# command:# Prefix for input files set to /projects/compbio/experiments/undertaker/atoms-inputs/ # command:# reading dunbrack-2191.atoms # #computed average backbone with maximum peptide_sq_deviance = 0.002 # computed average trans backbone unit from 53157 examples # computed average trans backbone unit before proline from 2010 examples # computed average cis backbone unit from 97 examples # trans (non-proline) backbone unit: # CA= -2.2087 1.0126 -0.0030 # O= -0.1499 2.2440 0.0016 # C= -0.6889 1.1368 -0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4581 -0.0000 0.0000 # cis backbone unit: # CA= -0.1436 2.4534 -0.0002 # O= -2.0284 0.9742 0.0015 # C= -0.8018 1.0771 -0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4668 0.0000 0.0000 # trans backbone unit before proline: # CA= -2.2100 1.0631 -0.0014 # O= -0.1236 2.2458 0.0075 # C= -0.6872 1.1517 -0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4660 0.0000 0.0000 # After reading dunbrack-2191.atoms have 2191 chains in training database # Count of chains,residues,atoms: 2191,500310,3902258 # 493341 residues have no bad marker # 3226 residues lack atoms needed to compute omega # 1453 residues have cis peptide # number of each bad type: # NON_STANDARD_RESIDUE 4 # HAS_OXT 1167 # TOO_MANY_ATOMS 1 # TOO_FEW_ATOMS 3052 # HAS_UNKNOWN_ATOMS 9 # HAS_DUPLICATE_ATOMS 0 # CHAIN_BREAK_BEFORE 979 # NON_PLANAR_PEPTIDE 888 # BAD_PEPTIDE 2680 # Note: may sum to more than number of residues, # because one residue may have multiple problems # command:# Reading rotamer library from dunbrack-2191.rot # command:# Prefix for input files set to /projects/compbio/experiments/undertaker/spots/ # command:# ReadAtomType exp-pdb.types Read AtomType exp-pdb with 49 types. # command:# ReadClashTable exp-pdb-2191-2symm.clash # Read ClashTable exp-pdb-2191-2symm checking bonds symmetric at MaxSep 2 # command:# command:# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/T0322/ # command:# Making conformation for sequence T0322 numbered 1 through 157 Created new target T0322 from T0322.a2m # command:# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/T0322/ # command:Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0322//projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0322/manyalignments-good-all.under or /projects/compbio/experiments/protein-predict/casp7/T0322//projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0322/manyalignments-good-all.under.gz for input Trying /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0322/manyalignments-good-all.under # reading script from file /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0322/manyalignments-good-all.under # Reading fragments from alignment file # Attempting to read fragment alignments from file 1bvqA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1bvqA expands to /projects/compbio/data/pdb/1bvq.pdb.gz 1bvqA:# T0322 read from 1bvqA/merged-good-all-a2m # 1bvqA read from 1bvqA/merged-good-all-a2m # adding 1bvqA to template set # found chain 1bvqA in template set T0322 42 :QARLAFRVEEHHTNGLGNCHGGMLMSFADMAWGRIISLQ 1bvqA 4 :SITMQQRIEFGDCDPAGIVWYPNYHRWLDAASRNYFIKC # choosing archetypes in rotamer library T0322 82 :SY 1bvqA 43 :GL T0322 84 :SWVTVRLMCDFLSGAKLGDWVEGEGELISEEDMLFTVRGRIWA 1bvqA 58 :GTPIVSCNASFVCTASYDDVLTIETCIKEWRRKSFVQRHSVSR T0322 127 :GE 1bvqA 103 :PG T0322 129 :RTLITGTGVF 1bvqA 108 :QLVMRADEIR T0322 139 :KALSAR 1bvqA 120 :AMNDGE Number of specific fragments extracted= 6 number of extra gaps= 0 total=6 Number of alignments=1 # 1bvqA read from 1bvqA/merged-good-all-a2m # found chain 1bvqA in template set Warning: unaligning (T0322)Y153 because of BadResidue code BAD_PEPTIDE in next template residue (1bvqA)D135 Warning: unaligning (T0322)K154 because of BadResidue code BAD_PEPTIDE at template residue (1bvqA)D135 T0322 42 :QARLAFRVEEHHTNGLGNCHGGMLMSFADMAWGRIISLQ 1bvqA 4 :SITMQQRIEFGDCDPAGIVWYPNYHRWLDAASRNYFIKC T0322 83 :YSWV 1bvqA 54 :RGIV T0322 87 :TVRLMCDFLSGAKLGDWVEGEGELISEEDMLFTVRGRIWA 1bvqA 61 :IVSCNASFVCTASYDDVLTIETCIKEWRRKSFVQRHSVSR T0322 127 :GE 1bvqA 103 :PG T0322 129 :RTLITGTGV 1bvqA 108 :QLVMRADEI T0322 138 :FKALSARKPRPGELA 1bvqA 119 :FAMNDGERLRAIEVP Number of specific fragments extracted= 6 number of extra gaps= 1 total=12 Number of alignments=2 # 1bvqA read from 1bvqA/merged-good-all-a2m # found chain 1bvqA in template set T0322 42 :QARLAFRVEEHHTNGLGNC 1bvqA 4 :SITMQQRIEFGDCDPAGIV T0322 64 :MLMSFADMAWGRIISLQK 1bvqA 26 :NYHRWLDAASRNYFIKCG T0322 83 :YSWV 1bvqA 54 :RGIV T0322 87 :TVRLMCDFLSGAKLGDWVEGEGELISEEDMLFTVRGRI 1bvqA 61 :IVSCNASFVCTASYDDVLTIETCIKEWRRKSFVQRHSV T0322 125 :WAGER 1bvqA 101 :TTPGG T0322 130 :TLITGT 1bvqA 108 :QLVMRA Number of specific fragments extracted= 6 number of extra gaps= 0 total=18 Number of alignments=3 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1tbuA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1tbuA expands to /projects/compbio/data/pdb/1tbu.pdb.gz 1tbuA:# T0322 read from 1tbuA/merged-good-all-a2m # 1tbuA read from 1tbuA/merged-good-all-a2m # adding 1tbuA to template set # found chain 1tbuA in template set Warning: unaligning (T0322)G31 because first residue in template chain is (1tbuA)K13 Warning: unaligning (T0322)P32 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1tbuA)I14 Warning: unaligning (T0322)L33 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1tbuA)L15 Warning: unaligning (T0322)V49 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1tbuA)T40 Warning: unaligning (T0322)C60 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1tbuA)T40 T0322 34 :FEHREGPGQARLAFR 1tbuA 16 :ELVPLSPTSFVTKYL T0322 61 :HGGMLMSFA 1tbuA 41 :FGGTLVSQS T0322 74 :GRIISLQKSYSWVTVRLMCDFLSGAKLGDWVEGEGELISEEDMLFTVRGRIWAGERTLITGTGVFK 1tbuA 50 :LLASLHTVPLNFFPTSLHSYFIKGGDPRTKITYHVQNLRNGRNFIHKQVSAYQHDKLIFTSMILFA Number of specific fragments extracted= 3 number of extra gaps= 0 total=21 Number of alignments=4 # 1tbuA read from 1tbuA/merged-good-all-a2m # found chain 1tbuA in template set Warning: unaligning (T0322)G31 because first residue in template chain is (1tbuA)K13 Warning: unaligning (T0322)P32 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1tbuA)I14 Warning: unaligning (T0322)L33 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1tbuA)L15 Warning: unaligning (T0322)V49 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1tbuA)T40 Warning: unaligning (T0322)C60 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1tbuA)T40 T0322 34 :FEHREGPGQARLAFR 1tbuA 16 :ELVPLSPTSFVTKYL T0322 61 :HGGMLM 1tbuA 41 :FGGTLV T0322 71 :MAWGRIISLQKSYSWVTVRLMCDFLSGAKLGDWVEGEGELISEEDMLFTVRGRIWAGERTLITGTGVFK 1tbuA 47 :SQSLLASLHTVPLNFFPTSLHSYFIKGGDPRTKITYHVQNLRNGRNFIHKQVSAYQHDKLIFTSMILFA Number of specific fragments extracted= 3 number of extra gaps= 0 total=24 Number of alignments=5 # 1tbuA read from 1tbuA/merged-good-all-a2m # found chain 1tbuA in template set Warning: unaligning (T0322)V49 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1tbuA)T40 Warning: unaligning (T0322)C60 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1tbuA)T40 Warning: unaligning (T0322)A140 because last residue in template chain is (1tbuA)V116 T0322 35 :EHREGPGQARLAFR 1tbuA 17 :LVPLSPTSFVTKYL T0322 61 :HGGMLM 1tbuA 41 :FGGTLV T0322 71 :MAWGRIISLQK 1tbuA 47 :SQSLLASLHTV T0322 82 :SYSWV 1tbuA 60 :NFFPT T0322 89 :RLMCDFLSGAKLGDWVEGEGELISEEDMLFTVRGRIWAGERTLITGTGVFK 1tbuA 65 :SLHSYFIKGGDPRTKITYHVQNLRNGRNFIHKQVSAYQHDKLIFTSMILFA Number of specific fragments extracted= 5 number of extra gaps= 0 total=29 Number of alignments=6 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1j1yA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0322 read from 1j1yA/merged-good-all-a2m # 1j1yA read from 1j1yA/merged-good-all-a2m # found chain 1j1yA in training set Warning: unaligning (T0322)S23 because first residue in template chain is (1j1yA)R2 Warning: unaligning (T0322)L141 because last residue in template chain is (1j1yA)L117 T0322 24 :RGFGRQIG 1j1yA 3 :DPFMEALG T0322 33 :LFEHREGPGQARLAFRVEEHHTNGLGNCHGGMLMSFADMAWGRIISL 1j1yA 11 :LKVLHLAPGEAVVAGEVRADHLNLHGTAHGGFLYALADSAFALASNT T0322 82 :SYSWVTVRLMCDFLSGAKLGDWVEGEGELISEEDMLFTVRGRIWAGERTLITGTGVFKA 1j1yA 58 :RGPAVALSCRMDYFRPLGAGARVEARAVEVNLSRRTATYRVEVVSEGKLVALFTGTVFR Number of specific fragments extracted= 3 number of extra gaps= 0 total=32 Number of alignments=7 # 1j1yA read from 1j1yA/merged-good-all-a2m # found chain 1j1yA in training set Warning: unaligning (T0322)S23 because first residue in template chain is (1j1yA)R2 Warning: unaligning (T0322)L141 because last residue in template chain is (1j1yA)L117 T0322 24 :RGFGRQIG 1j1yA 3 :DPFMEALG T0322 33 :LFEHREGPGQARLAFRVEEHHTNGLGNCHGGMLMSFADMAWGRIISLQ 1j1yA 11 :LKVLHLAPGEAVVAGEVRADHLNLHGTAHGGFLYALADSAFALASNTR T0322 83 :YSWVTVRLMCDFLSGAKLGDWVEGEGELISEEDMLFTVRGRIWAGERTLITGTGVFKA 1j1yA 59 :GPAVALSCRMDYFRPLGAGARVEARAVEVNLSRRTATYRVEVVSEGKLVALFTGTVFR Number of specific fragments extracted= 3 number of extra gaps= 0 total=35 Number of alignments=8 # 1j1yA read from 1j1yA/merged-good-all-a2m # found chain 1j1yA in training set Warning: unaligning (T0322)R24 because first residue in template chain is (1j1yA)R2 Warning: unaligning (T0322)L141 because last residue in template chain is (1j1yA)L117 T0322 25 :GFGRQIGPLFEHREGPGQARLAFRVEEHHTNGLGNCHGGMLMSFADMAWGRIISLQ 1j1yA 3 :DPFMEALGLKVLHLAPGEAVVAGEVRADHLNLHGTAHGGFLYALADSAFALASNTR T0322 83 :YSWVTVRLMCDFLSGAKLGDWVEGEGELISEEDMLFTVRGRIWAGERTLITGTGVFKA 1j1yA 59 :GPAVALSCRMDYFRPLGAGARVEARAVEVNLSRRTATYRVEVVSEGKLVALFTGTVFR Number of specific fragments extracted= 2 number of extra gaps= 0 total=37 Number of alignments=9 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1z6bA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1z6bA expands to /projects/compbio/data/pdb/1z6b.pdb.gz 1z6bA:# T0322 read from 1z6bA/merged-good-all-a2m # 1z6bA read from 1z6bA/merged-good-all-a2m # adding 1z6bA to template set # found chain 1z6bA in template set Warning: unaligning (T0322)H53 because of BadResidue code BAD_PEPTIDE in next template residue (1z6bA)F134 Warning: unaligning (T0322)T54 because of BadResidue code BAD_PEPTIDE at template residue (1z6bA)F134 Warning: unaligning (T0322)K81 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1z6bA)N166 Warning: unaligning (T0322)S112 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1z6bA)S200 Warning: unaligning (T0322)E113 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1z6bA)S200 T0322 2 :SDDLTDAQ 1z6bA 86 :SIDIEDIK T0322 11 :AAIPEGFSQLNW 1z6bA 94 :KILPHRYPFLLV T0322 32 :PLFEHREGPGQARLAFRVEEH 1z6bA 106 :DKVIYMQPNKTIIGLKQVSTN T0322 55 :NGLGNCHGGMLMSFADMAWGRIISLQ 1z6bA 135 :PQKQIMPGVLQIEALAQLAGILCLKS T0322 84 :SWVTVRLM 1z6bA 168 :LFLFAGVD T0322 92 :CDFLSGAKLGDWVEGEGELI 1z6bA 177 :VRWKKPVLPGDTLTMQANLI T0322 114 :EDMLFTVRGRIWAGERTLITGT 1z6bA 201 :SLGIAKLSGVGYVNGKVVINIS T0322 136 :GVFKA 1z6bA 224 :MTFAL Number of specific fragments extracted= 8 number of extra gaps= 2 total=45 Number of alignments=10 # 1z6bA read from 1z6bA/merged-good-all-a2m # found chain 1z6bA in template set Warning: unaligning (T0322)A8 because first residue in template chain is (1z6bA)D84 Warning: unaligning (T0322)H53 because of BadResidue code BAD_PEPTIDE in next template residue (1z6bA)F134 Warning: unaligning (T0322)T54 because of BadResidue code BAD_PEPTIDE at template residue (1z6bA)F134 Warning: unaligning (T0322)K81 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1z6bA)N166 Warning: unaligning (T0322)E113 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1z6bA)S200 T0322 9 :QTAAIPEGFSQLNWSRGFGRQIG 1z6bA 85 :TSIDIEDIKKILPHRYPFLLVDK T0322 34 :FEHREGPGQARLAFRVEE 1z6bA 108 :VIYMQPNKTIIGLKQVST T0322 52 :H 1z6bA 132 :G T0322 55 :NGLGNCHGGMLMSFADMAWGRIISLQ 1z6bA 135 :PQKQIMPGVLQIEALAQLAGILCLKS T0322 83 :YSWVTVRLM 1z6bA 167 :NLFLFAGVD T0322 92 :CDFLSGAKLGDWVEGEGELIS 1z6bA 177 :VRWKKPVLPGDTLTMQANLIS T0322 114 :EDMLFTVRGRIWAGERTLITGT 1z6bA 201 :SLGIAKLSGVGYVNGKVVINIS T0322 136 :GVFKA 1z6bA 224 :MTFAL Number of specific fragments extracted= 8 number of extra gaps= 2 total=53 Number of alignments=11 # 1z6bA read from 1z6bA/merged-good-all-a2m # found chain 1z6bA in template set Warning: unaligning (T0322)H53 because of BadResidue code BAD_PEPTIDE in next template residue (1z6bA)F134 Warning: unaligning (T0322)T54 because of BadResidue code BAD_PEPTIDE at template residue (1z6bA)F134 Warning: unaligning (T0322)K81 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1z6bA)N166 Warning: unaligning (T0322)S82 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1z6bA)N166 Warning: unaligning (T0322)S112 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1z6bA)S200 Warning: unaligning (T0322)E113 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1z6bA)S200 Warning: unaligning (T0322)S142 because last residue in template chain is (1z6bA)S229 T0322 7 :DAQTAAIP 1z6bA 86 :SIDIEDIK T0322 19 :Q 1z6bA 94 :K T0322 21 :NWSRGFGRQIGPLFEHREGPGQARLAFRVEEH 1z6bA 95 :ILPHRYPFLLVDKVIYMQPNKTIIGLKQVSTN T0322 55 :NGLGNCHGGMLMSFADMAWGRIISLQ 1z6bA 135 :PQKQIMPGVLQIEALAQLAGILCLKS T0322 83 :YSWVTVRLM 1z6bA 167 :NLFLFAGVD T0322 92 :CDFLSGAKLGDWVEGEGELI 1z6bA 177 :VRWKKPVLPGDTLTMQANLI T0322 114 :EDMLFTVRGRIWAGERTLITGTGVFKAL 1z6bA 201 :SLGIAKLSGVGYVNGKVVINISEMTFAL Number of specific fragments extracted= 7 number of extra gaps= 2 total=60 Number of alignments=12 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1psuA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1psuA expands to /projects/compbio/data/pdb/1psu.pdb.gz 1psuA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0322 read from 1psuA/merged-good-all-a2m # 1psuA read from 1psuA/merged-good-all-a2m # adding 1psuA to template set # found chain 1psuA in template set Warning: unaligning (T0322)A140 because last residue in template chain is (1psuA)R131 T0322 21 :NWSRGFGRQIG 1psuA 13 :YENDACAKALG T0322 33 :LFEHREGPGQARLAFRVEEHHTNGLGNCHGGMLMSFADMAWGRIISLQ 1psuA 24 :IDIISMDEGFAVVTMTVTAQMLNGHQSCHGGQLFSLADTAFAYACNSQ T0322 82 :SYSWVTVRLMCDFLSGAKLGDWVEGEGELISEEDMLFTVRGRIWA 1psuA 72 :GLAAVASACTIDFLRPGFAGDTLTATAQVRHQGKQTGVYDIEIVN T0322 127 :GERTLITGTGVFK 1psuA 118 :QQKTVALFRGKSH Number of specific fragments extracted= 4 number of extra gaps= 0 total=64 Number of alignments=13 # 1psuA read from 1psuA/merged-good-all-a2m # found chain 1psuA in template set Warning: unaligning (T0322)A140 because last residue in template chain is (1psuA)R131 T0322 14 :PEGFSQLN 1psuA 16 :DACAKALG T0322 33 :LFEHREGPGQARLAFRVEEHHTNGLGNCHGGMLMSFADMAWGRIISLQ 1psuA 24 :IDIISMDEGFAVVTMTVTAQMLNGHQSCHGGQLFSLADTAFAYACNSQ T0322 82 :SYSWVTVRLMCDFLSGAKLGDWVEGEGELISEEDMLFTVRGRIWA 1psuA 72 :GLAAVASACTIDFLRPGFAGDTLTATAQVRHQGKQTGVYDIEIVN T0322 127 :GERTLITGTGVFK 1psuA 118 :QQKTVALFRGKSH Number of specific fragments extracted= 4 number of extra gaps= 0 total=68 Number of alignments=14 # 1psuA read from 1psuA/merged-good-all-a2m # found chain 1psuA in template set Warning: unaligning (T0322)L141 because last residue in template chain is (1psuA)R131 T0322 12 :AIPEGFSQLNWSRGFGRQIGPLFEHREGPGQARLAFRVEEHHTNGLGNCHGGMLMSFADMAWGRIISLQ 1psuA 3 :HKAWQNAHAMYENDACAKALGIDIISMDEGFAVVTMTVTAQMLNGHQSCHGGQLFSLADTAFAYACNSQ T0322 82 :SYSWVTVRLMCDFLSGAKLGDWVEGEGELISEEDMLFTVRGRIWAGERTLITGTGVFKA 1psuA 72 :GLAAVASACTIDFLRPGFAGDTLTATAQVRHQGKQTGVYDIEIVNQQQKTVALFRGKSH Number of specific fragments extracted= 2 number of extra gaps= 0 total=70 Number of alignments=15 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1vpmA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0322 read from 1vpmA/merged-good-all-a2m # 1vpmA read from 1vpmA/merged-good-all-a2m # found chain 1vpmA in training set Warning: unaligning (T0322)Y83 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (1vpmA)A53 Warning: unaligning (T0322)S84 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (1vpmA)A53 T0322 35 :EHREGPGQARLAFRVEEHHTNGLGNCHGGMLMSFADMAWGRIISLQKS 1vpmA 4 :SYPVERSRTIQTRLVLPPDTNHLGTIFGGKVLAYIDEIAALTAMKHAN T0322 85 :WVTVRLM 1vpmA 54 :VVTASID T0322 92 :CDFLSGAKLGDWVEGEGELISEEDMLFTVRGRIWA 1vpmA 62 :VDFKSSATVGDALELEGFVTHTGRTSMEVYVRVHS T0322 127 :GE 1vpmA 101 :TG T0322 129 :RTLITGTGVFKALSARKPRP 1vpmA 105 :TLTTESFLTMVAVDESGKPK T0322 149 :GELAYK 1vpmA 134 :EEEKRL Number of specific fragments extracted= 6 number of extra gaps= 1 total=76 Number of alignments=16 # 1vpmA read from 1vpmA/merged-good-all-a2m # found chain 1vpmA in training set Warning: unaligning (T0322)Y83 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (1vpmA)A53 Warning: unaligning (T0322)S84 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (1vpmA)A53 T0322 37 :REGPGQARLAFRVEEHHTNGLGNCHGGMLMSFADMAWGRIISLQKS 1vpmA 6 :PVERSRTIQTRLVLPPDTNHLGTIFGGKVLAYIDEIAALTAMKHAN T0322 85 :WVTVRLM 1vpmA 54 :VVTASID T0322 92 :CDFLSGAKLGDWVEGEGELISEEDMLFTVRGRIWA 1vpmA 62 :VDFKSSATVGDALELEGFVTHTGRTSMEVYVRVHS T0322 127 :G 1vpmA 100 :L T0322 128 :E 1vpmA 102 :G T0322 129 :RTLITGTGVFKALSARKPR 1vpmA 105 :TLTTESFLTMVAVDESGKP T0322 148 :PGEL 1vpmA 125 :PVPQ Number of specific fragments extracted= 7 number of extra gaps= 1 total=83 Number of alignments=17 # 1vpmA read from 1vpmA/merged-good-all-a2m # found chain 1vpmA in training set Warning: unaligning (T0322)Y83 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (1vpmA)A53 Warning: unaligning (T0322)S84 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (1vpmA)A53 T0322 41 :GQARLAFRVEEHHTNGLGNCHGGMLMSFADMAWGRIISLQKS 1vpmA 10 :SRTIQTRLVLPPDTNHLGTIFGGKVLAYIDEIAALTAMKHAN T0322 85 :WVTVRLM 1vpmA 54 :VVTASID T0322 92 :CDFLSGAKLGDWVEGEGELISEEDMLFTVRGRIW 1vpmA 62 :VDFKSSATVGDALELEGFVTHTGRTSMEVYVRVH T0322 126 :AGERTLITGTGVFKALSARKPR 1vpmA 101 :TGERTLTTESFLTMVAVDESGK Number of specific fragments extracted= 4 number of extra gaps= 1 total=87 Number of alignments=18 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1zkiA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1zkiA expands to /projects/compbio/data/pdb/1zki.pdb.gz 1zkiA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 33, because occupancy 0.5 <= existing 0.500 in 1zkiA Skipped atom 35, because occupancy 0.500 <= existing 0.500 in 1zkiA Skipped atom 37, because occupancy 0.500 <= existing 0.500 in 1zkiA Skipped atom 39, because occupancy 0.500 <= existing 0.500 in 1zkiA Skipped atom 41, because occupancy 0.500 <= existing 0.500 in 1zkiA Skipped atom 43, because occupancy 0.500 <= existing 0.500 in 1zkiA Skipped atom 45, because occupancy 0.500 <= existing 0.500 in 1zkiA Skipped atom 47, because occupancy 0.500 <= existing 0.500 in 1zkiA Skipped atom 49, because occupancy 0.500 <= existing 0.500 in 1zkiA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 141, because occupancy 0.500 <= existing 0.500 in 1zkiA Skipped atom 143, because occupancy 0.500 <= existing 0.500 in 1zkiA Skipped atom 145, because occupancy 0.500 <= existing 0.500 in 1zkiA Skipped atom 147, because occupancy 0.500 <= existing 0.500 in 1zkiA Skipped atom 149, because occupancy 0.500 <= existing 0.500 in 1zkiA Skipped atom 151, because occupancy 0.500 <= existing 0.500 in 1zkiA Skipped atom 153, because occupancy 0.500 <= existing 0.500 in 1zkiA Skipped atom 155, because occupancy 0.500 <= existing 0.500 in 1zkiA Skipped atom 201, because occupancy 0.500 <= existing 0.500 in 1zkiA Skipped atom 203, because occupancy 0.500 <= existing 0.500 in 1zkiA Skipped atom 205, because occupancy 0.500 <= existing 0.500 in 1zkiA Skipped atom 207, because occupancy 0.500 <= existing 0.500 in 1zkiA Skipped atom 209, because occupancy 0.500 <= existing 0.500 in 1zkiA Skipped atom 211, because occupancy 0.500 <= existing 0.500 in 1zkiA Skipped atom 213, because occupancy 0.500 <= existing 0.500 in 1zkiA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 299, because occupancy 0.500 <= existing 0.500 in 1zkiA Skipped atom 303, because occupancy 0.500 <= existing 0.500 in 1zkiA Skipped atom 305, because occupancy 0.500 <= existing 0.500 in 1zkiA Skipped atom 307, because occupancy 0.500 <= existing 0.500 in 1zkiA Skipped atom 309, because occupancy 0.500 <= existing 0.500 in 1zkiA Skipped atom 311, because occupancy 0.500 <= existing 0.500 in 1zkiA Skipped atom 313, because occupancy 0.500 <= existing 0.500 in 1zkiA Skipped atom 315, because occupancy 0.500 <= existing 0.500 in 1zkiA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 528, because occupancy 0.500 <= existing 0.500 in 1zkiA Skipped atom 532, because occupancy 0.500 <= existing 0.500 in 1zkiA Skipped atom 534, because occupancy 0.500 <= existing 0.500 in 1zkiA Skipped atom 536, because occupancy 0.500 <= existing 0.500 in 1zkiA Skipped atom 538, because occupancy 0.500 <= existing 0.500 in 1zkiA Skipped atom 540, because occupancy 0.500 <= existing 0.500 in 1zkiA Skipped atom 542, because occupancy 0.500 <= existing 0.500 in 1zkiA Skipped atom 544, because occupancy 0.500 <= existing 0.500 in 1zkiA Skipped atom 754, because occupancy 0.500 <= existing 0.500 in 1zkiA Skipped atom 756, because occupancy 0.500 <= existing 0.500 in 1zkiA Skipped atom 758, because occupancy 0.500 <= existing 0.500 in 1zkiA Skipped atom 760, because occupancy 0.500 <= existing 0.500 in 1zkiA Skipped atom 762, because occupancy 0.500 <= existing 0.500 in 1zkiA Skipped atom 764, because occupancy 0.500 <= existing 0.500 in 1zkiA Skipped atom 766, because occupancy 0.500 <= existing 0.500 in 1zkiA Skipped atom 768, because occupancy 0.500 <= existing 0.500 in 1zkiA Skipped atom 770, because occupancy 0.500 <= existing 0.500 in 1zkiA Skipped atom 772, because occupancy 0.500 <= existing 0.500 in 1zkiA Skipped atom 887, because occupancy 0.500 <= existing 0.500 in 1zkiA Skipped atom 889, because occupancy 0.500 <= existing 0.500 in 1zkiA Skipped atom 891, because occupancy 0.500 <= existing 0.500 in 1zkiA Skipped atom 893, because occupancy 0.500 <= existing 0.500 in 1zkiA Skipped atom 895, because occupancy 0.500 <= existing 0.500 in 1zkiA Skipped atom 897, because occupancy 0.500 <= existing 0.500 in 1zkiA Skipped atom 899, because occupancy 0.500 <= existing 0.500 in 1zkiA Skipped atom 901, because occupancy 0.500 <= existing 0.500 in 1zkiA # T0322 read from 1zkiA/merged-good-all-a2m # 1zkiA read from 1zkiA/merged-good-all-a2m # adding 1zkiA to template set # found chain 1zkiA in template set Warning: unaligning (T0322)T6 because first residue in template chain is (1zkiA)M4 Warning: unaligning (T0322)L141 because last residue in template chain is (1zkiA)L129 T0322 7 :DAQTAAIPEGF 1zkiA 5 :PAREQMISAYS T0322 28 :RQIG 1zkiA 16 :ELVG T0322 33 :LFEHREGPGQARLAFRVEEHHTNGLGNCHGGMLMSFADMAWGRIISLQKSY 1zkiA 20 :LDPVSLGDGVAEVRLPMAAHLRNRGGVMHGGALFSLMDVTMGLACSSSHGF T0322 84 :SWVTVRLMCDFLSGAK 1zkiA 73 :QSVTLECKINYIRAVA T0322 101 :GDWVEGEGELISEEDMLFTVRGRIWAGERTLITGTGVFKA 1zkiA 89 :DGEVRCVARVLHAGRRSLVVEAEVRQGDKLVAKGQGTFAQ Number of specific fragments extracted= 5 number of extra gaps= 0 total=92 Number of alignments=19 # 1zkiA read from 1zkiA/merged-good-all-a2m # found chain 1zkiA in template set Warning: unaligning (T0322)D4 because first residue in template chain is (1zkiA)M4 Warning: unaligning (T0322)L141 because last residue in template chain is (1zkiA)L129 T0322 5 :LTDAQTAA 1zkiA 5 :PAREQMIS T0322 15 :EGFSQLN 1zkiA 13 :AYSELVG T0322 33 :LFEHREGPGQARLAFRVEEHHTNGLGNCHGGMLMSFADMAWGRIISLQ 1zkiA 20 :LDPVSLGDGVAEVRLPMAAHLRNRGGVMHGGALFSLMDVTMGLACSSS T0322 81 :KSYSWVTVRLMCDFLSGAK 1zkiA 70 :FDRQSVTLECKINYIRAVA T0322 101 :GDWVEGEGELISEEDMLFTVRGRIWAGERTLITGTGVFKA 1zkiA 89 :DGEVRCVARVLHAGRRSLVVEAEVRQGDKLVAKGQGTFAQ Number of specific fragments extracted= 5 number of extra gaps= 0 total=97 Number of alignments=20 # 1zkiA read from 1zkiA/merged-good-all-a2m # found chain 1zkiA in template set T0322 26 :FGRQIGPLFEHREGPGQARLAFRVEEHHTNGLGNCHGGMLMSFADMAWGRIISLQK 1zkiA 13 :AYSELVGLDPVSLGDGVAEVRLPMAAHLRNRGGVMHGGALFSLMDVTMGLACSSSH T0322 82 :SYSWVTVRLMCDFLSGAK 1zkiA 71 :DRQSVTLECKINYIRAVA T0322 101 :GDWVEGEGELISEEDMLFTVRGRIWAGERTLITGTGVFKA 1zkiA 89 :DGEVRCVARVLHAGRRSLVVEAEVRQGDKLVAKGQGTFAQ Number of specific fragments extracted= 3 number of extra gaps= 0 total=100 Number of alignments=21 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1yocA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0322 read from 1yocA/merged-good-all-a2m # 1yocA read from 1yocA/merged-good-all-a2m # found chain 1yocA in training set T0322 17 :FSQLNWSRGFGRQIG 1yocA 17 :SAMIGQFAPYFASIA T0322 33 :LFEHREGPGQARLAFRVEEHHTNGLGNCHGGMLMSFADMAWGRIISLQKSY 1yocA 32 :PQFVELRPGYAEVTFPKRREVLNHIGTVHAIALCNAAELAAGTMTDASIPA T0322 84 :SWVTVRLMCDFLSGAK 1yocA 85 :RWIPRGMTVEYLAKAT T0322 101 :GD 1yocA 101 :GD T0322 104 :VEGEGEL 1yocA 103 :VRAVADG T0322 111 :ISEEDMLFTVRGRIWAGERTLITGTGVFKALS 1yocA 113 :DWQATGNLVVPVVAYVDDKPVFRAEITMYVSQ Number of specific fragments extracted= 6 number of extra gaps= 0 total=106 Number of alignments=22 # 1yocA read from 1yocA/merged-good-all-a2m # found chain 1yocA in training set T0322 13 :IPEGFSQLNWSRGFGRQIG 1yocA 13 :PAQFSAMIGQFAPYFASIA T0322 33 :LFEHREGPGQARLAFRVEEHHTNGLGNCHGGMLMSFADMAWGRIISLQ 1yocA 32 :PQFVELRPGYAEVTFPKRREVLNHIGTVHAIALCNAAELAAGTMTDAS T0322 81 :KSYSWVTVRLMCDFLSGAK 1yocA 82 :AGHRWIPRGMTVEYLAKAT T0322 101 :GD 1yocA 101 :GD T0322 104 :VEGEGELIS 1yocA 103 :VRAVADGSQ T0322 113 :EEDMLFTVRGRIWAGERTLITGTGVFKALS 1yocA 115 :QATGNLVVPVVAYVDDKPVFRAEITMYVSQ Number of specific fragments extracted= 6 number of extra gaps= 0 total=112 Number of alignments=23 # 1yocA read from 1yocA/merged-good-all-a2m # found chain 1yocA in training set T0322 12 :AIPEGFSQLNWSRGFGRQIGPLFEHREGPGQARLAFRVEEHHTNGLGNCHGGMLMSFADMAWGRIISLQK 1yocA 11 :VGPAQFSAMIGQFAPYFASIAPQFVELRPGYAEVTFPKRREVLNHIGTVHAIALCNAAELAAGTMTDASI T0322 82 :SYSWVTVRLMCDFLSGAK 1yocA 83 :GHRWIPRGMTVEYLAKAT T0322 101 :GD 1yocA 101 :GD T0322 104 :VEGEGE 1yocA 103 :VRAVAD T0322 113 :EEDMLFTVRGRIWAGERTLITGTGVFK 1yocA 115 :QATGNLVVPVVAYVDDKPVFRAEITMY Number of specific fragments extracted= 5 number of extra gaps= 0 total=117 Number of alignments=24 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1mkaA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1mkaA expands to /projects/compbio/data/pdb/1mka.pdb.gz 1mkaA:# T0322 read from 1mkaA/merged-good-all-a2m # 1mkaA read from 1mkaA/merged-good-all-a2m # adding 1mkaA to template set # found chain 1mkaA in template set Warning: unaligning (T0322)S23 because of BadResidue code BAD_PEPTIDE in next template residue (1mkaA)N32 Warning: unaligning (T0322)R24 because of BadResidue code BAD_PEPTIDE at template residue (1mkaA)N32 Warning: unaligning (T0322)L57 because of BadResidue code BAD_PEPTIDE in next template residue (1mkaA)F71 T0322 10 :TAAIPEGFSQLNW 1mkaA 18 :GELFGAKGPQLPA T0322 25 :GF 1mkaA 33 :ML T0322 29 :QIG 1mkaA 35 :MMD T0322 34 :FEHREGPG 1mkaA 38 :RVVKMTET T0322 42 :QARLAFRVEEHHT 1mkaA 53 :YVEAELDINPDLW T0322 55 :NG 1mkaA 68 :GC T0322 58 :GNCHGGMLMSFADMAWGRIISLQ 1mkaA 75 :PVMPGCLGLDAMWQLVGFYLGWL T0322 82 :SY 1mkaA 98 :GG T0322 84 :SWVTVRLM 1mkaA 102 :KGRALGVG T0322 92 :CDFLSGAKLG 1mkaA 111 :VKFTGQVLPT T0322 102 :DWVEGEGEL 1mkaA 122 :KKVTYRIHF T0322 111 :ISEEDMLFTVRGRIWAGERTLITGT 1mkaA 134 :VNRRLIMGLADGEVLVDGRLIYTAS T0322 136 :GVFKALSARK 1mkaA 160 :LKVGLFQDTS Number of specific fragments extracted= 13 number of extra gaps= 2 total=130 Number of alignments=25 # 1mkaA read from 1mkaA/merged-good-all-a2m # found chain 1mkaA in template set Warning: unaligning (T0322)I30 because of BadResidue code BAD_PEPTIDE in next template residue (1mkaA)N32 Warning: unaligning (T0322)L57 because of BadResidue code BAD_PEPTIDE in next template residue (1mkaA)F71 T0322 7 :DAQTAAIPEGFS 1mkaA 3 :KRESYTKEDLLA T0322 19 :QLNWSRGFGRQ 1mkaA 20 :LFGAKGPQLPA T0322 31 :G 1mkaA 37 :D T0322 34 :FEHREGPG 1mkaA 38 :RVVKMTET T0322 42 :QARLAFRVEEHH 1mkaA 53 :YVEAELDINPDL T0322 54 :TNG 1mkaA 67 :FGC T0322 58 :GNCHGGMLMSFADMAWGRIISLQ 1mkaA 75 :PVMPGCLGLDAMWQLVGFYLGWL T0322 82 :S 1mkaA 98 :G T0322 83 :YSWVTVRLM 1mkaA 101 :GKGRALGVG T0322 92 :CDFLSGAKLGD 1mkaA 111 :VKFTGQVLPTA T0322 103 :WVEGEGELIS 1mkaA 123 :KVTYRIHFKR T0322 113 :EEDMLFTVRGRIWAGERTLITGT 1mkaA 136 :RRLIMGLADGEVLVDGRLIYTAS T0322 136 :GVFKALSARK 1mkaA 160 :LKVGLFQDTS Number of specific fragments extracted= 13 number of extra gaps= 2 total=143 Number of alignments=26 # 1mkaA read from 1mkaA/merged-good-all-a2m # found chain 1mkaA in template set Warning: unaligning (T0322)F26 because of BadResidue code BAD_PEPTIDE in next template residue (1mkaA)N32 Warning: unaligning (T0322)G27 because of BadResidue code BAD_PEPTIDE at template residue (1mkaA)N32 T0322 3 :DDLTDAQTAAIPEGFSQLNWSRG 1mkaA 2 :DKRESYTKEDLLASGRGELFGAK T0322 28 :RQIGP 1mkaA 33 :MLMMD T0322 34 :FEHREGP 1mkaA 38 :RVVKMTE T0322 41 :GQARLAFRVEEHHT 1mkaA 52 :GYVEAELDINPDLW T0322 56 :GLGNCHGGMLMSFADMAWGRIISLQK 1mkaA 73 :GDPVMPGCLGLDAMWQLVGFYLGWLG T0322 82 :SYSWVTVRLM 1mkaA 100 :EGKGRALGVG T0322 92 :CDFLSGAKLG 1mkaA 111 :VKFTGQVLPT T0322 102 :DWVEGEGE 1mkaA 122 :KKVTYRIH T0322 110 :LISEEDMLFTVRGRIWAGERTLITGTGVFKALSARK 1mkaA 133 :IVNRRLIMGLADGEVLVDGRLIYTASDLKVGLFQDT Number of specific fragments extracted= 9 number of extra gaps= 1 total=152 Number of alignments=27 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1lo7A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0322 read from 1lo7A/merged-good-all-a2m # 1lo7A read from 1lo7A/merged-good-all-a2m # found chain 1lo7A in training set T0322 42 :QARLAFRVEEHHTNGLGNCHGGMLMSFADMAWGRIISLQ 1lo7A 4 :SITMQQRIEFGDCDPAGIVWYPNYHRWLDAASRNYFIKC T0322 82 :SY 1lo7A 43 :GL T0322 84 :SWVTVRLMCDFLSGAKLGDWVEGEGELISEEDMLFTVRGRIWA 1lo7A 58 :GTPIVSCNASFVCTASYDDVLTIETCIKEWRRKSFVQRHSVSR T0322 127 :GE 1lo7A 104 :GG T0322 129 :RTLITGTGV 1lo7A 108 :QLVMRADEI T0322 138 :FKALSAR 1lo7A 119 :FAMNDGE Number of specific fragments extracted= 6 number of extra gaps= 0 total=158 Number of alignments=28 # 1lo7A read from 1lo7A/merged-good-all-a2m # found chain 1lo7A in training set T0322 42 :QARLAFRVEEHHTNGLGNCHGGMLMSFADMAWGRIISLQ 1lo7A 4 :SITMQQRIEFGDCDPAGIVWYPNYHRWLDAASRNYFIKC T0322 82 :S 1lo7A 43 :G T0322 83 :YSWVTVRLMCDFLSGAKLGDWVEGEGELISEEDMLFTVRGRIWA 1lo7A 57 :VGTPIVSCNASFVCTASYDDVLTIETCIKEWRRKSFVQRHSVSR T0322 127 :GE 1lo7A 104 :GG T0322 129 :RTLITGTGV 1lo7A 108 :QLVMRADEI T0322 138 :FKALSARKPRPGELAYK 1lo7A 119 :FAMNDGERLRAIEVPAD Number of specific fragments extracted= 6 number of extra gaps= 0 total=164 Number of alignments=29 # 1lo7A read from 1lo7A/merged-good-all-a2m # found chain 1lo7A in training set T0322 42 :QARLAFRVEEHHTNGLGNC 1lo7A 4 :SITMQQRIEFGDCDPAGIV T0322 65 :LMSFADMAWGRIISLQK 1lo7A 27 :YHRWLDAASRNYFIKCG T0322 83 :YS 1lo7A 59 :TP T0322 87 :TVRLMCDFLSGAKLGDWVEGEGELISEEDMLFTVRGRIWA 1lo7A 61 :IVSCNASFVCTASYDDVLTIETCIKEWRRKSFVQRHSVSR T0322 127 :GER 1lo7A 103 :PGG T0322 130 :TLITGTGVFK 1lo7A 111 :MRADEIRVFA Number of specific fragments extracted= 6 number of extra gaps= 0 total=170 Number of alignments=30 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1wluA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1wluA expands to /projects/compbio/data/pdb/1wlu.pdb.gz 1wluA:# T0322 read from 1wluA/merged-good-all-a2m # 1wluA read from 1wluA/merged-good-all-a2m # adding 1wluA to template set # found chain 1wluA in template set Warning: unaligning (T0322)L141 because last residue in template chain is (1wluA)L117 T0322 23 :SRGFGRQIG 1wluA 2 :RDPFMEALG T0322 33 :LFEHREGPGQARLAFRVEEHHTNGLGNCHGGMLMSFADMAWGRIISL 1wluA 11 :LKVLHLAPGEAVVAGEVRADHLNLHGTAHGGFLYALADSAFALASNT T0322 82 :SYSWVTVRLMCDFLSGAKLGDWVEGEGELISEEDMLFTVRGRIWAGERTLITGTGVFKA 1wluA 58 :RGPAVALSCRMDYFRPLGAGARVEARAVEVNLSRRTATYRVEVVSEGKLVALFTGTVFR Number of specific fragments extracted= 3 number of extra gaps= 0 total=173 Number of alignments=31 # 1wluA read from 1wluA/merged-good-all-a2m # found chain 1wluA in template set Warning: unaligning (T0322)L141 because last residue in template chain is (1wluA)L117 T0322 23 :SRGFGRQIG 1wluA 2 :RDPFMEALG T0322 33 :LFEHREGPGQARLAFRVEEHHTNGLGNCHGGMLMSFADMAWGRIISLQ 1wluA 11 :LKVLHLAPGEAVVAGEVRADHLNLHGTAHGGFLYALADSAFALASNTR T0322 83 :YSWVTVRLMCDFLSGAKLGDWVEGEGELISEEDMLFTVRGRIWAGERTLITGTGVFKA 1wluA 59 :GPAVALSCRMDYFRPLGAGARVEARAVEVNLSRRTATYRVEVVSEGKLVALFTGTVFR Number of specific fragments extracted= 3 number of extra gaps= 0 total=176 Number of alignments=32 # 1wluA read from 1wluA/merged-good-all-a2m # found chain 1wluA in template set Warning: unaligning (T0322)L141 because last residue in template chain is (1wluA)L117 T0322 24 :RGFGRQIGPLFEHREGPGQARLAFRVEEHHTNGLGNCHGGMLMSFADMAWGRIISLQ 1wluA 2 :RDPFMEALGLKVLHLAPGEAVVAGEVRADHLNLHGTAHGGFLYALADSAFALASNTR T0322 83 :YSWVTVRLMCDFLSGAKLGDWVEGEGELISEEDMLFTVRGRIWAGERTLITGTGVFKA 1wluA 59 :GPAVALSCRMDYFRPLGAGARVEARAVEVNLSRRTATYRVEVVSEGKLVALFTGTVFR Number of specific fragments extracted= 2 number of extra gaps= 0 total=178 Number of alignments=33 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1t82A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0322 read from 1t82A/merged-good-all-a2m # 1t82A read from 1t82A/merged-good-all-a2m # found chain 1t82A in training set Warning: unaligning (T0322)Q9 because first residue in template chain is (1t82A)M1 Warning: unaligning (T0322)S142 because last residue in template chain is (1t82A)P143 T0322 10 :TAAIPEGFSQLNWSRGFGRQIG 1t82A 2 :DELLNRLRQTWHSTIPVSEFMQ T0322 33 :LFEHREGPGQARLAFRVEE 1t82A 24 :IAPLSFTDGELSVSAPLAP T0322 53 :HTNGLGNCHGGM 1t82A 43 :NINLHHTMFAGS T0322 65 :LMSFADMAWGRIISLQKSY 1t82A 58 :IMTLTGWGMVWLQQQLLNV T0322 84 :SWVTVRLMCDFLSGAKLGDWVEGE 1t82A 79 :DIVLADAHIRYLAPVTSAPEVKVR T0322 111 :ISEEDMLFTVRGRIWAGERTLITGTGVFKAL 1t82A 112 :QRGRKAKVKLEVQLFCDGKLCAQFDGLYVSV Number of specific fragments extracted= 6 number of extra gaps= 0 total=184 Number of alignments=34 # 1t82A read from 1t82A/merged-good-all-a2m # found chain 1t82A in training set Warning: unaligning (T0322)I13 because first residue in template chain is (1t82A)M1 Warning: unaligning (T0322)S142 because last residue in template chain is (1t82A)P143 T0322 14 :PEGFSQL 1t82A 2 :DELLNRL T0322 21 :NWSRGFGRQIG 1t82A 13 :HSTIPVSEFMQ T0322 33 :LFEHREGPGQARLAFRVEEH 1t82A 24 :IAPLSFTDGELSVSAPLAPN T0322 54 :TNGLGNCHGGMLMSFADMAWGRIISLQ 1t82A 44 :INLHHTMFAGSIYTIMTLTGWGMVWLQ T0322 81 :KS 1t82A 74 :LN T0322 83 :YSWVTVRLMCDFLSGAKLGD 1t82A 78 :GDIVLADAHIRYLAPVTSAP T0322 105 :EGEGELIS 1t82A 98 :EVKVRWPD T0322 113 :EEDMLFTVRGRIWAGERTLITGTGVFKAL 1t82A 114 :GRKAKVKLEVQLFCDGKLCAQFDGLYVSV Number of specific fragments extracted= 8 number of extra gaps= 0 total=192 Number of alignments=35 # 1t82A read from 1t82A/merged-good-all-a2m # found chain 1t82A in training set Warning: unaligning (T0322)T10 because first residue in template chain is (1t82A)M1 T0322 11 :AAIPEGFSQLNWSRGFGRQIGPLFEHREGPGQARLAFRV 1t82A 2 :DELLNRLRQTWHSTIPVSEFMQIAPLSFTDGELSVSAPL T0322 51 :EHHTNGLGNCHGGM 1t82A 41 :APNINLHHTMFAGS T0322 65 :LMSFADMAWGRIISLQK 1t82A 58 :IMTLTGWGMVWLQQQLL T0322 82 :SYSWVTVRLMCDFLSGAKLGDWVEGE 1t82A 77 :DGDIVLADAHIRYLAPVTSAPEVKVR T0322 112 :SEEDMLFTVRGRIWAGERTLITGTGVFK 1t82A 113 :RGRKAKVKLEVQLFCDGKLCAQFDGLYV Number of specific fragments extracted= 5 number of extra gaps= 0 total=197 Number of alignments=36 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2cyeA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2cyeA expands to /projects/compbio/data/pdb/2cye.pdb.gz 2cyeA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0322 read from 2cyeA/merged-good-all-a2m # 2cyeA read from 2cyeA/merged-good-all-a2m # adding 2cyeA to template set # found chain 2cyeA in template set Warning: unaligning (T0322)Q80 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2cyeA)D46 Warning: unaligning (T0322)Y83 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2cyeA)D46 T0322 40 :PG 2cyeA 2 :EG T0322 42 :QARLAFRVEEHHTNGLGNCHGGMLMSFADMAWGRIISL 2cyeA 5 :PVRVRVDVRFRDLDPLGHVNNAVFLSYMELARIRYFQR T0322 84 :SWVTVRLMCDFLSGAKLGDWVEGEGELISEEDMLFTVRGRIWAGERTLITGTGVFKALSARKPRP 2cyeA 52 :HFVVARMEVDYLRPILLGDEVFVGVRTVGLGRSSLRMEHLVTANGESAAKGLGVLVWLEGGRPAP T0322 149 :GELAYKE 2cyeA 118 :PEAIRER Number of specific fragments extracted= 4 number of extra gaps= 0 total=201 Number of alignments=37 # 2cyeA read from 2cyeA/merged-good-all-a2m # found chain 2cyeA in template set Warning: unaligning (T0322)Q80 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2cyeA)D46 T0322 40 :PG 2cyeA 2 :EG T0322 42 :QARLAFRVEEHHTNGLGNCHGGMLMSFADMAWGRIISL 2cyeA 5 :PVRVRVDVRFRDLDPLGHVNNAVFLSYMELARIRYFQR T0322 83 :YSWVTVRLMCDFLSGAKLGDWVEGEGELISEEDMLFTVRGRIWAGERTLITGTGVFKALSARKPRPGE 2cyeA 51 :GHFVVARMEVDYLRPILLGDEVFVGVRTVGLGRSSLRMEHLVTANGESAAKGLGVLVWLEGGRPAPLP Number of specific fragments extracted= 3 number of extra gaps= 0 total=204 Number of alignments=38 # 2cyeA read from 2cyeA/merged-good-all-a2m # found chain 2cyeA in template set Warning: unaligning (T0322)Q80 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2cyeA)D46 T0322 39 :GPGQARLAFRVEEHHTNGLGNCHGGMLMSFADMAWGRIISL 2cyeA 2 :EGFPVRVRVDVRFRDLDPLGHVNNAVFLSYMELARIRYFQR T0322 82 :SYSWVTVRLMCDFLSGAKLGDWVEGEGELISEEDMLFTVRGRIWAGERTLITGTGVFKALSARKPRPGELAYKEEA 2cyeA 50 :EGHFVVARMEVDYLRPILLGDEVFVGVRTVGLGRSSLRMEHLVTANGESAAKGLGVLVWLEGGRPAPLPEAIRERI Number of specific fragments extracted= 2 number of extra gaps= 0 total=206 Number of alignments=39 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1y7uA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0322/1y7uA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0322/1y7uA/merged-good-all-a2m.gz for input Trying 1y7uA/merged-good-all-a2m Error: Couldn't open file 1y7uA/merged-good-all-a2m or 1y7uA/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1s5uA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0322 read from 1s5uA/merged-good-all-a2m # 1s5uA read from 1s5uA/merged-good-all-a2m # found chain 1s5uA in training set Warning: unaligning (T0322)G41 because first residue in template chain is (1s5uA)T4 T0322 42 :QARLAFRVEEHHTNGLGNCHGGMLMSFADMAWGRIISLQ 1s5uA 5 :LFRWPVRVYYEDTDAGGVVYHASYVAFYERARTEMLRHH T0322 82 :SY 1s5uA 44 :HF T0322 84 :SWVTVRLMCDFLSGAKLGDWVEGEGELISEEDMLFTVRGRIWA 1s5uA 56 :AFVVRKMTVEYYAPARLDDMLEIQTEITSMRGTSLVFTQRIVN T0322 127 :GERTLITGTGVFKALSARKPRP 1s5uA 100 :ENTLLNEAEVLVVCVDPLKMKP T0322 149 :GELAYK 1s5uA 125 :PKSIVA Number of specific fragments extracted= 5 number of extra gaps= 0 total=211 Number of alignments=40 # 1s5uA read from 1s5uA/merged-good-all-a2m # found chain 1s5uA in training set Warning: unaligning (T0322)G41 because first residue in template chain is (1s5uA)T4 T0322 42 :QARLAFRVEEHHTNGLGNCHGGMLMSFADMAWGRIISLQ 1s5uA 5 :LFRWPVRVYYEDTDAGGVVYHASYVAFYERARTEMLRHH T0322 81 :KSYSWVTVRLMCDFLSGAKLGDWVEGEGELISEEDMLFTVRGRIWA 1s5uA 53 :ERVAFVVRKMTVEYYAPARLDDMLEIQTEITSMRGTSLVFTQRIVN T0322 127 :GERTLITGTGVFKALSARKPRPGELAYK 1s5uA 100 :ENTLLNEAEVLVVCVDPLKMKPRALPKS Number of specific fragments extracted= 3 number of extra gaps= 0 total=214 Number of alignments=41 # 1s5uA read from 1s5uA/merged-good-all-a2m # found chain 1s5uA in training set T0322 42 :QARLAFRVEEHHTNGLGNCHGGMLMSFADMAWGRIISLQK 1s5uA 5 :LFRWPVRVYYEDTDAGGVVYHASYVAFYERARTEMLRHHH T0322 82 :SYSWVTVRLMCDFLSGAKLGDWVEGEGELISEEDMLFTVRGRIWAGERTLITGTGVFKALSAR 1s5uA 54 :RVAFVVRKMTVEYYAPARLDDMLEIQTEITSMRGTSLVFTQRIVNAENTLLNEAEVLVVCVDP Number of specific fragments extracted= 2 number of extra gaps= 0 total=216 Number of alignments=42 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1yliA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1yliA expands to /projects/compbio/data/pdb/1yli.pdb.gz 1yliA:Skipped atom 122, because occupancy 0.500 <= existing 0.500 in 1yliA Skipped atom 124, because occupancy 0.500 <= existing 0.500 in 1yliA Skipped atom 588, because occupancy 0.500 <= existing 0.500 in 1yliA Skipped atom 590, because occupancy 0.500 <= existing 0.500 in 1yliA Skipped atom 592, because occupancy 0.500 <= existing 0.500 in 1yliA Skipped atom 594, because occupancy 0.500 <= existing 0.500 in 1yliA Skipped atom 596, because occupancy 0.500 <= existing 0.500 in 1yliA Skipped atom 598, because occupancy 0.500 <= existing 0.500 in 1yliA Skipped atom 600, because occupancy 0.500 <= existing 0.500 in 1yliA # T0322 read from 1yliA/merged-good-all-a2m # 1yliA read from 1yliA/merged-good-all-a2m # adding 1yliA to template set # found chain 1yliA in template set Warning: unaligning (T0322)A46 because of BadResidue code BAD_PEPTIDE in next template residue (1yliA)T21 Warning: unaligning (T0322)F47 because of BadResidue code BAD_PEPTIDE at template residue (1yliA)T21 T0322 40 :PGQARL 1yliA 14 :KGVLLL T0322 48 :RVEEHHTNGLGNCHGGMLMSFADMAWGRIISLQKSYSWVTVRLM 1yliA 22 :LAMPSDTNANGDIFGGWIMSQMDMGGAILAKEIAHGRVVTVAVE T0322 92 :CDFLSGAKLGDWVEGEGELISEEDMLFTVRGRIWA 1yliA 67 :MNFIKPISVGDVVCCYGQCLKVGRSSIKIKVEVWV T0322 127 :G 1yliA 107 :E T0322 128 :ER 1yliA 110 :GE T0322 130 :TLITGTGVFKALSARKPRP 1yliA 114 :CVTDAVFTFVAVDNNGRSR T0322 149 :GELA 1yliA 140 :QELE Number of specific fragments extracted= 7 number of extra gaps= 1 total=223 Number of alignments=43 # 1yliA read from 1yliA/merged-good-all-a2m # found chain 1yliA in template set Warning: unaligning (T0322)A46 because of BadResidue code BAD_PEPTIDE in next template residue (1yliA)T21 Warning: unaligning (T0322)F47 because of BadResidue code BAD_PEPTIDE at template residue (1yliA)T21 T0322 41 :GQARL 1yliA 15 :GVLLL T0322 48 :RVEEHHTNGLGNCHGGMLMSFADMAWGRIISLQKSYSWVTVRLM 1yliA 22 :LAMPSDTNANGDIFGGWIMSQMDMGGAILAKEIAHGRVVTVAVE T0322 92 :CDFLSGAKLGDWVEGEGELISEEDMLFTVRGRIW 1yliA 67 :MNFIKPISVGDVVCCYGQCLKVGRSSIKIKVEVW T0322 126 :AG 1yliA 106 :SE T0322 128 :E 1yliA 110 :G T0322 130 :TLITGTGVFKALSARKPR 1yliA 114 :CVTDAVFTFVAVDNNGRS T0322 149 :GELAYKE 1yliA 132 :RTIPREN Number of specific fragments extracted= 7 number of extra gaps= 1 total=230 Number of alignments=44 # 1yliA read from 1yliA/merged-good-all-a2m # found chain 1yliA in template set Warning: unaligning (T0322)A46 because of BadResidue code BAD_PEPTIDE in next template residue (1yliA)T21 Warning: unaligning (T0322)F47 because of BadResidue code BAD_PEPTIDE at template residue (1yliA)T21 T0322 40 :PGQARL 1yliA 14 :KGVLLL T0322 48 :RVEEHHTNGLGNCHGGMLMSFADMAWGRIISLQKSYSWVTVRLM 1yliA 22 :LAMPSDTNANGDIFGGWIMSQMDMGGAILAKEIAHGRVVTVAVE T0322 92 :CDFLSGAKLGDWVEGEGELISEEDMLFTVRGRIWA 1yliA 67 :MNFIKPISVGDVVCCYGQCLKVGRSSIKIKVEVWV T0322 127 :GERTLITGTGVFKALSARK 1yliA 110 :GERYCVTDAVFTFVAVDNN T0322 146 :PRPGELAYKE 1yliA 135 :PRENNQELEK Number of specific fragments extracted= 5 number of extra gaps= 1 total=235 Number of alignments=45 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1njkA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1njkA expands to /projects/compbio/data/pdb/1njk.pdb.gz 1njkA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0322 read from 1njkA/merged-good-all-a2m # 1njkA read from 1njkA/merged-good-all-a2m # adding 1njkA to template set # found chain 1njkA in template set Warning: unaligning (T0322)Q42 because first residue in template chain is (1njkA)H0 T0322 43 :ARLAFRVEEHHTNGLGNCHGGMLMSFADMAWGRIIS 1njkA 1 :MQTQIKVRGYHLDVYQHVNNARYLEFLEEARWDGLE T0322 82 :SY 1njkA 37 :NS T0322 84 :SWVTVRLMCDFLSGAKLGDWVEGEGELISEEDMLFTVRGRIWA 1njkA 50 :AFVVVNININYRRPAVLSDLLTITSQLQQLNGKSGILSQVITL T0322 127 :GERTLITGTGVFKALSARKPRP 1njkA 95 :EGQVVADALITFVCIDLKTQKA T0322 149 :GELAY 1njkA 121 :GELRE Number of specific fragments extracted= 5 number of extra gaps= 0 total=240 Number of alignments=46 # 1njkA read from 1njkA/merged-good-all-a2m # found chain 1njkA in template set Warning: unaligning (T0322)Q42 because first residue in template chain is (1njkA)H0 T0322 43 :ARLAFRVEEHHTNGLGNCHGGMLMSFADMAWGRIISLQ 1njkA 1 :MQTQIKVRGYHLDVYQHVNNARYLEFLEEARWDGLENS T0322 81 :KSYSWVTVRLMCDFLSGAKLGDWVEGEGELISEEDMLFTVRGRIWA 1njkA 47 :HNIAFVVVNININYRRPAVLSDLLTITSQLQQLNGKSGILSQVITL T0322 128 :ERTLITGTGVFKALSARKPR 1njkA 96 :GQVVADALITFVCIDLKTQK Number of specific fragments extracted= 3 number of extra gaps= 0 total=243 Number of alignments=47 # 1njkA read from 1njkA/merged-good-all-a2m # found chain 1njkA in template set Warning: unaligning (T0322)Q42 because first residue in template chain is (1njkA)H0 T0322 43 :ARLAFRVEEHHTNGLGNCHGGMLMSFADMAWGRII 1njkA 1 :MQTQIKVRGYHLDVYQHVNNARYLEFLEEARWDGL T0322 78 :SLQKSYSWVTVRLMCDFLSGAKLGDWVEGEGELISEEDMLFTVRGRIWAG 1njkA 44 :MTAHNIAFVVVNININYRRPAVLSDLLTITSQLQQLNGKSGILSQVITLE T0322 128 :ERTLITGTGVFKALS 1njkA 95 :EGQVVADALITFVCI Number of specific fragments extracted= 3 number of extra gaps= 0 total=246 Number of alignments=48 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1o0iA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1o0iA expands to /projects/compbio/data/pdb/1o0i.pdb.gz 1o0iA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0322 read from 1o0iA/merged-good-all-a2m # 1o0iA read from 1o0iA/merged-good-all-a2m # adding 1o0iA to template set # found chain 1o0iA in template set Warning: unaligning (T0322)A143 because last residue in template chain is (1o0iA)L138 T0322 19 :QLNW 1o0iA 14 :QLCS T0322 24 :RGFGRQIG 1o0iA 18 :NSAVSHLG T0322 33 :LFEHREGPGQARLAFRVEEHHTNGLGNCHGGMLMSFADMAWGRIISLQKSY 1o0iA 26 :IEISAFGEDWIEATMPVDHRTMQPFGVLHGGVSVALAETIGSLAGSLCLEE T0322 84 :SWVTVRLMCDFLSGAKLG 1o0iA 79 :TVVGLDINANHLRPVRSG T0322 103 :WVEGEGELISEEDMLFTVRGRIWA 1o0iA 97 :KVTARATPINLGRNIQVWQIDIRT T0322 127 :GERTLITGTGVFKALS 1o0iA 122 :ENKLCCVSRLTLSVIN Number of specific fragments extracted= 6 number of extra gaps= 0 total=252 Number of alignments=49 # 1o0iA read from 1o0iA/merged-good-all-a2m # found chain 1o0iA in template set Warning: unaligning (T0322)T6 because first residue in template chain is (1o0iA)L2 Warning: unaligning (T0322)A143 because last residue in template chain is (1o0iA)L138 T0322 7 :DAQTAAIPEGFSQLN 1o0iA 3 :WKKTFTLENLNQLCS T0322 24 :RGFGRQIG 1o0iA 18 :NSAVSHLG T0322 33 :LFEHREGPGQARLAFRVEEHHTNGLGNCHGGMLMSFADMAWGRIISLQ 1o0iA 26 :IEISAFGEDWIEATMPVDHRTMQPFGVLHGGVSVALAETIGSLAGSLC T0322 81 :KSYSWVTVRLMCDFLSGAKLG 1o0iA 76 :EGKTVVGLDINANHLRPVRSG T0322 103 :WVEGEGELISEEDMLFTVRGRIWA 1o0iA 97 :KVTARATPINLGRNIQVWQIDIRT T0322 127 :GERTLITGTGVFKALS 1o0iA 122 :ENKLCCVSRLTLSVIN Number of specific fragments extracted= 6 number of extra gaps= 0 total=258 Number of alignments=50 # 1o0iA read from 1o0iA/merged-good-all-a2m # found chain 1o0iA in template set T0322 7 :DAQTAAIPEGF 1o0iA 6 :TFTLENLNQLC T0322 24 :RGFGRQIGPLFEHREGPGQARLAFRVEEHHTNGLGNCHGGMLMSFADMAWGRIISLQK 1o0iA 17 :SNSAVSHLGIEISAFGEDWIEATMPVDHRTMQPFGVLHGGVSVALAETIGSLAGSLCL T0322 82 :SYSWVTVRLMCDFLSGAK 1o0iA 77 :GKTVVGLDINANHLRPVR T0322 101 :GDWVEGEGELISEEDMLFTVRGRIWAGERTLITGTGVFKALSA 1o0iA 95 :SGKVTARATPINLGRNIQVWQIDIRTEENKLCCVSRLTLSVIN Number of specific fragments extracted= 4 number of extra gaps= 0 total=262 Number of alignments=51 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2aliA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2aliA expands to /projects/compbio/data/pdb/2ali.pdb.gz 2aliA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 157, because occupancy 0.500 <= existing 0.500 in 2aliA Skipped atom 161, because occupancy 0.500 <= existing 0.500 in 2aliA Skipped atom 163, because occupancy 0.500 <= existing 0.500 in 2aliA Skipped atom 165, because occupancy 0.500 <= existing 0.500 in 2aliA Skipped atom 167, because occupancy 0.500 <= existing 0.500 in 2aliA Skipped atom 169, because occupancy 0.500 <= existing 0.500 in 2aliA Skipped atom 171, because occupancy 0.500 <= existing 0.500 in 2aliA Skipped atom 197, because occupancy 0.500 <= existing 0.500 in 2aliA Skipped atom 201, because occupancy 0.500 <= existing 0.500 in 2aliA Skipped atom 203, because occupancy 0.500 <= existing 0.500 in 2aliA Skipped atom 205, because occupancy 0.500 <= existing 0.500 in 2aliA Skipped atom 718, because occupancy 0.500 <= existing 0.500 in 2aliA Skipped atom 722, because occupancy 0.500 <= existing 0.500 in 2aliA Skipped atom 724, because occupancy 0.500 <= existing 0.500 in 2aliA Skipped atom 726, because occupancy 0.500 <= existing 0.500 in 2aliA Skipped atom 728, because occupancy 0.500 <= existing 0.500 in 2aliA Skipped atom 730, because occupancy 0.500 <= existing 0.500 in 2aliA Skipped atom 732, because occupancy 0.500 <= existing 0.500 in 2aliA Skipped atom 734, because occupancy 0.500 <= existing 0.500 in 2aliA Skipped atom 745, because occupancy 0.400 <= existing 0.600 in 2aliA Skipped atom 749, because occupancy 0.400 <= existing 0.600 in 2aliA Skipped atom 751, because occupancy 0.400 <= existing 0.600 in 2aliA Skipped atom 753, because occupancy 0.400 <= existing 0.600 in 2aliA Skipped atom 755, because occupancy 0.400 <= existing 0.600 in 2aliA Skipped atom 757, because occupancy 0.400 <= existing 0.600 in 2aliA Skipped atom 759, because occupancy 0.400 <= existing 0.600 in 2aliA Skipped atom 860, because occupancy 0.400 <= existing 0.600 in 2aliA Skipped atom 864, because occupancy 0.400 <= existing 0.600 in 2aliA Skipped atom 866, because occupancy 0.400 <= existing 0.600 in 2aliA Skipped atom 886, because occupancy 0.400 <= existing 0.600 in 2aliA Skipped atom 890, because occupancy 0.400 <= existing 0.600 in 2aliA Skipped atom 892, because occupancy 0.400 <= existing 0.600 in 2aliA Skipped atom 894, because occupancy 0.400 <= existing 0.600 in 2aliA # T0322 read from 2aliA/merged-good-all-a2m # 2aliA read from 2aliA/merged-good-all-a2m # adding 2aliA to template set # found chain 2aliA in template set Warning: unaligning (T0322)F34 because first residue in template chain is (2aliA)Q5 T0322 35 :EH 2aliA 6 :LL T0322 43 :ARLAFRVEEHHTNGLGNCHGGMLMSFADMAWGRIISLQ 2aliA 8 :HTAHIPVRWGDMDSYGHVNNTLYFQYLEEARVAWFETL T0322 82 :SY 2aliA 46 :GI T0322 84 :SWVTVRLMCDFLSGAKLGDWVEGEGELISEEDMLFTVRGRIWA 2aliA 55 :GPVVLQSLHTYLKPVVHPATVVVELYAGRLGTSSLVLEHRLHT T0322 127 :GER 2aliA 102 :QGT T0322 130 :TLITGTGVFKALSARKPRP 2aliA 106 :GEGHCKLVWVRHAENRSTP T0322 149 :GELAYKE 2aliA 126 :PDSIRAA Number of specific fragments extracted= 7 number of extra gaps= 0 total=269 Number of alignments=52 # 2aliA read from 2aliA/merged-good-all-a2m # found chain 2aliA in template set Warning: unaligning (T0322)F34 because first residue in template chain is (2aliA)Q5 T0322 35 :EH 2aliA 6 :LL T0322 43 :ARLAFRVEEHHTNGLGNCHGGMLMSFADMAWGRIISLQ 2aliA 8 :HTAHIPVRWGDMDSYGHVNNTLYFQYLEEARVAWFETL T0322 83 :YSWVTVRLMCDFLSGAKLGDWVEGEGELISEEDMLFTVRGRIWA 2aliA 54 :EGPVVLQSLHTYLKPVVHPATVVVELYAGRLGTSSLVLEHRLHT T0322 127 :G 2aliA 99 :E T0322 128 :ERTLITGTGVFKALSARKPRPGELAYKE 2aliA 102 :QGTYGEGHCKLVWVRHAENRSTPVPDSI Number of specific fragments extracted= 5 number of extra gaps= 0 total=274 Number of alignments=53 # 2aliA read from 2aliA/merged-good-all-a2m # found chain 2aliA in template set Warning: unaligning (T0322)F34 because first residue in template chain is (2aliA)Q5 T0322 35 :EHR 2aliA 6 :LLH T0322 44 :RLAFRVEEHHTNGLGNC 2aliA 9 :TAHIPVRWGDMDSYGHV T0322 64 :MLMSFADMAWGRIISLQK 2aliA 29 :LYFQYLEEARVAWFETLG T0322 82 :SYSWVTVRLM 2aliA 51 :GAAEGPVVLQ T0322 92 :CDFLSGAKLGDWVEGEGELISEEDMLFTVRGRIWAGER 2aliA 63 :HTYLKPVVHPATVVVELYAGRLGTSSLVLEHRLHTLED T0322 130 :TLITGTGVFKALSARKPRPGELAYKE 2aliA 106 :GEGHCKLVWVRHAENRSTPVPDSIRA Number of specific fragments extracted= 6 number of extra gaps= 0 total=280 Number of alignments=54 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1z54A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1z54A expands to /projects/compbio/data/pdb/1z54.pdb.gz 1z54A:# T0322 read from 1z54A/merged-good-all-a2m # 1z54A read from 1z54A/merged-good-all-a2m # adding 1z54A to template set # found chain 1z54A in template set T0322 43 :ARLAFRVEEHHTNGLGNCHGGMLMSFADMAWGRIISLQ 1z54A 3 :SVTRIKVRYAETDQMGVVHHSVYAVYLEAARVDFLERA T0322 82 :SY 1z54A 41 :GL T0322 84 :SWVTVRLMCDFLSGAKLGDWVEGEGELISEEDMLFTVRGRIWAGERTLITGTGVFKALSARKPRP 1z54A 53 :FFPVVELGLTFRAPARFGEVVEVRTRLAELSSRALLFRYRVEREGVLLAEGFTRHLCQVGERAAR T0322 149 :GELAYKE 1z54A 119 :PEDIYRA Number of specific fragments extracted= 4 number of extra gaps= 0 total=284 Number of alignments=55 # 1z54A read from 1z54A/merged-good-all-a2m # found chain 1z54A in template set T0322 43 :ARLAFRVEEHHTNGLGNCHGGMLMSFADMAWGRIISLQ 1z54A 3 :SVTRIKVRYAETDQMGVVHHSVYAVYLEAARVDFLERA T0322 81 :KSYSWVTVRLMCDFLSGAKLGDWVEGEGELISEEDMLFTVRGRIWAGERTLITGTGVFKALSARKPRPGE 1z54A 50 :RGVFFPVVELGLTFRAPARFGEVVEVRTRLAELSSRALLFRYRVEREGVLLAEGFTRHLCQVGERAARIP Number of specific fragments extracted= 2 number of extra gaps= 0 total=286 Number of alignments=56 # 1z54A read from 1z54A/merged-good-all-a2m # found chain 1z54A in template set T0322 43 :ARLAFRVEEHHTNGLGNCH 1z54A 3 :SVTRIKVRYAETDQMGVVH T0322 64 :MLMSFADMAWGRIISLQK 1z54A 24 :VYAVYLEAARVDFLERAG T0322 82 :SYSWVTVRLMCDFLSGAKLGDWVEGEGELISEEDMLFTVRGRIWAGERTLITGTGVFKALSARKPRPGELAYKEE 1z54A 51 :GVFFPVVELGLTFRAPARFGEVVEVRTRLAELSSRALLFRYRVEREGVLLAEGFTRHLCQVGERAARIPEDIYRA Number of specific fragments extracted= 3 number of extra gaps= 0 total=289 Number of alignments=57 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2bi0A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2bi0A expands to /projects/compbio/data/pdb/2bi0.pdb.gz 2bi0A:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0322 read from 2bi0A/merged-good-all-a2m # 2bi0A read from 2bi0A/merged-good-all-a2m # adding 2bi0A to template set # found chain 2bi0A in template set T0322 50 :EEHHTNGL 2bi0A 239 :DWRVSGRR T0322 59 :NCHGGMLMSFA 2bi0A 247 :LVYGGHTIGLA T0322 74 :GRIISLQKSYSWVTVRLM 2bi0A 258 :LAQATRLLPNLATVLDWE T0322 92 :CDFLSGAKLGDWVEGEGELISE 2bi0A 277 :CDHTAPVHEGDTLYSELHIESA T0322 114 :EDMLFTVRGRIWA 2bi0A 303 :DGGVLGLRSLVYA T0322 127 :G 2bi0A 318 :D T0322 129 :RTLITGTGVFKA 2bi0A 325 :RQVLDWRFSALQ Number of specific fragments extracted= 7 number of extra gaps= 0 total=296 Number of alignments=58 # 2bi0A read from 2bi0A/merged-good-all-a2m # found chain 2bi0A in template set T0322 8 :AQTAAIPEGFSQLNWSRGFGRQIG 2bi0A 187 :TAHWDGAVFRKRVPGPHFDAGIAG T0322 34 :FEHREGP 2bi0A 211 :AVLHSTA T0322 47 :FRV 2bi0A 218 :DLV T0322 50 :EEHHTNGL 2bi0A 239 :DWRVSGRR T0322 59 :NCHGGMLMSFA 2bi0A 247 :LVYGGHTIGLA T0322 73 :WGRIISLQ 2bi0A 258 :LAQATRLL T0322 82 :SYSWVTVRLM 2bi0A 266 :PNLATVLDWE T0322 92 :CDFLSGAKLGDWVEGEGELIS 2bi0A 277 :CDHTAPVHEGDTLYSELHIES T0322 113 :EEDMLFTVRGRIWA 2bi0A 302 :ADGGVLGLRSLVYA T0322 127 :G 2bi0A 318 :D T0322 128 :E 2bi0A 320 :A T0322 129 :RTLITGTGVFKA 2bi0A 325 :RQVLDWRFSALQ Number of specific fragments extracted= 12 number of extra gaps= 0 total=308 Number of alignments=59 # 2bi0A read from 2bi0A/merged-good-all-a2m # found chain 2bi0A in template set T0322 53 :HTNGLGNCHGGMLMSF 2bi0A 241 :RVSGRRLVYGGHTIGL T0322 72 :AWGRIISLQKSYSWVTVRLMCDFLSGAKLGDWVEGEGELISEED 2bi0A 257 :ALAQATRLLPNLATVLDWESCDHTAPVHEGDTLYSELHIESAQA T0322 116 :MLFTVRGRIWA 2bi0A 305 :GVLGLRSLVYA Number of specific fragments extracted= 3 number of extra gaps= 0 total=311 Number of alignments=60 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2b3nA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2b3nA expands to /projects/compbio/data/pdb/2b3n.pdb.gz 2b3nA:Skipped atom 125, because occupancy 0.330 <= existing 0.330 in 2b3nA Skipped atom 126, because occupancy 0.330 <= existing 0.330 in 2b3nA Skipped atom 130, because occupancy 0.330 <= existing 0.330 in 2b3nA Skipped atom 131, because occupancy 0.330 <= existing 0.330 in 2b3nA Skipped atom 133, because occupancy 0.330 <= existing 0.330 in 2b3nA Skipped atom 134, because occupancy 0.330 <= existing 0.330 in 2b3nA Skipped atom 146, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 150, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 152, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 154, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 156, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 158, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 254, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 258, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 260, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 262, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 264, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 266, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 269, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 273, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 275, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 277, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 279, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 338, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 342, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 344, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 346, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 348, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 350, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 365, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 369, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 371, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 373, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 375, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 377, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 448, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 450, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 452, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 454, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 456, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 458, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 460, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 462, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 676, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 680, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 682, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 684, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 731, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 735, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 737, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 827, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 831, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 833, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 835, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 853, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 855, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 857, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 859, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 861, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 863, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 865, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 867, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 869, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 880, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 882, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 884, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 886, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 888, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 890, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 1017, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 1021, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 1023, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 1025, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 1027, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 1029, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 1036, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 1040, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 1042, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 1044, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 1054, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 1058, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 1060, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 1092, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 1096, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 1098, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 1100, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 1102, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 1245, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 1249, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 1251, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 1253, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 1262, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 1264, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 1266, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 1268, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 1270, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 1272, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 1274, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 1276, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 1278, because occupancy 0.500 <= existing 0.500 in 2b3nA # T0322 read from 2b3nA/merged-good-all-a2m # 2b3nA read from 2b3nA/merged-good-all-a2m # adding 2b3nA to template set # found chain 2b3nA in template set Warning: unaligning (T0322)S2 because first residue in template chain is (2b3nA)E5 Warning: unaligning (T0322)D3 because of BadResidue code BAD_PEPTIDE at template residue (2b3nA)V6 Warning: unaligning (T0322)D4 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2b3nA)K7 Warning: unaligning (T0322)R24 because of BadResidue code BAD_PEPTIDE in next template residue (2b3nA)K27 Warning: unaligning (T0322)W125 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (2b3nA)T144 Warning: unaligning (T0322)A126 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (2b3nA)T144 T0322 5 :LTDAQTAA 2b3nA 8 :MMSLLEEM T0322 14 :PEGFSQLNWS 2b3nA 16 :KGIYSKKGGK T0322 25 :GFGRQIG 2b3nA 28 :PFEKFEG T0322 37 :REGPG 2b3nA 35 :ELKEG T0322 42 :QARLAFRV 2b3nA 41 :RFEYEKKL T0322 50 :EEH 2b3nA 76 :TRF T0322 56 :GLGNCHGGMLMSFA 2b3nA 79 :GGRVVHGMLTTSLV T0322 74 :GRIISLQ 2b3nA 93 :SAAVARL T0322 82 :SYSWVTVRLMCDFLSGAKLGDWVEGEGELISEEDMLFTVRGRI 2b3nA 100 :PGTVVLLEQSFRYTSPVRIGDVVRVEGVVSGVEKNRYTIDVKC T0322 127 :GERTLITGTGVFKA 2b3nA 145 :GDKVVAEGVVKVLI Number of specific fragments extracted= 10 number of extra gaps= 2 total=321 Number of alignments=61 # 2b3nA read from 2b3nA/merged-good-all-a2m # found chain 2b3nA in template set Warning: unaligning (T0322)G27 because of BadResidue code BAD_PEPTIDE in next template residue (2b3nA)K27 Warning: unaligning (T0322)R28 because of BadResidue code BAD_PEPTIDE at template residue (2b3nA)K27 Warning: unaligning (T0322)W125 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (2b3nA)T144 Warning: unaligning (T0322)A126 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (2b3nA)T144 T0322 14 :PEGFSQLNWSRGF 2b3nA 13 :EEMKGIYSKKGGK T0322 29 :QIGPLFE 2b3nA 28 :PFEKFEG T0322 37 :REGPG 2b3nA 35 :ELKEG T0322 42 :QARLAFRV 2b3nA 41 :RFEYEKKL T0322 50 :EEH 2b3nA 76 :TRF T0322 56 :GLGNCHGGMLMSFAD 2b3nA 79 :GGRVVHGMLTTSLVS T0322 75 :RIISLQ 2b3nA 94 :AAVARL T0322 82 :SYSWVTVRLMCDFLSGAKLGDWVEGEGELISEEDMLFTVRGRI 2b3nA 100 :PGTVVLLEQSFRYTSPVRIGDVVRVEGVVSGVEKNRYTIDVKC T0322 127 :GERTLITGTGVFKA 2b3nA 145 :GDKVVAEGVVKVLI Number of specific fragments extracted= 9 number of extra gaps= 2 total=330 Number of alignments=62 # 2b3nA read from 2b3nA/merged-good-all-a2m # found chain 2b3nA in template set Warning: unaligning (T0322)W125 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (2b3nA)T144 Warning: unaligning (T0322)A126 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (2b3nA)T144 T0322 56 :GLGNCHGG 2b3nA 79 :GGRVVHGM T0322 68 :FADMAWGRIISLQ 2b3nA 87 :LTTSLVSAAVARL T0322 82 :SYSWVTVRLMCDFLSGAKLGDWVEGEGELISEEDMLFTVRGRI 2b3nA 100 :PGTVVLLEQSFRYTSPVRIGDVVRVEGVVSGVEKNRYTIDVKC T0322 127 :GERTLITGTGV 2b3nA 145 :GDKVVAEGVVK Number of specific fragments extracted= 4 number of extra gaps= 1 total=334 Number of alignments=63 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1q4uA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0322 read from 1q4uA/merged-good-all-a2m # 1q4uA read from 1q4uA/merged-good-all-a2m # found chain 1q4uA in training set Warning: unaligning (T0322)R144 because last residue in template chain is (1q4uA)R150 T0322 3 :DDLTDAQ 1q4uA 13 :GNLPDVA T0322 11 :AAIPEGFSQLNW 1q4uA 20 :SHYPVAYEQTLD T0322 28 :RQIG 1q4uA 32 :GTVG T0322 33 :LFEHREGPGQARLAFRVEEHHTNGLGNCHGGMLMSFADMAWGRIISLQKSY 1q4uA 36 :FVIDEMTPERATASVEVTDTLRQRWGLVHGGAYCALAEMLATEATVAVVHE T0322 84 :SWVTVRLMCDFLSGAKLG 1q4uA 90 :MAVGQSNHTSFFRPVKEG T0322 103 :WVEGEGELISEEDMLFTVRGRIWAG 1q4uA 108 :HVRAEAVRIHAGSTTWFWDVSLRDD T0322 128 :ERTLITGTGVFKALSA 1q4uA 134 :GRLCAVSSMSIAVRPR Number of specific fragments extracted= 7 number of extra gaps= 0 total=341 Number of alignments=64 # 1q4uA read from 1q4uA/merged-good-all-a2m # found chain 1q4uA in training set Warning: unaligning (T0322)R144 because last residue in template chain is (1q4uA)R150 T0322 6 :TDAQ 1q4uA 19 :ASHY T0322 23 :SRGFGRQI 1q4uA 23 :PVAYEQTL T0322 31 :G 1q4uA 35 :G T0322 33 :LFEHREGPGQARLAFRVEEHHTNGLGNCHGGMLMSFADMAWGRIISLQ 1q4uA 36 :FVIDEMTPERATASVEVTDTLRQRWGLVHGGAYCALAEMLATEATVAV T0322 81 :KSYSWVTVRLMCDFLSGAKLG 1q4uA 87 :KGMMAVGQSNHTSFFRPVKEG T0322 103 :WVEGEGELISEEDMLFTVRGRIWAG 1q4uA 108 :HVRAEAVRIHAGSTTWFWDVSLRDD T0322 128 :ERTLITGTGVFKALSA 1q4uA 134 :GRLCAVSSMSIAVRPR Number of specific fragments extracted= 7 number of extra gaps= 0 total=348 Number of alignments=65 # 1q4uA read from 1q4uA/merged-good-all-a2m # found chain 1q4uA in training set Warning: unaligning (T0322)K145 because last residue in template chain is (1q4uA)R150 T0322 7 :DAQTAAIPEG 1q4uA 23 :PVAYEQTLDG T0322 30 :IGPLFEHREGPGQARLAFRVEEHHTNGLGNCHGGMLMSFADMAWGRIISLQK 1q4uA 33 :TVGFVIDEMTPERATASVEVTDTLRQRWGLVHGGAYCALAEMLATEATVAVV T0322 82 :SYSWVTVRLMCDFLSGAKLG 1q4uA 88 :GMMAVGQSNHTSFFRPVKEG T0322 103 :WVEGEGELISEEDMLFTVRGRIWAGERTLITGTGVFKALSAR 1q4uA 108 :HVRAEAVRIHAGSTTWFWDVSLRDDAGRLCAVSSMSIAVRPR Number of specific fragments extracted= 4 number of extra gaps= 0 total=352 Number of alignments=66 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2av9A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2av9A expands to /projects/compbio/data/pdb/2av9.pdb.gz 2av9A:Skipped atom 226, because occupancy 0.500 <= existing 0.500 in 2av9A Skipped atom 230, because occupancy 0.500 <= existing 0.500 in 2av9A Skipped atom 232, because occupancy 0.500 <= existing 0.500 in 2av9A Skipped atom 234, because occupancy 0.500 <= existing 0.500 in 2av9A Skipped atom 236, because occupancy 0.500 <= existing 0.500 in 2av9A Skipped atom 238, because occupancy 0.500 <= existing 0.500 in 2av9A Skipped atom 240, because occupancy 0.500 <= existing 0.500 in 2av9A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0322 read from 2av9A/merged-good-all-a2m # 2av9A read from 2av9A/merged-good-all-a2m # adding 2av9A to template set # found chain 2av9A in template set Warning: unaligning (T0322)K99 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2av9A)F78 Warning: unaligning (T0322)L100 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2av9A)F78 T0322 26 :FGRQ 2av9A 9 :REQY T0322 33 :LFEH 2av9A 13 :LHFQ T0322 46 :AFRVEEHHTNGLGNCHGGMLMSFADMAWGRIISLQKSY 2av9A 17 :PISTRWHDNDIYGHVNNVTYYAFFDTAVNTYLIERGGL T0322 84 :SWVTVRLMCDFLSGA 2av9A 62 :IGLVVSSSCDYFAPV T0322 101 :GDWVEGEGELISEEDMLFTVRGRIWAGE 2av9A 79 :PQRIEMGLRVARLGNSSVQYELALFLEG T0322 129 :RTLITGTGVFKALSARKPRP 2av9A 109 :EACAAGRFVHVFVERRSSRP T0322 149 :GELAY 2av9A 133 :QELRD Number of specific fragments extracted= 7 number of extra gaps= 1 total=359 Number of alignments=67 # 2av9A read from 2av9A/merged-good-all-a2m # found chain 2av9A in template set Warning: unaligning (T0322)D3 because first residue in template chain is (2av9A)P5 Warning: unaligning (T0322)K99 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2av9A)F78 Warning: unaligning (T0322)L100 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2av9A)F78 T0322 4 :DLTDAQT 2av9A 6 :RPLREQY T0322 33 :LFEHREG 2av9A 13 :LHFQPIS T0322 49 :VEEHHTNGLGNCHGGMLMSFADMAWGRIISLQ 2av9A 20 :TRWHDNDIYGHVNNVTYYAFFDTAVNTYLIER T0322 81 :KS 2av9A 57 :QG T0322 83 :YSWVTVRLMCDFLSGA 2av9A 61 :VIGLVVSSSCDYFAPV T0322 101 :GDWVEGEGELISEEDMLFTVRGRIWAGE 2av9A 79 :PQRIEMGLRVARLGNSSVQYELALFLEG T0322 129 :RTLITGTGVFKALSARKPRPGELAYK 2av9A 109 :EACAAGRFVHVFVERRSSRPVAIPQE Number of specific fragments extracted= 7 number of extra gaps= 1 total=366 Number of alignments=68 # 2av9A read from 2av9A/merged-good-all-a2m # found chain 2av9A in template set Warning: unaligning (T0322)S23 because first residue in template chain is (2av9A)P5 Warning: unaligning (T0322)K99 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2av9A)F78 Warning: unaligning (T0322)L100 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2av9A)F78 T0322 24 :RGFGRQIGPLFEHR 2av9A 6 :RPLREQYLHFQPIS T0322 49 :VEEHHTNGLGNC 2av9A 20 :TRWHDNDIYGHV T0322 64 :MLMSFADMAWGRIISLQK 2av9A 35 :TYYAFFDTAVNTYLIERG T0322 82 :SYSWVTVRLMCDFLSGA 2av9A 60 :EVIGLVVSSSCDYFAPV T0322 101 :GDWVEGEGELISEEDMLFTVRGRIWAGERTL 2av9A 79 :PQRIEMGLRVARLGNSSVQYELALFLEGQRE T0322 132 :ITGTGVFKALSARKPRPGE 2av9A 112 :AAGRFVHVFVERRSSRPVA T0322 151 :LAYKEE 2av9A 133 :QELRDA Number of specific fragments extracted= 7 number of extra gaps= 1 total=373 Number of alignments=69 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1sbkA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0322/1sbkA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0322/1sbkA/merged-good-all-a2m.gz for input Trying 1sbkA/merged-good-all-a2m Error: Couldn't open file 1sbkA/merged-good-all-a2m or 1sbkA/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 2cwzA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2cwzA expands to /projects/compbio/data/pdb/2cwz.pdb.gz 2cwzA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0322 read from 2cwzA/merged-good-all-a2m # 2cwzA read from 2cwzA/merged-good-all-a2m # adding 2cwzA to template set # found chain 2cwzA in template set T0322 38 :EGPG 2cwzA 4 :IPEG T0322 42 :QARLAFRVEEHHT 2cwzA 9 :EAVFETVVTPEMT T0322 55 :NGLGNCHGGMLMSFADMAWGRIISLQKSY 2cwzA 29 :PVHPVYATYWMVKHMELAGRKIILPFLEE T0322 84 :SWVTVRLMCDFLSGAKLGDWVEGEGELISEEDMLFTVRGRIWAG 2cwzA 60 :EGIGSYVEARHLASALPGMRVRVVARHEKTEGNRVYARVEAYNE T0322 128 :ERTLITGTGVFKALSA 2cwzA 105 :GDLIGVGRTEQVILPK T0322 150 :ELAYKEE 2cwzA 121 :AKVEALF Number of specific fragments extracted= 6 number of extra gaps= 0 total=379 Number of alignments=70 # 2cwzA read from 2cwzA/merged-good-all-a2m # found chain 2cwzA in template set T0322 39 :GPG 2cwzA 5 :PEG T0322 42 :QARLAFRVEEHHT 2cwzA 9 :EAVFETVVTPEMT T0322 55 :NGLGNCHGGMLMSFADMAWGRIISLQ 2cwzA 29 :PVHPVYATYWMVKHMELAGRKIILPF T0322 81 :KSYSWVTVRLMCDFLSGAKLGDWVEGEGELISEEDMLFTVRGRIWAG 2cwzA 57 :EGEEGIGSYVEARHLASALPGMRVRVVARHEKTEGNRVYARVEAYNE T0322 128 :ERTLITGTGVFKALS 2cwzA 105 :GDLIGVGRTEQVILP Number of specific fragments extracted= 5 number of extra gaps= 0 total=384 Number of alignments=71 # 2cwzA read from 2cwzA/merged-good-all-a2m # found chain 2cwzA in template set T0322 38 :EGPGQARLAFRVEEHHT 2cwzA 5 :PEGYEAVFETVVTPEMT T0322 64 :MLMSFADMAWGRIISLQK 2cwzA 38 :WMVKHMELAGRKIILPFL T0322 82 :SYSWVTVRLMCDFLSGAKLGDWVEGEGELISEEDMLFTVRGRIWAGERTLITGTGVFKALSA 2cwzA 58 :GEEGIGSYVEARHLASALPGMRVRVVARHEKTEGNRVYARVEAYNELGDLIGVGRTEQVILP T0322 150 :ELAYKEE 2cwzA 120 :KAKVEAL Number of specific fragments extracted= 4 number of extra gaps= 0 total=388 Number of alignments=72 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2gvhA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2gvhA expands to /projects/compbio/data/pdb/2gvh.pdb.gz 2gvhA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0322 read from 2gvhA/merged-good-all-a2m # 2gvhA read from 2gvhA/merged-good-all-a2m # adding 2gvhA to template set # found chain 2gvhA in template set Warning: unaligning (T0322)P40 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2gvhA)A147 Warning: unaligning (T0322)Q42 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2gvhA)A147 Warning: unaligning (T0322)S142 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2gvhA)R258 Warning: unaligning (T0322)P146 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2gvhA)R258 T0322 27 :GRQIGPLFEHREG 2gvhA 130 :SYVLPELLTEETP T0322 43 :ARLAFRVEEHHTNGLGNCHGGMLMSFADMAWGRIISLQKSYSWVTVRLM 2gvhA 148 :VTMVEIVFPDQANSAGRMFGGEAIAYMTKAAFVAASRYCGKLVVLASSE T0322 92 :CDFLSGAKLGDWVEGEGELISEEDMLFTVRGRIWA 2gvhA 198 :IDFARAIEIGEIVEAQAHVERVGRSSMSIQTKLWS T0322 127 :G 2gvhA 237 :T T0322 130 :TLITGTGVFKAL 2gvhA 242 :ITATGHFTMVAV T0322 147 :RP 2gvhA 259 :PA Number of specific fragments extracted= 6 number of extra gaps= 0 total=394 Number of alignments=73 # 2gvhA read from 2gvhA/merged-good-all-a2m # found chain 2gvhA in template set Warning: unaligning (T0322)E38 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2gvhA)A147 Warning: unaligning (T0322)Q42 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2gvhA)A147 Warning: unaligning (T0322)S142 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2gvhA)R258 Warning: unaligning (T0322)P146 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2gvhA)R258 T0322 5 :LTDAQTAAI 2gvhA 123 :PEGEDAASY T0322 23 :SRGFGRQIG 2gvhA 132 :VLPELLTEE T0322 34 :F 2gvhA 141 :T T0322 37 :R 2gvhA 142 :P T0322 43 :ARLAFRVEEHHTNGLGNCHGGMLMSFADMAWGRIISLQKSYSWVTVRLM 2gvhA 148 :VTMVEIVFPDQANSAGRMFGGEAIAYMTKAAFVAASRYCGKLVVLASSE T0322 92 :CDFLSGAKLGDWVEGEGELISEEDMLFTVRGRIWA 2gvhA 198 :IDFARAIEIGEIVEAQAHVERVGRSSMSIQTKLWS T0322 128 :E 2gvhA 237 :T T0322 129 :RTLITGTGVFKAL 2gvhA 241 :HITATGHFTMVAV T0322 147 :RPG 2gvhA 259 :PAT Number of specific fragments extracted= 9 number of extra gaps= 0 total=403 Number of alignments=74 # 2gvhA read from 2gvhA/merged-good-all-a2m # found chain 2gvhA in template set Warning: unaligning (T0322)Q42 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2gvhA)A147 Warning: unaligning (T0322)A143 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2gvhA)R258 Warning: unaligning (T0322)R147 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2gvhA)R258 T0322 25 :GFGRQIGPLFEHREGP 2gvhA 127 :DAASYVLPELLTEETP T0322 43 :ARLAFRVEEHHTNGLGNCHGGMLMSFADMAWGRIISLQKSYSWVTVRLM 2gvhA 148 :VTMVEIVFPDQANSAGRMFGGEAIAYMTKAAFVAASRYCGKLVVLASSE T0322 92 :CDFLSGAKLGDWVEGEGELISEEDMLFTVRGRIW 2gvhA 198 :IDFARAIEIGEIVEAQAHVERVGRSSMSIQTKLW T0322 126 :AGERTLITGTGVFKALS 2gvhA 237 :TGERHITATGHFTMVAV Number of specific fragments extracted= 4 number of extra gaps= 0 total=407 Number of alignments=75 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ixlA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1ixlA expands to /projects/compbio/data/pdb/1ixl.pdb.gz 1ixlA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0322 read from 1ixlA/merged-good-all-a2m # 1ixlA read from 1ixlA/merged-good-all-a2m # adding 1ixlA to template set # found chain 1ixlA in template set Warning: unaligning (T0322)R147 because last residue in template chain is (1ixlA)D130 T0322 15 :EGFSQLNW 1ixlA 10 :KLTSRILV T0322 33 :LFEHREGPGQARLAFRVEEHHT 1ixlA 18 :GKPILIKEGYAEVELETIDEMK T0322 55 :NGLGNCHGGMLMSFADMAWGRIIS 1ixlA 41 :DEKGLVHGGFTFGLADYAAMLAVN T0322 82 :SYSWVTVRLMCDFLSGAKLGDWVEGEGELISEEDMLFTVRGRIWAGERTLITGTGVFKALSARKP 1ixlA 65 :EPTVVLGKAEVRFTKPVKVGDKLVAKAKIIEDLGKKKIVEVKVYREEEVVLEGKFYCYVLEKHVL Number of specific fragments extracted= 4 number of extra gaps= 0 total=411 Number of alignments=76 # 1ixlA read from 1ixlA/merged-good-all-a2m # found chain 1ixlA in template set Warning: unaligning (T0322)R147 because last residue in template chain is (1ixlA)D130 T0322 4 :DLTDAQT 1ixlA 11 :LTSRILV T0322 33 :LFEHREGPGQARLAFRVEEHH 1ixlA 18 :GKPILIKEGYAEVELETIDEM T0322 54 :TNGLGNCHGGMLMSFADMAWGRIIS 1ixlA 40 :VDEKGLVHGGFTFGLADYAAMLAVN T0322 82 :SYSWVTVRLMCDFLSGAKLGDWVEGEGELISEEDMLFTVRGRIWAGERTLITGTGVFKALSARKP 1ixlA 65 :EPTVVLGKAEVRFTKPVKVGDKLVAKAKIIEDLGKKKIVEVKVYREEEVVLEGKFYCYVLEKHVL Number of specific fragments extracted= 4 number of extra gaps= 0 total=415 Number of alignments=77 # 1ixlA read from 1ixlA/merged-good-all-a2m # found chain 1ixlA in template set T0322 33 :LFEHREGPGQARLAFRVEEHHT 1ixlA 18 :GKPILIKEGYAEVELETIDEMK T0322 55 :NGLGNCHGGMLMSFADMAWGRIISLQ 1ixlA 41 :DEKGLVHGGFTFGLADYAAMLAVNEP T0322 84 :SWVTVRLMCDFLSGAKLGDWVEGEGELISEEDMLFTVRGRIWAGERTLITGTGVFKALSAR 1ixlA 67 :TVVLGKAEVRFTKPVKVGDKLVAKAKIIEDLGKKKIVEVKVYREEEVVLEGKFYCYVLEKH Number of specific fragments extracted= 3 number of extra gaps= 0 total=418 Number of alignments=78 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2gf6A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2gf6A expands to /projects/compbio/data/pdb/2gf6.pdb.gz 2gf6A:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0322 read from 2gf6A/merged-good-all-a2m # 2gf6A read from 2gf6A/merged-good-all-a2m # adding 2gf6A to template set # found chain 2gf6A in template set Warning: unaligning (T0322)L141 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2gf6A)N114 Warning: unaligning (T0322)S142 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2gf6A)N114 T0322 44 :RLAFRVEEHHTNGLGNCHGGMLMSFADMAWGRIISLQKSY 2gf6A 7 :VFEDVVRIYDTDAQGIAHYAAYYRFFTNTIEKFIKEKVGI T0322 84 :SWVTVRLMCDFLSGAKLGDWVEGEGELISEEDMLFTVRGRIWAGERTLITGTGVFKA 2gf6A 56 :WFVIAESHAIYHRPVKLGDKLTVLLNPKILSNKTIKFEFKVLKDGELTTEGYVIQIA T0322 143 :ARKPRP 2gf6A 115 :PKIWKS T0322 149 :GELAYKE 2gf6A 125 :KEIMDKL Number of specific fragments extracted= 4 number of extra gaps= 1 total=422 Number of alignments=79 # 2gf6A read from 2gf6A/merged-good-all-a2m # found chain 2gf6A in template set Warning: unaligning (T0322)L141 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2gf6A)N114 Warning: unaligning (T0322)S142 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2gf6A)N114 T0322 44 :RLAFRVEEHHTNGLGNCHGGMLMSFADMAWGRIISLQ 2gf6A 7 :VFEDVVRIYDTDAQGIAHYAAYYRFFTNTIEKFIKEK T0322 81 :KSYSWVTVRLMCDFLSGAKLGDWVEGEGELISEEDMLFTVRGRIWAGERTLITGTGVFKA 2gf6A 53 :ENLWFVIAESHAIYHRPVKLGDKLTVLLNPKILSNKTIKFEFKVLKDGELTTEGYVIQIA T0322 143 :ARKPRPGELAYK 2gf6A 115 :PKIWKSTEMPKE Number of specific fragments extracted= 3 number of extra gaps= 1 total=425 Number of alignments=80 # 2gf6A read from 2gf6A/merged-good-all-a2m # found chain 2gf6A in template set Warning: unaligning (T0322)L141 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2gf6A)N114 Warning: unaligning (T0322)S142 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2gf6A)N114 T0322 44 :RLAFRVEEHHTNGLGNCHGGMLMSFADMAWGRIISLQK 2gf6A 7 :VFEDVVRIYDTDAQGIAHYAAYYRFFTNTIEKFIKEKV T0322 82 :SYSWVTVRLMCDFLSGAKLGDWVEGEGELISEEDMLFTVRGRIWAGERTLITGTGVFKA 2gf6A 54 :NLWFVIAESHAIYHRPVKLGDKLTVLLNPKILSNKTIKFEFKVLKDGELTTEGYVIQIA T0322 143 :ARK 2gf6A 115 :PKI Number of specific fragments extracted= 3 number of extra gaps= 1 total=428 Number of alignments=81 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1iq6A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0322 read from 1iq6A/merged-good-all-a2m # 1iq6A read from 1iq6A/merged-good-all-a2m # found chain 1iq6A in training set T0322 56 :GLGNCHGGMLMSFA 1iq6A 48 :ERPIVHGMLLASLF T0322 73 :WGRIISLQKSYSWVTVRLMCDFLSGAKLGDWVEGEGELISE 1iq6A 62 :SGLLGQQLPGKGSIYLGQSLSFKLPVFVGDEVTAEVEVTAL T0322 114 :EDMLFTVRGRIWA 1iq6A 105 :DKPIATLTTRIFT T0322 127 :GERTLITGTGVFK 1iq6A 119 :GGALAVTGEAVVK Number of specific fragments extracted= 4 number of extra gaps= 0 total=432 Number of alignments=82 # 1iq6A read from 1iq6A/merged-good-all-a2m # found chain 1iq6A in training set T0322 54 :TNGLGNCHGGMLMSFADMAWG 1iq6A 46 :AFERPIVHGMLLASLFSGLLG T0322 78 :SLQKSYSWVTVRLMCDFLSGAKLGDWVEGEGELIS 1iq6A 67 :QQLPGKGSIYLGQSLSFKLPVFVGDEVTAEVEVTA T0322 113 :EEDMLFTVRGRIWA 1iq6A 104 :EDKPIATLTTRIFT T0322 127 :GERTLITGTGVFKA 1iq6A 119 :GGALAVTGEAVVKL Number of specific fragments extracted= 4 number of extra gaps= 0 total=436 Number of alignments=83 # 1iq6A read from 1iq6A/merged-good-all-a2m # found chain 1iq6A in training set T0322 59 :NCHGGMLMS 1iq6A 51 :IVHGMLLAS T0322 72 :AWGRIISLQK 1iq6A 60 :LFSGLLGQQL T0322 82 :SYSWV 1iq6A 73 :GSIYL T0322 89 :RLMCDFLSGAKLGDWVEGEGELIS 1iq6A 78 :GQSLSFKLPVFVGDEVTAEVEVTA T0322 113 :EEDMLFTVRGRIWAGERTLITGTGVFKA 1iq6A 104 :EDKPIATLTTRIFTQGGALAVTGEAVVK Number of specific fragments extracted= 5 number of extra gaps= 0 total=441 Number of alignments=84 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1sh8A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0322 read from 1sh8A/merged-good-all-a2m # 1sh8A read from 1sh8A/merged-good-all-a2m # found chain 1sh8A in training set T0322 18 :SQLNWSRGFGRQIG 1sh8A 10 :HLTEEKIAFVQRSG T0322 33 :LFEHREGPGQARLAFR 1sh8A 24 :LRAEVLEPGYVRLRMP T0322 50 :EEHHTNGLGNCHGGMLMSFADMAWGRIISLQKSY 1sh8A 40 :GAGNENHIGSMYAGALFTLAELPGGALFLTSFDS T0322 84 :SWVTVRLMCDFLSGAK 1sh8A 77 :YPIVKEMTLRFRRPAK T0322 101 :GD 1sh8A 93 :GD T0322 104 :VEGEGEL 1sh8A 95 :IRVEARL T0322 114 :EDMLFTVRGRIWA 1sh8A 117 :GKAEYSLELQLTD T0322 127 :GERTLITGTGVFKALSARKPR 1sh8A 131 :QGEVVAESAALYQLRSHARPG Number of specific fragments extracted= 8 number of extra gaps= 0 total=449 Number of alignments=85 # 1sh8A read from 1sh8A/merged-good-all-a2m # found chain 1sh8A in training set T0322 10 :TAAIPEGFSQLNWSRGFGRQIG 1sh8A 2 :PLPTELARHLTEEKIAFVQRSG T0322 33 :LFEHREGPGQARLAFR 1sh8A 24 :LRAEVLEPGYVRLRMP T0322 50 :EEHHTNGLGNCHGGMLMSFADMAWGRIISLQ 1sh8A 40 :GAGNENHIGSMYAGALFTLAELPGGALFLTS T0322 81 :KSYSWVTVRLMCDFLSGAK 1sh8A 74 :ARFYPIVKEMTLRFRRPAK T0322 101 :GD 1sh8A 93 :GD T0322 104 :VEGEGELIS 1sh8A 95 :IRVEARLDA T0322 113 :EEDMLFTVRGRIWA 1sh8A 116 :RGKAEYSLELQLTD T0322 127 :GERTLITGTGVFKALSARKP 1sh8A 131 :QGEVVAESAALYQLRSHARP Number of specific fragments extracted= 8 number of extra gaps= 0 total=457 Number of alignments=86 # 1sh8A read from 1sh8A/merged-good-all-a2m # found chain 1sh8A in training set T0322 7 :DAQTAAIPEGFSQL 1sh8A 2 :PLPTELARHLTEEK T0322 25 :GFGRQIGPLFEHREGPGQARLAFR 1sh8A 16 :IAFVQRSGLRAEVLEPGYVRLRMP T0322 50 :EEHHTNGLGNCHGGMLMSFADMAWGRIISLQK 1sh8A 40 :GAGNENHIGSMYAGALFTLAELPGGALFLTSF T0322 82 :SYSWVTVRLMCDFLSGAK 1sh8A 75 :RFYPIVKEMTLRFRRPAK T0322 101 :GD 1sh8A 93 :GD T0322 104 :VEGEGE 1sh8A 95 :IRVEAR T0322 114 :EDMLFTVRGRIWAGERTLITGTGVFKALSA 1sh8A 117 :GKAEYSLELQLTDEQGEVVAESAALYQLRS T0322 145 :KPRPG 1sh8A 147 :HARPG Number of specific fragments extracted= 8 number of extra gaps= 0 total=465 Number of alignments=87 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2b6eA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2b6eA expands to /projects/compbio/data/pdb/2b6e.pdb.gz 2b6eA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0322 read from 2b6eA/merged-good-all-a2m # 2b6eA read from 2b6eA/merged-good-all-a2m # adding 2b6eA to template set # found chain 2b6eA in template set Warning: unaligning (T0322)S142 because last residue in template chain is (2b6eA)N137 T0322 17 :FSQLNW 2b6eA 12 :LNQLCS T0322 24 :RGFGRQIG 2b6eA 18 :NSAVSHLG T0322 33 :LFEHREGPGQARLAFRVEEHHTNGLGNCHGGMLMSFADMAWGRIISLQKSY 2b6eA 26 :IEISAFGEDWIEATMPVDHRTMQPFGVLHGGVSVALAETIGSLAGSLCLEE T0322 84 :SWVTVRLMCDFLSGAKLG 2b6eA 79 :TVVGLDINANHLRPVRSG T0322 103 :WVEGEGELISEEDMLFTVRGRIWA 2b6eA 97 :KVTARATPINLGRNIQVWQIDIRT T0322 127 :GERTLITGTGVFKAL 2b6eA 122 :ENKLCCVSRLTLSVI Number of specific fragments extracted= 6 number of extra gaps= 0 total=471 Number of alignments=88 # 2b6eA read from 2b6eA/merged-good-all-a2m # found chain 2b6eA in template set Warning: unaligning (T0322)S142 because last residue in template chain is (2b6eA)N137 T0322 8 :AQTAAIPEGFSQLN 2b6eA 4 :KKTFTLENLNQLCS T0322 24 :RGFGRQIG 2b6eA 18 :NSAVSHLG T0322 33 :LFEHREGPGQARLAFRVEEHHTNGLGNCHGGMLMSFADMAWGRIISLQ 2b6eA 26 :IEISAFGEDWIEATMPVDHRTMQPFGVLHGGVSVALAETIGSLAGSLC T0322 81 :KSYSWVTVRLMCDFLSGAKLG 2b6eA 76 :EGKTVVGLDINANHLRPVRSG T0322 103 :WVEGEGELISEEDMLFTVRGRIWA 2b6eA 97 :KVTARATPINLGRNIQVWQIDIRT T0322 127 :GERTLITGTGVFKAL 2b6eA 122 :ENKLCCVSRLTLSVI Number of specific fragments extracted= 6 number of extra gaps= 0 total=477 Number of alignments=89 # 2b6eA read from 2b6eA/merged-good-all-a2m # found chain 2b6eA in template set Warning: unaligning (T0322)A143 because last residue in template chain is (2b6eA)N137 T0322 6 :TDAQTAAIPEGF 2b6eA 5 :KTFTLENLNQLC T0322 24 :RGFGRQIGPLFEHREGPGQARLAFRVEEHHTNGLGNCHGGMLMSFADMAWGRIISLQK 2b6eA 17 :SNSAVSHLGIEISAFGEDWIEATMPVDHRTMQPFGVLHGGVSVALAETIGSLAGSLCL T0322 82 :SYSWVTVRLMCDFLSGAK 2b6eA 77 :GKTVVGLDINANHLRPVR T0322 101 :GDWVEGEGELISEEDMLFTVRGRIWAGERTLITGTGVFKALS 2b6eA 95 :SGKVTARATPINLGRNIQVWQIDIRTEENKLCCVSRLTLSVI Number of specific fragments extracted= 4 number of extra gaps= 0 total=481 Number of alignments=90 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1vh5A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0322 read from 1vh5A/merged-good-all-a2m # 1vh5A read from 1vh5A/merged-good-all-a2m # found chain 1vh5A in training set Warning: unaligning (T0322)S142 because last residue in template chain is (1vh5A)E137 T0322 16 :GFSQLNW 1vh5A 11 :ALNAMGE T0322 24 :RGFGRQIG 1vh5A 18 :GNMVGFLD T0322 33 :LFEHREGPGQARLAFRVEEHHTNGLGNCHGGMLMSFADMAWGRIISLQKSY 1vh5A 26 :IRFEHIGDDTLEATMPVDSRTKQPFGLLHGGASVVLAESIGSVAGYLCTEG T0322 84 :SWVTVRLMCDFLSGAKLG 1vh5A 79 :KVVGLEINANHVRSAREG T0322 103 :WVEGEGELISEEDMLFTVRGRIWA 1vh5A 97 :RVRGVCKPLHLGSRHQVWQIEIFD T0322 127 :GERTLITGTGVFKAL 1vh5A 122 :KGRLCCSSRLTTAIL Number of specific fragments extracted= 6 number of extra gaps= 0 total=487 Number of alignments=91 # 1vh5A read from 1vh5A/merged-good-all-a2m # found chain 1vh5A in training set Warning: unaligning (T0322)S2 because first residue in template chain is (1vh5A)S0 Warning: unaligning (T0322)S142 because last residue in template chain is (1vh5A)E137 T0322 3 :DDLTD 1vh5A 1 :LIWKR T0322 10 :TAAIPEGFSQLN 1vh5A 6 :KITLEALNAMGE T0322 24 :RGFGRQIG 1vh5A 18 :GNMVGFLD T0322 33 :LFEHREGPGQARLAFRVEEHHTNGLGNCHGGMLMSFADMAWGRIISLQ 1vh5A 26 :IRFEHIGDDTLEATMPVDSRTKQPFGLLHGGASVVLAESIGSVAGYLC T0322 81 :KSYSWVTVRLMCDFLSGAKLG 1vh5A 76 :GEQKVVGLEINANHVRSAREG T0322 103 :WVEGEGELISEEDMLFTVRGRIWAG 1vh5A 97 :RVRGVCKPLHLGSRHQVWQIEIFDE T0322 128 :ERTLITGTGVFKAL 1vh5A 123 :GRLCCSSRLTTAIL Number of specific fragments extracted= 7 number of extra gaps= 0 total=494 Number of alignments=92 # 1vh5A read from 1vh5A/merged-good-all-a2m # found chain 1vh5A in training set Warning: unaligning (T0322)A143 because last residue in template chain is (1vh5A)E137 T0322 22 :WSRGFGRQIGPLFEHREGPGQARLAFRVEEHHTNGLGNCHGGMLMSFADMAWGRIISLQK 1vh5A 15 :MGEGNMVGFLDIRFEHIGDDTLEATMPVDSRTKQPFGLLHGGASVVLAESIGSVAGYLCT T0322 82 :SYSWVTVRLMCDFLSGAK 1vh5A 77 :EQKVVGLEINANHVRSAR T0322 101 :GDWVEGEGELISEEDMLFTVRGRIWAGERTLITGTGVFKALS 1vh5A 95 :EGRVRGVCKPLHLGSRHQVWQIEIFDEKGRLCCSSRLTTAIL Number of specific fragments extracted= 3 number of extra gaps= 0 total=497 Number of alignments=93 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2fs2A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2fs2A expands to /projects/compbio/data/pdb/2fs2.pdb.gz 2fs2A:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0322 read from 2fs2A/merged-good-all-a2m # 2fs2A read from 2fs2A/merged-good-all-a2m # adding 2fs2A to template set # found chain 2fs2A in template set Warning: unaligning (T0322)F47 because of BadResidue code BAD_PEPTIDE in next template residue (2fs2A)T39 Warning: unaligning (T0322)R48 because of BadResidue code BAD_PEPTIDE at template residue (2fs2A)T39 Warning: unaligning (T0322)C92 because of BadResidue code BAD_PEPTIDE in next template residue (2fs2A)D83 Warning: unaligning (T0322)D93 because of BadResidue code BAD_PEPTIDE at template residue (2fs2A)D83 Warning: unaligning (T0322)G134 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2fs2A)R126 Warning: unaligning (T0322)T135 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2fs2A)R126 Warning: unaligning (T0322)K139 because of BadResidue code BAD_PEPTIDE in next template residue (2fs2A)R131 Warning: unaligning (T0322)A140 because of BadResidue code BAD_PEPTIDE at template residue (2fs2A)R131 T0322 25 :GFGRQIG 2fs2A 17 :ACAKALG T0322 33 :LFEHREGPGQARLA 2fs2A 24 :IDIISMDEGFAVVT T0322 49 :VEEHHTNGLGNCHGGMLMSFADMAWGRIISLQ 2fs2A 40 :VTAQMLNGHQSCHGGQLFSLADTAFAYACNSQ T0322 82 :SYSWVTVRLM 2fs2A 72 :GLAAVASACT T0322 94 :FLSGAKLGDWVEGEGELISEEDMLFTVRGRIWA 2fs2A 84 :FLRPGFAGDTLTATAQVRHQGKQTGVYDIEIVN T0322 127 :GERTLIT 2fs2A 118 :QQKTVAL T0322 136 :GVF 2fs2A 127 :GKS Number of specific fragments extracted= 7 number of extra gaps= 4 total=504 Number of alignments=94 # 2fs2A read from 2fs2A/merged-good-all-a2m # found chain 2fs2A in template set Warning: unaligning (T0322)F47 because of BadResidue code BAD_PEPTIDE in next template residue (2fs2A)T39 Warning: unaligning (T0322)R48 because of BadResidue code BAD_PEPTIDE at template residue (2fs2A)T39 Warning: unaligning (T0322)C92 because of BadResidue code BAD_PEPTIDE in next template residue (2fs2A)D83 Warning: unaligning (T0322)D93 because of BadResidue code BAD_PEPTIDE at template residue (2fs2A)D83 Warning: unaligning (T0322)G134 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2fs2A)R126 Warning: unaligning (T0322)T135 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2fs2A)R126 Warning: unaligning (T0322)K139 because of BadResidue code BAD_PEPTIDE in next template residue (2fs2A)R131 Warning: unaligning (T0322)A140 because of BadResidue code BAD_PEPTIDE at template residue (2fs2A)R131 T0322 14 :PEGFSQLN 2fs2A 16 :DACAKALG T0322 33 :LFEHREGPGQARLA 2fs2A 24 :IDIISMDEGFAVVT T0322 49 :VEEHHTNGLGNCHGGMLMSFADMAWGRIISLQ 2fs2A 40 :VTAQMLNGHQSCHGGQLFSLADTAFAYACNSQ T0322 82 :SYSWVTVRLM 2fs2A 72 :GLAAVASACT T0322 94 :FLSGAKLGDWVEGEGELISEEDMLFTVRGRIWA 2fs2A 84 :FLRPGFAGDTLTATAQVRHQGKQTGVYDIEIVN T0322 127 :GERTLIT 2fs2A 118 :QQKTVAL T0322 136 :GVF 2fs2A 127 :GKS Number of specific fragments extracted= 7 number of extra gaps= 4 total=511 Number of alignments=95 # 2fs2A read from 2fs2A/merged-good-all-a2m # found chain 2fs2A in template set Warning: unaligning (T0322)T10 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2fs2A)L1 Warning: unaligning (T0322)F47 because of BadResidue code BAD_PEPTIDE in next template residue (2fs2A)T39 Warning: unaligning (T0322)R48 because of BadResidue code BAD_PEPTIDE at template residue (2fs2A)T39 Warning: unaligning (T0322)C92 because of BadResidue code BAD_PEPTIDE in next template residue (2fs2A)D83 Warning: unaligning (T0322)D93 because of BadResidue code BAD_PEPTIDE at template residue (2fs2A)D83 Warning: unaligning (T0322)T135 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2fs2A)R126 Warning: unaligning (T0322)G136 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2fs2A)R126 Warning: unaligning (T0322)A140 because of BadResidue code BAD_PEPTIDE in next template residue (2fs2A)R131 Warning: unaligning (T0322)L141 because of BadResidue code BAD_PEPTIDE at template residue (2fs2A)R131 T0322 11 :AAIPEGFSQLNWSRGFGRQIGPLFEHREGPGQARLA 2fs2A 2 :SHKAWQNAHAMYENDACAKALGIDIISMDEGFAVVT T0322 49 :VEEHHTNGLGNCHGGMLMSFADMAWGRIISLQ 2fs2A 40 :VTAQMLNGHQSCHGGQLFSLADTAFAYACNSQ T0322 82 :SYSWVTVRLM 2fs2A 72 :GLAAVASACT T0322 94 :FLSGAKLGDWVEGEGELISEEDMLFTVRGRIWAGERTLITG 2fs2A 84 :FLRPGFAGDTLTATAQVRHQGKQTGVYDIEIVNQQQKTVAL T0322 137 :VFK 2fs2A 127 :GKS Number of specific fragments extracted= 5 number of extra gaps= 5 total=516 Number of alignments=96 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1c8uA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1c8uA expands to /projects/compbio/data/pdb/1c8u.pdb.gz 1c8uA:# T0322 read from 1c8uA/merged-good-all-a2m # 1c8uA read from 1c8uA/merged-good-all-a2m # adding 1c8uA to template set # found chain 1c8uA in template set Warning: unaligning (T0322)G56 because of BadResidue code BAD_PEPTIDE in next template residue (1c8uA)G30 Warning: unaligning (T0322)L57 because of BadResidue code BAD_PEPTIDE at template residue (1c8uA)G30 Warning: unaligning (T0322)G58 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1c8uA)R32 T0322 20 :LNWS 1c8uA 8 :LLTL T0322 33 :LFEHREGPGQARL 1c8uA 12 :LNLEKIEEGLFRG T0322 51 :E 1c8uA 25 :Q T0322 53 :HTN 1c8uA 26 :SED T0322 59 :NCHGGMLMSFA 1c8uA 33 :QVFGGQVVGQA T0322 74 :GRIISLQKSYSWVTVRLMCDFLSGAKLGDWVEGEGELISEEDMLFTVRGRIWAGERTLITGTGVFKALSARKP 1c8uA 44 :LYAAKETVPEERLVHSFHSYFLRPGDSKKPIIYDVETLRDGNSFSARRVAAIQNGKPIFYMTASFQAPEAGFE T0322 149 :GELAYKEEA 1c8uA 145 :PPVLKDKFI Number of specific fragments extracted= 7 number of extra gaps= 2 total=523 Number of alignments=97 # 1c8uA read from 1c8uA/merged-good-all-a2m # found chain 1c8uA in template set Warning: unaligning (T0322)N55 because of BadResidue code BAD_PEPTIDE in next template residue (1c8uA)G30 Warning: unaligning (T0322)G56 because of BadResidue code BAD_PEPTIDE at template residue (1c8uA)G30 Warning: unaligning (T0322)L57 because of BadResidue code BAD_PEPTIDE at template residue (1c8uA)L31 Warning: unaligning (T0322)G58 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1c8uA)R32 T0322 13 :IPEGFSQLN 1c8uA 5 :LKNLLTLLN T0322 35 :EHREGPGQARL 1c8uA 14 :LEKIEEGLFRG T0322 48 :RVE 1c8uA 25 :QSE T0322 54 :T 1c8uA 28 :D T0322 59 :NCHGGMLMSF 1c8uA 33 :QVFGGQVVGQ T0322 72 :AWGRIISLQKS 1c8uA 43 :ALYAAKETVPE T0322 85 :WVTVRLMCDFLSGAKLGDWVEGEGELISEEDMLFTVRGRIWAGERTLITGTGVFKALSARKPR 1c8uA 55 :RLVHSFHSYFLRPGDSKKPIIYDVETLRDGNSFSARRVAAIQNGKPIFYMTASFQAPEAGFEH T0322 148 :PGELA 1c8uA 123 :SAPAP Number of specific fragments extracted= 8 number of extra gaps= 1 total=531 Number of alignments=98 # 1c8uA read from 1c8uA/merged-good-all-a2m # found chain 1c8uA in template set Warning: unaligning (T0322)N55 because of BadResidue code BAD_PEPTIDE in next template residue (1c8uA)G30 Warning: unaligning (T0322)G56 because of BadResidue code BAD_PEPTIDE at template residue (1c8uA)G30 Warning: unaligning (T0322)L57 because of BadResidue code BAD_PEPTIDE at template residue (1c8uA)L31 Warning: unaligning (T0322)G58 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1c8uA)R32 T0322 36 :HREGPGQARL 1c8uA 15 :EKIEEGLFRG T0322 51 :EHHT 1c8uA 25 :QSED T0322 59 :NCHGGMLMSFA 1c8uA 33 :QVFGGQVVGQA T0322 73 :WGRIISLQK 1c8uA 44 :LYAAKETVP T0322 82 :SYSWV 1c8uA 54 :ERLVH T0322 89 :RLMCDFLSGAKLGDWVEGEGELISEEDMLFTVRGRIWAGERTLITGTGVFKA 1c8uA 59 :SFHSYFLRPGDSKKPIIYDVETLRDGNSFSARRVAAIQNGKPIFYMTASFQA Number of specific fragments extracted= 6 number of extra gaps= 1 total=537 Number of alignments=99 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1vh9A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0322/1vh9A/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0322/1vh9A/merged-good-all-a2m.gz for input Trying 1vh9A/merged-good-all-a2m Error: Couldn't open file 1vh9A/merged-good-all-a2m or 1vh9A/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 2essA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2essA expands to /projects/compbio/data/pdb/2ess.pdb.gz 2essA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 3, because occupancy 0.500 <= existing 0.500 in 2essA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 7, because occupancy 0.500 <= existing 0.500 in 2essA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 9, because occupancy 0.500 <= existing 0.500 in 2essA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 13, because occupancy 0.500 <= existing 0.500 in 2essA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 331, because occupancy 0.500 <= existing 0.500 in 2essA Skipped atom 335, because occupancy 0.500 <= existing 0.500 in 2essA Skipped atom 337, because occupancy 0.500 <= existing 0.500 in 2essA Skipped atom 472, because occupancy 0.500 <= existing 0.500 in 2essA Skipped atom 476, because occupancy 0.500 <= existing 0.500 in 2essA Skipped atom 478, because occupancy 0.500 <= existing 0.500 in 2essA Skipped atom 480, because occupancy 0.500 <= existing 0.500 in 2essA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1165, because occupancy 0.500 <= existing 0.500 in 2essA Skipped atom 1169, because occupancy 0.500 <= existing 0.500 in 2essA Skipped atom 1171, because occupancy 0.500 <= existing 0.500 in 2essA Skipped atom 1173, because occupancy 0.500 <= existing 0.500 in 2essA Skipped atom 1175, because occupancy 0.500 <= existing 0.500 in 2essA Skipped atom 1177, because occupancy 0.500 <= existing 0.500 in 2essA Skipped atom 1179, because occupancy 0.500 <= existing 0.500 in 2essA Skipped atom 1181, because occupancy 0.500 <= existing 0.500 in 2essA Skipped atom 1218, because occupancy 0.500 <= existing 0.500 in 2essA Skipped atom 1222, because occupancy 0.500 <= existing 0.500 in 2essA Skipped atom 1224, because occupancy 0.500 <= existing 0.500 in 2essA Skipped atom 1226, because occupancy 0.500 <= existing 0.500 in 2essA Skipped atom 1228, because occupancy 0.500 <= existing 0.500 in 2essA Skipped atom 1255, because occupancy 0.500 <= existing 0.500 in 2essA Skipped atom 1259, because occupancy 0.500 <= existing 0.500 in 2essA Skipped atom 1261, because occupancy 0.500 <= existing 0.500 in 2essA Skipped atom 1263, because occupancy 0.500 <= existing 0.500 in 2essA Skipped atom 1357, because occupancy 0.500 <= existing 0.500 in 2essA Skipped atom 1361, because occupancy 0.500 <= existing 0.500 in 2essA Skipped atom 1363, because occupancy 0.500 <= existing 0.500 in 2essA Skipped atom 1365, because occupancy 0.500 <= existing 0.500 in 2essA Skipped atom 1367, because occupancy 0.500 <= existing 0.500 in 2essA Skipped atom 1369, because occupancy 0.500 <= existing 0.500 in 2essA Skipped atom 1371, because occupancy 0.500 <= existing 0.500 in 2essA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0322 read from 2essA/merged-good-all-a2m # 2essA read from 2essA/merged-good-all-a2m # adding 2essA to template set # found chain 2essA in template set Warning: unaligning (T0322)K145 because of BadResidue code BAD_PEPTIDE in next template residue (2essA)R121 Warning: unaligning (T0322)P146 because of BadResidue code BAD_PEPTIDE at template residue (2essA)R121 Warning: unaligning (T0322)P148 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2essA)A124 T0322 27 :GRQIG 2essA 4 :ENKIG T0322 44 :RLAFRVEEHHTNGLGNCHGGMLMSFADMAWGRIISLQ 2essA 9 :TYQFVAEPFHVDFNGRLTMGVLGNHLLNCAGFHASDR T0322 82 :SY 2essA 46 :GF T0322 84 :SWVTVRLMCDFLSGAKLGDWVEGEGELISEEDMLFTVRGRIWA 2essA 58 :TWVLSRLAIELDEMPYQYEKFSVQTWVENVYRLFTDRNFAVID T0322 127 :GERTLITGTGVFKALSAR 2essA 102 :DGKKIGYARSVWAMINLN T0322 147 :R 2essA 122 :K Number of specific fragments extracted= 6 number of extra gaps= 2 total=543 Number of alignments=100 # 2essA read from 2essA/merged-good-all-a2m # found chain 2essA in template set Warning: unaligning (T0322)K145 because of BadResidue code BAD_PEPTIDE in next template residue (2essA)R121 Warning: unaligning (T0322)P146 because of BadResidue code BAD_PEPTIDE at template residue (2essA)R121 Warning: unaligning (T0322)P148 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2essA)A124 Warning: unaligning (T0322)G149 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2essA)A124 Warning: unaligning (T0322)K154 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2essA)L129 T0322 7 :DAQTA 2essA 3 :EENKI T0322 43 :ARLAFRVEEHHTNGLGNCHGGMLMSFADMAWGRIISLQ 2essA 8 :GTYQFVAEPFHVDFNGRLTMGVLGNHLLNCAGFHASDR T0322 81 :KSYSWVTVRLMCDFLSGAKLGDWVEGEGELISEEDMLFTVRGRIWA 2essA 55 :DNYTWVLSRLAIELDEMPYQYEKFSVQTWVENVYRLFTDRNFAVID T0322 127 :GERTLITGTGVFKALSAR 2essA 102 :DGKKIGYARSVWAMINLN T0322 147 :R 2essA 122 :K Number of specific fragments extracted= 5 number of extra gaps= 2 total=548 Number of alignments=101 # 2essA read from 2essA/merged-good-all-a2m # found chain 2essA in template set T0322 43 :ARLAFRVEEHHTNGLGNCHGGMLMSFADMAWGRIISLQK 2essA 8 :GTYQFVAEPFHVDFNGRLTMGVLGNHLLNCAGFHASDRG T0322 82 :SYSWVTVRLMCDFLSGAKLGDWVEGEGELISEEDMLFTVRGRIWAGERTLITGTGVFKALSAR 2essA 56 :NYTWVLSRLAIELDEMPYQYEKFSVQTWVENVYRLFTDRNFAVIDKDGKKIGYARSVWAMINL Number of specific fragments extracted= 2 number of extra gaps= 0 total=550 Number of alignments=102 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1u1zA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1u1zA expands to /projects/compbio/data/pdb/1u1z.pdb.gz 1u1zA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0322 read from 1u1zA/merged-good-all-a2m # 1u1zA read from 1u1zA/merged-good-all-a2m # adding 1u1zA to template set # found chain 1u1zA in template set Warning: unaligning (T0322)S2 because first residue in template chain is (1u1zA)M1 Warning: unaligning (T0322)H53 because of BadResidue code BAD_PEPTIDE in next template residue (1u1zA)F50 Warning: unaligning (T0322)T54 because of BadResidue code BAD_PEPTIDE at template residue (1u1zA)F50 Warning: unaligning (T0322)S142 because last residue in template chain is (1u1zA)K145 T0322 3 :DDLTDAQ 1u1zA 2 :MDINEIR T0322 11 :AAIPEGFSQLNW 1u1zA 9 :EYLPHRYPFLLV T0322 33 :LFEHREG 1u1zA 21 :DRVVELD T0322 40 :PGQARLAFRVEEH 1u1zA 30 :GKRIRAYKNVSIN T0322 55 :NGLGNCHGGMLMSFADMAWGRIISLQKSY 1u1zA 51 :PEHPIMPGVLIIEAMAQAAGILGFKMLDV T0322 84 :SWVTVRLM 1u1zA 86 :LYYFVGSD T0322 92 :CDFLSGAKLGDWVEGEGELISEEDMLFTVRGRIWAGERTLITGTGVFKAL 1u1zA 95 :LRFRQPVLPGDQLQLHAKFISVKRSIWKFDCHATVDDKPVCSAEIICAER Number of specific fragments extracted= 7 number of extra gaps= 1 total=557 Number of alignments=103 # 1u1zA read from 1u1zA/merged-good-all-a2m # found chain 1u1zA in template set Warning: unaligning (T0322)T10 because first residue in template chain is (1u1zA)M1 Warning: unaligning (T0322)H53 because of BadResidue code BAD_PEPTIDE in next template residue (1u1zA)F50 Warning: unaligning (T0322)T54 because of BadResidue code BAD_PEPTIDE at template residue (1u1zA)F50 Warning: unaligning (T0322)Y83 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1u1zA)T85 Warning: unaligning (T0322)S142 because last residue in template chain is (1u1zA)K145 T0322 11 :AAIPEGFSQLNWSRGFGRQIG 1u1zA 2 :MDINEIREYLPHRYPFLLVDR T0322 33 :LFEHREGPGQARLAFRVE 1u1zA 23 :VVELDIEGKRIRAYKNVS T0322 51 :EH 1u1zA 47 :NG T0322 55 :NGLGNCHGGMLMSFADMAWGRIISLQKS 1u1zA 51 :PEHPIMPGVLIIEAMAQAAGILGFKMLD T0322 84 :SWVTVRLM 1u1zA 86 :LYYFVGSD T0322 92 :CDFLSGAKLGDWVEGEGELISEEDMLFTVRGRIWAGERTLITGTGVFKAL 1u1zA 95 :LRFRQPVLPGDQLQLHAKFISVKRSIWKFDCHATVDDKPVCSAEIICAER Number of specific fragments extracted= 6 number of extra gaps= 1 total=563 Number of alignments=104 # 1u1zA read from 1u1zA/merged-good-all-a2m # found chain 1u1zA in template set Warning: unaligning (T0322)H53 because of BadResidue code BAD_PEPTIDE in next template residue (1u1zA)F50 Warning: unaligning (T0322)T54 because of BadResidue code BAD_PEPTIDE at template residue (1u1zA)F50 Warning: unaligning (T0322)Y83 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1u1zA)T85 T0322 14 :PEGFSQLNWSRGFGRQIGPLFEHREGPGQARLAFRVE 1u1zA 4 :INEIREYLPHRYPFLLVDRVVELDIEGKRIRAYKNVS T0322 51 :EH 1u1zA 47 :NG T0322 55 :NGLGNCHGGMLMSFADMAWGRIISLQK 1u1zA 51 :PEHPIMPGVLIIEAMAQAAGILGFKML T0322 84 :SWVTVRLM 1u1zA 86 :LYYFVGSD T0322 92 :CDFLSGAKLGDWVEGEGELISEEDMLFTVRGRIWAGERTLITGTGVF 1u1zA 95 :LRFRQPVLPGDQLQLHAKFISVKRSIWKFDCHATVDDKPVCSAEIIC Number of specific fragments extracted= 5 number of extra gaps= 1 total=568 Number of alignments=105 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2cy9A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0322/2cy9A/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0322/2cy9A/merged-good-all-a2m.gz for input Trying 2cy9A/merged-good-all-a2m Error: Couldn't open file 2cy9A/merged-good-all-a2m or 2cy9A/merged-good-all-a2m.gz for input # command:Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0322//projects/compbio/experiments/protein-predict/casp7/T0322/align.constraints_v3.costfcn or /projects/compbio/experiments/protein-predict/casp7/T0322//projects/compbio/experiments/protein-predict/casp7/T0322/align.constraints_v3.costfcn.gz for input Trying /projects/compbio/experiments/protein-predict/casp7/T0322/align.constraints_v3.costfcn # reading script from file /projects/compbio/experiments/protein-predict/casp7/T0322/align.constraints_v3.costfcn # future Constraint commands -> align # future HelixConstraint commands -> align # future StrandConstraint commands -> align # future SheetConstraint commands -> align # future Hbond commands -> align # future SSbond commands -> align # Constraint # added constraint: constraint((T0322)G106.CA, (T0322)R123.CB) [> 3.8948 = 6.4914 < 8.4388] w=1.0000 to align # Constraint # added constraint: constraint((T0322)G106.CA, (T0322)G122.CA) [> 3.9862 = 6.6437 < 8.6368] w=1.0000 to align # Constraint # added constraint: constraint((T0322)E105.CB, (T0322)I124.CB) [> 4.2225 = 7.0375 < 9.1487] w=1.0000 to align # Constraint # added constraint: constraint((T0322)L65.CB, (T0322)I124.CB) [> 3.6647 = 6.1078 < 7.9401] w=0.9899 to align # Constraint # added constraint: constraint((T0322)V104.CB, (T0322)I124.CB) [> 3.4001 = 5.6669 < 7.3669] w=0.9899 to align # Constraint # added constraint: constraint((T0322)L95.CB, (T0322)L131.CB) [> 3.5949 = 5.9914 < 7.7889] w=0.9862 to align # Constraint # added constraint: constraint((T0322)V120.CB, (T0322)G136.CA) [> 3.3075 = 5.5125 < 7.1662] w=0.9849 to align # Constraint # added constraint: constraint((T0322)T119.CB, (T0322)G136.CA) [> 3.7632 = 6.2721 < 8.1537] w=0.9849 to align # Constraint # added constraint: constraint((T0322)G108.CA, (T0322)G122.CA) [> 2.6912 = 4.4854 < 5.8310] w=0.9798 to align # Constraint # added constraint: constraint((T0322)G108.CA, (T0322)V120.CB) [> 3.6052 = 6.0086 < 7.8112] w=0.9798 to align # Constraint # added constraint: constraint((T0322)G106.CA, (T0322)I124.CB) [> 2.9884 = 4.9807 < 6.4749] w=0.9798 to align # Constraint # added constraint: constraint((T0322)G122.CA, (T0322)G134.CA) [> 3.1933 = 5.3222 < 6.9189] w=0.9758 to align # Constraint # added constraint: constraint((T0322)L90.CB, (T0322)V137.CB) [> 4.1495 = 6.9158 < 8.9905] w=0.9749 to align # Constraint # added constraint: constraint((T0322)E105.CB, (T0322)W125.CB) [> 2.8953 = 4.8255 < 6.2732] w=0.9697 to align # Constraint # added constraint: constraint((T0322)C60.CB, (T0322)A98.CB) [> 2.4803 = 4.1339 < 5.3740] w=0.9670 to align # Constraint # added constraint: constraint((T0322)C60.CB, (T0322)G97.CA) [> 4.0169 = 6.6948 < 8.7032] w=0.9670 to align # Constraint # added constraint: constraint((T0322)R123.CB, (T0322)T133.CB) [> 3.3227 = 5.5378 < 7.1992] w=0.9658 to align # Constraint # added constraint: constraint((T0322)L95.CB, (T0322)I132.CB) [> 3.7977 = 6.3296 < 8.2284] w=0.9658 to align # Constraint # added constraint: constraint((T0322)F94.CB, (T0322)I132.CB) [> 3.4616 = 5.7693 < 7.5001] w=0.9658 to align # Constraint # added constraint: constraint((T0322)T119.CB, (T0322)V137.CB) [> 3.3498 = 5.5830 < 7.2579] w=0.9648 to align # Constraint # added constraint: constraint((T0322)R89.CB, (T0322)V137.CB) [> 2.9497 = 4.9161 < 6.3909] w=0.9648 to align # Constraint # added constraint: constraint((T0322)L90.CB, (T0322)G136.CA) [> 3.0192 = 5.0320 < 6.5415] w=0.9648 to align # Constraint # added constraint: constraint((T0322)V104.CB, (T0322)W125.CB) [> 4.1490 = 6.9149 < 8.9894] w=0.9595 to align # Constraint # added constraint: constraint((T0322)R121.CB, (T0322)G134.CA) [> 4.0169 = 6.6949 < 8.7033] w=0.9556 to align # Constraint # added constraint: constraint((T0322)R121.CB, (T0322)G136.CA) [> 4.3978 = 7.3297 < 9.5286] w=0.9547 to align # Constraint # added constraint: constraint((T0322)L117.CB, (T0322)F138.CB) [> 4.0020 = 6.6700 < 8.6710] w=0.9537 to align # Constraint # added constraint: constraint((T0322)A69.CB, (T0322)G122.CA) [> 3.6204 = 6.0340 < 7.8442] w=0.9507 to align # Constraint # added constraint: constraint((T0322)E109.CB, (T0322)R121.CB) [> 3.1450 = 5.2417 < 6.8142] w=0.9494 to align # Constraint # added constraint: constraint((T0322)G108.CA, (T0322)R123.CB) [> 4.2379 = 7.0632 < 9.1821] w=0.9494 to align # Constraint # added constraint: constraint((T0322)G108.CA, (T0322)R121.CB) [> 3.7704 = 6.2840 < 8.1692] w=0.9494 to align # Constraint # added constraint: constraint((T0322)E107.CB, (T0322)R123.CB) [> 3.0157 = 5.0261 < 6.5340] w=0.9494 to align # Constraint # added constraint: constraint((T0322)E107.CB, (T0322)G122.CA) [> 3.6432 = 6.0721 < 7.8937] w=0.9494 to align # Constraint # added constraint: constraint((T0322)G106.CA, (T0322)W125.CB) [> 3.9440 = 6.5733 < 8.5453] w=0.9484 to align # Constraint # added constraint: constraint((T0322)T87.CB, (T0322)V137.CB) [> 4.1947 = 6.9912 < 9.0886] w=0.9473 to align # Constraint # added constraint: constraint((T0322)I76.CB, (T0322)G108.CA) [> 3.5945 = 5.9908 < 7.7880] w=0.9461 to align # Constraint # added constraint: constraint((T0322)R123.CB, (T0322)G134.CA) [> 4.1945 = 6.9909 < 9.0882] w=0.9456 to align # Constraint # added constraint: constraint((T0322)M91.CB, (T0322)T135.CB) [> 3.0485 = 5.0809 < 6.6052] w=0.9455 to align # Constraint # added constraint: constraint((T0322)C92.CB, (T0322)T133.CB) [> 4.1852 = 6.9753 < 9.0679] w=0.9455 to align # Constraint # added constraint: constraint((T0322)V86.CB, (T0322)K139.CB) [> 3.3516 = 5.5859 < 7.2617] w=0.9445 to align # Constraint # added constraint: constraint((T0322)E109.CB, (T0322)G122.CA) [> 4.0920 = 6.8200 < 8.8661] w=0.9393 to align # Constraint # added constraint: constraint((T0322)N59.CB, (T0322)A98.CB) [> 3.8110 = 6.3516 < 8.2570] w=0.9367 to align # Constraint # added constraint: constraint((T0322)N59.CB, (T0322)G97.CA) [> 3.1032 = 5.1720 < 6.7236] w=0.9367 to align # Constraint # added constraint: constraint((T0322)S96.CB, (T0322)L131.CB) [> 3.3141 = 5.5235 < 7.1805] w=0.9358 to align # Constraint # added constraint: constraint((T0322)C92.CB, (T0322)G134.CA) [> 3.0301 = 5.0501 < 6.5651] w=0.9354 to align # Constraint # added constraint: constraint((T0322)R121.CB, (T0322)T135.CB) [> 3.4858 = 5.8097 < 7.5525] w=0.9354 to align # Constraint # added constraint: constraint((T0322)I124.CB, (T0322)T133.CB) [> 4.1181 = 6.8635 < 8.9225] w=0.9354 to align # Constraint # added constraint: constraint((T0322)L90.CB, (T0322)T135.CB) [> 4.1830 = 6.9717 < 9.0632] w=0.9353 to align # Constraint # added constraint: constraint((T0322)M91.CB, (T0322)G136.CA) [> 3.8608 = 6.4347 < 8.3651] w=0.9344 to align # Constraint # added constraint: constraint((T0322)F68.CB, (T0322)G106.CA) [> 3.9607 = 6.6012 < 8.5816] w=0.9326 to align # Constraint # added constraint: constraint((T0322)W85.CB, (T0322)K139.CB) [> 3.8546 = 6.4243 < 8.3516] w=0.9268 to align # Constraint # added constraint: constraint((T0322)L65.CB, (T0322)I132.CB) [> 3.3770 = 5.6283 < 7.3169] w=0.9246 to align # Constraint # added constraint: constraint((T0322)F118.CB, (T0322)F138.CB) [> 3.1205 = 5.2008 < 6.7611] w=0.9234 to align # Constraint # added constraint: constraint((T0322)M66.CB, (T0322)L90.CB) [> 4.2391 = 7.0651 < 9.1847] w=0.9222 to align # Constraint # added constraint: constraint((T0322)L110.CB, (T0322)V120.CB) [> 3.4430 = 5.7383 < 7.4598] w=0.9213 to align # Constraint # added constraint: constraint((T0322)L45.CB, (T0322)E105.CB) [> 4.3784 = 7.2973 < 9.4865] w=0.9181 to align # Constraint # added constraint: constraint((T0322)R44.CB, (T0322)G106.CA) [> 3.7178 = 6.1963 < 8.0552] w=0.9181 to align # Constraint # added constraint: constraint((T0322)T87.CB, (T0322)F138.CB) [> 3.5656 = 5.9427 < 7.7255] w=0.9161 to align # Constraint # added constraint: constraint((T0322)V88.CB, (T0322)F138.CB) [> 3.8515 = 6.4191 < 8.3448] w=0.9161 to align # Constraint # added constraint: constraint((T0322)F68.CB, (T0322)I124.CB) [> 4.0505 = 6.7508 < 8.7760] w=0.9151 to align # Constraint # added constraint: constraint((T0322)M66.CB, (T0322)C92.CB) [> 3.7174 = 6.1957 < 8.0543] w=0.9143 to align # Constraint # added constraint: constraint((T0322)A72.CB, (T0322)G106.CA) [> 3.3154 = 5.5257 < 7.1834] w=0.9140 to align # Constraint # added constraint: constraint((T0322)E109.CB, (T0322)V120.CB) [> 4.0955 = 6.8258 < 8.8735] w=0.9090 to align # Constraint # added constraint: constraint((T0322)V104.CB, (T0322)A126.CB) [> 3.4687 = 5.7812 < 7.5155] w=0.9080 to align # Constraint # added constraint: constraint((T0322)C60.CB, (T0322)K99.CB) [> 4.3395 = 7.2326 < 9.4023] w=0.9065 to align # Constraint # added constraint: constraint((T0322)N59.CB, (T0322)K99.CB) [> 3.5572 = 5.9286 < 7.7072] w=0.9065 to align # Constraint # added constraint: constraint((T0322)G122.CA, (T0322)T135.CB) [> 4.1250 = 6.8749 < 8.9374] w=0.9051 to align # Constraint # added constraint: constraint((T0322)I111.CB, (T0322)R121.CB) [> 3.1572 = 5.2620 < 6.8406] w=0.9032 to align # Constraint # added constraint: constraint((T0322)I111.CB, (T0322)V120.CB) [> 3.9511 = 6.5852 < 8.5608] w=0.9032 to align # Constraint # added constraint: constraint((T0322)L117.CB, (T0322)K139.CB) [> 3.4763 = 5.7938 < 7.5320] w=0.9022 to align # Constraint # added constraint: constraint((T0322)D93.CB, (T0322)T133.CB) [> 3.2195 = 5.3659 < 6.9757] w=0.8950 to align # Constraint # added constraint: constraint((T0322)G62.CA, (T0322)F94.CB) [> 3.9153 = 6.5254 < 8.4830] w=0.8888 to align # Constraint # added constraint: constraint((T0322)R44.CB, (T0322)E105.CB) [> 3.7478 = 6.2463 < 8.1202] w=0.8878 to align # Constraint # added constraint: constraint((T0322)L95.CB, (T0322)T133.CB) [> 4.1398 = 6.8997 < 8.9696] w=0.8855 to align # Constraint # added constraint: constraint((T0322)W73.CB, (T0322)V120.CB) [> 3.0645 = 5.1074 < 6.6397] w=0.8850 to align # Constraint # added constraint: constraint((T0322)V88.CB, (T0322)K139.CB) [> 3.2675 = 5.4458 < 7.0796] w=0.8847 to align # Constraint # added constraint: constraint((T0322)R89.CB, (T0322)G136.CA) [> 3.8201 = 6.3668 < 8.2768] w=0.8838 to align # Constraint # added constraint: constraint((T0322)F68.CB, (T0322)V104.CB) [> 3.9173 = 6.5288 < 8.4874] w=0.8812 to align # Constraint # added constraint: constraint((T0322)V49.CB, (T0322)G101.CA) [> 3.0655 = 5.1092 < 6.6420] w=0.8790 to align # Constraint # added constraint: constraint((T0322)V49.CB, (T0322)A98.CB) [> 3.5158 = 5.8597 < 7.6177] w=0.8790 to align # Constraint # added constraint: constraint((T0322)L110.CB, (T0322)T119.CB) [> 4.4774 = 7.4624 < 9.7011] w=0.8786 to align # Constraint # added constraint: constraint((T0322)L95.CB, (T0322)T130.CB) [> 3.4999 = 5.8331 < 7.5831] w=0.8756 to align # Constraint # added constraint: constraint((T0322)L45.CB, (T0322)G106.CA) [> 3.2752 = 5.4587 < 7.0963] w=0.8750 to align # Constraint # added constraint: constraint((T0322)L65.CB, (T0322)F94.CB) [> 4.3962 = 7.3270 < 9.5251] w=0.8749 to align # Constraint # added constraint: constraint((T0322)V49.CB, (T0322)C60.CB) [> 3.3224 = 5.5374 < 7.1986] w=0.8689 to align # Constraint # added constraint: constraint((T0322)G122.CA, (T0322)T133.CB) [> 3.8691 = 6.4485 < 8.3830] w=0.8649 to align # Constraint # added constraint: constraint((T0322)A72.CB, (T0322)G108.CA) [> 3.3554 = 5.5924 < 7.2701] w=0.8648 to align # Constraint # added constraint: constraint((T0322)L45.CB, (T0322)A72.CB) [> 2.8260 = 4.7100 < 6.1230] w=0.8601 to align # Constraint # added constraint: constraint((T0322)A69.CB, (T0322)G106.CA) [> 4.1763 = 6.9605 < 9.0487] w=0.8570 to align # Constraint # added constraint: constraint((T0322)R44.CB, (T0322)G108.CA) [> 4.3630 = 7.2716 < 9.4531] w=0.8449 to align # Constraint # added constraint: constraint((T0322)R44.CB, (T0322)E107.CB) [> 3.1339 = 5.2231 < 6.7901] w=0.8449 to align # Constraint # added constraint: constraint((T0322)A46.CB, (T0322)V104.CB) [> 4.0859 = 6.8098 < 8.8528] w=0.8347 to align # Constraint # added constraint: constraint((T0322)F118.CB, (T0322)V137.CB) [> 4.3792 = 7.2987 < 9.4883] w=0.8338 to align # Constraint # added constraint: constraint((T0322)E107.CB, (T0322)W125.CB) [> 4.3064 = 7.1773 < 9.3305] w=0.8270 to align # Constraint # added constraint: constraint((T0322)L117.CB, (T0322)V137.CB) [> 3.6708 = 6.1180 < 7.9534] w=0.8258 to align # Constraint # added constraint: constraint((T0322)A46.CB, (T0322)E105.CB) [> 3.0996 = 5.1661 < 6.7159] w=0.8246 to align # Constraint # added constraint: constraint((T0322)D93.CB, (T0322)I132.CB) [> 4.0451 = 6.7419 < 8.7645] w=0.8236 to align # Constraint # added constraint: constraint((T0322)D102.CB, (T0322)A126.CB) [> 3.3459 = 5.5766 < 7.2496] w=0.8223 to align # Constraint # added constraint: constraint((T0322)V120.CB, (T0322)F138.CB) [> 4.1462 = 6.9103 < 8.9835] w=0.8190 to align # Constraint # added constraint: constraint((T0322)V49.CB, (T0322)V104.CB) [> 3.8256 = 6.3760 < 8.2887] w=0.8183 to align # Constraint # added constraint: constraint((T0322)A43.CB, (T0322)I76.CB) [> 2.7270 = 4.5450 < 5.9084] w=0.8175 to align # Constraint # added constraint: constraint((T0322)C92.CB, (T0322)I132.CB) [> 3.7030 = 6.1717 < 8.0232] w=0.8157 to align # Constraint # added constraint: constraint((T0322)W85.CB, (T0322)F138.CB) [> 2.8495 = 4.7492 < 6.1739] w=0.8155 to align # Constraint # added constraint: constraint((T0322)R123.CB, (T0322)I132.CB) [> 4.2736 = 7.1226 < 9.2594] w=0.8136 to align # Constraint # added constraint: constraint((T0322)A69.CB, (T0322)G134.CA) [> 3.9621 = 6.6035 < 8.5846] w=0.8090 to align # Constraint # added constraint: constraint((T0322)V88.CB, (T0322)V137.CB) [> 2.9993 = 4.9988 < 6.4984] w=0.8082 to align # Constraint # added constraint: constraint((T0322)T87.CB, (T0322)G136.CA) [> 3.9632 = 6.6054 < 8.5870] w=0.8082 to align # Constraint # added constraint: constraint((T0322)A98.CB, (T0322)L131.CB) [> 3.3187 = 5.5312 < 7.1906] w=0.8035 to align # Constraint # added constraint: constraint((T0322)G97.CA, (T0322)L131.CB) [> 3.6822 = 6.1370 < 7.9781] w=0.8035 to align # Constraint # added constraint: constraint((T0322)V88.CB, (T0322)L117.CB) [> 4.3766 = 7.2944 < 9.4826] w=0.8017 to align # Constraint # added constraint: constraint((T0322)A69.CB, (T0322)I124.CB) [> 3.8911 = 6.4851 < 8.4307] w=0.8007 to align # Constraint # added constraint: constraint((T0322)T119.CB, (T0322)F138.CB) [> 4.2531 = 7.0885 < 9.2150] w=0.7997 to align # Constraint # added constraint: constraint((T0322)F47.CB, (T0322)F68.CB) [> 3.2110 = 5.3516 < 6.9571] w=0.7982 to align # Constraint # added constraint: constraint((T0322)G58.CA, (T0322)K99.CB) [> 3.9865 = 6.6442 < 8.6375] w=0.7978 to align # Constraint # added constraint: constraint((T0322)A46.CB, (T0322)G106.CA) [> 4.3099 = 7.1831 < 9.3380] w=0.7952 to align # Constraint # added constraint: constraint((T0322)A43.CB, (T0322)G108.CA) [> 3.3473 = 5.5788 < 7.2524] w=0.7947 to align # Constraint # added constraint: constraint((T0322)V86.CB, (T0322)F138.CB) [> 3.9583 = 6.5971 < 8.5762] w=0.7944 to align # Constraint # added constraint: constraint((T0322)H53.CB, (T0322)M64.CB) [> 2.7206 = 4.5344 < 5.8947] w=0.7906 to align # Constraint # added constraint: constraint((T0322)F47.CB, (T0322)V104.CB) [> 3.0771 = 5.1286 < 6.6671] w=0.7881 to align # Constraint # added constraint: constraint((T0322)A43.CB, (T0322)E107.CB) [> 4.3702 = 7.2836 < 9.4687] w=0.7872 to align # Constraint # added constraint: constraint((T0322)W73.CB, (T0322)G108.CA) [> 3.9672 = 6.6120 < 8.5955] w=0.7807 to align # Constraint # added constraint: constraint((T0322)A43.CB, (T0322)A72.CB) [> 3.5159 = 5.8598 < 7.6178] w=0.7796 to align # Constraint # added constraint: constraint((T0322)M116.CB, (T0322)A140.CB) [> 3.3679 = 5.6132 < 7.2972] w=0.7790 to align # Constraint # added constraint: constraint((T0322)A43.CB, (T0322)R75.CB) [> 3.3297 = 5.5495 < 7.2144] w=0.7742 to align # Constraint # added constraint: constraint((T0322)T119.CB, (T0322)T135.CB) [> 3.7635 = 6.2725 < 8.1543] w=0.7695 to align # Constraint # added constraint: constraint((T0322)A72.CB, (T0322)G122.CA) [> 4.1611 = 6.9352 < 9.0158] w=0.7640 to align # Constraint # added constraint: constraint((T0322)R48.CB, (T0322)W103.CB) [> 3.3107 = 5.5179 < 7.1733] w=0.7603 to align # Constraint # added constraint: constraint((T0322)V49.CB, (T0322)L100.CB) [> 2.9802 = 4.9671 < 6.4572] w=0.7578 to align # Constraint # added constraint: constraint((T0322)V49.CB, (T0322)D102.CB) [> 3.0234 = 5.0390 < 6.5507] w=0.7576 to align # Constraint # added constraint: constraint((T0322)M116.CB, (T0322)K139.CB) [> 3.9248 = 6.5413 < 8.5037] w=0.7531 to align # Constraint # added constraint: constraint((T0322)L45.CB, (T0322)R75.CB) [> 3.8692 = 6.4486 < 8.3832] w=0.7502 to align # Constraint # added constraint: constraint((T0322)A46.CB, (T0322)W103.CB) [> 3.5195 = 5.8658 < 7.6255] w=0.7437 to align # Constraint # added constraint: constraint((T0322)D70.CB, (T0322)T87.CB) [> 3.8559 = 6.4265 < 8.3545] w=0.7404 to align # Constraint # added constraint: constraint((T0322)L90.CB, (T0322)G134.CA) [> 4.1355 = 6.8925 < 8.9602] w=0.7327 to align # Constraint # added constraint: constraint((T0322)R48.CB, (T0322)G101.CA) [> 3.8483 = 6.4139 < 8.3380] w=0.7266 to align # Constraint # added constraint: constraint((T0322)F94.CB, (T0322)L131.CB) [> 4.4138 = 7.3563 < 9.5632] w=0.7222 to align # Constraint # added constraint: constraint((T0322)I76.CB, (T0322)V120.CB) [> 3.7717 = 6.2861 < 8.1719] w=0.7185 to align # Constraint # added constraint: constraint((T0322)L45.CB, (T0322)F68.CB) [> 3.9467 = 6.5778 < 8.5511] w=0.7179 to align # Constraint # added constraint: constraint((T0322)W103.CB, (T0322)A126.CB) [> 4.1672 = 6.9453 < 9.0289] w=0.7174 to align # Constraint # added constraint: constraint((T0322)Q42.CB, (T0322)G108.CA) [> 3.6796 = 6.1326 < 7.9724] w=0.7169 to align # Constraint # added constraint: constraint((T0322)L117.CB, (T0322)A140.CB) [> 4.1016 = 6.8359 < 8.8867] w=0.7078 to align # Constraint # added constraint: constraint((T0322)L65.CB, (T0322)V104.CB) [> 4.2000 = 6.9999 < 9.0999] w=0.7049 to align # Constraint # added constraint: constraint((T0322)R121.CB, (T0322)T133.CB) [> 4.3598 = 7.2664 < 9.4463] w=0.7023 to align # Constraint # added constraint: constraint((T0322)A69.CB, (T0322)C92.CB) [> 4.2263 = 7.0439 < 9.1571] w=0.6941 to align # Constraint # added constraint: constraint((T0322)E105.CB, (T0322)A126.CB) [> 4.4570 = 7.4284 < 9.6569] w=0.6934 to align # Constraint # added constraint: constraint((T0322)F47.CB, (T0322)W103.CB) [> 4.2536 = 7.0893 < 9.2161] w=0.6870 to align # Constraint # added constraint: constraint((T0322)L45.CB, (T0322)M71.CB) [> 3.7155 = 6.1924 < 8.0502] w=0.6805 to align # Constraint # added constraint: constraint((T0322)G74.CA, (T0322)W85.CB) [> 3.7381 = 6.2302 < 8.0992] w=0.6780 to align # Constraint # added constraint: constraint((T0322)I76.CB, (T0322)L110.CB) [> 3.8974 = 6.4956 < 8.4443] w=0.6762 to align # Constraint # added constraint: constraint((T0322)Q42.CB, (T0322)E109.CB) [> 3.0839 = 5.1398 < 6.6817] w=0.6639 to align # Constraint # added constraint: constraint((T0322)A43.CB, (T0322)L79.CB) [> 4.0768 = 6.7946 < 8.8330] w=0.6521 to align # Constraint # added constraint: constraint((T0322)W85.CB, (T0322)F118.CB) [> 4.1391 = 6.8984 < 8.9680] w=0.6521 to align # Constraint # added constraint: constraint((T0322)E50.CB, (T0322)L100.CB) [> 3.9669 = 6.6116 < 8.5950] w=0.6425 to align # Constraint # added constraint: constraint((T0322)E107.CB, (T0322)I124.CB) [> 4.6162 = 7.6936 < 10.0017] w=0.6425 to align # Constraint # added constraint: constraint((T0322)L65.CB, (T0322)C92.CB) [> 4.0149 = 6.6915 < 8.6989] w=0.6416 to align # Constraint # added constraint: constraint((T0322)G122.CA, (T0322)G136.CA) [> 4.3572 = 7.2621 < 9.4407] w=0.6363 to align # Constraint # added constraint: constraint((T0322)V120.CB, (T0322)V137.CB) [> 4.1525 = 6.9208 < 8.9971] w=0.6233 to align # Constraint # added constraint: constraint((T0322)S84.CB, (T0322)A140.CB) [> 4.1970 = 6.9950 < 9.0936] w=0.6201 to align # Constraint # added constraint: constraint((T0322)R48.CB, (T0322)D102.CB) [> 4.2552 = 7.0920 < 9.2196] w=0.6109 to align # Constraint # added constraint: constraint((T0322)W73.CB, (T0322)G136.CA) [> 3.8963 = 6.4938 < 8.4420] w=0.6042 to align # Constraint # added constraint: constraint((T0322)L65.CB, (T0322)L131.CB) [> 4.2344 = 7.0572 < 9.1744] w=0.5965 to align # Constraint # added constraint: constraint((T0322)W73.CB, (T0322)G122.CA) [> 3.9781 = 6.6301 < 8.6191] w=0.5915 to align # Constraint # added constraint: constraint((T0322)S84.CB, (T0322)L141.CB) [> 3.5176 = 5.8628 < 7.6216] w=0.5900 to align # Constraint # added constraint: constraint((T0322)C60.CB, (T0322)V104.CB) [> 4.3128 = 7.1880 < 9.3444] w=0.5883 to align # Constraint # added constraint: constraint((T0322)S96.CB, (T0322)A126.CB) [> 4.3611 = 7.2685 < 9.4491] w=0.5822 to align # Constraint # added constraint: constraint((T0322)I77.CB, (T0322)V120.CB) [> 3.9221 = 6.5369 < 8.4980] w=0.5727 to align # Constraint # added constraint: constraint((T0322)A69.CB, (T0322)I132.CB) [> 4.1075 = 6.8458 < 8.8995] w=0.5716 to align # Constraint # added constraint: constraint((T0322)A72.CB, (T0322)E107.CB) [> 4.2910 = 7.1517 < 9.2972] w=0.5662 to align # Constraint # added constraint: constraint((T0322)W73.CB, (T0322)F138.CB) [> 4.1521 = 6.9202 < 8.9962] w=0.5604 to align # Constraint # added constraint: constraint((T0322)F118.CB, (T0322)K139.CB) [> 4.1048 = 6.8414 < 8.8938] w=0.5591 to align # Constraint # added constraint: constraint((T0322)G58.CA, (T0322)L100.CB) [> 4.0396 = 6.7327 < 8.7525] w=0.5553 to align # Constraint # added constraint: constraint((T0322)I77.CB, (T0322)F118.CB) [> 3.3526 = 5.5876 < 7.2639] w=0.5497 to align # Constraint # added constraint: constraint((T0322)T54.CB, (T0322)L100.CB) [> 3.5397 = 5.8995 < 7.6693] w=0.5456 to align # Constraint # added constraint: constraint((T0322)T87.CB, (T0322)K139.CB) [> 4.3077 = 7.1795 < 9.3333] w=0.5409 to align # Constraint # added constraint: constraint((T0322)E35.CB, (T0322)R44.CB) [> 4.1841 = 6.9734 < 9.0655] w=0.5218 to align # Constraint # added constraint: constraint((T0322)F47.CB, (T0322)G106.CA) [> 4.4958 = 7.4931 < 9.7410] w=0.5212 to align # Constraint # added constraint: constraint((T0322)C60.CB, (T0322)L100.CB) [> 4.1522 = 6.9203 < 8.9964] w=0.5187 to align # Constraint # added constraint: constraint((T0322)Q42.CB, (T0322)I76.CB) [> 4.0303 = 6.7171 < 8.7322] w=0.5158 to align # Constraint # added constraint: constraint((T0322)W85.CB, (T0322)L141.CB) [> 4.1691 = 6.9485 < 9.0330] w=0.5132 to align # Constraint # added constraint: constraint((T0322)V86.CB, (T0322)L141.CB) [> 3.6860 = 6.1434 < 7.9864] w=0.5090 to align # Constraint # added constraint: constraint((T0322)E50.CB, (T0322)G101.CA) [> 4.2366 = 7.0610 < 9.1793] w=0.5076 to align # Constraint # added constraint: constraint((T0322)I77.CB, (T0322)F138.CB) [> 3.2961 = 5.4934 < 7.1415] w=0.5051 to align # Constraint # added constraint: constraint((T0322)G41.CA, (T0322)L110.CB) [> 2.9902 = 4.9836 < 6.4787] w=0.4956 to align # Constraint # added constraint: constraint((T0322)C92.CB, (T0322)T135.CB) [> 4.0426 = 6.7377 < 8.7590] w=0.4891 to align # Constraint # added constraint: constraint((T0322)I111.CB, (T0322)T135.CB) [> 4.3812 = 7.3019 < 9.4925] w=0.4864 to align # Constraint # added constraint: constraint((T0322)A69.CB, (T0322)L90.CB) [> 4.3409 = 7.2348 < 9.4052] w=0.4839 to align # Constraint # added constraint: constraint((T0322)H36.CB, (T0322)L45.CB) [> 3.8786 = 6.4644 < 8.4037] w=0.4814 to align # Constraint # added constraint: constraint((T0322)W73.CB, (T0322)T87.CB) [> 4.2365 = 7.0609 < 9.1791] w=0.4788 to align # Constraint # added constraint: constraint((T0322)W103.CB, (T0322)G127.CA) [> 3.7644 = 6.2740 < 8.1562] w=0.4782 to align # Constraint # added constraint: constraint((T0322)D70.CB, (T0322)L90.CB) [> 3.9351 = 6.5585 < 8.5261] w=0.4688 to align # Constraint # added constraint: constraint((T0322)F34.CB, (T0322)A46.CB) [> 3.3250 = 5.5416 < 7.2041] w=0.4638 to align # Constraint # added constraint: constraint((T0322)H36.CB, (T0322)A46.CB) [> 3.2952 = 5.4920 < 7.1396] w=0.4613 to align # Constraint # added constraint: constraint((T0322)L33.CB, (T0322)L45.CB) [> 3.3128 = 5.5213 < 7.1777] w=0.4551 to align # Constraint # added constraint: constraint((T0322)L110.CB, (T0322)R121.CB) [> 4.6009 = 7.6682 < 9.9686] w=0.4494 to align # Constraint # added constraint: constraint((T0322)Q80.CB, (T0322)L110.CB) [> 3.8951 = 6.4918 < 8.4394] w=0.4423 to align # Constraint # added constraint: constraint((T0322)I76.CB, (T0322)E109.CB) [> 4.1732 = 6.9553 < 9.0419] w=0.4267 to align # Constraint # added constraint: constraint((T0322)C60.CB, (T0322)D102.CB) [> 4.4863 = 7.4772 < 9.7204] w=0.4265 to align # Constraint # added constraint: constraint((T0322)L33.CB, (T0322)A46.CB) [> 4.2431 = 7.0718 < 9.1934] w=0.4248 to align # Constraint # added constraint: constraint((T0322)G62.CA, (T0322)C92.CB) [> 4.5754 = 7.6257 < 9.9134] w=0.4156 to align # Constraint # added constraint: constraint((T0322)Y83.CB, (T0322)A140.CB) [> 3.4886 = 5.8143 < 7.5585] w=0.3961 to align # Constraint # added constraint: constraint((T0322)H53.CB, (T0322)L100.CB) [> 4.1383 = 6.8972 < 8.9664] w=0.3804 to align # Constraint # added constraint: constraint((T0322)F34.CB, (T0322)F47.CB) [> 4.3100 = 7.1833 < 9.3383] w=0.3794 to align # Constraint # added constraint: constraint((T0322)L33.CB, (T0322)M71.CB) [> 3.4104 = 5.6841 < 7.3893] w=0.3743 to align # Constraint # added constraint: constraint((T0322)H36.CB, (T0322)E105.CB) [> 4.2567 = 7.0945 < 9.2228] w=0.3741 to align # Constraint # added constraint: constraint((T0322)S84.CB, (T0322)S142.CB) [> 3.9288 = 6.5480 < 8.5124] w=0.3572 to align # Constraint # added constraint: constraint((T0322)A43.CB, (T0322)E109.CB) [> 4.4127 = 7.3545 < 9.5609] w=0.3462 to align # Constraint # added constraint: constraint((T0322)V86.CB, (T0322)A140.CB) [> 3.9131 = 6.5219 < 8.4784] w=0.3369 to align # Constraint # added constraint: constraint((T0322)F47.CB, (T0322)M64.CB) [> 4.3579 = 7.2632 < 9.4421] w=0.3338 to align # Constraint # added constraint: constraint((T0322)Y83.CB, (T0322)L141.CB) [> 3.7765 = 6.2941 < 8.1824] w=0.3286 to align # Constraint # added constraint: constraint((T0322)G97.CA, (T0322)A126.CB) [> 4.3547 = 7.2578 < 9.4352] w=0.3276 to align # Constraint # added constraint: constraint((T0322)F47.CB, (T0322)E105.CB) [> 4.5648 = 7.6081 < 9.8905] w=0.3165 to align # Constraint # added constraint: constraint((T0322)Q80.CB, (T0322)F118.CB) [> 3.9165 = 6.5275 < 8.4858] w=0.3113 to align # Constraint # added constraint: constraint((T0322)M66.CB, (T0322)I132.CB) [> 4.3346 = 7.2244 < 9.3917] w=0.3043 to align # Constraint # added constraint: constraint((T0322)G62.CA, (T0322)A98.CB) [> 4.4294 = 7.3823 < 9.5970] w=0.3004 to align # Constraint # added constraint: constraint((T0322)G62.CA, (T0322)I132.CB) [> 4.3602 = 7.2670 < 9.4471] w=0.2968 to align # Constraint # added constraint: constraint((T0322)V49.CB, (T0322)M64.CB) [> 4.3923 = 7.3205 < 9.5166] w=0.2962 to align # Constraint # added constraint: constraint((T0322)R89.CB, (T0322)T135.CB) [> 4.4667 = 7.4444 < 9.6778] w=0.2818 to align # Constraint # added constraint: constraint((T0322)I77.CB, (T0322)L110.CB) [> 4.3021 = 7.1702 < 9.3212] w=0.2709 to align # Constraint # added constraint: constraint((T0322)E109.CB, (T0322)R123.CB) [> 4.5710 = 7.6184 < 9.9039] w=0.2706 to align # Constraint # added constraint: constraint((T0322)Q80.CB, (T0322)E113.CB) [> 3.7261 = 6.2102 < 8.0733] w=0.2529 to align # Constraint # added constraint: constraint((T0322)L95.CB, (T0322)R129.CB) [> 4.5913 = 7.6521 < 9.9477] w=0.2518 to align # Constraint # added constraint: constraint((T0322)G27.CA, (T0322)S67.CB) [> 4.4002 = 7.3337 < 9.5338] w=0.2428 to align # Constraint # added constraint: constraint((T0322)A43.CB, (T0322)G74.CA) [> 4.4224 = 7.3707 < 9.5819] w=0.2427 to align # Constraint # added constraint: constraint((T0322)L33.CB, (T0322)S67.CB) [> 4.4332 = 7.3888 < 9.6054] w=0.2326 to align # Constraint # added constraint: constraint((T0322)D70.CB, (T0322)G136.CA) [> 4.2449 = 7.0748 < 9.1972] w=0.2282 to align # Constraint # added constraint: constraint((T0322)L45.CB, (T0322)E107.CB) [> 4.6949 = 7.8248 < 10.1722] w=0.2216 to align # Constraint # added constraint: constraint((T0322)I30.CB, (T0322)M64.CB) [> 3.8642 = 6.4403 < 8.3724] w=0.2203 to align # Constraint # added constraint: constraint((T0322)G27.CA, (T0322)M71.CB) [> 3.6948 = 6.1580 < 8.0054] w=0.2203 to align # Constraint # added constraint: constraint((T0322)N59.CB, (T0322)L100.CB) [> 4.4344 = 7.3906 < 9.6078] w=0.2004 to align # Constraint # added constraint: constraint((T0322)I30.CB, (T0322)F68.CB) [> 4.0329 = 6.7215 < 8.7379] w=0.1979 to align # Constraint # added constraint: constraint((T0322)G101.CA, (T0322)A126.CB) [> 4.0986 = 6.8311 < 8.8804] w=0.1922 to align # Constraint # added constraint: constraint((T0322)F26.CB, (T0322)S67.CB) [> 4.2190 = 7.0316 < 9.1411] w=0.1922 to align # Constraint # added constraint: constraint((T0322)R75.CB, (T0322)G108.CA) [> 4.5293 = 7.5489 < 9.8135] w=0.1896 to align # Constraint # added constraint: constraint((T0322)A43.CB, (T0322)G106.CA) [> 3.9497 = 6.5828 < 8.5576] w=0.1881 to align # Constraint # added constraint: constraint((T0322)K81.CB, (T0322)F118.CB) [> 3.9353 = 6.5589 < 8.5266] w=0.1880 to align # Constraint # added constraint: constraint((T0322)M66.CB, (T0322)G134.CA) [> 4.4874 = 7.4790 < 9.7227] w=0.1861 to align # Constraint # added constraint: constraint((T0322)Q42.CB, (T0322)L79.CB) [> 4.3008 = 7.1680 < 9.3184] w=0.1821 to align # Constraint # added constraint: constraint((T0322)C60.CB, (T0322)L131.CB) [> 4.5262 = 7.5436 < 9.8067] w=0.1819 to align # Constraint # added constraint: constraint((T0322)F17.CB, (T0322)E35.CB) [> 3.2983 = 5.4972 < 7.1463] w=0.1720 to align # Constraint # added constraint: constraint((T0322)V49.CB, (T0322)N59.CB) [> 4.6801 = 7.8002 < 10.1403] w=0.1710 to align # Constraint # added constraint: constraint((T0322)L90.CB, (T0322)F138.CB) [> 4.4367 = 7.3944 < 9.6128] w=0.1692 to align # Constraint # added constraint: constraint((T0322)R89.CB, (T0322)F138.CB) [> 2.5578 = 4.2631 < 5.5420] w=0.1692 to align # Constraint # added constraint: constraint((T0322)V88.CB, (T0322)G136.CA) [> 4.5164 = 7.5274 < 9.7856] w=0.1692 to align # Constraint # added constraint: constraint((T0322)Y83.CB, (T0322)A143.CB) [> 4.0793 = 6.7989 < 8.8386] w=0.1690 to align # Constraint # added constraint: constraint((T0322)I77.CB, (T0322)T87.CB) [> 4.3979 = 7.3298 < 9.5288] w=0.1668 to align # Constraint # added constraint: constraint((T0322)A140.CB, (T0322)G149.CA) [> 3.3791 = 5.6318 < 7.3213] w=0.1627 to align # Constraint # added constraint: constraint((T0322)D93.CB, (T0322)T135.CB) [> 4.4767 = 7.4612 < 9.6996] w=0.1623 to align # Constraint # added constraint: constraint((T0322)G122.CA, (T0322)V137.CB) [> 4.3231 = 7.2051 < 9.3667] w=0.1591 to align # Constraint # added constraint: constraint((T0322)E35.CB, (T0322)A46.CB) [> 4.4424 = 7.4040 < 9.6252] w=0.1543 to align # Constraint # added constraint: constraint((T0322)F94.CB, (T0322)T133.CB) [> 3.2026 = 5.3377 < 6.9390] w=0.1522 to align # Constraint # added constraint: constraint((T0322)V88.CB, (T0322)A140.CB) [> 3.0655 = 5.1092 < 6.6419] w=0.1492 to align # Constraint # added constraint: constraint((T0322)I30.CB, (T0322)M71.CB) [> 4.2712 = 7.1187 < 9.2543] w=0.1473 to align # Constraint # added constraint: constraint((T0322)M116.CB, (T0322)G149.CA) [> 3.3147 = 5.5245 < 7.1819] w=0.1424 to align # Constraint # added constraint: constraint((T0322)M91.CB, (T0322)V137.CB) [> 4.5500 = 7.5833 < 9.8583] w=0.1415 to align # Constraint # added constraint: constraint((T0322)P32.CB, (T0322)R48.CB) [> 3.3913 = 5.6522 < 7.3479] w=0.1394 to align # Constraint # added constraint: constraint((T0322)P32.CB, (T0322)F47.CB) [> 3.4566 = 5.7610 < 7.4893] w=0.1394 to align # Constraint # added constraint: constraint((T0322)R28.CB, (T0322)M71.CB) [> 3.3602 = 5.6002 < 7.2803] w=0.1394 to align # Constraint # added constraint: constraint((T0322)P40.CB, (T0322)L110.CB) [> 4.0106 = 6.6842 < 8.6895] w=0.1314 to align # Constraint # added constraint: constraint((T0322)T54.CB, (T0322)M64.CB) [> 4.5534 = 7.5890 < 9.8657] w=0.1314 to align # Constraint # added constraint: constraint((T0322)F26.CB, (T0322)M71.CB) [> 4.4476 = 7.4127 < 9.6365] w=0.1293 to align # Constraint # added constraint: constraint((T0322)L20.CB, (T0322)L33.CB) [> 3.8897 = 6.4828 < 8.4277] w=0.1213 to align # Constraint # added constraint: constraint((T0322)D70.CB, (T0322)V137.CB) [> 3.8347 = 6.3911 < 8.3084] w=0.1189 to align # Constraint # added constraint: constraint((T0322)G62.CA, (T0322)G97.CA) [> 4.6632 = 7.7720 < 10.1035] w=0.1148 to align # Constraint # added constraint: constraint((T0322)A43.CB, (T0322)S78.CB) [> 4.4828 = 7.4713 < 9.7127] w=0.1111 to align # Constraint # added constraint: constraint((T0322)G63.CA, (T0322)C92.CB) [> 4.5626 = 7.6043 < 9.8856] w=0.1105 to align # Constraint # added constraint: constraint((T0322)D102.CB, (T0322)L131.CB) [> 4.4132 = 7.3554 < 9.5620] w=0.1091 to align # Constraint # added constraint: constraint((T0322)R121.CB, (T0322)V137.CB) [> 4.6251 = 7.7085 < 10.0210] w=0.1085 to align # Constraint # added constraint: constraint((T0322)A43.CB, (T0322)E105.CB) [> 4.0873 = 6.8122 < 8.8559] w=0.1036 to align # Constraint # added constraint: constraint((T0322)L95.CB, (T0322)G134.CA) [> 4.2921 = 7.1535 < 9.2995] w=0.1019 to align # Constraint # added constraint: constraint((T0322)R24.CB, (T0322)M71.CB) [> 4.2550 = 7.0917 < 9.2192] w=0.1012 to align # Constraint # added constraint: constraint((T0322)D115.CB, (T0322)G149.CA) [> 4.1892 = 6.9820 < 9.0766] w=0.1011 to align # Constraint # added constraint: constraint((T0322)K81.CB, (T0322)F138.CB) [> 3.8726 = 6.4544 < 8.3907] w=0.0930 to align # Constraint # added constraint: constraint((T0322)G31.CA, (T0322)M64.CB) [> 4.2734 = 7.1223 < 9.2590] w=0.0910 to align # Constraint # added constraint: constraint((T0322)F47.CB, (T0322)D102.CB) [> 4.3082 = 7.1803 < 9.3344] w=0.0910 to align # Constraint # added constraint: constraint((T0322)M64.CB, (T0322)V104.CB) [> 4.5374 = 7.5623 < 9.8310] w=0.0910 to align # Constraint # added constraint: constraint((T0322)F17.CB, (T0322)R75.CB) [> 4.1015 = 6.8358 < 8.8865] w=0.0910 to align # Constraint # added constraint: constraint((T0322)M66.CB, (T0322)T135.CB) [> 4.2306 = 7.0511 < 9.1664] w=0.0908 to align # Constraint # added constraint: constraint((T0322)R123.CB, (T0322)T135.CB) [> 4.5693 = 7.6154 < 9.9001] w=0.0908 to align # Constraint # added constraint: constraint((T0322)L20.CB, (T0322)S78.CB) [> 3.5726 = 5.9544 < 7.7407] w=0.0888 to align # Constraint # added constraint: constraint((T0322)E105.CB, (T0322)E128.CB) [> 4.6523 = 7.7538 < 10.0799] w=0.0844 to align # Constraint # added constraint: constraint((T0322)Y83.CB, (T0322)F118.CB) [> 4.2652 = 7.1087 < 9.2413] w=0.0823 to align # Constraint # added constraint: constraint((T0322)L117.CB, (T0322)P148.CB) [> 4.5505 = 7.5842 < 9.8595] w=0.0817 to align # Constraint # added constraint: constraint((T0322)I13.CB, (T0322)E38.CB) [> 4.0330 = 6.7217 < 8.7382] w=0.0809 to align # Constraint # added constraint: constraint((T0322)I111.CB, (T0322)G136.CA) [> 4.5473 = 7.5788 < 9.8525] w=0.0809 to align # Constraint # added constraint: constraint((T0322)S67.CB, (T0322)T87.CB) [> 4.3745 = 7.2909 < 9.4782] w=0.0743 to align # Constraint # added constraint: constraint((T0322)R44.CB, (T0322)W103.CB) [> 3.3805 = 5.6341 < 7.3243] w=0.0732 to align # Constraint # added constraint: constraint((T0322)R44.CB, (T0322)V104.CB) [> 4.3343 = 7.2238 < 9.3910] w=0.0732 to align # Constraint # added constraint: constraint((T0322)L45.CB, (T0322)W103.CB) [> 3.8829 = 6.4714 < 8.4129] w=0.0732 to align # Constraint # added constraint: constraint((T0322)Q80.CB, (T0322)V120.CB) [> 4.0897 = 6.8161 < 8.8610] w=0.0728 to align # Constraint # added constraint: constraint((T0322)F34.CB, (T0322)R48.CB) [> 4.5167 = 7.5278 < 9.7861] w=0.0708 to align # Constraint # added constraint: constraint((T0322)M66.CB, (T0322)I124.CB) [> 4.0925 = 6.8208 < 8.8670] w=0.0701 to align # Constraint # added constraint: constraint((T0322)G16.CA, (T0322)E35.CB) [> 3.8453 = 6.4089 < 8.3315] w=0.0686 to align # Constraint # added constraint: constraint((T0322)I77.CB, (T0322)G136.CA) [> 4.0781 = 6.7968 < 8.8358] w=0.0633 to align # Constraint # added constraint: constraint((T0322)C60.CB, (T0322)I132.CB) [> 4.4407 = 7.4012 < 9.6216] w=0.0607 to align # Constraint # added constraint: constraint((T0322)G16.CA, (T0322)R75.CB) [> 4.1630 = 6.9383 < 9.0198] w=0.0607 to align # Constraint # added constraint: constraint((T0322)H52.CB, (T0322)M64.CB) [> 4.1464 = 6.9106 < 8.9838] w=0.0606 to align # Constraint # added constraint: constraint((T0322)T10.CB, (T0322)E35.CB) [> 3.4390 = 5.7316 < 7.4511] w=0.0585 to align # Constraint # added constraint: constraint((T0322)Q80.CB, (T0322)G108.CA) [> 3.9895 = 6.6492 < 8.6439] w=0.0566 to align # Constraint # added constraint: constraint((T0322)Q29.CB, (T0322)M71.CB) [> 3.4971 = 5.8286 < 7.5771] w=0.0563 to align # Constraint # added constraint: constraint((T0322)S84.CB, (T0322)F138.CB) [> 3.9980 = 6.6633 < 8.6623] w=0.0558 to align # Constraint # added constraint: constraint((T0322)A43.CB, (T0322)Q80.CB) [> 4.2673 = 7.1121 < 9.2458] w=0.0535 to align # Constraint # added constraint: constraint((T0322)H61.CB, (T0322)L100.CB) [> 4.6084 = 7.6806 < 9.9848] w=0.0530 to align # Constraint # added constraint: constraint((T0322)F118.CB, (T0322)L151.CB) [> 4.0239 = 6.7066 < 8.7185] w=0.0515 to align # Constraint # added constraint: constraint((T0322)E114.CB, (T0322)L151.CB) [> 4.3749 = 7.2915 < 9.4789] w=0.0515 to align # Constraint # added constraint: constraint((T0322)I13.CB, (T0322)H36.CB) [> 4.3786 = 7.2977 < 9.4870] w=0.0506 to align # Constraint # added constraint: constraint((T0322)I13.CB, (T0322)R37.CB) [> 4.4296 = 7.3827 < 9.5975] w=0.0506 to align # Constraint # added constraint: constraint((T0322)E107.CB, (T0322)R121.CB) [> 4.5895 = 7.6491 < 9.9439] w=0.0506 to align # Constraint # added constraint: constraint((T0322)F47.CB, (T0322)L65.CB) [> 4.0227 = 6.7045 < 8.7158] w=0.0506 to align # Constraint # added constraint: constraint((T0322)Q19.CB, (T0322)R75.CB) [> 3.9391 = 6.5652 < 8.5347] w=0.0506 to align # Constraint # added constraint: constraint((T0322)I13.CB, (T0322)R75.CB) [> 3.9700 = 6.6167 < 8.6017] w=0.0506 to align # Constraint # added constraint: constraint((T0322)C60.CB, (T0322)A126.CB) [> 4.5960 = 7.6601 < 9.9581] w=0.0505 to align # Constraint # added constraint: constraint((T0322)Q80.CB, (T0322)A152.CB) [> 3.6990 = 6.1650 < 8.0145] w=0.0505 to align # Constraint # added constraint: constraint((T0322)G62.CA, (T0322)T133.CB) [> 4.2791 = 7.1318 < 9.2714] w=0.0503 to align # Constraint # added constraint: constraint((T0322)M66.CB, (T0322)T133.CB) [> 4.4276 = 7.3794 < 9.5932] w=0.0503 to align # Constraint # added constraint: constraint((T0322)E105.CB, (T0322)R129.CB) [> 4.6394 = 7.7323 < 10.0520] w=0.0503 to align # Constraint # added constraint: constraint((T0322)I13.CB, (T0322)G31.CA) [> 3.6912 = 6.1520 < 7.9976] w=0.0462 to align # Constraint # added constraint: constraint((T0322)Q80.CB, (T0322)F138.CB) [> 3.6536 = 6.0894 < 7.9162] w=0.0443 to align # Constraint # added constraint: constraint((T0322)M71.CB, (T0322)W85.CB) [> 4.0786 = 6.7977 < 8.8370] w=0.0440 to align # Constraint # added constraint: constraint((T0322)A11.CB, (T0322)L79.CB) [> 3.8585 = 6.4309 < 8.3602] w=0.0405 to align # Constraint # added constraint: constraint((T0322)Q19.CB, (T0322)S78.CB) [> 3.1200 = 5.2000 < 6.7600] w=0.0405 to align # Constraint # added constraint: constraint((T0322)L20.CB, (T0322)M64.CB) [> 4.3003 = 7.1671 < 9.3172] w=0.0404 to align # Constraint # added constraint: constraint((T0322)T10.CB, (T0322)E38.CB) [> 4.2564 = 7.0939 < 9.2221] w=0.0383 to align # Constraint # added constraint: constraint((T0322)Q29.CB, (T0322)M64.CB) [> 4.0077 = 6.6795 < 8.6833] w=0.0383 to align # Constraint # added constraint: constraint((T0322)I30.CB, (T0322)L45.CB) [> 3.7759 = 6.2932 < 8.1812] w=0.0383 to align # Constraint # added constraint: constraint((T0322)W85.CB, (T0322)V137.CB) [> 4.2409 = 7.0682 < 9.1886] w=0.0376 to align # Constraint # added constraint: constraint((T0322)G74.CA, (T0322)L90.CB) [> 4.2966 = 7.1610 < 9.3092] w=0.0329 to align # Constraint # added constraint: constraint((T0322)G74.CA, (T0322)V86.CB) [> 4.4614 = 7.4356 < 9.6663] w=0.0303 to align # Constraint # added constraint: constraint((T0322)G41.CA, (T0322)R121.CB) [> 4.6555 = 7.7592 < 10.0869] w=0.0303 to align # Constraint # added constraint: constraint((T0322)G74.CA, (T0322)S84.CB) [> 4.6746 = 7.7910 < 10.1283] w=0.0303 to align # Constraint # added constraint: constraint((T0322)V49.CB, (T0322)G58.CA) [> 4.1532 = 6.9220 < 8.9986] w=0.0303 to align # Constraint # added constraint: constraint((T0322)W85.CB, (T0322)M116.CB) [> 4.6730 = 7.7883 < 10.1248] w=0.0303 to align # Constraint # added constraint: constraint((T0322)S23.CB, (T0322)M71.CB) [> 4.2270 = 7.0450 < 9.1585] w=0.0303 to align # Constraint # added constraint: constraint((T0322)N21.CB, (T0322)M64.CB) [> 3.8059 = 6.3431 < 8.2460] w=0.0303 to align # Constraint # added constraint: constraint((T0322)A12.CB, (T0322)R75.CB) [> 3.2383 = 5.3971 < 7.0163] w=0.0303 to align # Constraint # added constraint: constraint((T0322)N55.CB, (T0322)M64.CB) [> 4.7041 = 7.8402 < 10.1923] w=0.0303 to align # Constraint # added constraint: constraint((T0322)H53.CB, (T0322)G63.CA) [> 4.7570 = 7.9284 < 10.3069] w=0.0303 to align # Constraint # added constraint: constraint((T0322)Q80.CB, (T0322)L151.CB) [> 3.3250 = 5.5416 < 7.2042] w=0.0303 to align # Constraint # added constraint: constraint((T0322)L65.CB, (T0322)T130.CB) [> 3.4215 = 5.7024 < 7.4132] w=0.0302 to align # Constraint # added constraint: constraint((T0322)R89.CB, (T0322)G134.CA) [> 3.8622 = 6.4370 < 8.3681] w=0.0302 to align # Constraint # added constraint: constraint((T0322)M91.CB, (T0322)T133.CB) [> 3.5055 = 5.8424 < 7.5952] w=0.0302 to align # Constraint # added constraint: constraint((T0322)D93.CB, (T0322)T130.CB) [> 3.8145 = 6.3574 < 8.2647] w=0.0302 to align # Constraint # added constraint: constraint((T0322)D93.CB, (T0322)L131.CB) [> 3.1929 = 5.3214 < 6.9179] w=0.0302 to align # Constraint # added constraint: constraint((T0322)F94.CB, (T0322)T130.CB) [> 3.3324 = 5.5540 < 7.2202] w=0.0302 to align # Constraint # added constraint: constraint((T0322)I111.CB, (T0322)T133.CB) [> 3.7495 = 6.2492 < 8.1240] w=0.0302 to align # Constraint # added constraint: constraint((T0322)L117.CB, (T0322)T135.CB) [> 3.6495 = 6.0824 < 7.9071] w=0.0302 to align # Constraint # added constraint: constraint((T0322)L117.CB, (T0322)G136.CA) [> 3.3527 = 5.5878 < 7.2642] w=0.0302 to align # Constraint # added constraint: constraint((T0322)T119.CB, (T0322)T133.CB) [> 3.2790 = 5.4651 < 7.1046] w=0.0302 to align # Constraint # added constraint: constraint((T0322)T119.CB, (T0322)G134.CA) [> 3.7545 = 6.2576 < 8.1348] w=0.0302 to align # Constraint # added constraint: constraint((T0322)R121.CB, (T0322)I132.CB) [> 4.4344 = 7.3906 < 9.6078] w=0.0302 to align # Constraint # added constraint: constraint((T0322)G122.CA, (T0322)L131.CB) [> 3.5581 = 5.9301 < 7.7091] w=0.0302 to align # Constraint # added constraint: constraint((T0322)N59.CB, (T0322)S96.CB) [> 4.6999 = 7.8331 < 10.1830] w=0.0294 to align # Constraint # added constraint: constraint((T0322)V86.CB, (T0322)V137.CB) [> 3.2491 = 5.4151 < 7.0396] w=0.0278 to align # Constraint # added constraint: constraint((T0322)W85.CB, (T0322)G136.CA) [> 3.6056 = 6.0094 < 7.8122] w=0.0278 to align # Constraint # added constraint: constraint((T0322)L57.CB, (T0322)L100.CB) [> 4.1026 = 6.8377 < 8.8890] w=0.0277 to align # Constraint # added constraint: constraint((T0322)Q80.CB, (T0322)S112.CB) [> 3.1149 = 5.1916 < 6.7490] w=0.0260 to align # Constraint # added constraint: constraint((T0322)H61.CB, (T0322)A98.CB) [> 4.7432 = 7.9053 < 10.2769] w=0.0229 to align # Constraint # added constraint: constraint((T0322)W103.CB, (T0322)W125.CB) [> 2.7546 = 4.5910 < 5.9683] w=0.0212 to align # Constraint # added constraint: constraint((T0322)G97.CA, (T0322)T130.CB) [> 4.4298 = 7.3829 < 9.5978] w=0.0212 to align # Constraint # added constraint: constraint((T0322)E105.CB, (T0322)G122.CA) [> 3.8826 = 6.4710 < 8.4123] w=0.0202 to align # Constraint # added constraint: constraint((T0322)R75.CB, (T0322)W85.CB) [> 3.8363 = 6.3939 < 8.3120] w=0.0202 to align # Constraint # added constraint: constraint((T0322)M71.CB, (T0322)F138.CB) [> 4.1953 = 6.9922 < 9.0899] w=0.0202 to align # Constraint # added constraint: constraint((T0322)M71.CB, (T0322)T87.CB) [> 4.3039 = 7.1732 < 9.3251] w=0.0202 to align # Constraint # added constraint: constraint((T0322)M66.CB, (T0322)V104.CB) [> 3.4237 = 5.7062 < 7.4181] w=0.0202 to align # Constraint # added constraint: constraint((T0322)M66.CB, (T0322)G122.CA) [> 3.4016 = 5.6693 < 7.3701] w=0.0202 to align # Constraint # added constraint: constraint((T0322)L5.CB, (T0322)M71.CB) [> 4.0451 = 6.7419 < 8.7645] w=0.0202 to align # Constraint # added constraint: constraint((T0322)G16.CA, (T0322)F26.CB) [> 4.7900 = 7.9833 < 10.3784] w=0.0202 to align # Constraint # added constraint: constraint((T0322)G16.CA, (T0322)S84.CB) [> 4.3887 = 7.3144 < 9.5088] w=0.0202 to align # Constraint # added constraint: constraint((T0322)G27.CA, (T0322)F68.CB) [> 4.4854 = 7.4757 < 9.7184] w=0.0202 to align # Constraint # added constraint: constraint((T0322)A11.CB, (T0322)L33.CB) [> 3.2919 = 5.4865 < 7.1325] w=0.0202 to align # Constraint # added constraint: constraint((T0322)A11.CB, (T0322)R75.CB) [> 4.4053 = 7.3421 < 9.5447] w=0.0202 to align # Constraint # added constraint: constraint((T0322)M66.CB, (T0322)F94.CB) [> 4.7913 = 7.9856 < 10.3812] w=0.0202 to align # Constraint # added constraint: constraint((T0322)E38.CB, (T0322)S82.CB) [> 4.6518 = 7.7530 < 10.0789] w=0.0202 to align # Constraint # added constraint: constraint((T0322)Q80.CB, (T0322)Y153.CB) [> 3.5965 = 5.9941 < 7.7924] w=0.0202 to align # Constraint # added constraint: constraint((T0322)Q80.CB, (T0322)E156.CB) [> 3.1713 = 5.2854 < 6.8710] w=0.0202 to align # Constraint # added constraint: constraint((T0322)S23.CB, (T0322)L33.CB) [> 3.5024 = 5.8374 < 7.5886] w=0.0202 to align # Constraint # added constraint: constraint((T0322)L90.CB, (T0322)T133.CB) [> 4.4233 = 7.3723 < 9.5839] w=0.0202 to align # Constraint # added constraint: constraint((T0322)V88.CB, (T0322)T135.CB) [> 3.0241 = 5.0403 < 6.5523] w=0.0202 to align # Constraint # added constraint: constraint((T0322)T87.CB, (T0322)T135.CB) [> 4.1818 = 6.9697 < 9.0605] w=0.0202 to align # Constraint # added constraint: constraint((T0322)T87.CB, (T0322)G134.CA) [> 3.7096 = 6.1827 < 8.0375] w=0.0202 to align # Constraint # added constraint: constraint((T0322)G27.CA, (T0322)E107.CB) [> 4.0740 = 6.7900 < 8.8270] w=0.0201 to align # Constraint # added constraint: constraint((T0322)Q29.CB, (T0322)E107.CB) [> 3.0942 = 5.1570 < 6.7041] w=0.0201 to align # Constraint # added constraint: constraint((T0322)E107.CB, (T0322)T130.CB) [> 4.3222 = 7.2036 < 9.3647] w=0.0201 to align # Constraint # added constraint: constraint((T0322)R75.CB, (T0322)G122.CA) [> 3.8741 = 6.4569 < 8.3939] w=0.0201 to align # Constraint # added constraint: constraint((T0322)S23.CB, (T0322)R75.CB) [> 3.6828 = 6.1380 < 7.9794] w=0.0101 to align # Constraint # added constraint: constraint((T0322)L20.CB, (T0322)E50.CB) [> 4.1862 = 6.9769 < 9.0700] w=0.0101 to align # Constraint # added constraint: constraint((T0322)H52.CB, (T0322)H61.CB) [> 3.1176 = 5.1961 < 6.7549] w=0.0101 to align # Constraint # added constraint: constraint((T0322)L110.CB, (T0322)A157.CB) [> 3.2179 = 5.3632 < 6.9722] w=0.0101 to align # Constraint # added constraint: constraint((T0322)E113.CB, (T0322)A157.CB) [> 4.0095 = 6.6824 < 8.6872] w=0.0101 to align # Constraint # added constraint: constraint((T0322)F118.CB, (T0322)A157.CB) [> 4.5893 = 7.6489 < 9.9435] w=0.0101 to align # Constraint # added constraint: constraint((T0322)L5.CB, (T0322)Q80.CB) [> 3.8071 = 6.3451 < 8.2487] w=0.0101 to align # Constraint # added constraint: constraint((T0322)L5.CB, (T0322)R75.CB) [> 3.2056 = 5.3427 < 6.9455] w=0.0101 to align # Constraint # added constraint: constraint((T0322)M66.CB, (T0322)V137.CB) [> 4.6308 = 7.7180 < 10.0334] w=0.0101 to align # Constraint # added constraint: constraint((T0322)F26.CB, (T0322)R48.CB) [> 3.0480 = 5.0799 < 6.6039] w=0.0101 to align # Constraint # added constraint: constraint((T0322)M91.CB, (T0322)F138.CB) [> 4.7100 = 7.8500 < 10.2050] w=0.0101 to align # Constraint # added constraint: constraint((T0322)V86.CB, (T0322)P148.CB) [> 4.6193 = 7.6989 < 10.0086] w=0.0101 to align # Constraint # added constraint: constraint((T0322)V86.CB, (T0322)A152.CB) [> 3.7805 = 6.3008 < 8.1911] w=0.0101 to align # Constraint # added constraint: constraint((T0322)V86.CB, (T0322)Y153.CB) [> 3.7911 = 6.3185 < 8.2141] w=0.0101 to align # Constraint # added constraint: constraint((T0322)V86.CB, (T0322)G136.CA) [> 3.7841 = 6.3069 < 8.1989] w=0.0101 to align # Constraint # added constraint: constraint((T0322)V88.CB, (T0322)L141.CB) [> 4.7024 = 7.8374 < 10.1886] w=0.0101 to align # Constraint # added constraint: constraint((T0322)R89.CB, (T0322)T133.CB) [> 4.7109 = 7.8516 < 10.2071] w=0.0101 to align # Constraint # added constraint: constraint((T0322)F118.CB, (T0322)Y153.CB) [> 3.8830 = 6.4716 < 8.4131] w=0.0101 to align # Constraint # added constraint: constraint((T0322)R24.CB, (T0322)L95.CB) [> 2.9722 = 4.9538 < 6.4399] w=0.0101 to align # Constraint # added constraint: constraint((T0322)F26.CB, (T0322)T130.CB) [> 3.1860 = 5.3099 < 6.9029] w=0.0101 to align # Constraint # added constraint: constraint((T0322)G27.CA, (T0322)R123.CB) [> 4.2295 = 7.0492 < 9.1639] w=0.0101 to align # Constraint # added constraint: constraint((T0322)G27.CA, (T0322)L131.CB) [> 4.7476 = 7.9126 < 10.2864] w=0.0101 to align # Constraint # added constraint: constraint((T0322)L5.CB, (T0322)E107.CB) [> 4.5323 = 7.5539 < 9.8200] w=0.0101 to align # Constraint # added constraint: constraint((T0322)V88.CB, (T0322)P148.CB) [> 4.7462 = 7.9103 < 10.2833] w=0.0101 to align # Constraint # added constraint: constraint((T0322)S23.CB, (T0322)M64.CB) [> 4.2902 = 7.1502 < 9.2953] w=0.0101 to align # Constraint # added constraint: constraint((T0322)L20.CB, (T0322)T54.CB) [> 4.3188 = 7.1981 < 9.3575] w=0.0101 to align # Constraint # added constraint: constraint((T0322)I77.CB, (T0322)V86.CB) [> 4.7937 = 7.9894 < 10.3863] w=0.0101 to align # Constraint # added constraint: constraint((T0322)R75.CB, (T0322)E107.CB) [> 4.4442 = 7.4070 < 9.6291] w=0.0099 to align # Constraint # added constraint: constraint((T0322)V86.CB, (T0322)L117.CB) [> 4.1097 = 6.8494 < 8.9043] w=0.0099 to align # Constraint # added constraint: constraint((T0322)A11.CB, (T0322)E107.CB) [> 3.1122 = 5.1871 < 6.7432] w=0.0098 to align # Constraint # added constraint: constraint((T0322)R75.CB, (T0322)E105.CB) [> 4.1565 = 6.9275 < 9.0057] w=0.0079 to align # Constraint # added constraint: constraint((T0322)A8.CB, (T0322)V88.CB) [> 4.5687 = 7.6146 < 9.8989] w=0.0040 to align # Constraint # added constraint: constraint((T0322)M66.CB, (T0322)R89.CB) [> 4.4607 = 7.4345 < 9.6649] w=0.0040 to align # Constraint # added constraint: constraint((T0322)G62.CA, (T0322)M91.CB) [> 4.6770 = 7.7950 < 10.1335] w=0.0040 to align # Constraint # added constraint: constraint((T0322)I30.CB, (T0322)T119.CB) [> 4.4201 = 7.3668 < 9.5769] w=0.0040 to align # SetCost created cost = # ( 1.0000 * align ) # command:# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0322/ # command:# reading script from file servers-clean.under # Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/T0322/decoys/ # ReadConformPDB reading from PDB file tr322.gromacs0.pdb.gz looking for model 1 # Found a chain break before 155 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file tr322.gromacs0.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 155 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file tr322.pdb.gz looking for model 1 # Found a chain break before 155 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file tr322.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 155 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file ../dimer/decoys/dimer-tr322-2fs2A.pdb.gz looking for chain 'A' model 1 # Found a chain break before 155 # copying to AlignedFragments data structure # naming current conformation dimer//dimer-tr322-2fs2A # ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0322 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_POPULUS_TS1 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0322 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_POPULUS_TS2 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0322 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_POPULUS_TS3 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0322 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_POPULUS_TS4 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0322 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_POPULUS_TS5 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_RECOM_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0322 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_RECOM_TS1 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_RECOM_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0322 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_RECOM_TS2 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_RECOM_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0322 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_RECOM_TS3 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_RECOM_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0322 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_RECOM_TS4 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_RECOM_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0322 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_RECOM_TS5 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0322 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_TS1 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0322 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_TS2 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0322 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_TS3 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0322 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_TS4 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0322 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_TS5 # ReadConformPDB reading from PDB file servers/3Dpro_TS1.pdb.gz looking for model 1 # Found a chain break before 131 # copying to AlignedFragments data structure # naming current conformation 3Dpro_TS1 # ReadConformPDB reading from PDB file servers/3Dpro_TS2.pdb.gz looking for model 1 # Found a chain break before 130 # copying to AlignedFragments data structure # naming current conformation 3Dpro_TS2 # ReadConformPDB reading from PDB file servers/3Dpro_TS3.pdb.gz looking for model 1 # Found a chain break before 76 # copying to AlignedFragments data structure # naming current conformation 3Dpro_TS3 # ReadConformPDB reading from PDB file servers/3Dpro_TS4.pdb.gz looking for model 1 # Found a chain break before 138 # copying to AlignedFragments data structure # naming current conformation 3Dpro_TS4 # ReadConformPDB reading from PDB file servers/3Dpro_TS5.pdb.gz looking for model 1 # Found a chain break before 100 # copying to AlignedFragments data structure # naming current conformation 3Dpro_TS5 # ReadConformPDB reading from PDB file servers/ABIpro_TS1.pdb.gz looking for model 1 # Found a chain break before 152 # copying to AlignedFragments data structure # naming current conformation ABIpro_TS1 # ReadConformPDB reading from PDB file servers/ABIpro_TS2.pdb.gz looking for model 1 # Found a chain break before 145 # copying to AlignedFragments data structure # naming current conformation ABIpro_TS2 # ReadConformPDB reading from PDB file servers/ABIpro_TS3.pdb.gz looking for model 1 # Found a chain break before 152 # copying to AlignedFragments data structure # naming current conformation ABIpro_TS3 # ReadConformPDB reading from PDB file servers/ABIpro_TS4.pdb.gz looking for model 1 # Found a chain break before 152 # copying to AlignedFragments data structure # naming current conformation ABIpro_TS4 # ReadConformPDB reading from PDB file servers/ABIpro_TS5.pdb.gz looking for model 1 # Found a chain break before 153 # copying to AlignedFragments data structure # naming current conformation ABIpro_TS5 # ReadConformPDB reading from PDB file servers/BayesHH_TS1.pdb.gz looking for model 1 # Found a chain break before 31 # copying to AlignedFragments data structure # naming current conformation BayesHH_TS1 # ReadConformPDB reading from PDB file servers/Bilab-ENABLE_TS1.pdb.gz looking for model 1 # Found a chain break before 103 # copying to AlignedFragments data structure # naming current conformation Bilab-ENABLE_TS1 # ReadConformPDB reading from PDB file servers/CIRCLE_TS1.pdb.gz looking for model 1 # Found a chain break before 148 # copying to AlignedFragments data structure # naming current conformation CIRCLE_TS1 # ReadConformPDB reading from PDB file servers/CIRCLE_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0322 can't currently be optimized by undertaker # naming current conformation CIRCLE_TS2 # ReadConformPDB reading from PDB file servers/CIRCLE_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0322 can't currently be optimized by undertaker # naming current conformation CIRCLE_TS3 # ReadConformPDB reading from PDB file servers/CIRCLE_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0322 can't currently be optimized by undertaker # naming current conformation CIRCLE_TS4 # ReadConformPDB reading from PDB file servers/CIRCLE_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0322 can't currently be optimized by undertaker # naming current conformation CIRCLE_TS5 # ReadConformPDB reading from PDB file servers/CPHmodels_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0322 can't currently be optimized by undertaker # naming current conformation CPHmodels_TS1 # ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0322 can't currently be optimized by undertaker # naming current conformation CaspIta-FOX_TS1 # ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0322 can't currently be optimized by undertaker # naming current conformation CaspIta-FOX_TS2 # ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0322 can't currently be optimized by undertaker # naming current conformation CaspIta-FOX_TS3 # ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0322 can't currently be optimized by undertaker # naming current conformation CaspIta-FOX_TS4 # ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0322 can't currently be optimized by undertaker # naming current conformation CaspIta-FOX_TS5 # ReadConformPDB reading from PDB file servers/Distill_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0322 can't currently be optimized by undertaker # naming current conformation Distill_TS1 # ReadConformPDB reading from PDB file servers/Distill_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0322 can't currently be optimized by undertaker # naming current conformation Distill_TS2 # ReadConformPDB reading from PDB file servers/Distill_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0322 can't currently be optimized by undertaker # naming current conformation Distill_TS3 # ReadConformPDB reading from PDB file servers/Distill_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0322 can't currently be optimized by undertaker # naming current conformation Distill_TS4 # ReadConformPDB reading from PDB file servers/Distill_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0322 can't currently be optimized by undertaker # naming current conformation Distill_TS5 # ReadConformPDB reading from PDB file servers/FAMSD_TS1.pdb.gz looking for model 1 # Found a chain break before 149 # copying to AlignedFragments data structure # naming current conformation FAMSD_TS1 # ReadConformPDB reading from PDB file servers/FAMSD_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0322 can't currently be optimized by undertaker # naming current conformation FAMSD_TS2 # ReadConformPDB reading from PDB file servers/FAMSD_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0322 can't currently be optimized by undertaker # naming current conformation FAMSD_TS3 # ReadConformPDB reading from PDB file servers/FAMSD_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0322 can't currently be optimized by undertaker # naming current conformation FAMSD_TS4 # ReadConformPDB reading from PDB file servers/FAMSD_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0322 can't currently be optimized by undertaker # naming current conformation FAMSD_TS5 # ReadConformPDB reading from PDB file servers/FAMS_TS1.pdb.gz looking for model 1 # Found a chain break before 149 # copying to AlignedFragments data structure # naming current conformation FAMS_TS1 # ReadConformPDB reading from PDB file servers/FAMS_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0322 can't currently be optimized by undertaker # naming current conformation FAMS_TS2 # ReadConformPDB reading from PDB file servers/FAMS_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0322 can't currently be optimized by undertaker # naming current conformation FAMS_TS3 # ReadConformPDB reading from PDB file servers/FAMS_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0322 can't currently be optimized by undertaker # naming current conformation FAMS_TS4 # ReadConformPDB reading from PDB file servers/FAMS_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0322 can't currently be optimized by undertaker # naming current conformation FAMS_TS5 # ReadConformPDB reading from PDB file servers/FOLDpro_TS1.pdb.gz looking for model 1 # Found a chain break before 129 # copying to AlignedFragments data structure # naming current conformation FOLDpro_TS1 # ReadConformPDB reading from PDB file servers/FOLDpro_TS2.pdb.gz looking for model 1 # Found a chain break before 142 # copying to AlignedFragments data structure # naming current conformation FOLDpro_TS2 # ReadConformPDB reading from PDB file servers/FOLDpro_TS3.pdb.gz looking for model 1 # Found a chain break before 111 # copying to AlignedFragments data structure # naming current conformation FOLDpro_TS3 # ReadConformPDB reading from PDB file servers/FOLDpro_TS4.pdb.gz looking for model 1 # Found a chain break before 88 # copying to AlignedFragments data structure # naming current conformation FOLDpro_TS4 # ReadConformPDB reading from PDB file servers/FOLDpro_TS5.pdb.gz looking for model 1 # Found a chain break before 41 # copying to AlignedFragments data structure # naming current conformation FOLDpro_TS5 # ReadConformPDB reading from PDB file servers/FORTE1_AL1.pdb.gz looking for model 1 Skipped atom 79, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz Skipped atom 96, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz Skipped atom 337, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz Skipped atom 346, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz Skipped atom 391, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz Skipped atom 404, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz # WARNING: incomplete conformation T0322 can't currently be optimized by undertaker # naming current conformation FORTE1_AL1 # ReadConformPDB reading from PDB file servers/FORTE1_AL2.pdb.gz looking for model 1 Skipped atom 103, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL2.pdb.gz # WARNING: incomplete conformation T0322 can't currently be optimized by undertaker # naming current conformation FORTE1_AL2 # ReadConformPDB reading from PDB file servers/FORTE1_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0322 can't currently be optimized by undertaker # naming current conformation FORTE1_AL3 # ReadConformPDB reading from PDB file servers/FORTE1_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0322 can't currently be optimized by undertaker # naming current conformation FORTE1_AL4 # ReadConformPDB reading from PDB file servers/FORTE1_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0322 can't currently be optimized by undertaker # naming current conformation FORTE1_AL5 # ReadConformPDB reading from PDB file servers/FORTE2_AL1.pdb.gz looking for model 1 Skipped atom 79, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz Skipped atom 96, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz Skipped atom 337, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz Skipped atom 346, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz Skipped atom 391, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz Skipped atom 404, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz # WARNING: incomplete conformation T0322 can't currently be optimized by undertaker # naming current conformation FORTE2_AL1 # ReadConformPDB reading from PDB file servers/FORTE2_AL2.pdb.gz looking for model 1 Skipped atom 103, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL2.pdb.gz # WARNING: incomplete conformation T0322 can't currently be optimized by undertaker # naming current conformation FORTE2_AL2 # ReadConformPDB reading from PDB file servers/FORTE2_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0322 can't currently be optimized by undertaker # naming current conformation FORTE2_AL3 # ReadConformPDB reading from PDB file servers/FORTE2_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0322 can't currently be optimized by undertaker # naming current conformation FORTE2_AL4 # ReadConformPDB reading from PDB file servers/FORTE2_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0322 can't currently be optimized by undertaker # naming current conformation FORTE2_AL5 # ReadConformPDB reading from PDB file servers/FPSOLVER-SERVER_TS1.pdb.gz looking for model 1 # Found a chain break before 156 # copying to AlignedFragments data structure # naming current conformation FPSOLVER-SERVER_TS1 # ReadConformPDB reading from PDB file servers/FPSOLVER-SERVER_TS2.pdb.gz looking for model 1 # Found a chain break before 134 # copying to AlignedFragments data structure # naming current conformation FPSOLVER-SERVER_TS2 # ReadConformPDB reading from PDB file servers/FPSOLVER-SERVER_TS3.pdb.gz looking for model 1 # Found a chain break before 153 # copying to AlignedFragments data structure # naming current conformation FPSOLVER-SERVER_TS3 # ReadConformPDB reading from PDB file servers/FPSOLVER-SERVER_TS4.pdb.gz looking for model 1 # Found a chain break before 120 # copying to AlignedFragments data structure # naming current conformation FPSOLVER-SERVER_TS4 # ReadConformPDB reading from PDB file servers/FPSOLVER-SERVER_TS5.pdb.gz looking for model 1 # Found a chain break before 156 # copying to AlignedFragments data structure # naming current conformation FPSOLVER-SERVER_TS5 # ReadConformPDB reading from PDB file servers/FUGMOD_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0322 can't currently be optimized by undertaker # naming current conformation FUGMOD_TS1 # ReadConformPDB reading from PDB file servers/FUGMOD_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0322 can't currently be optimized by undertaker # naming current conformation FUGMOD_TS2 # ReadConformPDB reading from PDB file servers/FUGMOD_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0322 can't currently be optimized by undertaker # naming current conformation FUGMOD_TS3 # ReadConformPDB reading from PDB file servers/FUGMOD_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0322 can't currently be optimized by undertaker # naming current conformation FUGMOD_TS4 # ReadConformPDB reading from PDB file servers/FUGMOD_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0322 can't currently be optimized by undertaker # naming current conformation FUGMOD_TS5 # ReadConformPDB reading from PDB file servers/FUGUE_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0322 can't currently be optimized by undertaker # naming current conformation FUGUE_AL1 # ReadConformPDB reading from PDB file servers/FUGUE_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0322 can't currently be optimized by undertaker # naming current conformation FUGUE_AL2 # ReadConformPDB reading from PDB file servers/FUGUE_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0322 can't currently be optimized by undertaker # naming current conformation FUGUE_AL3 # ReadConformPDB reading from PDB file servers/FUGUE_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0322 can't currently be optimized by undertaker # naming current conformation FUGUE_AL4 # ReadConformPDB reading from PDB file servers/FUGUE_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0322 can't currently be optimized by undertaker # naming current conformation FUGUE_AL5 # ReadConformPDB reading from PDB file servers/FUNCTION_TS1.pdb.gz looking for model 1 # Found a chain break before 149 # copying to AlignedFragments data structure # naming current conformation FUNCTION_TS1 # ReadConformPDB reading from PDB file servers/FUNCTION_TS2.pdb.gz looking for model 1 # Found a chain break before 156 # copying to AlignedFragments data structure # naming current conformation FUNCTION_TS2 # ReadConformPDB reading from PDB file servers/FUNCTION_TS3.pdb.gz looking for model 1 # Found a chain break before 154 # copying to AlignedFragments data structure # naming current conformation FUNCTION_TS3 # ReadConformPDB reading from PDB file servers/FUNCTION_TS4.pdb.gz looking for model 1 # Found a chain break before 151 # copying to AlignedFragments data structure # naming current conformation FUNCTION_TS4 # ReadConformPDB reading from PDB file servers/FUNCTION_TS5.pdb.gz looking for model 1 # Found a chain break before 121 # copying to AlignedFragments data structure # naming current conformation FUNCTION_TS5 # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0322 can't currently be optimized by undertaker # naming current conformation GeneSilicoMetaServer_TS1 # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0322 can't currently be optimized by undertaker # naming current conformation GeneSilicoMetaServer_TS2 # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0322 can't currently be optimized by undertaker # naming current conformation GeneSilicoMetaServer_TS3 # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0322 can't currently be optimized by undertaker # naming current conformation GeneSilicoMetaServer_TS4 # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0322 can't currently be optimized by undertaker # naming current conformation GeneSilicoMetaServer_TS5 # ReadConformPDB reading from PDB file servers/HHpred1_TS1.pdb.gz looking for model 1 # Found a chain break before 103 # copying to AlignedFragments data structure # naming current conformation HHpred1_TS1 # ReadConformPDB reading from PDB file servers/HHpred2_TS1.pdb.gz looking for model 1 # Found a chain break before 103 # copying to AlignedFragments data structure # naming current conformation HHpred2_TS1 # ReadConformPDB reading from PDB file servers/HHpred3_TS1.pdb.gz looking for model 1 # Found a chain break before 103 # copying to AlignedFragments data structure # naming current conformation HHpred3_TS1 # ReadConformPDB reading from PDB file servers/Huber-Torda-Server_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0322 can't currently be optimized by undertaker # naming current conformation Huber-Torda-Server_TS1 # ReadConformPDB reading from PDB file servers/Huber-Torda-Server_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0322 can't currently be optimized by undertaker # naming current conformation Huber-Torda-Server_TS2 # ReadConformPDB reading from PDB file servers/Huber-Torda-Server_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0322 can't currently be optimized by undertaker # naming current conformation Huber-Torda-Server_TS3 # ReadConformPDB reading from PDB file servers/Huber-Torda-Server_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0322 can't currently be optimized by undertaker # naming current conformation Huber-Torda-Server_TS4 # ReadConformPDB reading from PDB file servers/Huber-Torda-Server_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0322 can't currently be optimized by undertaker # naming current conformation Huber-Torda-Server_TS5 # ReadConformPDB reading from PDB file servers/LOOPP_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0322 can't currently be optimized by undertaker # naming current conformation LOOPP_TS1 # ReadConformPDB reading from PDB file servers/LOOPP_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0322 can't currently be optimized by undertaker # naming current conformation LOOPP_TS2 # ReadConformPDB reading from PDB file servers/LOOPP_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0322 can't currently be optimized by undertaker # naming current conformation LOOPP_TS3 # ReadConformPDB reading from PDB file servers/LOOPP_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0322 can't currently be optimized by undertaker # naming current conformation LOOPP_TS4 # ReadConformPDB reading from PDB file servers/LOOPP_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0322 can't currently be optimized by undertaker # naming current conformation LOOPP_TS5 # ReadConformPDB reading from PDB file servers/MIG_FROST_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0322 can't currently be optimized by undertaker # naming current conformation MIG_FROST_AL1 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server2_TS1.pdb.gz looking for model 1 # Found a chain break before 76 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server2_TS1 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server2_TS2.pdb.gz looking for model 1 # Found a chain break before 62 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server2_TS2 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server2_TS3.pdb.gz looking for model 1 # Found a chain break before 76 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server2_TS3 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server2_TS4.pdb.gz looking for model 1 # Found a chain break before 79 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server2_TS4 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server2_TS5.pdb.gz looking for model 1 # Found a chain break before 143 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server2_TS5 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS1.pdb.gz looking for model 1 # Found a chain break before 29 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server_TS1 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS2.pdb.gz looking for model 1 # Found a chain break before 76 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server_TS2 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS3.pdb.gz looking for model 1 # Found a chain break before 31 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server_TS3 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS4.pdb.gz looking for model 1 # Found a chain break before 143 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server_TS4 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS5.pdb.gz looking for model 1 # Found a chain break before 76 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server_TS5 # ReadConformPDB reading from PDB file servers/MetaTasser_TS1.pdb.gz looking for model 1 # Found a chain break before 156 # copying to AlignedFragments data structure # naming current conformation MetaTasser_TS1 # ReadConformPDB reading from PDB file servers/MetaTasser_TS2.pdb.gz looking for model 1 # Found a chain break before 156 # copying to AlignedFragments data structure # naming current conformation MetaTasser_TS2 # ReadConformPDB reading from PDB file servers/MetaTasser_TS3.pdb.gz looking for model 1 # Found a chain break before 156 # copying to AlignedFragments data structure # naming current conformation MetaTasser_TS3 # ReadConformPDB reading from PDB file servers/MetaTasser_TS4.pdb.gz looking for model 1 # Found a chain break before 154 # copying to AlignedFragments data structure # naming current conformation MetaTasser_TS4 # ReadConformPDB reading from PDB file servers/MetaTasser_TS5.pdb.gz looking for model 1 # Found a chain break before 154 # copying to AlignedFragments data structure # naming current conformation MetaTasser_TS5 # ReadConformPDB reading from PDB file servers/NN_PUT_lab_TS1.pdb.gz looking for model 1 # Found a chain break before 31 # copying to AlignedFragments data structure # naming current conformation NN_PUT_lab_TS1 # ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS1.pdb.gz looking for model 1 # naming current conformation PROTINFO-AB_TS1 # ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS2.pdb.gz looking for model 1 # naming current conformation PROTINFO-AB_TS2 # ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS3.pdb.gz looking for model 1 # naming current conformation PROTINFO-AB_TS3 # ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS4.pdb.gz looking for model 1 # naming current conformation PROTINFO-AB_TS4 # ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS5.pdb.gz looking for model 1 # naming current conformation PROTINFO-AB_TS5 # ReadConformPDB reading from PDB file servers/PROTINFO_TS1.pdb.gz looking for model 1 # naming current conformation PROTINFO_TS1 # ReadConformPDB reading from PDB file servers/PROTINFO_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0322 can't currently be optimized by undertaker # naming current conformation PROTINFO_TS2 # ReadConformPDB reading from PDB file servers/PROTINFO_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0322 can't currently be optimized by undertaker # naming current conformation PROTINFO_TS3 # ReadConformPDB reading from PDB file servers/PROTINFO_TS4.pdb.gz looking for model 1 # naming current conformation PROTINFO_TS4 # ReadConformPDB reading from PDB file servers/PROTINFO_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0322 can't currently be optimized by undertaker # naming current conformation PROTINFO_TS5 # ReadConformPDB reading from PDB file servers/Pcons6_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0322 can't currently be optimized by undertaker # naming current conformation Pcons6_TS1 # ReadConformPDB reading from PDB file servers/Pcons6_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0322 can't currently be optimized by undertaker # naming current conformation Pcons6_TS2 # ReadConformPDB reading from PDB file servers/Pcons6_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0322 can't currently be optimized by undertaker # naming current conformation Pcons6_TS3 # ReadConformPDB reading from PDB file servers/Pcons6_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0322 can't currently be optimized by undertaker # naming current conformation Pcons6_TS4 # ReadConformPDB reading from PDB file servers/Pcons6_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0322 can't currently be optimized by undertaker # naming current conformation Pcons6_TS5 # ReadConformPDB reading from PDB file servers/Phyre-1_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0322 can't currently be optimized by undertaker # naming current conformation Phyre-1_TS1 # ReadConformPDB reading from PDB file servers/Phyre-2_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0322 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation Phyre-2_TS1 # ReadConformPDB reading from PDB file servers/Phyre-2_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0322 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation Phyre-2_TS2 # ReadConformPDB reading from PDB file servers/Phyre-2_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0322 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation Phyre-2_TS3 # ReadConformPDB reading from PDB file servers/Phyre-2_TS4.pdb.gz looking for model 1 # Found a chain break before 155 # copying to AlignedFragments data structure # naming current conformation Phyre-2_TS4 # ReadConformPDB reading from PDB file servers/Phyre-2_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0322 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation Phyre-2_TS5 # ReadConformPDB reading from PDB file servers/Pmodeller6_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0322 can't currently be optimized by undertaker # naming current conformation Pmodeller6_TS1 # ReadConformPDB reading from PDB file servers/Pmodeller6_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0322 can't currently be optimized by undertaker # naming current conformation Pmodeller6_TS2 # ReadConformPDB reading from PDB file servers/Pmodeller6_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0322 can't currently be optimized by undertaker # naming current conformation Pmodeller6_TS3 # ReadConformPDB reading from PDB file servers/Pmodeller6_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0322 can't currently be optimized by undertaker # naming current conformation Pmodeller6_TS4 # ReadConformPDB reading from PDB file servers/Pmodeller6_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0322 can't currently be optimized by undertaker # naming current conformation Pmodeller6_TS5 # ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS1.pdb.gz looking for model 1 # Found a chain break before 31 # copying to AlignedFragments data structure # naming current conformation RAPTOR-ACE_TS1 # ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS2.pdb.gz looking for model 1 # Found a chain break before 31 # copying to AlignedFragments data structure # naming current conformation RAPTOR-ACE_TS2 # ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS3.pdb.gz looking for model 1 # Found a chain break before 137 # copying to AlignedFragments data structure # naming current conformation RAPTOR-ACE_TS3 # ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS4.pdb.gz looking for model 1 # Found a chain break before 82 # copying to AlignedFragments data structure # naming current conformation RAPTOR-ACE_TS4 # ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS5.pdb.gz looking for model 1 # Found a chain break before 80 # copying to AlignedFragments data structure # naming current conformation RAPTOR-ACE_TS5 # ReadConformPDB reading from PDB file servers/RAPTORESS_TS1.pdb.gz looking for model 1 # Found a chain break before 151 # copying to AlignedFragments data structure # naming current conformation RAPTORESS_TS1 # ReadConformPDB reading from PDB file servers/RAPTORESS_TS2.pdb.gz looking for model 1 # Found a chain break before 147 # copying to AlignedFragments data structure # naming current conformation RAPTORESS_TS2 # ReadConformPDB reading from PDB file servers/RAPTORESS_TS3.pdb.gz looking for model 1 # Found a chain break before 152 # copying to AlignedFragments data structure # naming current conformation RAPTORESS_TS3 # ReadConformPDB reading from PDB file servers/RAPTORESS_TS4.pdb.gz looking for model 1 # Found a chain break before 152 # copying to AlignedFragments data structure # naming current conformation RAPTORESS_TS4 # ReadConformPDB reading from PDB file servers/RAPTORESS_TS5.pdb.gz looking for model 1 # Found a chain break before 147 # copying to AlignedFragments data structure # naming current conformation RAPTORESS_TS5 # ReadConformPDB reading from PDB file servers/RAPTOR_TS1.pdb.gz looking for model 1 # naming current conformation RAPTOR_TS1 # ReadConformPDB reading from PDB file servers/RAPTOR_TS2.pdb.gz looking for model 1 # Found a chain break before 82 # copying to AlignedFragments data structure # naming current conformation RAPTOR_TS2 # ReadConformPDB reading from PDB file servers/RAPTOR_TS3.pdb.gz looking for model 1 # Found a chain break before 55 # copying to AlignedFragments data structure # naming current conformation RAPTOR_TS3 # ReadConformPDB reading from PDB file servers/RAPTOR_TS4.pdb.gz looking for model 1 # Found a chain break before 55 # copying to AlignedFragments data structure # naming current conformation RAPTOR_TS4 # ReadConformPDB reading from PDB file servers/RAPTOR_TS5.pdb.gz looking for model 1 # Found a chain break before 29 # copying to AlignedFragments data structure # naming current conformation RAPTOR_TS5 # ReadConformPDB reading from PDB file servers/ROBETTA_TS1.pdb.gz looking for model 1 # Found a chain break before 146 # copying to AlignedFragments data structure # naming current conformation ROBETTA_TS1 # ReadConformPDB reading from PDB file servers/ROBETTA_TS2.pdb.gz looking for model 1 # Found a chain break before 150 # copying to AlignedFragments data structure # naming current conformation ROBETTA_TS2 # ReadConformPDB reading from PDB file servers/ROBETTA_TS3.pdb.gz looking for model 1 # Found a chain break before 89 # copying to AlignedFragments data structure # naming current conformation ROBETTA_TS3 # ReadConformPDB reading from PDB file servers/ROBETTA_TS4.pdb.gz looking for model 1 # Found a chain break before 81 # copying to AlignedFragments data structure # naming current conformation ROBETTA_TS4 # ReadConformPDB reading from PDB file servers/ROBETTA_TS5.pdb.gz looking for model 1 # Found a chain break before 94 # copying to AlignedFragments data structure # naming current conformation ROBETTA_TS5 # ReadConformPDB reading from PDB file servers/ROKKY_TS1.pdb.gz looking for model 1 # naming current conformation ROKKY_TS1 # ReadConformPDB reading from PDB file servers/ROKKY_TS2.pdb.gz looking for model 1 # naming current conformation ROKKY_TS2 # ReadConformPDB reading from PDB file servers/ROKKY_TS3.pdb.gz looking for model 1 # Found a chain break before 125 # copying to AlignedFragments data structure # naming current conformation ROKKY_TS3 # ReadConformPDB reading from PDB file servers/ROKKY_TS4.pdb.gz looking for model 1 # Found a chain break before 31 # copying to AlignedFragments data structure # naming current conformation ROKKY_TS4 # ReadConformPDB reading from PDB file servers/ROKKY_TS5.pdb.gz looking for model 1 # Found a chain break before 31 # copying to AlignedFragments data structure # naming current conformation ROKKY_TS5 # ReadConformPDB reading from PDB file servers/SAM-T02_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0322 can't currently be optimized by undertaker # naming current conformation SAM-T02_AL1 # ReadConformPDB reading from PDB file servers/SAM-T02_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0322 can't currently be optimized by undertaker # naming current conformation SAM-T02_AL2 # ReadConformPDB reading from PDB file servers/SAM-T02_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0322 can't currently be optimized by undertaker # naming current conformation SAM-T02_AL3 # ReadConformPDB reading from PDB file servers/SAM-T02_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0322 can't currently be optimized by undertaker # naming current conformation SAM-T02_AL4 # ReadConformPDB reading from PDB file servers/SAM-T02_AL5.pdb.gz looking for model 1 Skipped atom 38, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL5.pdb.gz Skipped atom 40, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL5.pdb.gz Skipped atom 42, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL5.pdb.gz Skipped atom 44, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL5.pdb.gz Skipped atom 74, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL5.pdb.gz Skipped atom 76, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL5.pdb.gz Skipped atom 78, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL5.pdb.gz Skipped atom 80, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL5.pdb.gz Skipped atom 127, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL5.pdb.gz Skipped atom 244, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL5.pdb.gz Skipped atom 356, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL5.pdb.gz Skipped atom 358, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL5.pdb.gz Skipped atom 360, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL5.pdb.gz Skipped atom 362, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL5.pdb.gz Skipped atom 424, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL5.pdb.gz Skipped atom 426, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL5.pdb.gz Skipped atom 428, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL5.pdb.gz Skipped atom 430, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL5.pdb.gz # WARNING: incomplete conformation T0322 can't currently be optimized by undertaker # naming current conformation SAM-T02_AL5 # ReadConformPDB reading from PDB file servers/SAM-T99_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0322 can't currently be optimized by undertaker # naming current conformation SAM-T99_AL1 # ReadConformPDB reading from PDB file servers/SAM-T99_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0322 can't currently be optimized by undertaker # naming current conformation SAM-T99_AL2 # ReadConformPDB reading from PDB file servers/SAM-T99_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0322 can't currently be optimized by undertaker # naming current conformation SAM-T99_AL3 # ReadConformPDB reading from PDB file servers/SAM-T99_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0322 can't currently be optimized by undertaker # naming current conformation SAM-T99_AL4 # ReadConformPDB reading from PDB file servers/SAM-T99_AL5.pdb.gz looking for model 1 Skipped atom 43, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL5.pdb.gz Skipped atom 91, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL5.pdb.gz Skipped atom 93, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL5.pdb.gz Skipped atom 95, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL5.pdb.gz Skipped atom 97, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL5.pdb.gz Skipped atom 152, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL5.pdb.gz Skipped atom 257, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL5.pdb.gz Skipped atom 322, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL5.pdb.gz Skipped atom 395, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL5.pdb.gz # WARNING: incomplete conformation T0322 can't currently be optimized by undertaker # naming current conformation SAM-T99_AL5 # ReadConformPDB reading from PDB file servers/SAM_T06_server_TS1.pdb.gz looking for model 1 # Found a chain break before 142 # copying to AlignedFragments data structure # naming current conformation SAM_T06_server_TS1 # ReadConformPDB reading from PDB file servers/SAM_T06_server_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0322 can't currently be optimized by undertaker # naming current conformation SAM_T06_server_TS2 # ReadConformPDB reading from PDB file servers/SAM_T06_server_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0322 can't currently be optimized by undertaker # naming current conformation SAM_T06_server_TS3 # ReadConformPDB reading from PDB file servers/SAM_T06_server_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0322 can't currently be optimized by undertaker # naming current conformation SAM_T06_server_TS4 # ReadConformPDB reading from PDB file servers/SAM_T06_server_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0322 can't currently be optimized by undertaker # naming current conformation SAM_T06_server_TS5 # ReadConformPDB reading from PDB file servers/SP3_TS1.pdb.gz looking for model 1 # Found a chain break before 31 # copying to AlignedFragments data structure # naming current conformation SP3_TS1 # ReadConformPDB reading from PDB file servers/SP3_TS2.pdb.gz looking for model 1 # naming current conformation SP3_TS2 # ReadConformPDB reading from PDB file servers/SP3_TS3.pdb.gz looking for model 1 # Found a chain break before 76 # copying to AlignedFragments data structure # naming current conformation SP3_TS3 # ReadConformPDB reading from PDB file servers/SP3_TS4.pdb.gz looking for model 1 # Found a chain break before 71 # copying to AlignedFragments data structure # naming current conformation SP3_TS4 # ReadConformPDB reading from PDB file servers/SP3_TS5.pdb.gz looking for model 1 # Found a chain break before 108 # copying to AlignedFragments data structure # naming current conformation SP3_TS5 # ReadConformPDB reading from PDB file servers/SP4_TS1.pdb.gz looking for model 1 # Found a chain break before 82 # copying to AlignedFragments data structure # naming current conformation SP4_TS1 # ReadConformPDB reading from PDB file servers/SP4_TS2.pdb.gz looking for model 1 # naming current conformation SP4_TS2 # ReadConformPDB reading from PDB file servers/SP4_TS3.pdb.gz looking for model 1 # naming current conformation SP4_TS3 # ReadConformPDB reading from PDB file servers/SP4_TS4.pdb.gz looking for model 1 # Found a chain break before 103 # copying to AlignedFragments data structure # naming current conformation SP4_TS4 # ReadConformPDB reading from PDB file servers/SP4_TS5.pdb.gz looking for model 1 # Found a chain break before 63 # copying to AlignedFragments data structure # naming current conformation SP4_TS5 # ReadConformPDB reading from PDB file servers/SPARKS2_TS1.pdb.gz looking for model 1 # Found a chain break before 31 # copying to AlignedFragments data structure # naming current conformation SPARKS2_TS1 # ReadConformPDB reading from PDB file servers/SPARKS2_TS2.pdb.gz looking for model 1 # Found a chain break before 71 # copying to AlignedFragments data structure # naming current conformation SPARKS2_TS2 # ReadConformPDB reading from PDB file servers/SPARKS2_TS3.pdb.gz looking for model 1 # Found a chain break before 72 # copying to AlignedFragments data structure # naming current conformation SPARKS2_TS3 # ReadConformPDB reading from PDB file servers/SPARKS2_TS4.pdb.gz looking for model 1 # Found a chain break before 137 # copying to AlignedFragments data structure # naming current conformation SPARKS2_TS4 # ReadConformPDB reading from PDB file servers/SPARKS2_TS5.pdb.gz looking for model 1 # Found a chain break before 46 # copying to AlignedFragments data structure # naming current conformation SPARKS2_TS5 # ReadConformPDB reading from PDB file servers/UNI-EID_bnmx_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0322 can't currently be optimized by undertaker # naming current conformation UNI-EID_bnmx_TS1 # ReadConformPDB reading from PDB file servers/UNI-EID_bnmx_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0322 can't currently be optimized by undertaker # naming current conformation UNI-EID_bnmx_TS2 # ReadConformPDB reading from PDB file servers/UNI-EID_bnmx_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0322 can't currently be optimized by undertaker # naming current conformation UNI-EID_bnmx_TS3 # ReadConformPDB reading from PDB file servers/UNI-EID_bnmx_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0322 can't currently be optimized by undertaker # naming current conformation UNI-EID_bnmx_TS4 # ReadConformPDB reading from PDB file servers/UNI-EID_bnmx_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0322 can't currently be optimized by undertaker # naming current conformation UNI-EID_bnmx_TS5 # ReadConformPDB reading from PDB file servers/UNI-EID_expm_TS1.pdb.gz looking for model 1 WARNING: atoms too close: (T0322)D7.CA and (T0322)E15.CA only 0.000 apart, marking (T0322)E15.CA as missing # WARNING: incomplete conformation T0322 can't currently be optimized by undertaker # naming current conformation UNI-EID_expm_TS1 # ReadConformPDB reading from PDB file servers/UNI-EID_sfst_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0322 can't currently be optimized by undertaker # naming current conformation UNI-EID_sfst_AL1 # ReadConformPDB reading from PDB file servers/UNI-EID_sfst_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0322 can't currently be optimized by undertaker # naming current conformation UNI-EID_sfst_AL2 # ReadConformPDB reading from PDB file servers/UNI-EID_sfst_AL3.pdb.gz looking for model 1 Skipped atom 38, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL3.pdb.gz Skipped atom 40, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL3.pdb.gz Skipped atom 42, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL3.pdb.gz Skipped atom 44, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL3.pdb.gz Skipped atom 74, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL3.pdb.gz Skipped atom 76, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL3.pdb.gz Skipped atom 78, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL3.pdb.gz Skipped atom 80, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL3.pdb.gz Skipped atom 127, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL3.pdb.gz Skipped atom 244, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL3.pdb.gz Skipped atom 356, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL3.pdb.gz Skipped atom 358, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL3.pdb.gz Skipped atom 360, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL3.pdb.gz Skipped atom 362, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL3.pdb.gz Skipped atom 424, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL3.pdb.gz Skipped atom 426, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL3.pdb.gz Skipped atom 428, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL3.pdb.gz Skipped atom 430, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL3.pdb.gz # WARNING: incomplete conformation T0322 can't currently be optimized by undertaker # naming current conformation UNI-EID_sfst_AL3 # ReadConformPDB reading from PDB file servers/UNI-EID_sfst_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0322 can't currently be optimized by undertaker # naming current conformation UNI-EID_sfst_AL4 # ReadConformPDB reading from PDB file servers/Zhang-Server_TS1.pdb.gz looking for model 1 # Found a chain break before 151 # copying to AlignedFragments data structure # naming current conformation Zhang-Server_TS1 # ReadConformPDB reading from PDB file servers/Zhang-Server_TS2.pdb.gz looking for model 1 # Found a chain break before 153 # copying to AlignedFragments data structure # naming current conformation Zhang-Server_TS2 # ReadConformPDB reading from PDB file servers/Zhang-Server_TS3.pdb.gz looking for model 1 # Found a chain break before 84 # copying to AlignedFragments data structure # naming current conformation Zhang-Server_TS3 # ReadConformPDB reading from PDB file servers/Zhang-Server_TS4.pdb.gz looking for model 1 # Found a chain break before 155 # copying to AlignedFragments data structure # naming current conformation Zhang-Server_TS4 # ReadConformPDB reading from PDB file servers/Zhang-Server_TS5.pdb.gz looking for model 1 # Found a chain break before 29 # copying to AlignedFragments data structure # naming current conformation Zhang-Server_TS5 # ReadConformPDB reading from PDB file servers/beautshot_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0322 can't currently be optimized by undertaker # naming current conformation beautshot_TS1 # ReadConformPDB reading from PDB file servers/beautshotbase_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0322 can't currently be optimized by undertaker # naming current conformation beautshotbase_TS1 # ReadConformPDB reading from PDB file servers/forecast-s_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0322 can't currently be optimized by undertaker # naming current conformation forecast-s_AL1 # ReadConformPDB reading from PDB file servers/forecast-s_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0322 can't currently be optimized by undertaker # naming current conformation forecast-s_AL2 # ReadConformPDB reading from PDB file servers/forecast-s_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0322 can't currently be optimized by undertaker # naming current conformation forecast-s_AL3 # ReadConformPDB reading from PDB file servers/forecast-s_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0322 can't currently be optimized by undertaker # naming current conformation forecast-s_AL4 # ReadConformPDB reading from PDB file servers/forecast-s_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0322 can't currently be optimized by undertaker # naming current conformation forecast-s_AL5 # ReadConformPDB reading from PDB file servers/gtg_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0322 can't currently be optimized by undertaker # naming current conformation gtg_AL1 # ReadConformPDB reading from PDB file servers/gtg_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0322 can't currently be optimized by undertaker # naming current conformation gtg_AL2 # ReadConformPDB reading from PDB file servers/gtg_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0322 can't currently be optimized by undertaker # naming current conformation gtg_AL3 # ReadConformPDB reading from PDB file servers/gtg_AL4.pdb.gz looking for model 1 Skipped atom 14, because occupancy 1.000 <= existing 1.000 in servers/gtg_AL4.pdb.gz Skipped atom 16, because occupancy 1.000 <= existing 1.000 in servers/gtg_AL4.pdb.gz Skipped atom 18, because occupancy 1.000 <= existing 1.000 in servers/gtg_AL4.pdb.gz Skipped atom 20, because occupancy 1.000 <= existing 1.000 in servers/gtg_AL4.pdb.gz Skipped atom 70, because occupancy 1.000 <= existing 1.000 in servers/gtg_AL4.pdb.gz Skipped atom 72, because occupancy 1.000 <= existing 1.000 in servers/gtg_AL4.pdb.gz Skipped atom 74, because occupancy 1.000 <= existing 1.000 in servers/gtg_AL4.pdb.gz Skipped atom 76, because occupancy 1.000 <= existing 1.000 in servers/gtg_AL4.pdb.gz Skipped atom 106, because occupancy 1.000 <= existing 1.000 in servers/gtg_AL4.pdb.gz Skipped atom 108, because occupancy 1.000 <= existing 1.000 in servers/gtg_AL4.pdb.gz Skipped atom 110, because occupancy 1.000 <= existing 1.000 in servers/gtg_AL4.pdb.gz Skipped atom 112, because occupancy 1.000 <= existing 1.000 in servers/gtg_AL4.pdb.gz Skipped atom 159, because occupancy 1.000 <= existing 1.000 in servers/gtg_AL4.pdb.gz Skipped atom 276, because occupancy 1.000 <= existing 1.000 in servers/gtg_AL4.pdb.gz Skipped atom 388, because occupancy 1.000 <= existing 1.000 in servers/gtg_AL4.pdb.gz Skipped atom 390, because occupancy 1.000 <= existing 1.000 in servers/gtg_AL4.pdb.gz Skipped atom 392, because occupancy 1.000 <= existing 1.000 in servers/gtg_AL4.pdb.gz Skipped atom 394, because occupancy 1.000 <= existing 1.000 in servers/gtg_AL4.pdb.gz Skipped atom 456, because occupancy 1.000 <= existing 1.000 in servers/gtg_AL4.pdb.gz Skipped atom 458, because occupancy 1.000 <= existing 1.000 in servers/gtg_AL4.pdb.gz Skipped atom 460, because occupancy 1.000 <= existing 1.000 in servers/gtg_AL4.pdb.gz Skipped atom 462, because occupancy 1.000 <= existing 1.000 in servers/gtg_AL4.pdb.gz # WARNING: incomplete conformation T0322 can't currently be optimized by undertaker # naming current conformation gtg_AL4 # ReadConformPDB reading from PDB file servers/gtg_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0322 can't currently be optimized by undertaker # naming current conformation gtg_AL5 # ReadConformPDB reading from PDB file servers/karypis.srv.2_TS1.pdb.gz looking for model 1 # Found a chain break before 31 # copying to AlignedFragments data structure # naming current conformation karypis.srv.2_TS1 # ReadConformPDB reading from PDB file servers/karypis.srv.2_TS2.pdb.gz looking for model 1 # Found a chain break before 81 # copying to AlignedFragments data structure # naming current conformation karypis.srv.2_TS2 # ReadConformPDB reading from PDB file servers/karypis.srv.2_TS3.pdb.gz looking for model 1 # naming current conformation karypis.srv.2_TS3 # ReadConformPDB reading from PDB file servers/karypis.srv.2_TS4.pdb.gz looking for model 1 # Found a chain break before 82 # copying to AlignedFragments data structure # naming current conformation karypis.srv.2_TS4 # ReadConformPDB reading from PDB file servers/karypis.srv.2_TS5.pdb.gz looking for model 1 # Found a chain break before 104 # copying to AlignedFragments data structure # naming current conformation karypis.srv.2_TS5 # ReadConformPDB reading from PDB file servers/karypis.srv.4_TS1.pdb.gz looking for model 1 WARNING: atoms too close: (T0322)A143.O and (T0322)R144.N only 0.000 apart, marking (T0322)R144.N as missing # WARNING: incomplete conformation T0322 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation karypis.srv.4_TS1 # ReadConformPDB reading from PDB file servers/karypis.srv.4_TS2.pdb.gz looking for model 1 # Found a chain break before 156 # copying to AlignedFragments data structure # naming current conformation karypis.srv.4_TS2 # ReadConformPDB reading from PDB file servers/karypis.srv.4_TS3.pdb.gz looking for model 1 # Found a chain break before 156 # copying to AlignedFragments data structure # naming current conformation karypis.srv.4_TS3 # ReadConformPDB reading from PDB file servers/karypis.srv.4_TS4.pdb.gz looking for model 1 # Found a chain break before 154 # copying to AlignedFragments data structure # naming current conformation karypis.srv.4_TS4 # ReadConformPDB reading from PDB file servers/karypis.srv.4_TS5.pdb.gz looking for model 1 # Found a chain break before 156 # copying to AlignedFragments data structure # naming current conformation karypis.srv.4_TS5 # ReadConformPDB reading from PDB file servers/karypis.srv_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0322 can't currently be optimized by undertaker # naming current conformation karypis.srv_TS1 # ReadConformPDB reading from PDB file servers/karypis.srv_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0322 can't currently be optimized by undertaker # naming current conformation karypis.srv_TS2 # ReadConformPDB reading from PDB file servers/karypis.srv_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0322 can't currently be optimized by undertaker # naming current conformation karypis.srv_TS3 # ReadConformPDB reading from PDB file servers/karypis.srv_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0322 can't currently be optimized by undertaker # naming current conformation karypis.srv_TS4 # ReadConformPDB reading from PDB file servers/karypis.srv_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0322 can't currently be optimized by undertaker # naming current conformation karypis.srv_TS5 # ReadConformPDB reading from PDB file servers/keasar-server_TS1.pdb.gz looking for model 1 # Found a chain break before 145 # copying to AlignedFragments data structure # naming current conformation keasar-server_TS1 # ReadConformPDB reading from PDB file servers/keasar-server_TS2.pdb.gz looking for model 1 # Found a chain break before 145 # copying to AlignedFragments data structure # naming current conformation keasar-server_TS2 # ReadConformPDB reading from PDB file servers/keasar-server_TS3.pdb.gz looking for model 1 # Found a chain break before 147 # copying to AlignedFragments data structure # naming current conformation keasar-server_TS3 # ReadConformPDB reading from PDB file servers/keasar-server_TS4.pdb.gz looking for model 1 # Found a chain break before 142 # copying to AlignedFragments data structure # naming current conformation keasar-server_TS4 # ReadConformPDB reading from PDB file servers/keasar-server_TS5.pdb.gz looking for model 1 # Found a chain break before 138 # copying to AlignedFragments data structure # naming current conformation keasar-server_TS5 # ReadConformPDB reading from PDB file servers/mGen-3D_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0322 can't currently be optimized by undertaker # naming current conformation mGen-3D_TS1 # ReadConformPDB reading from PDB file servers/nFOLD_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0322 can't currently be optimized by undertaker # naming current conformation nFOLD_TS1 # ReadConformPDB reading from PDB file servers/nFOLD_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0322 can't currently be optimized by undertaker # naming current conformation nFOLD_TS2 # ReadConformPDB reading from PDB file servers/nFOLD_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0322 can't currently be optimized by undertaker # naming current conformation nFOLD_TS3 # ReadConformPDB reading from PDB file servers/nFOLD_TS4.pdb.gz looking for model 1 WARNING: atom 1 has residue number 1 < previous residue 141 in servers/nFOLD_TS4.pdb.gz # WARNING: incomplete conformation T0322 can't currently be optimized by undertaker # naming current conformation nFOLD_TS4 # ReadConformPDB reading from PDB file servers/nFOLD_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0322 can't currently be optimized by undertaker # naming current conformation nFOLD_TS5 # ReadConformPDB reading from PDB file servers/panther2_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0322 can't currently be optimized by undertaker # naming current conformation panther2_TS1 # ReadConformPDB reading from PDB file servers/shub_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0322 can't currently be optimized by undertaker # naming current conformation shub_TS1 # command:Using radius: 8.0000 Using models AND alignments for constraints model score -0.6572 model score -0.6558 model score -0.6578 model score -0.6574 model score -0.6558 model score -0.6805 model score -0.6762 model score -0.6784 model score -0.6772 model score -0.6775 model score -0.6788 model score -0.6487 model score -0.6755 model score -0.6792 model score -0.6676 model score 0.7048 model score 0.7220 model score 0.6933 model score -0.6076 model score -0.5615 model score -0.5917 model score -0.5782 model score -0.3568 model score 0.0921 model score -0.0481 model score 1.2878 model score 0.9840 model score 1.2413 model score 1.2463 model score 1.3755 model score -0.6266 model score -0.4048 model score -0.5611 model score -0.5769 model score -0.6396 model score -0.6483 model score -0.6494 model score 0.5206 model score -0.6737 model score -0.6546 model score -0.6451 model score -0.4275 model score -0.4132 model score 1.2436 model score 1.2444 model score 1.2450 model score 1.2428 model score 1.2480 model score -0.5962 model score -0.6515 model score -0.6484 model score -0.6457 model score -0.6008 model score -0.6673 model score -0.5769 model score -0.6483 model score -0.6494 model score -0.6396 model score -0.5907 model score -0.6247 model score -0.2472 model score 0.1477 model score -0.4367 model score 1.2325 model score 1.2325 model score 1.2327 model score 1.2332 model score 1.2331 model score 1.2325 model score 1.2325 model score 1.2327 model score 1.2332 model score 1.2331 model score 1.9279 model score 2.1282 model score 2.4433 model score 1.8085 model score 1.9075 model score -0.5766 model score -0.3392 model score -0.3555 model score 0.8490 model score -0.3038 model score 1.2303 model score 1.2339 model score 1.2319 model score 1.2720 model score 1.2329 model score -0.6568 model score -0.6102 model score -0.6350 model score -0.6255 model score -0.5752 model score -0.6100 model score -0.6351 model score -0.6292 model score -0.6513 model score -0.5754 model score -0.6280 model score -0.6406 model score -0.6406 model score -0.5295 model score 0.4572 model score -0.5712 model score 1.7349 model score 2.0342 model score -0.6134 model score -0.6438 model score -0.2716 model score -0.5607 model score -0.5640 model score 1.2836 model score -0.2544 model score -0.6436 model score -0.5713 model score -0.6498 model score -0.5723 model score -0.6365 model score -0.5937 model score -0.6585 model score -0.5723 model score -0.5876 model score -0.5321 model score -0.5588 model score -0.5761 model score -0.5674 model score -0.5607 model score -0.6428 model score -0.5987 model score -0.5808 model score -0.5919 model score -0.5787 model score -0.5995 model score -0.5871 model score -0.5791 model score -0.5680 model score -0.5725 model score -0.5551 model score -0.6568 model score -0.6493 model score -0.6367 model score -0.6216 model score -0.6488 model score -0.5546 model score -0.6140 model score -0.6571 model score -0.6579 model score -0.6131 model score -0.6358 model score -0.6489 model score -0.6568 model score -0.6609 model score -0.6259 model score -0.5415 model score -0.6522 model score -0.6428 model score -0.6194 model score -0.6458 model score -0.5778 model score -0.5110 model score -0.4027 model score -0.5624 model score -0.5624 model score -0.5672 model score -0.5592 model score -0.4053 model score -0.6319 model score -0.6319 model score -0.6326 model score -0.5540 model score -0.4946 model score -0.5037 model score -0.4886 model score -0.6164 model score -0.5082 model score -0.4743 model score -0.5749 model score -0.6583 model score -0.6415 model score 1.2346 model score 1.2346 model score 1.2351 model score 1.2350 model score 1.2337 model score 1.2339 model score 1.2336 model score 1.2334 model score 1.2340 model score 1.2343 model score -0.5804 model score -0.4121 model score -0.5184 model score -0.6611 model score -0.6241 model score -0.6428 model score -0.5842 model score -0.4088 model score -0.3224 model score -0.4084 model score -0.6590 model score -0.5578 model score -0.5353 model score -0.1886 model score -0.5010 model score -0.6428 model score -0.3224 model score -0.5776 model score -0.3973 model score -0.5787 model score 1.2350 model score 1.2339 model score 1.2337 model score 1.2332 model score 1.2339 model score -0.6822 model score 1.2350 model score 1.2339 model score 1.2337 model score 1.2332 model score -0.6458 model score -0.6763 model score -0.6356 model score -0.6578 model score -0.6476 model score -0.5925 model score -0.6214 model score 1.2339 model score 1.2325 model score 1.2314 model score 1.2313 model score 1.2329 model score 1.2340 model score 1.2316 model score 1.2319 model score 1.2337 model score 1.2720 model score -0.6315 model score -0.6380 model score -0.5789 model score -0.6470 model score -0.5869 model score 1.4027 model score 1.7805 model score 1.8482 model score 2.0753 model score 1.8340 model score -0.6694 model score -0.6039 model score -0.6162 model score -0.6291 model score -0.3803 model score -0.5320 model score -0.5431 model score -0.5185 model score -0.5282 model score -0.5498 model score -0.6309 model score -0.6196 model score -0.5786 model score -0.6505 model score -0.6523 model score -0.4025 model score -0.6338 model score -0.6079 USE_META, weight: 0.9928 cost: -0.6572 min: -0.6822 max: 2.4433 USE_META, weight: 0.9924 cost: -0.6558 min: -0.6822 max: 2.4433 USE_META, weight: 0.9930 cost: -0.6578 min: -0.6822 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cost: -0.5185 min: -0.6822 max: 2.4433 USE_META, weight: 0.9557 cost: -0.5282 min: -0.6822 max: 2.4433 USE_META, weight: 0.9619 cost: -0.5498 min: -0.6822 max: 2.4433 USE_META, weight: 0.9852 cost: -0.6309 min: -0.6822 max: 2.4433 USE_META, weight: 0.9820 cost: -0.6196 min: -0.6822 max: 2.4433 USE_META, weight: 0.9702 cost: -0.5786 min: -0.6822 max: 2.4433 USE_META, weight: 0.9909 cost: -0.6505 min: -0.6822 max: 2.4433 USE_META, weight: 0.9914 cost: -0.6523 min: -0.6822 max: 2.4433 USE_META, weight: 0.9195 cost: -0.4025 min: -0.6822 max: 2.4433 USE_META, weight: 0.9861 cost: -0.6338 min: -0.6822 max: 2.4433 USE_META, weight: 0.9786 cost: -0.6079 min: -0.6822 max: 2.4433 USE_EVALUE, weight: 0.1000 eval: 0.0071 min: 0.0000 max: 0.0071 USE_EVALUE, weight: 0.1000 eval: 0.0071 min: 0.0000 max: 0.0071 USE_EVALUE, weight: 0.1000 eval: 0.0071 min: 0.0000 max: 0.0071 USE_EVALUE, weight: 0.7533 eval: 0.0019 min: 0.0000 max: 0.0071 USE_EVALUE, weight: 0.7533 eval: 0.0019 min: 0.0000 max: 0.0071 USE_EVALUE, weight: 0.7533 eval: 0.0019 min: 0.0000 max: 0.0071 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0071 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0071 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0071 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0071 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0071 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0071 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0071 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0071 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0071 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0071 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0071 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0071 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0071 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0071 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0071 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0071 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0071 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0071 USE_EVALUE, weight: 0.7833 eval: 0.0017 min: 0.0000 max: 0.0071 USE_EVALUE, weight: 0.7833 eval: 0.0017 min: 0.0000 max: 0.0071 USE_EVALUE, weight: 0.7833 eval: 0.0017 min: 0.0000 max: 0.0071 USE_EVALUE, weight: 0.9952 eval: 0.0000 min: 0.0000 max: 0.0071 USE_EVALUE, weight: 0.9952 eval: 0.0000 min: 0.0000 max: 0.0071 USE_EVALUE, weight: 0.9952 eval: 0.0000 min: 0.0000 max: 0.0071 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0071 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0071 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0071 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0071 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0071 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0071 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0071 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0071 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0071 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0071 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0071 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0071 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0071 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0071 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0071 USE_EVALUE, weight: 0.9997 eval: 0.0000 min: 0.0000 max: 0.0071 USE_EVALUE, weight: 0.9997 eval: 0.0000 min: 0.0000 max: 0.0071 USE_EVALUE, weight: 0.9997 eval: 0.0000 min: 0.0000 max: 0.0071 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0071 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0071 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0071 USE_EVALUE, weight: 0.9974 eval: 0.0000 min: 0.0000 max: 0.0071 USE_EVALUE, weight: 0.9974 eval: 0.0000 min: 0.0000 max: 0.0071 USE_EVALUE, weight: 0.9974 eval: 0.0000 min: 0.0000 max: 0.0071 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0071 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0071 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0071 USE_EVALUE, weight: 0.3919 eval: 0.0048 min: 0.0000 max: 0.0071 USE_EVALUE, weight: 0.3919 eval: 0.0048 min: 0.0000 max: 0.0071 USE_EVALUE, weight: 0.3919 eval: 0.0048 min: 0.0000 max: 0.0071 USE_EVALUE, weight: 0.9999 eval: 0.0000 min: 0.0000 max: 0.0071 USE_EVALUE, weight: 0.9999 eval: 0.0000 min: 0.0000 max: 0.0071 USE_EVALUE, weight: 0.9999 eval: 0.0000 min: 0.0000 max: 0.0071 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0071 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0071 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0071 USE_EVALUE, weight: 0.9957 eval: 0.0000 min: 0.0000 max: 0.0071 USE_EVALUE, weight: 0.9957 eval: 0.0000 min: 0.0000 max: 0.0071 USE_EVALUE, weight: 0.9957 eval: 0.0000 min: 0.0000 max: 0.0071 USE_EVALUE, weight: 0.9984 eval: 0.0000 min: 0.0000 max: 0.0071 USE_EVALUE, weight: 0.9984 eval: 0.0000 min: 0.0000 max: 0.0071 USE_EVALUE, weight: 0.9984 eval: 0.0000 min: 0.0000 max: 0.0071 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0071 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0071 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0071 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0071 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0071 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0071 USE_EVALUE, weight: 0.9996 eval: 0.0000 min: 0.0000 max: 0.0071 USE_EVALUE, weight: 0.9996 eval: 0.0000 min: 0.0000 max: 0.0071 USE_EVALUE, weight: 0.9996 eval: 0.0000 min: 0.0000 max: 0.0071 USE_EVALUE, weight: 0.9768 eval: 0.0002 min: 0.0000 max: 0.0071 USE_EVALUE, weight: 0.9768 eval: 0.0002 min: 0.0000 max: 0.0071 USE_EVALUE, weight: 0.9768 eval: 0.0002 min: 0.0000 max: 0.0071 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0071 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0071 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0071 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0071 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0071 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0071 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0071 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0071 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0071 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0071 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0071 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0071 USE_EVALUE, weight: 0.9937 eval: 0.0000 min: 0.0000 max: 0.0071 USE_EVALUE, weight: 0.9937 eval: 0.0000 min: 0.0000 max: 0.0071 USE_EVALUE, weight: 0.9937 eval: 0.0000 min: 0.0000 max: 0.0071 USE_EVALUE, weight: 0.9690 eval: 0.0002 min: 0.0000 max: 0.0071 USE_EVALUE, weight: 0.9690 eval: 0.0002 min: 0.0000 max: 0.0071 USE_EVALUE, weight: 0.9690 eval: 0.0002 min: 0.0000 max: 0.0071 USE_EVALUE, weight: 0.9999 eval: 0.0000 min: 0.0000 max: 0.0071 USE_EVALUE, weight: 0.9999 eval: 0.0000 min: 0.0000 max: 0.0071 USE_EVALUE, weight: 0.9999 eval: 0.0000 min: 0.0000 max: 0.0071 Number of contacts in models: 264 Number of contacts in alignments: 105 NUMB_ALIGNS: 105 Adding 4513 constraints to all3.constraints Done adding distance constraints # command:Reading probabilities from probabilities.dat Reading constraints from ConstraintSet all3.constraints maxweight: 1.0000 Optimizing... Probability sum: -290.6547, CN propb: -290.6547 weights: 0.3584 constraints: 518 # command:Found ConstraintSet # PrintContacts align.constraints_meta03 Number of constraints in align3.constraints 518 # command:Found ConstraintSet # PrintContacts align_bonus.constraints_meta03 Number of constraints in align3.constraints.bonus 518 # command:Found ConstraintSet # PrintContacts rejected.constraints_meta03 Number of constraints in rejected3.constraints 3995 # command:Found ConstraintSet # PrintContacts rejected_bonus.constraints_meta03 Number of constraints in rejected3.constraints.bonus 3995 # command:Found ConstraintSet # PrintContacts non_contacts.constraints_meta03 Number of constraints in noncontact3.constraints 0 # command:Found ConstraintSet # PrintContacts non_contacts_bonus.constraints_meta03 Number of constraints in noncontact3.constraints.bonus 0 # command:Found ConstraintSet # PrintContacts all.constraints_meta03 Number of constraints in all3.constraints 4513 # command: