIAELKGLSYEEVCEQTTKNAEKLFNLNS 1xwyA 216 :PSSRRNEPAHLPHILQRIAHWRGEDAAWLAATTDANVKTLFGIAF Number of specific fragments extracted= 5 number of extra gaps= 1 total=41 Will force an alignment to be made, even if fragment is small Number of alignments=9 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1zzmA/T0315-1zzmA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1zzmA expands to /projects/compbio/data/pdb/1zzm.pdb.gz 1zzmA:# T0315 read from 1zzmA/T0315-1zzmA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1zzmA read from 1zzmA/T0315-1zzmA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1zzmA to template set # found chain 1zzmA in template set Warning: unaligning (T0315)G91 because of BadResidue code BAD_PEPTIDE in next template residue (1zzmA)E97 Warning: unaligning (T0315)E92 because of BadResidue code BAD_PEPTIDE at template residue (1zzmA)E97 Warning: unaligning (T0315)N256 because last residue in template chain is (1zzmA)P259 T0315 1 :MLIDTHVHLNDEQYDDDLSEVITRAREAGVDRMFVVGFNKSTIERAMKLIDEYDFLYGIIGWHPVDAIDFTEEHLEWIESLAQHP 1zzmA 4 :RFIDTHCHFDFPPFSGDEEASLQRAAQAGVGKIIVPATEAENFARVLALAENYQPLYAALGLHPGMLEKHSDVSLEQLQQALERR T0315 86 :KVIGI 1zzmA 91 :KVVAV T0315 93 :MGLDYHWDKSPADVQKEVFRKQIALAKRLKLPIIIHNREATQDCIDILLEEHA 1zzmA 98 :IGLDLFGDDPQFERQQWLLDEQLKLAKRYDLPVILHSRRTHDKLAMHLKRHDL T0315 147 :EVGGIMHSFSGSPEIADIVTN 1zzmA 151 :PRTGVVHGFSGSLQQAERFVQ T0315 169 :LNFYISLGGPVTFKNAKQPKEVAKHVSMERLLVETDAPYLSPHPYRGKRNEPARVTLVAEQIAELKGLSYEEVCEQTTKNAEKLFNL 1zzmA 172 :LGYKIGVGGTITYPRASKTRDVIAKLPLASLLLETDAPDMPLNGFQGQPNRPEQAARVFAVLCELRREPADEIAQALLNNTYTLFNV Number of specific fragments extracted= 5 number of extra gaps= 1 total=46 Will force an alignment to be made, even if fragment is small Number of alignments=10 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1zzmA/T0315-1zzmA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0315 read from 1zzmA/T0315-1zzmA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1zzmA read from 1zzmA/T0315-1zzmA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1zzmA in template set Warning: unaligning (T0315)G91 because of BadResidue code BAD_PEPTIDE in next template residue (1zzmA)E97 Warning: unaligning (T0315)E92 because of BadResidue code BAD_PEPTIDE at template residue (1zzmA)E97 Warning: unaligning (T0315)N256 because last residue in template chain is (1zzmA)P259 T0315 1 :MLIDTHVHLNDEQYDDDLSEVITRAREAGVDRMFVVGFNKSTIERAMKLIDEYDFLYGIIGWHPVDAIDFTEEHLEWIESLAQ 1zzmA 4 :RFIDTHCHFDFPPFSGDEEASLQRAAQAGVGKIIVPATEAENFARVLALAENYQPLYAALGLHPGMLEKHSDVSLEQLQQALE T0315 84 :HPKVIGI 1zzmA 89 :PAKVVAV T0315 93 :MGLDYHWDKSPADVQKEVFRKQIALAKRLKLPIIIHNREATQDCIDILLEEHA 1zzmA 98 :IGLDLFGDDPQFERQQWLLDEQLKLAKRYDLPVILHSRRTHDKLAMHLKRHDL T0315 147 :EVGGIMHSFSGSPEIADIVTN 1zzmA 151 :PRTGVVHGFSGSLQQAERFVQ T0315 169 :LNFYISLGGPVTFKNAKQPKEVAKHVSMERLLVETDAPYLSPHPYRGKRNEPARVTLVAEQIAELKGLSYEEVCEQTTKNAEKLFNL 1zzmA 172 :LGYKIGVGGTITYPRASKTRDVIAKLPLASLLLETDAPDMPLNGFQGQPNRPEQAARVFAVLCELRREPADEIAQALLNNTYTLFNV Number of specific fragments extracted= 5 number of extra gaps= 1 total=51 Will force an alignment to be made, even if fragment is small Number of alignments=11 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1zzmA/T0315-1zzmA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0315 read from 1zzmA/T0315-1zzmA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1zzmA read from 1zzmA/T0315-1zzmA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1zzmA in template set Warning: unaligning (T0315)G91 because of BadResidue code BAD_PEPTIDE in next template residue (1zzmA)E97 Warning: unaligning (T0315)E92 because of BadResidue code BAD_PEPTIDE at template residue (1zzmA)E97 Warning: unaligning (T0315)N256 because last residue in template chain is (1zzmA)P259 T0315 2 :LIDTHVHLNDEQYDDDLSEVITRAREAGVDRMFVVGFNKSTIERAMKLIDEYDFLYGIIGWHPVDAIDFTEEHLEWIESLA 1zzmA 5 :FIDTHCHFDFPPFSGDEEASLQRAAQAGVGKIIVPATEAENFARVLALAENYQPLYAALGLHPGMLEKHSDVSLEQLQQAL T0315 83 :QHPKVIGI 1zzmA 88 :RPAKVVAV T0315 93 :MGLDYHWDKSPADVQKEVFRKQIALAKRLKLPIIIHNREATQDCIDILLEEHAE 1zzmA 98 :IGLDLFGDDPQFERQQWLLDEQLKLAKRYDLPVILHSRRTHDKLAMHLKRHDLP T0315 148 :VGGIMHSFSGSPEIADI 1zzmA 152 :RTGVVHGFSGSLQQAER T0315 166 :TNKLNFYISLGGPVTFKNAKQPKEVAKHVSMERLLVETDAPYLSPHPYRGKRNEPARVTLVAEQIAELKGLSYEEVCEQTTKNAEKLFNL 1zzmA 169 :FVQLGYKIGVGGTITYPRASKTRDVIAKLPLASLLLETDAPDMPLNGFQGQPNRPEQAARVFAVLCELRREPADEIAQALLNNTYTLFNV Number of specific fragments extracted= 5 number of extra gaps= 1 total=56 Will force an alignment to be made, even if fragment is small Number of alignments=12 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1bf6A/T0315-1bf6A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1bf6A expands to /projects/compbio/data/pdb/1bf6.pdb.gz 1bf6A:# T0315 read from 1bf6A/T0315-1bf6A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1bf6A read from 1bf6A/T0315-1bf6A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1bf6A to template set # found chain 1bf6A in template set Warning: unaligning (T0315)G91 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1bf6A)E125 Warning: unaligning (T0315)E92 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1bf6A)E125 T0315 1 :MLIDTHVHL 1bf6A 7 :GYTLAHEHL T0315 10 :NDEQYDD 1bf6A 18 :DLSGFKN T0315 17 :DLSEVITRAREAGVDRMFVVGFNK 1bf6A 35 :FICQEMNDLMTRGVRNVIEMTNRY T0315 41 :STIERAMKLIDEYD 1bf6A 61 :RNAQFMLDVMRETG T0315 55 :FLYGIIGWHPVDAIDFT 1bf6A 76 :NVVACTGYYQDAFFPEH T0315 72 :EEHLEWIESLAQHP 1bf6A 99 :QELAQEMVDEIEQG T0315 86 :KVIGI 1bf6A 119 :KAGII T0315 93 :MGL 1bf6A 126 :IGT T0315 99 :WDKSPADVQKEVFRKQIALAKRLKLPIIIHN 1bf6A 129 :SEGKITPLEEKVFIAAALAHNQTGRPISTHT T0315 130 :REATQDCIDILLEEHAEEVGGIM 1bf6A 162 :STMGLEQLALLQAHGVDLSRVTV T0315 153 :HS 1bf6A 186 :HC T0315 155 :FSGSPEIADIVTN 1bf6A 189 :LKDNLDNILKMID T0315 169 :LNFYISLGGPVTF 1bf6A 202 :LGAYVQFDTIGKN T0315 182 :KNA 1bf6A 217 :YPD T0315 185 :KQPKEVAKHVSMERLLVETDAPYLSPHPYRGKRNEPARVTLVAEQIAE 1bf6A 224 :AMLHALRDRGLLNRVMLSMDITRRSHLKANGGYGYDYLLTTFIPQLRQ T0315 234 :KGLSYEEVCEQTTKNAEKLF 1bf6A 272 :SGFSQADVDVMLRENPSQFF Number of specific fragments extracted= 16 number of extra gaps= 1 total=72 Will force an alignment to be made, even if fragment is small Number of alignments=13 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1bf6A/T0315-1bf6A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0315 read from 1bf6A/T0315-1bf6A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1bf6A read from 1bf6A/T0315-1bf6A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1bf6A in template set Warning: unaligning (T0315)G91 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1bf6A)E125 Warning: unaligning (T0315)E92 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1bf6A)E125 T0315 1 :MLIDTHVHL 1bf6A 7 :GYTLAHEHL T0315 10 :NDEQY 1bf6A 18 :DLSGF T0315 15 :DDDLSEVITRAREAGVDRMFVVGFNK 1bf6A 33 :YAFICQEMNDLMTRGVRNVIEMTNRY T0315 41 :STIERAMKLIDEYD 1bf6A 61 :RNAQFMLDVMRETG T0315 55 :FLYGIIGWHPVDA 1bf6A 76 :NVVACTGYYQDAF T0315 68 :IDF 1bf6A 90 :PEH T0315 71 :TEEHLEWIESLAQ 1bf6A 98 :VQELAQEMVDEIE T0315 84 :HPKVIGI 1bf6A 117 :ELKAGII T0315 93 :MGLD 1bf6A 126 :IGTS T0315 100 :DKSPADVQKEVFRKQIALAKRLKLPIIIHNRE 1bf6A 130 :EGKITPLEEKVFIAAALAHNQTGRPISTHTSF T0315 132 :ATQDCIDILLEEHAEEVGGIM 1bf6A 164 :MGLEQLALLQAHGVDLSRVTV T0315 153 :HSFSG 1bf6A 186 :HCDLK T0315 158 :SPEIADIVTN 1bf6A 192 :NLDNILKMID T0315 169 :LNFYISLGGPVT 1bf6A 202 :LGAYVQFDTIGK T0315 181 :FKNAKQ 1bf6A 216 :YYPDEK T0315 187 :PKEVAKHVSMERLLVETDAPYLSPHPYRGKRNEPARVTLVAEQIAEL 1bf6A 226 :LHALRDRGLLNRVMLSMDITRRSHLKANGGYGYDYLLTTFIPQLRQS T0315 235 :GLSYEEVCEQTTKNAEKLF 1bf6A 273 :GFSQADVDVMLRENPSQFF Number of specific fragments extracted= 17 number of extra gaps= 1 total=89 Will force an alignment to be made, even if fragment is small Number of alignments=14 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1bf6A/T0315-1bf6A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0315 read from 1bf6A/T0315-1bf6A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1bf6A read from 1bf6A/T0315-1bf6A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1bf6A in template set Warning: unaligning (T0315)G91 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1bf6A)E125 Warning: unaligning (T0315)E92 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1bf6A)E125 T0315 2 :LIDTHVHLNDEQYDD 1bf6A 10 :LAHEHLHIDLSGFKN T0315 17 :DLSEVITRAREAGVDRMFVVGFNKS 1bf6A 35 :FICQEMNDLMTRGVRNVIEMTNRYM T0315 43 :IERAMKLIDEYDF 1bf6A 63 :AQFMLDVMRETGI T0315 56 :LYGIIGWHPVDAIDFT 1bf6A 77 :VVACTGYYQDAFFPEH T0315 72 :EEHLEWIESLA 1bf6A 99 :QELAQEMVDEI T0315 84 :HPKVIGI 1bf6A 117 :ELKAGII T0315 93 :MGLD 1bf6A 126 :IGTS T0315 100 :DKSPADVQKEVFRKQIALAKRLKLPIIIHN 1bf6A 130 :EGKITPLEEKVFIAAALAHNQTGRPISTHT T0315 130 :REATQDCIDILLEEHAEEVGGIMHSF 1bf6A 162 :STMGLEQLALLQAHGVDLSRVTVGHC T0315 156 :SGSPEIADI 1bf6A 190 :KDNLDNILK T0315 166 :TNKLNFYISLGGPVTFK 1bf6A 199 :MIDLGAYVQFDTIGKNS T0315 183 :NAKQPKEVAKHV 1bf6A 218 :PDEKRIAMLHAL T0315 195 :SMERLLVETDAPYLSPHPYRGKRNEPARVTLVAEQIAE 1bf6A 234 :LLNRVMLSMDITRRSHLKANGGYGYDYLLTTFIPQLRQ T0315 234 :KGLSYEEVCEQTTKNAEKLF 1bf6A 272 :SGFSQADVDVMLRENPSQFF Number of specific fragments extracted= 14 number of extra gaps= 1 total=103 Will force an alignment to be made, even if fragment is small Number of alignments=15 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1i0dA/T0315-1i0dA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1i0dA expands to /projects/compbio/data/pdb/1i0d.pdb.gz 1i0dA:Skipped atom 584, because occupancy 0.5 <= existing 0.500 in 1i0dA Skipped atom 586, because occupancy 0.500 <= existing 0.500 in 1i0dA Skipped atom 593, because occupancy 0.500 <= existing 0.500 in 1i0dA Skipped atom 953, because occupancy 0.500 <= existing 0.500 in 1i0dA Skipped atom 955, because occupancy 0.500 <= existing 0.500 in 1i0dA Skipped atom 957, because occupancy 0.500 <= existing 0.500 in 1i0dA Skipped atom 959, because occupancy 0.500 <= existing 0.500 in 1i0dA Skipped atom 961, because occupancy 0.500 <= existing 0.500 in 1i0dA Skipped atom 963, because occupancy 0.500 <= existing 0.500 in 1i0dA Skipped atom 965, because occupancy 0.500 <= existing 0.500 in 1i0dA Skipped atom 967, because occupancy 0.500 <= existing 0.500 in 1i0dA Skipped atom 1246, because occupancy 0.500 <= existing 0.500 in 1i0dA Skipped atom 1248, because occupancy 0.500 <= existing 0.500 in 1i0dA Skipped atom 1250, because occupancy 0.500 <= existing 0.500 in 1i0dA Skipped atom 1442, because occupancy 0.300 <= existing 0.700 in 1i0dA Skipped atom 1561, because occupancy 0.500 <= existing 0.500 in 1i0dA Skipped atom 1587, because occupancy 0.500 <= existing 0.500 in 1i0dA Skipped atom 1589, because occupancy 0.500 <= existing 0.500 in 1i0dA Skipped atom 1591, because occupancy 0.500 <= existing 0.500 in 1i0dA Skipped atom 1997, because occupancy 0.330 <= existing 0.330 in 1i0dA Skipped atom 1998, because occupancy 0.330 <= existing 0.330 in 1i0dA Skipped atom 2000, because occupancy 0.330 <= existing 0.330 in 1i0dA Skipped atom 2001, because occupancy 0.330 <= existing 0.330 in 1i0dA Skipped atom 2003, because occupancy 0.330 <= existing 0.330 in 1i0dA Skipped atom 2004, because occupancy 0.330 <= existing 0.330 in 1i0dA Skipped atom 2006, because occupancy 0.330 <= existing 0.330 in 1i0dA Skipped atom 2007, because occupancy 0.330 <= existing 0.330 in 1i0dA Skipped atom 2512, because occupancy 0.500 <= existing 0.500 in 1i0dA # T0315 read from 1i0dA/T0315-1i0dA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1i0dA read from 1i0dA/T0315-1i0dA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1i0dA to template set # found chain 1i0dA in template set T0315 1 :MLIDTHVHLN 1i0dA 50 :GFTLTHEHIC T0315 11 :DEQYDDDLSEV 1i0dA 69 :WPEFFGSRKAL T0315 22 :ITRAREAGVDRMFVVGF 1i0dA 87 :LRRARAAGVRTIVDVST T0315 42 :TIERAMKLIDEYD 1i0dA 109 :DVSLLAEVSRAAD T0315 55 :FLYGIIGWH 1i0dA 123 :HIVAATGLW T0315 64 :PVDAIDFT 1i0dA 135 :PLSMRLRS T0315 72 :EEHLEWIESLAQHP 1i0dA 144 :EELTQFFLREIQYG T0315 86 :KVIGIG 1i0dA 166 :GIIKVA T0315 99 :WDKSPADVQKEVFRKQIALAKRLKLPIIIHN 1i0dA 172 :TTGKATPFQELVLKAAARASLATGVPVTTHT T0315 130 :REATQDCIDILLEEHAEEVGGIM 1i0dA 206 :QRDGEQQAAIFESEGLSPSRVCI T0315 153 :HS 1i0dA 230 :HS T0315 155 :FSGSPEIADIVTN 1i0dA 233 :DTDDLSYLTALAA T0315 169 :LNFYISLGGPVTF 1i0dA 246 :RGYLIGLDHIPHS T0315 182 :KNAKQPKEVAKHVSMERLLVETDAPYLSPH 1i0dA 279 :TRALLIKALIDQGYMKQILVSNDWLFGFSS T0315 217 :RNEPARVTL 1i0dA 322 :PDGMAFIPL T0315 226 :VAEQIAE 1i0dA 332 :VIPFLRE T0315 234 :KGLSYEEVCEQTTKNAEKLFNLN 1i0dA 339 :KGVPQETLAGITVTNPARFLSPT Number of specific fragments extracted= 17 number of extra gaps= 0 total=120 Will force an alignment to be made, even if fragment is small Number of alignments=16 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1i0dA/T0315-1i0dA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0315 read from 1i0dA/T0315-1i0dA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1i0dA read from 1i0dA/T0315-1i0dA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1i0dA in template set T0315 1 :MLIDTHVHL 1i0dA 50 :GFTLTHEHI T0315 10 :NDEQY 1i0dA 69 :WPEFF T0315 15 :DDDLSEVITRAREAGVDRMFVVGF 1i0dA 80 :AEKAVRGLRRARAAGVRTIVDVST T0315 41 :STIERAMKLIDEYD 1i0dA 108 :RDVSLLAEVSRAAD T0315 55 :FLYGIIGWHPV 1i0dA 123 :HIVAATGLWFD T0315 68 :IDFT 1i0dA 139 :RLRS T0315 72 :EEHLEWIESLAQ 1i0dA 144 :EELTQFFLREIQ T0315 84 :HPKVIG 1i0dA 160 :DTGIRA T0315 91 :GEMG 1i0dA 166 :GIIK T0315 97 :YHWDKSPADVQKEVFRKQIALAKRLKLPIIIHN 1i0dA 170 :VATTGKATPFQELVLKAAARASLATGVPVTTHT T0315 130 :REATQDCIDILLEEHAEEVGGIM 1i0dA 206 :QRDGEQQAAIFESEGLSPSRVCI T0315 153 :HSF 1i0dA 230 :HSD T0315 156 :SGSPEIADIVTN 1i0dA 234 :TDDLSYLTALAA T0315 169 :LNFYISLGGPVTF 1i0dA 246 :RGYLIGLDHIPHS T0315 182 :KNAKQ 1i0dA 275 :RSWQT T0315 187 :PKEVAKHVSMERLLVETDAPYLSPHPYRGK 1i0dA 284 :IKALIDQGYMKQILVSNDWLFGFSSYVTNI T0315 217 :RNEPARVTL 1i0dA 322 :PDGMAFIPL T0315 226 :VAEQIAEL 1i0dA 332 :VIPFLREK T0315 235 :GLSYEEVCEQTTKNAEKLFNLN 1i0dA 340 :GVPQETLAGITVTNPARFLSPT Number of specific fragments extracted= 19 number of extra gaps= 0 total=139 Will force an alignment to be made, even if fragment is small Number of alignments=17 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1i0dA/T0315-1i0dA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0315 read from 1i0dA/T0315-1i0dA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1i0dA read from 1i0dA/T0315-1i0dA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1i0dA in template set T0315 2 :LIDTHVHL 1i0dA 51 :FTLTHEHI T0315 11 :DEQYDDDLSEVITRA 1i0dA 69 :WPEFFGSRKALAEKA T0315 26 :REAGVDRMFVVGF 1i0dA 91 :RAAGVRTIVDVST T0315 43 :IERAMKLIDEYDF 1i0dA 110 :VSLLAEVSRAADV T0315 56 :LYGIIGW 1i0dA 124 :IVAATGL T0315 63 :HPVDAIDFT 1i0dA 134 :PPLSMRLRS T0315 72 :EEHLEWIESLA 1i0dA 144 :EELTQFFLREI T0315 84 :HPKVIGIGE 1i0dA 164 :RAGIIKVAT T0315 100 :DKSPADVQKEVFRKQIALAKRLKLPIIIHN 1i0dA 173 :TGKATPFQELVLKAAARASLATGVPVTTHT T0315 130 :REATQDCIDILLEEHAE 1i0dA 206 :QRDGEQQAAIFESEGLS T0315 148 :VGGIMHSF 1i0dA 223 :PSRVCIGH T0315 156 :SGSPEIADI 1i0dA 234 :TDDLSYLTA T0315 166 :TNKLNFYISLGGPV 1i0dA 243 :LAARGYLIGLDHIP T0315 180 :TFKNAKQPKEVAKHVS 1i0dA 261 :GLEDNASASALLGIRS T0315 196 :MERLLVETDAPYLSPHP 1i0dA 293 :MKQILVSNDWLFGFSSY T0315 220 :PARVTL 1i0dA 325 :MAFIPL T0315 226 :VAEQIAE 1i0dA 332 :VIPFLRE T0315 234 :KGLSYEEVCEQTTKNAEKLFNLNS 1i0dA 339 :KGVPQETLAGITVTNPARFLSPTL Number of specific fragments extracted= 18 number of extra gaps= 0 total=157 Will force an alignment to be made, even if fragment is small Number of alignments=18 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2d2jA/T0315-2d2jA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2d2jA expands to /projects/compbio/data/pdb/2d2j.pdb.gz 2d2jA:# T0315 read from 2d2jA/T0315-2d2jA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2d2jA read from 2d2jA/T0315-2d2jA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2d2jA to template set # found chain 2d2jA in template set Warning: unaligning (T0315)M93 because of BadResidue code BAD_PEPTIDE in next template residue (2d2jA)T172 Warning: unaligning (T0315)W99 because of BadResidue code BAD_PEPTIDE at template residue (2d2jA)T172 Warning: unaligning (T0315)N129 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2d2jA)S203 Warning: unaligning (T0315)L175 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2d2jA)D253 Warning: unaligning (T0315)G176 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2d2jA)D253 T0315 1 :MLIDTHVHLN 2d2jA 50 :GFTLTHEHIC T0315 11 :DEQYDDDLSEVITR 2d2jA 69 :WPEFFGSRKALAEK T0315 25 :AREAGVDRMFVVGF 2d2jA 90 :ARAAGVQTIVDVST T0315 42 :TIERAMKLIDEYD 2d2jA 109 :DVRLLAEVSRAAD T0315 55 :FLYGIIGWH 2d2jA 123 :HIVAATGLW T0315 64 :PVDAIDFT 2d2jA 135 :PLSMRMRS T0315 72 :EEHLEWIESLAQHP 2d2jA 144 :EELTQFFLREIQHG T0315 86 :KVIGIGE 2d2jA 164 :RAGIIKV T0315 100 :DKSPADVQKEVFRKQIALAKRLKLPIIIH 2d2jA 173 :TGKATPFQELVLKAAARASLATGVPVTTH T0315 130 :REATQDCIDILLEEHAEEVGGIM 2d2jA 206 :QRDGEQQAAIFESEGLSPSRVCI T0315 153 :HS 2d2jA 230 :HS T0315 155 :FSGSPEIADIVTN 2d2jA 233 :DTDDLSYLTGLAA T0315 169 :LNFYIS 2d2jA 246 :RGYLVG T0315 177 :GPVTF 2d2jA 254 :RMPYS T0315 182 :KNAKQPKEVAKHVSMERLLVETDAPYLSPH 2d2jA 279 :TRALLIKALIDRGYKDRILVSHDWLFGFSS T0315 218 :NEPARVTLVAEQIAE 2d2jA 324 :GMAFVPLRVIPFLRE T0315 234 :KGLSYEEVCEQTTKNAEKLFNL 2d2jA 339 :KGVPPETLAGVTVANPARFLSP Number of specific fragments extracted= 17 number of extra gaps= 3 total=174 Will force an alignment to be made, even if fragment is small Number of alignments=19 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2d2jA/T0315-2d2jA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0315 read from 2d2jA/T0315-2d2jA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2d2jA read from 2d2jA/T0315-2d2jA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2d2jA in template set Warning: unaligning (T0315)H98 because of BadResidue code BAD_PEPTIDE in next template residue (2d2jA)T172 Warning: unaligning (T0315)W99 because of BadResidue code BAD_PEPTIDE at template residue (2d2jA)T172 Warning: unaligning (T0315)N129 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2d2jA)S203 Warning: unaligning (T0315)R130 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2d2jA)S203 Warning: unaligning (T0315)L175 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2d2jA)D253 Warning: unaligning (T0315)G176 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2d2jA)D253 T0315 1 :MLIDTHVHL 2d2jA 50 :GFTLTHEHI T0315 10 :NDEQY 2d2jA 69 :WPEFF T0315 15 :DDDLSEVITRAREAGVDRMFVVGF 2d2jA 80 :AEKAVRGLRHARAAGVQTIVDVST T0315 41 :STIERAMKLIDEYD 2d2jA 108 :RDVRLLAEVSRAAD T0315 55 :FLYGIIGWHPV 2d2jA 123 :HIVAATGLWFD T0315 66 :DA 2d2jA 142 :SV T0315 72 :EEHLEWIESLAQ 2d2jA 144 :EELTQFFLREIQ T0315 84 :HPKVIG 2d2jA 160 :DTGIRA T0315 91 :GEMG 2d2jA 166 :GIIK T0315 97 :Y 2d2jA 170 :V T0315 100 :DKSPADVQKEVFRKQIALAKRLKLPIIIH 2d2jA 173 :TGKATPFQELVLKAAARASLATGVPVTTH T0315 132 :ATQDCIDILLEEHAEEVGGIM 2d2jA 208 :DGEQQAAIFESEGLSPSRVCI T0315 153 :HSF 2d2jA 230 :HSD T0315 156 :SGSPEIADIVTN 2d2jA 234 :TDDLSYLTGLAA T0315 169 :LNFYIS 2d2jA 246 :RGYLVG T0315 177 :GPVTF 2d2jA 255 :MPYSA T0315 182 :KN 2d2jA 275 :RS T0315 187 :PKEVAKHVSMERLLVETDAPYLSPHPYRGK 2d2jA 284 :IKALIDRGYKDRILVSHDWLFGFSSYVTNI T0315 217 :RNEPARVTL 2d2jA 322 :PDGMAFVPL T0315 226 :VAEQIAEL 2d2jA 332 :VIPFLREK T0315 235 :GLSYEEVCEQTTKNAEKLFNL 2d2jA 340 :GVPPETLAGVTVANPARFLSP Number of specific fragments extracted= 21 number of extra gaps= 3 total=195 Will force an alignment to be made, even if fragment is small Number of alignments=20 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2d2jA/T0315-2d2jA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0315 read from 2d2jA/T0315-2d2jA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2d2jA read from 2d2jA/T0315-2d2jA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2d2jA in template set Warning: unaligning (T0315)G91 because of BadResidue code BAD_PEPTIDE in next template residue (2d2jA)T172 Warning: unaligning (T0315)E92 because of BadResidue code BAD_PEPTIDE at template residue (2d2jA)T172 Warning: unaligning (T0315)N129 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2d2jA)S203 Warning: unaligning (T0315)L175 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2d2jA)D253 Warning: unaligning (T0315)G176 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2d2jA)D253 T0315 2 :LIDTHVHL 2d2jA 51 :FTLTHEHI T0315 11 :DEQYDDDLSEVITRA 2d2jA 69 :WPEFFGSRKALAEKA T0315 26 :REAGVDRMFVVGF 2d2jA 91 :RAAGVQTIVDVST T0315 43 :IERAMKLIDEYDF 2d2jA 110 :VRLLAEVSRAADV T0315 56 :LYGIIGW 2d2jA 124 :IVAATGL T0315 63 :HPVDAIDFT 2d2jA 134 :PPLSMRMRS T0315 72 :EEHLEWIESLA 2d2jA 144 :EELTQFFLREI T0315 84 :HPKVIGI 2d2jA 164 :RAGIIKV T0315 100 :DKSPADVQKEVFRKQIALAKRLKLPIIIH 2d2jA 173 :TGKATPFQELVLKAAARASLATGVPVTTH T0315 130 :REATQDCIDILLEEHAEEVGGIM 2d2jA 206 :QRDGEQQAAIFESEGLSPSRVCI T0315 154 :SF 2d2jA 229 :GH T0315 156 :SGSPEIADI 2d2jA 234 :TDDLSYLTG T0315 166 :TNKLNFYIS 2d2jA 243 :LAARGYLVG T0315 177 :GPVT 2d2jA 254 :RMPY T0315 181 :FKNAKQPKEVAKHVS 2d2jA 262 :LEGNASALALFGTRS T0315 196 :MERLLVETDAPYLSPHP 2d2jA 293 :KDRILVSHDWLFGFSSY T0315 221 :ARVTL 2d2jA 326 :AFVPL T0315 226 :VAEQI 2d2jA 332 :VIPFL T0315 232 :ELKGLSYEEVCEQTTKNAEKLFN 2d2jA 337 :REKGVPPETLAGVTVANPARFLS Number of specific fragments extracted= 19 number of extra gaps= 3 total=214 Will force an alignment to be made, even if fragment is small Number of alignments=21 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1xrtA/T0315-1xrtA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1xrtA expands to /projects/compbio/data/pdb/1xrt.pdb.gz 1xrtA:# T0315 read from 1xrtA/T0315-1xrtA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1xrtA read from 1xrtA/T0315-1xrtA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1xrtA to template set # found chain 1xrtA in template set Warning: unaligning (T0315)M93 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1xrtA)G154 Warning: unaligning (T0315)G94 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1xrtA)G154 Warning: unaligning (T0315)E131 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1xrtA)A209 Warning: unaligning (T0315)K182 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1xrtA)E285 Warning: unaligning (T0315)P212 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1xrtA)G323 T0315 1 :MLIDTHVHLNDEQYDD 1xrtA 56 :GFIDIHVHLRDPGQTY T0315 17 :DLSEVITRAREAGVDRMFVVG 1xrtA 74 :DIESGSRCAVAGGFTTIVCMP T0315 38 :FN 1xrtA 96 :TN T0315 40 :KSTIERAMKLIDEYD 1xrtA 103 :TTVVNYILQKSKSVG T0315 55 :FLYGIIGWHPVDAIDFT 1xrtA 119 :CRVLPTGTITKGRKGKE T0315 72 :EEHLEW 1xrtA 140 :YSLKEA T0315 86 :KVIGIGE 1xrtA 146 :GCVAFTD T0315 95 :LDYH 1xrtA 155 :SPVM T0315 103 :P 1xrtA 159 :D T0315 108 :KEVFRKQIALAKRLKLPIIIHN 1xrtA 160 :SSVMRKALELASQLGVPIMDHC T0315 132 :ATQ 1xrtA 210 :EEI T0315 135 :DCIDILLEE 1xrtA 216 :RDGILAQRT T0315 147 :EVGGIM 1xrtA 225 :GGHVHI T0315 153 :HSF 1xrtA 232 :HVS T0315 157 :GSP 1xrtA 235 :TKL T0315 160 :EIADIVTN 1xrtA 240 :EIIEFFKE T0315 169 :LNFYISLGGPVTF 1xrtA 248 :KGVKITCEVNPNH T0315 183 :NAKQPKEVAKHVSME 1xrtA 286 :DRLALIEGVKRGIID T0315 200 :LVETD 1xrtA 301 :CFATD T0315 207 :YLSPH 1xrtA 306 :HAPHQ T0315 217 :RNEPARVTLVAEQIAE 1xrtA 324 :IIGLQTALPSALELYR T0315 234 :KGL 1xrtA 340 :KGI T0315 237 :SYEEVCEQTTKNAEKLFNLN 1xrtA 344 :SLKKLIEMFTINPARIIGVD Number of specific fragments extracted= 23 number of extra gaps= 1 total=237 Will force an alignment to be made, even if fragment is small Number of alignments=22 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1xrtA/T0315-1xrtA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0315 read from 1xrtA/T0315-1xrtA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1xrtA read from 1xrtA/T0315-1xrtA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1xrtA in template set Warning: unaligning (T0315)D100 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1xrtA)G154 Warning: unaligning (T0315)K101 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1xrtA)G154 Warning: unaligning (T0315)K182 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1xrtA)E285 Warning: unaligning (T0315)S209 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1xrtA)G323 T0315 1 :MLIDTHVHLNDEQYDD 1xrtA 56 :GFIDIHVHLRDPGQTY T0315 17 :DLSEVITRAREAGVDRMFVV 1xrtA 74 :DIESGSRCAVAGGFTTIVCM T0315 37 :GF 1xrtA 99 :PI T0315 41 :STIERAMKLIDEYDFLYGIIGWHPV 1xrtA 104 :TVVNYILQKSKSVGLCRVLPTGTIT T0315 66 :DAIDF 1xrtA 130 :GRKGK T0315 72 :EEHLEW 1xrtA 140 :YSLKEA T0315 86 :KVIG 1xrtA 146 :GCVA T0315 97 :YHW 1xrtA 150 :FTD T0315 102 :SP 1xrtA 155 :SP T0315 104 :A 1xrtA 158 :M T0315 107 :QKEVFRKQIALAKRLKLPIIIHNRE 1xrtA 159 :DSSVMRKALELASQLGVPIMDHCED T0315 132 :ATQDCIDILLEE 1xrtA 213 :QIARDGILAQRT T0315 146 :EEVGGIMHSFSG 1xrtA 225 :GGHVHIQHVSTK T0315 158 :SPEIADIVTN 1xrtA 238 :SLEIIEFFKE T0315 169 :LNFYISLGGPVTF 1xrtA 248 :KGVKITCEVNPNH T0315 183 :NAKQPKEVAKHVSME 1xrtA 286 :DRLALIEGVKRGIID T0315 200 :LVETD 1xrtA 301 :CFATD T0315 205 :APYL 1xrtA 307 :APHQ T0315 217 :RNEPARVTLVAEQIAE 1xrtA 324 :IIGLQTALPSALELYR T0315 234 :KG 1xrtA 340 :KG T0315 236 :LSYEEVCEQTTKNAEKLFNLN 1xrtA 343 :ISLKKLIEMFTINPARIIGVD Number of specific fragments extracted= 21 number of extra gaps= 1 total=258 Will force an alignment to be made, even if fragment is small Number of alignments=23 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1xrtA/T0315-1xrtA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0315 read from 1xrtA/T0315-1xrtA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1xrtA read from 1xrtA/T0315-1xrtA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1xrtA in template set Warning: unaligning (T0315)M93 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1xrtA)G154 Warning: unaligning (T0315)G94 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1xrtA)G154 Warning: unaligning (T0315)R130 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1xrtA)L186 Warning: unaligning (T0315)E131 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1xrtA)L186 Warning: unaligning (T0315)A132 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1xrtA)A187 Warning: unaligning (T0315)T133 because of BadResidue code BAD_PEPTIDE at template residue (1xrtA)Y188 Warning: unaligning (T0315)G157 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1xrtA)A209 Warning: unaligning (T0315)L208 because of BadResidue code BAD_PEPTIDE in next template residue (1xrtA)L262 Warning: unaligning (T0315)S209 because of BadResidue code BAD_PEPTIDE at template residue (1xrtA)L262 Warning: unaligning (T0315)K216 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1xrtA)G323 T0315 2 :LIDTHVHLNDEQYDD 1xrtA 57 :FIDIHVHLRDPGQTY T0315 17 :DLSEVITRAREAGVDRMFVV 1xrtA 74 :DIESGSRCAVAGGFTTIVCM T0315 37 :GFNKSTIERAMKLIDEYDF 1xrtA 100 :IDNTTVVNYILQKSKSVGL T0315 56 :LYGIIGWHPVDAIDFT 1xrtA 120 :RVLPTGTITKGRKGKE T0315 72 :EEHLEW 1xrtA 140 :YSLKEA T0315 86 :KVIGIGE 1xrtA 146 :GCVAFTD T0315 95 :LDY 1xrtA 155 :SPV T0315 102 :SPAD 1xrtA 158 :MDSS T0315 110 :VFRKQIALAKRLKLPIIIHN 1xrtA 162 :VMRKALELASQLGVPIMDHC T0315 158 :SPEIADI 1xrtA 210 :EEIQIAR T0315 165 :VTNKLNFYISLGGPVTFKNAKQPKEVAKH 1xrtA 220 :LAQRTGGHVHIQHVSTKLSLEIIEFFKEK T0315 198 :RLLVETDAPY 1xrtA 251 :KITCEVNPNH T0315 217 :RNEPARVTLVAEQIAE 1xrtA 324 :IIGLQTALPSALELYR T0315 234 :KGL 1xrtA 340 :KGI T0315 237 :SYEEVCEQTTKNAEKLFNLN 1xrtA 344 :SLKKLIEMFTINPARIIGVD Number of specific fragments extracted= 15 number of extra gaps= 3 total=273 Will force an alignment to be made, even if fragment is small Number of alignments=24 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2gwgA/T0315-2gwgA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2gwgA expands to /projects/compbio/data/pdb/2gwg.pdb.gz 2gwgA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0315 read from 2gwgA/T0315-2gwgA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2gwgA read from 2gwgA/T0315-2gwgA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2gwgA to template set # found chain 2gwgA in template set Warning: unaligning (T0315)N39 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2gwgA)G80 T0315 1 :MLIDTHVHLN 2gwgA 1 :MIIDIHGHYT T0315 15 :DD 2gwgA 13 :PK T0315 17 :DLSEV 2gwgA 45 :ELQAS T0315 22 :ITRAREAGVDRMFVVGF 2gwgA 55 :LKKMQERGSDLTVFSPR T0315 43 :IERAMKLIDEYD 2gwgA 93 :NELCYRVSQLFP T0315 55 :FLYGIIGWH 2gwgA 106 :NFIGAAMLP T0315 64 :PVDA 2gwgA 121 :PKTC T0315 75 :LEWIESLAQHPKVIGIGE 2gwgA 125 :IPELEKCVKEYGFVAINL T0315 94 :GLDY 2gwgA 143 :NPDP T0315 98 :HWDKSP 2gwgA 150 :HWTSPP T0315 112 :RKQIALAKRLKLPIIIHN 2gwgA 162 :YPIYEKMVELEIPAMIHV T0315 134 :QDCID 2gwgA 203 :MQCVA T0315 139 :ILLEE 2gwgA 210 :LFKDF T0315 146 :EEVGGIM 2gwgA 215 :PELKFVI T0315 153 :HSFSG 2gwgA 223 :HGGGA T0315 158 :SPEIADIVTN 2gwgA 231 :HWGRFRGLAQ T0315 168 :KLNFYISL 2gwgA 252 :LNNIFFDT T0315 178 :PVT 2gwgA 260 :CVY T0315 183 :NAKQPKEVAKHVSMERLLVETDAP 2gwgA 263 :HQPGIDLLNTVIPVDNVLFASEMI T0315 208 :LSPH 2gwgA 287 :GAVR T0315 212 :PYRGKRNEP 2gwgA 294 :PRTGFYYDD T0315 223 :V 2gwgA 303 :T T0315 227 :AEQIAELKGLSYEEVCEQTTKNAEKLF 2gwgA 304 :KRYIEASTILTPEEKQQIYEGNARRVY Number of specific fragments extracted= 23 number of extra gaps= 0 total=296 Will force an alignment to be made, even if fragment is small Number of alignments=25 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2gwgA/T0315-2gwgA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0315 read from 2gwgA/T0315-2gwgA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2gwgA read from 2gwgA/T0315-2gwgA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2gwgA in template set Warning: unaligning (T0315)N39 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2gwgA)G80 Warning: unaligning (T0315)R130 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2gwgA)T190 Warning: unaligning (T0315)E131 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2gwgA)T190 T0315 1 :MLIDTHVHLNDEQY 2gwgA 1 :MIIDIHGHYTTAPK T0315 15 :DDDLSE 2gwgA 43 :DDELQA T0315 21 :VITRAREAGVDRMFVVGF 2gwgA 54 :QLKKMQERGSDLTVFSPR T0315 43 :IERAMKLIDEYDFLYGIIGWHPV 2gwgA 93 :NELCYRVSQLFPDNFIGAAMLPQ T0315 66 :DA 2gwgA 120 :DP T0315 72 :EEHLEWIESLAQHPKVIGIG 2gwgA 122 :KTCIPELEKCVKEYGFVAIN T0315 95 :LDYHWDKSPAD 2gwgA 142 :LNPDPSGGHWT T0315 106 :VQKEVFRKQIALAKRLKLPIIIHN 2gwgA 156 :LTDRIWYPIYEKMVELEIPAMIHV T0315 132 :ATQDCID 2gwgA 201 :AFMQCVA T0315 140 :LLEEHAEEVGGIMHSFSG 2gwgA 210 :LFKDFPELKFVIPHGGGA T0315 158 :SPEIADIVTN 2gwgA 231 :HWGRFRGLAQ T0315 168 :K 2gwgA 242 :M T0315 169 :LNFYISLGG 2gwgA 253 :NNIFFDTCV T0315 182 :KNAKQPKEVAKHVSMERLLVETD 2gwgA 262 :YHQPGIDLLNTVIPVDNVLFASE T0315 205 :APYLSPHPYRGKRNE 2gwgA 287 :GAVRGIDPRTGFYYD T0315 222 :RVTLVAEQ 2gwgA 302 :DTKRYIEA T0315 233 :L 2gwgA 310 :S T0315 235 :G 2gwgA 311 :T T0315 236 :LSYEEVCEQTTKNAEKLF 2gwgA 313 :LTPEEKQQIYEGNARRVY Number of specific fragments extracted= 19 number of extra gaps= 1 total=315 Will force an alignment to be made, even if fragment is small Number of alignments=26 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2gwgA/T0315-2gwgA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0315 read from 2gwgA/T0315-2gwgA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2gwgA read from 2gwgA/T0315-2gwgA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2gwgA in template set Warning: unaligning (T0315)N39 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2gwgA)G80 T0315 1 :MLIDTHVHL 2gwgA 1 :MIIDIHGHY T0315 11 :DEQYD 2gwgA 36 :VSELK T0315 16 :DDLSE 2gwgA 44 :DELQA T0315 21 :VITRAREAGVDRMFVVGF 2gwgA 54 :QLKKMQERGSDLTVFSPR T0315 43 :IERAMKLIDEYDFLYGIIGWHPVD 2gwgA 93 :NELCYRVSQLFPDNFIGAAMLPQS T0315 68 :IDFT 2gwgA 117 :PGVD T0315 72 :EEHLEWIESLAQHPKVIGIG 2gwgA 122 :KTCIPELEKCVKEYGFVAIN T0315 95 :LDYHW 2gwgA 142 :LNPDP T0315 101 :KSP 2gwgA 150 :HWT T0315 112 :RKQIALAKRLKLPIIIHN 2gwgA 162 :YPIYEKMVELEIPAMIHV T0315 130 :REATQDCIDILLE 2gwgA 195 :LNADTTAFMQCVA T0315 145 :AEEVGGIM 2gwgA 214 :FPELKFVI T0315 159 :PEIADIVTNKL 2gwgA 232 :WGRFRGLAQEM T0315 173 :ISLGGPVT 2gwgA 255 :IFFDTCVY T0315 183 :NAKQPKEVAKHVSMERLLVETDAP 2gwgA 263 :HQPGIDLLNTVIPVDNVLFASEMI T0315 208 :LSPHP 2gwgA 287 :GAVRG T0315 220 :PARVTLVAEQ 2gwgA 300 :YDDTKRYIEA T0315 236 :LSYEE 2gwgA 313 :LTPEE T0315 242 :CEQTTK 2gwgA 318 :KQQIYE T0315 248 :NAEKLF 2gwgA 325 :NARRVY Number of specific fragments extracted= 20 number of extra gaps= 0 total=335 Will force an alignment to be made, even if fragment is small Number of alignments=27 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2f6kA/T0315-2f6kA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2f6kA expands to /projects/compbio/data/pdb/2f6k.pdb.gz 2f6kA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0315 read from 2f6kA/T0315-2f6kA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2f6kA read from 2f6kA/T0315-2f6kA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2f6kA to template set # found chain 2f6kA in template set T0315 1 :MLIDTHVHLNDEQYDD 2f6kA 2 :SKIDFHTHYLPTSYVE T0315 17 :DLSEVITRAREAGVDRMFVV 2f6kA 36 :TPQLTLNFMRDNDISYSILS T0315 37 :GFNKST 2f6kA 60 :HVNFGD T0315 43 :IERAMKLIDEYD 2f6kA 77 :NDDGKSLAQQYP T0315 55 :FLYGIIG 2f6kA 90 :QLGYLAS T0315 63 :HP 2f6kA 97 :LP T0315 68 :IDFTEEHLEWIESLAQHPK 2f6kA 99 :IPYELDAVKTVQQALDQDG T0315 87 :VIGIGEMGLDYHWDKSP 2f6kA 119 :LGVTVPTNSRGLYFGSP T0315 111 :FRKQIALAKRLKLPIIIHN 2f6kA 137 :LERVYQELDARQAIVALHP T0315 136 :CIDILLEE 2f6kA 184 :FINMLKYH T0315 144 :HAEEVGGIM 2f6kA 195 :KYPNIKVII T0315 153 :HSFSG 2f6kA 205 :HAGAF T0315 160 :EIADI 2f6kA 219 :QYAQK T0315 165 :VTN 2f6kA 232 :VMH T0315 171 :FYISLGGPVT 2f6kA 236 :VYFDVAGAVL T0315 184 :AKQPKEVAKHVSMERLLVETDAPY 2f6kA 246 :PRQLPTLMSLAQPEHLLYGSDIPY T0315 218 :NEPARVTLVAEQIAELKGLSYEEVCEQTTKNAEKLF 2f6kA 270 :TPLDGSRQLGHALATTDLLTNEQKQAIFYDNAHRLL Number of specific fragments extracted= 17 number of extra gaps= 0 total=352 Will force an alignment to be made, even if fragment is small Number of alignments=28 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2f6kA/T0315-2f6kA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0315 read from 2f6kA/T0315-2f6kA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2f6kA read from 2f6kA/T0315-2f6kA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2f6kA in template set T0315 2 :LIDTHVHLNDEQY 2f6kA 3 :KIDFHTHYLPTSY T0315 15 :DDDLSEVITRAREAGVDRMFVV 2f6kA 34 :EWTPQLTLNFMRDNDISYSILS T0315 37 :GFNKST 2f6kA 60 :HVNFGD T0315 43 :IERAMKLIDEYDFLYGIIGWHPV 2f6kA 77 :NDDGKSLAQQYPDQLGYLASLPI T0315 69 :DFTEEHLEWIESLAQHPKVIGIGEM 2f6kA 100 :PYELDAVKTVQQALDQDGALGVTVP T0315 94 :GLDYHWDKSP 2f6kA 126 :NSRGLYFGSP T0315 111 :FRKQIALAKRLKLPIIIHNRE 2f6kA 137 :LERVYQELDARQAIVALHPNE T0315 132 :ATQDCIDILL 2f6kA 180 :TTMTFINMLK T0315 142 :EEHAEEVGGIMHSFSG 2f6kA 194 :EKYPNIKVIIPHAGAF T0315 158 :SP 2f6kA 211 :GI T0315 160 :EIADI 2f6kA 219 :QYAQK T0315 165 :VTN 2f6kA 232 :VMH T0315 171 :FYISLGGPV 2f6kA 236 :VYFDVAGAV T0315 183 :NAKQPKEVAKHVSMERLLVETDAPYLSP 2f6kA 245 :LPRQLPTLMSLAQPEHLLYGSDIPYTPL T0315 221 :ARVTLVAEQIAELKGLSYEEVCEQTTKNAEKLF 2f6kA 273 :DGSRQLGHALATTDLLTNEQKQAIFYDNAHRLL Number of specific fragments extracted= 15 number of extra gaps= 0 total=367 Will force an alignment to be made, even if fragment is small Number of alignments=29 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2f6kA/T0315-2f6kA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0315 read from 2f6kA/T0315-2f6kA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2f6kA read from 2f6kA/T0315-2f6kA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2f6kA in template set T0315 2 :LIDTHVHLNDEQYDD 2f6kA 3 :KIDFHTHYLPTSYVE T0315 17 :DLSEVITRAREAGVDRMFVVGF 2f6kA 36 :TPQLTLNFMRDNDISYSILSLS T0315 39 :NKST 2f6kA 65 :DKAE T0315 43 :IERAMKLIDEYDFLYGIIGWHPV 2f6kA 77 :NDDGKSLAQQYPDQLGYLASLPI T0315 69 :DFTEEHLEWIESLA 2f6kA 100 :PYELDAVKTVQQAL T0315 83 :QHPKVIGIGEMGLDYHWDKSP 2f6kA 115 :QDGALGVTVPTNSRGLYFGSP T0315 111 :FRKQIALAKRLKLPIIIHN 2f6kA 137 :LERVYQELDARQAIVALHP T0315 136 :CIDILL 2f6kA 184 :FINMLK T0315 143 :EH 2f6kA 190 :YH T0315 145 :AEEVGGIM 2f6kA 196 :YPNIKVII T0315 159 :PEIADIV 2f6kA 218 :AQYAQKV T0315 166 :TNKL 2f6kA 229 :VYDV T0315 170 :NFYISLGGPVTF 2f6kA 235 :HVYFDVAGAVLP T0315 185 :KQPKEVAKHVSMERLLVETDAPYLSP 2f6kA 247 :RQLPTLMSLAQPEHLLYGSDIPYTPL T0315 221 :ARVTLVAEQIAELKGLSYEE 2f6kA 273 :DGSRQLGHALATTDLLTNEQ T0315 242 :CEQT 2f6kA 293 :KQAI T0315 246 :TKNAEKLF 2f6kA 298 :YDNAHRLL Number of specific fragments extracted= 17 number of extra gaps= 0 total=384 Will force an alignment to be made, even if fragment is small Number of alignments=30 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1hzyA/T0315-1hzyA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1hzyA expands to /projects/compbio/data/pdb/1hzy.pdb.gz 1hzyA:Skipped atom 583, because occupancy 0.500 <= existing 0.500 in 1hzyA Skipped atom 585, because occupancy 0.500 <= existing 0.500 in 1hzyA Skipped atom 587, because occupancy 0.500 <= existing 0.500 in 1hzyA Skipped atom 594, because occupancy 0.500 <= existing 0.500 in 1hzyA Skipped atom 979, because occupancy 0.500 <= existing 0.500 in 1hzyA Skipped atom 981, because occupancy 0.500 <= existing 0.500 in 1hzyA Skipped atom 983, because occupancy 0.500 <= existing 0.500 in 1hzyA Skipped atom 985, because occupancy 0.500 <= existing 0.500 in 1hzyA Skipped atom 1243, because occupancy 0.500 <= existing 0.500 in 1hzyA Skipped atom 1245, because occupancy 0.500 <= existing 0.500 in 1hzyA Skipped atom 1247, because occupancy 0.500 <= existing 0.500 in 1hzyA Skipped atom 1439, because occupancy 0.300 <= existing 0.700 in 1hzyA Skipped atom 1558, because occupancy 0.500 <= existing 0.500 in 1hzyA Skipped atom 1584, because occupancy 0.500 <= existing 0.500 in 1hzyA Skipped atom 1586, because occupancy 0.500 <= existing 0.500 in 1hzyA Skipped atom 1588, because occupancy 0.500 <= existing 0.500 in 1hzyA Skipped atom 1994, because occupancy 0.330 <= existing 0.330 in 1hzyA Skipped atom 1995, because occupancy 0.330 <= existing 0.330 in 1hzyA Skipped atom 1997, because occupancy 0.330 <= existing 0.330 in 1hzyA Skipped atom 1998, because occupancy 0.330 <= existing 0.330 in 1hzyA Skipped atom 2000, because occupancy 0.330 <= existing 0.330 in 1hzyA Skipped atom 2001, because occupancy 0.330 <= existing 0.330 in 1hzyA Skipped atom 2003, because occupancy 0.330 <= existing 0.330 in 1hzyA Skipped atom 2004, because occupancy 0.330 <= existing 0.330 in 1hzyA Skipped atom 2509, because occupancy 0.500 <= existing 0.500 in 1hzyA # T0315 read from 1hzyA/T0315-1hzyA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1hzyA read from 1hzyA/T0315-1hzyA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1hzyA to template set # found chain 1hzyA in template set T0315 1 :MLIDTHVHLN 1hzyA 50 :GFTLTHEHIC T0315 11 :DEQYDDDLSEV 1hzyA 69 :WPEFFGSRKAL T0315 22 :ITRAREAGVDRMFVVGF 1hzyA 87 :LRRARAAGVRTIVDVST T0315 42 :TIERAMKLIDEYD 1hzyA 109 :DVSLLAEVSRAAD T0315 55 :FLYGIIGWH 1hzyA 123 :HIVAATGLW T0315 64 :PVDAIDFT 1hzyA 135 :PLSMRLRS T0315 72 :EEHLEWIESLAQHP 1hzyA 144 :EELTQFFLREIQYG T0315 86 :KVIGIGEM 1hzyA 164 :RAGIIKVA T0315 99 :WDKSPADVQKEVFRKQIALAKRLKLPIIIHN 1hzyA 172 :TTGKATPFQELVLKAAARASLATGVPVTTHT T0315 130 :REATQDCIDILLEEHAEEVGGIM 1hzyA 206 :QRDGEQQAAIFESEGLSPSRVCI T0315 153 :HS 1hzyA 230 :HS T0315 155 :FSGSPEIADIVTN 1hzyA 233 :DTDDLSYLTALAA T0315 169 :LNFYISLGGPVTF 1hzyA 246 :RGYLIGLDHIPHS T0315 182 :KNAKQPKEVAKHVSMERLLVETDAPYLSPHPYRG 1hzyA 279 :TRALLIKALIDQGYMKQILVSNDWLFGFSSYVTN T0315 217 :RNEPARVTL 1hzyA 322 :PDGMAFIPL T0315 226 :VAEQIAE 1hzyA 332 :VIPFLRE T0315 234 :KGLSYEEVCEQTTKNAEKLFNLN 1hzyA 339 :KGVPQETLAGITVTNPARFLSPT Number of specific fragments extracted= 17 number of extra gaps= 0 total=401 Will force an alignment to be made, even if fragment is small Number of alignments=31 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1hzyA/T0315-1hzyA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0315 read from 1hzyA/T0315-1hzyA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1hzyA read from 1hzyA/T0315-1hzyA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1hzyA in template set T0315 1 :MLIDTHVHL 1hzyA 50 :GFTLTHEHI T0315 10 :NDEQY 1hzyA 69 :WPEFF T0315 15 :DDDLSEVITRAREAGVDRMFVVGF 1hzyA 80 :AEKAVRGLRRARAAGVRTIVDVST T0315 41 :STIERAMKLIDEYD 1hzyA 108 :RDVSLLAEVSRAAD T0315 55 :FLYGIIGWHPV 1hzyA 123 :HIVAATGLWFD T0315 69 :DFT 1hzyA 140 :LRS T0315 72 :EEHLEWIESLAQ 1hzyA 144 :EELTQFFLREIQ T0315 84 :HPKVIG 1hzyA 160 :DTGIRA T0315 91 :GEMG 1hzyA 166 :GIIK T0315 97 :YHWDKSPADVQKEVFRKQIALAKRLKLPIIIHN 1hzyA 170 :VATTGKATPFQELVLKAAARASLATGVPVTTHT T0315 130 :REATQDCIDILLEEHAEEVGGIM 1hzyA 206 :QRDGEQQAAIFESEGLSPSRVCI T0315 153 :HSF 1hzyA 230 :HSD T0315 156 :SGSPEIADIVTN 1hzyA 234 :TDDLSYLTALAA T0315 169 :LNFYISLGGPVTF 1hzyA 246 :RGYLIGLDHIPHS T0315 182 :KNAKQ 1hzyA 275 :RSWQT T0315 187 :PKEVAKHVSMERLLVETDAPYLSPHPYRGK 1hzyA 284 :IKALIDQGYMKQILVSNDWLFGFSSYVTNI T0315 217 :RNEPARVTL 1hzyA 322 :PDGMAFIPL T0315 226 :VAEQIAEL 1hzyA 332 :VIPFLREK T0315 235 :GLSYEEVCEQTTKNAEKLFNLN 1hzyA 340 :GVPQETLAGITVTNPARFLSPT Number of specific fragments extracted= 19 number of extra gaps= 0 total=420 Will force an alignment to be made, even if fragment is small Number of alignments=32 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1hzyA/T0315-1hzyA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0315 read from 1hzyA/T0315-1hzyA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1hzyA read from 1hzyA/T0315-1hzyA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1hzyA in template set T0315 2 :LIDTHVHL 1hzyA 51 :FTLTHEHI T0315 11 :DEQYDDDLSEVITRA 1hzyA 69 :WPEFFGSRKALAEKA T0315 26 :REAGVDRMFVVGF 1hzyA 91 :RAAGVRTIVDVST T0315 43 :IERAMKLIDEYDF 1hzyA 110 :VSLLAEVSRAADV T0315 56 :LYGIIGW 1hzyA 124 :IVAATGL T0315 63 :HPVDAIDFT 1hzyA 134 :PPLSMRLRS T0315 72 :EEHLEWIESLA 1hzyA 144 :EELTQFFLREI T0315 84 :HPKVIGIGE 1hzyA 164 :RAGIIKVAT T0315 100 :DKSPADVQKEVFRKQIALAKRLKLPIIIHN 1hzyA 173 :TGKATPFQELVLKAAARASLATGVPVTTHT T0315 130 :REATQDCIDILLEEHAE 1hzyA 206 :QRDGEQQAAIFESEGLS T0315 148 :VGGIMHSF 1hzyA 223 :PSRVCIGH T0315 156 :SGSPEIADI 1hzyA 234 :TDDLSYLTA T0315 166 :TNKLNFYISLGGPV 1hzyA 243 :LAARGYLIGLDHIP T0315 180 :TFKNAKQPKEVAKHVS 1hzyA 261 :GLEDNASASALLGIRS T0315 196 :MERLLVETDAPYLSPHP 1hzyA 293 :MKQILVSNDWLFGFSSY T0315 220 :PARVTL 1hzyA 325 :MAFIPL T0315 226 :VAEQIAE 1hzyA 332 :VIPFLRE T0315 234 :KGLSYEEVCEQTTKNAEKLFNLNS 1hzyA 339 :KGVPQETLAGITVTNPARFLSPTL Number of specific fragments extracted= 18 number of extra gaps= 0 total=438 Will force an alignment to be made, even if fragment is small Number of alignments=33 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1gkpA/T0315-1gkpA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1gkpA expands to /projects/compbio/data/pdb/1gkp.pdb.gz 1gkpA:Bad short name: CX for alphabet: pdb_atoms Bad short name: OQ1 for alphabet: pdb_atoms Bad short name: OQ2 for alphabet: pdb_atoms # T0315 read from 1gkpA/T0315-1gkpA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1gkpA read from 1gkpA/T0315-1gkpA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1gkpA to template set # found chain 1gkpA in template set Warning: unaligning (T0315)I88 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1gkpA)I151 Warning: unaligning (T0315)I90 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1gkpA)I151 T0315 1 :MLIDTHVHLND 1gkpA 54 :GFIDPHVHIYL T0315 14 :YDD 1gkpA 66 :FMA T0315 17 :DLSEVITRAREAGVDRMFVVGFN 1gkpA 74 :THETGSKAALMGGTTTYIEMCCP T0315 40 :KSTIERAMKLID 1gkpA 103 :LEGYQLWKSKAE T0315 54 :DFLYGIIGWH 1gkpA 115 :GNSYCDYTFH T0315 65 :VDAIDFTEEHLEWIESLAQHP 1gkpA 125 :MAVSKFDEKTEGQLREIVADG T0315 86 :KV 1gkpA 147 :SS T0315 91 :GEM 1gkpA 152 :FLS T0315 97 :YHWDKSPA 1gkpA 155 :YKNFFGVD T0315 108 :KEVFRKQIALAKRLKLPIIIHN 1gkpA 163 :DGEMYQTLRLAKELGVIVTAHC T0315 130 :REATQDCIDILLEEH 1gkpA 218 :AEGTARFATFLETTG T0315 148 :VGGIM 1gkpA 233 :ATGYV T0315 153 :HSF 1gkpA 239 :HLS T0315 157 :GSP 1gkpA 242 :CKP T0315 160 :EIADIVTN 1gkpA 247 :DAAMAAKA T0315 169 :LNFYISLGGPVTF 1gkpA 255 :RGVPIYIESVIPH T0315 182 :KNAKQPKEVAKHVSME 1gkpA 295 :RNQKVLWDALAQGFID T0315 200 :LVETDA 1gkpA 311 :TVGTDH T0315 207 :YLSPHPYRGK 1gkpA 325 :LLGKEAFTAI T0315 217 :RNEPARVTLVAEQI 1gkpA 339 :PAIEDRVNLLYTYG T0315 235 :GLSYEEVCEQTTKNAEKLFNL 1gkpA 357 :RLDIHRFVDAASTKAAKLFGL Number of specific fragments extracted= 21 number of extra gaps= 0 total=459 Will force an alignment to be made, even if fragment is small Number of alignments=34 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1gkpA/T0315-1gkpA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0315 read from 1gkpA/T0315-1gkpA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1gkpA read from 1gkpA/T0315-1gkpA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1gkpA in template set Warning: unaligning (T0315)D15 because of BadResidue code BAD_PEPTIDE at template residue (1gkpA)K72 Warning: unaligning (T0315)I90 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1gkpA)I151 Warning: unaligning (T0315)E92 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1gkpA)I151 T0315 1 :MLIDTHVHLND 1gkpA 54 :GFIDPHVHIYL T0315 14 :Y 1gkpA 67 :M T0315 16 :DDLSEVITRAREAGVDRMFVVGFNK 1gkpA 73 :DTHETGSKAALMGGTTTYIEMCCPS T0315 41 :ST 1gkpA 99 :ND T0315 43 :IERAMKLID 1gkpA 106 :YQLWKSKAE T0315 54 :DFLYGIIGWHPV 1gkpA 115 :GNSYCDYTFHMA T0315 67 :AIDFTEEHLEWIESLAQH 1gkpA 127 :VSKFDEKTEGQLREIVAD T0315 86 :KVIG 1gkpA 145 :GISS T0315 93 :M 1gkpA 152 :F T0315 95 :LDYHWDKSP 1gkpA 153 :LSYKNFFGV T0315 107 :QKEVFRKQIALAKRLKLPIIIHNRE 1gkpA 162 :DDGEMYQTLRLAKELGVIVTAHCEN T0315 132 :ATQDCIDILLEE 1gkpA 220 :GTARFATFLETT T0315 146 :EEVGGIMHSFSGS 1gkpA 232 :GATGYVVHLSCKP T0315 160 :EIADIVTN 1gkpA 247 :DAAMAAKA T0315 169 :LNFYIS 1gkpA 255 :RGVPIY T0315 175 :LGGPVT 1gkpA 287 :MSPPLR T0315 181 :FKNAKQPKEVAKHVSME 1gkpA 294 :KRNQKVLWDALAQGFID T0315 200 :LVETD 1gkpA 311 :TVGTD T0315 205 :AP 1gkpA 317 :CP T0315 207 :YLSPHPYRGKRNEPAR 1gkpA 325 :LLGKEAFTAIPNGIPA T0315 223 :VTLVAEQI 1gkpA 345 :VNLLYTYG T0315 234 :KGLSYEEVCEQTTKNAEKLFNL 1gkpA 356 :GRLDIHRFVDAASTKAAKLFGL Number of specific fragments extracted= 22 number of extra gaps= 1 total=481 Will force an alignment to be made, even if fragment is small Number of alignments=35 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1gkpA/T0315-1gkpA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0315 read from 1gkpA/T0315-1gkpA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1gkpA read from 1gkpA/T0315-1gkpA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1gkpA in template set Warning: unaligning (T0315)M33 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1gkpA)I151 Warning: unaligning (T0315)V35 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1gkpA)I151 T0315 2 :LIDTHVHLNDEQYDDDLSEVITRAREAGVDR 1gkpA 118 :YCDYTFHMAVSKFDEKTEGQLREIVADGISS T0315 36 :V 1gkpA 152 :F T0315 37 :GFNKSTIERAMKLIDEYD 1gkpA 160 :GVDDGEMYQTLRLAKELG T0315 56 :LYGIIGWH 1gkpA 178 :VIVTAHCE T0315 70 :FTEEHLEWIESLAQHPK 1gkpA 186 :NAELVGRLQQKLLSEGK T0315 93 :MGLDYHWDKSPADVQKEVFRKQIALAKRLKLPIIIHN 1gkpA 203 :TGPEWHEPSRPEAVEAEGTARFATFLETTGATGYVVH T0315 132 :ATQDCIDILLEEHAEEVGGIMHSF 1gkpA 241 :SCKPALDAAMAAKARGVPIYIESV T0315 156 :SGSPEIADI 1gkpA 277 :RGGVEAMKY T0315 175 :LGGPVTFK 1gkpA 287 :MSPPLRDK T0315 183 :NAKQPKEVAKH 1gkpA 296 :NQKVLWDALAQ T0315 194 :V 1gkpA 309 :I T0315 197 :E 1gkpA 310 :D T0315 200 :LVETDA 1gkpA 311 :TVGTDH T0315 209 :SPHP 1gkpA 317 :CPFD T0315 213 :YRG 1gkpA 354 :SRG T0315 235 :GLSYEEVCEQTTKNAEKLFN 1gkpA 357 :RLDIHRFVDAASTKAAKLFG Number of specific fragments extracted= 16 number of extra gaps= 0 total=497 Will force an alignment to be made, even if fragment is small Number of alignments=36 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1onwA/T0315-1onwA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1onwA expands to /projects/compbio/data/pdb/1onw.pdb.gz 1onwA:Skipped atom 408, because occupancy 0.500 <= existing 0.500 in 1onwA Skipped atom 410, because occupancy 0.500 <= existing 0.500 in 1onwA Skipped atom 630, because occupancy 0.500 <= existing 0.500 in 1onwA Skipped atom 632, because occupancy 0.500 <= existing 0.500 in 1onwA Skipped atom 634, because occupancy 0.500 <= existing 0.500 in 1onwA Skipped atom 723, because occupancy 0.500 <= existing 0.500 in 1onwA Skipped atom 725, because occupancy 0.500 <= existing 0.500 in 1onwA Skipped atom 727, because occupancy 0.500 <= existing 0.500 in 1onwA Skipped atom 920, because occupancy 0.500 <= existing 0.500 in 1onwA Skipped atom 922, because occupancy 0.500 <= existing 0.500 in 1onwA Skipped atom 924, because occupancy 0.500 <= existing 0.500 in 1onwA Skipped atom 926, because occupancy 0.500 <= existing 0.500 in 1onwA Skipped atom 928, because occupancy 0.500 <= existing 0.500 in 1onwA Bad short name: CX for alphabet: pdb_atoms Bad short name: OQ1 for alphabet: pdb_atoms Bad short name: OQ2 for alphabet: pdb_atoms Skipped atom 2591, because occupancy 0.330 <= existing 0.670 in 1onwA Skipped atom 2593, because occupancy 0.330 <= existing 0.670 in 1onwA Skipped atom 2595, because occupancy 0.330 <= existing 0.670 in 1onwA Skipped atom 2597, because occupancy 0.330 <= existing 0.670 in 1onwA Skipped atom 2599, because occupancy 0.330 <= existing 0.670 in 1onwA Skipped atom 2601, because occupancy 0.330 <= existing 0.670 in 1onwA Skipped atom 2603, because occupancy 0.330 <= existing 0.670 in 1onwA # T0315 read from 1onwA/T0315-1onwA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1onwA read from 1onwA/T0315-1onwA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1onwA to template set # found chain 1onwA in template set Warning: unaligning (T0315)I90 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1onwA)C163 Warning: unaligning (T0315)E92 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1onwA)C163 Warning: unaligning (T0315)L208 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1onwA)G303 Warning: unaligning (T0315)K234 because of BadResidue code BAD_PEPTIDE in next template residue (1onwA)D322 Warning: unaligning (T0315)G235 because of BadResidue code BAD_PEPTIDE at template residue (1onwA)D322 T0315 2 :LIDTHVHL 1onwA 64 :FIDQHVHL T0315 11 :DEQYDDDLS 1onwA 80 :PTTRTPEVA T0315 22 :ITRAREAGVDRMFVV 1onwA 89 :LSRLTEAGVTSVVGL T0315 37 :GFN 1onwA 105 :GTD T0315 42 :TIERAMKLIDEY 1onwA 112 :HPESLLAKTRAL T0315 54 :D 1onwA 127 :G T0315 55 :FLYGIIGWHPVDAIDFTEEHLEWIESL 1onwA 129 :SAWMLTGAYHVPSRTITGSVEKDVAII T0315 85 :PKVIG 1onwA 156 :DRVIG T0315 93 :MGLDYHWDKSPADVQKEVFRKQIALAKRLKLP 1onwA 164 :AISDHRSAAPDVYHLANMAAESRVGGLLGGKP T0315 125 :IIIHN 1onwA 198 :TVFHM T0315 130 :REATQDCIDILLEEHAE 1onwA 206 :KKALQPIYDLLENCDVP T0315 147 :EVGGIMHSFS 1onwA 224 :SKLLPTHVNR T0315 158 :SP 1onwA 234 :NV T0315 160 :EIADIVTN 1onwA 239 :EQALEFAR T0315 169 :LNFYISLGGPVTF 1onwA 247 :KGGTIDITSSIDE T0315 184 :AKQPKEVAK 1onwA 260 :PVAPAEGIA T0315 193 :HVSMERLLVETDAPY 1onwA 274 :GIPLARVTLSSDGNG T0315 217 :RNEPARVTLVAEQIAEL 1onwA 304 :VAGFETLLETVQVLVKD T0315 236 :LSYEEVCEQTTKNAEKLFNLN 1onwA 323 :FSISDALRPLTSSVAGFLNLT Number of specific fragments extracted= 19 number of extra gaps= 1 total=516 Will force an alignment to be made, even if fragment is small Number of alignments=37 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1onwA/T0315-1onwA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0315 read from 1onwA/T0315-1onwA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1onwA read from 1onwA/T0315-1onwA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1onwA in template set Warning: unaligning (T0315)I90 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1onwA)C163 Warning: unaligning (T0315)E92 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1onwA)C163 Warning: unaligning (T0315)L208 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1onwA)G303 Warning: unaligning (T0315)K234 because of BadResidue code BAD_PEPTIDE in next template residue (1onwA)D322 Warning: unaligning (T0315)G235 because of BadResidue code BAD_PEPTIDE at template residue (1onwA)D322 T0315 1 :MLIDTHVHL 1onwA 63 :GFIDQHVHL T0315 10 :NDEQYDDDLS 1onwA 79 :GPTTRTPEVA T0315 22 :ITRAREAGVDRMFVV 1onwA 89 :LSRLTEAGVTSVVGL T0315 37 :GFNKST 1onwA 105 :GTDSIS T0315 43 :IERAMKLIDEY 1onwA 113 :PESLLAKTRAL T0315 54 :D 1onwA 127 :G T0315 55 :FLYGIIGWHPVDAIDFTEEHLEWIESL 1onwA 129 :SAWMLTGAYHVPSRTITGSVEKDVAII T0315 85 :PKVIG 1onwA 156 :DRVIG T0315 93 :MGLDYHWDKSPADVQKEVFRKQIALAKRLKLP 1onwA 164 :AISDHRSAAPDVYHLANMAAESRVGGLLGGKP T0315 125 :IIIHNRE 1onwA 198 :TVFHMGD T0315 132 :AT 1onwA 208 :AL T0315 135 :DCIDILLEEHA 1onwA 210 :QPIYDLLENCD T0315 146 :EEVGGIMHSFSGSP 1onwA 223 :ISKLLPTHVNRNVP T0315 160 :EIADIVTN 1onwA 239 :EQALEFAR T0315 169 :LNFYISLGGPVTFKN 1onwA 247 :KGGTIDITSSIDEPV T0315 186 :Q 1onwA 262 :A T0315 187 :PKEVAKH 1onwA 267 :IARAVQA T0315 194 :VSMERLLVETDAPY 1onwA 275 :IPLARVTLSSDGNG T0315 217 :RNEPARVTLVAEQIAEL 1onwA 304 :VAGFETLLETVQVLVKD T0315 236 :LSYEEVCEQTTKNAEKLFNLN 1onwA 323 :FSISDALRPLTSSVAGFLNLT Number of specific fragments extracted= 20 number of extra gaps= 1 total=536 Will force an alignment to be made, even if fragment is small Number of alignments=38 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1onwA/T0315-1onwA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0315 read from 1onwA/T0315-1onwA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1onwA read from 1onwA/T0315-1onwA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1onwA in template set Warning: unaligning (T0315)I90 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1onwA)C163 Warning: unaligning (T0315)E92 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1onwA)C163 Warning: unaligning (T0315)L208 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1onwA)G303 Warning: unaligning (T0315)K216 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1onwA)G303 Warning: unaligning (T0315)K234 because of BadResidue code BAD_PEPTIDE in next template residue (1onwA)D322 Warning: unaligning (T0315)G235 because of BadResidue code BAD_PEPTIDE at template residue (1onwA)D322 T0315 2 :LIDTHVHL 1onwA 64 :FIDQHVHL T0315 10 :NDEQYDD 1onwA 79 :GPTTRTP T0315 22 :ITRAREAGVDRMFVVGFN 1onwA 89 :LSRLTEAGVTSVVGLLGT T0315 40 :KS 1onwA 108 :SI T0315 43 :IERAMKLIDEYDF 1onwA 113 :PESLLAKTRALNE T0315 56 :LYGIIGWHPVDAIDFTEEHLEWIESL 1onwA 130 :AWMLTGAYHVPSRTITGSVEKDVAII T0315 85 :PKVIG 1onwA 156 :DRVIG T0315 93 :MGLDYHWDKSPADVQKEVFRKQIALAKRLKLP 1onwA 164 :AISDHRSAAPDVYHLANMAAESRVGGLLGGKP T0315 125 :IIIHN 1onwA 198 :TVFHM T0315 130 :REATQDCIDILLEEHAEEVGGIMHSFSGSPEIADI 1onwA 206 :KKALQPIYDLLENCDVPISKLLPTHVNRNVPLFEQ T0315 166 :TNKL 1onwA 241 :ALEF T0315 170 :NFYISLGGPVT 1onwA 248 :GGTIDITSSID T0315 183 :NAKQPKEVA 1onwA 259 :EPVAPAEGI T0315 194 :VSMERLLVETDAPY 1onwA 275 :IPLARVTLSSDGNG T0315 217 :RNEPARVTLVAEQIAEL 1onwA 304 :VAGFETLLETVQVLVKD T0315 236 :LSYEEV 1onwA 323 :FSISDA Number of specific fragments extracted= 16 number of extra gaps= 1 total=552 Will force an alignment to be made, even if fragment is small Number of alignments=39 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1p1mA/T0315-1p1mA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1p1mA expands to /projects/compbio/data/pdb/1p1m.pdb.gz 1p1mA:# T0315 read from 1p1mA/T0315-1p1mA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1p1mA read from 1p1mA/T0315-1p1mA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1p1mA to template set # found chain 1p1mA in template set T0315 2 :LIDTHVHLNDEQYDD 1p1mA 51 :LFNTHTHAPMTLLRG T0315 24 :RAREAGVDRMFVVGFN 1p1mA 102 :EMARHGIAGFVDMYFH T0315 43 :IERAMKLIDEYD 1p1mA 118 :EEWIAKAVRDFG T0315 55 :FLYGIIGWHP 1p1mA 131 :RALLTRGLVD T0315 67 :AIDFTEEHLEWIESLAQ 1p1mA 141 :SNGDDGGRLEENLKLYN T0315 84 :HPKVIGIGEM 1p1mA 164 :GRIFVGFGPH T0315 98 :HWDKSP 1p1mA 174 :SPYLCS T0315 108 :KEVFRKQIALAKRLKLPIIIHN 1p1mA 180 :EEYLKRVFDTAKSLNAPVTIHL T0315 130 :REA 1p1mA 209 :YDL T0315 134 :QDCI 1p1mA 212 :EDIL T0315 142 :EEHAEEVGGIM 1p1mA 216 :NIGLKEVKTIA T0315 153 :HSFSGSPE 1p1mA 228 :HCVHLPER T0315 168 :KLN 1p1mA 236 :YFG T0315 171 :FYISLG 1p1mA 245 :FFVSHN T0315 177 :GPV 1p1mA 260 :GIA T0315 186 :QPKEVAKHVS 1p1mA 263 :PVQRMIEHGM T0315 198 :RLLVETDAPY 1p1mA 273 :KVTLGTDGAA T0315 217 :RNEPARVTLVAEQIAEL 1p1mA 283 :SNNSLNLFFEMRLASLL T0315 234 :KGLSYEEVCEQTTKNAEKLFNLN 1p1mA 306 :RNLDVNTCLKMVTYDGAQAMGFK Number of specific fragments extracted= 19 number of extra gaps= 0 total=571 Will force an alignment to be made, even if fragment is small Number of alignments=40 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1p1mA/T0315-1p1mA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0315 read from 1p1mA/T0315-1p1mA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1p1mA read from 1p1mA/T0315-1p1mA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1p1mA in template set T0315 2 :LIDTHVHLNDEQY 1p1mA 51 :LFNTHTHAPMTLL T0315 15 :DDDLSEV 1p1mA 88 :TEKMAYY T0315 22 :ITRAREAGVDRMFVVGF 1p1mA 100 :QMEMARHGIAGFVDMYF T0315 42 :TIERAMKLIDEYD 1p1mA 117 :HEEWIAKAVRDFG T0315 55 :FLYGIIGWHPV 1p1mA 131 :RALLTRGLVDS T0315 66 :DAIDFTEEHLEWIESLAQHPKVIGIGEM 1p1mA 144 :DDGGRLEENLKLYNEWNGFEGRIFVGFG T0315 96 :DYHWDKSP 1p1mA 172 :PHSPYLCS T0315 108 :KEVFRKQIALAKRLKLPIIIHNRE 1p1mA 180 :EEYLKRVFDTAKSLNAPVTIHLYE T0315 132 :ATQDCI 1p1mA 210 :DLEDIL T0315 142 :EEHA 1p1mA 216 :NIGL T0315 146 :EEVGGIMHSFSGSP 1p1mA 221 :EVKTIAAHCVHLPE T0315 168 :KLN 1p1mA 236 :YFG T0315 171 :FYISLG 1p1mA 245 :FFVSHN T0315 177 :GPV 1p1mA 260 :GIA T0315 186 :QPKEVAKHVS 1p1mA 263 :PVQRMIEHGM T0315 198 :RLLVETDAPYL 1p1mA 273 :KVTLGTDGAAS T0315 218 :NEPARVTLVAEQIAEL 1p1mA 284 :NNSLNLFFEMRLASLL T0315 234 :KG 1p1mA 305 :PR T0315 236 :LSYEEVCEQTTKNAEKLFNLNS 1p1mA 308 :LDVNTCLKMVTYDGAQAMGFKS Number of specific fragments extracted= 19 number of extra gaps= 0 total=590 Will force an alignment to be made, even if fragment is small Number of alignments=41 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1p1mA/T0315-1p1mA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0315 read from 1p1mA/T0315-1p1mA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1p1mA read from 1p1mA/T0315-1p1mA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1p1mA in template set T0315 2 :LIDTHVHLNDEQYDD 1p1mA 51 :LFNTHTHAPMTLLRG T0315 17 :DLSEVIT 1p1mA 71 :SFEEWLF T0315 24 :RAREAGVDRMFVVGFN 1p1mA 102 :EMARHGIAGFVDMYFH T0315 43 :IERAMKLIDEYDF 1p1mA 118 :EEWIAKAVRDFGM T0315 56 :LYGIIGWHPV 1p1mA 132 :ALLTRGLVDS T0315 66 :DAIDFTEEHLEWIESLA 1p1mA 144 :DDGGRLEENLKLYNEWN T0315 83 :QHPKVIGIGE 1p1mA 163 :EGRIFVGFGP T0315 97 :YHWDKSP 1p1mA 173 :HSPYLCS T0315 108 :KEVFRKQIALAKRLKLPIIIHN 1p1mA 180 :EEYLKRVFDTAKSLNAPVTIHL T0315 130 :RE 1p1mA 209 :YD T0315 133 :TQDC 1p1mA 211 :LEDI T0315 141 :LEEHAEEVGGIMHSFSG 1p1mA 215 :LNIGLKEVKTIAAHCVH T0315 166 :TNKLNFYISLG 1p1mA 240 :LKDIPFFVSHN T0315 183 :NAK 1p1mA 258 :GNG T0315 186 :QPKEVAKH 1p1mA 263 :PVQRMIEH T0315 198 :RLLVETDAPYL 1p1mA 273 :KVTLGTDGAAS T0315 218 :NEPARVTLVAEQIAEL 1p1mA 284 :NNSLNLFFEMRLASLL T0315 234 :KGLSYEEVCEQTTKNAEKLFNLN 1p1mA 306 :RNLDVNTCLKMVTYDGAQAMGFK Number of specific fragments extracted= 18 number of extra gaps= 0 total=608 Will force an alignment to be made, even if fragment is small Number of alignments=42 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2gokA/T0315-2gokA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2gokA expands to /projects/compbio/data/pdb/2gok.pdb.gz 2gokA:# T0315 read from 2gokA/T0315-2gokA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2gokA read from 2gokA/T0315-2gokA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2gokA to template set # found chain 2gokA in template set T0315 2 :LIDTHVHLNDEQYDD 2gokA 82 :LIDCHTHLVFGGNRA T0315 17 :DLSEVITRAREAGVDRMFVVG 2gokA 136 :QALPRLDTLLSEGVSTIEIKS T0315 38 :FNKSTIERAMKLIDEY 2gokA 160 :LDIETELKMLRVARRL T0315 54 :DFLYGIIGWH 2gokA 180 :PVRIVTSYLA T0315 64 :PVDAIDFTEEH 2gokA 194 :PADYKGRNADY T0315 75 :LEWIESLAQHPKVIGIGEMG 2gokA 210 :LPGLEKAHAEGLADAVDGFC T0315 99 :WDKSP 2gokA 230 :EGIAF T0315 108 :KEVFRKQIALAKRLKLPIIIHN 2gokA 236 :VKEIDRVFAAAQQRGLPVKLHA T0315 130 :RE 2gokA 263 :LG T0315 136 :CIDILLEEHA 2gokA 265 :GAELAASYNA T0315 149 :GGIMHSFSGSPEIADIVTN 2gokA 275 :LSADHLEYLDETGAKALAK T0315 169 :LNFYISLG 2gokA 294 :AGTVAVLL T0315 182 :KNAKQPKEV 2gokA 314 :PPVQALRDA T0315 198 :RLLVETDAPY 2gokA 325 :EIALATDCNP T0315 216 :KRNEPARVTLVAEQIAELKGLSYEEVCEQTTKNAEKLFNL 2gokA 335 :GTSPLTSLLLTMNMGATLFRMTVEECLTATTRNAAKALGL Number of specific fragments extracted= 15 number of extra gaps= 0 total=623 Will force an alignment to be made, even if fragment is small Number of alignments=43 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2gokA/T0315-2gokA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0315 read from 2gokA/T0315-2gokA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2gokA read from 2gokA/T0315-2gokA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2gokA in template set T0315 2 :LIDTHVHLNDEQY 2gokA 82 :LIDCHTHLVFGGN T0315 15 :DDDLSEVITRAREAGVDRMFVV 2gokA 134 :VAQALPRLDTLLSEGVSTIEIK T0315 37 :GFNKSTIERAMKLIDEY 2gokA 159 :GLDIETELKMLRVARRL T0315 55 :FLYGIIGWHPV 2gokA 180 :PVRIVTSYLAA T0315 66 :DAIDFTEE 2gokA 196 :DYKGRNAD T0315 74 :HLEWIESLAQHPKVIGI 2gokA 209 :VLPGLEKAHAEGLADAV T0315 91 :GEM 2gokA 227 :GFC T0315 102 :SPADVQKEVFRKQIALAKRLKLPIIIHNRE 2gokA 230 :EGIAFSVKEIDRVFAAAQQRGLPVKLHAEQ T0315 132 :ATQDCIDILLEEH 2gokA 261 :SNLGGAELAASYN T0315 148 :VGGIMHSFSGSPEIADIVTN 2gokA 274 :ALSADHLEYLDETGAKALAK T0315 169 :LNFYIS 2gokA 294 :AGTVAV T0315 176 :GGP 2gokA 311 :KQL T0315 182 :KNAKQPKEV 2gokA 314 :PPVQALRDA T0315 198 :RLLVETD 2gokA 325 :EIALATD T0315 205 :APYLSPHP 2gokA 333 :NPGTSPLT T0315 222 :RVTLVAEQIAELKGLSYEEVCEQTTKNAEKLFNL 2gokA 341 :SLLLTMNMGATLFRMTVEECLTATTRNAAKALGL Number of specific fragments extracted= 16 number of extra gaps= 0 total=639 Will force an alignment to be made, even if fragment is small Number of alignments=44 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2gokA/T0315-2gokA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0315 read from 2gokA/T0315-2gokA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2gokA read from 2gokA/T0315-2gokA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2gokA in template set T0315 2 :LIDTHVHLNDEQYDD 2gokA 82 :LIDCHTHLVFGGNRA T0315 17 :DLSEVITRAREAGVDRMFVV 2gokA 136 :QALPRLDTLLSEGVSTIEIK T0315 37 :GFNKSTIERAMKLIDEYDF 2gokA 159 :GLDIETELKMLRVARRLET T0315 57 :YGIIGW 2gokA 183 :IVTSYL T0315 63 :HPVDAIDFTEEH 2gokA 193 :TPADYKGRNADY T0315 75 :LEWIESLAQHPKVIGIGEMGLDYHW 2gokA 210 :LPGLEKAHAEGLADAVDGFCEGIAF T0315 103 :P 2gokA 235 :S T0315 108 :KEVFRKQIALAKRLKLPIIIHN 2gokA 236 :VKEIDRVFAAAQQRGLPVKLHA T0315 136 :CIDILLEEH 2gokA 265 :GAELAASYN T0315 148 :VGGIMHSFSGSPEIADI 2gokA 274 :ALSADHLEYLDETGAKA T0315 166 :TNKLNFYISLG 2gokA 291 :LAKAGTVAVLL T0315 181 :FK 2gokA 310 :EK T0315 183 :NAKQPKEV 2gokA 315 :PVQALRDA T0315 195 :SM 2gokA 323 :GA T0315 198 :RLLVETDAPYLSPH 2gokA 325 :EIALATDCNPGTSP T0315 220 :PARVTLVAEQIAELKGLSYEEVCEQTTKNAEKLFNL 2gokA 339 :LTSLLLTMNMGATLFRMTVEECLTATTRNAAKALGL Number of specific fragments extracted= 16 number of extra gaps= 0 total=655 Will force an alignment to be made, even if fragment is small Number of alignments=45 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2ftwA/T0315-2ftwA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2ftwA expands to /projects/compbio/data/pdb/2ftw.pdb.gz 2ftwA:Skipped atom 14, because occupancy 0.500 <= existing 0.500 in 2ftwA Skipped atom 18, because occupancy 0.500 <= existing 0.500 in 2ftwA Skipped atom 20, because occupancy 0.500 <= existing 0.500 in 2ftwA Skipped atom 22, because occupancy 0.500 <= existing 0.500 in 2ftwA Skipped atom 322, because occupancy 0.500 <= existing 0.500 in 2ftwA Skipped atom 326, because occupancy 0.500 <= existing 0.500 in 2ftwA Skipped atom 328, because occupancy 0.500 <= existing 0.500 in 2ftwA Skipped atom 330, because occupancy 0.500 <= existing 0.500 in 2ftwA Skipped atom 332, because occupancy 0.500 <= existing 0.500 in 2ftwA Skipped atom 334, because occupancy 0.500 <= existing 0.500 in 2ftwA Skipped atom 594, because occupancy 0.500 <= existing 0.500 in 2ftwA Skipped atom 598, because occupancy 0.500 <= existing 0.500 in 2ftwA Skipped atom 600, because occupancy 0.500 <= existing 0.500 in 2ftwA Skipped atom 602, because occupancy 0.500 <= existing 0.500 in 2ftwA Skipped atom 604, because occupancy 0.500 <= existing 0.500 in 2ftwA Bad short name: CX for alphabet: pdb_atoms Bad short name: OQ1 for alphabet: pdb_atoms Bad short name: OQ2 for alphabet: pdb_atoms Skipped atom 1397, because occupancy 0.500 <= existing 0.500 in 2ftwA Skipped atom 1401, because occupancy 0.500 <= existing 0.500 in 2ftwA Skipped atom 1403, because occupancy 0.500 <= existing 0.500 in 2ftwA Skipped atom 1405, because occupancy 0.500 <= existing 0.500 in 2ftwA Skipped atom 1407, because occupancy 0.500 <= existing 0.500 in 2ftwA Skipped atom 1409, because occupancy 0.500 <= existing 0.500 in 2ftwA Skipped atom 1821, because occupancy 0.500 <= existing 0.500 in 2ftwA Skipped atom 1825, because occupancy 0.500 <= existing 0.500 in 2ftwA Skipped atom 1827, because occupancy 0.500 <= existing 0.500 in 2ftwA Skipped atom 1923, because occupancy 0.500 <= existing 0.500 in 2ftwA Skipped atom 1927, because occupancy 0.500 <= existing 0.500 in 2ftwA Skipped atom 1929, because occupancy 0.500 <= existing 0.500 in 2ftwA Skipped atom 1931, because occupancy 0.500 <= existing 0.500 in 2ftwA Skipped atom 1933, because occupancy 0.500 <= existing 0.500 in 2ftwA Skipped atom 2340, because occupancy 0.500 <= existing 0.500 in 2ftwA Skipped atom 2344, because occupancy 0.500 <= existing 0.500 in 2ftwA Skipped atom 2346, because occupancy 0.500 <= existing 0.500 in 2ftwA Skipped atom 2348, because occupancy 0.500 <= existing 0.500 in 2ftwA Skipped atom 2350, because occupancy 0.500 <= existing 0.500 in 2ftwA Skipped atom 2352, because occupancy 0.500 <= existing 0.500 in 2ftwA Skipped atom 2354, because occupancy 0.500 <= existing 0.500 in 2ftwA Skipped atom 2356, because occupancy 0.500 <= existing 0.500 in 2ftwA Skipped atom 2491, because occupancy 0.500 <= existing 0.500 in 2ftwA Skipped atom 2495, because occupancy 0.500 <= existing 0.500 in 2ftwA Skipped atom 2497, because occupancy 0.500 <= existing 0.500 in 2ftwA Skipped atom 2499, because occupancy 0.500 <= existing 0.500 in 2ftwA Skipped atom 2542, because occupancy 0.500 <= existing 0.500 in 2ftwA Skipped atom 2546, because occupancy 0.500 <= existing 0.500 in 2ftwA Skipped atom 2548, because occupancy 0.500 <= existing 0.500 in 2ftwA Skipped atom 2737, because occupancy 0.500 <= existing 0.500 in 2ftwA Skipped atom 2741, because occupancy 0.500 <= existing 0.500 in 2ftwA Skipped atom 2743, because occupancy 0.500 <= existing 0.500 in 2ftwA Skipped atom 3160, because occupancy 0.500 <= existing 0.500 in 2ftwA Skipped atom 3164, because occupancy 0.500 <= existing 0.500 in 2ftwA Skipped atom 3166, because occupancy 0.500 <= existing 0.500 in 2ftwA Skipped atom 3168, because occupancy 0.500 <= existing 0.500 in 2ftwA Skipped atom 3170, because occupancy 0.500 <= existing 0.500 in 2ftwA Skipped atom 3172, because occupancy 0.500 <= existing 0.500 in 2ftwA Skipped atom 3205, because occupancy 0.500 <= existing 0.500 in 2ftwA Skipped atom 3209, because occupancy 0.500 <= existing 0.500 in 2ftwA Skipped atom 3211, because occupancy 0.500 <= existing 0.500 in 2ftwA Skipped atom 3488, because occupancy 0.500 <= existing 0.500 in 2ftwA Skipped atom 3492, because occupancy 0.500 <= existing 0.500 in 2ftwA Skipped atom 3494, because occupancy 0.500 <= existing 0.500 in 2ftwA Skipped atom 3496, because occupancy 0.500 <= existing 0.500 in 2ftwA Skipped atom 3498, because occupancy 0.500 <= existing 0.500 in 2ftwA Skipped atom 3500, because occupancy 0.500 <= existing 0.500 in 2ftwA Skipped atom 3767, because occupancy 0.500 <= existing 0.500 in 2ftwA Skipped atom 3771, because occupancy 0.500 <= existing 0.500 in 2ftwA Skipped atom 3773, because occupancy 0.500 <= existing 0.500 in 2ftwA Skipped atom 3775, because occupancy 0.500 <= existing 0.500 in 2ftwA Skipped atom 3777, because occupancy 0.500 <= existing 0.500 in 2ftwA Skipped atom 3779, because occupancy 0.500 <= existing 0.500 in 2ftwA Skipped atom 3781, because occupancy 0.500 <= existing 0.500 in 2ftwA Skipped atom 3783, because occupancy 0.500 <= existing 0.500 in 2ftwA # T0315 read from 2ftwA/T0315-2ftwA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2ftwA read from 2ftwA/T0315-2ftwA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2ftwA to template set # found chain 2ftwA in template set Warning: unaligning (T0315)I90 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2ftwA)C159 Warning: unaligning (T0315)E92 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2ftwA)C159 T0315 2 :LIDTHVHLND 2ftwA 62 :GIDTHTHFQL T0315 13 :QYDD 2ftwA 72 :PFMG T0315 17 :DLSEVITRAREAGVDRMFVVGFN 2ftwA 81 :DFDIGTQAAVAGGTTFIIDFVIP T0315 40 :KSTIERAMKLIDEYDFLYGIIGWH 2ftwA 110 :LEAYDQWKKWADEKVNCDYSLHVA T0315 67 :AIDFTEEHLEWIESLAQHPKVIG 2ftwA 134 :ITWWSEQVSREMEILVKERGVNS T0315 93 :MGL 2ftwA 160 :FMA T0315 97 :YHWDKSPA 2ftwA 163 :YKNSFMVT T0315 108 :KEVFRKQIALAKRLKLPIIIHN 2ftwA 171 :DQEMYHIFKRCKELGAIAQVHA T0315 130 :REATQDCIDILLEE 2ftwA 226 :AEATNRAIVIADSV T0315 147 :EVGGIM 2ftwA 240 :CTPVYI T0315 153 :HSF 2ftwA 247 :HVQ T0315 158 :SPEIADIVTN 2ftwA 250 :SIGAADVICK T0315 168 :KLNFYISLGGP 2ftwA 262 :KEGVRVYGEPI T0315 179 :VTFKNAKQPKEVAKHVS 2ftwA 280 :GSHMWNHDWRHAAAFVM T0315 205 :APY 2ftwA 297 :GPP T0315 216 :KRNEPARVTLVAEQIAE 2ftwA 300 :IRPDPRTKGVLMDYLAR Number of specific fragments extracted= 16 number of extra gaps= 0 total=671 Will force an alignment to be made, even if fragment is small Number of alignments=46 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2ftwA/T0315-2ftwA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0315 read from 2ftwA/T0315-2ftwA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2ftwA read from 2ftwA/T0315-2ftwA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2ftwA in template set Warning: unaligning (T0315)I90 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2ftwA)C159 Warning: unaligning (T0315)E92 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2ftwA)C159 Warning: unaligning (T0315)S195 because of BadResidue code BAD_PEPTIDE in next template residue (2ftwA)L319 Warning: unaligning (T0315)M196 because of BadResidue code BAD_PEPTIDE at template residue (2ftwA)L319 T0315 1 :MLIDTHVHLNDEQY 2ftwA 61 :GGIDTHTHFQLPFM T0315 15 :DDDLSEVITRAREAGVDRMFVVGF 2ftwA 79 :VDDFDIGTQAAVAGGTTFIIDFVI T0315 39 :NKST 2ftwA 104 :TRGQ T0315 43 :IERAMKLIDE 2ftwA 113 :YDQWKKWADE T0315 55 :FLYGIIGWHPV 2ftwA 123 :KVNCDYSLHVA T0315 67 :AIDFTEEHLEWIESLAQHPKVIG 2ftwA 134 :ITWWSEQVSREMEILVKERGVNS T0315 93 :M 2ftwA 160 :F T0315 97 :YHWDKS 2ftwA 161 :MAYKNS T0315 104 :ADVQKEVFRKQIALAKRLKLPIIIHNRE 2ftwA 167 :FMVTDQEMYHIFKRCKELGAIAQVHAEN T0315 132 :ATQDCIDILLEE 2ftwA 228 :ATNRAIVIADSV T0315 146 :EEVGGIMHS 2ftwA 240 :CTPVYIVHV T0315 157 :GSPEIADIVTN 2ftwA 249 :QSIGAADVICK T0315 168 :KLNFYIS 2ftwA 262 :KEGVRVY T0315 175 :LGGPVTF 2ftwA 296 :MGPPIRP T0315 182 :KNAKQPKEVAKHV 2ftwA 305 :RTKGVLMDYLARG T0315 197 :E 2ftwA 320 :D T0315 200 :LVETD 2ftwA 321 :CVGTD T0315 205 :AP 2ftwA 327 :CT T0315 217 :RNEPARVTLVAEQIAELKG 2ftwA 348 :VNGVEDRMSIVWENGVNTG T0315 236 :LSYEEVCEQTTKNAEKLFNL 2ftwA 368 :LTWCQFVRATSSERARIFNI Number of specific fragments extracted= 20 number of extra gaps= 1 total=691 Will force an alignment to be made, even if fragment is small Number of alignments=47 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2ftwA/T0315-2ftwA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0315 read from 2ftwA/T0315-2ftwA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2ftwA read from 2ftwA/T0315-2ftwA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2ftwA in template set Warning: unaligning (T0315)I90 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2ftwA)C159 Warning: unaligning (T0315)E92 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2ftwA)C159 T0315 2 :LIDTHVHLND 2ftwA 62 :GIDTHTHFQL T0315 13 :QYDD 2ftwA 72 :PFMG T0315 17 :DLSEVITRAREAGVDRMFVVGFN 2ftwA 81 :DFDIGTQAAVAGGTTFIIDFVIP T0315 40 :KSTIERAMKLIDEYDFLYGIIGWH 2ftwA 110 :LEAYDQWKKWADEKVNCDYSLHVA T0315 67 :AIDFTEEHLEWIESLAQHPKVIG 2ftwA 134 :ITWWSEQVSREMEILVKERGVNS T0315 93 :MGLDYHWDKSPADVQKEVF 2ftwA 160 :FMAYKNSFMVTDQEMYHIF T0315 116 :ALAKRLKLPIIIHNRE 2ftwA 179 :KRCKELGAIAQVHAEN T0315 133 :TQDCIDILLEEHAEE 2ftwA 195 :GDMVFEGQKKMLEMG T0315 148 :VGGIMHSFSGSPEIADI 2ftwA 240 :CTPVYIVHVQSIGAADV T0315 166 :TNKL 2ftwA 257 :ICKH T0315 170 :NFYISLGGPV 2ftwA 264 :GVRVYGEPIA T0315 180 :TFKNAKQPKEVAKHV 2ftwA 281 :SHMWNHDWRHAAAFV T0315 205 :APYLSPHP 2ftwA 297 :GPPIRPDP T0315 213 :YRGKRNEPARVTLVAEQIAELKG 2ftwA 364 :NTGKLTWCQFVRATSSERARIFN Number of specific fragments extracted= 14 number of extra gaps= 0 total=705 Will force an alignment to be made, even if fragment is small Number of alignments=48 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ra0A/T0315-1ra0A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0315 read from 1ra0A/T0315-1ra0A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ra0A read from 1ra0A/T0315-1ra0A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1ra0A in training set T0315 2 :LIDTHVHLNDEQYDD 1ra0A 57 :FVEPHIHLDTTQTAG T0315 17 :DLSEVITRAREAGVDRM 1ra0A 103 :RAWQTLKWQIANGIQHV T0315 34 :FVVGFN 1ra0A 121 :THVDVS T0315 40 :K 1ra0A 128 :A T0315 41 :STIERAMKLIDEYD 1ra0A 131 :TALKAMLEVKQEVA T0315 55 :FLYGIIGWHPVDAIDFTEEHLEWIESLAQHP 1ra0A 146 :WIDLQIVAFPQEGILSYPNGEALLEEALRLG T0315 86 :KV 1ra0A 178 :DV T0315 90 :IGEM 1ra0A 180 :VGAI T0315 96 :DYH 1ra0A 184 :PHF T0315 101 :KSPADVQKEVFRKQIALAKRLKLPIIIHN 1ra0A 187 :EFTREYGVESLHKTFALAQKYDRLIDVHC T0315 130 :REATQDCIDILLEEHAEEVGGIMHS 1ra0A 223 :SRFVETVAALAHHEGMGARVTASHT T0315 155 :FSGSPEIADIVTN 1ra0A 251 :HSYNGAYTSRLFR T0315 168 :KLNFYISLG 1ra0A 267 :MSGINFVAN T0315 177 :GPVTFKNA 1ra0A 285 :RFDTYPKR T0315 185 :KQPKEVAKHVS 1ra0A 296 :TRVKEMLESGI T0315 198 :RLLVETDA 1ra0A 307 :NVCFGHDG T0315 206 :PYLSP 1ra0A 318 :PWYPL T0315 219 :EPARVTLVAEQIAELKG 1ra0A 323 :GTANMLQVLHMGLHVCQ T0315 236 :LSYEEVCE 1ra0A 341 :MGYGQIND T0315 245 :TTKNAEKLFNLN 1ra0A 353 :ITHHSARTLNLQ Number of specific fragments extracted= 20 number of extra gaps= 0 total=725 Will force an alignment to be made, even if fragment is small Number of alignments=49 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ra0A/T0315-1ra0A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0315 read from 1ra0A/T0315-1ra0A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ra0A read from 1ra0A/T0315-1ra0A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1ra0A in training set T0315 2 :LIDTHVHLNDEQY 1ra0A 57 :FVEPHIHLDTTQT T0315 15 :DDDLSEVITRAREAGVDRMFV 1ra0A 101 :KQRAWQTLKWQIANGIQHVRT T0315 36 :VGFNKST 1ra0A 123 :VDVSDAT T0315 43 :IERAMKLIDEYD 1ra0A 133 :LKAMLEVKQEVA T0315 55 :FLYGIIGWHPVDAIDFTEEHLEWIESLAQH 1ra0A 146 :WIDLQIVAFPQEGILSYPNGEALLEEALRL T0315 86 :KVIGIGEM 1ra0A 176 :GADVVGAI T0315 98 :HWDKSPADVQKEVFRKQIALAKRLKLPIIIHN 1ra0A 184 :PHFEFTREYGVESLHKTFALAQKYDRLIDVHC T0315 132 :ATQDCIDILLEEHAEEVGGIMHSF 1ra0A 225 :FVETVAALAHHEGMGARVTASHTT T0315 156 :SGSPEIADIVTN 1ra0A 252 :SYNGAYTSRLFR T0315 168 :KLNFYIS 1ra0A 267 :MSGINFV T0315 177 :GPVTFKNAKQ 1ra0A 285 :RFDTYPKRRG T0315 187 :PKEVAKHVS 1ra0A 298 :VKEMLESGI T0315 198 :RLLVETD 1ra0A 307 :NVCFGHD T0315 205 :APYLSP 1ra0A 317 :DPWYPL T0315 219 :EPARVTLVAEQIAELKG 1ra0A 323 :GTANMLQVLHMGLHVCQ T0315 236 :LSYEEVCEQT 1ra0A 341 :MGYGQINDGL T0315 246 :TKNAEKLFNLN 1ra0A 354 :THHSARTLNLQ Number of specific fragments extracted= 17 number of extra gaps= 0 total=742 Will force an alignment to be made, even if fragment is small Number of alignments=50 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ra0A/T0315-1ra0A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0315 read from 1ra0A/T0315-1ra0A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ra0A read from 1ra0A/T0315-1ra0A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1ra0A in training set T0315 9 :LNDEQYDDDLSEVITRAREAGVDRMFVVG 1ra0A 95 :LTHDDVKQRAWQTLKWQIANGIQHVRTHV T0315 38 :FNKST 1ra0A 125 :VSDAT T0315 43 :IERAMKLIDEYDF 1ra0A 133 :LKAMLEVKQEVAP T0315 56 :LYGIIGWHPVDAIDFTEEHLEWIESLAQH 1ra0A 147 :IDLQIVAFPQEGILSYPNGEALLEEALRL T0315 86 :KVIGIGEMGLDY 1ra0A 176 :GADVVGAIPHFE T0315 102 :SPADVQKEVFRKQIALAKRLKLPIIIHN 1ra0A 188 :FTREYGVESLHKTFALAQKYDRLIDVHC T0315 130 :REATQDCIDILLEEHAEEVGGIMHS 1ra0A 223 :SRFVETVAALAHHEGMGARVTASHT T0315 155 :FSGSPEIADI 1ra0A 251 :HSYNGAYTSR T0315 166 :TNKL 1ra0A 261 :LFRL T0315 170 :NFYISLG 1ra0A 269 :GINFVAN T0315 178 :PVTFKNAK 1ra0A 286 :FDTYPKRR T0315 186 :QPKEVAKH 1ra0A 297 :RVKEMLES T0315 198 :RLLVETDAPYLSPHPYR 1ra0A 307 :NVCFGHDGVFDPWYPLG T0315 220 :PARVTLVAEQIAELKG 1ra0A 324 :TANMLQVLHMGLHVCQ T0315 236 :LSYEEVCE 1ra0A 341 :MGYGQIND Number of specific fragments extracted= 15 number of extra gaps= 0 total=757 Will force an alignment to be made, even if fragment is small Number of alignments=51 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1j79A/T0315-1j79A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1j79A expands to /projects/compbio/data/pdb/1j79.pdb.gz 1j79A:Skipped atom 64, because occupancy 0.500 <= existing 0.500 in 1j79A Skipped atom 66, because occupancy 0.500 <= existing 0.500 in 1j79A Skipped atom 68, because occupancy 0.500 <= existing 0.500 in 1j79A Skipped atom 70, because occupancy 0.500 <= existing 0.500 in 1j79A Skipped atom 72, because occupancy 0.500 <= existing 0.500 in 1j79A Skipped atom 74, because occupancy 0.500 <= existing 0.500 in 1j79A Skipped atom 76, because occupancy 0.500 <= existing 0.500 in 1j79A Skipped atom 194, because occupancy 0.500 <= existing 0.500 in 1j79A Skipped atom 196, because occupancy 0.500 <= existing 0.500 in 1j79A Skipped atom 198, because occupancy 0.500 <= existing 0.500 in 1j79A Skipped atom 200, because occupancy 0.500 <= existing 0.500 in 1j79A Skipped atom 464, because occupancy 0.500 <= existing 0.500 in 1j79A Skipped atom 466, because occupancy 0.500 <= existing 0.500 in 1j79A Skipped atom 468, because occupancy 0.500 <= existing 0.500 in 1j79A Skipped atom 470, because occupancy 0.500 <= existing 0.500 in 1j79A Skipped atom 472, because occupancy 0.500 <= existing 0.500 in 1j79A Bad short name: CX for alphabet: pdb_atoms Bad short name: OQ1 for alphabet: pdb_atoms Bad short name: OQ2 for alphabet: pdb_atoms Skipped atom 840, because occupancy 0.500 <= existing 0.500 in 1j79A Skipped atom 842, because occupancy 0.500 <= existing 0.500 in 1j79A Skipped atom 844, because occupancy 0.500 <= existing 0.500 in 1j79A Skipped atom 846, because occupancy 0.500 <= existing 0.500 in 1j79A Skipped atom 1020, because occupancy 0.500 <= existing 0.500 in 1j79A Skipped atom 1022, because occupancy 0.500 <= existing 0.500 in 1j79A Skipped atom 1024, because occupancy 0.500 <= existing 0.500 in 1j79A Skipped atom 1026, because occupancy 0.500 <= existing 0.500 in 1j79A Skipped atom 1028, because occupancy 0.500 <= existing 0.500 in 1j79A Skipped atom 1107, because occupancy 0.500 <= existing 0.500 in 1j79A Skipped atom 1109, because occupancy 0.500 <= existing 0.500 in 1j79A Skipped atom 1111, because occupancy 0.500 <= existing 0.500 in 1j79A Skipped atom 1215, because occupancy 0.500 <= existing 0.500 in 1j79A Skipped atom 1217, because occupancy 0.500 <= existing 0.500 in 1j79A Skipped atom 1219, because occupancy 0.500 <= existing 0.500 in 1j79A Skipped atom 1221, because occupancy 0.500 <= existing 0.500 in 1j79A Skipped atom 1223, because occupancy 0.500 <= existing 0.500 in 1j79A Skipped atom 1225, because occupancy 0.500 <= existing 0.500 in 1j79A Skipped atom 1227, because occupancy 0.500 <= existing 0.500 in 1j79A Skipped atom 1534, because occupancy 0.500 <= existing 0.500 in 1j79A Skipped atom 1536, because occupancy 0.500 <= existing 0.500 in 1j79A Skipped atom 1538, because occupancy 0.500 <= existing 0.500 in 1j79A Skipped atom 1540, because occupancy 0.500 <= existing 0.500 in 1j79A Skipped atom 1542, because occupancy 0.500 <= existing 0.500 in 1j79A Skipped atom 1544, because occupancy 0.500 <= existing 0.500 in 1j79A Skipped atom 1546, because occupancy 0.500 <= existing 0.500 in 1j79A Skipped atom 1963, because occupancy 0.500 <= existing 0.500 in 1j79A Skipped atom 1965, because occupancy 0.500 <= existing 0.500 in 1j79A Skipped atom 1967, because occupancy 0.500 <= existing 0.500 in 1j79A Skipped atom 2044, because occupancy 0.500 <= existing 0.500 in 1j79A Skipped atom 2046, because occupancy 0.500 <= existing 0.500 in 1j79A Skipped atom 2048, because occupancy 0.500 <= existing 0.500 in 1j79A Skipped atom 2050, because occupancy 0.500 <= existing 0.500 in 1j79A Skipped atom 2052, because occupancy 0.500 <= existing 0.500 in 1j79A Skipped atom 2054, because occupancy 0.500 <= existing 0.500 in 1j79A Skipped atom 2056, because occupancy 0.500 <= existing 0.500 in 1j79A Skipped atom 2387, because occupancy 0.500 <= existing 0.500 in 1j79A Skipped atom 2389, because occupancy 0.500 <= existing 0.500 in 1j79A Skipped atom 2391, because occupancy 0.500 <= existing 0.500 in 1j79A Skipped atom 2393, because occupancy 0.500 <= existing 0.500 in 1j79A Skipped atom 2395, because occupancy 0.500 <= existing 0.500 in 1j79A # T0315 read from 1j79A/T0315-1j79A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1j79A read from 1j79A/T0315-1j79A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1j79A to template set # found chain 1j79A in template set Warning: unaligning (T0315)I90 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1j79A)L103 Warning: unaligning (T0315)E92 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1j79A)L103 T0315 4 :DTHVHLNDEQ 1j79A 14 :DWHLHLRDGD T0315 17 :DLSEVITRAREA 1j79A 24 :MLKTVVPYTSEI T0315 30 :VDRMFVVG 1j79A 36 :YGRAIVMP T0315 38 :FNKSTIERAMKLIDEY 1j79A 50 :TTVEAAVAYRQRILDA T0315 54 :D 1j79A 69 :P T0315 55 :FLYGIIGWHP 1j79A 71 :DFTPLMTCYL T0315 67 :AIDFT 1j79A 81 :TDSLD T0315 75 :LEWIESLAQHPKVIG 1j79A 86 :PNELERGFNEGVFTA T0315 93 :MGLDYHWDKSP 1j79A 104 :YPANATTNSSH T0315 111 :FRKQIALAKRLKLPIIIHN 1j79A 122 :IMPVLERMEKIGMPLLVHG T0315 130 :REATQDCIDI 1j79A 147 :IDIFDREARF T0315 140 :LLE 1j79A 164 :LRQ T0315 144 :HAEEVGGIM 1j79A 167 :RLTALKVVF T0315 153 :HSF 1j79A 177 :HIT T0315 158 :SPEIADIVTN 1j79A 180 :TKDAADYVRD T0315 168 :KLNFYISLGGP 1j79A 191 :NERLAATITPQ T0315 182 :KNAKQPKEVAKHVS 1j79A 229 :IHQQALRELVASGF T0315 197 :ERLLVETDAPYL 1j79A 243 :QRVFLGTDSAPH T0315 209 :SPHPYRGKRNEPARVTLVAEQIAEL 1j79A 261 :SSCGCAGCFNAPTALGSYATVFEEM T0315 235 :GL 1j79A 286 :NA T0315 238 :YEEVCEQTTKNAEKLFNLN 1j79A 288 :LQHFEAFCSVNGPQFYGLP Number of specific fragments extracted= 21 number of extra gaps= 0 total=778 Will force an alignment to be made, even if fragment is small Number of alignments=52 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1j79A/T0315-1j79A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0315 read from 1j79A/T0315-1j79A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1j79A read from 1j79A/T0315-1j79A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1j79A in template set Warning: unaligning (T0315)I90 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1j79A)L103 Warning: unaligning (T0315)Y97 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1j79A)L103 T0315 4 :DTHVHLNDE 1j79A 14 :DWHLHLRDG T0315 16 :DDLSEVITRAREA 1j79A 23 :DMLKTVVPYTSEI T0315 30 :VDRMFVVGFNKST 1j79A 36 :YGRAIVMPNLAPP T0315 43 :IERAMKLIDEY 1j79A 52 :VEAAVAYRQRI T0315 54 :D 1j79A 69 :P T0315 55 :FLYGIIGWHPV 1j79A 71 :DFTPLMTCYLT T0315 68 :IDFT 1j79A 82 :DSLD T0315 75 :LEWIESLAQHPKVIG 1j79A 86 :PNELERGFNEGVFTA T0315 98 :HW 1j79A 104 :YP T0315 102 :SPADV 1j79A 117 :TSVDA T0315 111 :FRKQIALAKRLKLPIIIHNRE 1j79A 122 :IMPVLERMEKIGMPLLVHGEV T0315 132 :ATQDCIDILLEEHAEEVGGIMHSF 1j79A 156 :FIESVMEPLRQRLTALKVVFEHIT T0315 158 :SPEIADIVTN 1j79A 180 :TKDAADYVRD T0315 168 :KLNFYIS 1j79A 191 :NERLAAT T0315 175 :LGGPVTF 1j79A 221 :CLPILKR T0315 182 :KNAKQPKEVAKHVS 1j79A 229 :IHQQALRELVASGF T0315 197 :ERLLVETD 1j79A 243 :QRVFLGTD T0315 205 :APYL 1j79A 252 :APHA T0315 209 :SPHPYRGKRNEPARVTLVAEQIAEL 1j79A 261 :SSCGCAGCFNAPTALGSYATVFEEM T0315 235 :G 1j79A 286 :N T0315 237 :SYEEVCEQTTKNAEKLFNLN 1j79A 287 :ALQHFEAFCSVNGPQFYGLP Number of specific fragments extracted= 21 number of extra gaps= 0 total=799 Will force an alignment to be made, even if fragment is small Number of alignments=53 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1j79A/T0315-1j79A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0315 read from 1j79A/T0315-1j79A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1j79A read from 1j79A/T0315-1j79A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1j79A in template set Warning: unaligning (T0315)I90 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1j79A)L103 Warning: unaligning (T0315)E92 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1j79A)L103 T0315 4 :DTHVHLND 1j79A 14 :DWHLHLRD T0315 15 :DDDLSEVITRARE 1j79A 22 :GDMLKTVVPYTSE T0315 29 :GVDRMFVV 1j79A 35 :IYGRAIVM T0315 37 :GFNKSTIERAMKLI 1j79A 49 :VTTVEAAVAYRQRI T0315 51 :DEYDF 1j79A 64 :DAVPA T0315 56 :LYGIIGWH 1j79A 74 :PLMTCYLT T0315 68 :IDFT 1j79A 82 :DSLD T0315 75 :LEWIESLAQHPKVIG 1j79A 86 :PNELERGFNEGVFTA T0315 93 :M 1j79A 104 :Y T0315 97 :YHWDKSP 1j79A 105 :PANATTN T0315 112 :RKQIALAKRLKLPIIIHN 1j79A 123 :MPVLERMEKIGMPLLVHG T0315 130 :RE 1j79A 150 :FD T0315 132 :ATQDCIDILLEEHAE 1j79A 156 :FIESVMEPLRQRLTA T0315 148 :VGGIMHSFS 1j79A 171 :LKVVFEHIT T0315 158 :SPEIADI 1j79A 180 :TKDAADY T0315 166 :TNKL 1j79A 187 :VRDG T0315 170 :NFYISLG 1j79A 193 :RLAATIT T0315 178 :PVTFK 1j79A 223 :PILKR T0315 184 :AKQPKEVAKH 1j79A 231 :QQALRELVAS T0315 195 :SMERLLVETDA 1j79A 241 :GFQRVFLGTDS T0315 209 :SPHP 1j79A 252 :APHA T0315 213 :YRGKRNEPARVTLVAEQIAELK 1j79A 265 :CAGCFNAPTALGSYATVFEEMN T0315 237 :SYEEVCEQTTKNAEKLFNLNS 1j79A 287 :ALQHFEAFCSVNGPQFYGLPV Number of specific fragments extracted= 23 number of extra gaps= 0 total=822 Will force an alignment to be made, even if fragment is small Number of alignments=54 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ejxC/T0315-1ejxC-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1ejxC expands to /projects/compbio/data/pdb/1ejx.pdb.gz 1ejxC:Skipped atom 387, because occupancy 0.500 <= existing 0.500 in 1ejxC Skipped atom 389, because occupancy 0.500 <= existing 0.500 in 1ejxC Skipped atom 391, because occupancy 0.500 <= existing 0.500 in 1ejxC Skipped atom 700, because occupancy 0.500 <= existing 0.500 in 1ejxC Skipped atom 702, because occupancy 0.500 <= existing 0.500 in 1ejxC Skipped atom 704, because occupancy 0.500 <= existing 0.500 in 1ejxC Skipped atom 1365, because occupancy 0.500 <= existing 0.500 in 1ejxC Skipped atom 1367, because occupancy 0.500 <= existing 0.500 in 1ejxC Skipped atom 1369, because occupancy 0.500 <= existing 0.500 in 1ejxC Bad short name: CX for alphabet: pdb_atoms Bad short name: OQ1 for alphabet: pdb_atoms Bad short name: OQ2 for alphabet: pdb_atoms Skipped atom 1699, because occupancy 0.500 <= existing 0.500 in 1ejxC Skipped atom 1701, because occupancy 0.500 <= existing 0.500 in 1ejxC Skipped atom 1703, because occupancy 0.500 <= existing 0.500 in 1ejxC Skipped atom 2582, because occupancy 0.500 <= existing 0.500 in 1ejxC # T0315 read from 1ejxC/T0315-1ejxC-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ejxC read from 1ejxC/T0315-1ejxC-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1ejxC to template set # found chain 1ejxC in template set Warning: unaligning (T0315)L95 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ejxC)I1218 Warning: unaligning (T0315)Y97 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ejxC)I1218 Warning: unaligning (T0315)V194 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ejxC)V1330 T0315 2 :LIDTHVHLNDEQ 1ejxC 1130 :GIDTHIHWICPQ T0315 21 :VITRAREAGVDRMFVVGFNK 1ejxC 1142 :QAEEALVSGVTTMVGGGTGP T0315 41 :ST 1ejxC 1163 :AG T0315 43 :IERAMKLIDEYD 1ejxC 1174 :PWYISRMLQAAD T0315 55 :FLYGIIGWH 1ejxC 1189 :VNIGLLGKG T0315 66 :DAID 1ejxC 1198 :NVSQ T0315 75 :LEWIESLAQH 1ejxC 1202 :PDALREQVAA T0315 91 :GEMG 1ejxC 1212 :GVIG T0315 98 :HWDKSPA 1ejxC 1219 :HEDWGAT T0315 108 :KEVFRKQIALAKRLKLPIIIHN 1ejxC 1226 :PAAIDCALTVADEMDIQVALHS T0315 130 :REATQDCIDIL 1ejxC 1253 :SGFVEDTLAAI T0315 146 :EEVGGIM 1ejxC 1264 :GGRTIHT T0315 153 :H 1ejxC 1272 :H T0315 154 :SFSGSP 1ejxC 1276 :AGGGHA T0315 165 :VTNKLNFYISLGGPVTF 1ejxC 1287 :ACAHPNILPSSTNPTLP T0315 182 :KNA 1ejxC 1306 :LNT T0315 185 :KQPKEVAKH 1ejxC 1310 :DEHLDMLMV Number of specific fragments extracted= 17 number of extra gaps= 0 total=839 Will force an alignment to be made, even if fragment is small Number of alignments=55 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ejxC/T0315-1ejxC-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0315 read from 1ejxC/T0315-1ejxC-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ejxC read from 1ejxC/T0315-1ejxC-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1ejxC in template set Warning: unaligning (T0315)L95 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ejxC)I1218 Warning: unaligning (T0315)Y97 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ejxC)I1218 T0315 1 :MLIDTHVHLNDEQ 1ejxC 1129 :GGIDTHIHWICPQ T0315 21 :VITRAREAGVDRMFVVGFNK 1ejxC 1142 :QAEEALVSGVTTMVGGGTGP T0315 41 :ST 1ejxC 1163 :AG T0315 43 :IERAMKLIDEYDFLYGIIGWHPV 1ejxC 1174 :PWYISRMLQAADSLPVNIGLLGK T0315 66 :DAID 1ejxC 1198 :NVSQ T0315 75 :LEWIESLAQH 1ejxC 1202 :PDALREQVAA T0315 91 :GEMG 1ejxC 1212 :GVIG T0315 98 :HWDKSPAD 1ejxC 1219 :HEDWGATP T0315 109 :EVFRKQIALAKRLKLPIIIHN 1ejxC 1227 :AAIDCALTVADEMDIQVALHS T0315 132 :ATQDCIDIL 1ejxC 1255 :FVEDTLAAI T0315 145 :AEEVGGIMHS 1ejxC 1264 :GGRTIHTFHT T0315 155 :FSGSP 1ejxC 1277 :GGGHA T0315 165 :VTNKLNFYISLG 1ejxC 1287 :ACAHPNILPSST T0315 177 :GPVTF 1ejxC 1300 :PTLPY Number of specific fragments extracted= 14 number of extra gaps= 0 total=853 Will force an alignment to be made, even if fragment is small Number of alignments=56 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ejxC/T0315-1ejxC-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0315 read from 1ejxC/T0315-1ejxC-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ejxC read from 1ejxC/T0315-1ejxC-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1ejxC in template set Warning: unaligning (T0315)I88 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ejxC)I1218 Warning: unaligning (T0315)I90 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ejxC)I1218 T0315 2 :LIDTHVHLNDEQ 1ejxC 1130 :GIDTHIHWICPQ T0315 21 :VITRAREAGVDRMFVVGFNKST 1ejxC 1142 :QAEEALVSGVTTMVGGGTGPAA T0315 43 :IERAMKLIDEYDFLYGIIGWHPVDAIDFTEEHLEWIESLA 1ejxC 1174 :PWYISRMLQAADSLPVNIGLLGKGNVSQPDALREQVAAGV T0315 87 :V 1ejxC 1215 :G T0315 91 :GE 1ejxC 1219 :HE T0315 96 :DYHWD 1ejxC 1221 :DWGAT T0315 108 :KEVFRKQIALAKRLKLPIIIHN 1ejxC 1226 :PAAIDCALTVADEMDIQVALHS T0315 130 :REATQDCIDIL 1ejxC 1253 :SGFVEDTLAAI T0315 146 :EEVGGIMHSFSG 1ejxC 1264 :GGRTIHTFHTEG T0315 176 :GGPVT 1ejxC 1277 :GGGHA T0315 188 :KEVAKHVSMERLLVETDAPYLSPHPY 1ejxC 1282 :PDIITACAHPNILPSSTNPTLPYTLN T0315 238 :YEEVCEQTTK 1ejxC 1309 :IDEHLDMLMV Number of specific fragments extracted= 12 number of extra gaps= 0 total=865 Will force an alignment to be made, even if fragment is small Number of alignments=57 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1onxA/T0315-1onxA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1onxA expands to /projects/compbio/data/pdb/1onx.pdb.gz 1onxA:Bad short name: CX for alphabet: pdb_atoms Bad short name: OX1 for alphabet: pdb_atoms Bad short name: OX2 for alphabet: pdb_atoms Skipped atom 2519, because occupancy 0.500 <= existing 0.500 in 1onxA Skipped atom 2521, because occupancy 0.500 <= existing 0.500 in 1onxA Skipped atom 2523, because occupancy 0.500 <= existing 0.500 in 1onxA Skipped atom 2525, because occupancy 0.500 <= existing 0.500 in 1onxA # T0315 read from 1onxA/T0315-1onxA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1onxA read from 1onxA/T0315-1onxA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1onxA to template set # found chain 1onxA in template set Warning: unaligning (T0315)I90 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1onxA)C163 Warning: unaligning (T0315)E92 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1onxA)C163 Warning: unaligning (T0315)L233 because of BadResidue code BAD_PEPTIDE in next template residue (1onxA)Y321 Warning: unaligning (T0315)K234 because of BadResidue code BAD_PEPTIDE at template residue (1onxA)Y321 T0315 2 :LIDTHVHL 1onxA 64 :FIDQHVHL T0315 11 :DEQYDDDLS 1onxA 80 :PTTRTPEVA T0315 22 :ITRAREAGVDRMFVV 1onxA 89 :LSRLTEAGVTSVVGL T0315 37 :GFN 1onxA 105 :GTD T0315 42 :TIERAMKLIDEY 1onxA 112 :HPESLLAKTRAL T0315 54 :D 1onxA 127 :G T0315 55 :FLYGIIGWHPVDAIDFTEEHLEWIES 1onxA 129 :SAWMLTGAYHVPSRTITGSVEKDVAI T0315 84 :HPKVIG 1onxA 155 :IDRVIG T0315 93 :MGLDYHWDKSPADVQKEVFRKQIALAKRLKLP 1onxA 164 :AISDHRSAAPDVYHLANMAAESRVGGLLGGKP T0315 125 :IIIHN 1onxA 198 :TVFHM T0315 130 :REATQDCIDILLEEHAEEVGGIM 1onxA 206 :KKALQPIYDLLENCDVPISKLLP T0315 153 :HS 1onxA 230 :HV T0315 156 :SGSPEIADIVTN 1onxA 232 :NRNVPLFEQALE T0315 168 :KLNFYISLGGPVTF 1onxA 246 :RKGGTIDITSSIDE T0315 182 :KNAKQPKEVAKH 1onxA 262 :APAEGIARAVQA T0315 194 :VSMERLLVETDAP 1onxA 275 :IPLARVTLSSDGN T0315 207 :YLSPHP 1onxA 292 :FFDDEG T0315 217 :RNEPARVTLVAEQIAE 1onxA 304 :VAGFETLLETVQVLVK T0315 235 :GLSYEEVCEQTTKNAEKLFNLN 1onxA 322 :DFSISDALRPLTSSVAGFLNLT Number of specific fragments extracted= 19 number of extra gaps= 1 total=884 Will force an alignment to be made, even if fragment is small Number of alignments=58 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1onxA/T0315-1onxA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0315 read from 1onxA/T0315-1onxA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1onxA read from 1onxA/T0315-1onxA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1onxA in template set Warning: unaligning (T0315)I90 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1onxA)C163 Warning: unaligning (T0315)M93 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1onxA)C163 Warning: unaligning (T0315)L233 because of BadResidue code BAD_PEPTIDE in next template residue (1onxA)Y321 Warning: unaligning (T0315)K234 because of BadResidue code BAD_PEPTIDE at template residue (1onxA)Y321 T0315 1 :MLIDTHVHLNDEQY 1onxA 63 :GFIDQHVHLIGGGG T0315 15 :DDDLS 1onxA 84 :TPEVA T0315 22 :ITRAREAGVDRMFVV 1onxA 89 :LSRLTEAGVTSVVGL T0315 37 :GFNKST 1onxA 105 :GTDSIS T0315 43 :IERAMKLIDEY 1onxA 113 :PESLLAKTRAL T0315 54 :D 1onxA 127 :G T0315 55 :FLYGIIGWHPVDAIDFTEEHLEWIES 1onxA 129 :SAWMLTGAYHVPSRTITGSVEKDVAI T0315 84 :HPKVIG 1onxA 155 :IDRVIG T0315 94 :GLDYHWDKSP 1onxA 164 :AISDHRSAAP T0315 104 :ADVQKEVFRKQIALAKRLKLP 1onxA 175 :VYHLANMAAESRVGGLLGGKP T0315 125 :IIIHNRE 1onxA 198 :TVFHMGD T0315 132 :ATQDCID 1onxA 208 :ALQPIYD T0315 140 :LLEEHA 1onxA 215 :LLENCD T0315 146 :EEV 1onxA 222 :PIS T0315 149 :GGIMHSFS 1onxA 226 :LLPTHVNR T0315 158 :SPEIADIVTN 1onxA 234 :NVPLFEQALE T0315 168 :KLNFYISLGGPVTFKNA 1onxA 246 :RKGGTIDITSSIDEPVA T0315 187 :PKEVAKH 1onxA 267 :IARAVQA T0315 194 :VSMERLLVETDAPYLSPHPYRGK 1onxA 275 :IPLARVTLSSDGNGSQPFFDDEG T0315 217 :RNEPARVTLVAEQIAE 1onxA 304 :VAGFETLLETVQVLVK T0315 235 :GLSYEEVCEQTTKNAEKLFNLN 1onxA 322 :DFSISDALRPLTSSVAGFLNLT Number of specific fragments extracted= 21 number of extra gaps= 1 total=905 Will force an alignment to be made, even if fragment is small Number of alignments=59 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1onxA/T0315-1onxA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0315 read from 1onxA/T0315-1onxA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1onxA read from 1onxA/T0315-1onxA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1onxA in template set Warning: unaligning (T0315)I90 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1onxA)C163 Warning: unaligning (T0315)E92 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1onxA)C163 Warning: unaligning (T0315)L233 because of BadResidue code BAD_PEPTIDE in next template residue (1onxA)Y321 Warning: unaligning (T0315)K234 because of BadResidue code BAD_PEPTIDE at template residue (1onxA)Y321 T0315 2 :LIDTHVHL 1onxA 64 :FIDQHVHL T0315 10 :NDEQYDD 1onxA 79 :GPTTRTP T0315 22 :ITRAREAGVDRMFVV 1onxA 89 :LSRLTEAGVTSVVGL T0315 37 :GFNKST 1onxA 105 :GTDSIS T0315 43 :IERAMKLIDEYDF 1onxA 113 :PESLLAKTRALNE T0315 56 :LYGIIGWHPVDAIDFTEEHLEWIESL 1onxA 130 :AWMLTGAYHVPSRTITGSVEKDVAII T0315 85 :PKVIG 1onxA 156 :DRVIG T0315 93 :MGLDYHWDKSPADVQKEVFRKQIALAKRLKLP 1onxA 164 :AISDHRSAAPDVYHLANMAAESRVGGLLGGKP T0315 125 :IIIHN 1onxA 198 :TVFHM T0315 130 :REATQDCIDILLEEHAEEVGGIMHSFSGSPEIADI 1onxA 206 :KKALQPIYDLLENCDVPISKLLPTHVNRNVPLFEQ T0315 166 :TNKL 1onxA 241 :ALEF T0315 170 :NFYISLGGPVTFK 1onxA 248 :GGTIDITSSIDEP T0315 185 :KQPKEVAKH 1onxA 261 :VAPAEGIAR T0315 194 :VSMERLLVETDA 1onxA 275 :IPLARVTLSSDG T0315 206 :PYLSPHPYRG 1onxA 291 :PFFDDEGNLT T0315 216 :KRNEPARVTLVAEQIAE 1onxA 303 :GVAGFETLLETVQVLVK T0315 235 :GLSYEEV 1onxA 322 :DFSISDA Number of specific fragments extracted= 17 number of extra gaps= 1 total=922 Will force an alignment to be made, even if fragment is small Number of alignments=60 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1o12A/T0315-1o12A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1o12A expands to /projects/compbio/data/pdb/1o12.pdb.gz 1o12A:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0315 read from 1o12A/T0315-1o12A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1o12A read from 1o12A/T0315-1o12A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1o12A to template set # found chain 1o12A in template set T0315 1 :MLIDTHVHLN 1o12A 44 :GFVDPHIHGV T0315 15 :DD 1o12A 54 :VG T0315 17 :DLSEVITRAREAGVDRMFVVG 1o12A 62 :DFSEMEEFLYSQGVTTFLATT T0315 38 :FNKST 1o12A 85 :TSLEK T0315 43 :IERAMKLIDEYD 1o12A 94 :LRKARDYILENP T0315 55 :FLYGIIGWHPVDAIDFT 1o12A 108 :SLLGVHLEGPYISKEKK T0315 72 :EEHL 1o12A 137 :EREL T0315 80 :SLAQH 1o12A 141 :SEIDS T0315 86 :KVIGIGEM 1o12A 146 :PAKMLTFA T0315 95 :LDYHW 1o12A 159 :SELLL T0315 122 :KLPIII 1o12A 169 :DIVLSA T0315 128 :HNREATQDCIDILL 1o12A 176 :HSIATFEEFMKFYK T0315 146 :EEVGGIMHSF 1o12A 190 :EGVKRITHFP T0315 156 :SGSPEIADIVTNKLNFYISLGGPVTFKNAKQPKEVAKHVSMERLLVETDAPYLSPHP 1o12A 207 :HREIGITGAGLLLDDVKLELICDGVHLSREMVKLVYKVKKANGIVLVTDSISAAGLK T0315 215 :GK 1o12A 264 :DG T0315 217 :RNEPARVTLVAEQIAELKGLSYEEVCEQTTKNAEKLFNLN 1o12A 289 :AGSTLFFSQAVKNFRKFTGCSITELAKVSSYNSCVELGLD Number of specific fragments extracted= 16 number of extra gaps= 0 total=938 Will force an alignment to be made, even if fragment is small Number of alignments=61 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1o12A/T0315-1o12A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0315 read from 1o12A/T0315-1o12A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1o12A read from 1o12A/T0315-1o12A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1o12A in template set T0315 1 :MLIDTHVHLNDEQY 1o12A 44 :GFVDPHIHGVVGAD T0315 15 :DDDLSEVITRAREAGVDRMFVV 1o12A 60 :NCDFSEMEEFLYSQGVTTFLAT T0315 37 :GFNKST 1o12A 84 :STSLEK T0315 43 :IERAMKLIDEYD 1o12A 94 :LRKARDYILENP T0315 55 :FLYGIIGWHPV 1o12A 108 :SLLGVHLEGPY T0315 66 :DAIDFTEEHL 1o12A 131 :HIRPPSEREL T0315 83 :Q 1o12A 141 :S T0315 84 :HPKVIGIGEM 1o12A 144 :DSPAKMLTFA T0315 99 :W 1o12A 154 :P T0315 131 :E 1o12A 155 :E T0315 144 :HAEEVGGIMHS 1o12A 167 :KRDIVLSAGHS T0315 156 :SGSPEIADIVTN 1o12A 178 :IATFEEFMKFYK T0315 169 :LNFYIS 1o12A 190 :EGVKRI T0315 175 :LGGPVTFKNAKQPKEVAKHVSMERLLVETD 1o12A 226 :LICDGVHLSREMVKLVYKVKKANGIVLVTD T0315 205 :APYLSP 1o12A 257 :ISAAGL T0315 214 :RGK 1o12A 263 :KDG T0315 217 :RNEPARVTLVAEQIAELKGLSYEEVCEQTTKNAEKLFNLN 1o12A 289 :AGSTLFFSQAVKNFRKFTGCSITELAKVSSYNSCVELGLD Number of specific fragments extracted= 17 number of extra gaps= 0 total=955 Will force an alignment to be made, even if fragment is small Number of alignments=62 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1o12A/T0315-1o12A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0315 read from 1o12A/T0315-1o12A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1o12A read from 1o12A/T0315-1o12A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1o12A in template set T0315 2 :LIDTHVHLNDEQ 1o12A 45 :FVDPHIHGVVGA T0315 14 :YDDDLSEVITRAREAGVDRMFVV 1o12A 59 :MNCDFSEMEEFLYSQGVTTFLAT T0315 37 :GFNKST 1o12A 84 :STSLEK T0315 43 :IERAMKLIDEYDF 1o12A 94 :LRKARDYILENPS T0315 56 :LYGIIGWHPVDAIDFT 1o12A 109 :LLGVHLEGPYISKEKK T0315 79 :ESLAQHPKVIGIGEM 1o12A 163 :LRLVKRDIVLSAGHS T0315 101 :KSPADVQKEVF 1o12A 178 :IATFEEFMKFY T0315 120 :RLKLPIIIHN 1o12A 189 :KEGVKRITHF T0315 130 :RE 1o12A 208 :RE T0315 135 :DCIDIL 1o12A 211 :GITGAG T0315 143 :EHAEEVGGIMHSFSG 1o12A 217 :LLLDDVKLELICDGV T0315 158 :SPEIAD 1o12A 234 :SREMVK T0315 189 :EVAKHVSMERLLVETDAPYLSPHP 1o12A 240 :LVYKVKKANGIVLVTDSISAAGLK T0315 213 :YRGKR 1o12A 284 :EDGTL T0315 218 :NEPARVTLVAEQIAELKGLSYEEVCEQTTKNAEKLFNLN 1o12A 290 :GSTLFFSQAVKNFRKFTGCSITELAKVSSYNSCVELGLD Number of specific fragments extracted= 15 number of extra gaps= 0 total=970 Will force an alignment to be made, even if fragment is small Number of alignments=63 # Reading fragments from alignment file # Attempting to read fragment alignments from file 4ubpC/T0315-4ubpC-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 4ubpC expands to /projects/compbio/data/pdb/4ubp.pdb.gz 4ubpC:# T0315 read from 4ubpC/T0315-4ubpC-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 4ubpC read from 4ubpC/T0315-4ubpC-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 4ubpC to template set # found chain 4ubpC in template set Warning: unaligning (T0315)I90 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (4ubpC)I221 Warning: unaligning (T0315)E92 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (4ubpC)I221 Warning: unaligning (T0315)I127 because of BadResidue code BAD_PEPTIDE in next template residue (4ubpC)H249 Warning: unaligning (T0315)H128 because of BadResidue code BAD_PEPTIDE at template residue (4ubpC)H249 Warning: unaligning (T0315)Y238 because of BadResidue code BAD_PEPTIDE in next template residue (4ubpC)N328 T0315 2 :LIDTHVHLNDEQ 4ubpC 133 :GIDTHVHFINPD T0315 21 :VITRAREAGVDRMFVVGFNK 4ubpC 145 :QVDVALANGITTLFGGGTGP T0315 41 :STIER 4ubpC 166 :EGSKA T0315 46 :AMKLIDEYDFLYGIIGWHPVDAIDFTEEHLEWIESLA 4ubpC 180 :IEKMLKSTEGLPINVGILGKGHGSSIAPIMEQIDAGA T0315 88 :IG 4ubpC 217 :AG T0315 93 :M 4ubpC 222 :H T0315 95 :LDYHWD 4ubpC 223 :EDWGAT T0315 108 :KEVFRKQIALAKRLKLPII 4ubpC 229 :PASIDRSLTVADEADVQVA T0315 129 :N 4ubpC 250 :S T0315 130 :REATQDCIDIL 4ubpC 256 :AGFLEDTLRAI T0315 146 :EEVGGIM 4ubpC 267 :NGRVIHS T0315 153 :HSFS 4ubpC 275 :HVEG T0315 169 :LN 4ubpC 279 :AG T0315 176 :GGPVT 4ubpC 281 :GGHAP T0315 189 :EVAKHVSMERLLVETDAPYLSPHP 4ubpC 286 :DIMAMAGHPNVLPSSTNPTRPFTV T0315 221 :ARVTLVAEQIAELKGLS 4ubpC 310 :NTIDEHLDMLMVCHHLK Number of specific fragments extracted= 16 number of extra gaps= 2 total=986 Will force an alignment to be made, even if fragment is small Number of alignments=64 # Reading fragments from alignment file # Attempting to read fragment alignments from file 4ubpC/T0315-4ubpC-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0315 read from 4ubpC/T0315-4ubpC-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 4ubpC read from 4ubpC/T0315-4ubpC-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 4ubpC in template set Warning: unaligning (T0315)L95 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (4ubpC)I221 Warning: unaligning (T0315)Y97 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (4ubpC)I221 Warning: unaligning (T0315)I127 because of BadResidue code BAD_PEPTIDE in next template residue (4ubpC)H249 Warning: unaligning (T0315)H128 because of BadResidue code BAD_PEPTIDE at template residue (4ubpC)H249 T0315 1 :MLIDTHVHLNDEQ 4ubpC 132 :GGIDTHVHFINPD T0315 21 :VITRAREAGVDRMFVVGFNK 4ubpC 145 :QVDVALANGITTLFGGGTGP T0315 41 :ST 4ubpC 166 :EG T0315 43 :IERAMKLIDEYDFLYGIIGWHPVDAIDFTEEHLEWIES 4ubpC 177 :PWNIEKMLKSTEGLPINVGILGKGHGSSIAPIMEQIDA T0315 91 :GEMG 4ubpC 215 :GAAG T0315 98 :HWDKSPAD 4ubpC 222 :HEDWGATP T0315 109 :EVFRKQIALAKRLKLPII 4ubpC 230 :ASIDRSLTVADEADVQVA T0315 129 :N 4ubpC 250 :S T0315 132 :ATQDCIDIL 4ubpC 258 :FLEDTLRAI T0315 145 :AEEVGGIMHSFS 4ubpC 267 :NGRVIHSFHVEG T0315 169 :LN 4ubpC 279 :AG T0315 176 :GGPVT 4ubpC 281 :GGHAP T0315 189 :EVAKHVSMERLLVETDAPYLSPHP 4ubpC 286 :DIMAMAGHPNVLPSSTNPTRPFTV T0315 221 :ARVTLVAEQIAELKGLS 4ubpC 310 :NTIDEHLDMLMVCHHLK T0315 238 :YEEVC 4ubpC 330 :PEDVA Number of specific fragments extracted= 15 number of extra gaps= 1 total=1001 Will force an alignment to be made, even if fragment is small Number of alignments=65 # Reading fragments from alignment file # Attempting to read fragment alignments from file 4ubpC/T0315-4ubpC-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0315 read from 4ubpC/T0315-4ubpC-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 4ubpC read from 4ubpC/T0315-4ubpC-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 4ubpC in template set Warning: unaligning (T0315)I88 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (4ubpC)I221 Warning: unaligning (T0315)I90 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (4ubpC)I221 Warning: unaligning (T0315)I127 because of BadResidue code BAD_PEPTIDE in next template residue (4ubpC)H249 Warning: unaligning (T0315)H128 because of BadResidue code BAD_PEPTIDE at template residue (4ubpC)H249 T0315 2 :LIDTHVHLNDEQ 4ubpC 133 :GIDTHVHFINPD T0315 21 :VITRAREAGVDRMFVVGFNK 4ubpC 145 :QVDVALANGITTLFGGGTGP T0315 41 :ST 4ubpC 166 :EG T0315 43 :IERAMKLIDEYDFLYGIIGWHPVDAIDFTEEHLEWIESLA 4ubpC 177 :PWNIEKMLKSTEGLPINVGILGKGHGSSIAPIMEQIDAGA T0315 86 :KV 4ubpC 217 :AG T0315 91 :GE 4ubpC 222 :HE T0315 96 :DYHWD 4ubpC 224 :DWGAT T0315 108 :KEVFRKQIALAKRLKLPII 4ubpC 229 :PASIDRSLTVADEADVQVA T0315 129 :N 4ubpC 250 :S T0315 130 :REATQDCIDIL 4ubpC 256 :AGFLEDTLRAI T0315 148 :VGGIMHSFS 4ubpC 267 :NGRVIHSFH T0315 176 :GGPVT 4ubpC 281 :GGHAP T0315 189 :EVAKHVSMERLLVETDAPYLSPHPY 4ubpC 286 :DIMAMAGHPNVLPSSTNPTRPFTVN T0315 222 :RVTLVAEQIAELKGLS 4ubpC 311 :TIDEHLDMLMVCHHLK Number of specific fragments extracted= 14 number of extra gaps= 1 total=1015 Will force an alignment to be made, even if fragment is small Number of alignments=66 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1rk6A/T0315-1rk6A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1rk6A expands to /projects/compbio/data/pdb/1rk6.pdb.gz 1rk6A:Skipped atom 424, because occupancy 0.500 <= existing 0.500 in 1rk6A Skipped atom 426, because occupancy 0.500 <= existing 0.500 in 1rk6A Skipped atom 428, because occupancy 0.500 <= existing 0.500 in 1rk6A Skipped atom 430, because occupancy 0.500 <= existing 0.500 in 1rk6A Skipped atom 432, because occupancy 0.500 <= existing 0.500 in 1rk6A Skipped atom 434, because occupancy 0.500 <= existing 0.500 in 1rk6A # T0315 read from 1rk6A/T0315-1rk6A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1rk6A read from 1rk6A/T0315-1rk6A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1rk6A to template set # found chain 1rk6A in template set Warning: unaligning (T0315)D4 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1rk6A)S66 Warning: unaligning (T0315)T5 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1rk6A)S66 T0315 1 :MLI 1rk6A 62 :GFI T0315 6 :HVHLN 1rk6A 67 :HTHDD T0315 17 :DLSEVITRARE 1rk6A 125 :RFSDYLEALRA T0315 31 :DRMFVV 1rk6A 140 :VNAACM T0315 37 :GFNKSTIERAMKLIDEY 1rk6A 162 :EATADEIQAMQALADDA T0315 54 :DFLYGIIG 1rk6A 182 :GAIGISTG T0315 62 :WHP 1rk6A 191 :FYP T0315 66 :DAIDFTE 1rk6A 194 :PAAHAST T0315 76 :EWIESLAQ 1rk6A 201 :EEIIEVCR T0315 84 :HPKVIGIGEM 1rk6A 212 :THGGVYATHM T0315 101 :KSPADVQKEVFRKQIALAKRLKLPIII 1rk6A 222 :RDEGEHIVQALEETFRIGRELDVPVVI T0315 128 :HN 1rk6A 250 :HH T0315 130 :REATQDCIDILLEE 1rk6A 259 :FGRSKETLALIEAA T0315 166 :TNKLNFYISLGGPVTF 1rk6A 273 :MASQDVSLDAYPYVAG T0315 185 :KQPKEVAKH 1rk6A 350 :PDVQRILAF T0315 197 :ERLLVETDAPYLSP 1rk6A 359 :GPTMIGSDGLPHDE T0315 217 :RNEPAR 1rk6A 373 :RPHPRL T0315 223 :VTLVAEQIAELKG 1rk6A 382 :FPRVLGHYSRDLG T0315 236 :LSYEEVCEQTTKNAEKLFNLN 1rk6A 396 :FPLETAVWKMTGLTAAKFGLA Number of specific fragments extracted= 19 number of extra gaps= 1 total=1034 Will force an alignment to be made, even if fragment is small Number of alignments=67 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1rk6A/T0315-1rk6A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0315 read from 1rk6A/T0315-1rk6A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1rk6A read from 1rk6A/T0315-1rk6A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1rk6A in template set Warning: unaligning (T0315)D4 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1rk6A)S66 Warning: unaligning (T0315)T5 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1rk6A)S66 T0315 1 :MLI 1rk6A 62 :GFI T0315 6 :HVHLN 1rk6A 67 :HTHDD T0315 11 :DEQY 1rk6A 77 :HRDM T0315 23 :TRAREAGVDRMFVV 1rk6A 81 :TPKISQGVTTVVTG T0315 37 :GFNK 1rk6A 99 :SLAP T0315 41 :ST 1rk6A 106 :AN T0315 43 :IERAMKLIDEYDFLYGIIGWHPV 1rk6A 126 :FSDYLEALRAAPPAVNAACMVGH T0315 66 :DA 1rk6A 158 :DL T0315 68 :IDFTEEHLEWIESLAQ 1rk6A 161 :REATADEIQAMQALAD T0315 84 :HPKVIGIGEMGLDYHWDKSP 1rk6A 180 :ASGAIGISTGAFYPPAAHAS T0315 108 :KEVFRKQIALAKRLKLPIIIHNRE 1rk6A 200 :TEEIIEVCRPLITHGGVYATHMRD T0315 132 :ATQDCIDILLEE 1rk6A 231 :ALEETFRIGREL T0315 146 :EEVGGIMHSFSGSP 1rk6A 243 :DVPVVISHHKVMGK T0315 160 :EIADIVTNKLNFYISLGGPVTF 1rk6A 267 :ALIEAAMASQDVSLDAYPYVAG T0315 183 :NAKQ 1rk6A 347 :MDEP T0315 187 :PKEVAK 1rk6A 352 :VQRILA T0315 194 :V 1rk6A 358 :F T0315 197 :ERLLVETDAPYLSPHPYR 1rk6A 359 :GPTMIGSDGLPHDERPHP T0315 218 :NEPARVTLVAEQIAELKG 1rk6A 377 :RLWGTFPRVLGHYSRDLG T0315 236 :LSYEEVCEQTTKNAEKLFNLN 1rk6A 396 :FPLETAVWKMTGLTAAKFGLA Number of specific fragments extracted= 20 number of extra gaps= 1 total=1054 Will force an alignment to be made, even if fragment is small Number of alignments=68 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1rk6A/T0315-1rk6A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0315 read from 1rk6A/T0315-1rk6A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1rk6A read from 1rk6A/T0315-1rk6A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1rk6A in template set T0315 9 :LNDEQYDD 1rk6A 112 :LDLLDEGG T0315 17 :DLSEVITRARE 1rk6A 125 :RFSDYLEALRA T0315 31 :DRMFVVG 1rk6A 140 :VNAACMV T0315 38 :FNKSTIERAMKLIDEYDF 1rk6A 163 :ATADEIQAMQALADDALA T0315 56 :LYGIIGWHPVDAIDFTEEHLEWIESLA 1rk6A 184 :IGISTGAFYPPAAHASTEEIIEVCRPL T0315 83 :QHPKVIGIGE 1rk6A 212 :THGGVYATHM T0315 97 :YHW 1rk6A 222 :RDE T0315 100 :DK 1rk6A 226 :EH T0315 107 :QKEVFRKQIALAKRLKLPIIIHN 1rk6A 228 :IVQALEETFRIGRELDVPVVISH T0315 130 :REATQDCIDILLEEHAE 1rk6A 259 :FGRSKETLALIEAAMAS T0315 148 :VGGIMHSFSGS 1rk6A 276 :QDVSLDAYPYV T0315 176 :GGPVTFKNAK 1rk6A 287 :AGSTMLKQDR T0315 192 :KHVSMERLLVETD 1rk6A 297 :VLLAGRTLITWCK T0315 205 :APYLSPHP 1rk6A 311 :YPELSGRD T0315 227 :AEQIAELKGLSYEEVC 1rk6A 319 :LEEIAAERGKSKYDVV Number of specific fragments extracted= 15 number of extra gaps= 0 total=1069 Will force an alignment to be made, even if fragment is small Number of alignments=69 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1j6pA/T0315-1j6pA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1j6pA expands to /projects/compbio/data/pdb/1j6p.pdb.gz 1j6pA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0315 read from 1j6pA/T0315-1j6pA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1j6pA read from 1j6pA/T0315-1j6pA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1j6pA to template set # found chain 1j6pA in template set Warning: unaligning (T0315)N218 because of BadResidue code BAD_PEPTIDE in next template residue (1j6pA)N285 Warning: unaligning (T0315)E219 because of BadResidue code BAD_PEPTIDE at template residue (1j6pA)N285 T0315 2 :LIDTHVHLNDEQYDD 1j6pA 51 :LFNTHTHAPMTLLRG T0315 24 :RAREAGVDRMFVVGFN 1j6pA 102 :EMARHGIAGFVDMYFH T0315 43 :IERAMKLIDEYD 1j6pA 118 :EEWIAKAVRDFG T0315 55 :FLYGIIGWHP 1j6pA 131 :RALLTRGLVD T0315 67 :AIDFTEEHLEWIESLAQ 1j6pA 141 :SNGDDGGRLEENLKLYN T0315 84 :HPKVIGIGEM 1j6pA 164 :GRIFVGFGPH T0315 98 :HWDKSP 1j6pA 174 :SPYLCS T0315 108 :KEVFRKQIALAKRLKLPIIIHN 1j6pA 180 :EEYLKRVFDTAKSLNAPVTIHL T0315 130 :REA 1j6pA 209 :YDL T0315 134 :QDCI 1j6pA 212 :EDIL T0315 142 :EEHAEEVGGIM 1j6pA 216 :NIGLKEVKTIA T0315 153 :HSFSGSP 1j6pA 228 :HCVHLPE T0315 166 :TNKLNFYISLG 1j6pA 240 :LKDIPFFVSHN T0315 183 :NAKQPKEVAKHVS 1j6pA 260 :GIAPVQRMIEHGM T0315 198 :RLLVETDAPY 1j6pA 273 :KVTLGTDGAA T0315 217 :R 1j6pA 283 :S T0315 220 :PARVTLVAEQIAEL 1j6pA 286 :SLNLFFEMRLASLL T0315 234 :KGLSYEEVCEQTTKNAEKLFNLN 1j6pA 306 :RNLDVNTCLKMVTYDGAQAMGFK Number of specific fragments extracted= 18 number of extra gaps= 1 total=1087 Will force an alignment to be made, even if fragment is small Number of alignments=70 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1j6pA/T0315-1j6pA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0315 read from 1j6pA/T0315-1j6pA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1j6pA read from 1j6pA/T0315-1j6pA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1j6pA in template set Warning: unaligning (T0315)S209 because of BadResidue code BAD_PEPTIDE in next template residue (1j6pA)N285 Warning: unaligning (T0315)E219 because of BadResidue code BAD_PEPTIDE at template residue (1j6pA)N285 T0315 2 :LIDTHVHLNDEQY 1j6pA 51 :LFNTHTHAPMTLL T0315 15 :DDDLSEV 1j6pA 88 :TEKMAYY T0315 22 :ITRAREAGVDRMFVVGF 1j6pA 100 :QMEMARHGIAGFVDMYF T0315 42 :TIERAMKLIDEYD 1j6pA 117 :HEEWIAKAVRDFG T0315 55 :FLYGIIGWHPV 1j6pA 131 :RALLTRGLVDS T0315 66 :DAIDFTEEHLEWIESLAQHPK 1j6pA 144 :DDGGRLEENLKLYNEWNGFEG T0315 87 :VIGIGE 1j6pA 167 :FVGFGP T0315 97 :YHWDKSP 1j6pA 173 :HSPYLCS T0315 108 :KEVFRKQIALAKRLKLPIIIHNRE 1j6pA 180 :EEYLKRVFDTAKSLNAPVTIHLYE T0315 132 :ATQD 1j6pA 210 :DLED T0315 140 :LLEEHA 1j6pA 214 :ILNIGL T0315 146 :EEVGGIMHSFSGSP 1j6pA 221 :EVKTIAAHCVHLPE T0315 167 :N 1j6pA 242 :D T0315 169 :LNFYISLG 1j6pA 243 :IPFFVSHN T0315 177 :GPV 1j6pA 260 :GIA T0315 186 :QPKEVAKHVS 1j6pA 263 :PVQRMIEHGM T0315 198 :RLLVETDAPYL 1j6pA 273 :KVTLGTDGAAS T0315 220 :PARVTLVAEQIAEL 1j6pA 286 :SLNLFFEMRLASLL T0315 234 :KG 1j6pA 305 :PR T0315 236 :LSYEEVCEQTTKNAEKLFNLNS 1j6pA 308 :LDVNTCLKMVTYDGAQAMGFKS Number of specific fragments extracted= 20 number of extra gaps= 1 total=1107 Will force an alignment to be made, even if fragment is small Number of alignments=71 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1j6pA/T0315-1j6pA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0315 read from 1j6pA/T0315-1j6pA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1j6pA read from 1j6pA/T0315-1j6pA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1j6pA in template set Warning: unaligning (T0315)N218 because of BadResidue code BAD_PEPTIDE in next template residue (1j6pA)N285 Warning: unaligning (T0315)E219 because of BadResidue code BAD_PEPTIDE at template residue (1j6pA)N285 T0315 2 :LIDTHVHLNDEQYDD 1j6pA 51 :LFNTHTHAPMTLLRG T0315 17 :DLSEVIT 1j6pA 71 :SFEEWLF T0315 24 :RAREAGVDRMFVVGFN 1j6pA 102 :EMARHGIAGFVDMYFH T0315 43 :IERAMKLIDEYDF 1j6pA 118 :EEWIAKAVRDFGM T0315 56 :LYGIIGWHPV 1j6pA 132 :ALLTRGLVDS T0315 66 :DAIDFTEEHLEWIESLA 1j6pA 144 :DDGGRLEENLKLYNEWN T0315 83 :QHPKVIGIGE 1j6pA 163 :EGRIFVGFGP T0315 97 :YHWDKSP 1j6pA 173 :HSPYLCS T0315 108 :KEVFRKQIALAKRLKLPIIIHN 1j6pA 180 :EEYLKRVFDTAKSLNAPVTIHL T0315 130 :RE 1j6pA 209 :YD T0315 133 :TQDC 1j6pA 211 :LEDI T0315 141 :LEEHAEEVGGIMHSFSG 1j6pA 215 :LNIGLKEVKTIAAHCVH T0315 166 :TNKLNFYISLGGPV 1j6pA 240 :LKDIPFFVSHNPAS T0315 183 :NAK 1j6pA 258 :GNG T0315 186 :QPKEVAKH 1j6pA 263 :PVQRMIEH T0315 198 :RLLVETDAPYL 1j6pA 273 :KVTLGTDGAAS T0315 220 :PARVTLVAEQIAEL 1j6pA 286 :SLNLFFEMRLASLL T0315 234 :KGLSYEEVCEQTTKNAEKLFNLN 1j6pA 306 :RNLDVNTCLKMVTYDGAQAMGFK Number of specific fragments extracted= 18 number of extra gaps= 1 total=1125 Will force an alignment to be made, even if fragment is small Number of alignments=72 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1un7A/T0315-1un7A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1un7A expands to Error: no filename for 1un7A # T0315 read from 1un7A/T0315-1un7A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1un7A read from 1un7A/T0315-1un7A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1un7A to template set Error: can't find template for 1un7A or 1un7A, so skipping it. # Reading fragments from alignment file # Attempting to read fragment alignments from file 1un7A/T0315-1un7A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1un7A expands to Error: no filename for 1un7A # T0315 read from 1un7A/T0315-1un7A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1un7A read from 1un7A/T0315-1un7A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1un7A to template set Error: can't find template for 1un7A or 1un7A, so skipping it. # Reading fragments from alignment file # Attempting to read fragment alignments from file 1un7A/T0315-1un7A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1un7A expands to Error: no filename for 1un7A # T0315 read from 1un7A/T0315-1un7A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1un7A read from 1un7A/T0315-1un7A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1un7A to template set Error: can't find template for 1un7A or 1un7A, so skipping it. # Reading fragments from alignment file # Attempting to read fragment alignments from file 1m65A/T0315-1m65A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1m65A expands to /projects/compbio/data/pdb/1m65.pdb.gz 1m65A:Skipped atom 249, because occupancy 0.500 <= existing 0.500 in 1m65A Skipped atom 251, because occupancy 0.500 <= existing 0.500 in 1m65A Skipped atom 253, because occupancy 0.500 <= existing 0.500 in 1m65A Skipped atom 255, because occupancy 0.500 <= existing 0.500 in 1m65A # T0315 read from 1m65A/T0315-1m65A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1m65A read from 1m65A/T0315-1m65A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1m65A to template set # found chain 1m65A in template set Warning: unaligning (T0315)S154 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1m65A)N172 Warning: unaligning (T0315)T180 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1m65A)T195 Warning: unaligning (T0315)F181 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1m65A)T195 T0315 3 :IDTHVHLN 1m65A 4 :VDLHMHTV T0315 11 :DEQYDDDLSEVITRAREAGVDRMFVVGFN 1m65A 13 :STHAYSTLSDYIAQAKQKGIKLFAITDHG T0315 40 :KSTIE 1m65A 50 :HWHFI T0315 52 :EY 1m65A 55 :NM T0315 54 :D 1m65A 65 :G T0315 55 :FLYGIIGWH 1m65A 67 :GILRGIEAN T0315 72 :EEHLEWI 1m65A 87 :GKMFDSL T0315 86 :KVIGIGE 1m65A 94 :DLIIAGF T0315 95 :LDYHWDKSPADVQKEVFRKQIA 1m65A 101 :HEPVFAPHDKATNTQAMIATIA T0315 122 :KLPIIIHN 1m65A 125 :NVHIISHP T0315 131 :EA 1m65A 138 :EI T0315 133 :TQDCIDILLEEHA 1m65A 141 :VKAVAEAAAKHQV T0315 149 :GGIMH 1m65A 154 :ALEIN T0315 160 :EIADIVTN 1m65A 175 :EVAAAVRD T0315 169 :LNFYISLGGPV 1m65A 183 :AGGWVALGSDS T0315 182 :KN 1m65A 197 :FT T0315 184 :AKQPKEVAKHV 1m65A 202 :FEECLKILDAV T0315 195 :SMERL 1m65A 215 :PPERI T0315 205 :AP 1m65A 220 :LN T0315 221 :ARVTLVAEQIAE 1m65A 222 :VSPRRLLNFLES T0315 234 :KGLS 1m65A 234 :RGMA Number of specific fragments extracted= 21 number of extra gaps= 1 total=1146 Will force an alignment to be made, even if fragment is small Number of alignments=73 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1m65A/T0315-1m65A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0315 read from 1m65A/T0315-1m65A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1m65A read from 1m65A/T0315-1m65A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1m65A in template set Warning: unaligning (T0315)T180 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1m65A)T195 Warning: unaligning (T0315)F181 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1m65A)T195 T0315 3 :IDTHVHL 1m65A 4 :VDLHMHT T0315 10 :NDEQYDDDLSEVITRAREAGVDRMFVV 1m65A 12 :ASTHAYSTLSDYIAQAKQKGIKLFAIT T0315 37 :GFNKST 1m65A 47 :APHHWH T0315 54 :D 1m65A 65 :G T0315 55 :FLYGIIGWHPVDAIDF 1m65A 67 :GILRGIEANIKNVDGE T0315 71 :TEEHLEWI 1m65A 86 :SGKMFDSL T0315 86 :KVIGIGEM 1m65A 94 :DLIIAGFH T0315 96 :DYHWDKSPADVQKEVFRKQIA 1m65A 102 :EPVFAPHDKATNTQAMIATIA T0315 121 :LK 1m65A 123 :SG T0315 123 :LPIIIHNRE 1m65A 126 :VHIISHPGN T0315 132 :ATQDCIDILLEE 1m65A 140 :DVKAVAEAAAKH T0315 146 :EEVGGIM 1m65A 152 :QVALEIN T0315 160 :EIADIVTN 1m65A 175 :EVAAAVRD T0315 169 :LNFYISLGGPV 1m65A 183 :AGGWVALGSDS T0315 182 :KNAKQPKEVAKHV 1m65A 200 :GEFEECLKILDAV T0315 195 :SMERLL 1m65A 215 :PPERIL T0315 207 :YL 1m65A 221 :NV T0315 222 :RVTLVAEQIAEL 1m65A 223 :SPRRLLNFLESR T0315 235 :GLS 1m65A 235 :GMA Number of specific fragments extracted= 19 number of extra gaps= 1 total=1165 Will force an alignment to be made, even if fragment is small Number of alignments=74 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1m65A/T0315-1m65A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0315 read from 1m65A/T0315-1m65A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1m65A read from 1m65A/T0315-1m65A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1m65A in template set Warning: unaligning (T0315)S158 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1m65A)N172 Warning: unaligning (T0315)T180 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1m65A)T195 T0315 3 :IDTHVH 1m65A 4 :VDLHMH T0315 11 :DEQYDD 1m65A 10 :TVASTH T0315 17 :DLSEVITRAREAGVDRMFVVGFNK 1m65A 19 :TLSDYIAQAKQKGIKLFAITDHGP T0315 41 :STIER 1m65A 51 :WHFIN T0315 50 :IDEYDF 1m65A 56 :MRIWPR T0315 56 :LYGIIGWHPVDA 1m65A 68 :ILRGIEANIKNV T0315 69 :DFT 1m65A 80 :DGE T0315 72 :EEHLEWI 1m65A 87 :GKMFDSL T0315 86 :KVIGIGEM 1m65A 94 :DLIIAGFH T0315 96 :DYHWDKSPADVQKEVFRKQIA 1m65A 102 :EPVFAPHDKATNTQAMIATIA T0315 122 :KLPIIIHN 1m65A 125 :NVHIISHP T0315 133 :TQDCIDILLEE 1m65A 141 :VKAVAEAAAKH T0315 149 :GGIMHSFSG 1m65A 152 :QVALEINNS T0315 159 :PEIADI 1m65A 174 :REVAAA T0315 166 :TNKLNFYISLGGPV 1m65A 180 :VRDAGGWVALGSDS T0315 181 :FK 1m65A 196 :AF T0315 183 :NAKQPKEVAKH 1m65A 201 :EFEECLKILDA T0315 194 :VSMERLL 1m65A 214 :FPPERIL T0315 237 :SYEEVCEQTTK 1m65A 223 :SPRRLLNFLES Number of specific fragments extracted= 19 number of extra gaps= 1 total=1184 Will force an alignment to be made, even if fragment is small Number of alignments=75 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1yrrA/T0315-1yrrA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1yrrA expands to /projects/compbio/data/pdb/1yrr.pdb.gz 1yrrA:Skipped atom 62, because occupancy 0.500 <= existing 0.500 in 1yrrA Skipped atom 64, because occupancy 0.500 <= existing 0.500 in 1yrrA Skipped atom 66, because occupancy 0.500 <= existing 0.500 in 1yrrA Skipped atom 68, because occupancy 0.500 <= existing 0.500 in 1yrrA Skipped atom 847, because occupancy 0.500 <= existing 0.500 in 1yrrA Skipped atom 849, because occupancy 0.500 <= existing 0.500 in 1yrrA Skipped atom 851, because occupancy 0.500 <= existing 0.500 in 1yrrA Skipped atom 872, because occupancy 0.500 <= existing 0.500 in 1yrrA Skipped atom 874, because occupancy 0.500 <= existing 0.500 in 1yrrA Skipped atom 876, because occupancy 0.500 <= existing 0.500 in 1yrrA Skipped atom 878, because occupancy 0.500 <= existing 0.500 in 1yrrA Skipped atom 880, because occupancy 0.500 <= existing 0.500 in 1yrrA Skipped atom 882, because occupancy 0.500 <= existing 0.500 in 1yrrA Skipped atom 884, because occupancy 0.500 <= existing 0.500 in 1yrrA Skipped atom 985, because occupancy 0.500 <= existing 0.500 in 1yrrA Skipped atom 987, because occupancy 0.500 <= existing 0.500 in 1yrrA Skipped atom 989, because occupancy 0.500 <= existing 0.500 in 1yrrA Skipped atom 1181, because occupancy 0.500 <= existing 0.500 in 1yrrA Skipped atom 1183, because occupancy 0.500 <= existing 0.500 in 1yrrA Skipped atom 1185, because occupancy 0.500 <= existing 0.500 in 1yrrA Skipped atom 1187, because occupancy 0.500 <= existing 0.500 in 1yrrA Skipped atom 1588, because occupancy 0.500 <= existing 0.500 in 1yrrA Skipped atom 1590, because occupancy 0.500 <= existing 0.500 in 1yrrA Skipped atom 1592, because occupancy 0.500 <= existing 0.500 in 1yrrA Skipped atom 1704, because occupancy 0.500 <= existing 0.500 in 1yrrA Skipped atom 1706, because occupancy 0.500 <= existing 0.500 in 1yrrA Skipped atom 1708, because occupancy 0.500 <= existing 0.500 in 1yrrA Skipped atom 1710, because occupancy 0.500 <= existing 0.500 in 1yrrA Skipped atom 1712, because occupancy 0.500 <= existing 0.500 in 1yrrA Skipped atom 1714, because occupancy 0.500 <= existing 0.500 in 1yrrA Skipped atom 1716, because occupancy 0.500 <= existing 0.500 in 1yrrA Skipped atom 1832, because occupancy 0.500 <= existing 0.500 in 1yrrA Skipped atom 1834, because occupancy 0.500 <= existing 0.500 in 1yrrA Skipped atom 1836, because occupancy 0.500 <= existing 0.500 in 1yrrA Skipped atom 1838, because occupancy 0.500 <= existing 0.500 in 1yrrA Skipped atom 2009, because occupancy 0.500 <= existing 0.500 in 1yrrA Skipped atom 2011, because occupancy 0.500 <= existing 0.500 in 1yrrA Skipped atom 2013, because occupancy 0.500 <= existing 0.500 in 1yrrA Skipped atom 2015, because occupancy 0.500 <= existing 0.500 in 1yrrA Skipped atom 2459, because occupancy 0.500 <= existing 0.500 in 1yrrA Skipped atom 2461, because occupancy 0.500 <= existing 0.500 in 1yrrA Skipped atom 2463, because occupancy 0.500 <= existing 0.500 in 1yrrA Skipped atom 2660, because occupancy 0.500 <= existing 0.500 in 1yrrA Skipped atom 2662, because occupancy 0.500 <= existing 0.500 in 1yrrA Skipped atom 2664, because occupancy 0.500 <= existing 0.500 in 1yrrA Skipped atom 2666, because occupancy 0.500 <= existing 0.500 in 1yrrA Skipped atom 2668, because occupancy 0.500 <= existing 0.500 in 1yrrA # T0315 read from 1yrrA/T0315-1yrrA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1yrrA read from 1yrrA/T0315-1yrrA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1yrrA to template set # found chain 1yrrA in template set Warning: unaligning (T0315)P64 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1yrrA)P145 Warning: unaligning (T0315)H128 because of BadResidue code BAD_PEPTIDE in next template residue (1yrrA)S196 Warning: unaligning (T0315)N129 because of BadResidue code BAD_PEPTIDE at template residue (1yrrA)S196 T0315 2 :LIDTHVHL 1yrrA 55 :FIDVQLNG T0315 10 :NDEQ 1yrrA 70 :DTAE T0315 17 :DLSEVITRAREAGVDRM 1yrrA 79 :TLEIMQKANEKSGCTNY T0315 34 :FVVGFNKSTIERAMKLIDEY 1yrrA 98 :TLITTSDELMKQGVRVMREY T0315 54 :D 1yrrA 122 :P T0315 55 :FLYGIIG 1yrrA 126 :LGLHLEG T0315 63 :H 1yrrA 134 :W T0315 65 :VDAIDFTEEHLEWIESLA 1yrrA 146 :NFVRKPDAALVDFLCENA T0315 85 :PKVIGIGEM 1yrrA 164 :DVITKVTLA T0315 95 :LDYHW 1yrrA 173 :PEMVP T0315 112 :RKQIALAKRLKLPIII 1yrrA 178 :AEVISKLANAGIVVSA T0315 130 :REATQDC 1yrrA 197 :NATLKEA T0315 138 :DILLEEHA 1yrrA 204 :KAGFRAGI T0315 149 :GGIMHSF 1yrrA 212 :TFATHLY T0315 156 :SGSPEIADIVTNKLNFYISLGGPVTFKNAKQPKEVAKHVS 1yrrA 226 :GREPGLAGAILDEADIYCGIIADGLHVDYANIRNAKRLKG T0315 197 :ERLLVETDAPYLSPHPYRGK 1yrrA 266 :DKLCLVTDATAPAGANIEQF T0315 219 :EPARVTLVAEQIAELKGLSYEEVCEQTTKNAEKLFNL 1yrrA 309 :SSLTMIEGVRNLVEHCGIALDEVLRMATLYPARAIGV Number of specific fragments extracted= 17 number of extra gaps= 2 total=1201 Will force an alignment to be made, even if fragment is small Number of alignments=76 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1yrrA/T0315-1yrrA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0315 read from 1yrrA/T0315-1yrrA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1yrrA read from 1yrrA/T0315-1yrrA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1yrrA in template set Warning: unaligning (T0315)D66 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1yrrA)N144 Warning: unaligning (T0315)A67 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1yrrA)P145 Warning: unaligning (T0315)N129 because of BadResidue code BAD_PEPTIDE in next template residue (1yrrA)S196 Warning: unaligning (T0315)R130 because of BadResidue code BAD_PEPTIDE at template residue (1yrrA)S196 T0315 1 :MLIDTHVH 1yrrA 54 :GFIDVQLN T0315 9 :LNDEQY 1yrrA 68 :FNDTAE T0315 15 :DDDLSEVITRAREAGVDRMFVV 1yrrA 77 :VETLEIMQKANEKSGCTNYLPT T0315 37 :GFNKSTIERAMKLIDEY 1yrrA 101 :TTSDELMKQGVRVMREY T0315 54 :D 1yrrA 122 :P T0315 55 :FLYGIIGWHPV 1yrrA 124 :QALGLHLEGPW T0315 68 :IDFTEEHLEWIESLAQHPKVIGIGEMGLDYHW 1yrrA 146 :NFVRKPDAALVDFLCENADVITKVTLAPEMVP T0315 112 :RKQIALAKRLKLPIIIH 1yrrA 178 :AEVISKLANAGIVVSAG T0315 131 :EATQDCIDILLEEHA 1yrrA 197 :NATLKEAKAGFRAGI T0315 149 :GGIMHSF 1yrrA 212 :TFATHLY T0315 156 :SGSPEIADIVTNKLNFYISLGGPVTFKNAKQPKEVAKHVS 1yrrA 226 :GREPGLAGAILDEADIYCGIIADGLHVDYANIRNAKRLKG T0315 197 :ERLLVETD 1yrrA 266 :DKLCLVTD T0315 205 :APY 1yrrA 276 :APA T0315 208 :LSPHPYRGK 1yrrA 282 :IEQFIFAGK T0315 217 :RNEPARVTLVAEQI 1yrrA 311 :LTMIEGVRNLVEHC T0315 235 :GLSYEEVCEQTTKNAEKLFNL 1yrrA 325 :GIALDEVLRMATLYPARAIGV Number of specific fragments extracted= 16 number of extra gaps= 2 total=1217 Will force an alignment to be made, even if fragment is small Number of alignments=77 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1yrrA/T0315-1yrrA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0315 read from 1yrrA/T0315-1yrrA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1yrrA read from 1yrrA/T0315-1yrrA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1yrrA in template set Warning: unaligning (T0315)V65 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1yrrA)L137 Warning: unaligning (T0315)D66 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1yrrA)L137 Warning: unaligning (T0315)D69 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1yrrA)T142 Warning: unaligning (T0315)T71 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1yrrA)T142 Warning: unaligning (T0315)N129 because of BadResidue code BAD_PEPTIDE in next template residue (1yrrA)S196 Warning: unaligning (T0315)R130 because of BadResidue code BAD_PEPTIDE at template residue (1yrrA)S196 T0315 2 :LIDTHVH 1yrrA 55 :FIDVQLN T0315 10 :NDEQ 1yrrA 70 :DTAE T0315 14 :YDDDLSEVITRAREAGVDRMFVVGF 1yrrA 76 :SVETLEIMQKANEKSGCTNYLPTLI T0315 39 :NKSTIERAMKLI 1yrrA 103 :SDELMKQGVRVM T0315 51 :DEYDF 1yrrA 119 :AKHPN T0315 56 :LYGIIGWHP 1yrrA 127 :GLHLEGPWL T0315 67 :AI 1yrrA 138 :VK T0315 72 :EEHLEWIESLA 1yrrA 153 :AALVDFLCENA T0315 85 :PKVIGI 1yrrA 164 :DVITKV T0315 92 :EMGLDYHW 1yrrA 170 :TLAPEMVP T0315 112 :RKQIALAKRLKLPIIIH 1yrrA 178 :AEVISKLANAGIVVSAG T0315 131 :EATQDCIDILLEEH 1yrrA 197 :NATLKEAKAGFRAG T0315 148 :VGGIMHSF 1yrrA 211 :ITFATHLY T0315 156 :SGSPEIADIVTNKLNFYISLGGPVTFKNAKQPKEVAKHV 1yrrA 226 :GREPGLAGAILDEADIYCGIIADGLHVDYANIRNAKRLK T0315 196 :MERLLVETDAPYLSPHP 1yrrA 265 :GDKLCLVTDATAPAGAN T0315 214 :RGKR 1yrrA 303 :NGTL T0315 218 :NEPARVTLVAEQIAELKGLSYEEVCEQTTKNAEKLFNL 1yrrA 308 :GSSLTMIEGVRNLVEHCGIALDEVLRMATLYPARAIGV Number of specific fragments extracted= 17 number of extra gaps= 2 total=1234 Will force an alignment to be made, even if fragment is small Number of alignments=78 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1kcxA/T0315-1kcxA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1kcxA expands to /projects/compbio/data/pdb/1kcx.pdb.gz 1kcxA:# T0315 read from 1kcxA/T0315-1kcxA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1kcxA read from 1kcxA/T0315-1kcxA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1kcxA to template set # found chain 1kcxA in template set Warning: unaligning (T0315)S237 because last residue in template chain is (1kcxA)G490 T0315 1 :MLIDTHVHLND 1kcxA 68 :GGIDVNTYLQK T0315 15 :DD 1kcxA 81 :QG T0315 17 :DLSEVITRAREAGVDRMFVVGFN 1kcxA 88 :DFFQGTKAALAGGTTMIIDHVVP T0315 40 :KSTIERAMKLIDEYDFLYGIIGWH 1kcxA 117 :LTSFEKWHEAADTKSCCDYSLHVD T0315 67 :AIDFTEEHLEWIESLAQHPKVIGIGEM 1kcxA 141 :ITSWYDGVREELEVLVQDKGVNSFQVY T0315 95 :LDYHWDKSPA 1kcxA 168 :MAYKDLYQMS T0315 108 :KEVFRKQIALAKRLKLPIIIHNREA 1kcxA 178 :DSQLYEAFTFLKGLGAVILVHAENG T0315 134 :QDCIDILLEEHAEE 1kcxA 203 :DLIAQEQKRILEMG T0315 155 :FSGSP 1kcxA 217 :ITGPE T0315 160 :EIADIVTN 1kcxA 234 :EAVFRAIA T0315 168 :KLNFYISLGGPVTFKNAKQPKEVAKHVS 1kcxA 245 :RINCPVYITKVMSKSAADIIALARKKGP T0315 198 :RLLVE 1kcxA 273 :LVFGE T0315 203 :TDAPYL 1kcxA 285 :TDGTHY T0315 214 :RGK 1kcxA 291 :WSK T0315 217 :RNEPARVTLVAEQIAEL 1kcxA 472 :KPFPEHLYQRVRIRSKV T0315 236 :L 1kcxA 489 :F Number of specific fragments extracted= 16 number of extra gaps= 0 total=1250 Will force an alignment to be made, even if fragment is small Number of alignments=79 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1kcxA/T0315-1kcxA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0315 read from 1kcxA/T0315-1kcxA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1kcxA read from 1kcxA/T0315-1kcxA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1kcxA in template set T0315 1 :MLIDTHVHLND 1kcxA 68 :GGIDVNTYLQK T0315 15 :DDDLSEVITRAREAGVDRMFVVGF 1kcxA 86 :ADDFFQGTKAALAGGTTMIIDHVV T0315 39 :NKST 1kcxA 111 :EPGS T0315 43 :IERAMKLIDEY 1kcxA 120 :FEKWHEAADTK T0315 56 :LYGIIGWHPV 1kcxA 131 :SCCDYSLHVD T0315 67 :AIDFTEEHLEWIESLAQHPKVIGIGEM 1kcxA 141 :ITSWYDGVREELEVLVQDKGVNSFQVY T0315 97 :YHW 1kcxA 168 :MAY T0315 100 :DKSP 1kcxA 172 :DLYQ T0315 107 :QKEVFRKQIALAKRLKLPIIIHNRE 1kcxA 177 :SDSQLYEAFTFLKGLGAVILVHAEN T0315 132 :ATQDCIDILLEE 1kcxA 235 :AVFRAIAIAGRI T0315 146 :EEVGGIM 1kcxA 247 :NCPVYIT T0315 158 :SP 1kcxA 257 :SK T0315 160 :EIADIVTN 1kcxA 262 :DIIALARK T0315 169 :LN 1kcxA 270 :KG T0315 171 :FYIS 1kcxA 273 :LVFG T0315 177 :GPVTFKNAKQPKEVAKHV 1kcxA 285 :TDGTHYWSKNWAKAAAFV T0315 207 :YLSPHPYRGK 1kcxA 303 :TSPPLSPDPT T0315 217 :RNEPARVTLVAEQIAELKG 1kcxA 355 :VNGIEERMTVVWDKAVATG T0315 236 :LSYEEVCEQTTKNAEKLFNL 1kcxA 375 :MDENQFVAVTSTNAAKIFNL Number of specific fragments extracted= 19 number of extra gaps= 0 total=1269 Will force an alignment to be made, even if fragment is small Number of alignments=80 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1kcxA/T0315-1kcxA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0315 read from 1kcxA/T0315-1kcxA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1kcxA read from 1kcxA/T0315-1kcxA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1kcxA in template set Warning: unaligning (T0315)G235 because last residue in template chain is (1kcxA)G490 T0315 2 :LIDTHVHLND 1kcxA 69 :GIDVNTYLQK T0315 14 :YDD 1kcxA 80 :SQG T0315 17 :DLSEVITRAREAGVDRMFVVGFN 1kcxA 88 :DFFQGTKAALAGGTTMIIDHVVP T0315 40 :KSTIERAMKLIDEYDFLYGIIGWH 1kcxA 117 :LTSFEKWHEAADTKSCCDYSLHVD T0315 67 :AIDFTEEHLEWIESLAQHPKVIGIGEMGLDYHWDKSPADVQKEVFR 1kcxA 141 :ITSWYDGVREELEVLVQDKGVNSFQVYMAYKDLYQMSDSQLYEAFT T0315 117 :LAKRLKLPIIIHNRE 1kcxA 187 :FLKGLGAVILVHAEN T0315 133 :TQDCIDILLEEHAEE 1kcxA 202 :GDLIAQEQKRILEMG T0315 159 :PEIADI 1kcxA 237 :FRAIAI T0315 166 :TNKLNFYISLGGPVT 1kcxA 243 :AGRINCPVYITKVMS T0315 185 :KQPKEVAKH 1kcxA 258 :KSAADIIAL T0315 196 :MERLLVE 1kcxA 271 :GPLVFGE T0315 203 :TDAPYLSPHP 1kcxA 285 :TDGTHYWSKN T0315 213 :YRGKRNEPARVTLVAEQIAELK 1kcxA 468 :FIPRKPFPEHLYQRVRIRSKVF Number of specific fragments extracted= 13 number of extra gaps= 0 total=1282 Will force an alignment to be made, even if fragment is small Number of alignments=81 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1k6wA/T0315-1k6wA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1k6wA expands to /projects/compbio/data/pdb/1k6w.pdb.gz 1k6wA:# T0315 read from 1k6wA/T0315-1k6wA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1k6wA read from 1k6wA/T0315-1k6wA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1k6wA to template set # found chain 1k6wA in template set T0315 2 :LIDTHVHLNDEQYDD 1k6wA 57 :FVEPHIHLDTTQTAG T0315 17 :DLSEVITRAREAGVDRMFVVG 1k6wA 103 :RAWQTLKWQIANGIQHVRTHV T0315 38 :FN 1k6wA 125 :VS T0315 40 :K 1k6wA 128 :A T0315 41 :STIERAMKLIDEYD 1k6wA 131 :TALKAMLEVKQEVA T0315 55 :FLYGIIGWHPVDAIDFTEEHLEWIESLAQHP 1k6wA 146 :WIDLQIVAFPQEGILSYPNGEALLEEALRLG T0315 86 :KVI 1k6wA 178 :DVV T0315 91 :GE 1k6wA 181 :GA T0315 95 :LDYH 1k6wA 183 :IPHF T0315 101 :KSPADVQKEVFRKQIALAKRLKLPIIIHN 1k6wA 187 :EFTREYGVESLHKTFALAQKYDRLIDVHC T0315 130 :REATQDCIDILLEEHAEEVGGIMHS 1k6wA 223 :SRFVETVAALAHHEGMGARVTASHT T0315 155 :FSGSPEIADIVTN 1k6wA 251 :HSYNGAYTSRLFR T0315 168 :KLNFYISLG 1k6wA 267 :MSGINFVAN T0315 182 :KNA 1k6wA 290 :PKR T0315 185 :KQPKEVAKHVS 1k6wA 296 :TRVKEMLESGI T0315 198 :RLLVETDAPYL 1k6wA 307 :NVCFGHDDVFD T0315 214 :RGKRNEPARVTLVAEQIAELKG 1k6wA 318 :PWYPLGTANMLQVLHMGLHVCQ T0315 236 :LSYEEVCEQT 1k6wA 341 :MGYGQINDGL T0315 246 :TKNAEKLFNLN 1k6wA 354 :THHSARTLNLQ Number of specific fragments extracted= 19 number of extra gaps= 0 total=1301 Will force an alignment to be made, even if fragment is small Number of alignments=82 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1k6wA/T0315-1k6wA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0315 read from 1k6wA/T0315-1k6wA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1k6wA read from 1k6wA/T0315-1k6wA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1k6wA in template set T0315 2 :LIDTHVHLNDEQY 1k6wA 57 :FVEPHIHLDTTQT T0315 15 :DDDLSEVITRAREAGVDRMFV 1k6wA 101 :KQRAWQTLKWQIANGIQHVRT T0315 36 :VGFNKST 1k6wA 123 :VDVSDAT T0315 43 :IERAMKLIDEYD 1k6wA 133 :LKAMLEVKQEVA T0315 55 :FLYGIIGWHPVDAIDFTEEHLEWIESLAQH 1k6wA 146 :WIDLQIVAFPQEGILSYPNGEALLEEALRL T0315 86 :KVIGIGEM 1k6wA 176 :GADVVGAI T0315 98 :HWDKSPADVQKEVFRKQIALAKRLKLPIIIHN 1k6wA 184 :PHFEFTREYGVESLHKTFALAQKYDRLIDVHC T0315 132 :ATQDCIDILLEEHAEEVGGIMHSF 1k6wA 225 :FVETVAALAHHEGMGARVTASHTT T0315 156 :SGSPEIADIVTN 1k6wA 252 :SYNGAYTSRLFR T0315 168 :KLNFYIS 1k6wA 267 :MSGINFV T0315 175 :LGGPVTFKNAKQ 1k6wA 283 :QGRFDTYPKRRG T0315 187 :PKEVAKHVS 1k6wA 298 :VKEMLESGI T0315 198 :RLLVETDA 1k6wA 307 :NVCFGHDD T0315 211 :HPYRGKRNEPARVTLVAEQIAELKG 1k6wA 315 :VFDPWYPLGTANMLQVLHMGLHVCQ T0315 236 :LSYEEVCEQT 1k6wA 341 :MGYGQINDGL T0315 246 :TKNAEKLFNLN 1k6wA 354 :THHSARTLNLQ Number of specific fragments extracted= 16 number of extra gaps= 0 total=1317 Will force an alignment to be made, even if fragment is small Number of alignments=83 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1k6wA/T0315-1k6wA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0315 read from 1k6wA/T0315-1k6wA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1k6wA read from 1k6wA/T0315-1k6wA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1k6wA in template set T0315 9 :LNDEQYDDDLSEVITRAREAGVDRMFVVG 1k6wA 95 :LTHDDVKQRAWQTLKWQIANGIQHVRTHV T0315 38 :FNKST 1k6wA 125 :VSDAT T0315 43 :IERAMKLIDEYDF 1k6wA 133 :LKAMLEVKQEVAP T0315 56 :LYGIIGWHPVDAIDFTEEHLEWIESLAQH 1k6wA 147 :IDLQIVAFPQEGILSYPNGEALLEEALRL T0315 86 :KVIGIGEMGLD 1k6wA 176 :GADVVGAIPHF T0315 101 :KSPADVQKEVFRKQIALAKRLKLPIIIHN 1k6wA 187 :EFTREYGVESLHKTFALAQKYDRLIDVHC T0315 130 :REATQDCIDILLEEHAEEVGGIMHS 1k6wA 223 :SRFVETVAALAHHEGMGARVTASHT T0315 155 :FSGSPEIADI 1k6wA 251 :HSYNGAYTSR T0315 166 :TNKL 1k6wA 261 :LFRL T0315 170 :NFYISLG 1k6wA 269 :GINFVAN T0315 180 :TFKNAK 1k6wA 288 :TYPKRR T0315 186 :QPKEVAKH 1k6wA 297 :RVKEMLES T0315 198 :RLLVETDAPYLSPHPY 1k6wA 307 :NVCFGHDDVFDPWYPL T0315 219 :EPARVTLVAEQIAELKG 1k6wA 323 :GTANMLQVLHMGLHVCQ T0315 236 :LSYEEVCE 1k6wA 341 :MGYGQIND Number of specific fragments extracted= 15 number of extra gaps= 0 total=1332 Will force an alignment to be made, even if fragment is small Number of alignments=84 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1j5sA/T0315-1j5sA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1j5sA expands to /projects/compbio/data/pdb/1j5s.pdb.gz 1j5sA:# T0315 read from 1j5sA/T0315-1j5sA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1j5sA read from 1j5sA/T0315-1j5sA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1j5sA to template set # found chain 1j5sA in template set Warning: unaligning (T0315)G176 because of BadResidue code BAD_PEPTIDE in next template residue (1j5sA)W366 Warning: unaligning (T0315)G177 because of BadResidue code BAD_PEPTIDE at template residue (1j5sA)W366 T0315 1 :MLIDTHVHLNDEQYDD 1j5sA 25 :PIVDPHNHLDAKDIVE T0315 17 :DLSEVITRAREA 1j5sA 119 :TAEEIWEETKKK T0315 29 :GVDRMFVVG 1j5sA 144 :KVEILCTTD T0315 38 :FNKSTIERAM 1j5sA 156 :STLEHHRKAK T0315 51 :DEYDFLYGIIGWHPVDAIDFT 1j5sA 166 :EAVEGVTILPTWRPDRAMNVD T0315 72 :EEHLEWIE 1j5sA 209 :DGFLNALW T0315 80 :SLAQHPKVIGIGEMGLDYHWDKSPADVQKEVFRKQ 1j5sA 220 :EHFKEHGCVASDHALLEPSVYYVDENRARAVHEKA T0315 115 :IALAKRLKLPIIIHN 1j5sA 277 :GKMNQETNWVTQLHI T0315 130 :REATQDCIDILLEEH 1j5sA 318 :LRIAEGLRYFLNEFD T0315 146 :EEVGGIMHSFSGS 1j5sA 333 :GKLKIVLYVLDPT T0315 159 :PEIADIVTN 1j5sA 347 :LPTISTIAR T0315 168 :KLNFYISL 1j5sA 357 :FPNVYVGA T0315 178 :PVTF 1j5sA 367 :WFND T0315 185 :KQPKEVAKHVSMERL 1j5sA 377 :MHLKYLASVDLLYNL T0315 202 :ETDAPYLS 1j5sA 395 :VTDSRKLL T0315 218 :NEPARVTLVAEQIAEL 1j5sA 403 :SFGSRTEMFRRVLSNV T0315 234 :KG 1j5sA 425 :KG T0315 236 :LSYEEVCEQT 1j5sA 428 :IPIKEARELV T0315 246 :TKNAEKLF 1j5sA 442 :YDGPKALF Number of specific fragments extracted= 19 number of extra gaps= 1 total=1351 Will force an alignment to be made, even if fragment is small Number of alignments=85 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1j5sA/T0315-1j5sA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0315 read from 1j5sA/T0315-1j5sA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1j5sA read from 1j5sA/T0315-1j5sA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1j5sA in template set Warning: unaligning (T0315)G176 because of BadResidue code BAD_PEPTIDE in next template residue (1j5sA)W366 Warning: unaligning (T0315)G177 because of BadResidue code BAD_PEPTIDE at template residue (1j5sA)W366 T0315 1 :MLIDTHVHLNDEQY 1j5sA 25 :PIVDPHNHLDAKDI T0315 15 :DDDLSEVITRAREA 1j5sA 117 :EETAEEIWEETKKK T0315 29 :GVDRMFVVGFNKSTIERAMKLIDEYDFLYGIIGWHPV 1j5sA 144 :KVEILCTTDDPVSTLEHHRKAKEAVEGVTILPTWRPD T0315 66 :DAIDF 1j5sA 204 :DTSTL T0315 72 :EEHLEWIESLAQ 1j5sA 209 :DGFLNALWKSHE T0315 84 :HPKVIGIGEMGLDYHWDKSPADVQKEVFRK 1j5sA 224 :EHGCVASDHALLEPSVYYVDENRARAVHEK T0315 114 :QIALAKRLKLPIIIHN 1j5sA 276 :FGKMNQETNWVTQLHI T0315 130 :RE 1j5sA 295 :RD T0315 132 :ATQDCIDILLEEHAEEVGGIMHSFSGS 1j5sA 319 :RIAEGLRYFLNEFDGKLKIVLYVLDPT T0315 159 :PEIADIVTNKLNFYISL 1j5sA 348 :PTISTIARAFPNVYVGA T0315 178 :PVTF 1j5sA 367 :WFND T0315 187 :PKEVAKHVSMERL 1j5sA 379 :LKYLASVDLLYNL T0315 201 :VETDAPYL 1j5sA 394 :MVTDSRKL T0315 217 :RNEPARVTLVAEQIAEL 1j5sA 402 :LSFGSRTEMFRRVLSNV T0315 234 :KG 1j5sA 425 :KG T0315 236 :LSYEEVCEQT 1j5sA 428 :IPIKEARELV T0315 246 :TKNAEKLF 1j5sA 442 :YDGPKALF Number of specific fragments extracted= 17 number of extra gaps= 1 total=1368 Will force an alignment to be made, even if fragment is small Number of alignments=86 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1j5sA/T0315-1j5sA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0315 read from 1j5sA/T0315-1j5sA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1j5sA read from 1j5sA/T0315-1j5sA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1j5sA in template set Warning: unaligning (T0315)G176 because of BadResidue code BAD_PEPTIDE in next template residue (1j5sA)W366 Warning: unaligning (T0315)G177 because of BadResidue code BAD_PEPTIDE at template residue (1j5sA)W366 T0315 15 :DDDLSEVITRARE 1j5sA 117 :EETAEEIWEETKK T0315 28 :AGVDRMFVVGFNKSTIERAMKLIDEYDFLYGIIGWHPVDAIDFT 1j5sA 143 :MKVEILCTTDDPVSTLEHHRKAKEAVEGVTILPTWRPDRAMNVD T0315 72 :EEHLEWIESLA 1j5sA 209 :DGFLNALWKSH T0315 83 :QHPKVIGIGEMGLDYHWDKSPADVQKEVFRK 1j5sA 223 :KEHGCVASDHALLEPSVYYVDENRARAVHEK T0315 114 :QIALAKRLKLPIIIHN 1j5sA 276 :FGKMNQETNWVTQLHI T0315 130 :REATQD 1j5sA 295 :RDYRDS T0315 136 :CIDILLEEHAEEVGGIMHSFSGS 1j5sA 323 :GLRYFLNEFDGKLKIVLYVLDPT T0315 159 :PEIADIVTNKL 1j5sA 347 :LPTISTIARAF T0315 170 :NFYISL 1j5sA 359 :NVYVGA T0315 178 :PVTFK 1j5sA 367 :WFNDS T0315 187 :PKEVAKHVSMERL 1j5sA 379 :LKYLASVDLLYNL T0315 203 :TDAPYLSP 1j5sA 396 :TDSRKLLS T0315 221 :ARVTLVAEQIAELK 1j5sA 406 :SRTEMFRRVLSNVV T0315 235 :GLSYEEVCEQTTK 1j5sA 427 :QIPIKEARELVKH T0315 248 :NAEKLF 1j5sA 444 :GPKALF Number of specific fragments extracted= 15 number of extra gaps= 1 total=1383 Will force an alignment to be made, even if fragment is small Number of alignments=87 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1vflA/T0315-1vflA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1vflA expands to /projects/compbio/data/pdb/1vfl.pdb.gz 1vflA:# T0315 read from 1vflA/T0315-1vflA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1vflA read from 1vflA/T0315-1vflA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1vflA to template set # found chain 1vflA in template set Warning: unaligning (T0315)N254 because last residue in template chain is (1vflA)R349 T0315 2 :LIDTHVHLNDEQYDD 1vflA 94 :YVEVRYSPHLLANSK T0315 17 :DLSEVITRA 1vflA 122 :TPDEVVSLV T0315 43 :IERAMKLIDEYD 1vflA 131 :NQGLQEGERDFG T0315 55 :FLYGIIGWHP 1vflA 144 :KVRSILCCMR T0315 66 :DAIDFTEEHLEWIESLAQHP 1vflA 154 :HQPSWSSEVVELCKKYREQT T0315 87 :VIGIGEMG 1vflA 174 :VVAIDLAG T0315 96 :DYHWDKSP 1vflA 182 :DETIEGSS T0315 104 :ADV 1vflA 191 :FPG T0315 111 :FRKQIALAKRLKLPIIIHN 1vflA 194 :HVQAYAEAVKSGVHRTVHA T0315 132 :ATQDCIDILLEE 1vflA 216 :GSANVVKEAVDT T0315 147 :EVGGIMHSF 1vflA 229 :KTERLGHGY T0315 157 :GSPEIADIVTN 1vflA 241 :EDTTLYNRLRQ T0315 169 :LNFYISLG 1vflA 252 :ENMHFEIC T0315 182 :KNAKQ 1vflA 270 :KPDTE T0315 187 :PKEVAKH 1vflA 277 :VIRFKND T0315 198 :RLLVETDAP 1vflA 286 :NYSLNTDDP T0315 219 :EPARVTLVAEQIAELKGLSYEEV 1vflA 297 :FKSTLDTDYQMTKKDMGFTEEEF T0315 242 :CEQTTKNAEKLF 1vflA 337 :KKELLDLLYKAY Number of specific fragments extracted= 18 number of extra gaps= 0 total=1401 Will force an alignment to be made, even if fragment is small Number of alignments=88 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1vflA/T0315-1vflA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0315 read from 1vflA/T0315-1vflA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1vflA read from 1vflA/T0315-1vflA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1vflA in template set Warning: unaligning (T0315)N254 because last residue in template chain is (1vflA)R349 T0315 1 :MLIDTHVHLND 1vflA 7 :PKVELHVHLDG T0315 14 :Y 1vflA 18 :A T0315 18 :LSEVITRAREAGVDRMFVV 1vflA 80 :AYEFVEMKAKDGVVYVEVR T0315 37 :GFNK 1vflA 105 :ANSK T0315 41 :ST 1vflA 110 :EP T0315 43 :IERAMKLIDEYD 1vflA 131 :NQGLQEGERDFG T0315 55 :FLYGIIGWHPV 1vflA 144 :KVRSILCCMRH T0315 67 :AIDFTEEHLEWIESLAQHP 1vflA 155 :QPSWSSEVVELCKKYREQT T0315 87 :VIGIGEMG 1vflA 174 :VVAIDLAG T0315 96 :DYHWDKSP 1vflA 182 :DETIEGSS T0315 104 :A 1vflA 191 :F T0315 109 :EVFRKQIALAKRLKLPIIIHNRE 1vflA 192 :PGHVQAYAEAVKSGVHRTVHAGE T0315 132 :ATQDCIDILLEEH 1vflA 216 :GSANVVKEAVDTL T0315 147 :EVGGIMHSF 1vflA 229 :KTERLGHGY T0315 156 :SGSPEIADIVTN 1vflA 240 :LEDTTLYNRLRQ T0315 169 :LNFYISLG 1vflA 252 :ENMHFEIC T0315 177 :GPV 1vflA 267 :GAW T0315 182 :KNAKQ 1vflA 270 :KPDTE T0315 187 :PKEVAKH 1vflA 277 :VIRFKND T0315 198 :RLLVETDAP 1vflA 286 :NYSLNTDDP T0315 220 :PARVTLVAEQIAELKGLSYEEV 1vflA 298 :KSTLDTDYQMTKKDMGFTEEEF T0315 242 :CEQTTKNAEKLF 1vflA 337 :KKELLDLLYKAY Number of specific fragments extracted= 22 number of extra gaps= 0 total=1423 Will force an alignment to be made, even if fragment is small Number of alignments=89 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1vflA/T0315-1vflA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0315 read from 1vflA/T0315-1vflA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1vflA read from 1vflA/T0315-1vflA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1vflA in template set Warning: unaligning (T0315)N254 because last residue in template chain is (1vflA)R349 T0315 2 :LIDTHVHLNDEQYDD 1vflA 94 :YVEVRYSPHLLANSK T0315 17 :DLSEVITRARE 1vflA 122 :TPDEVVSLVNQ T0315 45 :RAMKLIDEYDFLYGIIGWHPVDAIDFTEEHLEWIESLAQHP 1vflA 133 :GLQEGERDFGVKVRSILCCMRHQPSWSSEVVELCKKYREQT T0315 87 :VIGIGEMGLDYHWDKSPADVQKEVFRK 1vflA 174 :VVAIDLAGDETIEGSSLFPGHVQAYAE T0315 118 :AKRLKLPIIIHN 1vflA 201 :AVKSGVHRTVHA T0315 132 :ATQDCIDILLEEH 1vflA 216 :GSANVVKEAVDTL T0315 147 :EVGGIMHSFS 1vflA 229 :KTERLGHGYH T0315 157 :GSPEIADI 1vflA 241 :EDTTLYNR T0315 166 :TNKLNFYISLGGPV 1vflA 249 :LRQENMHFEICPWS T0315 180 :TFKNAKQ 1vflA 268 :AWKPDTE T0315 187 :PKEVAKH 1vflA 277 :VIRFKND T0315 198 :RLLVETDAP 1vflA 286 :NYSLNTDDP T0315 220 :PARVTLVAEQIAELKGLSYEEV 1vflA 298 :KSTLDTDYQMTKKDMGFTEEEF T0315 242 :CEQTTKNAEKLF 1vflA 337 :KKELLDLLYKAY Number of specific fragments extracted= 14 number of extra gaps= 0 total=1437 Will force an alignment to be made, even if fragment is small Number of alignments=90 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1pta/T0315-1pta-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1pta expands to /projects/compbio/data/pdb/1pta.pdb.gz 1pta:Warning: there is no chain 1pta will retry with 1ptaA # T0315 read from 1pta/T0315-1pta-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1pta read from 1pta/T0315-1pta-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1pta to template set # found chain 1pta in template set Warning: unaligning (T0315)D100 because of BadResidue code BAD_PEPTIDE in next template residue (1pta)G174 Warning: unaligning (T0315)K101 because of BadResidue code BAD_PEPTIDE at template residue (1pta)G174 Warning: unaligning (T0315)P210 because of BadResidue code BAD_PEPTIDE in next template residue (1pta)M317 Warning: unaligning (T0315)H211 because of BadResidue code BAD_PEPTIDE at template residue (1pta)M317 T0315 1 :MLIDTHVHLNDEQ 1pta 50 :GFTLTHEHICGSS T0315 15 :DD 1pta 63 :AG T0315 17 :DLSEVITRAREAGVDRMFVVGF 1pta 82 :KAVRGLRRARAAGVRTIVDVST T0315 42 :TIERAMKLIDEYD 1pta 109 :DVSLLAEVSRAAD T0315 55 :FLYGIIGWH 1pta 123 :HIVAATGLW T0315 64 :PVDAIDFT 1pta 135 :PLSMRLRS T0315 72 :EEHLEWIESLAQHP 1pta 144 :EELTQFFLREIQYG T0315 86 :KVIGIGEM 1pta 164 :RAGIIKVA T0315 99 :W 1pta 172 :T T0315 102 :SPADVQKEVFRKQIALAKRLKLPIIIHN 1pta 175 :KATPFQELVLKAAARASLATGVPVTTHT T0315 130 :REATQDCIDILLEEHAEEVGGIM 1pta 206 :QRDGEQQAAIFESEGLSPSRVCI T0315 153 :HS 1pta 230 :HS T0315 155 :FSGSPEIADIVTN 1pta 233 :DTDDLSYLTALAA T0315 169 :LNFYISLGGPVTF 1pta 246 :RGYLIGLDHIPHS T0315 182 :KNAKQPKEVAKHVSMERLLVETDA 1pta 279 :TRALLIKALIDQGYMKQILVSNDW T0315 206 :PYLS 1pta 312 :NIMD T0315 212 :PYRGKRNEPARVTLVAEQIAE 1pta 318 :DRVNPDGMAFIPLRVIPFLRE T0315 234 :KGLSYEEVCEQTTKNAEKLFNL 1pta 339 :KGVPQETLAGITVTNPARFLSP Number of specific fragments extracted= 18 number of extra gaps= 2 total=1455 Will force an alignment to be made, even if fragment is small Number of alignments=91 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1pta/T0315-1pta-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0315 read from 1pta/T0315-1pta-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1pta read from 1pta/T0315-1pta-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1pta in template set Warning: unaligning (T0315)D100 because of BadResidue code BAD_PEPTIDE in next template residue (1pta)G174 Warning: unaligning (T0315)K101 because of BadResidue code BAD_PEPTIDE at template residue (1pta)G174 Warning: unaligning (T0315)N183 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1pta)A270 Warning: unaligning (T0315)A184 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1pta)A270 Warning: unaligning (T0315)P210 because of BadResidue code BAD_PEPTIDE in next template residue (1pta)M317 Warning: unaligning (T0315)H211 because of BadResidue code BAD_PEPTIDE at template residue (1pta)M317 T0315 1 :MLIDTHVHLNDEQY 1pta 50 :GFTLTHEHICGSSA T0315 15 :DDDLSEVITRAREAGVDRMFVVGF 1pta 80 :AEKAVRGLRRARAAGVRTIVDVST T0315 39 :NK 1pta 105 :DI T0315 41 :STIERAMKLIDEYD 1pta 108 :RDVSLLAEVSRAAD T0315 55 :FLYGIIGWHPV 1pta 123 :HIVAATGLWFD T0315 66 :DA 1pta 142 :SV T0315 72 :EEHLEWIESLA 1pta 144 :EELTQFFLREI T0315 83 :QHPKVIG 1pta 159 :EDTGIRA T0315 91 :GEM 1pta 166 :GII T0315 96 :DYHW 1pta 169 :KVAT T0315 102 :SPADVQKEVFRKQIALAKRLKLPIIIHNRE 1pta 175 :KATPFQELVLKAAARASLATGVPVTTHTAA T0315 132 :ATQDCIDILLEEHAEEVGG 1pta 208 :DGEQQAAIFESEGLSPSRV T0315 151 :IMHS 1pta 228 :IGHS T0315 155 :FSGSPEIADIVTN 1pta 233 :DTDDLSYLTALAA T0315 169 :LNFYISLGGPVTFK 1pta 246 :RGYLIGLDHIPHSA T0315 185 :KQ 1pta 271 :LL T0315 187 :PKEVAKHVSMERLLVETDA 1pta 284 :IKALIDQGYMKQILVSNDW T0315 206 :PYLS 1pta 312 :NIMD T0315 212 :PYRGKRNEPARVTLVAEQIAEL 1pta 318 :DRVNPDGMAFIPLRVIPFLREK T0315 235 :GLSYEEVCEQTTKNAEKLFNL 1pta 340 :GVPQETLAGITVTNPARFLSP Number of specific fragments extracted= 20 number of extra gaps= 3 total=1475 Will force an alignment to be made, even if fragment is small Number of alignments=92 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1pta/T0315-1pta-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0315 read from 1pta/T0315-1pta-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1pta read from 1pta/T0315-1pta-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1pta in template set Warning: unaligning (T0315)D100 because of BadResidue code BAD_PEPTIDE in next template residue (1pta)G174 Warning: unaligning (T0315)K101 because of BadResidue code BAD_PEPTIDE at template residue (1pta)G174 Warning: unaligning (T0315)P210 because of BadResidue code BAD_PEPTIDE in next template residue (1pta)M317 Warning: unaligning (T0315)H211 because of BadResidue code BAD_PEPTIDE at template residue (1pta)M317 T0315 3 :IDTHVHL 1pta 52 :TLTHEHI T0315 10 :NDEQYDDDLSEVITRAREAGVDRMFVVGF 1pta 75 :SRKALAEKAVRGLRRARAAGVRTIVDVST T0315 43 :IERAMKLIDEYDF 1pta 110 :VSLLAEVSRAADV T0315 56 :LYGIIGWH 1pta 124 :IVAATGLW T0315 64 :PVDAIDFT 1pta 135 :PLSMRLRS T0315 72 :EEHLEWIESLA 1pta 144 :EELTQFFLREI T0315 84 :HPKVIGIG 1pta 164 :RAGIIKVA T0315 99 :W 1pta 172 :T T0315 102 :SPADVQKEVFRKQIALAKRLKLPIIIHNREA 1pta 175 :KATPFQELVLKAAARASLATGVPVTTHTAAS T0315 133 :TQDCIDILLEEHAEEVGGIMHSFSG 1pta 209 :GEQQAAIFESEGLSPSRVCIGHSDD T0315 158 :SPEIADI 1pta 236 :DLSYLTA T0315 166 :TNKLNFYISLGGPVTFK 1pta 243 :LAARGYLIGLDHIPHSA T0315 184 :AKQPKEVAKHVSMERLLV 1pta 281 :ALLIKALIDQGYMKQILV T0315 207 :YLS 1pta 313 :IMD T0315 212 :PYRGKRNEPARVTLVAEQIAE 1pta 318 :DRVNPDGMAFIPLRVIPFLRE T0315 234 :KGLSYEEVCEQTTKNAEKLFNLN 1pta 339 :KGVPQETLAGITVTNPARFLSPT Number of specific fragments extracted= 16 number of extra gaps= 2 total=1491 Will force an alignment to be made, even if fragment is small Number of alignments=93 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ituA/T0315-1ituA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1ituA expands to /projects/compbio/data/pdb/1itu.pdb.gz 1ituA:# T0315 read from 1ituA/T0315-1ituA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ituA read from 1ituA/T0315-1ituA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1ituA to template set # found chain 1ituA in template set T0315 1 :MLIDTHVHL 1ituA 15 :PVIDGHNDL T0315 11 :DEQY 1ituA 37 :DERA T0315 17 :DL 1ituA 51 :NI T0315 23 :TRAREAGVDRMFVVGFN 1ituA 53 :PKLRAGFVGGQFWSVYT T0315 40 :KSTIERAMKLIDEY 1ituA 83 :LEQMDVVHRMCRMY T0315 54 :DFLYGIIGWHPVDAIDFT 1ituA 116 :GKVASLIGVEGGHSIDSS T0315 75 :LEWIESLAQH 1ituA 134 :LGVLRALYQL T0315 86 :KVIGIGEMGLDYH 1ituA 144 :GMRYLTLTHSCNT T0315 100 :DKS 1ituA 173 :SQG T0315 104 :A 1ituA 177 :S T0315 109 :EVFRKQIALAKRLKLPIII 1ituA 178 :PFGQRVVKELNRLGVLIDL T0315 130 :REATQDCIDILLEE 1ituA 197 :AHVSVATMKATLQL T0315 146 :EEVGGIM 1ituA 211 :SRAPVIF T0315 153 :HSF 1ituA 219 :HSS T0315 158 :SPEIADIVTN 1ituA 233 :PDDVLRLVKQ T0315 169 :LNFYISLGGP 1ituA 243 :TDSLVMVNFY T0315 182 :KNAKQ 1ituA 260 :NKANL T0315 187 :PKEVAKHVSMERLLVETDAPYLSPH 1ituA 271 :LDHIKEVAGARAVGFGGDFDGVPRV T0315 214 :RGKRNEPARVTLVAEQIAE 1ituA 296 :PEGLEDVSKYPDLIAELLR T0315 234 :KGLSYEEVCEQTTKNAEKLF 1ituA 315 :RNWTEAEVKGALADNLLRVF Number of specific fragments extracted= 20 number of extra gaps= 0 total=1511 Will force an alignment to be made, even if fragment is small Number of alignments=94 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ituA/T0315-1ituA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0315 read from 1ituA/T0315-1ituA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ituA read from 1ituA/T0315-1ituA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1ituA in template set T0315 1 :MLIDTHVH 1ituA 15 :PVIDGHND T0315 9 :LNDEQY 1ituA 35 :LQDERA T0315 22 :ITRAREAGVDRMFVV 1ituA 52 :IPKLRAGFVGGQFWS T0315 37 :GFNKST 1ituA 68 :YTPCDT T0315 43 :IERAMKLIDEY 1ituA 86 :MDVVHRMCRMY T0315 54 :DFLYGIIGWHPVDAIDFT 1ituA 116 :GKVASLIGVEGGHSIDSS T0315 75 :LEWIESLAQH 1ituA 134 :LGVLRALYQL T0315 86 :KVIGIGEM 1ituA 144 :GMRYLTLT T0315 95 :L 1ituA 152 :H T0315 100 :DKSP 1ituA 172 :QSQG T0315 109 :EVFRKQIALAKRLKLPII 1ituA 178 :PFGQRVVKELNRLGVLID T0315 129 :NREATQDCIDILLEE 1ituA 196 :LAHVSVATMKATLQL T0315 145 :AEEVGGIMHSF 1ituA 211 :SRAPVIFSHSS T0315 158 :SPEIADIVTN 1ituA 233 :PDDVLRLVKQ T0315 169 :LNFYISLGGP 1ituA 243 :TDSLVMVNFY T0315 182 :KNAKQ 1ituA 260 :NKANL T0315 187 :PKEVAKHVSMERLLVETDAPYLSPHPY 1ituA 271 :LDHIKEVAGARAVGFGGDFDGVPRVPE T0315 216 :KRNEPARVTLVAEQIAE 1ituA 298 :GLEDVSKYPDLIAELLR T0315 234 :KGLSYEEVCEQTTKNAEKLF 1ituA 315 :RNWTEAEVKGALADNLLRVF Number of specific fragments extracted= 19 number of extra gaps= 0 total=1530 Will force an alignment to be made, even if fragment is small Number of alignments=95 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ituA/T0315-1ituA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0315 read from 1ituA/T0315-1ituA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ituA read from 1ituA/T0315-1ituA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1ituA in template set T0315 2 :LIDTHVHLNDEQYDD 1ituA 62 :GQFWSVYTPCDTQNK T0315 17 :DLSEVITRARE 1ituA 81 :RTLEQMDVVHR T0315 34 :FVVGFNKSTIERAMKL 1ituA 100 :FLYVTSSAGIRQAFRE T0315 54 :DFLYGIIGWHPVDAIDFT 1ituA 116 :GKVASLIGVEGGHSIDSS T0315 75 :LEWIESLAQH 1ituA 134 :LGVLRALYQL T0315 86 :KVIGIGEMG 1ituA 144 :GMRYLTLTH T0315 100 :DKSP 1ituA 168 :DSEP T0315 109 :EVFRKQIALAKRLKLPIII 1ituA 178 :PFGQRVVKELNRLGVLIDL T0315 130 :REATQDCIDILLEEHA 1ituA 197 :AHVSVATMKATLQLSR T0315 148 :VGGIM 1ituA 213 :APVIF T0315 154 :SFSG 1ituA 218 :SHSS T0315 158 :SPEIADI 1ituA 233 :PDDVLRL T0315 166 :TNKLNFYISLGGPV 1ituA 240 :VKQTDSLVMVNFYN T0315 180 :TFKNAK 1ituA 258 :CTNKAN T0315 187 :PKEVAKHVSMERLLVETDAPYLSPH 1ituA 271 :LDHIKEVAGARAVGFGGDFDGVPRV T0315 214 :RGKRNEPARVTLVAEQIAE 1ituA 296 :PEGLEDVSKYPDLIAELLR T0315 234 :KGLSYEEVCEQTTKNAEKLF 1ituA 315 :RNWTEAEVKGALADNLLRVF Number of specific fragments extracted= 17 number of extra gaps= 0 total=1547 Will force an alignment to be made, even if fragment is small Number of alignments=96 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1eywA/T0315-1eywA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1eywA expands to /projects/compbio/data/pdb/1eyw.pdb.gz 1eywA:Skipped atom 588, because occupancy 0.500 <= existing 0.500 in 1eywA Bad short name: CX for alphabet: pdb_atoms Bad short name: OQ1 for alphabet: pdb_atoms Bad short name: OQ2 for alphabet: pdb_atoms Skipped atom 2004, because occupancy 0.500 <= existing 0.500 in 1eywA Skipped atom 2006, because occupancy 0.500 <= existing 0.500 in 1eywA # T0315 read from 1eywA/T0315-1eywA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1eywA read from 1eywA/T0315-1eywA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1eywA to template set # found chain 1eywA in template set Warning: unaligning (T0315)I90 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1eywA)V170 Warning: unaligning (T0315)E92 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1eywA)V170 T0315 1 :MLIDTHVHL 1eywA 50 :GFTLTHEHI T0315 10 :NDEQYDD 1eywA 69 :WPEFFGS T0315 17 :DLSEVITRAREAGVDRMFVVGF 1eywA 82 :KAVRGLRRARAAGVRTIVDVST T0315 42 :TIERAMKLIDEYD 1eywA 109 :DVSLLAEVSRAAD T0315 55 :FLYGIIGWH 1eywA 123 :HIVAATGLW T0315 64 :PVDAIDFT 1eywA 135 :PLSMRLRS T0315 72 :EEHLEWIESLAQHP 1eywA 144 :EELTQFFLREIQYG T0315 86 :KVIG 1eywA 164 :RAGI T0315 93 :M 1eywA 171 :A T0315 99 :WDKSPADVQKEVFRKQIALAKRLKLPIIIHN 1eywA 172 :TTGKATPFQELVLKAAARASLATGVPVTTHT T0315 130 :REATQDCIDILLEEHAEEVGGIM 1eywA 206 :QRDGEQQAAIFESEGLSPSRVCI T0315 153 :HS 1eywA 230 :HS T0315 155 :FSGSPEIADIVTN 1eywA 233 :DTDDLSYLTALAA T0315 169 :LNFYISLGGPVTF 1eywA 246 :RGYLIGLDHIPHS T0315 182 :KNAKQPKEVAKHVSMERLLVETDAPYLS 1eywA 279 :TRALLIKALIDQGYMKQILVSNDWLFGF T0315 219 :EPARVTLVAEQIAE 1eywA 325 :MAFIPLRVIPFLRE T0315 234 :KGLSYEEVCEQTTKNAEKLFNLN 1eywA 339 :KGVPQETLAGITVTNPARFLSPT Number of specific fragments extracted= 17 number of extra gaps= 0 total=1564 Will force an alignment to be made, even if fragment is small Number of alignments=97 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1eywA/T0315-1eywA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0315 read from 1eywA/T0315-1eywA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1eywA read from 1eywA/T0315-1eywA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1eywA in template set Warning: unaligning (T0315)M93 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1eywA)V170 Warning: unaligning (T0315)Y97 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1eywA)V170 T0315 1 :MLIDTHVHL 1eywA 50 :GFTLTHEHI T0315 10 :NDEQY 1eywA 69 :WPEFF T0315 15 :DDDLSEVITRAREAGVDRMFVVGF 1eywA 80 :AEKAVRGLRRARAAGVRTIVDVST T0315 41 :STIERAMKLIDEYD 1eywA 108 :RDVSLLAEVSRAAD T0315 55 :FLYGIIGWHPV 1eywA 123 :HIVAATGLWFD T0315 69 :DFT 1eywA 140 :LRS T0315 72 :EEHLEWIESLAQ 1eywA 144 :EELTQFFLREIQ T0315 84 :HPKVIG 1eywA 160 :DTGIRA T0315 91 :GE 1eywA 166 :GI T0315 98 :HWDKSPADVQKEVFRKQIALAKRLKLPIIIHN 1eywA 171 :ATTGKATPFQELVLKAAARASLATGVPVTTHT T0315 130 :REATQDCIDILLEEHAEEVGGIM 1eywA 206 :QRDGEQQAAIFESEGLSPSRVCI T0315 153 :HSF 1eywA 230 :HSD T0315 156 :SGSPEIADIVTN 1eywA 234 :TDDLSYLTALAA T0315 169 :LNFYISLGGPVTF 1eywA 246 :RGYLIGLDHIPHS T0315 182 :KNAKQ 1eywA 275 :RSWQT T0315 187 :PKEVAKHVSMERLLVETDAPYLSPHPYRGK 1eywA 284 :IKALIDQGYMKQILVSNDWLFGFSSYVTNI T0315 217 :RNEPARVTL 1eywA 322 :PDGMAFIPL T0315 226 :VAEQIAEL 1eywA 332 :VIPFLREK T0315 235 :GLSYEEVCEQTTKNAEKLFNL 1eywA 340 :GVPQETLAGITVTNPARFLSP Number of specific fragments extracted= 19 number of extra gaps= 0 total=1583 Will force an alignment to be made, even if fragment is small Number of alignments=98 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1eywA/T0315-1eywA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0315 read from 1eywA/T0315-1eywA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1eywA read from 1eywA/T0315-1eywA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1eywA in template set Warning: unaligning (T0315)I88 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1eywA)V170 Warning: unaligning (T0315)I90 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1eywA)V170 T0315 2 :LIDTHVHL 1eywA 51 :FTLTHEHI T0315 10 :NDEQYDD 1eywA 69 :WPEFFGS T0315 17 :DLSEVITRAREAGVDRMFVVGF 1eywA 82 :KAVRGLRRARAAGVRTIVDVST T0315 43 :IERAMKLIDEYDF 1eywA 110 :VSLLAEVSRAADV T0315 56 :LYGIIGW 1eywA 124 :IVAATGL T0315 63 :HPVDAIDFT 1eywA 134 :PPLSMRLRS T0315 72 :EEHLEWIESLA 1eywA 144 :EELTQFFLREI T0315 84 :HPKV 1eywA 164 :RAGI T0315 91 :GE 1eywA 171 :AT T0315 100 :DKSPADVQKEVFRKQIALAKRLKLPIIIHN 1eywA 173 :TGKATPFQELVLKAAARASLATGVPVTTHT T0315 130 :REATQDCIDILLEEHAEEVGGIMH 1eywA 206 :QRDGEQQAAIFESEGLSPSRVCIG T0315 155 :F 1eywA 230 :H T0315 156 :SGSPEIADI 1eywA 234 :TDDLSYLTA T0315 166 :TNKLNFYISLGGPVT 1eywA 243 :LAARGYLIGLDHIPH T0315 181 :FKNAKQPKEVAKHVS 1eywA 262 :LEDNASASALLGIRS T0315 196 :MERLLVETDAPYLSPHP 1eywA 293 :MKQILVSNDWLFGFSSY T0315 221 :ARVTL 1eywA 326 :AFIPL T0315 226 :VAEQIAE 1eywA 332 :VIPFLRE T0315 234 :KGLSYEEVCEQTTKNAEKLFNLN 1eywA 339 :KGVPQETLAGITVTNPARFLSPT Number of specific fragments extracted= 19 number of extra gaps= 0 total=1602 Will force an alignment to be made, even if fragment is small Number of alignments=99 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2amxA/T0315-2amxA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2amxA expands to /projects/compbio/data/pdb/2amx.pdb.gz 2amxA:# T0315 read from 2amxA/T0315-2amxA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2amxA read from 2amxA/T0315-2amxA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2amxA to template set # found chain 2amxA in template set Warning: unaligning (T0315)M1 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2amxA)K51 Warning: unaligning (T0315)L2 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2amxA)K51 T0315 3 :IDTHVHLND 2amxA 52 :VELHCHLDL T0315 17 :DLSEVITRAREAGVD 2amxA 63 :SAEFFLKWARKYNLQ T0315 37 :GFNKST 2amxA 79 :NMSDDE T0315 43 :IERAMKLIDEY 2amxA 98 :LAEFIRKAISV T0315 65 :VDAIDFTEEHLEWIESLAQ 2amxA 109 :SDLYRDYDFIEDLAKWAVI T0315 84 :HPKVIGIGEMGLDY 2amxA 131 :KEGVVLMEFRYSPT T0315 100 :DKSPADVQKEVFRKQIALAKR 2amxA 150 :YGLDVELIHKAFIKGIKNATE T0315 121 :LK 2amxA 172 :LN T0315 123 :LPIIIHN 2amxA 176 :IHVALIC T0315 130 :REATQDCI 2amxA 187 :GHAAASIK T0315 138 :DILLEEH 2amxA 198 :DFAIKHK T0315 146 :EEVGGIMHSFSG 2amxA 205 :HDFVGFDHGGRE T0315 158 :S 2amxA 218 :D T0315 159 :PEIADIVTN 2amxA 223 :KDVYHSVRD T0315 169 :LNFYISLGGPV 2amxA 232 :HGLHLTVHAGE T0315 180 :TFKNAKQPKEVAKHVSMERL 2amxA 245 :TLPNLNTLYTAINILNVERI T0315 202 :ETDAPY 2amxA 265 :GHGIRV T0315 214 :RGK 2amxA 271 :SES T0315 221 :ARVTLVAEQIAELKGLSYEEVCEQTT 2amxA 330 :SNINDNYEKLYIHLNFTLEEFMIMNN Number of specific fragments extracted= 19 number of extra gaps= 1 total=1621 Will force an alignment to be made, even if fragment is small Number of alignments=100 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2amxA/T0315-2amxA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0315 read from 2amxA/T0315-2amxA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2amxA read from 2amxA/T0315-2amxA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2amxA in template set Warning: unaligning (T0315)M1 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2amxA)K51 Warning: unaligning (T0315)L2 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2amxA)K51 T0315 3 :IDTHVHLNDEQ 2amxA 52 :VELHCHLDLTF T0315 15 :DDDLSEVITRA 2amxA 115 :YDFIEDLAKWA T0315 26 :REAGVDRMFVV 2amxA 130 :YKEGVVLMEFR T0315 37 :GFNKST 2amxA 151 :GLDVEL T0315 43 :IERAMKLIDEY 2amxA 158 :HKAFIKGIKNA T0315 54 :DFLYGIIGWHPVDA 2amxA 174 :NKIHVALICISDTG T0315 70 :FTEEHLE 2amxA 188 :HAAASIK T0315 77 :WIESLAQH 2amxA 199 :FAIKHKHD T0315 87 :VIGI 2amxA 207 :FVGF T0315 96 :DYHWDKSP 2amxA 211 :DHGGREID T0315 104 :AD 2amxA 220 :KD T0315 107 :QKE 2amxA 222 :HKD T0315 114 :QIALAKRLKLPIIIHNRE 2amxA 225 :VYHSVRDHGLHLTVHAGE T0315 132 :ATQDCIDILLEE 2amxA 247 :PNLNTLYTAINI T0315 145 :AE 2amxA 259 :LN T0315 148 :VGGIMHSF 2amxA 261 :VERIGHGI T0315 156 :SGSPEIADIVTN 2amxA 271 :SESDELIELVKK T0315 169 :LNFYISLG 2amxA 283 :KDILLEVC T0315 182 :KNAKQ 2amxA 301 :KSMDT T0315 187 :PKEVAKHVS 2amxA 308 :IRKLYDAGV T0315 198 :RLLVETDAP 2amxA 317 :KVSVNSDDP T0315 221 :ARVTLVAEQIAELKGLSYEEVCEQT 2amxA 330 :SNINDNYEKLYIHLNFTLEEFMIMN Number of specific fragments extracted= 22 number of extra gaps= 1 total=1643 Will force an alignment to be made, even if fragment is small Number of alignments=101 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2amxA/T0315-2amxA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0315 read from 2amxA/T0315-2amxA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2amxA read from 2amxA/T0315-2amxA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2amxA in template set Warning: unaligning (T0315)L2 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2amxA)K51 T0315 3 :IDTHVHLNDEQ 2amxA 52 :VELHCHLDLTF T0315 17 :DLSEVITRAREAGVD 2amxA 63 :SAEFFLKWARKYNLQ T0315 37 :GFNKST 2amxA 79 :NMSDDE T0315 43 :IERAMKLIDEYD 2amxA 98 :LAEFIRKAISVS T0315 66 :DAIDFTEEHLEWIESLA 2amxA 110 :DLYRDYDFIEDLAKWAV T0315 84 :HPKVIGIGEM 2amxA 131 :KEGVVLMEFR T0315 95 :LDY 2amxA 141 :YSP T0315 100 :DKSPADVQKEVFRKQIALAKRL 2amxA 150 :YGLDVELIHKAFIKGIKNATEL T0315 123 :LPIIIHN 2amxA 178 :VALICIS T0315 130 :REATQDCI 2amxA 187 :GHAAASIK T0315 138 :DILLEEHA 2amxA 198 :DFAIKHKH T0315 149 :GGIMHSFSGS 2amxA 206 :DFVGFDHGGR T0315 159 :PEIADI 2amxA 223 :KDVYHS T0315 166 :TNKLNFYISLGGPV 2amxA 229 :VRDHGLHLTVHAGE T0315 180 :TFKNAKQPKEVAKHVSMERLLV 2amxA 245 :TLPNLNTLYTAINILNVERIGH T0315 205 :APYLSPHP 2amxA 267 :GIRVSESD T0315 221 :ARVTLVAEQIAELKGLSYEEVCEQTT 2amxA 330 :SNINDNYEKLYIHLNFTLEEFMIMNN Number of specific fragments extracted= 17 number of extra gaps= 1 total=1660 Will force an alignment to be made, even if fragment is small Number of alignments=102 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1pscA/T0315-1pscA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1pscA expands to /projects/compbio/data/pdb/1psc.pdb.gz 1pscA:# T0315 read from 1pscA/T0315-1pscA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1pscA read from 1pscA/T0315-1pscA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1pscA to template set # found chain 1pscA in template set T0315 1 :MLIDTHVHL 1pscA 50 :GFTLTHEHI T0315 10 :NDEQYDD 1pscA 69 :WPEFFGS T0315 17 :DLSEVITRAREAGVDRMFVVGF 1pscA 82 :KAVRGLRRARAAGVRTIVDVST T0315 42 :TIERAMKLIDEYD 1pscA 109 :DVSLLAEVSRAAD T0315 55 :FLYGIIGWH 1pscA 123 :HIVAATGLW T0315 64 :PVDAIDFT 1pscA 135 :PLSMRLRS T0315 72 :EEHLEWIESLAQHP 1pscA 144 :EELTQFFLREIQYG T0315 86 :KVIGIGEM 1pscA 164 :RAGIIKVA T0315 99 :WDKSPADVQKEVFRKQIALAKRLKLPIIIHN 1pscA 172 :TTGKATPFQELVLKAAARASLATGVPVTTHT T0315 130 :REATQDCIDILLEEHAEEVGGIM 1pscA 206 :QRDGEQQAAIFESEGLSPSRVCI T0315 153 :HS 1pscA 230 :HS T0315 155 :FSGSPEIADIVTN 1pscA 233 :DTDDLSYLTALAA T0315 169 :LNFYISLGGPVTF 1pscA 246 :RGYLIGLDHIPHS T0315 182 :KNAKQPKEVAKHVSMERLLVETDAPYLSPHP 1pscA 279 :TRALLIKALIDQGYMKQILVSNDWLFGFSSY T0315 217 :RNEPARVTLVAEQIAE 1pscA 323 :DGMAFIPLRVIPFLRE T0315 234 :KGLSYEEVCEQTTKNAEKLFNLN 1pscA 339 :KGVPQETLAGITVTNPARFLSPT Number of specific fragments extracted= 16 number of extra gaps= 0 total=1676 Will force an alignment to be made, even if fragment is small Number of alignments=103 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1pscA/T0315-1pscA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0315 read from 1pscA/T0315-1pscA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1pscA read from 1pscA/T0315-1pscA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1pscA in template set T0315 1 :MLIDTHVHL 1pscA 50 :GFTLTHEHI T0315 10 :NDEQY 1pscA 69 :WPEFF T0315 15 :DDDLSEVITRAREAGVDRMFVVGF 1pscA 80 :AEKAVRGLRRARAAGVRTIVDVST T0315 41 :STIERAMKLIDEYD 1pscA 108 :RDVSLLAEVSRAAD T0315 55 :FLYGIIGWHPV 1pscA 123 :HIVAATGLWFD T0315 69 :DFT 1pscA 140 :LRS T0315 72 :EEHLEWIESLAQ 1pscA 144 :EELTQFFLREIQ T0315 84 :HPKVIG 1pscA 160 :DTGIRA T0315 91 :GEMG 1pscA 166 :GIIK T0315 97 :YHWDKSPADVQKEVFRKQIALAKRLKLPIIIHN 1pscA 170 :VATTGKATPFQELVLKAAARASLATGVPVTTHT T0315 132 :ATQDCIDILLEEHAEEVGGIM 1pscA 208 :DGEQQAAIFESEGLSPSRVCI T0315 153 :HSF 1pscA 230 :HSD T0315 156 :SGSPEIADIVTN 1pscA 234 :TDDLSYLTALAA T0315 169 :LNFYISLGGPVTF 1pscA 246 :RGYLIGLDHIPHS T0315 182 :KNAKQ 1pscA 275 :RSWQT T0315 187 :PKEVAKHVSMERLLVETDAPYLSPHPYRGK 1pscA 284 :IKALIDQGYMKQILVSNDWLFGFSSYVTNI T0315 217 :RNEPARVTL 1pscA 322 :PDGMAFIPL T0315 226 :VAEQIAEL 1pscA 332 :VIPFLREK T0315 235 :GLSYEEVCEQTTKNAEKLFNLN 1pscA 340 :GVPQETLAGITVTNPARFLSPT Number of specific fragments extracted= 19 number of extra gaps= 0 total=1695 Will force an alignment to be made, even if fragment is small Number of alignments=104 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1pscA/T0315-1pscA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0315 read from 1pscA/T0315-1pscA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1pscA read from 1pscA/T0315-1pscA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1pscA in template set T0315 2 :LIDTHVHL 1pscA 51 :FTLTHEHI T0315 10 :NDEQYDD 1pscA 69 :WPEFFGS T0315 17 :DLSEVITRAREAGVDRMFVVGF 1pscA 82 :KAVRGLRRARAAGVRTIVDVST T0315 43 :IERAMKLIDEYDF 1pscA 110 :VSLLAEVSRAADV T0315 56 :LYGIIGW 1pscA 124 :IVAATGL T0315 63 :HPVDAIDFT 1pscA 134 :PPLSMRLRS T0315 72 :EEHLEWIESLA 1pscA 144 :EELTQFFLREI T0315 84 :HPKVIGIGE 1pscA 164 :RAGIIKVAT T0315 100 :DKSPADVQKEVFRKQIALAKRLKLPIIIHN 1pscA 173 :TGKATPFQELVLKAAARASLATGVPVTTHT T0315 130 :REATQDCIDILLEEHAEEVGGIM 1pscA 206 :QRDGEQQAAIFESEGLSPSRVCI T0315 154 :SF 1pscA 229 :GH T0315 156 :SGSPEIADI 1pscA 234 :TDDLSYLTA T0315 166 :TNKLNFYISLGGPVT 1pscA 243 :LAARGYLIGLDHIPH T0315 181 :FKNAKQPKEVAKHVS 1pscA 262 :LEDNASASALLGIRS T0315 196 :MERLLVETDAPYLSPHP 1pscA 293 :MKQILVSNDWLFGFSSY T0315 221 :ARVTL 1pscA 326 :AFIPL T0315 226 :VAEQIAE 1pscA 332 :VIPFLRE T0315 234 :KGLSYEEVCEQTTKNAEKLFNLNS 1pscA 339 :KGVPQETLAGITVTNPARFLSPTL Number of specific fragments extracted= 18 number of extra gaps= 0 total=1713 Will force an alignment to be made, even if fragment is small Number of alignments=105 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1dosA/T0315-1dosA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1dosA expands to /projects/compbio/data/pdb/1dos.pdb.gz 1dosA:Skipped atom 958, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 960, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 962, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 964, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 966, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 968, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 970, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 972, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 976, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 978, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 980, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 982, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 984, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 986, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 988, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 990, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 992, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 994, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 1000, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 1002, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 1004, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 1006, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 1008, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 1010, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 1301, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 1303, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 1305, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 1307, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 1309, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 1311, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 1313, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 1315, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 1319, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 1321, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 1323, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 1325, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 1327, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 1329, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 1331, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 1333, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 1337, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 1339, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 1341, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 1343, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 1345, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 1347, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 1349, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 1351, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 1620, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 1622, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 1624, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 1626, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 1628, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 1630, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 1632, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 1634, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 1638, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 1640, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 1642, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 1644, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 1646, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 1648, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 1650, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 1652, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 1654, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 1658, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 1660, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 1662, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 1664, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 1666, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 1668, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 1670, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 1672, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 2117, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 2119, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 2121, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 2123, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 2125, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 2127, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 2129, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 2133, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 2135, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 2137, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 2139, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 2141, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 2143, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 2145, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 2147, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 2149, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 2151, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 2158, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 2160, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 2162, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 2164, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 2517, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 2519, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 2521, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 2523, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 2525, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 2527, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 2529, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 2531, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 2533, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 2535, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 2537, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 2541, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 2543, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 2545, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 2547, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 2549, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 2551, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 2553, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 2555, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 2557, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 2559, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 2565, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 2567, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 2569, because occupancy 0.400 <= existing 0.600 in 1dosA Skipped atom 2571, because occupancy 0.400 <= existing 0.600 in 1dosA # T0315 read from 1dosA/T0315-1dosA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1dosA read from 1dosA/T0315-1dosA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1dosA to template set # found chain 1dosA in template set Warning: unaligning (T0315)Y213 because of BadResidue code BAD_PEPTIDE in next template residue (1dosA)A231 Warning: unaligning (T0315)R214 because of BadResidue code BAD_PEPTIDE at template residue (1dosA)A231 T0315 11 :DEQYDD 1dosA 3 :IFDFVK T0315 17 :DLSEVITRAREAGVDRMFVVGFNKSTIERAMKLIDEYD 1dosA 16 :DVQKVFQVAKENNFALPAVNCVGTDSINAVLETAAKVK T0315 55 :FLYGIIG 1dosA 55 :PVIVQFS T0315 75 :LEWIESLAQHP 1dosA 62 :NGGASFIAGKG T0315 95 :LD 1dosA 73 :VK T0315 99 :WDKSP 1dosA 75 :SDVPQ T0315 104 :ADVQKEVFRKQIALAKRLKLPIIIHN 1dosA 83 :ILGAISGAHHVHQMAEHYGVPVILHT T0315 130 :REATQDCIDILLEEH 1dosA 116 :LPWIDGLLDAGEKHF T0315 145 :AEEVGGIMHSF 1dosA 133 :TGKPLFSSHMI T0315 156 :SGSP 1dosA 147 :EESL T0315 160 :EIADIVTN 1dosA 159 :KYLERMSK T0315 169 :LNFYISLGGPVTF 1dosA 167 :IGMTLEIELGCTG T0315 184 :AKQPKEVAKHV 1dosA 199 :PEDVDYAYTEL T0315 195 :SMERLLVETDAPYLSPHP 1dosA 212 :ISPRFTIAASFGNVHGVY T0315 215 :GK 1dosA 232 :GN T0315 217 :RNEPARVTLVAEQIAELKGLS 1dosA 235 :VLTPTILRDSQEYVSKKHNLP Number of specific fragments extracted= 16 number of extra gaps= 1 total=1729 Will force an alignment to be made, even if fragment is small Number of alignments=106 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1dosA/T0315-1dosA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0315 read from 1dosA/T0315-1dosA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1dosA read from 1dosA/T0315-1dosA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1dosA in template set Warning: unaligning (T0315)Y213 because of BadResidue code BAD_PEPTIDE in next template residue (1dosA)A231 Warning: unaligning (T0315)R214 because of BadResidue code BAD_PEPTIDE at template residue (1dosA)A231 T0315 12 :EQY 1dosA 4 :FDF T0315 15 :DDDLSEVITRAREAGVDRMFVVGFNKSTIERAMKLIDEYD 1dosA 14 :GDDVQKVFQVAKENNFALPAVNCVGTDSINAVLETAAKVK T0315 55 :FLYGIIG 1dosA 55 :PVIVQFS T0315 75 :LEWIESLAQHP 1dosA 62 :NGGASFIAGKG T0315 95 :LD 1dosA 73 :VK T0315 100 :DKSP 1dosA 75 :SDVP T0315 104 :ADVQKEVFRKQIALAKRLKLPIIIHNRE 1dosA 83 :ILGAISGAHHVHQMAEHYGVPVILHTDH T0315 132 :ATQDCIDILLEEHA 1dosA 118 :WIDGLLDAGEKHFA T0315 146 :EEVGGIMHS 1dosA 134 :GKPLFSSHM T0315 155 :FSGSP 1dosA 146 :SEESL T0315 160 :EIADIVTN 1dosA 159 :KYLERMSK T0315 169 :LNFYISLGGPVTF 1dosA 167 :IGMTLEIELGCTG T0315 187 :PKEVAKHVS 1dosA 206 :YTELSKISP T0315 198 :RLLVETDAPYLSPHP 1dosA 215 :RFTIAASFGNVHGVY T0315 215 :GK 1dosA 232 :GN T0315 217 :RNEPARVTLVAEQIAEL 1dosA 235 :VLTPTILRDSQEYVSKK T0315 234 :KGLSYEEVCE 1dosA 267 :SGSTAQEIKD Number of specific fragments extracted= 17 number of extra gaps= 1 total=1746 Will force an alignment to be made, even if fragment is small Number of alignments=107 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1dosA/T0315-1dosA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0315 read from 1dosA/T0315-1dosA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1dosA read from 1dosA/T0315-1dosA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1dosA in template set Warning: unaligning (T0315)Y213 because of BadResidue code BAD_PEPTIDE in next template residue (1dosA)A231 Warning: unaligning (T0315)R214 because of BadResidue code BAD_PEPTIDE at template residue (1dosA)A231 T0315 14 :YDDDLSEVITRAREAGVDRMFVVGFNKSTIERAMKLIDEYDFLYGIIGW 1dosA 13 :TGDDVQKVFQVAKENNFALPAVNCVGTDSINAVLETAAKVKAPVIVQFS T0315 75 :LEWIESLAQHP 1dosA 62 :NGGASFIAGKG T0315 97 :YHWDKSP 1dosA 73 :VKSDVPQ T0315 104 :ADVQKEVFRKQIALAKRLKLPIIIHN 1dosA 83 :ILGAISGAHHVHQMAEHYGVPVILHT T0315 130 :REATQDCIDILLEEHAE 1dosA 116 :LPWIDGLLDAGEKHFAA T0315 148 :VGGIMHSFSGSPEI 1dosA 139 :SSHMIDLSEESLQE T0315 162 :ADI 1dosA 161 :LER T0315 166 :TNKLNFYISLGGPVTFK 1dosA 164 :MSKIGMTLEIELGCTGG T0315 185 :KQ 1dosA 181 :EE T0315 187 :PKEVAKHVS 1dosA 206 :YTELSKISP T0315 198 :RLLVETDAPYLSPHP 1dosA 215 :RFTIAASFGNVHGVY T0315 215 :G 1dosA 232 :G T0315 216 :KRNEPARVTLVAEQIAELKGLS 1dosA 234 :VVLTPTILRDSQEYVSKKHNLP Number of specific fragments extracted= 13 number of extra gaps= 1 total=1759 Will force an alignment to be made, even if fragment is small Number of alignments=108 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1bqcA/T0315-1bqcA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1bqcA expands to /projects/compbio/data/pdb/1bqc.pdb.gz 1bqcA:# T0315 read from 1bqcA/T0315-1bqcA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1bqcA read from 1bqcA/T0315-1bqcA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1bqcA to template set # found chain 1bqcA in template set Warning: unaligning (T0315)T203 because of BadResidue code BAD_PEPTIDE in next template residue (1bqcA)S255 Warning: unaligning (T0315)D204 because of BadResidue code BAD_PEPTIDE at template residue (1bqcA)S255 Warning: unaligning (T0315)P206 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1bqcA)E264 T0315 2 :LIDTHVHLNDEQYDD 1bqcA 22 :RGVSHPHNWYPQHTQ T0315 21 :VITRAREAGVDRMFVV 1bqcA 37 :AFADIKSHGANTVRVV T0315 37 :GFNKSTIERAMKLIDEYDFLYGII 1bqcA 61 :KNGPSDVANVISLCKQNRLICMLE T0315 62 :W 1bqcA 85 :V T0315 65 :VDAIDFT 1bqcA 86 :HDTTGYG T0315 72 :EEHLEWIESL 1bqcA 101 :DQAVDYWIEL T0315 82 :AQHP 1bqcA 114 :LQGE T0315 86 :KVIGIG 1bqcA 119 :DYVLIN T0315 93 :MGLDYH 1bqcA 125 :IGNEPY T0315 101 :KSPADVQ 1bqcA 131 :GNDSATV T0315 108 :KEVFRKQIALAKRLK 1bqcA 141 :ATDTSAAIQRLRAAG T0315 123 :LPIIIHN 1bqcA 158 :HTLVVDA T0315 130 :REATQDCID 1bqcA 176 :RNNADQVYA T0315 144 :HAEEVGGIMHSF 1bqcA 187 :PTGNTVFSIHMY T0315 156 :SGSPEIADIVTN 1bqcA 201 :YSQASTITSYLE T0315 168 :KLNFYISLGGPVTF 1bqcA 216 :NAGLPLIIGEFGHD T0315 182 :KNAKQPKEVAKHV 1bqcA 235 :PDEDTIMAEAERL T0315 197 :ERLLVE 1bqcA 248 :KLGYIG T0315 205 :A 1bqcA 256 :W T0315 207 :YLSPHPYRGKRNEPARVTLVA 1bqcA 265 :YLDMVYNFDGDNLSPWGERIF Number of specific fragments extracted= 20 number of extra gaps= 2 total=1779 Will force an alignment to be made, even if fragment is small Number of alignments=109 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1bqcA/T0315-1bqcA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0315 read from 1bqcA/T0315-1bqcA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1bqcA read from 1bqcA/T0315-1bqcA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1bqcA in template set Warning: unaligning (T0315)T203 because of BadResidue code BAD_PEPTIDE in next template residue (1bqcA)S255 Warning: unaligning (T0315)D204 because of BadResidue code BAD_PEPTIDE at template residue (1bqcA)S255 T0315 2 :LIDTHVHLNDEQYDD 1bqcA 22 :RGVSHPHNWYPQHTQ T0315 21 :VITRAREAGVDRMFVV 1bqcA 37 :AFADIKSHGANTVRVV T0315 37 :GFNKSTIERAMKLIDEY 1bqcA 61 :KNGPSDVANVISLCKQN T0315 55 :FLYGIIGWHPV 1bqcA 78 :RLICMLEVHDT T0315 72 :EEHLEWIESL 1bqcA 101 :DQAVDYWIEL T0315 82 :A 1bqcA 114 :L T0315 83 :QHPKVIGI 1bqcA 116 :GEEDYVLI T0315 94 :GLDYHWDKSPADVQ 1bqcA 124 :NIGNEPYGNDSATV T0315 108 :KEVFRKQIALAKRLK 1bqcA 141 :ATDTSAAIQRLRAAG T0315 123 :LPIIIHNRE 1bqcA 158 :HTLVVDAPN T0315 132 :ATQDCIDILLEEHA 1bqcA 174 :TMRNNADQVYASDP T0315 146 :EEVGGIMHSF 1bqcA 189 :GNTVFSIHMY T0315 156 :SGSPEIADIVTNK 1bqcA 201 :YSQASTITSYLEH T0315 169 :LNFYISLGGPVTF 1bqcA 217 :AGLPLIIGEFGHD T0315 182 :KNAKQPKEVAKHV 1bqcA 235 :PDEDTIMAEAERL T0315 197 :ERLLVE 1bqcA 248 :KLGYIG T0315 205 :AP 1bqcA 256 :WS T0315 207 :YLSPHPYRGKRNEPARVTLVAE 1bqcA 265 :YLDMVYNFDGDNLSPWGERIFY Number of specific fragments extracted= 18 number of extra gaps= 1 total=1797 Will force an alignment to be made, even if fragment is small Number of alignments=110 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1bqcA/T0315-1bqcA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0315 read from 1bqcA/T0315-1bqcA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1bqcA read from 1bqcA/T0315-1bqcA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1bqcA in template set Warning: unaligning (T0315)T203 because of BadResidue code BAD_PEPTIDE in next template residue (1bqcA)S255 Warning: unaligning (T0315)D204 because of BadResidue code BAD_PEPTIDE at template residue (1bqcA)S255 Warning: unaligning (T0315)P206 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1bqcA)E264 T0315 1 :MLIDTHVHLNDEQYDD 1bqcA 21 :IRGVSHPHNWYPQHTQ T0315 21 :VITRAREAGVDRMFVVGF 1bqcA 37 :AFADIKSHGANTVRVVLS T0315 39 :NKSTIERAMKLIDEYD 1bqcA 63 :GPSDVANVISLCKQNR T0315 56 :LYGIIGW 1bqcA 79 :LICMLEV T0315 65 :VDAIDFT 1bqcA 86 :HDTTGYG T0315 72 :EEHLEWIESLA 1bqcA 101 :DQAVDYWIELK T0315 83 :QHPKVIGIG 1bqcA 116 :GEEDYVLIN T0315 93 :MGLDYHW 1bqcA 125 :IGNEPYG T0315 102 :SPADV 1bqcA 132 :NDSAT T0315 107 :QKEVFRKQIALAKRLK 1bqcA 140 :WATDTSAAIQRLRAAG T0315 123 :LPIIIHN 1bqcA 158 :HTLVVDA T0315 130 :REATQDCID 1bqcA 176 :RNNADQVYA T0315 144 :HAEEVGGIMHSFS 1bqcA 187 :PTGNTVFSIHMYG T0315 157 :GSPEIADIV 1bqcA 202 :SQASTITSY T0315 167 :NKL 1bqcA 211 :LEH T0315 170 :NFYISLGGPVTFK 1bqcA 218 :GLPLIIGEFGHDH T0315 183 :NAKQPKEVAKH 1bqcA 236 :DEDTIMAEAER T0315 196 :MERLLVE 1bqcA 247 :LKLGYIG T0315 205 :A 1bqcA 256 :W T0315 207 :YLSPHPYRGKRNEPARVTLVA 1bqcA 265 :YLDMVYNFDGDNLSPWGERIF Number of specific fragments extracted= 20 number of extra gaps= 2 total=1817 Will force an alignment to be made, even if fragment is small Number of alignments=111 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1w8sA/T0315-1w8sA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1w8sA expands to /projects/compbio/data/pdb/1w8s.pdb.gz 1w8sA:Skipped atom 267, because occupancy 0.350 <= existing 0.650 in 1w8sA Skipped atom 269, because occupancy 0.350 <= existing 0.650 in 1w8sA Skipped atom 271, because occupancy 0.350 <= existing 0.650 in 1w8sA Skipped atom 273, because occupancy 0.350 <= existing 0.650 in 1w8sA Skipped atom 790, because occupancy 0.350 <= existing 0.650 in 1w8sA Skipped atom 792, because occupancy 0.350 <= existing 0.650 in 1w8sA Skipped atom 1672, because occupancy 0.350 <= existing 0.650 in 1w8sA Skipped atom 1674, because occupancy 0.350 <= existing 0.650 in 1w8sA Skipped atom 1676, because occupancy 0.350 <= existing 0.650 in 1w8sA Skipped atom 1678, because occupancy 0.350 <= existing 0.650 in 1w8sA Skipped atom 1680, because occupancy 0.350 <= existing 0.650 in 1w8sA # T0315 read from 1w8sA/T0315-1w8sA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1w8sA read from 1w8sA/T0315-1w8sA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1w8sA to template set # found chain 1w8sA in template set T0315 3 :IDTHVHL 1w8sA 19 :IILAYDH T0315 10 :NDEQYDD 1w8sA 30 :GPADFMD T0315 17 :DLSEVITRAREAGVDRMFVV 1w8sA 42 :DPEYILRLARDAGFDGVVFQ T0315 47 :MKLIDEY 1w8sA 62 :RGIAEKY T0315 54 :DFLYGIIGWH 1w8sA 71 :GSVPLILKLN T0315 68 :IDFT 1w8sA 84 :TLYN T0315 75 :LEWIESL 1w8sA 98 :VEEAVSL T0315 84 :HPKVIGIGE 1w8sA 105 :GASAVGYTI T0315 98 :HWDKSPADVQKEVFRKQIALAKRLKLPIIIHN 1w8sA 114 :YPGSGFEWKMFEELARIKRDAVKFDLPLVVES T0315 130 :REATQDCI 1w8sA 155 :ETAPEIVA T0315 138 :DILLEEHA 1w8sA 166 :RIALELGA T0315 149 :GGIMHSFSGSPEIADIVTNKLN 1w8sA 174 :DAMKIKYTGDPKTFSWAVKVAG T0315 171 :FYISLGGPVTFKNAKQPKEVAKHV 1w8sA 197 :VPVLMSGGPKTKTEEDFLKQVEGV T0315 196 :MERLLVETD 1w8sA 223 :AGALGIAVG T0315 206 :P 1w8sA 236 :Q T0315 220 :PARVTLVAEQIAEL 1w8sA 237 :RRDALKFARALAEL Number of specific fragments extracted= 16 number of extra gaps= 0 total=1833 Will force an alignment to be made, even if fragment is small Number of alignments=112 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1w8sA/T0315-1w8sA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0315 read from 1w8sA/T0315-1w8sA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1w8sA read from 1w8sA/T0315-1w8sA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1w8sA in template set T0315 2 :LIDTHVH 1w8sA 19 :IILAYDH T0315 10 :NDEQY 1w8sA 30 :GPADF T0315 15 :DDDLSEVITRAREAGVDRMFVV 1w8sA 40 :SADPEYILRLARDAGFDGVVFQ T0315 47 :MKLIDEY 1w8sA 62 :RGIAEKY T0315 54 :DFLYGIIGWHPV 1w8sA 71 :GSVPLILKLNGK T0315 66 :D 1w8sA 97 :S T0315 75 :LEWIESL 1w8sA 98 :VEEAVSL T0315 86 :KVIGIGEM 1w8sA 105 :GASAVGYT T0315 97 :YHWDKSPADVQKEVFRKQIALAKRLKLPIIIHNRE 1w8sA 113 :IYPGSGFEWKMFEELARIKRDAVKFDLPLVVESFP T0315 132 :ATQDCIDILLEEHA 1w8sA 160 :IVAYAARIALELGA T0315 149 :GGIMHSFSGSPEIADIVTNKLN 1w8sA 174 :DAMKIKYTGDPKTFSWAVKVAG T0315 171 :FYISLGGPVTFKNAKQPKEVAKHV 1w8sA 197 :VPVLMSGGPKTKTEEDFLKQVEGV T0315 196 :MERLLVETD 1w8sA 223 :AGALGIAVG T0315 205 :A 1w8sA 235 :W T0315 207 :YL 1w8sA 236 :QR T0315 221 :ARVTLVAEQIAEL 1w8sA 238 :RDALKFARALAEL Number of specific fragments extracted= 16 number of extra gaps= 0 total=1849 Will force an alignment to be made, even if fragment is small Number of alignments=113 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1w8sA/T0315-1w8sA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0315 read from 1w8sA/T0315-1w8sA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1w8sA read from 1w8sA/T0315-1w8sA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1w8sA in template set T0315 2 :LIDTHVH 1w8sA 19 :IILAYDH T0315 10 :NDEQYDD 1w8sA 30 :GPADFMD T0315 17 :DLSEVITRAREAGVDRMFVV 1w8sA 42 :DPEYILRLARDAGFDGVVFQ T0315 40 :KSTIE 1w8sA 62 :RGIAE T0315 51 :DEYDF 1w8sA 67 :KYYDG T0315 56 :LYGIIGWHPVDAIDFT 1w8sA 75 :LILKLNGKTTLYNGEP T0315 75 :LEWIESL 1w8sA 98 :VEEAVSL T0315 86 :KVIGIGEMGLDYH 1w8sA 105 :GASAVGYTIYPGS T0315 102 :SPADVQKEVFRKQIALAKRLKLPIIIHN 1w8sA 118 :GFEWKMFEELARIKRDAVKFDLPLVVES T0315 130 :REATQDCIDILLEEH 1w8sA 158 :PEIVAYAARIALELG T0315 148 :VGGIMHSFSGSPEIADIVTNKL 1w8sA 173 :ADAMKIKYTGDPKTFSWAVKVA T0315 170 :NFYISLGGPVTFKNAKQPKEVAKH 1w8sA 196 :KVPVLMSGGPKTKTEEDFLKQVEG T0315 195 :SMERLLVETD 1w8sA 222 :EAGALGIAVG T0315 213 :YRG 1w8sA 237 :RRD T0315 223 :VTLVAEQIAEL 1w8sA 240 :ALKFARALAEL Number of specific fragments extracted= 15 number of extra gaps= 0 total=1864 Will force an alignment to be made, even if fragment is small Number of alignments=114 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1n7kA/T0315-1n7kA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1n7kA expands to /projects/compbio/data/pdb/1n7k.pdb.gz 1n7kA:# T0315 read from 1n7kA/T0315-1n7kA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1n7kA read from 1n7kA/T0315-1n7kA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1n7kA to template set # found chain 1n7kA in template set T0315 3 :IDT 1n7kA 25 :IDS T0315 8 :HLNDEQYDD 1n7kA 28 :TLLSPRATE T0315 17 :DLSEVITRAREAGVDRMFV 1n7kA 38 :DVRNLVREASDYGFRCAVL T0315 39 :NKSTIERAMKLIDEYD 1n7kA 57 :TPVYTVKISGLAEKLG T0315 55 :FLYGIIGW 1n7kA 74 :KLCSVIGF T0315 65 :VDAIDFTEEHLEWIESLAQHP 1n7kA 82 :PLGQAPLEVKLVEAQTVLEAG T0315 86 :KVIGIG 1n7kA 104 :TELDVV T0315 97 :YHW 1n7kA 110 :PHL T0315 101 :KSPADVQKEVFRKQIALAKRLKLPIIIHN 1n7kA 113 :SLGPEAVYREVSGIVKLAKSYGAVVKVIL T0315 130 :REATQDCIDILLEEHAE 1n7kA 148 :DKTLSLLVDSSRRAGAD T0315 150 :GIM 1n7kA 165 :IVK T0315 153 :HSFSG 1n7kA 169 :STGVY T0315 158 :SPEIADIVTN 1n7kA 178 :DPVTVFRLAS T0315 168 :KLNFYISLGGPVT 1n7kA 191 :PLGMGVKASGGIR T0315 183 :NAKQPKEVAKHVSM 1n7kA 204 :SGIDAVLAVGAGAD T0315 200 :LVETD 1n7kA 218 :IIGTS T0315 222 :RVTLVAEQIA 1n7kA 223 :SAVKVLESFK Number of specific fragments extracted= 17 number of extra gaps= 0 total=1881 Will force an alignment to be made, even if fragment is small Number of alignments=115 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1n7kA/T0315-1n7kA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0315 read from 1n7kA/T0315-1n7kA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1n7kA read from 1n7kA/T0315-1n7kA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1n7kA in template set T0315 3 :IDT 1n7kA 25 :IDS T0315 8 :HLNDEQY 1n7kA 28 :TLLSPRA T0315 15 :DDDLSEVITRAREAGVDRMFV 1n7kA 36 :EEDVRNLVREASDYGFRCAVL T0315 39 :NKSTIERAMKLIDEYD 1n7kA 57 :TPVYTVKISGLAEKLG T0315 55 :FLYGIIGW 1n7kA 74 :KLCSVIGF T0315 65 :VDAIDFTEEHLEWIESLAQH 1n7kA 82 :PLGQAPLEVKLVEAQTVLEA T0315 86 :KVIGIGEM 1n7kA 102 :GATELDVV T0315 98 :HWDKSPADVQKEVFRKQIALAKRLKLPIIIHNRE 1n7kA 110 :PHLSLGPEAVYREVSGIVKLAKSYGAVVKVILEA T0315 132 :ATQDCIDILLEEHAE 1n7kA 150 :TLSLLVDSSRRAGAD T0315 149 :GGIMHSFSG 1n7kA 165 :IVKTSTGVY T0315 158 :SPEIADIVTN 1n7kA 178 :DPVTVFRLAS T0315 168 :KLNFYISLGGPV 1n7kA 191 :PLGMGVKASGGI T0315 182 :KNAKQPKEVAKHVS 1n7kA 203 :RSGIDAVLAVGAGA T0315 197 :E 1n7kA 217 :D T0315 200 :LVETD 1n7kA 218 :IIGTS T0315 222 :RVTLVAEQIA 1n7kA 223 :SAVKVLESFK Number of specific fragments extracted= 16 number of extra gaps= 0 total=1897 Will force an alignment to be made, even if fragment is small Number of alignments=116 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1n7kA/T0315-1n7kA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0315 read from 1n7kA/T0315-1n7kA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1n7kA read from 1n7kA/T0315-1n7kA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1n7kA in template set T0315 3 :IDT 1n7kA 25 :IDS T0315 7 :VHLNDEQYDDDLSEVITRAREAGVDRMFV 1n7kA 28 :TLLSPRATEEDVRNLVREASDYGFRCAVL T0315 39 :NKSTIERAMKLIDEYD 1n7kA 57 :TPVYTVKISGLAEKLG T0315 56 :LYGIIGWHPVDAIDFTEEHLEWIESLAQ 1n7kA 73 :VKLCSVIGFPLGQAPLEVKLVEAQTVLE T0315 84 :HPKVIGI 1n7kA 102 :GATELDV T0315 97 :YHWDKSPADVQKEVFRKQIALAKRLKLPIIIHN 1n7kA 109 :VPHLSLGPEAVYREVSGIVKLAKSYGAVVKVIL T0315 130 :REATQDCIDILLEEHAE 1n7kA 148 :DKTLSLLVDSSRRAGAD T0315 151 :IMHSFSG 1n7kA 165 :IVKTSTG T0315 158 :SPEIADI 1n7kA 178 :DPVTVFR T0315 166 :TNKL 1n7kA 185 :LASL T0315 170 :NFYISLGGPVT 1n7kA 193 :GMGVKASGGIR T0315 183 :NAKQPKEVAKH 1n7kA 204 :SGIDAVLAVGA T0315 196 :MERLL 1n7kA 216 :ADIIG T0315 203 :T 1n7kA 221 :T T0315 221 :ARVTLVAEQI 1n7kA 222 :SSAVKVLESF Number of specific fragments extracted= 15 number of extra gaps= 0 total=1912 Will force an alignment to be made, even if fragment is small Number of alignments=117 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1hjsA/T0315-1hjsA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1hjsA expands to /projects/compbio/data/pdb/1hjs.pdb.gz 1hjsA:Skipped atom 1871, because occupancy 0.500 <= existing 0.500 in 1hjsA Skipped atom 1875, because occupancy 0.500 <= existing 0.500 in 1hjsA Skipped atom 1877, because occupancy 0.500 <= existing 0.500 in 1hjsA Skipped atom 1879, because occupancy 0.500 <= existing 0.500 in 1hjsA Skipped atom 1881, because occupancy 0.500 <= existing 0.500 in 1hjsA # T0315 read from 1hjsA/T0315-1hjsA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1hjsA read from 1hjsA/T0315-1hjsA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1hjsA to template set # found chain 1hjsA in template set Warning: unaligning (T0315)K101 because of BadResidue code BAD_PEPTIDE in next template residue (1hjsA)E148 Warning: unaligning (T0315)S102 because of BadResidue code BAD_PEPTIDE at template residue (1hjsA)E148 T0315 21 :VITRAREAGVDRMFVVG 1hjsA 32 :LENILAANGVNTVRQRV T0315 38 :FNKST 1hjsA 50 :VNPAD T0315 43 :IERAMKLIDEY 1hjsA 59 :LDYNIAIAKRA T0315 54 :D 1hjsA 73 :G T0315 55 :FLYGIIGWH 1hjsA 75 :GVYIDFHYS T0315 64 :PVDAIDFTEEHLEWIESLAQ 1hjsA 95 :PAGWPSDIDNLSWKLYNYTL T0315 84 :HPKVIGIG 1hjsA 126 :QPTIVSIG T0315 92 :EMGLDYHW 1hjsA 135 :EIRAGLLW T0315 100 :D 1hjsA 146 :R T0315 103 :PADVQKEVFRKQIALAKRLKLP 1hjsA 149 :NWANIARLLHSAAWGIKDSSLS T0315 146 :EEVGGIMHSFSG 1hjsA 171 :PKPKIMIHLDNG T0315 158 :SPEIADIVTN 1hjsA 184 :DWGTQNWWYT T0315 168 :KLN 1hjsA 197 :KQG T0315 171 :FYISLGGPVTFKN 1hjsA 207 :DMMGVSFYPFYSS T0315 184 :AKQPKEVAKHV 1hjsA 223 :LSALKSSLDNM T0315 195 :SMERLLVETDAPYLSPHPYRGK 1hjsA 238 :NKEIAVVETNWPISCPNPRYSF T0315 217 :RNEPARVTLVAEQIAEL 1hjsA 267 :PFSPEGQTTFITNVANI T0315 245 :T 1hjsA 284 :V Number of specific fragments extracted= 18 number of extra gaps= 1 total=1930 Will force an alignment to be made, even if fragment is small Number of alignments=118 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1hjsA/T0315-1hjsA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0315 read from 1hjsA/T0315-1hjsA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1hjsA read from 1hjsA/T0315-1hjsA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1hjsA in template set T0315 21 :VITRAREAGVDRMFV 1hjsA 32 :LENILAANGVNTVRQ T0315 36 :VGFNKST 1hjsA 48 :VWVNPAD T0315 43 :IERAMKLIDEY 1hjsA 59 :LDYNIAIAKRA T0315 55 :FLYGIIGWHPV 1hjsA 73 :GLGVYIDFHYS T0315 66 :DAIDFTEEHLEWIESL 1hjsA 97 :GWPSDIDNLSWKLYNY T0315 111 :FRKQIALAKRLKLP 1hjsA 113 :TLDAANKLQNAGIQ T0315 125 :III 1hjsA 129 :IVS T0315 129 :NRE 1hjsA 132 :IGN T0315 132 :ATQDCIDILLE 1hjsA 149 :NWANIARLLHS T0315 143 :EH 1hjsA 163 :GI T0315 146 :EEVGGIMHSFSG 1hjsA 171 :PKPKIMIHLDNG T0315 158 :SP 1hjsA 184 :DW T0315 160 :EIADIVTN 1hjsA 190 :WWYTNVLK T0315 169 :LN 1hjsA 198 :QG T0315 171 :FYISLGGPVTFKNAKQ 1hjsA 207 :DMMGVSFYPFYSSSAT T0315 187 :PKEVAKHV 1hjsA 226 :LKSSLDNM T0315 195 :SMERLLVETDAPYLSPHPYRGK 1hjsA 238 :NKEIAVVETNWPISCPNPRYSF T0315 217 :RNEPARVTLVAEQIAEL 1hjsA 267 :PFSPEGQTTFITNVANI Number of specific fragments extracted= 18 number of extra gaps= 0 total=1948 Will force an alignment to be made, even if fragment is small Number of alignments=119 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1hjsA/T0315-1hjsA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0315 read from 1hjsA/T0315-1hjsA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1hjsA read from 1hjsA/T0315-1hjsA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1hjsA in template set Warning: unaligning (T0315)K101 because of BadResidue code BAD_PEPTIDE in next template residue (1hjsA)E148 Warning: unaligning (T0315)S102 because of BadResidue code BAD_PEPTIDE at template residue (1hjsA)E148 T0315 2 :LIDTHVHLNDEQYDDDLSEVIT 1hjsA 43 :TVRQRVWVNPADGNYNLDYNIA T0315 24 :RAREAGVDRMFVVGFNKS 1hjsA 68 :RAKAAGLGVYIDFHYSDT T0315 64 :PVDAIDFTEEHLEWIESLA 1hjsA 95 :PAGWPSDIDNLSWKLYNYT T0315 84 :HPKVIGIG 1hjsA 126 :QPTIVSIG T0315 92 :EMGLDYHW 1hjsA 135 :EIRAGLLW T0315 100 :D 1hjsA 146 :R T0315 103 :PADVQKEVFRKQIALAKRL 1hjsA 149 :NWANIARLLHSAAWGIKDS T0315 122 :KLPIIIHNREA 1hjsA 172 :KPKIMIHLDNG T0315 133 :TQDCIDILLEEH 1hjsA 185 :WGTQNWWYTNVL T0315 145 :AEEVGGIMHSF 1hjsA 203 :LSDFDMMGVSF T0315 156 :SGSPEIADIV 1hjsA 220 :SATLSALKSS T0315 187 :PKEVAKHVSMERLLVETDAPYLSPHP 1hjsA 230 :LDNMAKTWNKEIAVVETNWPISCPNP T0315 213 :YRGKRNEPARVTLVAEQIAEL 1hjsA 263 :VKNIPFSPEGQTTFITNVANI Number of specific fragments extracted= 13 number of extra gaps= 1 total=1961 Will force an alignment to be made, even if fragment is small Number of alignments=120 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1m7jA/T0315-1m7jA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1m7jA expands to /projects/compbio/data/pdb/1m7j.pdb.gz 1m7jA:# T0315 read from 1m7jA/T0315-1m7jA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1m7jA read from 1m7jA/T0315-1m7jA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1m7jA to template set # found chain 1m7jA in template set T0315 1 :MLIDTHVHLN 1m7jA 62 :GFIDSHTHDD T0315 17 :DLSEVITRARE 1m7jA 125 :RFSDYLEALRA T0315 31 :DRMFVV 1m7jA 140 :VNAACM T0315 37 :GFNKSTIERAMKLIDEY 1m7jA 162 :EATADEIQAMQALADDA T0315 54 :DFLYGIIG 1m7jA 182 :GAIGISTG T0315 62 :WHP 1m7jA 191 :FYP T0315 66 :DAIDFTEEHLEWIESLAQHPKVIGIGEM 1m7jA 194 :PAAHASTEEIIEVCRPLITHGGVYATHM T0315 101 :KSPADVQKEVFRKQIALAKRLKLPIII 1m7jA 222 :RDEGEHIVQALEETFRIGRELDVPVVI T0315 128 :HN 1m7jA 250 :HH T0315 130 :REATQDCIDILLEE 1m7jA 259 :FGRSKETLALIEAA T0315 166 :TNKLNFYISLGGPVTF 1m7jA 273 :MASQDVSLDAYPYVAG T0315 185 :KQPKEVAKH 1m7jA 350 :PDVQRILAF T0315 197 :ERLLVETDAPYLS 1m7jA 359 :GPTMIGSDGLPHD T0315 216 :KRNEPAR 1m7jA 372 :ERPHPRL T0315 223 :VTLVAEQIAELKG 1m7jA 382 :FPRVLGHYSRDLG T0315 236 :LSYEEVCEQTTKNAEKLFNLN 1m7jA 396 :FPLETAVWKMTGLTAAKFGLA Number of specific fragments extracted= 16 number of extra gaps= 0 total=1977 Will force an alignment to be made, even if fragment is small Number of alignments=121 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1m7jA/T0315-1m7jA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0315 read from 1m7jA/T0315-1m7jA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1m7jA read from 1m7jA/T0315-1m7jA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1m7jA in template set T0315 1 :MLIDTHVHLN 1m7jA 62 :GFIDSHTHDD T0315 11 :DEQY 1m7jA 77 :HRDM T0315 28 :AGVDRMFVV 1m7jA 86 :QGVTTVVTG T0315 37 :GFNK 1m7jA 99 :SLAP T0315 41 :ST 1m7jA 106 :AN T0315 43 :IERAMKLIDEYDFLYGIIGWHPV 1m7jA 126 :FSDYLEALRAAPPAVNAACMVGH T0315 66 :DA 1m7jA 158 :DL T0315 68 :IDFTEEHLEWIESLAQ 1m7jA 161 :REATADEIQAMQALAD T0315 84 :HPKVIGIGEMGLDYHWDKSP 1m7jA 180 :ASGAIGISTGAFYPPAAHAS T0315 108 :KEVFRKQIALAKRLKLPIIIHNRE 1m7jA 200 :TEEIIEVCRPLITHGGVYATHMRD T0315 132 :ATQDCIDILLEE 1m7jA 231 :ALEETFRIGREL T0315 146 :EEVGGIMHSFSGSP 1m7jA 243 :DVPVVISHHKVMGK T0315 160 :EIADIVTNKLNFYIS 1m7jA 267 :ALIEAAMASQDVSLD T0315 182 :KNAKQPKEVAKH 1m7jA 347 :MDEPDVQRILAF T0315 197 :ERLLVETDAPYLSPHPYR 1m7jA 359 :GPTMIGSDGLPHDERPHP T0315 218 :NEPARVTLVAEQIAELKG 1m7jA 377 :RLWGTFPRVLGHYSRDLG T0315 236 :LSYEEVCEQTTKNAEKLFNLN 1m7jA 396 :FPLETAVWKMTGLTAAKFGLA Number of specific fragments extracted= 17 number of extra gaps= 0 total=1994 Will force an alignment to be made, even if fragment is small Number of alignments=122 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1m7jA/T0315-1m7jA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0315 read from 1m7jA/T0315-1m7jA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1m7jA read from 1m7jA/T0315-1m7jA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1m7jA in template set T0315 11 :DEQYDD 1m7jA 114 :LLDEGG T0315 17 :DLSEVITRARE 1m7jA 125 :RFSDYLEALRA T0315 31 :DRMFVVG 1m7jA 140 :VNAACMV T0315 38 :FNKSTIERAMKLIDEYDF 1m7jA 163 :ATADEIQAMQALADDALA T0315 56 :LYGIIGWHPVDAIDFTEEHLEWIESLA 1m7jA 184 :IGISTGAFYPPAAHASTEEIIEVCRPL T0315 83 :QHPKVIGIGE 1m7jA 212 :THGGVYATHM T0315 97 :YHW 1m7jA 222 :RDE T0315 100 :DK 1m7jA 226 :EH T0315 107 :QKEVFRKQIALAKRLKLPIIIHN 1m7jA 228 :IVQALEETFRIGRELDVPVVISH T0315 130 :REATQDCIDILLEEHAE 1m7jA 259 :FGRSKETLALIEAAMAS T0315 148 :VGGIMHSFSG 1m7jA 276 :QDVSLDAYPY T0315 172 :Y 1m7jA 286 :V T0315 176 :GGPVTFKNAK 1m7jA 287 :AGSTMLKQDR T0315 192 :KHV 1m7jA 297 :VLL T0315 196 :MERLLVETD 1m7jA 300 :AGRTLITWC T0315 205 :APYLSPHP 1m7jA 311 :YPELSGRD T0315 227 :AEQIAELKGLSYEEVC 1m7jA 319 :LEEIAAERGKSKYDVV Number of specific fragments extracted= 17 number of extra gaps= 0 total=2011 Will force an alignment to be made, even if fragment is small Number of alignments=123 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1a4mA/T0315-1a4mA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1a4mA expands to /projects/compbio/data/pdb/1a4m.pdb.gz 1a4mA:# T0315 read from 1a4mA/T0315-1a4mA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1a4mA read from 1a4mA/T0315-1a4mA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1a4mA to template set # found chain 1a4mA in template set T0315 1 :MLIDTHVHLND 1a4mA 10 :PKVELHVHLDG T0315 14 :YDD 1a4mA 21 :AIK T0315 18 :LSEVITRAREAGVDRMFVVGFN 1a4mA 83 :AYEFVEMKAKEGVVYVEVRYSP T0315 40 :KST 1a4mA 126 :PDD T0315 43 :IERAMKLIDEYD 1a4mA 134 :NQGLQEGEQAFG T0315 55 :FLYGIIGWHP 1a4mA 147 :KVRSILCCMR T0315 66 :DAIDFTEEHLEWIESLAQHP 1a4mA 157 :HQPSWSLEVLELCKKYNQKT T0315 87 :VIGIGEMG 1a4mA 177 :VVAMDLAG T0315 96 :DYHWDKSP 1a4mA 185 :DETIEGSS T0315 104 :ADV 1a4mA 194 :FPG T0315 111 :FRKQIALAKRLKLPIIIHN 1a4mA 197 :HVEAYEGAVKNGIHRTVHA T0315 130 :REATQDCIDILL 1a4mA 218 :VGSPEVVREAVD T0315 144 :H 1a4mA 230 :I T0315 147 :EVGGIMHSF 1a4mA 232 :KTERVGHGY T0315 157 :GSPEIADIVTN 1a4mA 244 :EDEALYNRLLK T0315 169 :LNFYISLG 1a4mA 255 :ENMHFEVC T0315 177 :GPVTFKNAKQPKEVAKH 1a4mA 270 :GAWDPKTTHAVVRFKND T0315 198 :RLLVETDAPYLSP 1a4mA 289 :NYSLNTDDPLIFK T0315 221 :ARVTLVAEQIAELKGLSYEEVCEQTT 1a4mA 302 :STLDTDYQMTKKDMGFTEEEFKRLNI T0315 248 :NAEK 1a4mA 328 :NAAK Number of specific fragments extracted= 20 number of extra gaps= 0 total=2031 Will force an alignment to be made, even if fragment is small Number of alignments=124 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1a4mA/T0315-1a4mA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0315 read from 1a4mA/T0315-1a4mA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1a4mA read from 1a4mA/T0315-1a4mA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1a4mA in template set T0315 1 :MLIDTHVHLNDEQY 1a4mA 10 :PKVELHVHLDGAIK T0315 18 :LSEVITRAREAGVDRMFVV 1a4mA 83 :AYEFVEMKAKEGVVYVEVR T0315 37 :GFNKST 1a4mA 111 :KVDPMP T0315 43 :IERAMKLIDEYD 1a4mA 134 :NQGLQEGEQAFG T0315 55 :FLYGIIGWHPV 1a4mA 147 :KVRSILCCMRH T0315 67 :AIDFTEEHLEWIESLAQHP 1a4mA 158 :QPSWSLEVLELCKKYNQKT T0315 87 :VIGIGEMG 1a4mA 177 :VVAMDLAG T0315 96 :DYHWDKS 1a4mA 185 :DETIEGS T0315 104 :A 1a4mA 194 :F T0315 109 :EVFRKQIALAKRLKLPIIIHNRE 1a4mA 195 :PGHVEAYEGAVKNGIHRTVHAGE T0315 132 :ATQDCIDILLEEH 1a4mA 219 :GSPEVVREAVDIL T0315 147 :EVGGIMHSFSG 1a4mA 232 :KTERVGHGYHT T0315 158 :SPEIADIVTN 1a4mA 245 :DEALYNRLLK T0315 169 :LNFYIS 1a4mA 255 :ENMHFE T0315 175 :L 1a4mA 269 :T T0315 177 :GPV 1a4mA 270 :GAW T0315 183 :NAKQ 1a4mA 273 :DPKT T0315 187 :PKEVAKH 1a4mA 280 :VVRFKND T0315 198 :RLLVETDAPYLSP 1a4mA 289 :NYSLNTDDPLIFK T0315 221 :ARVTLVAEQIAELKGLSYEEVCEQTT 1a4mA 302 :STLDTDYQMTKKDMGFTEEEFKRLNI T0315 248 :NAEK 1a4mA 328 :NAAK Number of specific fragments extracted= 21 number of extra gaps= 0 total=2052 Will force an alignment to be made, even if fragment is small Number of alignments=125 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1a4mA/T0315-1a4mA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0315 read from 1a4mA/T0315-1a4mA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1a4mA read from 1a4mA/T0315-1a4mA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1a4mA in template set T0315 20 :EVITRAREAGVDRMFVVGFNK 1a4mA 85 :EFVEMKAKEGVVYVEVRYSPH T0315 43 :IERAMKLIDEYDFLYGIIGWHPVDAIDFTEEHLEWIESLAQH 1a4mA 134 :NQGLQEGEQAFGIKVRSILCCMRHQPSWSLEVLELCKKYNQK T0315 86 :KVIGIGEMGLDYHWDKSPADVQKEVFRK 1a4mA 176 :TVVAMDLAGDETIEGSSLFPGHVEAYEG T0315 118 :AKRLKLPIIIHN 1a4mA 204 :AVKNGIHRTVHA T0315 133 :TQ 1a4mA 221 :PE T0315 136 :CIDILLEEH 1a4mA 223 :VVREAVDIL T0315 147 :EVGGIMHSFS 1a4mA 232 :KTERVGHGYH T0315 157 :GSPEIADI 1a4mA 244 :EDEALYNR T0315 166 :TNKLNFYISL 1a4mA 252 :LLKENMHFEV T0315 176 :GGPVTFKNAKQPKEVAKH 1a4mA 269 :TGAWDPKTTHAVVRFKND T0315 198 :RLLVETDAPYLSPH 1a4mA 289 :NYSLNTDDPLIFKS T0315 222 :RVTLVAEQIAELKGLSYEEVCE 1a4mA 303 :TLDTDYQMTKKDMGFTEEEFKR T0315 245 :TTKNAEK 1a4mA 325 :LNINAAK Number of specific fragments extracted= 13 number of extra gaps= 0 total=2065 Will force an alignment to be made, even if fragment is small Number of alignments=126 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1fkx/T0315-1fkx-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1fkx expands to /projects/compbio/data/pdb/1fkx.pdb.gz 1fkx:Warning: there is no chain 1fkx will retry with 1fkxA # T0315 read from 1fkx/T0315-1fkx-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1fkx read from 1fkx/T0315-1fkx-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1fkx to template set # found chain 1fkx in template set T0315 1 :MLIDTHVHLND 1fkx 10 :PKVELHVHLDG T0315 15 :DD 1fkx 24 :PE T0315 18 :LSEVITRAREAGVDR 1fkx 83 :AYEFVEMKAKEGVVY T0315 58 :GIIGWHPVDAIDFT 1fkx 98 :VEVRYSPHLLANSK T0315 72 :EEHLEWIESLAQ 1fkx 127 :DDVVDLVNQGLQ T0315 84 :H 1fkx 145 :G T0315 86 :KVIGIGEMGL 1fkx 147 :KVRSILCCMR T0315 101 :KS 1fkx 157 :HQ T0315 108 :KEVFRKQIALAKRL 1fkx 159 :PSWSLEVLELCKKY T0315 123 :LPIIIHN 1fkx 176 :TVVAMDL T0315 133 :TQDCIDILLEEHAEEVGGIMHSF 1fkx 194 :FPGHVEAYEGAVKNGIHRTVHAG T0315 156 :SGSPEIADIVTNKLNFYISLGGPVTF 1fkx 218 :VGSPEVVREAVDILKTERVGHGYHTI T0315 182 :KNAKQPKEVAKH 1fkx 275 :KTTHAVVRFKND T0315 198 :RLLVETDAP 1fkx 289 :NYSLNTDAP T0315 221 :AR 1fkx 298 :LI T0315 223 :VTLVAEQIAELKGLSYEEVCE 1fkx 304 :LDTDYQMTKKDMGFTEEEFKR T0315 245 :TTKNAEK 1fkx 325 :LNINAAK Number of specific fragments extracted= 17 number of extra gaps= 0 total=2082 Will force an alignment to be made, even if fragment is small Number of alignments=127 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1fkx/T0315-1fkx-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0315 read from 1fkx/T0315-1fkx-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1fkx read from 1fkx/T0315-1fkx-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1fkx in template set T0315 1 :MLIDTHVHLNDEQY 1fkx 10 :PKVELHVHLDGAIK T0315 18 :LSEVITRAREAGVDRMFVV 1fkx 83 :AYEFVEMKAKEGVVYVEVR T0315 37 :GFNKST 1fkx 111 :KVDPMP T0315 43 :IERAMKLIDEYD 1fkx 134 :NQGLQEGEQAFG T0315 55 :FLYGIIGWHPV 1fkx 147 :KVRSILCCMRH T0315 67 :AIDFTEEHLEWIESLAQHP 1fkx 158 :QPSWSLEVLELCKKYNQKT T0315 87 :VIGIGEMG 1fkx 177 :VVAMDLAG T0315 96 :DYHWDKS 1fkx 185 :DETIEGS T0315 104 :A 1fkx 194 :F T0315 109 :EVFRKQIALAKRLKLPIIIHNRE 1fkx 195 :PGHVEAYEGAVKNGIHRTVHAGE T0315 132 :ATQDCIDILLEEH 1fkx 219 :GSPEVVREAVDIL T0315 147 :EVGGIMHSFSG 1fkx 232 :KTERVGHGYHT T0315 158 :SPEIADIVTN 1fkx 245 :DEALYNRLLK T0315 169 :LNFYISLG 1fkx 255 :ENMHFEVC T0315 177 :GPVTFKNAKQPKEVAKH 1fkx 270 :GAWDPKTTHAVVRFKND T0315 198 :RLLVETDAP 1fkx 289 :NYSLNTDAP T0315 223 :VTLVAEQIAELKGLSYEEVCE 1fkx 304 :LDTDYQMTKKDMGFTEEEFKR T0315 245 :TTKNAEK 1fkx 325 :LNINAAK Number of specific fragments extracted= 18 number of extra gaps= 0 total=2100 Will force an alignment to be made, even if fragment is small Number of alignments=128 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1fkx/T0315-1fkx-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0315 read from 1fkx/T0315-1fkx-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1fkx read from 1fkx/T0315-1fkx-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1fkx in template set T0315 2 :LIDTHVHLNDEQ 1fkx 11 :KVELHVHLDGAI T0315 17 :DLSEVITRAREAGVD 1fkx 23 :KPETILYFGKKRGIA T0315 35 :VVGFNKST 1fkx 38 :LPADTVEE T0315 43 :IERAMKLIDEYDFLYGIIGWHPVDAIDFT 1fkx 83 :AYEFVEMKAKEGVVYVEVRYSPHLLANSK T0315 72 :EEHLEWIESLA 1fkx 127 :DDVVDLVNQGL T0315 84 :HPKVIGIGEMGLD 1fkx 145 :GIKVRSILCCMRH T0315 107 :QKEVFRKQIALAKRL 1fkx 158 :QPSWSLEVLELCKKY T0315 122 :KLPIIIHN 1fkx 175 :KTVVAMDL T0315 132 :ATQDCIDILLEEHAEEVGGIMHSFS 1fkx 193 :LFPGHVEAYEGAVKNGIHRTVHAGE T0315 157 :GSPEIADI 1fkx 219 :GSPEVVRE T0315 166 :TNKL 1fkx 227 :AVDI T0315 170 :NFYISLGGPVTFKNAKQPKEVAKH 1fkx 232 :KTERVGHGYHTIEDEALYNRLLKE T0315 198 :RLLVETD 1fkx 256 :NMHFEVC T0315 207 :YLSPH 1fkx 269 :TGAWD T0315 222 :RVTLVAEQIAELKGLSYEEVC 1fkx 303 :TLDTDYQMTKKDMGFTEEEFK T0315 244 :QTTKNAEK 1fkx 324 :RLNINAAK Number of specific fragments extracted= 16 number of extra gaps= 0 total=2116 Will force an alignment to be made, even if fragment is small Number of alignments=129 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ur4A/T0315-1ur4A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1ur4A expands to /projects/compbio/data/pdb/1ur4.pdb.gz 1ur4A:# T0315 read from 1ur4A/T0315-1ur4A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ur4A read from 1ur4A/T0315-1ur4A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1ur4A to template set # found chain 1ur4A in template set T0315 17 :D 1ur4A 52 :D T0315 21 :VITRAREAGVDRMFVV 1ur4A 53 :IFKTLKEAGVNYVRVR T0315 37 :GFNKSTIERAMKLIDEYD 1ur4A 85 :NNDLEKAIQIGKRATANG T0315 55 :FLYGIIGWH 1ur4A 104 :KLLADFHYS T0315 64 :PVDAIDFT 1ur4A 124 :PKAWANLN T0315 72 :EEHLEWIESLAQ 1ur4A 133 :EDKKTALYQYTK T0315 84 :HP 1ur4A 153 :AG T0315 86 :KVIGIGE 1ur4A 156 :DIGMVQV T0315 94 :GLDY 1ur4A 163 :GNET T0315 98 :HWDKSPADVQKEVFRKQIALAKRL 1ur4A 170 :LAGETDWAKMSQLFNAGSQAVRET T0315 122 :KLPIIIHN 1ur4A 196 :NILVALHF T0315 130 :REATQDCIDILLEEHAE 1ur4A 209 :SGRYAWIAETLHRHHVD T0315 148 :VGGIMHSF 1ur4A 226 :YDVFASSY T0315 156 :SGSP 1ur4A 238 :HGTL T0315 160 :EIADIVTNKLNFYISLGGPVTF 1ur4A 246 :SVLTSVADTYGKKVMVAETSYT T0315 194 :VSME 1ur4A 268 :YTAE T0315 202 :ETDAPYLSPHPYRGKRNEPARVTLVAEQIAEL 1ur4A 272 :DGDGHGNTAPKNGQTLNNPVTVQGQANAVRDV T0315 249 :AEKLFNL 1ur4A 304 :IQAVSDV Number of specific fragments extracted= 18 number of extra gaps= 0 total=2134 Will force an alignment to be made, even if fragment is small Number of alignments=130 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ur4A/T0315-1ur4A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0315 read from 1ur4A/T0315-1ur4A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ur4A read from 1ur4A/T0315-1ur4A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1ur4A in template set T0315 15 :DDDLSEVITRAREAGVDRMFVV 1ur4A 47 :SGKKQDIFKTLKEAGVNYVRVR T0315 37 :GFNKST 1ur4A 73 :PYDANG T0315 43 :IERAMKLIDEY 1ur4A 88 :LEKAIQIGKRA T0315 54 :DFLYGIIGWHPV 1ur4A 101 :NGMKLLADFHYS T0315 66 :DAIDFT 1ur4A 126 :AWANLN T0315 72 :EEHLEWIESLAQ 1ur4A 133 :EDKKTALYQYTK T0315 84 :HPKVIGIGEMGLDYHWDKSPADVQKEVFRKQIALAKRL 1ur4A 156 :DIGMVQVGNETNGGLAGETDWAKMSQLFNAGSQAVRET T0315 122 :KLPIIIHNRE 1ur4A 196 :NILVALHFTN T0315 132 :ATQDCIDILLEEHAEEVGGIMHSF 1ur4A 211 :RYAWIAETLHRHHVDYDVFASSYY T0315 156 :SGSP 1ur4A 238 :HGTL T0315 160 :EIADIVTNKLNFYISLGGPVTFKNAKQ 1ur4A 246 :SVLTSVADTYGKKVMVAETSYTYTAED T0315 203 :TDAPYLSPHPYRGKRNEPARVTLVAEQIAEL 1ur4A 273 :GDGHGNTAPKNGQTLNNPVTVQGQANAVRDV T0315 249 :AEKLFNLN 1ur4A 304 :IQAVSDVG Number of specific fragments extracted= 13 number of extra gaps= 0 total=2147 Will force an alignment to be made, even if fragment is small Number of alignments=131 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ur4A/T0315-1ur4A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0315 read from 1ur4A/T0315-1ur4A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ur4A read from 1ur4A/T0315-1ur4A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1ur4A in template set T0315 21 :VITRAREAGVDRMFVVGF 1ur4A 53 :IFKTLKEAGVNYVRVRIW T0315 39 :NKSTIERAMKLIDEYDF 1ur4A 87 :DLEKAIQIGKRATANGM T0315 56 :LYGIIGW 1ur4A 105 :LLADFHY T0315 64 :PVDAIDFT 1ur4A 124 :PKAWANLN T0315 72 :EEHLEWIESLA 1ur4A 133 :EDKKTALYQYT T0315 84 :HPKVIGIGEMGLDYHWDKSPADVQKEVFRKQIALAKRL 1ur4A 156 :DIGMVQVGNETNGGLAGETDWAKMSQLFNAGSQAVRET T0315 122 :KLPIIIHN 1ur4A 196 :NILVALHF T0315 130 :REATQDCIDILLEEHAE 1ur4A 209 :SGRYAWIAETLHRHHVD T0315 148 :VGGIMHSF 1ur4A 226 :YDVFASSY T0315 156 :SGSPEIADIVTNKL 1ur4A 238 :HGTLKNLTSVLTSV T0315 170 :NFYISLGGPVTFKNAK 1ur4A 256 :GKKVMVAETSYTYTAE T0315 202 :ETDAPYLSPHPYRGKRNEPARVTLVAEQIAEL 1ur4A 272 :DGDGHGNTAPKNGQTLNNPVTVQGQANAVRDV T0315 249 :AEKLFNLN 1ur4A 304 :IQAVSDVG Number of specific fragments extracted= 13 number of extra gaps= 0 total=2160 Will force an alignment to be made, even if fragment is small Number of alignments=132 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1w3iA/T0315-1w3iA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1w3iA expands to /projects/compbio/data/pdb/1w3i.pdb.gz 1w3iA:Skipped atom 192, because occupancy 0.500 <= existing 0.500 in 1w3iA Skipped atom 194, because occupancy 0.500 <= existing 0.500 in 1w3iA Skipped atom 196, because occupancy 0.500 <= existing 0.500 in 1w3iA Skipped atom 198, because occupancy 0.500 <= existing 0.500 in 1w3iA Skipped atom 200, because occupancy 0.500 <= existing 0.500 in 1w3iA Skipped atom 202, because occupancy 0.500 <= existing 0.500 in 1w3iA Skipped atom 204, because occupancy 0.500 <= existing 0.500 in 1w3iA Skipped atom 206, because occupancy 0.500 <= existing 0.500 in 1w3iA Skipped atom 643, because occupancy 0.500 <= existing 0.500 in 1w3iA Skipped atom 645, because occupancy 0.500 <= existing 0.500 in 1w3iA Skipped atom 647, because occupancy 0.500 <= existing 0.500 in 1w3iA Skipped atom 649, because occupancy 0.500 <= existing 0.500 in 1w3iA Skipped atom 651, because occupancy 0.500 <= existing 0.500 in 1w3iA Skipped atom 653, because occupancy 0.500 <= existing 0.500 in 1w3iA Skipped atom 655, because occupancy 0.500 <= existing 0.500 in 1w3iA Skipped atom 657, because occupancy 0.500 <= existing 0.500 in 1w3iA Skipped atom 659, because occupancy 0.500 <= existing 0.500 in 1w3iA Skipped atom 661, because occupancy 0.500 <= existing 0.500 in 1w3iA Skipped atom 663, because occupancy 0.500 <= existing 0.500 in 1w3iA Skipped atom 853, because occupancy 0.400 <= existing 0.600 in 1w3iA Skipped atom 855, because occupancy 0.400 <= existing 0.600 in 1w3iA Skipped atom 857, because occupancy 0.400 <= existing 0.600 in 1w3iA Skipped atom 859, because occupancy 0.400 <= existing 0.600 in 1w3iA Skipped atom 861, because occupancy 0.400 <= existing 0.600 in 1w3iA Skipped atom 863, because occupancy 0.400 <= existing 0.600 in 1w3iA Skipped atom 865, because occupancy 0.400 <= existing 0.600 in 1w3iA Skipped atom 867, because occupancy 0.400 <= existing 0.600 in 1w3iA Skipped atom 1271, because occupancy 0.500 <= existing 0.500 in 1w3iA Skipped atom 1273, because occupancy 0.500 <= existing 0.500 in 1w3iA Skipped atom 1275, because occupancy 0.500 <= existing 0.500 in 1w3iA Skipped atom 1277, because occupancy 0.500 <= existing 0.500 in 1w3iA Skipped atom 1279, because occupancy 0.500 <= existing 0.500 in 1w3iA Skipped atom 1281, because occupancy 0.500 <= existing 0.500 in 1w3iA Skipped atom 1283, because occupancy 0.500 <= existing 0.500 in 1w3iA Skipped atom 1285, because occupancy 0.500 <= existing 0.500 in 1w3iA Skipped atom 1287, because occupancy 0.500 <= existing 0.500 in 1w3iA Skipped atom 1454, because occupancy 0.400 <= existing 0.600 in 1w3iA Skipped atom 1456, because occupancy 0.400 <= existing 0.600 in 1w3iA Skipped atom 1458, because occupancy 0.400 <= existing 0.600 in 1w3iA Skipped atom 1460, because occupancy 0.400 <= existing 0.600 in 1w3iA Skipped atom 1462, because occupancy 0.400 <= existing 0.600 in 1w3iA Skipped atom 1464, because occupancy 0.400 <= existing 0.600 in 1w3iA Skipped atom 1522, because occupancy 0.500 <= existing 0.500 in 1w3iA Skipped atom 1524, because occupancy 0.500 <= existing 0.500 in 1w3iA Skipped atom 1526, because occupancy 0.500 <= existing 0.500 in 1w3iA Skipped atom 1528, because occupancy 0.500 <= existing 0.500 in 1w3iA Skipped atom 1530, because occupancy 0.500 <= existing 0.500 in 1w3iA Skipped atom 1532, because occupancy 0.500 <= existing 0.500 in 1w3iA Skipped atom 1711, because occupancy 0.400 <= existing 0.600 in 1w3iA Skipped atom 1713, because occupancy 0.400 <= existing 0.600 in 1w3iA Skipped atom 1715, because occupancy 0.400 <= existing 0.600 in 1w3iA Skipped atom 1717, because occupancy 0.400 <= existing 0.600 in 1w3iA Skipped atom 1719, because occupancy 0.400 <= existing 0.600 in 1w3iA Skipped atom 1721, because occupancy 0.400 <= existing 0.600 in 1w3iA Skipped atom 1723, because occupancy 0.400 <= existing 0.600 in 1w3iA Skipped atom 1725, because occupancy 0.400 <= existing 0.600 in 1w3iA # T0315 read from 1w3iA/T0315-1w3iA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1w3iA read from 1w3iA/T0315-1w3iA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1w3iA to template set # found chain 1w3iA in template set Warning: unaligning (T0315)L56 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1w3iA)I70 Warning: unaligning (T0315)Y57 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1w3iA)I70 Warning: unaligning (T0315)E92 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1w3iA)Y99 Warning: unaligning (T0315)M93 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1w3iA)Y99 Warning: unaligning (T0315)T203 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (1w3iA)A197 Warning: unaligning (T0315)D204 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (1w3iA)A197 T0315 2 :LIDTHVHLNDEQ 1w3iA 4 :IITPIITPFTKD T0315 17 :DLSEVITRAREAGVDRMFVVG 1w3iA 22 :KLKIHAENLIRKGIDKLFVNG T0315 38 :FNKSTIERAMKLIDEYD 1w3iA 50 :LSPEEKLENLKAVYDVT T0315 55 :F 1w3iA 68 :K T0315 58 :GIIG 1w3iA 71 :FQVG T0315 68 :IDFTEEHLEWI 1w3iA 75 :GLNLDDAIRLA T0315 80 :SLAQHPKVIGIG 1w3iA 86 :KLSKDFDIVGIA T0315 95 :LDYHWDKSPADVQKEVFRKQIAL 1w3iA 100 :APYYYPRMSEKHLVKYFKTLCEV T0315 122 :KLPIIIHN 1w3iA 124 :PHPVYLYN T0315 137 :IDILLEE 1w3iA 142 :AKVAKEI T0315 146 :EEVGGIMH 1w3iA 149 :GCFTGVKD T0315 155 :FSGSPEIADIVTN 1w3iA 157 :TIENIIHTLDYKR T0315 168 :KLNFYISLGGPVT 1w3iA 171 :NPNMLVYSGSDML T0315 187 :PKEVAKHVS 1w3iA 184 :IATVASTGL T0315 197 :E 1w3iA 193 :D T0315 201 :VE 1w3iA 194 :GN T0315 205 :APYL 1w3iA 198 :AGSN T0315 218 :NEPARVTLVAEQI 1w3iA 202 :YLPEVTVTIKKLA T0315 234 :KGLSYEEVCEQT 1w3iA 215 :MERKIDEALKLQ T0315 247 :KNAEKLF 1w3iA 227 :FLHDEVI Number of specific fragments extracted= 20 number of extra gaps= 3 total=2180 Will force an alignment to be made, even if fragment is small Number of alignments=133 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1w3iA/T0315-1w3iA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0315 read from 1w3iA/T0315-1w3iA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1w3iA read from 1w3iA/T0315-1w3iA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1w3iA in template set Warning: unaligning (T0315)L56 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1w3iA)I70 Warning: unaligning (T0315)Y57 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1w3iA)I70 Warning: unaligning (T0315)E92 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1w3iA)Y99 Warning: unaligning (T0315)M93 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1w3iA)Y99 Warning: unaligning (T0315)L199 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (1w3iA)A197 Warning: unaligning (T0315)L200 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (1w3iA)A197 T0315 2 :LIDTHVHLNDEQY 1w3iA 4 :IITPIITPFTKDN T0315 15 :DDDLSEVITRAREAGVDRMFVV 1w3iA 20 :KEKLKIHAENLIRKGIDKLFVN T0315 37 :GFNKSTIERAMKLI 1w3iA 49 :SLSPEEKLENLKAV T0315 51 :DEYDF 1w3iA 64 :DVTNK T0315 58 :GIIG 1w3iA 71 :FQVG T0315 68 :IDFTEEHLEWIE 1w3iA 75 :GLNLDDAIRLAK T0315 81 :LAQHPKVIGIG 1w3iA 87 :LSKDFDIVGIA T0315 95 :LDYHWDKSPADVQKEVFRKQIAL 1w3iA 100 :APYYYPRMSEKHLVKYFKTLCEV T0315 122 :KLPIIIHNRE 1w3iA 124 :PHPVYLYNYP T0315 134 :QDC 1w3iA 134 :TAT T0315 137 :IDILLEE 1w3iA 142 :AKVAKEI T0315 146 :EEVGGIMHS 1w3iA 149 :GCFTGVKDT T0315 156 :SGSPEIADIVTN 1w3iA 158 :IENIIHTLDYKR T0315 169 :LNFYISLG 1w3iA 172 :PNMLVYSG T0315 177 :GP 1w3iA 181 :DM T0315 186 :QPKEVAKHVSMER 1w3iA 183 :LIATVASTGLDGN T0315 201 :VETD 1w3iA 198 :AGSN T0315 207 :Y 1w3iA 202 :Y T0315 219 :EPARVTLVAEQIA 1w3iA 203 :LPEVTVTIKKLAM T0315 235 :GLSYEEVCEQTT 1w3iA 216 :ERKIDEALKLQF Number of specific fragments extracted= 20 number of extra gaps= 3 total=2200 Will force an alignment to be made, even if fragment is small Number of alignments=134 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1w3iA/T0315-1w3iA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0315 read from 1w3iA/T0315-1w3iA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1w3iA read from 1w3iA/T0315-1w3iA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1w3iA in template set Warning: unaligning (T0315)L56 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1w3iA)I70 Warning: unaligning (T0315)Y57 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1w3iA)I70 Warning: unaligning (T0315)E92 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1w3iA)Y99 Warning: unaligning (T0315)M93 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1w3iA)Y99 Warning: unaligning (T0315)T203 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (1w3iA)A197 Warning: unaligning (T0315)D204 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (1w3iA)A197 T0315 1 :MLIDTHVHLNDEQ 1w3iA 4 :IITPIITPFTKDN T0315 14 :YDDDLSEVITRAREAGVDRMFVVG 1w3iA 19 :DKEKLKIHAENLIRKGIDKLFVNG T0315 38 :FNKSTIERAMKLIDEYDF 1w3iA 50 :LSPEEKLENLKAVYDVTN T0315 58 :GIIGW 1w3iA 71 :FQVGG T0315 69 :DF 1w3iA 76 :LN T0315 75 :LEWIESLA 1w3iA 78 :LDDAIRLA T0315 83 :QHPKVIGIG 1w3iA 89 :KDFDIVGIA T0315 95 :LDYHWDKSPADVQKEVFRKQIAL 1w3iA 100 :APYYYPRMSEKHLVKYFKTLCEV T0315 121 :LKLPIIIHNREAT 1w3iA 123 :SPHPVYLYNYPTA T0315 137 :IDILLEEH 1w3iA 142 :AKVAKEIG T0315 147 :EVGGIMHSF 1w3iA 150 :CFTGVKDTI T0315 157 :GSPEIADI 1w3iA 159 :ENIIHTLD T0315 166 :TNKL 1w3iA 167 :YKRL T0315 170 :NFYISLGGPVT 1w3iA 173 :NMLVYSGSDML T0315 187 :PKEVAKH 1w3iA 184 :IATVAST T0315 197 :E 1w3iA 193 :D T0315 201 :VE 1w3iA 194 :GN T0315 205 :APYLSP 1w3iA 198 :AGSNYL T0315 223 :VTLVAEQIAELKGLSYEEVCEQT 1w3iA 204 :PEVTVTIKKLAMERKIDEALKLQ T0315 247 :KNAEKL 1w3iA 227 :FLHDEV Number of specific fragments extracted= 20 number of extra gaps= 3 total=2220 Will force an alignment to be made, even if fragment is small Number of alignments=135 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1hl2A/T0315-1hl2A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1hl2A expands to /projects/compbio/data/pdb/1hl2.pdb.gz 1hl2A:# T0315 read from 1hl2A/T0315-1hl2A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1hl2A read from 1hl2A/T0315-1hl2A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1hl2A to template set # found chain 1hl2A in template set T0315 1 :MLIDTHVHLNDEQ 1hl2A 7 :GVMAALLTPFDQQ T0315 17 :DLSEVITRAREAGVDRMFVVG 1hl2A 26 :SLRRLVQFNIQQGIDGLYVGG T0315 38 :FNKSTIERAMKLIDEY 1hl2A 54 :QSLSEREQVLEIVAEE T0315 54 :DFLYGIIGWHPVDAID 1hl2A 72 :GKIKLIAHVGCVSTAE T0315 71 :TEEHLEWIESL 1hl2A 88 :SQQLAASAKRY T0315 86 :KVIGIGEM 1hl2A 99 :GFDAVSAV T0315 95 :L 1hl2A 107 :T T0315 98 :HWDKSP 1hl2A 108 :PFYYPF T0315 104 :ADVQKEVFRKQIALA 1hl2A 115 :FEEHCDHYRAIIDSA T0315 122 :KLPIIIHN 1hl2A 131 :GLPMVVYN T0315 130 :REATQDCIDIL 1hl2A 145 :VKLTLDQINTL T0315 144 :HAEEVGGIMH 1hl2A 157 :TLPGVGALKQ T0315 155 :FSGSPEIADIVTN 1hl2A 167 :TSGDLYQMEQIRR T0315 168 :KLNFYISLG 1hl2A 181 :HPDLVLYNG T0315 183 :NAKQPKEVAKHVS 1hl2A 190 :YDEIFASGLLAGA T0315 197 :ERLLVET 1hl2A 203 :DGGIGST T0315 219 :EPARVTLVAEQIAELKGLSYEEVCEQT 1hl2A 210 :YNIMGWRYQGIVKALKEGDIQTAQKLQ T0315 247 :KNAEKLFN 1hl2A 237 :TECNKVID Number of specific fragments extracted= 18 number of extra gaps= 0 total=2238 Will force an alignment to be made, even if fragment is small Number of alignments=136 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1hl2A/T0315-1hl2A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0315 read from 1hl2A/T0315-1hl2A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1hl2A read from 1hl2A/T0315-1hl2A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1hl2A in template set T0315 1 :MLIDTHVHLNDEQY 1hl2A 7 :GVMAALLTPFDQQQ T0315 15 :DDDLSEVITRAREAGVDRMFVVG 1hl2A 24 :KASLRRLVQFNIQQGIDGLYVGG T0315 38 :FNKSTIERAMKLI 1hl2A 54 :QSLSEREQVLEIV T0315 51 :DEY 1hl2A 68 :EEA T0315 54 :DFLYGIIGWHPVDAIDF 1hl2A 72 :GKIKLIAHVGCVSTAES T0315 72 :EEHLEWIESL 1hl2A 89 :QQLAASAKRY T0315 86 :KVIGIGEM 1hl2A 99 :GFDAVSAV T0315 98 :HWDKSP 1hl2A 107 :TPFYYP T0315 104 :ADVQKEVFRKQIALA 1hl2A 115 :FEEHCDHYRAIIDSA T0315 122 :KLPIIIHNRE 1hl2A 131 :GLPMVVYNIP T0315 132 :ATQDCIDILL 1hl2A 147 :LTLDQINTLV T0315 144 :HAEEVGGIMHS 1hl2A 157 :TLPGVGALKQT T0315 156 :SGSPEIADIVTN 1hl2A 168 :SGDLYQMEQIRR T0315 168 :KLNFYISLGG 1hl2A 181 :HPDLVLYNGY T0315 184 :AKQPKEVAKHVS 1hl2A 191 :DEIFASGLLAGA T0315 197 :ERLLVET 1hl2A 203 :DGGIGST T0315 221 :ARVTLVAEQIAELKGLSYEEVCEQTT 1hl2A 212 :IMGWRYQGIVKALKEGDIQTAQKLQT T0315 248 :NAEKLFN 1hl2A 238 :ECNKVID Number of specific fragments extracted= 18 number of extra gaps= 0 total=2256 Will force an alignment to be made, even if fragment is small Number of alignments=137 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1hl2A/T0315-1hl2A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0315 read from 1hl2A/T0315-1hl2A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1hl2A read from 1hl2A/T0315-1hl2A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1hl2A in template set T0315 1 :MLIDTHVHLNDEQ 1hl2A 8 :VMAALLTPFDQQQ T0315 14 :YDDDLSEVITRAREAGVDRMFVVG 1hl2A 23 :DKASLRRLVQFNIQQGIDGLYVGG T0315 38 :FNKSTIERAMKLI 1hl2A 54 :QSLSEREQVLEIV T0315 51 :DEYDF 1hl2A 68 :EEAKG T0315 56 :LYGIIGWHPVDAIDF 1hl2A 74 :IKLIAHVGCVSTAES T0315 72 :EEHLEWIESL 1hl2A 89 :QQLAASAKRY T0315 83 :QHPKVIGIG 1hl2A 99 :GFDAVSAVT T0315 97 :YHWDKSPADVQKEVFRKQIALA 1hl2A 108 :PFYYPFSFEEHCDHYRAIIDSA T0315 122 :KLPIIIHN 1hl2A 131 :GLPMVVYN T0315 133 :TQDCIDIL 1hl2A 149 :LDQINTLV T0315 144 :HAEEVGGIMH 1hl2A 157 :TLPGVGALKQ T0315 155 :FSGSPEIADI 1hl2A 167 :TSGDLYQMEQ T0315 166 :TNKL 1hl2A 177 :IRRE T0315 170 :NFYISLGGPVT 1hl2A 183 :DLVLYNGYDEI T0315 187 :PKEVAKH 1hl2A 194 :FASGLLA T0315 195 :SMERLLVET 1hl2A 201 :GADGGIGST T0315 221 :ARVTLVAEQIAELKGLSYEEVCEQ 1hl2A 212 :IMGWRYQGIVKALKEGDIQTAQKL T0315 245 :TTKNAEKL 1hl2A 239 :CNKVIDLL Number of specific fragments extracted= 18 number of extra gaps= 0 total=2274 Will force an alignment to be made, even if fragment is small Number of alignments=138 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1yxcA/T0315-1yxcA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1yxcA expands to /projects/compbio/data/pdb/1yxc.pdb.gz 1yxcA:# T0315 read from 1yxcA/T0315-1yxcA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1yxcA read from 1yxcA/T0315-1yxcA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1yxcA to template set # found chain 1yxcA in template set Warning: unaligning (T0315)V36 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1yxcA)G43 Warning: unaligning (T0315)G37 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1yxcA)G43 Warning: unaligning (T0315)V201 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1yxcA)S204 Warning: unaligning (T0315)E202 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1yxcA)S204 T0315 1 :MLIDTHVHLNDEQ 1yxcA 4 :GSIVAIVTPMDEK T0315 14 :YDDDLSEVITRAREAGVDRMFV 1yxcA 20 :CRASLKKLIDYHVASGTSAIVS T0315 38 :FNKST 1yxcA 51 :LNHDE T0315 43 :IERAMKLID 1yxcA 60 :VMMTLDLAD T0315 54 :DFLYGIIGWHPVD 1yxcA 69 :GRIPVIAGTGANA T0315 71 :TEEHLEWI 1yxcA 82 :TAEAISLT T0315 80 :SLAQHPKVIGIGEM 1yxcA 90 :QRFNDSGIVGCLTV T0315 96 :DYHWDKSPADVQKEVFRKQIA 1yxcA 104 :TPYYNRPSQEGLYQHFKAIAE T0315 120 :RLKLPIIIHN 1yxcA 125 :HTDLPQILYN T0315 130 :REATQDCIDILL 1yxcA 141 :CDLLPETVGRLA T0315 144 :HAEEVGGIM 1yxcA 153 :KVKNIIGIK T0315 154 :SFSGSPEIADIVTNKLN 1yxcA 162 :EATGNLTRVNQIKELVS T0315 171 :FYISL 1yxcA 182 :VLLSG T0315 183 :NAKQPKEVAKHVS 1yxcA 187 :DDASALDFMQLGG T0315 198 :RLL 1yxcA 200 :HGV T0315 203 :TDAPY 1yxcA 205 :VTANV T0315 222 :RVTLVAEQIAELKGLSYEEVCEQ 1yxcA 210 :AARDMAQMCKLAAEGHFAEARVI T0315 245 :TTKNAEKLF 1yxcA 236 :LMPLHNKLF Number of specific fragments extracted= 18 number of extra gaps= 2 total=2292 Will force an alignment to be made, even if fragment is small Number of alignments=139 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1yxcA/T0315-1yxcA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0315 read from 1yxcA/T0315-1yxcA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1yxcA read from 1yxcA/T0315-1yxcA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1yxcA in template set Warning: unaligning (T0315)V36 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1yxcA)G43 Warning: unaligning (T0315)G37 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1yxcA)G43 Warning: unaligning (T0315)V201 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1yxcA)S204 Warning: unaligning (T0315)E202 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1yxcA)S204 T0315 1 :MLIDTHVHLNDEQY 1yxcA 4 :GSIVAIVTPMDEKG T0315 15 :DDDLSEVITRAREAGVDRMFV 1yxcA 21 :RASLKKLIDYHVASGTSAIVS T0315 38 :F 1yxcA 44 :T T0315 41 :ST 1yxcA 49 :AT T0315 43 :IERAMKLIDEY 1yxcA 53 :HDEHADVVMMT T0315 54 :DFLYGIIGWHPVDA 1yxcA 69 :GRIPVIAGTGANAT T0315 72 :EEHLEWIES 1yxcA 83 :AEAISLTQR T0315 82 :AQHPKVIGIGEM 1yxcA 92 :FNDSGIVGCLTV T0315 98 :HWDKSP 1yxcA 104 :TPYYNR T0315 107 :QKEVFRKQIALAKRL 1yxcA 111 :SQEGLYQHFKAIAEH T0315 122 :KLPIIIHNRE 1yxcA 127 :DLPQILYNVP T0315 132 :ATQDCIDILLEE 1yxcA 143 :LLPETVGRLAKV T0315 146 :EEVGGIM 1yxcA 155 :KNIIGIK T0315 154 :SFSGSPEIADIVTNKLN 1yxcA 162 :EATGNLTRVNQIKELVS T0315 171 :FYISLG 1yxcA 182 :VLLSGD T0315 184 :AKQPKEVAKHVS 1yxcA 188 :DASALDFMQLGG T0315 198 :RLL 1yxcA 200 :HGV T0315 203 :TDAPY 1yxcA 205 :VTANV T0315 222 :RVTLVAEQIAELKGLSYEEVCEQ 1yxcA 210 :AARDMAQMCKLAAEGHFAEARVI T0315 245 :TTKNAEKLF 1yxcA 236 :LMPLHNKLF Number of specific fragments extracted= 20 number of extra gaps= 2 total=2312 Will force an alignment to be made, even if fragment is small Number of alignments=140 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1yxcA/T0315-1yxcA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0315 read from 1yxcA/T0315-1yxcA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1yxcA read from 1yxcA/T0315-1yxcA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1yxcA in template set Warning: unaligning (T0315)V36 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1yxcA)G43 Warning: unaligning (T0315)G37 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1yxcA)G43 Warning: unaligning (T0315)E202 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1yxcA)S204 Warning: unaligning (T0315)T203 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1yxcA)S204 T0315 2 :LIDTHVHLNDEQ 1yxcA 6 :IVAIVTPMDEKG T0315 14 :YDDDLSEVITRAREAGVDRMFV 1yxcA 20 :CRASLKKLIDYHVASGTSAIVS T0315 38 :FNKST 1yxcA 51 :LNHDE T0315 43 :IERAMKLI 1yxcA 60 :VMMTLDLA T0315 54 :DF 1yxcA 68 :DG T0315 56 :LYGIIGWHPV 1yxcA 71 :IPVIAGTGAN T0315 70 :FTEEHLEWIESLAQHPKVIGIGEM 1yxcA 81 :ATAEAISLTQRFNDSGIVGCLTVT T0315 97 :YHWDKSPADVQKEVFRKQ 1yxcA 105 :PYYNRPSQEGLYQHFKAI T0315 118 :AKRLKLPIIIHN 1yxcA 123 :AEHTDLPQILYN T0315 130 :REATQDCIDIL 1yxcA 141 :CDLLPETVGRL T0315 143 :EHAEEVGGIMHS 1yxcA 152 :AKVKNIIGIKEA T0315 156 :SGSPEIADI 1yxcA 164 :TGNLTRVNQ T0315 166 :TNKL 1yxcA 173 :IKEL T0315 170 :NFYISLG 1yxcA 180 :DFVLLSG T0315 183 :NAKQPKEVAKH 1yxcA 187 :DDASALDFMQL T0315 198 :R 1yxcA 200 :H T0315 200 :LV 1yxcA 201 :GV T0315 204 :DAPYLS 1yxcA 205 :VTANVA T0315 223 :VTLVAEQIAELKGLSYEEV 1yxcA 211 :ARDMAQMCKLAAEGHFAEA T0315 242 :CEQTTKNAEKLF 1yxcA 233 :NQRLMPLHNKLF Number of specific fragments extracted= 20 number of extra gaps= 2 total=2332 Will force an alignment to be made, even if fragment is small Number of alignments=141 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1o0yA/T0315-1o0yA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1o0yA expands to /projects/compbio/data/pdb/1o0y.pdb.gz 1o0yA:# T0315 read from 1o0yA/T0315-1o0yA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1o0yA read from 1o0yA/T0315-1o0yA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1o0yA to template set # found chain 1o0yA in template set Warning: unaligning (T0315)G150 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1o0yA)V178 Warning: unaligning (T0315)I151 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1o0yA)V178 Warning: unaligning (T0315)H153 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1o0yA)S181 Warning: unaligning (T0315)F155 because of BadResidue code BAD_PEPTIDE in next template residue (1o0yA)F184 Warning: unaligning (T0315)S156 because of BadResidue code BAD_PEPTIDE at template residue (1o0yA)F184 T0315 5 :THVHLNDEQYDDDLSEVITRAREAGVDRMFV 1o0yA 36 :EHTNLKPFATPDDIKKLCLEARENRFHGVCV T0315 39 :NKSTIERAMKLIDEYD 1o0yA 67 :NPCYVKLAREELEGTD T0315 55 :FLYGIIGW 1o0yA 84 :KVVTVVGF T0315 65 :VDAIDFTEEHLEWIESLAQHP 1o0yA 92 :PLGANETRTKAHEAIFAVESG T0315 86 :KVIGIG 1o0yA 114 :DEIDMV T0315 93 :MG 1o0yA 120 :IN T0315 97 :Y 1o0yA 122 :V T0315 100 :DKSPADVQKEVFRKQIAL 1o0yA 126 :KAKEWEYVYEDIRSVVES T0315 122 :KLPIIIHN 1o0yA 146 :GKVVKVII T0315 130 :RE 1o0yA 158 :LD T0315 133 :TQD 1o0yA 160 :TEE T0315 136 :CIDILLEEHA 1o0yA 166 :ACVISKLAGA T0315 149 :G 1o0yA 176 :H T0315 152 :M 1o0yA 179 :K T0315 154 :S 1o0yA 182 :T T0315 157 :G 1o0yA 185 :G T0315 158 :SPEIADIVTN 1o0yA 190 :TAEDVHLMKW T0315 168 :KLNFYISLGGPVT 1o0yA 202 :GDEMGVKASGGIR T0315 183 :NAKQPKEVAKHVS 1o0yA 215 :TFEDAVKMIMYGA T0315 197 :ERLL 1o0yA 228 :DRIG T0315 203 :TD 1o0yA 232 :TS T0315 222 :RVTLVAEQIAE 1o0yA 234 :SGVKIVQGGEE Number of specific fragments extracted= 22 number of extra gaps= 3 total=2354 Will force an alignment to be made, even if fragment is small Number of alignments=142 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1o0yA/T0315-1o0yA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0315 read from 1o0yA/T0315-1o0yA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1o0yA read from 1o0yA/T0315-1o0yA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1o0yA in template set Warning: unaligning (T0315)G149 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1o0yA)V178 Warning: unaligning (T0315)G150 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1o0yA)V178 Warning: unaligning (T0315)M152 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1o0yA)S181 Warning: unaligning (T0315)H153 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1o0yA)S181 Warning: unaligning (T0315)F155 because of BadResidue code BAD_PEPTIDE in next template residue (1o0yA)F184 Warning: unaligning (T0315)S156 because of BadResidue code BAD_PEPTIDE at template residue (1o0yA)F184 T0315 5 :THVHLNDEQYDDDLSEVITRAREAGVDRMFV 1o0yA 36 :EHTNLKPFATPDDIKKLCLEARENRFHGVCV T0315 39 :NKSTIERAMKLIDEYD 1o0yA 67 :NPCYVKLAREELEGTD T0315 55 :FLYGIIGW 1o0yA 84 :KVVTVVGF T0315 65 :VDAIDFTEEHLEWIESLAQ 1o0yA 92 :PLGANETRTKAHEAIFAVE T0315 84 :HPKVIGI 1o0yA 112 :GADEIDM T0315 92 :EMGLDYHWDK 1o0yA 119 :VINVGMLKAK T0315 107 :QKEVFRKQIALAKRL 1o0yA 129 :EWEYVYEDIRSVVES T0315 122 :KLPIIIHNRE 1o0yA 146 :GKVVKVIIET T0315 132 :ATQDCIDILL 1o0yA 159 :DTEEKIAACV T0315 143 :EHAEEV 1o0yA 171 :KLAGAH T0315 151 :I 1o0yA 179 :K T0315 154 :S 1o0yA 182 :T T0315 157 :G 1o0yA 185 :G T0315 158 :SPEIADIVTNKLN 1o0yA 190 :TAEDVHLMKWIVG T0315 171 :FYISLGGPV 1o0yA 205 :MGVKASGGI T0315 182 :KNAKQPKEVAKHVS 1o0yA 214 :RTFEDAVKMIMYGA T0315 197 :ERLLVET 1o0yA 228 :DRIGTSS T0315 223 :VTLVAEQIAE 1o0yA 235 :GVKIVQGGEE Number of specific fragments extracted= 18 number of extra gaps= 3 total=2372 Will force an alignment to be made, even if fragment is small Number of alignments=143 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1o0yA/T0315-1o0yA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0315 read from 1o0yA/T0315-1o0yA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1o0yA read from 1o0yA/T0315-1o0yA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1o0yA in template set Warning: unaligning (T0315)G150 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1o0yA)V178 Warning: unaligning (T0315)I151 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1o0yA)V178 Warning: unaligning (T0315)H153 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1o0yA)S181 Warning: unaligning (T0315)S154 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1o0yA)S181 Warning: unaligning (T0315)S156 because of BadResidue code BAD_PEPTIDE in next template residue (1o0yA)F184 Warning: unaligning (T0315)G157 because of BadResidue code BAD_PEPTIDE at template residue (1o0yA)F184 T0315 5 :THVHLNDEQYDDDLSEVITRAREAGVDRMFV 1o0yA 36 :EHTNLKPFATPDDIKKLCLEARENRFHGVCV T0315 39 :NKSTIERAMKLIDEYDFLYGII 1o0yA 67 :NPCYVKLAREELEGTDVKVVTV T0315 62 :WHPVDAIDFTEEHLEWIESLA 1o0yA 89 :VGFPLGANETRTKAHEAIFAV T0315 83 :QHPKVIGI 1o0yA 112 :GADEIDMV T0315 100 :DKSPADVQKEVFRKQIAL 1o0yA 126 :KAKEWEYVYEDIRSVVES T0315 122 :KLPIIIHN 1o0yA 146 :GKVVKVII T0315 130 :REATQD 1o0yA 156 :CYLDTE T0315 136 :CIDILLEEHA 1o0yA 166 :ACVISKLAGA T0315 149 :G 1o0yA 176 :H T0315 152 :M 1o0yA 179 :K T0315 155 :F 1o0yA 182 :T T0315 158 :SPEIADI 1o0yA 190 :TAEDVHL T0315 166 :TNKL 1o0yA 197 :MKWI T0315 170 :NFYISLGGPVT 1o0yA 204 :EMGVKASGGIR T0315 183 :NAKQPKEVAKH 1o0yA 215 :TFEDAVKMIMY T0315 195 :SMERLLV 1o0yA 226 :GADRIGT T0315 221 :ARVTLVAEQIAE 1o0yA 233 :SSGVKIVQGGEE Number of specific fragments extracted= 17 number of extra gaps= 3 total=2389 Will force an alignment to be made, even if fragment is small Number of alignments=144 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ojxA/T0315-1ojxA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1ojxA expands to /projects/compbio/data/pdb/1ojx.pdb.gz 1ojxA:# T0315 read from 1ojxA/T0315-1ojxA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ojxA read from 1ojxA/T0315-1ojxA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1ojxA to template set # found chain 1ojxA in template set T0315 2 :LIDTHVHL 1ojxA 18 :SIILAYDH T0315 10 :NDEQYDD 1ojxA 30 :GPADFMD T0315 17 :DLSEVITRAREAGVDRMFVV 1ojxA 42 :DPEYILRLARDAGFDGVVFQ T0315 47 :MKLIDEY 1ojxA 62 :RGIAEKY T0315 54 :DFLYGIIGWH 1ojxA 71 :GSVPLILKLN T0315 75 :LEWIESL 1ojxA 98 :VEEAVSL T0315 84 :HPKVIGIGE 1ojxA 105 :GASAVGYTI T0315 98 :HWDKSPADVQKEVFRKQIALAKRLKLPIIIHN 1ojxA 114 :YPGSGFEWKMFEELARIKRDAVKFDLPLVVWS T0315 130 :REATQDCIDILLEEHA 1ojxA 158 :PEIVAYAARIALELGA T0315 149 :GGIMHSFSGSPEIADIVTNKLN 1ojxA 174 :DAMKIKYTGDPKTFSWAVKVAG T0315 171 :FYISLGGPVTFKNAKQPKEVAKHV 1ojxA 197 :VPVLMSGGPKTKTEEDFLKQVEGV T0315 196 :MERLLVETD 1ojxA 223 :AGALGIAVG T0315 220 :PARVTLVAEQIAEL 1ojxA 237 :RRDALKFARALAEL Number of specific fragments extracted= 13 number of extra gaps= 0 total=2402 Will force an alignment to be made, even if fragment is small Number of alignments=145 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ojxA/T0315-1ojxA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0315 read from 1ojxA/T0315-1ojxA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ojxA read from 1ojxA/T0315-1ojxA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1ojxA in template set T0315 11 :DEQY 1ojxA 31 :PADF T0315 15 :DDDLSEVITRAREAGVDRMFVV 1ojxA 40 :SADPEYILRLARDAGFDGVVFQ T0315 47 :MKLIDEY 1ojxA 62 :RGIAEKY T0315 54 :DFLYGIIGWHPV 1ojxA 71 :GSVPLILKLNGK T0315 66 :D 1ojxA 97 :S T0315 75 :LEWIESL 1ojxA 98 :VEEAVSL T0315 86 :KVIGIGEM 1ojxA 105 :GASAVGYT T0315 97 :YHWDKSPADVQKEVFRKQIALAKRLKLPIIIHNRE 1ojxA 113 :IYPGSGFEWKMFEELARIKRDAVKFDLPLVVWSYP T0315 132 :ATQDCIDILLEEHA 1ojxA 160 :IVAYAARIALELGA T0315 149 :GGIMHSFSGSPEIADIVTNKLN 1ojxA 174 :DAMKIKYTGDPKTFSWAVKVAG T0315 171 :FYISLGGPVTFKNAKQPKEVAKHV 1ojxA 197 :VPVLMSGGPKTKTEEDFLKQVEGV T0315 195 :SMERLLVETD 1ojxA 222 :EAGALGIAVG T0315 205 :AP 1ojxA 235 :WQ T0315 208 :L 1ojxA 237 :R T0315 221 :ARVTLVAEQIAEL 1ojxA 238 :RDALKFARALAEL Number of specific fragments extracted= 15 number of extra gaps= 0 total=2417 Will force an alignment to be made, even if fragment is small Number of alignments=146 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ojxA/T0315-1ojxA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0315 read from 1ojxA/T0315-1ojxA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ojxA read from 1ojxA/T0315-1ojxA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1ojxA in template set T0315 2 :LIDTHVH 1ojxA 19 :IILAYDH T0315 10 :NDEQYDD 1ojxA 30 :GPADFMD T0315 17 :DLSEVITRAREAGVDRMFVV 1ojxA 42 :DPEYILRLARDAGFDGVVFQ T0315 40 :KS 1ojxA 62 :RG T0315 49 :LID 1ojxA 64 :IAE T0315 52 :EYDF 1ojxA 68 :YYDG T0315 56 :LYGIIGWHPVDAIDFT 1ojxA 75 :LILKLNGKTTLYNGEP T0315 75 :LEWIESL 1ojxA 98 :VEEAVSL T0315 86 :KVIGIGEMGLDYH 1ojxA 105 :GASAVGYTIYPGS T0315 102 :SPADVQKEVFRKQIALAKRLKLPIIIHN 1ojxA 118 :GFEWKMFEELARIKRDAVKFDLPLVVWS T0315 130 :REATQDCIDILLEEH 1ojxA 158 :PEIVAYAARIALELG T0315 148 :VGGIMHSFSGSPEIADIVTNKL 1ojxA 173 :ADAMKIKYTGDPKTFSWAVKVA T0315 170 :NFYISLGGPVTFKNAKQPKEVAKH 1ojxA 196 :KVPVLMSGGPKTKTEEDFLKQVEG T0315 195 :SMERLLVETD 1ojxA 222 :EAGALGIAVG T0315 213 :YRG 1ojxA 237 :RRD T0315 223 :VTLVAEQIAEL 1ojxA 240 :ALKFARALAEL Number of specific fragments extracted= 16 number of extra gaps= 0 total=2433 Will force an alignment to be made, even if fragment is small Number of alignments=147 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2a6lA/T0315-2a6lA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2a6lA expands to /projects/compbio/data/pdb/2a6l.pdb.gz 2a6lA:# T0315 read from 2a6lA/T0315-2a6lA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2a6lA read from 2a6lA/T0315-2a6lA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2a6lA to template set # found chain 2a6lA in template set Warning: unaligning (T0315)V201 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2a6lA)S204 Warning: unaligning (T0315)E202 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2a6lA)S204 T0315 1 :MLIDTHVHLNDEQ 2a6lA 4 :GSIVAIVTPMDEK T0315 14 :YDDDLSEVITRAREAGVDRMFVVG 2a6lA 20 :CRASLKKLIDYHVASGTSAIVSVG T0315 38 :FNKST 2a6lA 51 :LNHDE T0315 43 :IERAMKLID 2a6lA 60 :VMMTLDLAD T0315 54 :DFLYGIIGWHPVD 2a6lA 69 :GRIPVIAGTGANA T0315 71 :TEEHLEWI 2a6lA 82 :TAEAISLT T0315 80 :SLAQHPKVIGIGEM 2a6lA 90 :QRFNDSGIVGCLTV T0315 96 :DYHWDKSPADVQKEVFRKQIA 2a6lA 104 :TPYYNRPSQEGLYQHFKAIAE T0315 120 :RLKLPIIIHN 2a6lA 125 :HTDLPQILYN T0315 130 :REATQDCIDILLEE 2a6lA 141 :CDLLPETVGRLAKV T0315 146 :EEVGGIM 2a6lA 155 :KNIIGIK T0315 154 :SFSGSPEIADIVTNKLN 2a6lA 162 :EATGNLTRVNQIKELVS T0315 171 :FYISL 2a6lA 182 :VLLSG T0315 183 :NAKQPKEVAKHVS 2a6lA 187 :DDASALDFMQLGG T0315 198 :RLL 2a6lA 200 :HGV T0315 203 :TDAPY 2a6lA 205 :VTANV T0315 222 :RVTLVAEQIAELKGLSYEEVCEQ 2a6lA 210 :AARDMAQMCKLAAEGHFAEARVI T0315 245 :TTKNAEKLF 2a6lA 236 :LMPLHNKLF Number of specific fragments extracted= 18 number of extra gaps= 1 total=2451 Will force an alignment to be made, even if fragment is small Number of alignments=148 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2a6lA/T0315-2a6lA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0315 read from 2a6lA/T0315-2a6lA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2a6lA read from 2a6lA/T0315-2a6lA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2a6lA in template set Warning: unaligning (T0315)V201 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2a6lA)S204 Warning: unaligning (T0315)E202 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2a6lA)S204 T0315 1 :MLIDTHVHLNDEQY 2a6lA 4 :GSIVAIVTPMDEKG T0315 15 :DDDLSEVITRAREAGVDRMFVV 2a6lA 21 :RASLKKLIDYHVASGTSAIVSV T0315 37 :GFNKST 2a6lA 50 :TLNHDE T0315 43 :IERAMKLID 2a6lA 60 :VMMTLDLAD T0315 54 :DFLYGIIGWHPVDA 2a6lA 69 :GRIPVIAGTGANAT T0315 72 :EEHLEWIES 2a6lA 83 :AEAISLTQR T0315 82 :AQHPKVIGIGEM 2a6lA 92 :FNDSGIVGCLTV T0315 98 :HWDKSP 2a6lA 104 :TPYYNR T0315 107 :QKEVFRKQIALAKRL 2a6lA 111 :SQEGLYQHFKAIAEH T0315 122 :KLPIIIHNRE 2a6lA 127 :DLPQILYNVP T0315 132 :ATQDCIDILLEE 2a6lA 143 :LLPETVGRLAKV T0315 146 :EEVGGIM 2a6lA 155 :KNIIGIK T0315 154 :SFSGSPEIADIVTNKLN 2a6lA 162 :EATGNLTRVNQIKELVS T0315 171 :FYISLG 2a6lA 182 :VLLSGD T0315 184 :AKQPKEVAKHVS 2a6lA 188 :DASALDFMQLGG T0315 198 :RLL 2a6lA 200 :HGV T0315 203 :TDAPY 2a6lA 205 :VTANV T0315 222 :RVTLVAEQIAELKGLSYEEVCEQTT 2a6lA 210 :AARDMAQMCKLAAEGHFAEARVINQ Number of specific fragments extracted= 18 number of extra gaps= 1 total=2469 Will force an alignment to be made, even if fragment is small Number of alignments=149 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2a6lA/T0315-2a6lA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0315 read from 2a6lA/T0315-2a6lA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2a6lA read from 2a6lA/T0315-2a6lA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2a6lA in template set Warning: unaligning (T0315)E202 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2a6lA)S204 Warning: unaligning (T0315)T203 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2a6lA)S204 T0315 2 :LIDTHVHLNDEQ 2a6lA 6 :IVAIVTPMDEKG T0315 14 :YDDDLSEVITRAREAGVDRMFVVG 2a6lA 20 :CRASLKKLIDYHVASGTSAIVSVG T0315 38 :FNKST 2a6lA 51 :LNHDE T0315 43 :IERAMKLID 2a6lA 60 :VMMTLDLAD T0315 54 :DFLYGIIGWHP 2a6lA 69 :GRIPVIAGTGA T0315 69 :DFTEEHLEWIESLAQHPKVIGIGE 2a6lA 80 :NATAEAISLTQRFNDSGIVGCLTV T0315 96 :DYHWDKSPADVQKEVFRKQ 2a6lA 104 :TPYYNRPSQEGLYQHFKAI T0315 118 :AKRLKLPIIIHN 2a6lA 123 :AEHTDLPQILYN T0315 130 :REATQDCIDILL 2a6lA 141 :CDLLPETVGRLA T0315 144 :HAEEVGGIMHS 2a6lA 153 :KVKNIIGIKEA T0315 156 :SGSPEIADI 2a6lA 164 :TGNLTRVNQ T0315 166 :TNKL 2a6lA 173 :IKEL T0315 170 :NFYISLG 2a6lA 180 :DFVLLSG T0315 183 :NAKQPKEVAKH 2a6lA 187 :DDASALDFMQL T0315 200 :LV 2a6lA 201 :GV T0315 204 :DAPYLS 2a6lA 205 :VTANVA T0315 223 :VTLVAEQIAELKGLSYEEVCEQ 2a6lA 211 :ARDMAQMCKLAAEGHFAEARVI T0315 245 :TTKNAEKLF 2a6lA 236 :LMPLHNKLF Number of specific fragments extracted= 18 number of extra gaps= 1 total=2487 Will force an alignment to be made, even if fragment is small Number of alignments=150 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1nal1/T0315-1nal1-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1nal1 expands to /projects/compbio/data/pdb/1nal.pdb.gz 1nal1:# T0315 read from 1nal1/T0315-1nal1-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1nal1 read from 1nal1/T0315-1nal1-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1nal1 to template set # found chain 1nal1 in template set Warning: unaligning (T0315)D54 because of BadResidue code BAD_PEPTIDE in next template residue (1nal1)G72 T0315 1 :MLIDTHVHLNDEQ 1nal1 7 :GVMAALLTPFDQQ T0315 15 :DDDLSEVITRAREAGVDRMFVVG 1nal1 24 :KASLRRLVQFNIQQGIDGLYVGG T0315 38 :FNKSTIERAMKLIDEY 1nal1 54 :QSLSEREQVLEIVAEE T0315 55 :FLYGIIGWHP 1nal1 73 :KIKLIAHVGC T0315 69 :DFTEEHL 1nal1 83 :VTTAESQ T0315 76 :EWIESL 1nal1 93 :ASAKRY T0315 86 :KVIGIGEMG 1nal1 99 :GFDAVSAVT T0315 97 :YHWDKS 1nal1 108 :PFYYPF T0315 104 :ADVQKEVFRKQIALA 1nal1 115 :FEEHCDHYRAIIDSA T0315 122 :KLPIIIHN 1nal1 131 :GLPMVVYN T0315 130 :REATQDCIDIL 1nal1 145 :VKLTLDQINTL T0315 144 :HAEEVGGIMH 1nal1 157 :TLPGVGALKQ T0315 155 :FSGSPEIADIVTN 1nal1 167 :TSGDLYQMEQIRR T0315 168 :KLNFYISLG 1nal1 181 :HPDLVLYNG T0315 183 :NAKQPKEVAKHVS 1nal1 190 :YDEIFASGLLAGA T0315 197 :ERLLVET 1nal1 203 :DGGIGST T0315 219 :EPARVTLVAEQIAELKGLSYEEVCEQ 1nal1 210 :YNIMGWRYQGIVKALKEGDIQTAQKL T0315 245 :TTKNAE 1nal1 239 :CNKVID Number of specific fragments extracted= 18 number of extra gaps= 1 total=2505 Will force an alignment to be made, even if fragment is small Number of alignments=151 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1nal1/T0315-1nal1-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0315 read from 1nal1/T0315-1nal1-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1nal1 read from 1nal1/T0315-1nal1-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1nal1 in template set Warning: unaligning (T0315)D54 because of BadResidue code BAD_PEPTIDE in next template residue (1nal1)G72 T0315 1 :MLIDTHVHLNDEQY 1nal1 7 :GVMAALLTPFDQQQ T0315 15 :DDDLSEVITRAREAGVDRMFVVG 1nal1 24 :KASLRRLVQFNIQQGIDGLYVGG T0315 38 :FNKSTIERAMKLI 1nal1 54 :QSLSEREQVLEIV T0315 51 :DEY 1nal1 68 :EEG T0315 55 :FLYGIIGWHPVDA 1nal1 73 :KIKLIAHVGCVTT T0315 72 :EEHLEWIESLAQ 1nal1 86 :AESQQLAASAKR T0315 85 :PKVIGIGEM 1nal1 98 :YGFDAVSAV T0315 98 :HWDKSP 1nal1 107 :TPFYYP T0315 104 :ADVQKEVFRKQIALA 1nal1 115 :FEEHCDHYRAIIDSA T0315 122 :KLPIIIHN 1nal1 131 :GLPMVVYN T0315 130 :REATQDCIDIL 1nal1 145 :VKLTLDQINTL T0315 144 :HAEEVGGIMHS 1nal1 157 :TLPGVGALKQT T0315 156 :SGSPEIADIVTN 1nal1 168 :SGDLYQMEQIRR T0315 168 :KLNFYISLGG 1nal1 181 :HPDLVLYNGY T0315 184 :AKQPKEVAKHVS 1nal1 191 :DEIFASGLLAGA T0315 197 :ERLLVET 1nal1 203 :DGGIGST T0315 221 :ARVTLVAEQIAELKGLSYEEVCEQTTK 1nal1 212 :IMGWRYQGIVKALKEGDIQTAQKLQTE T0315 249 :AEKLFN 1nal1 239 :CNKVID Number of specific fragments extracted= 18 number of extra gaps= 1 total=2523 Will force an alignment to be made, even if fragment is small Number of alignments=152 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1nal1/T0315-1nal1-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0315 read from 1nal1/T0315-1nal1-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1nal1 read from 1nal1/T0315-1nal1-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1nal1 in template set Warning: unaligning (T0315)D54 because of BadResidue code BAD_PEPTIDE in next template residue (1nal1)G72 Warning: unaligning (T0315)F55 because of BadResidue code BAD_PEPTIDE at template residue (1nal1)G72 T0315 1 :MLIDTHVHLNDEQ 1nal1 8 :VMAALLTPFDQQQ T0315 14 :YDDDLSEVITRAREAGVDRMFVVG 1nal1 23 :DKASLRRLVQFNIQQGIDGLYVGG T0315 38 :FNKSTIERAMK 1nal1 54 :QSLSEREQVLE T0315 49 :LIDEY 1nal1 66 :VAEEG T0315 56 :LYGIIGWHPV 1nal1 74 :IKLIAHVGCV T0315 70 :FTEEHLEWIESLA 1nal1 84 :TTAESQQLAASAK T0315 83 :QHPKVIGI 1nal1 99 :GFDAVSAV T0315 96 :DYHWDKSPADVQKEVFRKQIALA 1nal1 107 :TPFYYPFSFEEHCDHYRAIIDSA T0315 122 :KLPIIIHN 1nal1 131 :GLPMVVYN T0315 130 :REAT 1nal1 145 :VKLT T0315 137 :IDILLEEHAEEVGGIMHSFSGSPEIADI 1nal1 149 :LDQINTLVTLPGVGALKQTSGDLYQMEQ T0315 166 :TNKL 1nal1 177 :IRRE T0315 170 :NFYISLG 1nal1 183 :DLVLYNG T0315 183 :NAKQPKEVAKHVSMERLL 1nal1 190 :YDEIFASGLLAGADGGIG T0315 221 :ARVTLVAEQIAELKGLSYEEVCEQ 1nal1 212 :IMGWRYQGIVKALKEGDIQTAQKL T0315 245 :TTKNAEKL 1nal1 239 :CNKVIDLL Number of specific fragments extracted= 16 number of extra gaps= 1 total=2539 Will force an alignment to be made, even if fragment is small Number of alignments=153 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1p6bA/T0315-1p6bA-t06-local-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1p6bA expands to /projects/compbio/data/pdb/1p6b.pdb.gz 1p6bA:Bad short name: CX for alphabet: pdb_atoms Bad short name: OX1 for alphabet: pdb_atoms Bad short name: OX2 for alphabet: pdb_atoms # T0315 read from 1p6bA/T0315-1p6bA-t06-local-adpstyle5.a2m # 1p6bA read from 1p6bA/T0315-1p6bA-t06-local-adpstyle5.a2m # adding 1p6bA to template set # found chain 1p6bA in template set T0315 20 :EVITRAREAGVDRMFVVG 1p6bA 85 :RGLRRARAAGVRTIVDVS T0315 38 :FNK 1p6bA 104 :FDI T0315 41 :STIERAMKLIDEYD 1p6bA 108 :RDVSLLAEVSRAAD T0315 55 :FLYGIIGWH 1p6bA 123 :HIVAATGLW T0315 64 :PVDAIDFTE 1p6bA 134 :PPLSMRLRS T0315 75 :LEWIESLAQHPKVIGIGEMGLDYHW 1p6bA 143 :VEELTQFFLREIQYGIEDTGIRAGI T0315 100 :DKSPADVQKEVFRKQIALAKRLKLPIIIHN 1p6bA 173 :TGKATPFQELVLKAAARASLATGVPVTTHT T0315 130 :REATQDCIDILLEEHAEEVGGIM 1p6bA 206 :QRDGEQQAAIFESEGLSPSRVCI T0315 153 :HS 1p6bA 230 :HS T0315 155 :FSGSPEIADIVTN 1p6bA 233 :DTDDLSYLTALAA T0315 169 :LNFYISLGGPVTF 1p6bA 246 :RGYLIGLDGIPWS T0315 182 :KNAKQPKEVAKHVSMERLLVETDAPYLSPH 1p6bA 279 :TRALLIKALIDQGYMKQILVSNDWTFGFSS T0315 217 :RNEPARVTLVAEQIAELKGLSYEEVCEQTTKNAEKLFN 1p6bA 322 :PDGMAFIPLRVIPFLREKGVPQETLAGITVTNPARFLS Number of specific fragments extracted= 13 number of extra gaps= 0 total=2552 Will force an alignment to be made, even if fragment is small Number of alignments=154 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1jgmA/T0315-1jgmA-t06-local-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1jgmA expands to /projects/compbio/data/pdb/1jgm.pdb.gz 1jgmA:Skipped atom 592, because occupancy 0.500 <= existing 0.500 in 1jgmA Skipped atom 594, because occupancy 0.500 <= existing 0.500 in 1jgmA Skipped atom 601, because occupancy 0.500 <= existing 0.500 in 1jgmA Bad short name: CX for alphabet: pdb_atoms Bad short name: OQ1 for alphabet: pdb_atoms Bad short name: OQ2 for alphabet: pdb_atoms Skipped atom 1250, because occupancy 0.500 <= existing 0.500 in 1jgmA Skipped atom 1252, because occupancy 0.500 <= existing 0.500 in 1jgmA Skipped atom 1444, because occupancy 0.300 <= existing 0.700 in 1jgmA Skipped atom 1995, because occupancy 0.500 <= existing 0.500 in 1jgmA Skipped atom 1997, because occupancy 0.500 <= existing 0.500 in 1jgmA Skipped atom 1999, because occupancy 0.500 <= existing 0.500 in 1jgmA Skipped atom 2001, because occupancy 0.500 <= existing 0.500 in 1jgmA Skipped atom 2508, because occupancy 0.500 <= existing 0.500 in 1jgmA # T0315 read from 1jgmA/T0315-1jgmA-t06-local-adpstyle5.a2m # 1jgmA read from 1jgmA/T0315-1jgmA-t06-local-adpstyle5.a2m # adding 1jgmA to template set # found chain 1jgmA in template set Warning: unaligning (T0315)S158 because of BadResidue code BAD_PEPTIDE in next template residue (1jgmA)L237 Warning: unaligning (T0315)P159 because of BadResidue code BAD_PEPTIDE at template residue (1jgmA)L237 T0315 20 :EVITRAREAGVDRMFVVG 1jgmA 85 :RGLRRARAAGVRTIVDVS T0315 38 :FNK 1jgmA 104 :FDI T0315 41 :STIERAMKLIDEYD 1jgmA 108 :RDVSLLAEVSRAAD T0315 55 :FLYGIIGWH 1jgmA 123 :HIVAATGLW T0315 64 :PVDAIDFTE 1jgmA 134 :PPLSMRLRS T0315 75 :LEWIESLAQHPKVIGIGEMGLDYHW 1jgmA 143 :VEELTQFFLREIQYGIEDTGIRAGI T0315 100 :DKSPADVQKEVFRKQIALAKRLKLPIIIHN 1jgmA 173 :TGKATPFQELVLKAAARASLATGVPVTTHT T0315 130 :REATQDCIDILLEEHAEEVGGIM 1jgmA 206 :QRDGEQQAAIFESEGLSPSRVCI T0315 153 :HS 1jgmA 230 :HS T0315 155 :FSG 1jgmA 233 :DTD T0315 160 :EIADIVTN 1jgmA 238 :SYLTALAA T0315 169 :LNFYISLGGPVTF 1jgmA 246 :RGYLIGLDHIPHS T0315 182 :KNAKQPKEVAKHVSMERLLVETDAPYLS 1jgmA 279 :TRALLIKALIDQGYMKQILVSNDWLFGF T0315 217 :RNEPARVTLVAEQIAELKGLSYEEVCEQTTKNAEKLFN 1jgmA 322 :PDGMAFIPLRVIPFLREKGVPQETLAGITVTNPARFLS Number of specific fragments extracted= 14 number of extra gaps= 1 total=2566 Will force an alignment to be made, even if fragment is small Number of alignments=155 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1dpmA/T0315-1dpmA-t06-local-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1dpmA expands to /projects/compbio/data/pdb/1dpm.pdb.gz 1dpmA:# T0315 read from 1dpmA/T0315-1dpmA-t06-local-adpstyle5.a2m # 1dpmA read from 1dpmA/T0315-1dpmA-t06-local-adpstyle5.a2m # adding 1dpmA to template set # found chain 1dpmA in template set Warning: unaligning (T0315)Y238 because of BadResidue code BAD_PEPTIDE in next template residue (1dpmA)E344 Warning: unaligning (T0315)E239 because of BadResidue code BAD_PEPTIDE at template residue (1dpmA)E344 T0315 20 :EVITRAREAGVDRMFVVG 1dpmA 85 :RGLRRARAAGVRTIVDVS T0315 38 :FNK 1dpmA 104 :FDI T0315 41 :STIERAMKLIDEYD 1dpmA 108 :RDVSLLAEVSRAAD T0315 55 :FLYGIIGWH 1dpmA 123 :HIVAATGLW T0315 64 :PVDAIDFTE 1dpmA 134 :PPLSMRLRS T0315 75 :LEWIESLAQHPKVIGIGEMGLDYHW 1dpmA 143 :VEELTQFFLREIQYGIEDTGIRAGI T0315 100 :DKSPADVQKEVFRKQIALAKRLKLPIIIHN 1dpmA 173 :TGKATPFQELVLKAAARASLATGVPVTTHT T0315 130 :REATQDCIDILLEEHAEEVGGIM 1dpmA 206 :QRDGEQQAAIFESEGLSPSRVCI T0315 153 :HS 1dpmA 230 :HS T0315 155 :FSGSPEIADIVTN 1dpmA 233 :DTDDLSYLTALAA T0315 169 :LNFYISLGGPVTF 1dpmA 246 :RGYLIGLDHIPHS T0315 182 :KNAKQPKEVAKHVSMERLLVETDAPYLS 1dpmA 279 :TRALLIKALIDQGYMKQILVSNDWLFGF T0315 217 :RNEPARVTLVAEQIAELKGLS 1dpmA 322 :PDGMAFIPLRVIPFLREKGVP T0315 240 :EVCEQTTKNAEKLFN 1dpmA 345 :TLAGITVTNPARFLS Number of specific fragments extracted= 14 number of extra gaps= 1 total=2580 Will force an alignment to be made, even if fragment is small Number of alignments=156 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1qw7A/T0315-1qw7A-t06-local-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1qw7A expands to /projects/compbio/data/pdb/1qw7.pdb.gz 1qw7A:Skipped atom 768, because occupancy 0.500 <= existing 0.500 in 1qw7A Skipped atom 770, because occupancy 0.500 <= existing 0.500 in 1qw7A Skipped atom 772, because occupancy 0.500 <= existing 0.500 in 1qw7A Skipped atom 774, because occupancy 0.500 <= existing 0.500 in 1qw7A Skipped atom 776, because occupancy 0.500 <= existing 0.500 in 1qw7A Skipped atom 778, because occupancy 0.500 <= existing 0.500 in 1qw7A Skipped atom 780, because occupancy 0.500 <= existing 0.500 in 1qw7A Skipped atom 782, because occupancy 0.500 <= existing 0.500 in 1qw7A Skipped atom 784, because occupancy 0.500 <= existing 0.500 in 1qw7A Skipped atom 786, because occupancy 0.500 <= existing 0.500 in 1qw7A Skipped atom 788, because occupancy 0.500 <= existing 0.500 in 1qw7A Bad short name: CX for alphabet: pdb_atoms Bad short name: OX1 for alphabet: pdb_atoms Bad short name: OX2 for alphabet: pdb_atoms Skipped atom 1113, because occupancy 0.500 <= existing 0.500 in 1qw7A Skipped atom 1115, because occupancy 0.500 <= existing 0.500 in 1qw7A Skipped atom 1117, because occupancy 0.500 <= existing 0.500 in 1qw7A Skipped atom 1119, because occupancy 0.500 <= existing 0.500 in 1qw7A Skipped atom 1121, because occupancy 0.500 <= existing 0.500 in 1qw7A Skipped atom 1123, because occupancy 0.500 <= existing 0.500 in 1qw7A Skipped atom 1125, because occupancy 0.500 <= existing 0.500 in 1qw7A # T0315 read from 1qw7A/T0315-1qw7A-t06-local-adpstyle5.a2m # 1qw7A read from 1qw7A/T0315-1qw7A-t06-local-adpstyle5.a2m # adding 1qw7A to template set # found chain 1qw7A in template set T0315 20 :EVITRAREAGVDRMFVVG 1qw7A 85 :RGLRRARAAGVRTIVDVS T0315 38 :FNK 1qw7A 104 :FDI T0315 41 :STIERAMKLIDEYD 1qw7A 108 :RDVSLLAEVSRAAD T0315 55 :FLYGIIGWH 1qw7A 123 :HIVAATGLW T0315 64 :PVDAIDFTE 1qw7A 134 :PPLSMRLRS T0315 75 :LEWIESLAQHPKVIGIGEMGLDYHW 1qw7A 143 :VEELTQFFLREIQYGIEDTGIRAGI T0315 100 :DKSPADVQKEVFRKQIALAKRLKLPIIIHN 1qw7A 173 :TGKATPFQELVLKAAARASLATGVPVTTHT T0315 130 :REATQDCIDILLEEHAEEVGGIM 1qw7A 206 :QRDGEQQAAIFESEGLSPSRVCI T0315 153 :HS 1qw7A 230 :HS T0315 155 :FSGSPEIADIVTN 1qw7A 233 :DTDDLSYLTALAA T0315 169 :LNFYISLGGPVTF 1qw7A 246 :RGYLIGLDRIPHS T0315 182 :KNAKQPKEVAKHVSMERLLVETDAPYLS 1qw7A 279 :TRALLIKALIDQGYMKQILVSNDWLFGF T0315 217 :RNEPARVTLVAEQIAELKGLSYEEVCEQTTKNAEKLFN 1qw7A 322 :PDGMAFIPLRVIPFLREKGVPQETLAGITVTNPARFLS Number of specific fragments extracted= 13 number of extra gaps= 0 total=2593 Will force an alignment to be made, even if fragment is small Number of alignments=157 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1fdyA/T0315-1fdyA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1fdyA expands to /projects/compbio/data/pdb/1fdy.pdb.gz 1fdyA:# T0315 read from 1fdyA/T0315-1fdyA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1fdyA read from 1fdyA/T0315-1fdyA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1fdyA to template set # found chain 1fdyA in template set T0315 1 :MLIDTHVHLNDEQ 1fdyA 7 :GVMAALLTPFDQQ T0315 17 :DLSEVITRAREAGVDRMFVVG 1fdyA 26 :SLRRLVQFNIQQGIDGLYVGG T0315 38 :FNKSTIERAMKLIDEY 1fdyA 54 :QSLSEREQVLEIVAEE T0315 54 :D 1fdyA 71 :K T0315 55 :FLYGIIGWHP 1fdyA 73 :KIKLIAHVGC T0315 68 :IDFT 1fdyA 83 :VTTA T0315 72 :EEHLEWIESL 1fdyA 89 :QQLAASAKRY T0315 86 :KVIGIGEMG 1fdyA 99 :GFDAVSAVT T0315 99 :WDKSP 1fdyA 108 :PFYYP T0315 104 :ADVQKEVFRKQIALA 1fdyA 115 :FEEHCDHYRAIIDSA T0315 122 :KLPIIIHN 1fdyA 131 :GLPMVVYN T0315 130 :REATQDCIDILLEE 1fdyA 145 :VKLTLDQINTLVTL T0315 146 :EEVGGIMH 1fdyA 159 :PGVGALKQ T0315 155 :FSGSPEIADIVTN 1fdyA 167 :TSGDLYQMEQIRR T0315 168 :KLNFYISLG 1fdyA 181 :HPDLVLYNG T0315 183 :NAKQPKEVAKHVS 1fdyA 190 :YDEIFASGLLAGA T0315 197 :ERLLVET 1fdyA 203 :DGGIGST T0315 219 :EPARVTLVAEQIAELKGLSYEEVCEQTTK 1fdyA 210 :YNIMGWRYQGIVKALKEGDIQTAQKLQTE T0315 249 :AEKLFN 1fdyA 239 :CNKVID Number of specific fragments extracted= 19 number of extra gaps= 0 total=2612 Will force an alignment to be made, even if fragment is small Number of alignments=158 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1fdyA/T0315-1fdyA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0315 read from 1fdyA/T0315-1fdyA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1fdyA read from 1fdyA/T0315-1fdyA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1fdyA in template set T0315 1 :MLIDTHVHLNDEQY 1fdyA 7 :GVMAALLTPFDQQQ T0315 15 :DDDLSEVITRAREAGVDRMFVVG 1fdyA 24 :KASLRRLVQFNIQQGIDGLYVGG T0315 38 :FNKSTIERAMKLI 1fdyA 54 :QSLSEREQVLEIV T0315 51 :DEYD 1fdyA 68 :EEGK T0315 55 :FLYGIIGWHPVDA 1fdyA 73 :KIKLIAHVGCVTT T0315 72 :EEHLEWIESLAQ 1fdyA 86 :AESQQLAASAKR T0315 85 :PKVIGIGEM 1fdyA 98 :YGFDAVSAV T0315 98 :HWDKSP 1fdyA 107 :TPFYYP T0315 104 :ADVQKEVFRKQIALA 1fdyA 115 :FEEHCDHYRAIIDSA T0315 122 :KLPIIIHN 1fdyA 131 :GLPMVVYN T0315 130 :REATQDCIDILLEE 1fdyA 145 :VKLTLDQINTLVTL T0315 146 :EEVGGIMHS 1fdyA 159 :PGVGALKQT T0315 156 :SGSPEIADIVTN 1fdyA 168 :SGDLYQMEQIRR T0315 168 :KLNFYISLGG 1fdyA 181 :HPDLVLYNGY T0315 184 :AKQPKEVAKHVS 1fdyA 191 :DEIFASGLLAGA T0315 197 :ERLLVET 1fdyA 203 :DGGIGST T0315 221 :ARVTLVAEQIAELKGLSYEEVCEQTTK 1fdyA 212 :IMGWRYQGIVKALKEGDIQTAQKLQTE T0315 249 :AEKLFN 1fdyA 239 :CNKVID Number of specific fragments extracted= 18 number of extra gaps= 0 total=2630 Will force an alignment to be made, even if fragment is small Number of alignments=159 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1fdyA/T0315-1fdyA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0315 read from 1fdyA/T0315-1fdyA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1fdyA read from 1fdyA/T0315-1fdyA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1fdyA in template set T0315 1 :MLIDTHVHLNDEQ 1fdyA 8 :VMAALLTPFDQQQ T0315 14 :YDDDLSEVITRAREAGVDRMFVVG 1fdyA 23 :DKASLRRLVQFNIQQGIDGLYVGG T0315 38 :FNKSTIERAMKLI 1fdyA 54 :QSLSEREQVLEIV T0315 51 :DEYDF 1fdyA 68 :EEGKG T0315 56 :LYGIIGWHPV 1fdyA 74 :IKLIAHVGCV T0315 70 :FTEEHLEWIESLA 1fdyA 84 :TTAESQQLAASAK T0315 83 :QHPKVIGI 1fdyA 99 :GFDAVSAV T0315 96 :DYHWDKSPADVQKEVFRKQIALA 1fdyA 107 :TPFYYPFSFEEHCDHYRAIIDSA T0315 122 :KLPIIIHNREA 1fdyA 131 :GLPMVVYNIPA T0315 133 :TQDCIDILL 1fdyA 149 :LDQINTLVT T0315 145 :AEEVGGIM 1fdyA 158 :LPGVGALK T0315 154 :SFSGSPEIADI 1fdyA 166 :QTSGDLYQMEQ T0315 166 :TNKL 1fdyA 177 :IRRE T0315 170 :NFYISLG 1fdyA 183 :DLVLYNG T0315 183 :NAKQPKEVAKHV 1fdyA 190 :YDEIFASGLLAG T0315 196 :MERLLVET 1fdyA 202 :ADGGIGST T0315 221 :ARVTLVAEQIAELKGLSYEEVCEQ 1fdyA 212 :IMGWRYQGIVKALKEGDIQTAQKL T0315 245 :TTKNAEK 1fdyA 239 :CNKVIDL Number of specific fragments extracted= 18 number of extra gaps= 0 total=2648 Will force an alignment to be made, even if fragment is small Number of alignments=160 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1k1dA/T0315-1k1dA-t06-local-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1k1dA expands to /projects/compbio/data/pdb/1k1d.pdb.gz 1k1dA:Bad short name: CX for alphabet: pdb_atoms Bad short name: OQ1 for alphabet: pdb_atoms Bad short name: OQ2 for alphabet: pdb_atoms # T0315 read from 1k1dA/T0315-1k1dA-t06-local-adpstyle5.a2m # 1k1dA read from 1k1dA/T0315-1k1dA-t06-local-adpstyle5.a2m # adding 1k1dA to template set # found chain 1k1dA in template set Warning: unaligning (T0315)G94 because of BadResidue code BAD_PEPTIDE in next template residue (1k1dA)L149 Warning: unaligning (T0315)L95 because of BadResidue code BAD_PEPTIDE at template residue (1k1dA)L149 Warning: unaligning (T0315)Y97 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1k1dA)V151 T0315 2 :LIDTHVHLNDE 1k1dA 54 :GIDPHTHLDMP T0315 13 :QYDDDLSEVITRAREAGVDRMFVVG 1k1dA 69 :VTKDDFESGTIAAAFGGTTTIIDFC T0315 38 :FNKSTIERAMKLIDEYD 1k1dA 96 :NKGEPLKKAIETWHNKA T0315 55 :FLYGIIGWH 1k1dA 115 :KAVIDYGFH T0315 65 :VDAIDFTEEHLEWIESLAQHP 1k1dA 124 :LMISEITDDVLEELPKVLEEE T0315 91 :GEM 1k1dA 145 :GIT T0315 98 :HWDKSP 1k1dA 152 :FMAYKN T0315 104 :ADVQKEVFRKQIALAKRLKLPIIIHNRE 1k1dA 159 :FQADDGTLYCTLLAAKELGALVMVHAEN T0315 134 :QDCIDIL 1k1dA 187 :GDVIDYL T0315 141 :LEEHAE 1k1dA 195 :KKALAD T0315 147 :EVGGIMHSFSGSP 1k1dA 202 :NTDPIYHALTRPP T0315 160 :EIADIVTNKLNFYISLGGPVTF 1k1dA 222 :GRACQLTELAGSQLYVVHVTCA T0315 223 :VTLVAEQIAELKGLSYEEVCEQTTKNAEKLFNL 1k1dA 346 :VSILFSEGVKKGRITLNQFVDIVSTRIAKLFGL Number of specific fragments extracted= 13 number of extra gaps= 1 total=2661 Will force an alignment to be made, even if fragment is small Number of alignments=161 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ynyA/T0315-1ynyA-t06-local-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1ynyA expands to /projects/compbio/data/pdb/1yny.pdb.gz 1ynyA:# T0315 read from 1ynyA/T0315-1ynyA-t06-local-adpstyle5.a2m # 1ynyA read from 1ynyA/T0315-1ynyA-t06-local-adpstyle5.a2m # adding 1ynyA to template set # found chain 1ynyA in template set T0315 2 :LIDTHVHLNDEQY 1ynyA 54 :GIDPHTHLDMPFG T0315 16 :D 1ynyA 67 :G T0315 17 :DLSEVITRAREAGVDRMFVVGFN 1ynyA 73 :DFFTGTRAAAFGGTTSIVDFCLT T0315 40 :KSTIERAMKLIDEY 1ynyA 98 :GESLKSAIATWHEK T0315 54 :DFLYGIIGWH 1ynyA 114 :GKAVIDYGFH T0315 65 :VDAIDFTEEHLEWIESLAQHP 1ynyA 124 :LMIAEANDQVLEELESVISSE T0315 91 :GEMGLDYHWDKSP 1ynyA 145 :GITSLKVFMAYKN T0315 104 :ADVQKEVFRKQIALAKRLKLPIIIHNRE 1ynyA 159 :FQADDETLFKTLVKAKELGALVQVHAEN T0315 134 :QDCIDILLEEHAE 1ynyA 187 :GDVLDYLTKKALA T0315 147 :EVGGIMHSFSGSP 1ynyA 202 :NTDPIYHAYTRPP T0315 163 :DIVTN 1ynyA 222 :GRAIA T0315 169 :LNFYISLGGP 1ynyA 227 :LTALAGSQLY T0315 182 :KNAKQPKEVAKHVSME 1ynyA 295 :WNQEVLWSALKNGILQ T0315 200 :LVETD 1ynyA 311 :TVGSD T0315 209 :SPHPYRGK 1ynyA 317 :CPFNFRGQ T0315 217 :RNEPARVTLVAEQIAELKGLSYEEVCEQTTKNAEKLFNL 1ynyA 340 :PLIEDRLTILYSEGVRQGRISLNQFVDISSTKAAKLFGM Number of specific fragments extracted= 16 number of extra gaps= 0 total=2677 Will force an alignment to be made, even if fragment is small Number of alignments=162 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2ffiA/T0315-2ffiA-t06-local-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2ffiA expands to /projects/compbio/data/pdb/2ffi.pdb.gz 2ffiA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0315 read from 2ffiA/T0315-2ffiA-t06-local-adpstyle5.a2m # 2ffiA read from 2ffiA/T0315-2ffiA-t06-local-adpstyle5.a2m # adding 2ffiA to template set # found chain 2ffiA in template set T0315 3 :IDTHVHLNDEQYDD 2ffiA 15 :IDSHAHVFSRGLNL T0315 17 :DLSEVITRAREAGVDRMFVVGFNK 2ffiA 41 :PLGDYLGQLRAHGFSHGVLVQPSF T0315 41 :STIERAMKLIDEYD 2ffiA 67 :TDNRYLLSALQTVP T0315 55 :FLYGII 2ffiA 82 :QLRGVV T0315 65 :VDAIDFTEEHLEWIESL 2ffiA 88 :MLERDVEQATLAEMARL T0315 91 :GEMGLDYHWDKSP 2ffiA 105 :GVRGVRLNLMGQD T0315 104 :ADVQKEVFRKQIALAKRLKLPIIIHN 2ffiA 119 :PDLTGAQWRPLLERIGEQGWHVELHR T0315 130 :REATQDCIDILLEEHA 2ffiA 146 :VADIPVLVRALQPYGL T0315 149 :GGIM 2ffiA 162 :DIVI T0315 153 :HSFSGSP 2ffiA 167 :HFGRPDA T0315 160 :EIADIVTN 2ffiA 184 :ELLTLSGR T0315 169 :LNFYISLGGPVTF 2ffiA 192 :GKVWVKVSGIYRL T0315 182 :KNAKQPKEVAKHVSMERLLVETDAPYLSP 2ffiA 214 :FARQALCALEAHYGAERLMWGSDWPHTQH T0315 219 :EPARVTLVAEQIAELKGLSYEEVCEQTTKNAEKLFNLN 2ffiA 243 :ESEVSFGSAVEQFEALGCSAQLRQALLLDTARALFGFE Number of specific fragments extracted= 14 number of extra gaps= 0 total=2691 Will force an alignment to be made, even if fragment is small Number of alignments=163 # command:CPU_time= 57.144 sec, elapsed time= 100.080 sec. # command:Using radius: 8.000 NUMB_ALIGNS: 163 Adding 32896 constraints to all_contacts Done adding distance constraints # command:CPU_time= 57.402 sec, elapsed time= 100.367 sec. # command:Reading probabilities from T0315.t06.CB8-sep9.rdb Reading constraints from ConstraintSet all_contacts maxweight: 43.381 Optimizing... Probability sum: -400.712, CN propb: -400.712 weights: 0.325 constraints: 941 # command:CPU_time= 287.672 sec, elapsed time= 330.757 sec. # command:Found ConstraintSet # PrintContacts log_align.constraints Number of constraints in align 941 # command:Found ConstraintSet # PrintContacts log_align_bonus.constraints Number of constraints in align.bonus 941 # command:Found ConstraintSet # PrintContacts log_rejected.constraints Number of constraints in rejected 4334 # command:Found ConstraintSet # PrintContacts log_rejected_bonus.constraints Number of constraints in rejected.bonus 4334 # command:Found ConstraintSet # PrintContacts log_noncontact.constraints Number of constraints in noncontact 25601 # command:Found ConstraintSet # PrintContacts log_noncontact_bonus.constraints Number of constraints in noncontact.bonus 25601 # command:CPU_time= 288.228 sec, elapsed time= 331.724 sec. # command: