# 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/T0362/ # command:# Making conformation for sequence T0362 numbered 1 through 151 Created new target T0362 from T0362.a2m # command:# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/T0362/ # command:Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0362//projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0362/manyalignments-good-all.under or /projects/compbio/experiments/protein-predict/casp7/T0362//projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0362/manyalignments-good-all.under.gz for input Trying /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0362/manyalignments-good-all.under # reading script from file /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0362/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:# T0362 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 Warning: unaligning (T0362)E134 because of BadResidue code BAD_PEPTIDE in next template residue (1bvqA)D135 Warning: unaligning (T0362)G135 because of BadResidue code BAD_PEPTIDE at template residue (1bvqA)D135 T0362 5 :NWLLLRRVVRFGDTDAAGVMHFHQLFRWCHESWEESLESYGLN 1bvqA 3 :RSITMQQRIEFGDCDPAGIVWYPNYHRWLDAASRNYFIKCGLP # choosing archetypes in rotamer library T0362 48 :PADIF 1bvqA 47 :WRQTV T0362 60 :VTPEV 1bvqA 52 :VERGI T0362 65 :ALPIIHCQADFRRPIHTGDALAMELRPERLNPNSFQVHFEFRC 1bvqA 58 :GTPIVSCNASFVCTASYDDVLTIETCIKEWRRKSFVQRHSVSR T0362 108 :EE 1bvqA 103 :PG T0362 110 :QIAAHALIRHLAI 1bvqA 108 :QLVMRADEIRVFA T0362 123 :NAQTRHRCALP 1bvqA 123 :DGERLRAIEVP T0362 136 :IDRW 1bvqA 136 :YIEL Number of specific fragments extracted= 8 number of extra gaps= 1 total=8 Number of alignments=1 # 1bvqA read from 1bvqA/merged-good-all-a2m # found chain 1bvqA in template set Warning: unaligning (T0362)E134 because of BadResidue code BAD_PEPTIDE in next template residue (1bvqA)D135 Warning: unaligning (T0362)G135 because of BadResidue code BAD_PEPTIDE at template residue (1bvqA)D135 T0362 5 :NWLLLRRVVRFGDTDAAGVMHFHQLFRWCHESWEESLESYGL 1bvqA 3 :RSITMQQRIEFGDCDPAGIVWYPNYHRWLDAASRNYFIKCGL T0362 47 :NPADIFPGS 1bvqA 46 :PWRQTVVER T0362 63 :EV 1bvqA 55 :GI T0362 65 :ALPIIHCQADFRRPIHTGDALAMELRPERLNPNSFQVHFEFRC 1bvqA 58 :GTPIVSCNASFVCTASYDDVLTIETCIKEWRRKSFVQRHSVSR T0362 108 :EE 1bvqA 103 :PG T0362 110 :QIAAHALIRHLAI 1bvqA 108 :QLVMRADEIRVFA T0362 123 :NAQTRHRCALP 1bvqA 123 :DGERLRAIEVP T0362 136 :IDRW 1bvqA 136 :YIEL Number of specific fragments extracted= 8 number of extra gaps= 1 total=16 Number of alignments=2 # 1bvqA read from 1bvqA/merged-good-all-a2m # found chain 1bvqA in template set Warning: unaligning (T0362)E134 because of BadResidue code BAD_PEPTIDE in next template residue (1bvqA)D135 Warning: unaligning (T0362)G135 because of BadResidue code BAD_PEPTIDE at template residue (1bvqA)D135 T0362 5 :NWLLLRRVVRFGDTDAAGVMHFHQLFRWCHESWEESLESYGLNPADIFP 1bvqA 3 :RSITMQQRIEFGDCDPAGIVWYPNYHRWLDAASRNYFIKCGLPPWRQTV T0362 60 :VTPEV 1bvqA 52 :VERGI T0362 65 :ALPIIHCQADFRRPIHTGDALAMELRPERLNPNSFQVHFEFRC 1bvqA 58 :GTPIVSCNASFVCTASYDDVLTIETCIKEWRRKSFVQRHSVSR T0362 108 :EE 1bvqA 104 :GG T0362 110 :QIAAHALIRHLAI 1bvqA 108 :QLVMRADEIRVFA T0362 123 :NAQTRHRCALP 1bvqA 123 :DGERLRAIEVP T0362 136 :IDRW 1bvqA 136 :YIEL Number of specific fragments extracted= 7 number of extra gaps= 1 total=23 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:# T0362 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 (T0362)V13 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1tbuA)T40 Warning: unaligning (T0362)M24 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1tbuA)T40 T0362 3 :PENWLLLRRV 1tbuA 21 :SPTSFVTKYL T0362 25 :HFHQ 1tbuA 41 :FGGT T0362 33 :CHESWEESLESY 1tbuA 45 :LVSQSLLASLHT T0362 60 :VTPEVA 1tbuA 57 :VPLNFF T0362 68 :IIHCQADFRRPIHTGDALAMELRPERLNPNSFQVHFEFRCEEQIAAHALIRHL 1tbuA 63 :PTSLHSYFIKGGDPRTKITYHVQNLRNGRNFIHKQVSAYQHDKLIFTSMILFA Number of specific fragments extracted= 5 number of extra gaps= 0 total=28 Number of alignments=4 # 1tbuA read from 1tbuA/merged-good-all-a2m # found chain 1tbuA in template set Warning: unaligning (T0362)V13 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1tbuA)T40 Warning: unaligning (T0362)M24 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1tbuA)T40 T0362 3 :PENWLLLRRV 1tbuA 21 :SPTSFVTKYL T0362 25 :HFHQLFRWCHESW 1tbuA 41 :FGGTLVSQSLLAS T0362 43 :SYGLNP 1tbuA 54 :LHTVPL T0362 63 :EVAL 1tbuA 60 :NFFP T0362 69 :IHCQADFRRPIHTGDALAMELRPERLNPNSFQVHFEFRCEEQIAAHALIRHL 1tbuA 64 :TSLHSYFIKGGDPRTKITYHVQNLRNGRNFIHKQVSAYQHDKLIFTSMILFA Number of specific fragments extracted= 5 number of extra gaps= 0 total=33 Number of alignments=5 # 1tbuA read from 1tbuA/merged-good-all-a2m # found chain 1tbuA in template set T0362 68 :IIHCQADFRRPIHTGDALAMELRPERLNPNSFQVHFEFRCEEQIAAHALIRHL 1tbuA 63 :PTSLHSYFIKGGDPRTKITYHVQNLRNGRNFIHKQVSAYQHDKLIFTSMILFA Number of specific fragments extracted= 1 number of extra gaps= 0 total=34 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 # T0362 read from 1j1yA/merged-good-all-a2m # 1j1yA read from 1j1yA/merged-good-all-a2m # found chain 1j1yA in training set Warning: unaligning (T0362)I122 because last residue in template chain is (1j1yA)L117 T0362 4 :ENWLLLRRVVRFGDTDAAGVMHFHQLFRWCHESWEESLESYGL 1j1yA 18 :PGEAVVAGEVRADHLNLHGTAHGGFLYALADSAFALASNTRGP T0362 66 :LPIIHCQADFRRPIHTGDALAMELRPERLNPNSFQVHFEFRCEEQIAAHALIRHLA 1j1yA 61 :AVALSCRMDYFRPLGAGARVEARAVEVNLSRRTATYRVEVVSEGKLVALFTGTVFR Number of specific fragments extracted= 2 number of extra gaps= 0 total=36 Number of alignments=7 # 1j1yA read from 1j1yA/merged-good-all-a2m # found chain 1j1yA in training set Warning: unaligning (T0362)I122 because last residue in template chain is (1j1yA)L117 T0362 4 :ENWLLLRRVVRFGDTDAAGVMHFHQLFRWCHESWEESLESYG 1j1yA 18 :PGEAVVAGEVRADHLNLHGTAHGGFLYALADSAFALASNTRG T0362 63 :EV 1j1yA 60 :PA T0362 67 :PIIHCQADFRRPIHTGDALAMELRPERLNPNSFQVHFEFRCEEQIAAHALIRHLA 1j1yA 62 :VALSCRMDYFRPLGAGARVEARAVEVNLSRRTATYRVEVVSEGKLVALFTGTVFR Number of specific fragments extracted= 3 number of extra gaps= 0 total=39 Number of alignments=8 # 1j1yA read from 1j1yA/merged-good-all-a2m # found chain 1j1yA in training set Warning: unaligning (T0362)I122 because last residue in template chain is (1j1yA)L117 T0362 4 :ENWLLLRRVVRFGDTDAAGVMHFHQLFRWCHESWEESLESYGL 1j1yA 18 :PGEAVVAGEVRADHLNLHGTAHGGFLYALADSAFALASNTRGP T0362 66 :LPIIHCQADFRRPIHTGDALAMELRPERLNPNSFQVHFEFRCEEQIAAHALIRHLA 1j1yA 61 :AVALSCRMDYFRPLGAGARVEARAVEVNLSRRTATYRVEVVSEGKLVALFTGTVFR Number of specific fragments extracted= 2 number of extra gaps= 0 total=41 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:# T0362 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 (T0362)V23 because of BadResidue code BAD_PEPTIDE in next template residue (1z6bA)F134 Warning: unaligning (T0362)G45 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1z6bA)N166 Warning: unaligning (T0362)E63 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1z6bA)N166 Warning: unaligning (T0362)N95 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1z6bA)S200 Warning: unaligning (T0362)P96 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1z6bA)S200 T0362 2 :NPENWLLLRRVVRFGDTDAAG 1z6bA 112 :QPNKTIIGLKQVSTNEPFFNG T0362 24 :MHFHQLFRWCHESWEESLESY 1z6bA 140 :MPGVLQIEALAQLAGILCLKS T0362 64 :VALPIIHCQ 1z6bA 167 :NLFLFAGVD T0362 73 :ADFRRPIHTGDALAMELRPERL 1z6bA 177 :VRWKKPVLPGDTLTMQANLISF T0362 97 :N 1z6bA 201 :S T0362 98 :SFQVHFEFRCEEQIAAHA 1z6bA 204 :IAKLSGVGYVNGKVVINI T0362 116 :LIRHLA 1z6bA 223 :EMTFAL Number of specific fragments extracted= 7 number of extra gaps= 2 total=48 Number of alignments=10 # 1z6bA read from 1z6bA/merged-good-all-a2m # found chain 1z6bA in template set Warning: unaligning (T0362)V23 because of BadResidue code BAD_PEPTIDE in next template residue (1z6bA)F134 Warning: unaligning (T0362)G45 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1z6bA)N166 Warning: unaligning (T0362)E63 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1z6bA)N166 Warning: unaligning (T0362)N95 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1z6bA)S200 Warning: unaligning (T0362)P96 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1z6bA)S200 T0362 2 :NPENWLLLRRVVRFGDTDAAG 1z6bA 112 :QPNKTIIGLKQVSTNEPFFNG T0362 24 :MHFHQLFRWCHESWEESLESY 1z6bA 140 :MPGVLQIEALAQLAGILCLKS T0362 64 :VALPIIHCQ 1z6bA 167 :NLFLFAGVD T0362 73 :ADFRRPIHTGDALAMELRPERL 1z6bA 177 :VRWKKPVLPGDTLTMQANLISF T0362 97 :N 1z6bA 201 :S T0362 98 :SFQVHFEFRCEEQIAAHA 1z6bA 204 :IAKLSGVGYVNGKVVINI T0362 116 :LIRHLA 1z6bA 223 :EMTFAL Number of specific fragments extracted= 7 number of extra gaps= 2 total=55 Number of alignments=11 # 1z6bA read from 1z6bA/merged-good-all-a2m # found chain 1z6bA in template set Warning: unaligning (T0362)A49 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1z6bA)N166 Warning: unaligning (T0362)T61 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1z6bA)N166 Warning: unaligning (T0362)N95 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1z6bA)S200 Warning: unaligning (T0362)P96 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1z6bA)S200 T0362 32 :WCHESWEESLESYGLNP 1z6bA 144 :LQIEALAQLAGILCLKS T0362 62 :PEVALPIIH 1z6bA 167 :NLFLFAGVD T0362 72 :QADFRRPIHTGDALAMELRPERL 1z6bA 176 :GVRWKKPVLPGDTLTMQANLISF T0362 97 :N 1z6bA 201 :S T0362 98 :SFQVHFEFRCEEQIAAHA 1z6bA 204 :IAKLSGVGYVNGKVVINI T0362 116 :LIRHL 1z6bA 223 :EMTFA T0362 122 :I 1z6bA 228 :L Number of specific fragments extracted= 7 number of extra gaps= 1 total=62 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 # T0362 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 T0362 4 :ENWLLLRRVVRFGDTDAAGVMHFHQLFRWCHESWEESL 1psuA 31 :EGFAVVTMTVTAQMLNGHQSCHGGQLFSLADTAFAYAC T0362 60 :VTPEVALPIIHCQADFRRPIHTGDALAMELRPERLNPNSFQVHFEFRC 1psuA 69 :NSQGLAAVASACTIDFLRPGFAGDTLTATAQVRHQGKQTGVYDIEIVN T0362 108 :EEQIAAHALIRHL 1psuA 118 :QQKTVALFRGKSH Number of specific fragments extracted= 3 number of extra gaps= 0 total=65 Number of alignments=13 # 1psuA read from 1psuA/merged-good-all-a2m # found chain 1psuA in template set T0362 3 :PENWLLLRRVVRFGDTDAAGVMHFHQLFRWCHESWEESL 1psuA 30 :DEGFAVVTMTVTAQMLNGHQSCHGGQLFSLADTAFAYAC T0362 43 :SYG 1psuA 69 :NSQ T0362 63 :EVALPIIHCQADFRRPIHTGDALAMELRPERLNPNSFQVHFEFRC 1psuA 72 :GLAAVASACTIDFLRPGFAGDTLTATAQVRHQGKQTGVYDIEIVN T0362 108 :EEQIAAHALIRHL 1psuA 118 :QQKTVALFRGKSH Number of specific fragments extracted= 4 number of extra gaps= 0 total=69 Number of alignments=14 # 1psuA read from 1psuA/merged-good-all-a2m # found chain 1psuA in template set T0362 4 :ENWLLLRRVVRFGDTDAAGVMHFHQLFRWCHESWEESL 1psuA 31 :EGFAVVTMTVTAQMLNGHQSCHGGQLFSLADTAFAYAC T0362 60 :VTPEVALPIIHCQADFRRPIHTGDALAMELRPERLNPNSFQVHFEFRC 1psuA 69 :NSQGLAAVASACTIDFLRPGFAGDTLTATAQVRHQGKQTGVYDIEIVN T0362 108 :EEQIAAHALIRH 1psuA 118 :QQKTVALFRGKS Number of specific fragments extracted= 3 number of extra gaps= 0 total=72 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 # T0362 read from 1vpmA/merged-good-all-a2m # 1vpmA read from 1vpmA/merged-good-all-a2m # found chain 1vpmA in training set Warning: unaligning (T0362)V64 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (1vpmA)A53 Warning: unaligning (T0362)A65 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (1vpmA)A53 T0362 6 :WLLLRRVVRFGDTDAAGVMHFHQLFRWCHESWEESLE 1vpmA 11 :RTIQTRLVLPPDTNHLGTIFGGKVLAYIDEIAALTAM T0362 60 :VTPE 1vpmA 48 :KHAN T0362 66 :LPIIHCQ 1vpmA 54 :VVTASID T0362 73 :ADFRRPIHTGDALAMELRPERLNPNSFQVHFEFRC 1vpmA 62 :VDFKSSATVGDALELEGFVTHTGRTSMEVYVRVHS T0362 108 :EE 1vpmA 101 :TG T0362 110 :QIAAHALIRHLAIN 1vpmA 105 :TLTTESFLTMVAVD T0362 125 :QTRHRCALP 1vpmA 119 :ESGKPKPVP T0362 134 :EGIDRWLEASG 1vpmA 134 :EEEKRLYETAP Number of specific fragments extracted= 8 number of extra gaps= 1 total=80 Number of alignments=16 # 1vpmA read from 1vpmA/merged-good-all-a2m # found chain 1vpmA in training set Warning: unaligning (T0362)V64 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (1vpmA)A53 Warning: unaligning (T0362)A65 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (1vpmA)A53 T0362 6 :WLLLRRVVRFGDTDAAGVMHFHQLFRWCHESWEESLESYG 1vpmA 11 :RTIQTRLVLPPDTNHLGTIFGGKVLAYIDEIAALTAMKHA T0362 63 :E 1vpmA 51 :N T0362 66 :LPIIHCQ 1vpmA 54 :VVTASID T0362 73 :ADFRRPIHTGDALAMELRPERLNPNSFQVHFEFRC 1vpmA 62 :VDFKSSATVGDALELEGFVTHTGRTSMEVYVRVHS T0362 108 :EE 1vpmA 101 :TG T0362 110 :QIAAHALIRHLAIN 1vpmA 105 :TLTTESFLTMVAVD T0362 125 :QTRHRCALP 1vpmA 119 :ESGKPKPVP T0362 134 :EGIDRWLEASG 1vpmA 134 :EEEKRLYETAP Number of specific fragments extracted= 8 number of extra gaps= 1 total=88 Number of alignments=17 # 1vpmA read from 1vpmA/merged-good-all-a2m # found chain 1vpmA in training set Warning: unaligning (T0362)V64 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (1vpmA)A53 Warning: unaligning (T0362)A65 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (1vpmA)A53 T0362 6 :WLLLRRVVRFGDTDAAGVMHFHQLFRWCHESWEESLESYG 1vpmA 11 :RTIQTRLVLPPDTNHLGTIFGGKVLAYIDEIAALTAMKHA T0362 63 :E 1vpmA 51 :N T0362 66 :LPIIHC 1vpmA 54 :VVTASI T0362 72 :QADFRRPIHTGDALAMELRPERLNPNSFQVHFEFRC 1vpmA 61 :SVDFKSSATVGDALELEGFVTHTGRTSMEVYVRVHS T0362 108 :EEQIAAHALIRHLAIN 1vpmA 103 :ERTLTTESFLTMVAVD T0362 125 :QTRHRCALP 1vpmA 119 :ESGKPKPVP T0362 134 :EGIDRWLEASG 1vpmA 134 :EEEKRLYETAP Number of specific fragments extracted= 7 number of extra gaps= 1 total=95 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 # T0362 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 T0362 4 :ENWLLLRRVVRFGDTDAAGVMHFHQLFRWCHESWEESLESY 1zkiA 27 :DGVAEVRLPMAAHLRNRGGVMHGGALFSLMDVTMGLACSSS T0362 60 :VTPEVALPIIHCQADFRRPIH 1zkiA 68 :HGFDRQSVTLECKINYIRAVA T0362 82 :GDALAMELRPERLNPNSFQVHFEFRCEEQIAAHALIRHL 1zkiA 89 :DGEVRCVARVLHAGRRSLVVEAEVRQGDKLVAKGQGTFA Number of specific fragments extracted= 3 number of extra gaps= 0 total=98 Number of alignments=19 # 1zkiA read from 1zkiA/merged-good-all-a2m # found chain 1zkiA in template set T0362 4 :ENWLLLRRVVRFGDTDAAGVMHFHQLFRWCHESWEESLES 1zkiA 27 :DGVAEVRLPMAAHLRNRGGVMHGGALFSLMDVTMGLACSS T0362 44 :YGL 1zkiA 68 :HGF T0362 63 :EVALPIIHCQADFRRPIH 1zkiA 71 :DRQSVTLECKINYIRAVA T0362 82 :GDALAMELRPERLNPNSFQVHFEFRCEEQIAAHALIRHL 1zkiA 89 :DGEVRCVARVLHAGRRSLVVEAEVRQGDKLVAKGQGTFA Number of specific fragments extracted= 4 number of extra gaps= 0 total=102 Number of alignments=20 # 1zkiA read from 1zkiA/merged-good-all-a2m # found chain 1zkiA in template set T0362 18 :TDAAGVMHFHQLFRWCHESWEESLESY 1zkiA 41 :RNRGGVMHGGALFSLMDVTMGLACSSS T0362 60 :VTPEVALPIIHCQADFRRPIH 1zkiA 68 :HGFDRQSVTLECKINYIRAVA T0362 82 :GDALAMELRPERLNPNSFQVHFEFRCEEQIAAHALIRHL 1zkiA 89 :DGEVRCVARVLHAGRRSLVVEAEVRQGDKLVAKGQGTFA Number of specific fragments extracted= 3 number of extra gaps= 0 total=105 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 # T0362 read from 1yocA/merged-good-all-a2m # 1yocA read from 1yocA/merged-good-all-a2m # found chain 1yocA in training set T0362 5 :NWLLLRRVVRFGDTDAAGVMHFHQLFRWCHESWEESLESY 1yocA 40 :GYAEVTFPKRREVLNHIGTVHAIALCNAAELAAGTMTDAS T0362 60 :VTPEVALPIIHCQADFRRPIH 1yocA 80 :IPAGHRWIPRGMTVEYLAKAT T0362 83 :DALAMELRPERLN 1yocA 101 :GDVRAVADGSQID T0362 96 :PNSFQVHFEFRCEEQIAAHALIRHLA 1yocA 117 :TGNLVVPVVAYVDDKPVFRAEITMYV Number of specific fragments extracted= 4 number of extra gaps= 0 total=109 Number of alignments=22 # 1yocA read from 1yocA/merged-good-all-a2m # found chain 1yocA in training set T0362 5 :NWLLLRRVVRFGDTDAAGVMHFHQLFRWCHESWEESLESY 1yocA 40 :GYAEVTFPKRREVLNHIGTVHAIALCNAAELAAGTMTDAS T0362 52 :FPG 1yocA 80 :IPA T0362 63 :EVALPIIHCQADFRRPIHT 1yocA 83 :GHRWIPRGMTVEYLAKATG T0362 84 :ALAMELRPERLN 1yocA 102 :DVRAVADGSQID T0362 96 :PNSFQVHFEFRCEEQIAAHALIRHLA 1yocA 117 :TGNLVVPVVAYVDDKPVFRAEITMYV Number of specific fragments extracted= 5 number of extra gaps= 0 total=114 Number of alignments=23 # 1yocA read from 1yocA/merged-good-all-a2m # found chain 1yocA in training set T0362 27 :HQLFRWCHESWEESL 1yocA 65 :CNAAELAAGTMTDAS T0362 60 :VTPEVALPIIHCQADFRRPIHT 1yocA 80 :IPAGHRWIPRGMTVEYLAKATG T0362 84 :ALAMELRP 1yocA 102 :DVRAVADG T0362 96 :PNSFQVHFEFRCEEQIAAHALIRHLA 1yocA 117 :TGNLVVPVVAYVDDKPVFRAEITMYV Number of specific fragments extracted= 4 number of extra gaps= 0 total=118 Number of alignments=24 # 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 # T0362 read from 1lo7A/merged-good-all-a2m # 1lo7A read from 1lo7A/merged-good-all-a2m # found chain 1lo7A in training set T0362 5 :NWLLLRRVVRFGDTDAAGVMHFHQLFRWCHESWEESLESYGLN 1lo7A 3 :RSITMQQRIEFGDCDPAGIVWYPNYHRWLDAASRNYFIKCGLP T0362 48 :PADIF 1lo7A 47 :WRQTV T0362 60 :VTPEV 1lo7A 52 :VERGI T0362 65 :ALPIIHCQADFRRPIHTGDALAMELRPERLNPNSFQVHFEFRC 1lo7A 58 :GTPIVSCNASFVCTASYDDVLTIETCIKEWRRKSFVQRHSVSR T0362 108 :EE 1lo7A 104 :GG T0362 110 :QIAAHALIRHLAI 1lo7A 108 :QLVMRADEIRVFA T0362 123 :NAQTRHRCALPEGIDRWL 1lo7A 123 :DGERLRAIEVPADYIELC Number of specific fragments extracted= 7 number of extra gaps= 0 total=125 Number of alignments=25 # 1lo7A read from 1lo7A/merged-good-all-a2m # found chain 1lo7A in training set T0362 5 :NWLLLRRVVRFGDTDAAGVMHFHQLFRWCHESWEESLESYGL 1lo7A 3 :RSITMQQRIEFGDCDPAGIVWYPNYHRWLDAASRNYFIKCGL T0362 47 :NPADIFPGS 1lo7A 46 :PWRQTVVER T0362 63 :EV 1lo7A 55 :GI T0362 65 :ALPIIHCQADFRRPIHTGDALAMELRPERLNPNSFQVHFEFRC 1lo7A 58 :GTPIVSCNASFVCTASYDDVLTIETCIKEWRRKSFVQRHSVSR T0362 108 :EE 1lo7A 104 :GG T0362 110 :QIAAHALIRHLAI 1lo7A 108 :QLVMRADEIRVFA T0362 123 :NAQTRHRCALPEGIDRWL 1lo7A 123 :DGERLRAIEVPADYIELC Number of specific fragments extracted= 7 number of extra gaps= 0 total=132 Number of alignments=26 # 1lo7A read from 1lo7A/merged-good-all-a2m # found chain 1lo7A in training set T0362 5 :NWLLLRRVVRFGDTDAAGVMHFHQLFRWCHESWEESLESYGLNPADIF 1lo7A 3 :RSITMQQRIEFGDCDPAGIVWYPNYHRWLDAASRNYFIKCGLPPWRQT T0362 58 :SEVTPEVALPIIHCQADFRRPIHTGDALAMELRPERLNPNSFQVHFEFRC 1lo7A 51 :VVERGIVGTPIVSCNASFVCTASYDDVLTIETCIKEWRRKSFVQRHSVSR T0362 108 :EE 1lo7A 104 :GG T0362 110 :QIAAHALIRHLAI 1lo7A 108 :QLVMRADEIRVFA T0362 123 :NAQTRHRCALPEGIDRWL 1lo7A 123 :DGERLRAIEVPADYIELC Number of specific fragments extracted= 5 number of extra gaps= 0 total=137 Number of alignments=27 # 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:# T0362 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 (T0362)I122 because last residue in template chain is (1wluA)L117 T0362 4 :ENWLLLRRVVRFGDTDAAGVMHFHQLFRWCHESWEESLESYGL 1wluA 18 :PGEAVVAGEVRADHLNLHGTAHGGFLYALADSAFALASNTRGP T0362 66 :LPIIHCQADFRRPIHTGDALAMELRPERLNPNSFQVHFEFRCEEQIAAHALIRHLA 1wluA 61 :AVALSCRMDYFRPLGAGARVEARAVEVNLSRRTATYRVEVVSEGKLVALFTGTVFR Number of specific fragments extracted= 2 number of extra gaps= 0 total=139 Number of alignments=28 # 1wluA read from 1wluA/merged-good-all-a2m # found chain 1wluA in template set Warning: unaligning (T0362)I122 because last residue in template chain is (1wluA)L117 T0362 4 :ENWLLLRRVVRFGDTDAAGVMHFHQLFRWCHESWEESLESYG 1wluA 18 :PGEAVVAGEVRADHLNLHGTAHGGFLYALADSAFALASNTRG T0362 63 :EV 1wluA 60 :PA T0362 67 :PIIHCQADFRRPIHTGDALAMELRPERLNPNSFQVHFEFRCEEQIAAHALIRHLA 1wluA 62 :VALSCRMDYFRPLGAGARVEARAVEVNLSRRTATYRVEVVSEGKLVALFTGTVFR Number of specific fragments extracted= 3 number of extra gaps= 0 total=142 Number of alignments=29 # 1wluA read from 1wluA/merged-good-all-a2m # found chain 1wluA in template set Warning: unaligning (T0362)I122 because last residue in template chain is (1wluA)L117 T0362 4 :ENWLLLRRVVRFGDTDAAGVMHFHQLFRWCHESWEESLESYGL 1wluA 18 :PGEAVVAGEVRADHLNLHGTAHGGFLYALADSAFALASNTRGP T0362 66 :LPIIHCQADFRRPIHTGDALAMELRPERLNPNSFQVHFEFRCEEQIAAHALIRHLA 1wluA 61 :AVALSCRMDYFRPLGAGARVEARAVEVNLSRRTATYRVEVVSEGKLVALFTGTVFR Number of specific fragments extracted= 2 number of extra gaps= 0 total=144 Number of alignments=30 # 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 # T0362 read from 1t82A/merged-good-all-a2m # 1t82A read from 1t82A/merged-good-all-a2m # found chain 1t82A in training set Warning: unaligning (T0362)N123 because last residue in template chain is (1t82A)P143 T0362 4 :ENWLL 1t82A 31 :DGELS T0362 11 :RVVRFG 1t82A 36 :VSAPLA T0362 17 :DTDAAGVMH 1t82A 43 :NINLHHTMF T0362 26 :FHQLFRWCHESWEESLES 1t82A 55 :IYTIMTLTGWGMVWLQQQ T0362 44 :YGL 1t82A 74 :LNV T0362 63 :EVALPIIHCQADFRRPIHTGD 1t82A 77 :DGDIVLADAHIRYLAPVTSAP T0362 86 :AMELRPERL 1t82A 98 :EVKVRWPDT T0362 95 :NPNSFQVHFEFRCEEQIAAHALIRHLAI 1t82A 115 :RKAKVKLEVQLFCDGKLCAQFDGLYVSV Number of specific fragments extracted= 8 number of extra gaps= 0 total=152 Number of alignments=31 # 1t82A read from 1t82A/merged-good-all-a2m # found chain 1t82A in training set Warning: unaligning (T0362)N123 because last residue in template chain is (1t82A)P143 T0362 8 :LLRRVVRFG 1t82A 33 :ELSVSAPLA T0362 17 :DTDAAGVMH 1t82A 43 :NINLHHTMF T0362 26 :FHQLFRWCHESWEESLES 1t82A 55 :IYTIMTLTGWGMVWLQQQ T0362 44 :YGL 1t82A 74 :LNV T0362 63 :EVALPIIHCQADFRRPIHTGDALAME 1t82A 77 :DGDIVLADAHIRYLAPVTSAPEVKVR T0362 91 :PERLNPNSFQVHFEFRCEEQIAAHALIRHLAI 1t82A 111 :LQRGRKAKVKLEVQLFCDGKLCAQFDGLYVSV Number of specific fragments extracted= 6 number of extra gaps= 0 total=158 Number of alignments=32 # 1t82A read from 1t82A/merged-good-all-a2m # found chain 1t82A in training set Warning: unaligning (T0362)N123 because last residue in template chain is (1t82A)P143 T0362 27 :HQLFRWCHESWEESLES 1t82A 56 :YTIMTLTGWGMVWLQQQ T0362 51 :I 1t82A 73 :L T0362 60 :VTPEVALPIIHCQADFRRPIHTGDALAME 1t82A 74 :LNVDGDIVLADAHIRYLAPVTSAPEVKVR T0362 95 :NPNSFQVHFEFRCEEQIAAHALIRHLAI 1t82A 115 :RKAKVKLEVQLFCDGKLCAQFDGLYVSV Number of specific fragments extracted= 4 number of extra gaps= 0 total=162 Number of alignments=33 # 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 # T0362 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 (T0362)Y44 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2cyeA)D46 Warning: unaligning (T0362)N47 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2cyeA)D46 Warning: unaligning (T0362)K147 because last residue in template chain is (2cyeA)P132 T0362 3 :PENWLLLRRVVRFGDTDAAGVMHFHQLFRWCHESWEESLES 2cyeA 2 :EGFPVRVRVDVRFRDLDPLGHVNNAVFLSYMELARIRYFQR T0362 48 :PADI 2cyeA 47 :WLEE T0362 64 :VALPIIHCQADFRRPIHTGDALAMELRPERLNPNSFQVHFEFRCEEQIAAHALIRHLAI 2cyeA 51 :GHFVVARMEVDYLRPILLGDEVFVGVRTVGLGRSSLRMEHLVTANGESAAKGLGVLVWL T0362 125 :QTRHRCALPEGIDRWLEASGVG 2cyeA 110 :EGGRPAPLPEAIRERIRALEGR Number of specific fragments extracted= 4 number of extra gaps= 0 total=166 Number of alignments=34 # 2cyeA read from 2cyeA/merged-good-all-a2m # found chain 2cyeA in template set Warning: unaligning (T0362)Y44 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2cyeA)D46 Warning: unaligning (T0362)N47 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2cyeA)D46 Warning: unaligning (T0362)K147 because last residue in template chain is (2cyeA)P132 T0362 3 :PENWLLLRRVVRFGDTDAAGVMHFHQLFRWCHESWEESLES 2cyeA 2 :EGFPVRVRVDVRFRDLDPLGHVNNAVFLSYMELARIRYFQR T0362 48 :PAD 2cyeA 47 :WLE T0362 63 :EVALPIIHCQADFRRPIHTGDALAMELRPERLNPNSFQVHFEFRCEEQIAAHALIRHLAIN 2cyeA 50 :EGHFVVARMEVDYLRPILLGDEVFVGVRTVGLGRSSLRMEHLVTANGESAAKGLGVLVWLE T0362 126 :TRHRCALPEGIDRWLEASGVG 2cyeA 111 :GGRPAPLPEAIRERIRALEGR Number of specific fragments extracted= 4 number of extra gaps= 0 total=170 Number of alignments=35 # 2cyeA read from 2cyeA/merged-good-all-a2m # found chain 2cyeA in template set Warning: unaligning (T0362)Y44 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2cyeA)D46 Warning: unaligning (T0362)N47 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2cyeA)D46 Warning: unaligning (T0362)K147 because last residue in template chain is (2cyeA)P132 T0362 3 :PENWLLLRRVVRFGDTDAAGVMHFHQLFRWCHESWEESLES 2cyeA 2 :EGFPVRVRVDVRFRDLDPLGHVNNAVFLSYMELARIRYFQR T0362 48 :PADIFP 2cyeA 47 :WLEEGH T0362 66 :LPIIHCQADFRRPIHTGDALAMELRPERLNPNSFQVHFEFRCEEQIAAHALIRHLAIN 2cyeA 53 :FVVARMEVDYLRPILLGDEVFVGVRTVGLGRSSLRMEHLVTANGESAAKGLGVLVWLE T0362 126 :TRHRCALPEGIDRWLEASGVG 2cyeA 111 :GGRPAPLPEAIRERIRALEGR Number of specific fragments extracted= 4 number of extra gaps= 0 total=174 Number of alignments=36 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1lo9A/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/T0362/1lo9A/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0362/1lo9A/merged-good-all-a2m.gz for input Trying 1lo9A/merged-good-all-a2m Error: Couldn't open file 1lo9A/merged-good-all-a2m or 1lo9A/merged-good-all-a2m.gz for input # 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/T0362/1y7uA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0362/1y7uA/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 # T0362 read from 1s5uA/merged-good-all-a2m # 1s5uA read from 1s5uA/merged-good-all-a2m # found chain 1s5uA in training set Warning: unaligning (T0362)N5 because first residue in template chain is (1s5uA)T4 Warning: unaligning (T0362)L140 because last residue in template chain is (1s5uA)F132 T0362 6 :WLLLRRVVRFGDTDAAGVMHFHQLFRWCHESWEESLESYGLNPADI 1s5uA 5 :LFRWPVRVYYEDTDAGGVVYHASYVAFYERARTEMLRHHHFSQQAL T0362 60 :VTPEVALPIIHCQADFRRPIHTGDALAMELRPERLNPNSFQVHFEFRC 1s5uA 51 :MAERVAFVVRKMTVEYYAPARLDDMLEIQTEITSMRGTSLVFTQRIVN T0362 108 :EEQIAAHALIRHLAINAQTRHRCALPEGIDRW 1s5uA 100 :ENTLLNEAEVLVVCVDPLKMKPRALPKSIVAE Number of specific fragments extracted= 3 number of extra gaps= 0 total=177 Number of alignments=37 # 1s5uA read from 1s5uA/merged-good-all-a2m # found chain 1s5uA in training set Warning: unaligning (T0362)N5 because first residue in template chain is (1s5uA)T4 Warning: unaligning (T0362)L140 because last residue in template chain is (1s5uA)F132 T0362 6 :WLLLRRVVRFGDTDAAGVMHFHQLFRWCHESWEESLESYGLNPADIFPG 1s5uA 5 :LFRWPVRVYYEDTDAGGVVYHASYVAFYERARTEMLRHHHFSQQALMAE T0362 63 :EVALPIIHCQADFRRPIHTGDALAMELRPERLNPNSFQVHFEFRC 1s5uA 54 :RVAFVVRKMTVEYYAPARLDDMLEIQTEITSMRGTSLVFTQRIVN T0362 108 :EEQIAAHALIRHLAINAQTRHRCALPEGIDRW 1s5uA 100 :ENTLLNEAEVLVVCVDPLKMKPRALPKSIVAE Number of specific fragments extracted= 3 number of extra gaps= 0 total=180 Number of alignments=38 # 1s5uA read from 1s5uA/merged-good-all-a2m # found chain 1s5uA in training set Warning: unaligning (T0362)N5 because first residue in template chain is (1s5uA)T4 T0362 6 :WLLLRRVVRFGDTDAAGVMHFHQLFRWCHESWEESLESYGLNPADI 1s5uA 5 :LFRWPVRVYYEDTDAGGVVYHASYVAFYERARTEMLRHHHFSQQAL T0362 60 :VTPEVALPIIHCQADFRRPIHTGDALAMELRPERLNPNSFQVHFEFRC 1s5uA 51 :MAERVAFVVRKMTVEYYAPARLDDMLEIQTEITSMRGTSLVFTQRIVN T0362 108 :EEQIAAHALIRHLAINAQTRHRCALPEGIDRW 1s5uA 100 :ENTLLNEAEVLVVCVDPLKMKPRALPKSIVAE Number of specific fragments extracted= 3 number of extra gaps= 0 total=183 Number of alignments=39 # 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 # T0362 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 (T0362)R10 because of BadResidue code BAD_PEPTIDE in next template residue (1yliA)T21 Warning: unaligning (T0362)R11 because of BadResidue code BAD_PEPTIDE at template residue (1yliA)T21 Warning: unaligning (T0362)G146 because last residue in template chain is (1yliA)Q152 T0362 8 :LL 1yliA 18 :LL T0362 12 :VVRFGDTDAAGVMHFHQLFRWCHESWEESLESY 1yliA 22 :LAMPSDTNANGDIFGGWIMSQMDMGGAILAKEI T0362 62 :PEVALPIIHCQ 1yliA 55 :AHGRVVTVAVE T0362 73 :ADFRRPIHTGDALAMELRPERLNPNSFQVHFEFRC 1yliA 67 :MNFIKPISVGDVVCCYGQCLKVGRSSIKIKVEVWV T0362 108 :EE 1yliA 106 :SE T0362 110 :QIAAHALIRHLAIN 1yliA 113 :YCVTDAVFTFVAVD T0362 125 :QTRHRCALP 1yliA 127 :NNGRSRTIP T0362 134 :EGIDRWLEASGV 1yliA 140 :QELEKALALISE Number of specific fragments extracted= 8 number of extra gaps= 1 total=191 Number of alignments=40 # 1yliA read from 1yliA/merged-good-all-a2m # found chain 1yliA in template set Warning: unaligning (T0362)R10 because of BadResidue code BAD_PEPTIDE in next template residue (1yliA)T21 Warning: unaligning (T0362)R11 because of BadResidue code BAD_PEPTIDE at template residue (1yliA)T21 Warning: unaligning (T0362)G146 because last residue in template chain is (1yliA)Q152 T0362 8 :LL 1yliA 18 :LL T0362 12 :VVRFGDTDAAGVMHFHQLFRWCHESWEESLESYG 1yliA 22 :LAMPSDTNANGDIFGGWIMSQMDMGGAILAKEIA T0362 63 :EVALPIIHCQ 1yliA 56 :HGRVVTVAVE T0362 73 :ADFRRPIHTGDALAMELRPERLNPNSFQVHFEFRC 1yliA 67 :MNFIKPISVGDVVCCYGQCLKVGRSSIKIKVEVWV T0362 108 :EE 1yliA 106 :SE T0362 110 :QIAAHALIRHLAIN 1yliA 113 :YCVTDAVFTFVAVD T0362 125 :QTRHRCALP 1yliA 127 :NNGRSRTIP T0362 134 :EGIDRWLEASGV 1yliA 140 :QELEKALALISE Number of specific fragments extracted= 8 number of extra gaps= 1 total=199 Number of alignments=41 # 1yliA read from 1yliA/merged-good-all-a2m # found chain 1yliA in template set Warning: unaligning (T0362)R10 because of BadResidue code BAD_PEPTIDE in next template residue (1yliA)T21 Warning: unaligning (T0362)R11 because of BadResidue code BAD_PEPTIDE at template residue (1yliA)T21 T0362 9 :L 1yliA 19 :L T0362 12 :VVRFGDTDAAGVMHFHQLFRWCHESWEESLES 1yliA 22 :LAMPSDTNANGDIFGGWIMSQMDMGGAILAKE T0362 60 :VTPEVALPIIHCQADFRRPIHTGDALAMELRPERLNPNSFQVHFEFRC 1yliA 54 :IAHGRVVTVAVESMNFIKPISVGDVVCCYGQCLKVGRSSIKIKVEVWV T0362 110 :QIAAHALIRHLAIN 1yliA 113 :YCVTDAVFTFVAVD T0362 125 :QTRHRCALP 1yliA 127 :NNGRSRTIP T0362 134 :EGIDRWLEASGV 1yliA 140 :QELEKALALISE Number of specific fragments extracted= 6 number of extra gaps= 1 total=205 Number of alignments=42 # 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 # T0362 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 (T0362)W6 because first residue in template chain is (1njkA)H0 Warning: unaligning (T0362)V145 because last residue in template chain is (1njkA)K132 T0362 7 :LLLRRVVRFGDTDAAGVMHFHQLFRWCHESWEESLE 1njkA 1 :MQTQIKVRGYHLDVYQHVNNARYLEFLEEARWDGLE T0362 45 :G 1njkA 37 :N T0362 48 :PADI 1njkA 41 :FQWM T0362 60 :VTPEVALPIIHCQADFRRPIHTGDALAMELRPERLNPNSFQVHFEFRC 1njkA 45 :TAHNIAFVVVNININYRRPAVLSDLLTITSQLQQLNGKSGILSQVITL T0362 108 :EEQIAAHALIRHLAINAQTRHRCALPEGIDRWLEASG 1njkA 95 :EGQVVADALITFVCIDLKTQKALALEGELREKLEQMV Number of specific fragments extracted= 5 number of extra gaps= 0 total=210 Number of alignments=43 # 1njkA read from 1njkA/merged-good-all-a2m # found chain 1njkA in template set Warning: unaligning (T0362)W6 because first residue in template chain is (1njkA)H0 T0362 7 :LLLRRVVRFGDTDAAGVMHFHQLFRWCHESWEESLE 1njkA 1 :MQTQIKVRGYHLDVYQHVNNARYLEFLEEARWDGLE T0362 48 :PADIFPG 1njkA 41 :FQWMTAH T0362 63 :EVALPIIHCQADFRRPIHTGDALAMELRPERLNPNSFQVHFEFRC 1njkA 48 :NIAFVVVNININYRRPAVLSDLLTITSQLQQLNGKSGILSQVITL T0362 108 :EEQIAAHALIRHLAINAQTRHRCALPEGIDRWLEAS 1njkA 95 :EGQVVADALITFVCIDLKTQKALALEGELREKLEQM Number of specific fragments extracted= 4 number of extra gaps= 0 total=214 Number of alignments=44 # 1njkA read from 1njkA/merged-good-all-a2m # found chain 1njkA in template set Warning: unaligning (T0362)W6 because first residue in template chain is (1njkA)H0 Warning: unaligning (T0362)V145 because last residue in template chain is (1njkA)K132 T0362 7 :LLLRRVVRFGDTDAAGVMHFHQLFRWCHESWEESLE 1njkA 1 :MQTQIKVRGYHLDVYQHVNNARYLEFLEEARWDGLE T0362 47 :NPADI 1njkA 40 :SFQWM T0362 60 :VTPEVALPIIHCQADFRRPIHTGDALAMELRPERLNPNSFQVHFEFRC 1njkA 45 :TAHNIAFVVVNININYRRPAVLSDLLTITSQLQQLNGKSGILSQVITL T0362 108 :EEQIAAHALIRHLAINAQTRHRCALPEGIDRWLEASG 1njkA 95 :EGQVVADALITFVCIDLKTQKALALEGELREKLEQMV Number of specific fragments extracted= 4 number of extra gaps= 0 total=218 Number of alignments=45 # 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 # T0362 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 T0362 3 :PENWLLLRRVVRFGDTDAAGVMHFHQLFRWCHESWEESLESY 1o0iA 32 :GEDWIEATMPVDHRTMQPFGVLHGGVSVALAETIGSLAGSLC T0362 60 :VTPEVALPIIHCQADFRRPIHT 1o0iA 74 :LEEGKTVVGLDINANHLRPVRS T0362 83 :DALAMELRPERLNPNSFQVHFEFRC 1o0iA 96 :GKVTARATPINLGRNIQVWQIDIRT T0362 108 :EEQIAAHALIRHLAIN 1o0iA 122 :ENKLCCVSRLTLSVIN Number of specific fragments extracted= 4 number of extra gaps= 0 total=222 Number of alignments=46 # 1o0iA read from 1o0iA/merged-good-all-a2m # found chain 1o0iA in template set T0362 3 :PENWLLLRRVVRFGDTDAAGVMHFHQLFRWCHESWEESLESY 1o0iA 32 :GEDWIEATMPVDHRTMQPFGVLHGGVSVALAETIGSLAGSLC T0362 52 :FPG 1o0iA 74 :LEE T0362 63 :EVALPIIHCQADFRRPIHTG 1o0iA 77 :GKTVVGLDINANHLRPVRSG T0362 84 :ALAMELRPERLNPNSFQVHFEFRC 1o0iA 97 :KVTARATPINLGRNIQVWQIDIRT T0362 108 :EEQIAAHALIRHLAIN 1o0iA 122 :ENKLCCVSRLTLSVIN Number of specific fragments extracted= 5 number of extra gaps= 0 total=227 Number of alignments=47 # 1o0iA read from 1o0iA/merged-good-all-a2m # found chain 1o0iA in template set T0362 3 :PENWLLLRRVVRFGDTDAAGVMHFHQLFRWCHESWEESLESY 1o0iA 32 :GEDWIEATMPVDHRTMQPFGVLHGGVSVALAETIGSLAGSLC T0362 60 :VTPEVALPIIHCQADFRRPIH 1o0iA 74 :LEEGKTVVGLDINANHLRPVR T0362 82 :GDALAMELRPERLNPNSFQVHFEFRC 1o0iA 95 :SGKVTARATPINLGRNIQVWQIDIRT T0362 108 :EEQIAAHALIRHLAI 1o0iA 122 :ENKLCCVSRLTLSVI Number of specific fragments extracted= 4 number of extra gaps= 0 total=231 Number of alignments=48 # 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 # T0362 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 (T0362)P48 because of BadResidue code BAD_PEPTIDE in next template residue (2aliA)E50 Warning: unaligning (T0362)V60 because of BadResidue code BAD_PEPTIDE at template residue (2aliA)E50 T0362 6 :WLLLRRVVRFGDTDAAGVMHFHQLFRWCHESWEESLESYGLN 2aliA 7 :LHTAHIPVRWGDMDSYGHVNNTLYFQYLEEARVAWFETLGID T0362 61 :TPEVALPIIHCQADFRRPIHTGDALAMELRPERLNPNSFQVHFEFRC 2aliA 51 :GAAEGPVVLQSLHTYLKPVVHPATVVVELYAGRLGTSSLVLEHRLHT T0362 108 :EEQIAAHALIRHLAINAQTRHRCALPEGIDRWL 2aliA 101 :PQGTYGEGHCKLVWVRHAENRSTPVPDSIRAAI Number of specific fragments extracted= 3 number of extra gaps= 1 total=234 Number of alignments=49 # 2aliA read from 2aliA/merged-good-all-a2m # found chain 2aliA in template set Warning: unaligning (T0362)I51 because of BadResidue code BAD_PEPTIDE in next template residue (2aliA)E50 Warning: unaligning (T0362)F52 because of BadResidue code BAD_PEPTIDE at template residue (2aliA)E50 T0362 5 :NWLLLRRVVRFGDTDAAGVMHFHQLFRWCHESWEESLESYGLN 2aliA 6 :LLHTAHIPVRWGDMDSYGHVNNTLYFQYLEEARVAWFETLGID T0362 53 :PG 2aliA 51 :GA T0362 63 :EVALPIIHCQADFRRPIHTGDALAMELRPERLNPNSFQVHFEFRC 2aliA 53 :AEGPVVLQSLHTYLKPVVHPATVVVELYAGRLGTSSLVLEHRLHT T0362 108 :EEQIAAHALIRHLAINAQTRHRCALPEGIDRWL 2aliA 101 :PQGTYGEGHCKLVWVRHAENRSTPVPDSIRAAI Number of specific fragments extracted= 4 number of extra gaps= 1 total=238 Number of alignments=50 # 2aliA read from 2aliA/merged-good-all-a2m # found chain 2aliA in template set Warning: unaligning (T0362)P48 because of BadResidue code BAD_PEPTIDE in next template residue (2aliA)E50 Warning: unaligning (T0362)V60 because of BadResidue code BAD_PEPTIDE at template residue (2aliA)E50 T0362 5 :NWLLLRRVVRFGDTDAAGVMHFHQLFRWCHESWEESLESYGLN 2aliA 6 :LLHTAHIPVRWGDMDSYGHVNNTLYFQYLEEARVAWFETLGID T0362 61 :TPEVALPIIHCQADFRRPIHTGDALAMELRPERLNPNSFQVHFEFRC 2aliA 51 :GAAEGPVVLQSLHTYLKPVVHPATVVVELYAGRLGTSSLVLEHRLHT T0362 108 :EEQIAAHALIRHLAINAQTRHRCALPEGIDRWL 2aliA 101 :PQGTYGEGHCKLVWVRHAENRSTPVPDSIRAAI Number of specific fragments extracted= 3 number of extra gaps= 1 total=241 Number of alignments=51 # 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:# T0362 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 Warning: unaligning (T0362)N5 because first residue in template chain is (1z54A)M1 T0362 6 :WLLLRRVVRFGDTDAAGVMHFHQLFRWCHESWEESLESYGLNPADI 1z54A 2 :ESVTRIKVRYAETDQMGVVHHSVYAVYLEAARVDFLERAGLPYHRV T0362 60 :VTPEVALPIIHCQADFRRPIHTGDALAMELRPERLNPNSFQVHFEFRCEEQIAAHALIRHLAIN 1z54A 48 :EARGVFFPVVELGLTFRAPARFGEVVEVRTRLAELSSRALLFRYRVEREGVLLAEGFTRHLCQV T0362 126 :TRHRCALPEGIDRWLEASGV 1z54A 112 :GERAARIPEDIYRALSVLHL Number of specific fragments extracted= 3 number of extra gaps= 0 total=244 Number of alignments=52 # 1z54A read from 1z54A/merged-good-all-a2m # found chain 1z54A in template set Warning: unaligning (T0362)N5 because first residue in template chain is (1z54A)M1 T0362 6 :WLLLRRVVRFGDTDAAGVMHFHQLFRWCHESWEESLESYGLNPADIFPG 1z54A 2 :ESVTRIKVRYAETDQMGVVHHSVYAVYLEAARVDFLERAGLPYHRVEAR T0362 63 :EVALPIIHCQADFRRPIHTGDALAMELRPERLNPNSFQVHFEFRCEEQIAAHALIRHLAIN 1z54A 51 :GVFFPVVELGLTFRAPARFGEVVEVRTRLAELSSRALLFRYRVEREGVLLAEGFTRHLCQV T0362 126 :TRHRCALPEGIDRWLEASGV 1z54A 112 :GERAARIPEDIYRALSVLHL Number of specific fragments extracted= 3 number of extra gaps= 0 total=247 Number of alignments=53 # 1z54A read from 1z54A/merged-good-all-a2m # found chain 1z54A in template set Warning: unaligning (T0362)N5 because first residue in template chain is (1z54A)M1 T0362 6 :WLLLRRVVRFGDTDAAGVMHFHQLFRWCHESWEESLESYGLNPADI 1z54A 2 :ESVTRIKVRYAETDQMGVVHHSVYAVYLEAARVDFLERAGLPYHRV T0362 60 :VTPEVALPIIHCQADFRRPIHTGDALAMELRPERLNPNSFQVHFEFRCEEQIAAHALIRHLAIN 1z54A 48 :EARGVFFPVVELGLTFRAPARFGEVVEVRTRLAELSSRALLFRYRVEREGVLLAEGFTRHLCQV T0362 126 :TRHRCALPEGIDRWLEASG 1z54A 112 :GERAARIPEDIYRALSVLH Number of specific fragments extracted= 3 number of extra gaps= 0 total=250 Number of alignments=54 # 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 # T0362 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 T0362 27 :HQ 2bi0A 251 :GH T0362 32 :WCHESWEESLE 2bi0A 253 :TIGLALAQATR T0362 60 :VTPEVALP 2bi0A 264 :LLPNLATV T0362 69 :IHCQ 2bi0A 272 :LDWE T0362 73 :ADFRRPIHTGDALAMELRPERLN 2bi0A 277 :CDHTAPVHEGDTLYSELHIESAQ T0362 96 :PNSFQVHFEFRC 2bi0A 304 :GGVLGLRSLVYA T0362 108 :EE 2bi0A 320 :AS T0362 110 :QIAAHALIRHLA 2bi0A 325 :RQVLDWRFSALQ Number of specific fragments extracted= 8 number of extra gaps= 0 total=258 Number of alignments=55 # 2bi0A read from 2bi0A/merged-good-all-a2m # found chain 2bi0A in template set T0362 23 :VMHFHQLFRW 2bi0A 247 :LVYGGHTIGL T0362 36 :SWEESLESY 2bi0A 257 :ALAQATRLL T0362 63 :EVALPIIHCQ 2bi0A 266 :PNLATVLDWE T0362 73 :ADFRRPIHTGDALAMELRPERLN 2bi0A 277 :CDHTAPVHEGDTLYSELHIESAQ T0362 96 :PNSFQVHFEFRC 2bi0A 304 :GGVLGLRSLVYA T0362 108 :EE 2bi0A 318 :DS T0362 110 :QIAAHALIRHLA 2bi0A 325 :RQVLDWRFSALQ Number of specific fragments extracted= 7 number of extra gaps= 0 total=265 Number of alignments=56 # 2bi0A read from 2bi0A/merged-good-all-a2m # found chain 2bi0A in template set T0362 26 :FHQL 2bi0A 250 :GGHT T0362 33 :CHESWEESLE 2bi0A 254 :IGLALAQATR T0362 60 :VTPEVALPIIHCQADFRRPIHTGDALAMELRPERLNP 2bi0A 264 :LLPNLATVLDWESCDHTAPVHEGDTLYSELHIESAQA T0362 97 :NSFQVHFEFRC 2bi0A 305 :GVLGLRSLVYA T0362 108 :EE 2bi0A 320 :AS T0362 110 :QIAAHALIRHLA 2bi0A 325 :RQVLDWRFSALQ Number of specific fragments extracted= 6 number of extra gaps= 0 total=271 Number of alignments=57 # 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 # T0362 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 (T0362)R106 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (2b3nA)T144 Warning: unaligning (T0362)C107 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (2b3nA)T144 T0362 1 :MNPENWLLLRRVVRFG 2b3nA 36 :LKEGYRFEYEKKLCEI T0362 29 :LFRWCH 2b3nA 52 :DVAMFG T0362 35 :ESWEESLE 2b3nA 90 :SLVSAAVA T0362 60 :VTPE 2b3nA 98 :RLPG T0362 65 :ALPIIHCQADFRRPIHTGDALAMELRPERLNPNSFQVHFEF 2b3nA 102 :TVVLLEQSFRYTSPVRIGDVVRVEGVVSGVEKNRYTIDVKC T0362 108 :EEQIAAHALIRHLA 2b3nA 145 :GDKVVAEGVVKVLI Number of specific fragments extracted= 6 number of extra gaps= 1 total=277 Number of alignments=58 # 2b3nA read from 2b3nA/merged-good-all-a2m # found chain 2b3nA in template set Warning: unaligning (T0362)R106 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (2b3nA)T144 Warning: unaligning (T0362)C107 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (2b3nA)T144 T0362 1 :MNPENWLLLRRVV 2b3nA 36 :LKEGYRFEYEKKL T0362 22 :GVMHFHQLFRWCHESW 2b3nA 81 :RVVHGMLTTSLVSAAV T0362 42 :ES 2b3nA 97 :AR T0362 46 :L 2b3nA 99 :L T0362 63 :EVALPIIHCQADFRRPIHTGDALAMELRPERLNPNSFQVHFEF 2b3nA 100 :PGTVVLLEQSFRYTSPVRIGDVVRVEGVVSGVEKNRYTIDVKC T0362 108 :EEQIAAHALIRHLA 2b3nA 145 :GDKVVAEGVVKVLI Number of specific fragments extracted= 6 number of extra gaps= 1 total=283 Number of alignments=59 # 2b3nA read from 2b3nA/merged-good-all-a2m # found chain 2b3nA in template set Warning: unaligning (T0362)R106 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (2b3nA)T144 Warning: unaligning (T0362)C107 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (2b3nA)T144 T0362 1 :MNPENWLLLRRVVR 2b3nA 36 :LKEGYRFEYEKKLC T0362 27 :HQLFRWCHE 2b3nA 50 :EIDVAMFGL T0362 36 :SWEESLESYG 2b3nA 87 :LTTSLVSAAV T0362 60 :VTPEVALPIIHCQADFRRPIHTGDALAMELRPERLNPNSFQVHFEF 2b3nA 97 :ARLPGTVVLLEQSFRYTSPVRIGDVVRVEGVVSGVEKNRYTIDVKC T0362 108 :EEQIAAHALIRHLA 2b3nA 145 :GDKVVAEGVVKVLI Number of specific fragments extracted= 5 number of extra gaps= 1 total=288 Number of alignments=60 # 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 # T0362 read from 1q4uA/merged-good-all-a2m # 1q4uA read from 1q4uA/merged-good-all-a2m # found chain 1q4uA in training set Warning: unaligning (T0362)A131 because last residue in template chain is (1q4uA)R150 T0362 4 :ENWLLLRRVVRFGDTDAAGVMHFHQLFRWCHESWEESLES 1q4uA 43 :PERATASVEVTDTLRQRWGLVHGGAYCALAEMLATEATVA T0362 44 :Y 1q4uA 84 :V T0362 60 :VTPEVALPIIHCQADFRRPIHTG 1q4uA 85 :HEKGMMAVGQSNHTSFFRPVKEG T0362 84 :ALAMELRPERLNPNSFQVHFEFRC 1q4uA 108 :HVRAEAVRIHAGSTTWFWDVSLRD T0362 108 :EEQIAAHALIRHLA 1q4uA 133 :AGRLCAVSSMSIAV T0362 128 :HRC 1q4uA 147 :RPR Number of specific fragments extracted= 6 number of extra gaps= 0 total=294 Number of alignments=61 # 1q4uA read from 1q4uA/merged-good-all-a2m # found chain 1q4uA in training set Warning: unaligning (T0362)A131 because last residue in template chain is (1q4uA)R150 T0362 6 :WLLLRRVVRFGDTDAAGVMHFHQLFRWCHESWEESLESY 1q4uA 45 :RATASVEVTDTLRQRWGLVHGGAYCALAEMLATEATVAV T0362 51 :IFPG 1q4uA 84 :VHEK T0362 63 :EVALPIIHCQADFRRPIHTG 1q4uA 88 :GMMAVGQSNHTSFFRPVKEG T0362 84 :ALAMELRPERLNPNSFQVHFEFRC 1q4uA 108 :HVRAEAVRIHAGSTTWFWDVSLRD T0362 108 :EEQIAAHALIRHLA 1q4uA 133 :AGRLCAVSSMSIAV T0362 128 :HRC 1q4uA 147 :RPR Number of specific fragments extracted= 6 number of extra gaps= 0 total=300 Number of alignments=62 # 1q4uA read from 1q4uA/merged-good-all-a2m # found chain 1q4uA in training set T0362 24 :MHFHQLFRWCHESWEESLESY 1q4uA 63 :VHGGAYCALAEMLATEATVAV T0362 51 :I 1q4uA 84 :V T0362 60 :VTPEVALPIIHCQADFRRPIHT 1q4uA 85 :HEKGMMAVGQSNHTSFFRPVKE T0362 83 :DALAMELRPERLNPNSFQVHFEFRC 1q4uA 107 :GHVRAEAVRIHAGSTTWFWDVSLRD T0362 108 :EEQIAAHALIRHLA 1q4uA 133 :AGRLCAVSSMSIAV T0362 128 :HRC 1q4uA 147 :RPR Number of specific fragments extracted= 6 number of extra gaps= 0 total=306 Number of alignments=63 # 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 # T0362 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 (T0362)H80 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2av9A)F78 Warning: unaligning (T0362)T81 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2av9A)F78 Warning: unaligning (T0362)K147 because last residue in template chain is (2av9A)A146 T0362 3 :PENWLLLRRVVRFGDTDAAGVMHFHQLFRWCHESWEESLES 2av9A 10 :EQYLHFQPISTRWHDNDIYGHVNNVTYYAFFDTAVNTYLIE T0362 44 :YGLNP 2av9A 52 :GGLDI T0362 60 :VTPEVALPIIHCQADFRRPI 2av9A 57 :QGGEVIGLVVSSSCDYFAPV T0362 82 :GDALAMELRPERLNPNSFQVHFEFRCEE 2av9A 79 :PQRIEMGLRVARLGNSSVQYELALFLEG T0362 110 :QIAAHALIRHLAINAQTRHRCALPEGIDRWLEASGVG 2av9A 109 :EACAAGRFVHVFVERRSSRPVAIPQELRDALAALQSS Number of specific fragments extracted= 5 number of extra gaps= 1 total=311 Number of alignments=64 # 2av9A read from 2av9A/merged-good-all-a2m # found chain 2av9A in template set Warning: unaligning (T0362)H80 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2av9A)F78 Warning: unaligning (T0362)T81 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2av9A)F78 Warning: unaligning (T0362)K147 because last residue in template chain is (2av9A)A146 T0362 3 :PENWLLLRRVVRFGDTDAAGVMHFHQLFRWCHESWEESLES 2av9A 10 :EQYLHFQPISTRWHDNDIYGHVNNVTYYAFFDTAVNTYLIE T0362 44 :YGLNPADI 2av9A 52 :GGLDIQGG T0362 63 :EVALPIIHCQADFRRPI 2av9A 60 :EVIGLVVSSSCDYFAPV T0362 82 :GDALAMELRPERLNPNSFQVHFEFRCEE 2av9A 79 :PQRIEMGLRVARLGNSSVQYELALFLEG T0362 110 :QIAAHALIRHLAINAQTRHRCALPEGIDRWLEASGVG 2av9A 109 :EACAAGRFVHVFVERRSSRPVAIPQELRDALAALQSS Number of specific fragments extracted= 5 number of extra gaps= 1 total=316 Number of alignments=65 # 2av9A read from 2av9A/merged-good-all-a2m # found chain 2av9A in template set Warning: unaligning (T0362)H80 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2av9A)F78 Warning: unaligning (T0362)T81 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2av9A)F78 Warning: unaligning (T0362)K147 because last residue in template chain is (2av9A)A146 T0362 5 :NWLLLRRVVRFGDTDAAGVMHFHQLFRWCHESWEESLESYG 2av9A 12 :YLHFQPISTRWHDNDIYGHVNNVTYYAFFDTAVNTYLIERG T0362 46 :LNP 2av9A 54 :LDI T0362 60 :VTPEVALPIIHCQADFRRPI 2av9A 57 :QGGEVIGLVVSSSCDYFAPV T0362 82 :GDALAMELRPERLNPNSFQVHFEFRCEE 2av9A 79 :PQRIEMGLRVARLGNSSVQYELALFLEG T0362 110 :QIAAHALIRHLAINAQTRHRCALPEGIDRWLEASGVG 2av9A 109 :EACAAGRFVHVFVERRSSRPVAIPQELRDALAALQSS Number of specific fragments extracted= 5 number of extra gaps= 1 total=321 Number of alignments=66 # 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 # T0362 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 T0362 1 :MNPENWLLLRRVVRFGDT 2cwzA 4 :IPEGYEAVFETVVTPEMT T0362 23 :VMHFHQLFRWCHESWEESLESY 2cwzA 33 :VYATYWMVKHMELAGRKIILPF T0362 60 :VTPEVALPIIHCQADFRRPIHTGDALAMELRPERLNPNSFQVHFEFRC 2cwzA 55 :LEEGEEGIGSYVEARHLASALPGMRVRVVARHEKTEGNRVYARVEAYN T0362 108 :EEQIAAHALIRHLAIN 2cwzA 104 :LGDLIGVGRTEQVILP T0362 133 :PEGIDRWLEASG 2cwzA 120 :KAKVEALFRRLK Number of specific fragments extracted= 5 number of extra gaps= 0 total=326 Number of alignments=67 # 2cwzA read from 2cwzA/merged-good-all-a2m # found chain 2cwzA in template set T0362 2 :NPENWLLLRRVVRFGDT 2cwzA 5 :PEGYEAVFETVVTPEMT T0362 23 :VMHFHQLFRWCHESWEESLE 2cwzA 33 :VYATYWMVKHMELAGRKIIL T0362 50 :DIFPG 2cwzA 53 :PFLEE T0362 63 :EVALPIIHCQADFRRPIHTGDALAMELRPERLNPNSFQVHFEFRC 2cwzA 58 :GEEGIGSYVEARHLASALPGMRVRVVARHEKTEGNRVYARVEAYN T0362 108 :EEQIAAHALIRHLAIN 2cwzA 104 :LGDLIGVGRTEQVILP T0362 133 :PEGIDRWLEAS 2cwzA 120 :KAKVEALFRRL Number of specific fragments extracted= 6 number of extra gaps= 0 total=332 Number of alignments=68 # 2cwzA read from 2cwzA/merged-good-all-a2m # found chain 2cwzA in template set T0362 1 :MNPENWLLLRRVV 2cwzA 4 :IPEGYEAVFETVV T0362 14 :RFGD 2cwzA 23 :RFEE T0362 26 :FHQLFRWCHESWEESLESY 2cwzA 36 :TYWMVKHMELAGRKIILPF T0362 60 :VTPEVALPIIHCQADFRRPIHTGDALAMELRPERLNPNSFQVHFEFRC 2cwzA 55 :LEEGEEGIGSYVEARHLASALPGMRVRVVARHEKTEGNRVYARVEAYN T0362 108 :EEQIAAHALIRHLAIN 2cwzA 104 :LGDLIGVGRTEQVILP T0362 133 :PEGIDRWLEAS 2cwzA 120 :KAKVEALFRRL Number of specific fragments extracted= 6 number of extra gaps= 0 total=338 Number of alignments=69 # 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 # T0362 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 (T0362)N2 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2gvhA)A147 Warning: unaligning (T0362)W6 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2gvhA)A147 Warning: unaligning (T0362)N123 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2gvhA)R258 Warning: unaligning (T0362)H128 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2gvhA)R258 Warning: unaligning (T0362)L132 because last residue in template chain is (2gvhA)I262 T0362 7 :LLLRRVVRFGDTDAAGVMHFHQLFRWCHESWEESLE 2gvhA 148 :VTMVEIVFPDQANSAGRMFGGEAIAYMTKAAFVAAS T0362 60 :VTPEVALPIIHCQ 2gvhA 184 :RYCGKLVVLASSE T0362 73 :ADFRRPIHTGDALAMELRPERLNPNSFQVHFEFRC 2gvhA 198 :IDFARAIEIGEIVEAQAHVERVGRSSMSIQTKLWS T0362 108 :EE 2gvhA 237 :TG T0362 110 :QIAAHALIRHLAI 2gvhA 241 :HITATGHFTMVAV T0362 129 :RCA 2gvhA 259 :PAT Number of specific fragments extracted= 6 number of extra gaps= 0 total=344 Number of alignments=70 # 2gvhA read from 2gvhA/merged-good-all-a2m # found chain 2gvhA in template set Warning: unaligning (T0362)W6 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2gvhA)A147 Warning: unaligning (T0362)N123 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2gvhA)R258 Warning: unaligning (T0362)H128 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2gvhA)R258 Warning: unaligning (T0362)L132 because last residue in template chain is (2gvhA)I262 T0362 7 :LLLRRVVRFGDTDAAGVMHFHQLFRWCHESWEESLESYG 2gvhA 148 :VTMVEIVFPDQANSAGRMFGGEAIAYMTKAAFVAASRYC T0362 63 :EVALPIIHCQ 2gvhA 187 :GKLVVLASSE T0362 73 :ADFRRPIHTGDALAMELRPERLNPNSFQVHFEFRC 2gvhA 198 :IDFARAIEIGEIVEAQAHVERVGRSSMSIQTKLWS T0362 108 :EE 2gvhA 237 :TG T0362 110 :QIAAHALIRHLAI 2gvhA 241 :HITATGHFTMVAV T0362 129 :RCA 2gvhA 259 :PAT Number of specific fragments extracted= 6 number of extra gaps= 0 total=350 Number of alignments=71 # 2gvhA read from 2gvhA/merged-good-all-a2m # found chain 2gvhA in template set Warning: unaligning (T0362)N2 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2gvhA)A147 Warning: unaligning (T0362)W6 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2gvhA)A147 Warning: unaligning (T0362)N123 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2gvhA)R258 Warning: unaligning (T0362)H128 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2gvhA)R258 Warning: unaligning (T0362)L132 because last residue in template chain is (2gvhA)I262 T0362 7 :LLLRRVVRFGDTDAAGVMHFHQLFRWCHESWEESLESY 2gvhA 148 :VTMVEIVFPDQANSAGRMFGGEAIAYMTKAAFVAASRY T0362 61 :T 2gvhA 186 :C T0362 63 :EVALPIIHC 2gvhA 187 :GKLVVLASS T0362 72 :QADFRRPIHTGDALAMELRPERLNPNSFQVHFEFRC 2gvhA 197 :RIDFARAIEIGEIVEAQAHVERVGRSSMSIQTKLWS T0362 108 :EEQIAAHALIRHLAI 2gvhA 239 :ERHITATGHFTMVAV T0362 129 :RCA 2gvhA 259 :PAT Number of specific fragments extracted= 6 number of extra gaps= 0 total=356 Number of alignments=72 # 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 # T0362 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 T0362 4 :ENWLLLRRVVRFGDT 1ixlA 25 :EGYAEVELETIDEMK T0362 19 :DAAGVMHFHQLFRWCHESWEESL 1ixlA 41 :DEKGLVHGGFTFGLADYAAMLAV T0362 60 :VTPE 1ixlA 64 :NEPT T0362 66 :LPIIHCQADFRRPIHTGDALAMELRPERLNPNSFQVHFEFRCEEQIAAHALIRHLA 1ixlA 68 :VVLGKAEVRFTKPVKVGDKLVAKAKIIEDLGKKKIVEVKVYREEEVVLEGKFYCYV Number of specific fragments extracted= 4 number of extra gaps= 0 total=360 Number of alignments=73 # 1ixlA read from 1ixlA/merged-good-all-a2m # found chain 1ixlA in template set T0362 4 :ENWLLLRRVVRFGDT 1ixlA 25 :EGYAEVELETIDEMK T0362 19 :DAAGVMHFHQLFRWCHESWEESL 1ixlA 41 :DEKGLVHGGFTFGLADYAAMLAV T0362 45 :G 1ixlA 64 :N T0362 63 :EVALPIIHCQADFRRPIHTGDALAMELRPERLNPNSFQVHFEFRCEEQIAAHALIRHLA 1ixlA 65 :EPTVVLGKAEVRFTKPVKVGDKLVAKAKIIEDLGKKKIVEVKVYREEEVVLEGKFYCYV Number of specific fragments extracted= 4 number of extra gaps= 0 total=364 Number of alignments=74 # 1ixlA read from 1ixlA/merged-good-all-a2m # found chain 1ixlA in template set T0362 18 :TDAAGVMHFHQLFRWCHESWEESL 1ixlA 40 :VDEKGLVHGGFTFGLADYAAMLAV T0362 60 :VTPEVA 1ixlA 64 :NEPTVV T0362 68 :IIHCQADFRRPIHTGDALAMELRPERLNPNSFQVHFEFRCEEQIAAHALIRHL 1ixlA 70 :LGKAEVRFTKPVKVGDKLVAKAKIIEDLGKKKIVEVKVYREEEVVLEGKFYCY Number of specific fragments extracted= 3 number of extra gaps= 0 total=367 Number of alignments=75 # 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 # T0362 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 (T0362)I122 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2gf6A)N114 Warning: unaligning (T0362)N123 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2gf6A)N114 T0362 1 :M 2gf6A 1 :M T0362 3 :PENWLLLRRVVRFGDTDAAGVMHFHQLFRWCHESWEESLES 2gf6A 2 :ENIEYVFEDVVRIYDTDAQGIAHYAAYYRFFTNTIEKFIKE T0362 44 :YGLNPAD 2gf6A 44 :VGIPYPI T0362 60 :VTPEVALPIIHCQADFRRPIHTGDALAMELRPERLNPNSFQVHFEFRCEEQIAAHALIRHLA 2gf6A 51 :VNENLWFVIAESHAIYHRPVKLGDKLTVLLNPKILSNKTIKFEFKVLKDGELTTEGYVIQIA T0362 124 :AQTRHRCALPEGIDRWL 2gf6A 115 :PKIWKSTEMPKEIMDKL Number of specific fragments extracted= 5 number of extra gaps= 1 total=372 Number of alignments=76 # 2gf6A read from 2gf6A/merged-good-all-a2m # found chain 2gf6A in template set Warning: unaligning (T0362)I122 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2gf6A)N114 Warning: unaligning (T0362)N123 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2gf6A)N114 T0362 3 :PENWLLLRRVVRFGDTDAAGVMHFHQLFRWCHESWEESLES 2gf6A 2 :ENIEYVFEDVVRIYDTDAQGIAHYAAYYRFFTNTIEKFIKE T0362 44 :YGLNPADIFP 2gf6A 44 :VGIPYPIVNE T0362 63 :EVALPIIHCQADFRRPIHTGDALAMELRPERLNPNSFQVHFEFRCEEQIAAHALIRHLA 2gf6A 54 :NLWFVIAESHAIYHRPVKLGDKLTVLLNPKILSNKTIKFEFKVLKDGELTTEGYVIQIA T0362 124 :AQTRHRCALPEGIDRWL 2gf6A 115 :PKIWKSTEMPKEIMDKL Number of specific fragments extracted= 4 number of extra gaps= 1 total=376 Number of alignments=77 # 2gf6A read from 2gf6A/merged-good-all-a2m # found chain 2gf6A in template set Warning: unaligning (T0362)N2 because first residue in template chain is (2gf6A)M1 Warning: unaligning (T0362)I122 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2gf6A)N114 Warning: unaligning (T0362)N123 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2gf6A)N114 T0362 3 :PENWLLLRRVVRFGDTDAAGVMHFHQLFRWCHESWEESLES 2gf6A 2 :ENIEYVFEDVVRIYDTDAQGIAHYAAYYRFFTNTIEKFIKE T0362 44 :YGLNPA 2gf6A 44 :VGIPYP T0362 51 :I 2gf6A 50 :I T0362 60 :VTPEVALPIIHCQADFRRPIHTGDALAMELRPERLNPNSFQVHFEFRCEEQIAAHALIRHLA 2gf6A 51 :VNENLWFVIAESHAIYHRPVKLGDKLTVLLNPKILSNKTIKFEFKVLKDGELTTEGYVIQIA T0362 124 :AQTRHRCALPEGIDRWL 2gf6A 115 :PKIWKSTEMPKEIMDKL Number of specific fragments extracted= 5 number of extra gaps= 1 total=381 Number of alignments=78 # 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 # T0362 read from 1iq6A/merged-good-all-a2m # 1iq6A read from 1iq6A/merged-good-all-a2m # found chain 1iq6A in training set T0362 31 :RWCHESWEESLESY 1iq6A 55 :MLLASLFSGLLGQQ T0362 50 :D 1iq6A 69 :L T0362 60 :VTPEVA 1iq6A 70 :PGKGSI T0362 68 :IIHCQADFRRPIHTGDALAMELRPERL 1iq6A 76 :YLGQSLSFKLPVFVGDEVTAEVEVTAL T0362 95 :NPNSFQVHFEFRC 1iq6A 105 :DKPIATLTTRIFT T0362 108 :EEQIAAHALIRH 1iq6A 119 :GGALAVTGEAVV Number of specific fragments extracted= 6 number of extra gaps= 0 total=387 Number of alignments=79 # 1iq6A read from 1iq6A/merged-good-all-a2m # found chain 1iq6A in training set T0362 23 :VMHFHQLFRWCHES 1iq6A 51 :IVHGMLLASLFSGL T0362 41 :LESY 1iq6A 65 :LGQQ T0362 51 :IFPG 1iq6A 69 :LPGK T0362 63 :EVA 1iq6A 73 :GSI T0362 68 :IIHCQADFRRPIHTGDALAMELRPERL 1iq6A 76 :YLGQSLSFKLPVFVGDEVTAEVEVTAL T0362 95 :NPNSFQVHFEFRC 1iq6A 105 :DKPIATLTTRIFT T0362 108 :EEQIAAHALIRH 1iq6A 119 :GGALAVTGEAVV Number of specific fragments extracted= 7 number of extra gaps= 0 total=394 Number of alignments=80 # 1iq6A read from 1iq6A/merged-good-all-a2m # found chain 1iq6A in training set T0362 31 :RWCHESWEESLESYG 1iq6A 55 :MLLASLFSGLLGQQL T0362 60 :VTPEVA 1iq6A 70 :PGKGSI T0362 68 :IIHCQADFRRPIHTGDALAMELRPERL 1iq6A 76 :YLGQSLSFKLPVFVGDEVTAEVEVTAL T0362 95 :NPNSFQVHFEFRC 1iq6A 105 :DKPIATLTTRIFT T0362 108 :EEQIAAHALIRH 1iq6A 119 :GGALAVTGEAVV Number of specific fragments extracted= 5 number of extra gaps= 0 total=399 Number of alignments=81 # 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 # T0362 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 (T0362)N123 because last residue in template chain is (2b6eA)N137 T0362 3 :PENWLLLRRVVRFGDTDAAGVMHFHQLFRWCHESWEESLESY 2b6eA 32 :GEDWIEATMPVDHRTMQPFGVLHGGVSVALAETIGSLAGSLC T0362 60 :VTPEVALPIIHCQADFRRPIHT 2b6eA 74 :LEEGKTVVGLDINANHLRPVRS T0362 83 :DALAMELRPERLNPNSFQVHFEFRC 2b6eA 96 :GKVTARATPINLGRNIQVWQIDIRT T0362 108 :EEQIAAHALIRHLAI 2b6eA 122 :ENKLCCVSRLTLSVI Number of specific fragments extracted= 4 number of extra gaps= 0 total=403 Number of alignments=82 # 2b6eA read from 2b6eA/merged-good-all-a2m # found chain 2b6eA in template set Warning: unaligning (T0362)N123 because last residue in template chain is (2b6eA)N137 T0362 3 :PENWLLLRRVVRFGDTDAAGVMHFHQLFRWCHESWEESLESY 2b6eA 32 :GEDWIEATMPVDHRTMQPFGVLHGGVSVALAETIGSLAGSLC T0362 52 :FPG 2b6eA 74 :LEE T0362 63 :EVALPIIHCQADFRRPIHTG 2b6eA 77 :GKTVVGLDINANHLRPVRSG T0362 84 :ALAMELRPERLNPNSFQVHFEFRC 2b6eA 97 :KVTARATPINLGRNIQVWQIDIRT T0362 108 :EEQIAAHALIRHLAI 2b6eA 122 :ENKLCCVSRLTLSVI Number of specific fragments extracted= 5 number of extra gaps= 0 total=408 Number of alignments=83 # 2b6eA read from 2b6eA/merged-good-all-a2m # found chain 2b6eA in template set Warning: unaligning (T0362)N123 because last residue in template chain is (2b6eA)N137 T0362 3 :PENWLLLRRVVRFGDTDAAGVMHFHQLFRWCHESWEESLESY 2b6eA 32 :GEDWIEATMPVDHRTMQPFGVLHGGVSVALAETIGSLAGSLC T0362 60 :VTPEVALPIIHCQADFRRPIH 2b6eA 74 :LEEGKTVVGLDINANHLRPVR T0362 82 :GDALAMELRPERLNPNSFQVHFEFRC 2b6eA 95 :SGKVTARATPINLGRNIQVWQIDIRT T0362 108 :EEQIAAHALIRHLAI 2b6eA 122 :ENKLCCVSRLTLSVI Number of specific fragments extracted= 4 number of extra gaps= 0 total=412 Number of alignments=84 # 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 # T0362 read from 1vh5A/merged-good-all-a2m # 1vh5A read from 1vh5A/merged-good-all-a2m # found chain 1vh5A in training set Warning: unaligning (T0362)N123 because last residue in template chain is (1vh5A)E137 T0362 4 :ENWLLLRRVVRFGDTDAAGVMHFHQLFRWCHESWEESLESY 1vh5A 33 :DDTLEATMPVDSRTKQPFGLLHGGASVVLAESIGSVAGYLC T0362 60 :VTPEVALPIIHCQADFRRPIHT 1vh5A 74 :TEGEQKVVGLEINANHVRSARE T0362 83 :DALAMELRPERLNPNSFQVHFEFRC 1vh5A 96 :GRVRGVCKPLHLGSRHQVWQIEIFD T0362 108 :EEQIAAHALIRHLAI 1vh5A 122 :KGRLCCSSRLTTAIL Number of specific fragments extracted= 4 number of extra gaps= 0 total=416 Number of alignments=85 # 1vh5A read from 1vh5A/merged-good-all-a2m # found chain 1vh5A in training set Warning: unaligning (T0362)N123 because last residue in template chain is (1vh5A)E137 T0362 4 :ENWLLLRRVVRFGDTDAAGVMHFHQLFRWCHESWEESLESYG 1vh5A 33 :DDTLEATMPVDSRTKQPFGLLHGGASVVLAESIGSVAGYLCT T0362 53 :PG 1vh5A 75 :EG T0362 63 :EVALPIIHCQADFRRPIHTG 1vh5A 77 :EQKVVGLEINANHVRSAREG T0362 84 :ALAMELRPERLNPNSFQVHFEFRC 1vh5A 97 :RVRGVCKPLHLGSRHQVWQIEIFD T0362 108 :EEQIAAHALIRHLAI 1vh5A 122 :KGRLCCSSRLTTAIL Number of specific fragments extracted= 5 number of extra gaps= 0 total=421 Number of alignments=86 # 1vh5A read from 1vh5A/merged-good-all-a2m # found chain 1vh5A in training set Warning: unaligning (T0362)N123 because last residue in template chain is (1vh5A)E137 T0362 4 :ENWLLLRRVVRFGDTDAAGVMHFHQLFRWCHESWEESLESY 1vh5A 33 :DDTLEATMPVDSRTKQPFGLLHGGASVVLAESIGSVAGYLC T0362 60 :VTPEVALPIIHCQADFRRPIH 1vh5A 74 :TEGEQKVVGLEINANHVRSAR T0362 82 :GDALAMELRPERLNPNSFQVHFEFRC 1vh5A 95 :EGRVRGVCKPLHLGSRHQVWQIEIFD T0362 108 :EEQIAAHALIRHLAI 1vh5A 122 :KGRLCCSSRLTTAIL Number of specific fragments extracted= 4 number of extra gaps= 0 total=425 Number of alignments=87 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2h4uA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2h4uA expands to /projects/compbio/data/pdb/2h4u.pdb.gz 2h4uA:# T0362 read from 2h4uA/merged-good-all-a2m # 2h4uA read from 2h4uA/merged-good-all-a2m # adding 2h4uA to template set # found chain 2h4uA in template set T0362 4 :ENWLLLRRVVRFGDTDAAGVMHFHQLFRWCHESWEESLES 2h4uA 35 :PGKVICEMKVEEEHTNAIGTLHGGLTATLVDNISTMALLC T0362 60 :VTPEVALPIIHCQADFRRPIHTGDALAMELRPERLNPNSFQVHFEFRC 2h4uA 75 :TERGAPGVSVDMNITYMSPAKLGEDIVITAHVLKQGKTLAFTSVDLTN T0362 108 :EEQIAAHALIRHL 2h4uA 125 :TGKLIAQGRHTKH Number of specific fragments extracted= 3 number of extra gaps= 0 total=428 Number of alignments=88 # 2h4uA read from 2h4uA/merged-good-all-a2m # found chain 2h4uA in template set T0362 4 :ENWLLLRRVVRFGDTDAAGVMHFHQLFRWCHESWEESLESYGL 2h4uA 35 :PGKVICEMKVEEEHTNAIGTLHGGLTATLVDNISTMALLCTER T0362 63 :EVALPIIHCQADFRRPIHTGDALAMELRPERLNPNSFQVHFEFRC 2h4uA 78 :GAPGVSVDMNITYMSPAKLGEDIVITAHVLKQGKTLAFTSVDLTN T0362 108 :EEQIAAHALIRHL 2h4uA 125 :TGKLIAQGRHTKH Number of specific fragments extracted= 3 number of extra gaps= 0 total=431 Number of alignments=89 # 2h4uA read from 2h4uA/merged-good-all-a2m # found chain 2h4uA in template set T0362 4 :ENWLLLRRVVRFGDTDAAGVMHFHQLFRWCHESWEESLES 2h4uA 35 :PGKVICEMKVEEEHTNAIGTLHGGLTATLVDNISTMALLC T0362 60 :VTPEVALPIIHCQADFRRPIHTGDALAMELRPERLNPNSFQVHFEFRC 2h4uA 75 :TERGAPGVSVDMNITYMSPAKLGEDIVITAHVLKQGKTLAFTSVDLTN T0362 108 :EEQIAAHALIRHL 2h4uA 125 :TGKLIAQGRHTKH Number of specific fragments extracted= 3 number of extra gaps= 0 total=434 Number of alignments=90 # 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 # T0362 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 (T0362)R11 because of BadResidue code BAD_PEPTIDE in next template residue (2fs2A)T39 Warning: unaligning (T0362)V12 because of BadResidue code BAD_PEPTIDE at template residue (2fs2A)T39 Warning: unaligning (T0362)A73 because of BadResidue code BAD_PEPTIDE in next template residue (2fs2A)D83 Warning: unaligning (T0362)D74 because of BadResidue code BAD_PEPTIDE at template residue (2fs2A)D83 Warning: unaligning (T0362)A115 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2fs2A)R126 Warning: unaligning (T0362)L116 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2fs2A)R126 Warning: unaligning (T0362)L120 because of BadResidue code BAD_PEPTIDE in next template residue (2fs2A)R131 T0362 4 :ENWLLLR 2fs2A 31 :EGFAVVT T0362 13 :VRFGDTDAAGVMHFHQLFRWCHESWEESLE 2fs2A 40 :VTAQMLNGHQSCHGGQLFSLADTAFAYACN T0362 61 :TPEVALPIIHCQ 2fs2A 70 :SQGLAAVASACT T0362 75 :FRRPIHTGDALAMELRPERLNPNSFQVHFEFRC 2fs2A 84 :FLRPGFAGDTLTATAQVRHQGKQTGVYDIEIVN T0362 108 :EEQIAAH 2fs2A 118 :QQKTVAL T0362 117 :IRH 2fs2A 127 :GKS Number of specific fragments extracted= 6 number of extra gaps= 4 total=440 Number of alignments=91 # 2fs2A read from 2fs2A/merged-good-all-a2m # found chain 2fs2A in template set Warning: unaligning (T0362)R11 because of BadResidue code BAD_PEPTIDE in next template residue (2fs2A)T39 Warning: unaligning (T0362)V12 because of BadResidue code BAD_PEPTIDE at template residue (2fs2A)T39 Warning: unaligning (T0362)A73 because of BadResidue code BAD_PEPTIDE in next template residue (2fs2A)D83 Warning: unaligning (T0362)D74 because of BadResidue code BAD_PEPTIDE at template residue (2fs2A)D83 Warning: unaligning (T0362)A115 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2fs2A)R126 Warning: unaligning (T0362)L116 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2fs2A)R126 Warning: unaligning (T0362)L120 because of BadResidue code BAD_PEPTIDE in next template residue (2fs2A)R131 T0362 3 :PENWLLLR 2fs2A 30 :DEGFAVVT T0362 13 :VRFGDTDAAGVMHFHQLFRWCHESWEESLESY 2fs2A 40 :VTAQMLNGHQSCHGGQLFSLADTAFAYACNSQ T0362 63 :EVALPIIHCQ 2fs2A 72 :GLAAVASACT T0362 75 :FRRPIHTGDALAMELRPERLNPNSFQVHFEFRC 2fs2A 84 :FLRPGFAGDTLTATAQVRHQGKQTGVYDIEIVN T0362 108 :EEQIAAH 2fs2A 118 :QQKTVAL T0362 117 :IRH 2fs2A 127 :GKS Number of specific fragments extracted= 6 number of extra gaps= 4 total=446 Number of alignments=92 # 2fs2A read from 2fs2A/merged-good-all-a2m # found chain 2fs2A in template set Warning: unaligning (T0362)R11 because of BadResidue code BAD_PEPTIDE in next template residue (2fs2A)T39 Warning: unaligning (T0362)V12 because of BadResidue code BAD_PEPTIDE at template residue (2fs2A)T39 Warning: unaligning (T0362)A73 because of BadResidue code BAD_PEPTIDE in next template residue (2fs2A)D83 Warning: unaligning (T0362)D74 because of BadResidue code BAD_PEPTIDE at template residue (2fs2A)D83 Warning: unaligning (T0362)A115 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2fs2A)R126 Warning: unaligning (T0362)L116 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2fs2A)R126 T0362 10 :R 2fs2A 37 :T T0362 13 :VRFGDTDAAGVMHFHQLFRWCHESWEESL 2fs2A 40 :VTAQMLNGHQSCHGGQLFSLADTAFAYAC T0362 60 :VTPEVALPIIHCQ 2fs2A 69 :NSQGLAAVASACT T0362 75 :FRRPIHTGDALAMELRPERLNPNSFQVHFEFRC 2fs2A 84 :FLRPGFAGDTLTATAQVRHQGKQTGVYDIEIVN T0362 108 :EEQIAAH 2fs2A 118 :QQKTVAL T0362 117 :IRH 2fs2A 127 :GKS Number of specific fragments extracted= 6 number of extra gaps= 3 total=452 Number of alignments=93 # 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:# T0362 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 T0362 23 :VMHFHQLFRWCHESWEE 1c8uA 33 :QVFGGQVVGQALYAAKE T0362 44 :Y 1c8uA 50 :T T0362 60 :VTPEVA 1c8uA 51 :VPEERL T0362 68 :IIHCQADFRRPIHTGDALAMELRPERLNPNSFQVHFEFRCEEQIAAHALIRHLAI 1c8uA 57 :VHSFHSYFLRPGDSKKPIIYDVETLRDGNSFSARRVAAIQNGKPIFYMTASFQAP T0362 125 :QTRHRCALPE 1c8uA 117 :HQKTMPSAPA Number of specific fragments extracted= 5 number of extra gaps= 0 total=457 Number of alignments=94 # 1c8uA read from 1c8uA/merged-good-all-a2m # found chain 1c8uA in template set T0362 23 :VMHFHQLFRWCHESWEE 1c8uA 33 :QVFGGQVVGQALYAAKE T0362 45 :GLN 1c8uA 50 :TVP T0362 54 :G 1c8uA 53 :E T0362 63 :EVA 1c8uA 54 :ERL T0362 68 :IIHCQADFRRPIHTGDALAMELRPERLNPNSFQVHFEFRCEEQIAAHALIRHLA 1c8uA 57 :VHSFHSYFLRPGDSKKPIIYDVETLRDGNSFSARRVAAIQNGKPIFYMTASFQA Number of specific fragments extracted= 5 number of extra gaps= 0 total=462 Number of alignments=95 # 1c8uA read from 1c8uA/merged-good-all-a2m # found chain 1c8uA in template set T0362 6 :WLLLRRVVRFGD 1c8uA 175 :EPHRQVWIRANG T0362 27 :HQLFRWCHES 1c8uA 193 :RVHQYLLGYA T0362 43 :SYGLNPADIFPGSRKSEVTPEVALPIIHCQADFRRPIHTGDALAMELRPERLNPNSFQVHFEFRC 1c8uA 203 :SDLNFLPVALQPHGIGFLEPGIQIATIDHSMWFHRPFNLNEWLLYSVESTSASSARGFVRGEFYT T0362 108 :EEQIAAHALIRHLA 1c8uA 269 :DGVLVASTVQEGVM Number of specific fragments extracted= 4 number of extra gaps= 0 total=466 Number of alignments=96 # 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 # T0362 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 (T0362)T126 because of BadResidue code BAD_PEPTIDE in next template residue (2essA)R121 Warning: unaligning (T0362)R127 because of BadResidue code BAD_PEPTIDE at template residue (2essA)R121 Warning: unaligning (T0362)R129 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2essA)A124 Warning: unaligning (T0362)C130 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2essA)A124 T0362 1 :MNPEN 2essA 1 :MSEEN T0362 6 :WLLLRRVVRFGDTDAAGVMHFHQLFRWCHESWEESLESYGLNPADI 2essA 7 :IGTYQFVAEPFHVDFNGRLTMGVLGNHLLNCAGFHASDRGFGIATL T0362 60 :VTPEVALPIIHCQADFRRPIHTGDALAMELRPERLNPNSFQVHFEFRC 2essA 53 :NEDNYTWVLSRLAIELDEMPYQYEKFSVQTWVENVYRLFTDRNFAVID T0362 108 :EEQIAAHALIRHLAINAQ 2essA 102 :DGKKIGYARSVWAMINLN T0362 128 :H 2essA 122 :K Number of specific fragments extracted= 5 number of extra gaps= 2 total=471 Number of alignments=97 # 2essA read from 2essA/merged-good-all-a2m # found chain 2essA in template set Warning: unaligning (T0362)T126 because of BadResidue code BAD_PEPTIDE in next template residue (2essA)R121 Warning: unaligning (T0362)R127 because of BadResidue code BAD_PEPTIDE at template residue (2essA)R121 Warning: unaligning (T0362)R129 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2essA)A124 Warning: unaligning (T0362)C130 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2essA)A124 T0362 1 :MNPEN 2essA 1 :MSEEN T0362 6 :WLLLRRVVRFGDTDAAGVMHFHQLFRWCHESWEESLESYGLNPADIFPG 2essA 7 :IGTYQFVAEPFHVDFNGRLTMGVLGNHLLNCAGFHASDRGFGIATLNED T0362 63 :EVALPIIHCQADFRRPIHTGDALAMELRPERLNPNSFQVHFEFRC 2essA 56 :NYTWVLSRLAIELDEMPYQYEKFSVQTWVENVYRLFTDRNFAVID T0362 108 :EEQIAAHALIRHLAINAQ 2essA 102 :DGKKIGYARSVWAMINLN T0362 128 :H 2essA 122 :K Number of specific fragments extracted= 5 number of extra gaps= 2 total=476 Number of alignments=98 # 2essA read from 2essA/merged-good-all-a2m # found chain 2essA in template set Warning: unaligning (T0362)T126 because of BadResidue code BAD_PEPTIDE in next template residue (2essA)R121 Warning: unaligning (T0362)R127 because of BadResidue code BAD_PEPTIDE at template residue (2essA)R121 Warning: unaligning (T0362)R129 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2essA)A124 Warning: unaligning (T0362)C130 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2essA)A124 T0362 3 :PENWLLLRRVVRFGDTDAAGVMHFHQLFRWCHESWEESLESYGLNPADI 2essA 4 :ENKIGTYQFVAEPFHVDFNGRLTMGVLGNHLLNCAGFHASDRGFGIATL T0362 60 :VTPEVALPIIHCQADFRRPIHTGDALAMELRPERLNPNSFQVHFEFRC 2essA 53 :NEDNYTWVLSRLAIELDEMPYQYEKFSVQTWVENVYRLFTDRNFAVID T0362 108 :EEQIAAHALIRHLAINAQ 2essA 102 :DGKKIGYARSVWAMINLN T0362 128 :H 2essA 122 :K Number of specific fragments extracted= 4 number of extra gaps= 2 total=480 Number of alignments=99 # 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 # T0362 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 (T0362)V23 because of BadResidue code BAD_PEPTIDE in next template residue (1u1zA)F50 Warning: unaligning (T0362)V60 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1u1zA)T85 Warning: unaligning (T0362)V64 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1u1zA)T85 T0362 3 :PENWLLLRRVVRFGDTDAAG 1u1zA 29 :EGKRIRAYKNVSINEPFFNG T0362 24 :MHFHQLFRWCHESWEESLES 1u1zA 56 :MPGVLIIEAMAQAAGILGFK T0362 44 :YGLN 1u1zA 77 :LDVK T0362 65 :ALPIIHCQ 1u1zA 86 :LYYFVGSD T0362 73 :ADFRRPIHTGDALAMELRPERLNPNSFQVHFEFRCEEQIAAHALIRHL 1u1zA 95 :LRFRQPVLPGDQLQLHAKFISVKRSIWKFDCHATVDDKPVCSAEIICA Number of specific fragments extracted= 5 number of extra gaps= 1 total=485 Number of alignments=100 # 1u1zA read from 1u1zA/merged-good-all-a2m # found chain 1u1zA in template set Warning: unaligning (T0362)V23 because of BadResidue code BAD_PEPTIDE in next template residue (1u1zA)F50 Warning: unaligning (T0362)P48 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1u1zA)T85 Warning: unaligning (T0362)V64 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1u1zA)T85 T0362 3 :PENWLLLRRVVRFGDTDAAG 1u1zA 29 :EGKRIRAYKNVSINEPFFNG T0362 24 :MHFHQLFRWCHESWEESLES 1u1zA 56 :MPGVLIIEAMAQAAGILGFK T0362 44 :YGLN 1u1zA 77 :LDVK T0362 65 :ALPIIHCQ 1u1zA 86 :LYYFVGSD T0362 73 :ADFRRPIHTGDALAMELRPERLNPNSFQVHFEFRCEEQIAAHALIRHL 1u1zA 95 :LRFRQPVLPGDQLQLHAKFISVKRSIWKFDCHATVDDKPVCSAEIICA Number of specific fragments extracted= 5 number of extra gaps= 1 total=490 Number of alignments=101 # 1u1zA read from 1u1zA/merged-good-all-a2m # found chain 1u1zA in template set Warning: unaligning (T0362)V60 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1u1zA)T85 Warning: unaligning (T0362)V64 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1u1zA)T85 T0362 32 :WCHESWEESLESYGLNPADIF 1u1zA 60 :LIIEAMAQAAGILGFKMLDVK T0362 65 :ALPIIHC 1u1zA 86 :LYYFVGS T0362 72 :QADFRRPIHTGDALAMELRPERLNPNSFQVHFEFRCEEQIAAHALIRHL 1u1zA 94 :KLRFRQPVLPGDQLQLHAKFISVKRSIWKFDCHATVDDKPVCSAEIICA Number of specific fragments extracted= 3 number of extra gaps= 0 total=493 Number of alignments=102 # command:Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0362//projects/compbio/experiments/protein-predict/casp7/T0362/align.constraints_v3.costfcn or /projects/compbio/experiments/protein-predict/casp7/T0362//projects/compbio/experiments/protein-predict/casp7/T0362/align.constraints_v3.costfcn.gz for input Trying /projects/compbio/experiments/protein-predict/casp7/T0362/align.constraints_v3.costfcn # reading script from file /projects/compbio/experiments/protein-predict/casp7/T0362/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((T0362)I69.CB, (T0362)R118.CB) [> 3.0026 = 5.0044 < 6.5057] w=1.0000 to align # Constraint # added constraint: constraint((T0362)F75.CB, (T0362)A113.CB) [> 3.1120 = 5.1867 < 6.7427] w=1.0000 to align # Constraint # added constraint: constraint((T0362)R76.CB, (T0362)A113.CB) [> 3.6965 = 6.1609 < 8.0092] w=1.0000 to align # Constraint # added constraint: constraint((T0362)I79.CB, (T0362)A112.CB) [> 3.2793 = 5.4656 < 7.1052] w=1.0000 to align # Constraint # added constraint: constraint((T0362)A86.CB, (T0362)F105.CB) [> 4.2467 = 7.0778 < 9.2011] w=1.0000 to align # Constraint # added constraint: constraint((T0362)M87.CB, (T0362)F103.CB) [> 3.5875 = 5.9792 < 7.7730] w=1.0000 to align # Constraint # added constraint: constraint((T0362)M87.CB, (T0362)E104.CB) [> 4.3597 = 7.2662 < 9.4461] w=1.0000 to align # Constraint # added constraint: constraint((T0362)S98.CB, (T0362)R118.CB) [> 3.5803 = 5.9672 < 7.7573] w=1.0000 to align # Constraint # added constraint: constraint((T0362)F105.CB, (T0362)H114.CB) [> 4.4238 = 7.3731 < 9.5850] w=1.0000 to align # Constraint # added constraint: constraint((T0362)E104.CB, (T0362)H114.CB) [> 3.2314 = 5.3857 < 7.0014] w=1.0000 to align # Constraint # added constraint: constraint((T0362)F103.CB, (T0362)I117.CB) [> 4.0054 = 6.6756 < 8.6783] w=1.0000 to align # Constraint # added constraint: constraint((T0362)F103.CB, (T0362)H114.CB) [> 4.2595 = 7.0992 < 9.2290] w=1.0000 to align # Constraint # added constraint: constraint((T0362)V101.CB, (T0362)H119.CB) [> 4.0085 = 6.6808 < 8.6851] w=1.0000 to align # Constraint # added constraint: constraint((T0362)V101.CB, (T0362)I117.CB) [> 2.9304 = 4.8839 < 6.3491] w=1.0000 to align # Constraint # added constraint: constraint((T0362)Q100.CB, (T0362)R118.CB) [> 3.0996 = 5.1659 < 6.7157] w=1.0000 to align # Constraint # added constraint: constraint((T0362)Q100.CB, (T0362)I117.CB) [> 4.3182 = 7.1970 < 9.3561] w=1.0000 to align # Constraint # added constraint: constraint((T0362)F99.CB, (T0362)H119.CB) [> 2.7802 = 4.6337 < 6.0239] w=1.0000 to align # Constraint # added constraint: constraint((T0362)F99.CB, (T0362)R118.CB) [> 4.2639 = 7.1065 < 9.2384] w=1.0000 to align # Constraint # added constraint: constraint((T0362)S98.CB, (T0362)H119.CB) [> 3.8629 = 6.4381 < 8.3696] w=1.0000 to align # Constraint # added constraint: constraint((T0362)I68.CB, (T0362)R118.CB) [> 4.3498 = 7.2496 < 9.4245] w=0.9910 to align # Constraint # added constraint: constraint((T0362)L85.CB, (T0362)F105.CB) [> 3.4422 = 5.7370 < 7.4581] w=0.9898 to align # Constraint # added constraint: constraint((T0362)C71.CB, (T0362)I117.CB) [> 2.9202 = 4.8671 < 6.3272] w=0.9898 to align # Constraint # added constraint: constraint((T0362)H70.CB, (T0362)R118.CB) [> 2.7070 = 4.5116 < 5.8651] w=0.9898 to align # Constraint # added constraint: constraint((T0362)I68.CB, (T0362)H119.CB) [> 3.5341 = 5.8902 < 7.6573] w=0.9808 to align # Constraint # added constraint: constraint((T0362)I68.CB, (T0362)I117.CB) [> 3.5506 = 5.9177 < 7.6931] w=0.9808 to align # Constraint # added constraint: constraint((T0362)M87.CB, (T0362)F105.CB) [> 3.1258 = 5.2097 < 6.7726] w=0.9796 to align # Constraint # added constraint: constraint((T0362)E88.CB, (T0362)F103.CB) [> 4.0688 = 6.7813 < 8.8157] w=0.9796 to align # Constraint # added constraint: constraint((T0362)E88.CB, (T0362)E104.CB) [> 2.9513 = 4.9189 < 6.3945] w=0.9796 to align # Constraint # added constraint: constraint((T0362)L89.CB, (T0362)V101.CB) [> 3.3308 = 5.5514 < 7.2168] w=0.9796 to align # Constraint # added constraint: constraint((T0362)L89.CB, (T0362)H102.CB) [> 4.1865 = 6.9775 < 9.0707] w=0.9796 to align # Constraint # added constraint: constraint((T0362)L89.CB, (T0362)F103.CB) [> 2.9423 = 4.9038 < 6.3749] w=0.9796 to align # Constraint # added constraint: constraint((T0362)R90.CB, (T0362)H102.CB) [> 3.0398 = 5.0664 < 6.5863] w=0.9796 to align # Constraint # added constraint: constraint((T0362)P91.CB, (T0362)V101.CB) [> 3.4380 = 5.7300 < 7.4490] w=0.9796 to align # Constraint # added constraint: constraint((T0362)I69.CB, (T0362)H119.CB) [> 3.9767 = 6.6279 < 8.6163] w=0.9716 to align # Constraint # added constraint: constraint((T0362)L85.CB, (T0362)A112.CB) [> 4.1591 = 6.9318 < 9.0113] w=0.9695 to align # Constraint # added constraint: constraint((T0362)A86.CB, (T0362)R106.CB) [> 2.9302 = 4.8837 < 6.3488] w=0.9692 to align # Constraint # added constraint: constraint((T0362)I79.CB, (T0362)C107.CB) [> 3.4940 = 5.8233 < 7.5703] w=0.9692 to align # Constraint # added constraint: constraint((T0362)F103.CB, (T0362)A115.CB) [> 2.7859 = 4.6432 < 6.0362] w=0.9692 to align # Constraint # added constraint: constraint((T0362)H102.CB, (T0362)L116.CB) [> 3.4169 = 5.6948 < 7.4033] w=0.9692 to align # Constraint # added constraint: constraint((T0362)V101.CB, (T0362)L116.CB) [> 4.2333 = 7.0555 < 9.1721] w=0.9692 to align # Constraint # added constraint: constraint((T0362)Q100.CB, (T0362)L116.CB) [> 3.8192 = 6.3653 < 8.2749] w=0.9692 to align # Constraint # added constraint: constraint((T0362)D74.CB, (T0362)A113.CB) [> 3.8526 = 6.4211 < 8.3474] w=0.9692 to align # Constraint # added constraint: constraint((T0362)A73.CB, (T0362)A115.CB) [> 2.5877 = 4.3128 < 5.6066] w=0.9692 to align # Constraint # added constraint: constraint((T0362)R76.CB, (T0362)I111.CB) [> 3.4259 = 5.7099 < 7.4228] w=0.9692 to align # Constraint # added constraint: constraint((T0362)R77.CB, (T0362)Q110.CB) [> 3.5603 = 5.9339 < 7.7141] w=0.9692 to align # Constraint # added constraint: constraint((T0362)I69.CB, (T0362)S98.CB) [> 4.2283 = 7.0472 < 9.1614] w=0.9685 to align # Constraint # added constraint: constraint((T0362)F75.CB, (T0362)A112.CB) [> 4.3543 = 7.2571 < 9.4342] w=0.9662 to align # Constraint # added constraint: constraint((T0362)H70.CB, (T0362)I117.CB) [> 4.1786 = 6.9644 < 9.0537] w=0.9593 to align # Constraint # added constraint: constraint((T0362)L85.CB, (T0362)R106.CB) [> 4.1939 = 6.9899 < 9.0868] w=0.9591 to align # Constraint # added constraint: constraint((T0362)C71.CB, (T0362)L116.CB) [> 4.2309 = 7.0516 < 9.1670] w=0.9590 to align # Constraint # added constraint: constraint((T0362)C71.CB, (T0362)A115.CB) [> 3.7740 = 6.2900 < 8.1770] w=0.9590 to align # Constraint # added constraint: constraint((T0362)E92.CB, (T0362)V101.CB) [> 3.9156 = 6.5260 < 8.4838] w=0.9577 to align # Constraint # added constraint: constraint((T0362)E92.CB, (T0362)H102.CB) [> 3.1421 = 5.2368 < 6.8078] w=0.9577 to align # Constraint # added constraint: constraint((T0362)R90.CB, (T0362)V101.CB) [> 4.1120 = 6.8534 < 8.9094] w=0.9476 to align # Constraint # added constraint: constraint((T0362)A73.CB, (T0362)A113.CB) [> 3.6159 = 6.0265 < 7.8345] w=0.9454 to align # Constraint # added constraint: constraint((T0362)H102.CB, (T0362)A115.CB) [> 4.4665 = 7.4441 < 9.6773] w=0.9387 to align # Constraint # added constraint: constraint((T0362)L85.CB, (T0362)C107.CB) [> 3.6086 = 6.0143 < 7.8187] w=0.9387 to align # Constraint # added constraint: constraint((T0362)Q72.CB, (T0362)A115.CB) [> 3.7280 = 6.2133 < 8.0773] w=0.9387 to align # Constraint # added constraint: constraint((T0362)A73.CB, (T0362)H114.CB) [> 4.2191 = 7.0318 < 9.1414] w=0.9385 to align # Constraint # added constraint: constraint((T0362)E104.CB, (T0362)A113.CB) [> 4.4488 = 7.4146 < 9.6390] w=0.9385 to align # Constraint # added constraint: constraint((T0362)P67.CB, (T0362)H119.CB) [> 4.0114 = 6.6856 < 8.6913] w=0.9357 to align # Constraint # added constraint: constraint((T0362)F103.CB, (T0362)L116.CB) [> 4.4007 = 7.3344 < 9.5348] w=0.9355 to align # Constraint # added constraint: constraint((T0362)Q72.CB, (T0362)L116.CB) [> 3.0193 = 5.0322 < 6.5418] w=0.9305 to align # Constraint # added constraint: constraint((T0362)W37.CB, (T0362)I117.CB) [> 3.3442 = 5.5737 < 7.2459] w=0.9305 to align # Constraint # added constraint: constraint((T0362)S98.CB, (T0362)L120.CB) [> 3.1807 = 5.3012 < 6.8916] w=0.9285 to align # Constraint # added constraint: constraint((T0362)W37.CB, (T0362)L89.CB) [> 3.3108 = 5.5181 < 7.1735] w=0.9231 to align # Constraint # added constraint: constraint((T0362)L29.CB, (T0362)F105.CB) [> 3.7416 = 6.2360 < 8.1068] w=0.9185 to align # Constraint # added constraint: constraint((T0362)E88.CB, (T0362)R106.CB) [> 4.3608 = 7.2680 < 9.4484] w=0.9181 to align # Constraint # added constraint: constraint((T0362)L66.CB, (T0362)H119.CB) [> 2.8143 = 4.6906 < 6.0978] w=0.9162 to align # Constraint # added constraint: constraint((T0362)D74.CB, (T0362)H114.CB) [> 3.0557 = 5.0928 < 6.6206] w=0.9077 to align # Constraint # added constraint: constraint((T0362)C33.CB, (T0362)F103.CB) [> 2.7977 = 4.6629 < 6.0617] w=0.9026 to align # Constraint # added constraint: constraint((T0362)I69.CB, (T0362)L120.CB) [> 3.0723 = 5.1205 < 6.6567] w=0.9001 to align # Constraint # added constraint: constraint((T0362)C71.CB, (T0362)R118.CB) [> 4.4215 = 7.3692 < 9.5799] w=0.8999 to align # Constraint # added constraint: constraint((T0362)S40.CB, (T0362)L89.CB) [> 2.8628 = 4.7714 < 6.2028] w=0.8988 to align # Constraint # added constraint: constraint((T0362)N97.CB, (T0362)L120.CB) [> 3.8059 = 6.3431 < 8.2460] w=0.8979 to align # Constraint # added constraint: constraint((T0362)W37.CB, (T0362)V101.CB) [> 3.0427 = 5.0711 < 6.5925] w=0.8924 to align # Constraint # added constraint: constraint((T0362)C33.CB, (T0362)M87.CB) [> 3.6098 = 6.0164 < 7.8213] w=0.8923 to align # Constraint # added constraint: constraint((T0362)P67.CB, (T0362)L120.CB) [> 3.1944 = 5.3240 < 6.9212] w=0.8868 to align # Constraint # added constraint: constraint((T0362)P91.CB, (T0362)Q100.CB) [> 4.4440 = 7.4066 < 9.6286] w=0.8832 to align # Constraint # added constraint: constraint((T0362)S36.CB, (T0362)L89.CB) [> 2.8151 = 4.6919 < 6.0994] w=0.8823 to align # Constraint # added constraint: constraint((T0362)R77.CB, (T0362)I111.CB) [> 4.3179 = 7.1965 < 9.3555] w=0.8771 to align # Constraint # added constraint: constraint((T0362)R76.CB, (T0362)H114.CB) [> 4.1821 = 6.9702 < 9.0613] w=0.8769 to align # Constraint # added constraint: constraint((T0362)W32.CB, (T0362)M87.CB) [> 3.2287 = 5.3811 < 6.9955] w=0.8721 to align # Constraint # added constraint: constraint((T0362)C33.CB, (T0362)I117.CB) [> 4.1358 = 6.8930 < 8.9608] w=0.8648 to align # Constraint # added constraint: constraint((T0362)L66.CB, (T0362)L120.CB) [> 4.0170 = 6.6950 < 8.7035] w=0.8641 to align # Constraint # added constraint: constraint((T0362)D83.CB, (T0362)C107.CB) [> 3.3741 = 5.6235 < 7.3106] w=0.8634 to align # Constraint # added constraint: constraint((T0362)C33.CB, (T0362)A115.CB) [> 3.1368 = 5.2280 < 6.7964] w=0.8510 to align # Constraint # added constraint: constraint((T0362)W32.CB, (T0362)F105.CB) [> 4.0800 = 6.8000 < 8.8400] w=0.8499 to align # Constraint # added constraint: constraint((T0362)L29.CB, (T0362)A113.CB) [> 3.2777 = 5.4628 < 7.1016] w=0.8499 to align # Constraint # added constraint: constraint((T0362)Q100.CB, (T0362)H119.CB) [> 4.4973 = 7.4955 < 9.7441] w=0.8431 to align # Constraint # added constraint: constraint((T0362)F26.CB, (T0362)F75.CB) [> 3.5728 = 5.9546 < 7.7410] w=0.8406 to align # Constraint # added constraint: constraint((T0362)L8.CB, (T0362)E88.CB) [> 3.1627 = 5.2711 < 6.8524] w=0.8330 to align # Constraint # added constraint: constraint((T0362)M24.CB, (T0362)H80.CB) [> 4.3436 = 7.2393 < 9.4111] w=0.8307 to align # Constraint # added constraint: constraint((T0362)W37.CB, (T0362)F103.CB) [> 3.6389 = 6.0648 < 7.8842] w=0.8279 to align # Constraint # added constraint: constraint((T0362)M24.CB, (T0362)P78.CB) [> 4.2667 = 7.1112 < 9.2446] w=0.8263 to align # Constraint # added constraint: constraint((T0362)L9.CB, (T0362)A86.CB) [> 4.3552 = 7.2587 < 9.4363] w=0.8249 to align # Constraint # added constraint: constraint((T0362)L8.CB, (T0362)M87.CB) [> 4.0829 = 6.8048 < 8.8462] w=0.8248 to align # Constraint # added constraint: constraint((T0362)L29.CB, (T0362)F75.CB) [> 4.3970 = 7.3283 < 9.5267] w=0.8238 to align # Constraint # added constraint: constraint((T0362)V13.CB, (T0362)I79.CB) [> 3.4214 = 5.7023 < 7.4130] w=0.8229 to align # Constraint # added constraint: constraint((T0362)L9.CB, (T0362)M87.CB) [> 2.9038 = 4.8397 < 6.2915] w=0.8229 to align # Constraint # added constraint: constraint((T0362)W32.CB, (T0362)L85.CB) [> 3.9408 = 6.5680 < 8.5384] w=0.8192 to align # Constraint # added constraint: constraint((T0362)L9.CB, (T0362)S36.CB) [> 2.7812 = 4.6353 < 6.0259] w=0.8136 to align # Constraint # added constraint: constraint((T0362)V13.CB, (T0362)L85.CB) [> 3.8193 = 6.3654 < 8.2751] w=0.8126 to align # Constraint # added constraint: constraint((T0362)R10.CB, (T0362)A86.CB) [> 3.1567 = 5.2612 < 6.8395] w=0.8126 to align # Constraint # added constraint: constraint((T0362)L8.CB, (T0362)A86.CB) [> 3.7098 = 6.1830 < 8.0379] w=0.8043 to align # Constraint # added constraint: constraint((T0362)R10.CB, (T0362)L85.CB) [> 4.0954 = 6.8257 < 8.8735] w=0.8024 to align # Constraint # added constraint: constraint((T0362)V23.CB, (T0362)I79.CB) [> 3.8234 = 6.3724 < 8.2841] w=0.8001 to align # Constraint # added constraint: constraint((T0362)V23.CB, (T0362)P78.CB) [> 2.6202 = 4.3670 < 5.6771] w=0.8001 to align # Constraint # added constraint: constraint((T0362)V13.CB, (T0362)G82.CA) [> 3.1099 = 5.1831 < 6.7381] w=0.7983 to align # Constraint # added constraint: constraint((T0362)L7.CB, (T0362)L89.CB) [> 2.9353 = 4.8921 < 6.3597] w=0.7942 to align # Constraint # added constraint: constraint((T0362)V13.CB, (T0362)M24.CB) [> 3.1893 = 5.3155 < 6.9101] w=0.7922 to align # Constraint # added constraint: constraint((T0362)H102.CB, (T0362)H114.CB) [> 4.4994 = 7.4990 < 9.7486] w=0.7860 to align # Constraint # added constraint: constraint((T0362)V13.CB, (T0362)D83.CB) [> 3.0972 = 5.1620 < 6.7106] w=0.7851 to align # Constraint # added constraint: constraint((T0362)V12.CB, (T0362)A84.CB) [> 3.2805 = 5.4675 < 7.1077] w=0.7838 to align # Constraint # added constraint: constraint((T0362)V101.CB, (T0362)R118.CB) [> 4.5712 = 7.6187 < 9.9043] w=0.7832 to align # Constraint # added constraint: constraint((T0362)F30.CB, (T0362)A73.CB) [> 3.7126 = 6.1877 < 8.0440] w=0.7796 to align # Constraint # added constraint: constraint((T0362)F30.CB, (T0362)C71.CB) [> 4.1742 = 6.9570 < 9.0442] w=0.7775 to align # Constraint # added constraint: constraint((T0362)L7.CB, (T0362)S40.CB) [> 2.7150 = 4.5251 < 5.8826] w=0.7726 to align # Constraint # added constraint: constraint((T0362)R11.CB, (T0362)L85.CB) [> 3.0591 = 5.0985 < 6.6281] w=0.7716 to align # Constraint # added constraint: constraint((T0362)R10.CB, (T0362)A84.CB) [> 3.5544 = 5.9239 < 7.7011] w=0.7716 to align # Constraint # added constraint: constraint((T0362)V23.CB, (T0362)H80.CB) [> 3.5831 = 5.9718 < 7.7634] w=0.7693 to align # Constraint # added constraint: constraint((T0362)D74.CB, (T0362)A115.CB) [> 4.3104 = 7.1840 < 9.3392] w=0.7615 to align # Constraint # added constraint: constraint((T0362)R11.CB, (T0362)W32.CB) [> 3.2769 = 5.4616 < 7.1000] w=0.7613 to align # Constraint # added constraint: constraint((T0362)L7.CB, (T0362)S36.CB) [> 3.6461 = 6.0768 < 7.8999] w=0.7429 to align # Constraint # added constraint: constraint((T0362)N97.CB, (T0362)A121.CB) [> 3.4101 = 5.6835 < 7.3885] w=0.7415 to align # Constraint # added constraint: constraint((T0362)D17.CB, (T0362)Q28.CB) [> 2.7497 = 4.5828 < 5.9576] w=0.7412 to align # Constraint # added constraint: constraint((T0362)H34.CB, (T0362)I68.CB) [> 3.9316 = 6.5527 < 8.5185] w=0.7375 to align # Constraint # added constraint: constraint((T0362)V13.CB, (T0362)T81.CB) [> 3.0324 = 5.0540 < 6.5702] w=0.7340 to align # Constraint # added constraint: constraint((T0362)V13.CB, (T0362)H80.CB) [> 4.0231 = 6.7051 < 8.7167] w=0.7307 to align # Constraint # added constraint: constraint((T0362)L9.CB, (T0362)E39.CB) [> 3.8141 = 6.3568 < 8.2638] w=0.7265 to align # Constraint # added constraint: constraint((T0362)L66.CB, (T0362)A121.CB) [> 3.3989 = 5.6648 < 7.3643] w=0.7256 to align # Constraint # added constraint: constraint((T0362)L7.CB, (T0362)E88.CB) [> 4.3256 = 7.2094 < 9.3722] w=0.7123 to align # Constraint # added constraint: constraint((T0362)A86.CB, (T0362)C107.CB) [> 4.5138 = 7.5230 < 9.7799] w=0.7110 to align # Constraint # added constraint: constraint((T0362)R10.CB, (T0362)M87.CB) [> 4.4598 = 7.4330 < 9.6630] w=0.7101 to align # Constraint # added constraint: constraint((T0362)R11.CB, (T0362)A84.CB) [> 4.2314 = 7.0523 < 9.1679] w=0.7101 to align # Constraint # added constraint: constraint((T0362)W6.CB, (T0362)L89.CB) [> 3.9952 = 6.6587 < 8.6563] w=0.7019 to align # Constraint # added constraint: constraint((T0362)S40.CB, (T0362)P91.CB) [> 3.9048 = 6.5080 < 8.4604] w=0.6999 to align # Constraint # added constraint: constraint((T0362)W6.CB, (T0362)R90.CB) [> 3.0318 = 5.0530 < 6.5689] w=0.6998 to align # Constraint # added constraint: constraint((T0362)L7.CB, (T0362)E39.CB) [> 3.3672 = 5.6120 < 7.2955] w=0.6896 to align # Constraint # added constraint: constraint((T0362)S98.CB, (T0362)A121.CB) [> 4.2744 = 7.1239 < 9.2611] w=0.6800 to align # Constraint # added constraint: constraint((T0362)A65.CB, (T0362)A121.CB) [> 4.2991 = 7.1651 < 9.3147] w=0.6799 to align # Constraint # added constraint: constraint((T0362)L8.CB, (T0362)L89.CB) [> 4.4679 = 7.4465 < 9.6804] w=0.6796 to align # Constraint # added constraint: constraint((T0362)W37.CB, (T0362)H119.CB) [> 4.2828 = 7.1379 < 9.2793] w=0.6795 to align # Constraint # added constraint: constraint((T0362)L41.CB, (T0362)L66.CB) [> 3.2696 = 5.4493 < 7.0841] w=0.6793 to align # Constraint # added constraint: constraint((T0362)G22.CA, (T0362)H80.CB) [> 3.9680 = 6.6133 < 8.5974] w=0.6753 to align # Constraint # added constraint: constraint((T0362)R11.CB, (T0362)M87.CB) [> 4.0995 = 6.8326 < 8.8823] w=0.6690 to align # Constraint # added constraint: constraint((T0362)L66.CB, (T0362)F99.CB) [> 4.1770 = 6.9616 < 9.0501] w=0.6646 to align # Constraint # added constraint: constraint((T0362)C33.CB, (T0362)A73.CB) [> 4.2145 = 7.0242 < 9.1315] w=0.6611 to align # Constraint # added constraint: constraint((T0362)L29.CB, (T0362)A73.CB) [> 4.0011 = 6.6685 < 8.6690] w=0.6602 to align # Constraint # added constraint: constraint((T0362)L9.CB, (T0362)E35.CB) [> 3.7799 = 6.2997 < 8.1897] w=0.6592 to align # Constraint # added constraint: constraint((T0362)V13.CB, (T0362)A84.CB) [> 4.3089 = 7.1815 < 9.3360] w=0.6486 to align # Constraint # added constraint: constraint((T0362)V12.CB, (T0362)D83.CB) [> 4.3986 = 7.3310 < 9.5303] w=0.6468 to align # Constraint # added constraint: constraint((T0362)F15.CB, (T0362)T81.CB) [> 3.3457 = 5.5761 < 7.2490] w=0.6452 to align # Constraint # added constraint: constraint((T0362)W6.CB, (T0362)E88.CB) [> 4.0171 = 6.6951 < 8.7037] w=0.6403 to align # Constraint # added constraint: constraint((T0362)V12.CB, (T0362)L85.CB) [> 4.5275 = 7.5458 < 9.8096] w=0.6350 to align # Constraint # added constraint: constraint((T0362)L29.CB, (T0362)A112.CB) [> 4.2468 = 7.0780 < 9.2014] w=0.6346 to align # Constraint # added constraint: constraint((T0362)V64.CB, (T0362)A121.CB) [> 3.4189 = 5.6981 < 7.4076] w=0.6185 to align # Constraint # added constraint: constraint((T0362)E104.CB, (T0362)A115.CB) [> 4.5883 = 7.6472 < 9.9413] w=0.6177 to align # Constraint # added constraint: constraint((T0362)C33.CB, (T0362)L89.CB) [> 4.3779 = 7.2966 < 9.4855] w=0.6148 to align # Constraint # added constraint: constraint((T0362)C33.CB, (T0362)A113.CB) [> 4.2105 = 7.0175 < 9.1228] w=0.6046 to align # Constraint # added constraint: constraint((T0362)R14.CB, (T0362)T81.CB) [> 3.8892 = 6.4820 < 8.4267] w=0.6043 to align # Constraint # added constraint: constraint((T0362)R77.CB, (T0362)A113.CB) [> 4.6180 = 7.6967 < 10.0057] w=0.6014 to align # Constraint # added constraint: constraint((T0362)F26.CB, (T0362)A73.CB) [> 4.4319 = 7.3865 < 9.6024] w=0.5994 to align # Constraint # added constraint: constraint((T0362)E88.CB, (T0362)F105.CB) [> 4.6187 = 7.6978 < 10.0072] w=0.5943 to align # Constraint # added constraint: constraint((T0362)F99.CB, (T0362)A121.CB) [> 4.0853 = 6.8088 < 8.8514] w=0.5877 to align # Constraint # added constraint: constraint((T0362)L41.CB, (T0362)H119.CB) [> 3.1371 = 5.2285 < 6.7971] w=0.5765 to align # Constraint # added constraint: constraint((T0362)T18.CB, (T0362)T81.CB) [> 3.4089 = 5.6815 < 7.3859] w=0.5636 to align # Constraint # added constraint: constraint((T0362)L41.CB, (T0362)V101.CB) [> 3.9328 = 6.5546 < 8.5210] w=0.5468 to align # Constraint # added constraint: constraint((T0362)D17.CB, (T0362)T81.CB) [> 4.3121 = 7.1868 < 9.3428] w=0.5428 to align # Constraint # added constraint: constraint((T0362)R14.CB, (T0362)G82.CA) [> 4.3107 = 7.1845 < 9.3399] w=0.5426 to align # Constraint # added constraint: constraint((T0362)Q72.CB, (T0362)I117.CB) [> 4.5698 = 7.6164 < 9.9013] w=0.5409 to align # Constraint # added constraint: constraint((T0362)L29.CB, (T0362)L85.CB) [> 4.2133 = 7.0221 < 9.1288] w=0.5392 to align # Constraint # added constraint: constraint((T0362)L41.CB, (T0362)F99.CB) [> 3.3532 = 5.5887 < 7.2653] w=0.5357 to align # Constraint # added constraint: constraint((T0362)P91.CB, (T0362)H102.CB) [> 4.5429 = 7.5714 < 9.8429] w=0.5349 to align # Constraint # added constraint: constraint((T0362)L9.CB, (T0362)W32.CB) [> 3.9843 = 6.6406 < 8.6327] w=0.5268 to align # Constraint # added constraint: constraint((T0362)L7.CB, (T0362)S43.CB) [> 4.0186 = 6.6977 < 8.7070] w=0.5169 to align # Constraint # added constraint: constraint((T0362)P67.CB, (T0362)I122.CB) [> 3.3604 = 5.6007 < 7.2809] w=0.5114 to align # Constraint # added constraint: constraint((T0362)S36.CB, (T0362)E88.CB) [> 4.2706 = 7.1177 < 9.2530] w=0.5053 to align # Constraint # added constraint: constraint((T0362)M24.CB, (T0362)L85.CB) [> 4.3305 = 7.2175 < 9.3828] w=0.5049 to align # Constraint # added constraint: constraint((T0362)F99.CB, (T0362)L120.CB) [> 4.6417 = 7.7361 < 10.0570] w=0.5021 to align # Constraint # added constraint: constraint((T0362)A65.CB, (T0362)I122.CB) [> 3.5135 = 5.8559 < 7.6126] w=0.5010 to align # Constraint # added constraint: constraint((T0362)L9.CB, (T0362)L89.CB) [> 4.4975 = 7.4958 < 9.7446] w=0.4919 to align # Constraint # added constraint: constraint((T0362)M87.CB, (T0362)R106.CB) [> 4.6380 = 7.7300 < 10.0490] w=0.4791 to align # Constraint # added constraint: constraint((T0362)V64.CB, (T0362)I122.CB) [> 4.1859 = 6.9764 < 9.0694] w=0.4703 to align # Constraint # added constraint: constraint((T0362)C33.CB, (T0362)C71.CB) [> 4.2984 = 7.1640 < 9.3132] w=0.4623 to align # Constraint # added constraint: constraint((T0362)S40.CB, (T0362)R90.CB) [> 4.1984 = 6.9973 < 9.0964] w=0.4611 to align # Constraint # added constraint: constraint((T0362)M24.CB, (T0362)T81.CB) [> 4.2243 = 7.0404 < 9.1525] w=0.4554 to align # Constraint # added constraint: constraint((T0362)A73.CB, (T0362)L116.CB) [> 4.6248 = 7.7080 < 10.0204] w=0.4470 to align # Constraint # added constraint: constraint((T0362)M24.CB, (T0362)D83.CB) [> 4.4981 = 7.4969 < 9.7460] w=0.4451 to align # Constraint # added constraint: constraint((T0362)R76.CB, (T0362)Q110.CB) [> 4.6125 = 7.6876 < 9.9938] w=0.4432 to align # Constraint # added constraint: constraint((T0362)I68.CB, (T0362)L120.CB) [> 4.6131 = 7.6884 < 9.9950] w=0.4363 to align # Constraint # added constraint: constraint((T0362)G22.CA, (T0362)T81.CB) [> 3.8658 = 6.4430 < 8.3759] w=0.4303 to align # Constraint # added constraint: constraint((T0362)E42.CB, (T0362)L66.CB) [> 3.6168 = 6.0280 < 7.8364] w=0.4230 to align # Constraint # added constraint: constraint((T0362)W37.CB, (T0362)I68.CB) [> 4.2639 = 7.1065 < 9.2384] w=0.4209 to align # Constraint # added constraint: constraint((T0362)L7.CB, (T0362)R90.CB) [> 4.3422 = 7.2370 < 9.4081] w=0.4099 to align # Constraint # added constraint: constraint((T0362)H70.CB, (T0362)L116.CB) [> 4.5318 = 7.5531 < 9.8190] w=0.3972 to align # Constraint # added constraint: constraint((T0362)W37.CB, (T0362)A115.CB) [> 4.3877 = 7.3128 < 9.5067] w=0.3942 to align # Constraint # added constraint: constraint((T0362)R11.CB, (T0362)A86.CB) [> 4.5957 = 7.6595 < 9.9573] w=0.3893 to align # Constraint # added constraint: constraint((T0362)H102.CB, (T0362)I117.CB) [> 4.6831 = 7.8052 < 10.1467] w=0.3821 to align # Constraint # added constraint: constraint((T0362)P96.CB, (T0362)A131.CB) [> 3.5332 = 5.8887 < 7.6554] w=0.3692 to align # Constraint # added constraint: constraint((T0362)N97.CB, (T0362)C130.CB) [> 3.7065 = 6.1776 < 8.0308] w=0.3692 to align # Constraint # added constraint: constraint((T0362)L120.CB, (T0362)R129.CB) [> 3.0489 = 5.0815 < 6.6059] w=0.3692 to align # Constraint # added constraint: constraint((T0362)A121.CB, (T0362)C130.CB) [> 3.1500 = 5.2500 < 6.8250] w=0.3692 to align # Constraint # added constraint: constraint((T0362)L66.CB, (T0362)I122.CB) [> 4.1634 = 6.9389 < 9.0206] w=0.3681 to align # Constraint # added constraint: constraint((T0362)W6.CB, (T0362)P91.CB) [> 4.0339 = 6.7232 < 8.7402] w=0.3625 to align # Constraint # added constraint: constraint((T0362)A121.CB, (T0362)L132.CB) [> 3.1101 = 5.1835 < 6.7386] w=0.3384 to align # Constraint # added constraint: constraint((T0362)F103.CB, (T0362)A113.CB) [> 4.6343 = 7.7239 < 10.0410] w=0.3308 to align # Constraint # added constraint: constraint((T0362)N95.CB, (T0362)L132.CB) [> 4.5705 = 7.6175 < 9.9027] w=0.3076 to align # Constraint # added constraint: constraint((T0362)F99.CB, (T0362)L132.CB) [> 3.9595 = 6.5992 < 8.5790] w=0.3076 to align # Constraint # added constraint: constraint((T0362)F26.CB, (T0362)A113.CB) [> 4.3666 = 7.2776 < 9.4609] w=0.2955 to align # Constraint # added constraint: constraint((T0362)F30.CB, (T0362)A113.CB) [> 4.4301 = 7.3835 < 9.5985] w=0.2905 to align # Constraint # added constraint: constraint((T0362)V64.CB, (T0362)C130.CB) [> 3.9892 = 6.6487 < 8.6433] w=0.2871 to align # Constraint # added constraint: constraint((T0362)L89.CB, (T0362)E104.CB) [> 4.6614 = 7.7689 < 10.0996] w=0.2867 to align # Constraint # added constraint: constraint((T0362)Y44.CB, (T0362)P91.CB) [> 3.8231 = 6.3718 < 8.2833] w=0.2785 to align # Constraint # added constraint: constraint((T0362)T18.CB, (T0362)H80.CB) [> 4.3564 = 7.2606 < 9.4388] w=0.2760 to align # Constraint # added constraint: constraint((T0362)Y44.CB, (T0362)L94.CB) [> 3.7260 = 6.2101 < 8.0731] w=0.2757 to align # Constraint # added constraint: constraint((T0362)V64.CB, (T0362)N123.CB) [> 3.7689 = 6.2815 < 8.1660] w=0.2666 to align # Constraint # added constraint: constraint((T0362)G16.CA, (T0362)T81.CB) [> 4.5394 = 7.5657 < 9.8355] w=0.2660 to align # Constraint # added constraint: constraint((T0362)W37.CB, (T0362)C71.CB) [> 4.4572 = 7.4286 < 9.6572] w=0.2552 to align # Constraint # added constraint: constraint((T0362)Y44.CB, (T0362)F99.CB) [> 3.9583 = 6.5971 < 8.5762] w=0.2530 to align # Constraint # added constraint: constraint((T0362)R90.CB, (T0362)E104.CB) [> 4.6099 = 7.6832 < 9.9882] w=0.2528 to align # Constraint # added constraint: constraint((T0362)L94.CB, (T0362)L132.CB) [> 3.7692 = 6.2820 < 8.1666] w=0.2461 to align # Constraint # added constraint: constraint((T0362)L94.CB, (T0362)D137.CB) [> 4.0232 = 6.7053 < 8.7169] w=0.2461 to align # Constraint # added constraint: constraint((T0362)E63.CB, (T0362)N123.CB) [> 3.5608 = 5.9346 < 7.7150] w=0.2461 to align # Constraint # added constraint: constraint((T0362)Y44.CB, (T0362)W139.CB) [> 3.0700 = 5.1166 < 6.6516] w=0.2359 to align # Constraint # added constraint: constraint((T0362)L7.CB, (T0362)W37.CB) [> 4.4495 = 7.4159 < 9.6406] w=0.2295 to align # Constraint # added constraint: constraint((T0362)R11.CB, (T0362)Q28.CB) [> 4.4711 = 7.4518 < 9.6873] w=0.2288 to align # Constraint # added constraint: constraint((T0362)P67.CB, (T0362)A121.CB) [> 4.5651 = 7.6085 < 9.8910] w=0.2253 to align # Constraint # added constraint: constraint((T0362)P91.CB, (T0362)L140.CB) [> 3.6329 = 6.0549 < 7.8713] w=0.2153 to align # Constraint # added constraint: constraint((T0362)L9.CB, (T0362)S40.CB) [> 4.2855 = 7.1425 < 9.2853] w=0.2153 to align # Constraint # added constraint: constraint((T0362)W37.CB, (T0362)L66.CB) [> 4.4424 = 7.4040 < 9.6252] w=0.1854 to align # Constraint # added constraint: constraint((T0362)L94.CB, (T0362)L140.CB) [> 3.7220 = 6.2033 < 8.0643] w=0.1846 to align # Constraint # added constraint: constraint((T0362)A65.CB, (T0362)A124.CB) [> 3.3732 = 5.6219 < 7.3085] w=0.1846 to align # Constraint # added constraint: constraint((T0362)E63.CB, (T0362)Q125.CB) [> 3.9446 = 6.5743 < 8.5466] w=0.1846 to align # Constraint # added constraint: constraint((T0362)L46.CB, (T0362)I136.CB) [> 3.8355 = 6.3926 < 8.3103] w=0.1846 to align # Constraint # added constraint: constraint((T0362)G45.CA, (T0362)W139.CB) [> 3.8165 = 6.3608 < 8.2691] w=0.1846 to align # Constraint # added constraint: constraint((T0362)R11.CB, (T0362)S36.CB) [> 4.3473 = 7.2456 < 9.4192] w=0.1844 to align # Constraint # added constraint: constraint((T0362)M24.CB, (T0362)A112.CB) [> 4.4878 = 7.4797 < 9.7236] w=0.1833 to align # Constraint # added constraint: constraint((T0362)F52.CB, (T0362)V64.CB) [> 3.4683 = 5.7806 < 7.5147] w=0.1812 to align # Constraint # added constraint: constraint((T0362)P67.CB, (T0362)R127.CB) [> 4.0810 = 6.8017 < 8.8422] w=0.1743 to align # Constraint # added constraint: constraint((T0362)I51.CB, (T0362)A65.CB) [> 4.0111 = 6.6852 < 8.6908] w=0.1743 to align # Constraint # added constraint: constraint((T0362)V13.CB, (T0362)V23.CB) [> 4.6993 = 7.8322 < 10.1818] w=0.1732 to align # Constraint # added constraint: constraint((T0362)L7.CB, (T0362)M87.CB) [> 4.6415 = 7.7358 < 10.0566] w=0.1659 to align # Constraint # added constraint: constraint((T0362)W37.CB, (T0362)M87.CB) [> 4.0591 = 6.7652 < 8.7947] w=0.1647 to align # Constraint # added constraint: constraint((T0362)L9.CB, (T0362)E88.CB) [> 4.6826 = 7.8043 < 10.1456] w=0.1578 to align # Constraint # added constraint: constraint((T0362)A121.CB, (T0362)I136.CB) [> 4.2663 = 7.1105 < 9.2437] w=0.1538 to align # Constraint # added constraint: constraint((T0362)A65.CB, (T0362)N123.CB) [> 4.3213 = 7.2022 < 9.3629] w=0.1538 to align # Constraint # added constraint: constraint((T0362)G16.CA, (T0362)Q28.CB) [> 4.6174 = 7.6957 < 10.0044] w=0.1528 to align # Constraint # added constraint: constraint((T0362)I69.CB, (T0362)I117.CB) [> 4.4678 = 7.4464 < 9.6803] w=0.1466 to align # Constraint # added constraint: constraint((T0362)I51.CB, (T0362)T61.CB) [> 4.0798 = 6.7997 < 8.8396] w=0.1435 to align # Constraint # added constraint: constraint((T0362)F15.CB, (T0362)G82.CA) [> 4.1942 = 6.9904 < 9.0875] w=0.1431 to align # Constraint # added constraint: constraint((T0362)A65.CB, (T0362)H119.CB) [> 3.9342 = 6.5570 < 8.5241] w=0.1384 to align # Constraint # added constraint: constraint((T0362)P48.CB, (T0362)A65.CB) [> 3.6600 = 6.1000 < 7.9300] w=0.1333 to align # Constraint # added constraint: constraint((T0362)F52.CB, (T0362)E63.CB) [> 4.0231 = 6.7052 < 8.7167] w=0.1332 to align # Constraint # added constraint: constraint((T0362)I51.CB, (T0362)L66.CB) [> 3.9532 = 6.5887 < 8.5653] w=0.1332 to align # Constraint # added constraint: constraint((T0362)P91.CB, (T0362)S143.CB) [> 3.5017 = 5.8362 < 7.5871] w=0.1231 to align # Constraint # added constraint: constraint((T0362)T18.CB, (T0362)Q28.CB) [> 4.6445 = 7.7409 < 10.0632] w=0.1231 to align # Constraint # added constraint: constraint((T0362)L46.CB, (T0362)W139.CB) [> 3.7960 = 6.3267 < 8.2247] w=0.1231 to align # Constraint # added constraint: constraint((T0362)G45.CA, (T0362)L66.CB) [> 4.0137 = 6.6896 < 8.6964] w=0.1229 to align # Constraint # added constraint: constraint((T0362)Y44.CB, (T0362)L140.CB) [> 3.6810 = 6.1350 < 7.9755] w=0.1128 to align # Constraint # added constraint: constraint((T0362)E88.CB, (T0362)H102.CB) [> 4.6655 = 7.7758 < 10.1085] w=0.1125 to align # Constraint # added constraint: constraint((T0362)L41.CB, (T0362)I68.CB) [> 4.4900 = 7.4833 < 9.7283] w=0.1033 to align # Constraint # added constraint: constraint((T0362)Y44.CB, (T0362)T61.CB) [> 4.0468 = 6.7446 < 8.7680] w=0.1024 to align # Constraint # added constraint: constraint((T0362)F52.CB, (T0362)A65.CB) [> 4.0369 = 6.7282 < 8.7466] w=0.0993 to align # Constraint # added constraint: constraint((T0362)A86.CB, (T0362)E109.CB) [> 4.6446 = 7.7411 < 10.0634] w=0.0934 to align # Constraint # added constraint: constraint((T0362)L120.CB, (T0362)C130.CB) [> 4.5342 = 7.5569 < 9.8240] w=0.0923 to align # Constraint # added constraint: constraint((T0362)V64.CB, (T0362)L132.CB) [> 4.6301 = 7.7169 < 10.0320] w=0.0923 to align # Constraint # added constraint: constraint((T0362)A86.CB, (T0362)E108.CB) [> 4.2016 = 7.0026 < 9.1034] w=0.0923 to align # Constraint # added constraint: constraint((T0362)N97.CB, (T0362)I122.CB) [> 4.4003 = 7.3339 < 9.5341] w=0.0923 to align # Constraint # added constraint: constraint((T0362)I51.CB, (T0362)A121.CB) [> 4.0489 = 6.7482 < 8.7726] w=0.0922 to align # Constraint # added constraint: constraint((T0362)W37.CB, (T0362)P91.CB) [> 4.4868 = 7.4781 < 9.7215] w=0.0890 to align # Constraint # added constraint: constraint((T0362)A65.CB, (T0362)L120.CB) [> 3.5689 = 5.9482 < 7.7327] w=0.0872 to align # Constraint # added constraint: constraint((T0362)A86.CB, (T0362)E104.CB) [> 4.4238 = 7.3730 < 9.5850] w=0.0819 to align # Constraint # added constraint: constraint((T0362)Y44.CB, (T0362)A121.CB) [> 4.1554 = 6.9257 < 9.0034] w=0.0797 to align # Constraint # added constraint: constraint((T0362)V64.CB, (T0362)L120.CB) [> 3.9128 = 6.5213 < 8.4777] w=0.0793 to align # Constraint # added constraint: constraint((T0362)Y44.CB, (T0362)G135.CA) [> 3.4870 = 5.8117 < 7.5553] w=0.0718 to align # Constraint # added constraint: constraint((T0362)G22.CA, (T0362)P78.CB) [> 4.7070 = 7.8450 < 10.1985] w=0.0718 to align # Constraint # added constraint: constraint((T0362)D19.CB, (T0362)Q28.CB) [> 4.3350 = 7.2250 < 9.3925] w=0.0715 to align # Constraint # added constraint: constraint((T0362)C33.CB, (T0362)E104.CB) [> 4.7291 = 7.8819 < 10.2465] w=0.0715 to align # Constraint # added constraint: constraint((T0362)L46.CB, (T0362)A65.CB) [> 4.2892 = 7.1486 < 9.2932] w=0.0615 to align # Constraint # added constraint: constraint((T0362)P91.CB, (T0362)W139.CB) [> 3.4249 = 5.7082 < 7.4206] w=0.0615 to align # Constraint # added constraint: constraint((T0362)R93.CB, (T0362)L140.CB) [> 3.5628 = 5.9381 < 7.7195] w=0.0615 to align # Constraint # added constraint: constraint((T0362)P62.CB, (T0362)A124.CB) [> 4.4068 = 7.3447 < 9.5481] w=0.0615 to align # Constraint # added constraint: constraint((T0362)R93.CB, (T0362)S143.CB) [> 3.0644 = 5.1073 < 6.6396] w=0.0615 to align # Constraint # added constraint: constraint((T0362)Y44.CB, (T0362)L66.CB) [> 3.9381 = 6.5635 < 8.5325] w=0.0615 to align # Constraint # added constraint: constraint((T0362)N123.CB, (T0362)P133.CB) [> 3.6828 = 6.1380 < 7.9794] w=0.0615 to align # Constraint # added constraint: constraint((T0362)A73.CB, (T0362)F103.CB) [> 4.5097 = 7.5162 < 9.7711] w=0.0615 to align # Constraint # added constraint: constraint((T0362)R11.CB, (T0362)R31.CB) [> 4.7090 = 7.8483 < 10.2028] w=0.0614 to align # Constraint # added constraint: constraint((T0362)R93.CB, (T0362)R118.CB) [> 4.7778 = 7.9630 < 10.3518] w=0.0546 to align # Constraint # added constraint: constraint((T0362)C33.CB, (T0362)A112.CB) [> 4.2260 = 7.0433 < 9.1562] w=0.0520 to align # Constraint # added constraint: constraint((T0362)A49.CB, (T0362)A65.CB) [> 3.3792 = 5.6320 < 7.3216] w=0.0513 to align # Constraint # added constraint: constraint((T0362)P96.CB, (T0362)L120.CB) [> 3.8245 = 6.3742 < 8.2865] w=0.0464 to align # Constraint # added constraint: constraint((T0362)N47.CB, (T0362)P62.CB) [> 3.0407 = 5.0679 < 6.5882] w=0.0410 to align # Constraint # added constraint: constraint((T0362)D50.CB, (T0362)A65.CB) [> 3.2764 = 5.4606 < 7.0988] w=0.0410 to align # Constraint # added constraint: constraint((T0362)L46.CB, (T0362)P67.CB) [> 4.5142 = 7.5237 < 9.7809] w=0.0410 to align # Constraint # added constraint: constraint((T0362)P62.CB, (T0362)H119.CB) [> 4.4477 = 7.4129 < 9.6367] w=0.0410 to align # Constraint # added constraint: constraint((T0362)I79.CB, (T0362)Q110.CB) [> 4.6822 = 7.8036 < 10.1447] w=0.0410 to align # Constraint # added constraint: constraint((T0362)E63.CB, (T0362)I122.CB) [> 4.3322 = 7.2204 < 9.3865] w=0.0409 to align # Constraint # added constraint: constraint((T0362)H27.CB, (T0362)A115.CB) [> 4.3699 = 7.2832 < 9.4682] w=0.0378 to align # Constraint # added constraint: constraint((T0362)H27.CB, (T0362)A73.CB) [> 3.3956 = 5.6594 < 7.3572] w=0.0378 to align # Constraint # added constraint: constraint((T0362)H27.CB, (T0362)C71.CB) [> 4.7195 = 7.8658 < 10.2256] w=0.0378 to align # Constraint # added constraint: constraint((T0362)P67.CB, (T0362)R118.CB) [> 3.9014 = 6.5024 < 8.4531] w=0.0364 to align # Constraint # added constraint: constraint((T0362)C33.CB, (T0362)F75.CB) [> 4.5257 = 7.5429 < 9.8057] w=0.0316 to align # Constraint # added constraint: constraint((T0362)Q100.CB, (T0362)S143.CB) [> 3.1984 = 5.3307 < 6.9299] w=0.0308 to align # Constraint # added constraint: constraint((T0362)Q72.CB, (T0362)R118.CB) [> 4.7246 = 7.8744 < 10.2367] w=0.0308 to align # Constraint # added constraint: constraint((T0362)V23.CB, (T0362)R77.CB) [> 4.5987 = 7.6645 < 9.9639] w=0.0308 to align # Constraint # added constraint: constraint((T0362)F75.CB, (T0362)H114.CB) [> 4.6156 = 7.6926 < 10.0004] w=0.0308 to align # Constraint # added constraint: constraint((T0362)E88.CB, (T0362)I111.CB) [> 4.3608 = 7.2679 < 9.4483] w=0.0308 to align # Constraint # added constraint: constraint((T0362)R90.CB, (T0362)I136.CB) [> 4.5188 = 7.5313 < 9.7907] w=0.0308 to align # Constraint # added constraint: constraint((T0362)A49.CB, (T0362)P67.CB) [> 4.3053 = 7.1755 < 9.3281] w=0.0308 to align # Constraint # added constraint: constraint((T0362)L94.CB, (T0362)R118.CB) [> 4.3762 = 7.2937 < 9.4819] w=0.0308 to align # Constraint # added constraint: constraint((T0362)I69.CB, (T0362)R129.CB) [> 4.7586 = 7.9310 < 10.3103] w=0.0308 to align # Constraint # added constraint: constraint((T0362)L46.CB, (T0362)L140.CB) [> 4.4024 = 7.3373 < 9.5385] w=0.0308 to align # Constraint # added constraint: constraint((T0362)R11.CB, (T0362)F105.CB) [> 4.7833 = 7.9721 < 10.3637] w=0.0308 to align # Constraint # added constraint: constraint((T0362)A121.CB, (T0362)L140.CB) [> 4.6197 = 7.6994 < 10.0093] w=0.0308 to align # Constraint # added constraint: constraint((T0362)P67.CB, (T0362)A124.CB) [> 4.6718 = 7.7863 < 10.1221] w=0.0308 to align # Constraint # added constraint: constraint((T0362)E92.CB, (T0362)R118.CB) [> 4.3654 = 7.2758 < 9.4585] w=0.0308 to align # Constraint # added constraint: constraint((T0362)I68.CB, (T0362)V101.CB) [> 4.7456 = 7.9093 < 10.2821] w=0.0308 to align # Constraint # added constraint: constraint((T0362)P78.CB, (T0362)Q110.CB) [> 4.7039 = 7.8399 < 10.1918] w=0.0307 to align # Constraint # added constraint: constraint((T0362)I122.CB, (T0362)P133.CB) [> 4.6810 = 7.8017 < 10.1422] w=0.0307 to align # Constraint # added constraint: constraint((T0362)I122.CB, (T0362)I136.CB) [> 3.3823 = 5.6373 < 7.3284] w=0.0307 to align # Constraint # added constraint: constraint((T0362)C71.CB, (T0362)F103.CB) [> 4.3363 = 7.2272 < 9.3953] w=0.0306 to align # Constraint # added constraint: constraint((T0362)Y44.CB, (T0362)A65.CB) [> 4.3440 = 7.2401 < 9.4121] w=0.0284 to align # Constraint # added constraint: constraint((T0362)H70.CB, (T0362)A115.CB) [> 3.9962 = 6.6603 < 8.6584] w=0.0284 to align # Constraint # added constraint: constraint((T0362)P67.CB, (T0362)I117.CB) [> 3.3954 = 5.6590 < 7.3567] w=0.0262 to align # Constraint # added constraint: constraint((T0362)W37.CB, (T0362)P67.CB) [> 4.3416 = 7.2360 < 9.4068] w=0.0262 to align # Constraint # added constraint: constraint((T0362)H25.CB, (T0362)T81.CB) [> 4.4593 = 7.4322 < 9.6619] w=0.0224 to align # Constraint # added constraint: constraint((T0362)I51.CB, (T0362)P67.CB) [> 4.2615 = 7.1025 < 9.2333] w=0.0205 to align # Constraint # added constraint: constraint((T0362)L8.CB, (T0362)F103.CB) [> 4.4735 = 7.4559 < 9.6926] w=0.0205 to align # Constraint # added constraint: constraint((T0362)R14.CB, (T0362)L29.CB) [> 2.9103 = 4.8505 < 6.3056] w=0.0205 to align # Constraint # added constraint: constraint((T0362)R14.CB, (T0362)F30.CB) [> 4.4121 = 7.3535 < 9.5595] w=0.0205 to align # Constraint # added constraint: constraint((T0362)D17.CB, (T0362)L85.CB) [> 4.5138 = 7.5230 < 9.7799] w=0.0205 to align # Constraint # added constraint: constraint((T0362)V12.CB, (T0362)M87.CB) [> 4.3520 = 7.2534 < 9.4294] w=0.0204 to align # Constraint # added constraint: constraint((T0362)V12.CB, (T0362)A86.CB) [> 3.6151 = 6.0252 < 7.8328] w=0.0204 to align # Constraint # added constraint: constraint((T0362)V12.CB, (T0362)L29.CB) [> 4.7628 = 7.9380 < 10.3194] w=0.0204 to align # Constraint # added constraint: constraint((T0362)F15.CB, (T0362)M24.CB) [> 3.5254 = 5.8757 < 7.6385] w=0.0204 to align # Constraint # added constraint: constraint((T0362)F15.CB, (T0362)I79.CB) [> 4.5879 = 7.6464 < 9.9404] w=0.0204 to align # Constraint # added constraint: constraint((T0362)F15.CB, (T0362)H80.CB) [> 4.7224 = 7.8706 < 10.2318] w=0.0204 to align # Constraint # added constraint: constraint((T0362)D17.CB, (T0362)F26.CB) [> 4.7846 = 7.9743 < 10.3667] w=0.0204 to align # Constraint # added constraint: constraint((T0362)F26.CB, (T0362)D83.CB) [> 4.6316 = 7.7194 < 10.0352] w=0.0204 to align # Constraint # added constraint: constraint((T0362)F26.CB, (T0362)F105.CB) [> 3.6952 = 6.1587 < 8.0063] w=0.0204 to align # Constraint # added constraint: constraint((T0362)A86.CB, (T0362)F103.CB) [> 4.4103 = 7.3506 < 9.5557] w=0.0204 to align # Constraint # added constraint: constraint((T0362)A84.CB, (T0362)R106.CB) [> 2.5927 = 4.3211 < 5.6175] w=0.0204 to align # Constraint # added constraint: constraint((T0362)A84.CB, (T0362)F105.CB) [> 4.3612 = 7.2687 < 9.4493] w=0.0204 to align # Constraint # added constraint: constraint((T0362)C33.CB, (T0362)A86.CB) [> 4.4067 = 7.3445 < 9.5479] w=0.0204 to align # Constraint # added constraint: constraint((T0362)F26.CB, (T0362)A112.CB) [> 4.7238 = 7.8729 < 10.2348] w=0.0204 to align # Constraint # added constraint: constraint((T0362)I68.CB, (T0362)S98.CB) [> 4.1919 = 6.9866 < 9.0825] w=0.0182 to align # Constraint # added constraint: constraint((T0362)Q72.CB, (T0362)H114.CB) [> 4.3272 = 7.2120 < 9.3756] w=0.0182 to align # Constraint # added constraint: constraint((T0362)C33.CB, (T0362)E88.CB) [> 4.2357 = 7.0595 < 9.1773] w=0.0175 to align # Constraint # added constraint: constraint((T0362)E38.CB, (T0362)C71.CB) [> 4.1934 = 6.9889 < 9.0856] w=0.0113 to align # Constraint # added constraint: constraint((T0362)L66.CB, (T0362)R118.CB) [> 4.6100 = 7.6834 < 9.9884] w=0.0112 to align # Constraint # added constraint: constraint((T0362)L66.CB, (T0362)I117.CB) [> 4.3466 = 7.2444 < 9.4177] w=0.0112 to align # Constraint # added constraint: constraint((T0362)H34.CB, (T0362)H70.CB) [> 4.2997 = 7.1662 < 9.3161] w=0.0103 to align # Constraint # added constraint: constraint((T0362)F30.CB, (T0362)H70.CB) [> 4.5250 = 7.5417 < 9.8043] w=0.0103 to align # Constraint # added constraint: constraint((T0362)L66.CB, (T0362)R127.CB) [> 4.1222 = 6.8704 < 8.9315] w=0.0103 to align # Constraint # added constraint: constraint((T0362)E63.CB, (T0362)I136.CB) [> 4.7976 = 7.9960 < 10.3948] w=0.0103 to align # Constraint # added constraint: constraint((T0362)R14.CB, (T0362)H27.CB) [> 3.0803 = 5.1339 < 6.6741] w=0.0103 to align # Constraint # added constraint: constraint((T0362)F15.CB, (T0362)F30.CB) [> 3.4248 = 5.7080 < 7.4204] w=0.0103 to align # Constraint # added constraint: constraint((T0362)R10.CB, (T0362)S40.CB) [> 4.6758 = 7.7929 < 10.1308] w=0.0103 to align # Constraint # added constraint: constraint((T0362)R10.CB, (T0362)S36.CB) [> 4.6758 = 7.7929 < 10.1308] w=0.0103 to align # Constraint # added constraint: constraint((T0362)L8.CB, (T0362)Y44.CB) [> 4.5042 = 7.5069 < 9.7590] w=0.0103 to align # Constraint # added constraint: constraint((T0362)G45.CA, (T0362)H119.CB) [> 3.8501 = 6.4168 < 8.3419] w=0.0103 to align # Constraint # added constraint: constraint((T0362)G45.CA, (T0362)I68.CB) [> 4.7682 = 7.9469 < 10.3310] w=0.0103 to align # Constraint # added constraint: constraint((T0362)Y44.CB, (T0362)F103.CB) [> 4.6442 = 7.7404 < 10.0625] w=0.0103 to align # Constraint # added constraint: constraint((T0362)Y44.CB, (T0362)M87.CB) [> 2.6206 = 4.3676 < 5.6779] w=0.0103 to align # Constraint # added constraint: constraint((T0362)L41.CB, (T0362)C71.CB) [> 4.1653 = 6.9422 < 9.0249] w=0.0103 to align # Constraint # added constraint: constraint((T0362)G16.CA, (T0362)F30.CB) [> 3.5529 = 5.9216 < 7.6981] w=0.0103 to align # Constraint # added constraint: constraint((T0362)H27.CB, (T0362)G82.CA) [> 4.6974 = 7.8291 < 10.1778] w=0.0103 to align # Constraint # added constraint: constraint((T0362)W37.CB, (T0362)F75.CB) [> 4.4784 = 7.4640 < 9.7032] w=0.0103 to align # Constraint # added constraint: constraint((T0362)W37.CB, (T0362)A112.CB) [> 3.7128 = 6.1880 < 8.0445] w=0.0103 to align # Constraint # added constraint: constraint((T0362)H34.CB, (T0362)I69.CB) [> 3.8836 = 6.4727 < 8.4144] w=0.0102 to align # Constraint # added constraint: constraint((T0362)E38.CB, (T0362)I69.CB) [> 4.7629 = 7.9382 < 10.3197] w=0.0102 to align # Constraint # added constraint: constraint((T0362)I69.CB, (T0362)A115.CB) [> 3.7677 = 6.2794 < 8.1632] w=0.0102 to align # Constraint # added constraint: constraint((T0362)I69.CB, (T0362)L116.CB) [> 4.1182 = 6.8636 < 8.9227] w=0.0102 to align # Constraint # added constraint: constraint((T0362)F99.CB, (T0362)I122.CB) [> 4.6924 = 7.8207 < 10.1669] w=0.0102 to align # Constraint # added constraint: constraint((T0362)R14.CB, (T0362)D83.CB) [> 3.7523 = 6.2538 < 8.1299] w=0.0102 to align # Constraint # added constraint: constraint((T0362)R14.CB, (T0362)A84.CB) [> 3.0015 = 5.0025 < 6.5032] w=0.0102 to align # Constraint # added constraint: constraint((T0362)F15.CB, (T0362)W32.CB) [> 4.1527 = 6.9212 < 8.9976] w=0.0102 to align # Constraint # added constraint: constraint((T0362)R10.CB, (T0362)E88.CB) [> 2.9468 = 4.9113 < 6.3847] w=0.0102 to align # Constraint # added constraint: constraint((T0362)P48.CB, (T0362)I68.CB) [> 3.6407 = 6.0679 < 7.8883] w=0.0102 to align # Constraint # added constraint: constraint((T0362)I51.CB, (T0362)Q100.CB) [> 3.8937 = 6.4895 < 8.4364] w=0.0102 to align # Constraint # added constraint: constraint((T0362)S43.CB, (T0362)C71.CB) [> 4.4257 = 7.3762 < 9.5890] w=0.0102 to align # Constraint # added constraint: constraint((T0362)Y44.CB, (T0362)I68.CB) [> 4.4611 = 7.4352 < 9.6657] w=0.0102 to align # Constraint # added constraint: constraint((T0362)Y44.CB, (T0362)C71.CB) [> 3.9116 = 6.5193 < 8.4750] w=0.0102 to align # Constraint # added constraint: constraint((T0362)F26.CB, (T0362)Q72.CB) [> 3.9593 = 6.5989 < 8.5786] w=0.0079 to align # Constraint # added constraint: constraint((T0362)C33.CB, (T0362)H70.CB) [> 4.5059 = 7.5098 < 9.7627] w=0.0079 to align # Constraint # added constraint: constraint((T0362)C33.CB, (T0362)Q72.CB) [> 4.3178 = 7.1963 < 9.3552] w=0.0079 to align # Constraint # added constraint: constraint((T0362)Q72.CB, (T0362)A113.CB) [> 4.2449 = 7.0749 < 9.1973] w=0.0079 to align # Constraint # added constraint: constraint((T0362)L8.CB, (T0362)A84.CB) [> 3.2626 = 5.4376 < 7.0689] w=0.0021 to align # SetCost created cost = # ( 1.0000 * align ) # command:# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0362/ # command:# reading script from file servers-clean.under # Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/T0362/decoys/ # ReadConformPDB reading from PDB file tr362.gromacs0.pdb.gz looking for model 1 # Found a chain break before 126 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file tr362.gromacs0.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 126 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file tr362.pdb.gz looking for model 1 # Found a chain break before 126 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file tr362.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 126 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file ../dimer/decoys/dimer-tr362-1s5uA.pdb.gz looking for chain 'A' model 1 # Found a chain break before 126 # copying to AlignedFragments data structure # naming current conformation dimer//dimer-tr362-1s5uA # ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0362 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 T0362 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 T0362 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 T0362 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 T0362 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 T0362 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 T0362 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 T0362 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 T0362 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 T0362 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 T0362 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 T0362 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 T0362 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 T0362 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 T0362 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 62 # 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 59 # 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 62 # copying to AlignedFragments data structure # naming current conformation 3Dpro_TS3 # ReadConformPDB reading from PDB file servers/3Dpro_TS4.pdb.gz looking for model 1 # naming current conformation 3Dpro_TS4 # ReadConformPDB reading from PDB file servers/3Dpro_TS5.pdb.gz looking for model 1 # naming current conformation 3Dpro_TS5 # ReadConformPDB reading from PDB file servers/ABIpro_TS1.pdb.gz looking for model 1 # Found a chain break before 126 # 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 95 # 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 95 # 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 141 # 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 147 # 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 82 # 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 # naming current conformation Bilab-ENABLE_TS1 # ReadConformPDB reading from PDB file servers/Bilab-ENABLE_TS2.pdb.gz looking for model 1 # Found a chain break before 43 # copying to AlignedFragments data structure # naming current conformation Bilab-ENABLE_TS2 # ReadConformPDB reading from PDB file servers/Bilab-ENABLE_TS3.pdb.gz looking for model 1 # naming current conformation Bilab-ENABLE_TS3 # ReadConformPDB reading from PDB file servers/Bilab-ENABLE_TS4.pdb.gz looking for model 1 # Found a chain break before 64 # copying to AlignedFragments data structure # naming current conformation Bilab-ENABLE_TS4 # ReadConformPDB reading from PDB file servers/Bilab-ENABLE_TS5.pdb.gz looking for model 1 # Found a chain break before 122 # copying to AlignedFragments data structure # naming current conformation Bilab-ENABLE_TS5 # ReadConformPDB reading from PDB file servers/CIRCLE_TS1.pdb.gz looking for model 1 # Found a chain break before 140 # copying to AlignedFragments data structure # naming current conformation CIRCLE_TS1 # ReadConformPDB reading from PDB file servers/CIRCLE_TS2.pdb.gz looking for model 1 # Found a chain break before 119 # copying to AlignedFragments data structure # naming current conformation CIRCLE_TS2 # ReadConformPDB reading from PDB file servers/CIRCLE_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0362 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 T0362 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 T0362 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 T0362 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 T0362 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: atoms too close: (T0362)A142.C and (T0362)S143.N only 0.000 apart, marking (T0362)S143.N as missing WARNING: atoms too close: (T0362)S143.N and (T0362)S143.CA only 0.000 apart, marking (T0362)S143.CA as missing WARNING: atoms too close: (T0362)A142.C and (T0362)S143.CA only 0.000 apart, marking (T0362)S143.CA as missing WARNING: atoms too close: (T0362)S143.CA and (T0362)S143.CB only 0.000 apart, marking (T0362)S143.CB as missing WARNING: atoms too close: (T0362)S143.N and (T0362)S143.CB only 0.000 apart, marking (T0362)S143.CB as missing WARNING: atoms too close: (T0362)A142.C and (T0362)S143.CB only 0.000 apart, marking (T0362)S143.CB as missing WARNING: atoms too close: (T0362)S143.CB and (T0362)S143.OG only 0.000 apart, marking (T0362)S143.OG as missing WARNING: atoms too close: (T0362)S143.CA and (T0362)S143.OG only 0.000 apart, marking (T0362)S143.OG as missing WARNING: atoms too close: (T0362)S143.N and (T0362)S143.OG only 0.000 apart, marking (T0362)S143.OG as missing WARNING: atoms too close: (T0362)A142.C and (T0362)S143.OG only 0.000 apart, marking (T0362)S143.OG as missing WARNING: atoms too close: (T0362)S143.OG and (T0362)S143.O only 0.000 apart, marking (T0362)S143.O as missing WARNING: atoms too close: (T0362)S143.CB and (T0362)S143.O only 0.000 apart, marking (T0362)S143.O as missing WARNING: atoms too close: (T0362)S143.CA and (T0362)S143.O only 0.000 apart, marking (T0362)S143.O as missing WARNING: atoms too close: (T0362)S143.N and (T0362)S143.O only 0.000 apart, marking (T0362)S143.O as missing WARNING: atoms too close: (T0362)A142.C and (T0362)S143.O only 0.000 apart, marking (T0362)S143.O as missing WARNING: atoms too close: (T0362)S143.O and (T0362)S143.C only 0.000 apart, marking (T0362)S143.C as missing WARNING: atoms too close: (T0362)S143.OG and (T0362)S143.C only 0.000 apart, marking (T0362)S143.C as missing WARNING: atoms too close: (T0362)S143.CB and (T0362)S143.C only 0.000 apart, marking (T0362)S143.C as missing WARNING: atoms too close: (T0362)S143.CA and (T0362)S143.C only 0.000 apart, marking (T0362)S143.C as missing WARNING: atoms too close: (T0362)S143.N and (T0362)S143.C only 0.000 apart, marking (T0362)S143.C as missing WARNING: atoms too close: (T0362)A142.C and (T0362)S143.C only 0.000 apart, marking (T0362)S143.C as missing # WARNING: incomplete conformation T0362 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 T0362 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 T0362 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 T0362 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 T0362 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 T0362 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 T0362 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 T0362 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 T0362 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 T0362 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 T0362 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 T0362 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 T0362 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 # Found a chain break before 140 # copying to AlignedFragments data structure # naming current conformation FAMS_TS2 # ReadConformPDB reading from PDB file servers/FAMS_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0362 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 # Found a chain break before 119 # copying to AlignedFragments data structure # naming current conformation FAMS_TS4 # ReadConformPDB reading from PDB file servers/FAMS_TS5.pdb.gz looking for model 1 # Found a chain break before 144 # copying to AlignedFragments data structure # naming current conformation FAMS_TS5 # ReadConformPDB reading from PDB file servers/FOLDpro_TS1.pdb.gz looking for model 1 # Found a chain break before 117 # 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 118 # copying to AlignedFragments data structure # naming current conformation FOLDpro_TS2 # ReadConformPDB reading from PDB file servers/FOLDpro_TS3.pdb.gz looking for model 1 # naming current conformation FOLDpro_TS3 # ReadConformPDB reading from PDB file servers/FOLDpro_TS4.pdb.gz looking for model 1 # Found a chain break before 136 # 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 9 # copying to AlignedFragments data structure # naming current conformation FOLDpro_TS5 # ReadConformPDB reading from PDB file servers/FORTE1_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0362 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 83, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL2.pdb.gz # WARNING: incomplete conformation T0362 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 T0362 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 T0362 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 T0362 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 # WARNING: incomplete conformation T0362 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 83, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL2.pdb.gz # WARNING: incomplete conformation T0362 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 T0362 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 T0362 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 T0362 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 129 # 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 87 # 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 58 # 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 84 # 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 144 # 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 T0362 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 T0362 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 T0362 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 T0362 can't currently be optimized by undertaker # naming current conformation FUGMOD_TS4 # ReadConformPDB reading from PDB file servers/FUGMOD_TS5.pdb.gz looking for model 1 # Found a chain break before 131 # copying to AlignedFragments data structure # naming current conformation FUGMOD_TS5 # ReadConformPDB reading from PDB file servers/FUGUE_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0362 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 T0362 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 T0362 can't currently be optimized by undertaker # naming current conformation FUGUE_AL3 # ReadConformPDB reading from PDB file servers/FUGUE_AL5.pdb.gz looking for model 1 Skipped atom 163, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL5.pdb.gz Skipped atom 232, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL5.pdb.gz # WARNING: incomplete conformation T0362 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 143 # 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 146 # 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 149 # 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 145 # 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 144 # 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 T0362 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 T0362 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 T0362 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 T0362 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 T0362 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 18 # 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 62 # 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 62 # 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 T0362 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 T0362 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 T0362 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 T0362 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 T0362 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 T0362 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 T0362 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 T0362 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 T0362 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 T0362 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 T0362 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 # 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 51 # 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 148 # 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 64 # 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 48 # 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 51 # 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 135 # 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 81 # 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 23 # 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 45 # 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 148 # 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 150 # 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 148 # 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 150 # 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 150 # 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 # WARNING: incomplete conformation T0362 can't currently be optimized by undertaker # 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 # Found a chain break before 90 # copying to AlignedFragments data structure # naming current conformation PROTINFO_TS1 # ReadConformPDB reading from PDB file servers/PROTINFO_TS2.pdb.gz looking for model 1 # naming current conformation PROTINFO_TS2 # ReadConformPDB reading from PDB file servers/PROTINFO_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0362 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 T0362 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 T0362 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 T0362 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 T0362 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 T0362 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 T0362 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 T0362 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 T0362 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 T0362 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 T0362 can't currently be optimized by undertaker # naming current conformation Phyre-2_TS3 # ReadConformPDB reading from PDB file servers/Phyre-2_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0362 can't currently be optimized by undertaker # 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 T0362 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 # Found a chain break before 122 # copying to AlignedFragments data structure # naming current conformation Pmodeller6_TS1 # ReadConformPDB reading from PDB file servers/Pmodeller6_TS2.pdb.gz looking for model 1 # Found a chain break before 122 # copying to AlignedFragments data structure # naming current conformation Pmodeller6_TS2 # ReadConformPDB reading from PDB file servers/Pmodeller6_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0362 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 T0362 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 # Found a chain break before 122 # copying to AlignedFragments data structure # naming current conformation Pmodeller6_TS5 # ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS1.pdb.gz looking for model 1 # Found a chain break before 139 # 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 # naming current conformation RAPTOR-ACE_TS2 # ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS3.pdb.gz looking for model 1 # 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 115 # 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 # 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 95 # 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 148 # 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 146 # 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 150 # 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 95 # copying to AlignedFragments data structure # naming current conformation RAPTORESS_TS5 # ReadConformPDB reading from PDB file servers/RAPTOR_TS1.pdb.gz looking for model 1 # Found a chain break before 64 # copying to AlignedFragments data structure # naming current conformation RAPTOR_TS1 # ReadConformPDB reading from PDB file servers/RAPTOR_TS2.pdb.gz looking for model 1 # naming current conformation RAPTOR_TS2 # ReadConformPDB reading from PDB file servers/RAPTOR_TS3.pdb.gz looking for model 1 # Found a chain break before 129 # copying to AlignedFragments data structure # naming current conformation RAPTOR_TS3 # ReadConformPDB reading from PDB file servers/RAPTOR_TS4.pdb.gz looking for model 1 # naming current conformation RAPTOR_TS4 # ReadConformPDB reading from PDB file servers/RAPTOR_TS5.pdb.gz looking for model 1 # naming current conformation RAPTOR_TS5 # ReadConformPDB reading from PDB file servers/ROBETTA_TS1.pdb.gz looking for model 1 # Found a chain break before 122 # 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 122 # 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 122 # 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 122 # 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 122 # 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 # Found a chain break before 59 # copying to AlignedFragments data structure # naming current conformation ROKKY_TS2 # ReadConformPDB reading from PDB file servers/ROKKY_TS3.pdb.gz looking for model 1 # naming current conformation ROKKY_TS3 # ReadConformPDB reading from PDB file servers/ROKKY_TS4.pdb.gz looking for model 1 # Found a chain break before 106 # copying to AlignedFragments data structure # naming current conformation ROKKY_TS4 # ReadConformPDB reading from PDB file servers/ROKKY_TS5.pdb.gz looking for model 1 # naming current conformation ROKKY_TS5 # ReadConformPDB reading from PDB file servers/SAM-T02_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0362 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 T0362 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 T0362 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 T0362 can't currently be optimized by undertaker # naming current conformation SAM-T02_AL4 # ReadConformPDB reading from PDB file servers/SAM-T02_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0362 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 T0362 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 T0362 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 T0362 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 T0362 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 # WARNING: incomplete conformation T0362 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 148 # 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 T0362 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 T0362 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 T0362 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 T0362 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 # naming current conformation SP3_TS1 # ReadConformPDB reading from PDB file servers/SP3_TS2.pdb.gz looking for model 1 # Found a chain break before 115 # copying to AlignedFragments data structure # naming current conformation SP3_TS2 # ReadConformPDB reading from PDB file servers/SP3_TS3.pdb.gz looking for model 1 # Found a chain break before 102 # copying to AlignedFragments data structure # naming current conformation SP3_TS3 # ReadConformPDB reading from PDB file servers/SP3_TS4.pdb.gz looking for model 1 # naming current conformation SP3_TS4 # ReadConformPDB reading from PDB file servers/SP3_TS5.pdb.gz looking for model 1 # naming current conformation SP3_TS5 # ReadConformPDB reading from PDB file servers/SP4_TS1.pdb.gz looking for model 1 # Found a chain break before 122 # 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 # naming current conformation SP4_TS4 # ReadConformPDB reading from PDB file servers/SP4_TS5.pdb.gz looking for model 1 # naming current conformation SP4_TS5 # ReadConformPDB reading from PDB file servers/SPARKS2_TS1.pdb.gz looking for model 1 # naming current conformation SPARKS2_TS1 # ReadConformPDB reading from PDB file servers/SPARKS2_TS2.pdb.gz looking for model 1 # Found a chain break before 115 # 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 28 # 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 135 # 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 51 # 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 T0362 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 T0362 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 T0362 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 T0362 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 T0362 can't currently be optimized by undertaker # naming current conformation UNI-EID_bnmx_TS5 # ReadConformPDB reading from PDB file servers/UNI-EID_expm_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0362 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation UNI-EID_expm_TS1 # ReadConformPDB reading from PDB file servers/UNI-EID_sfst_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0362 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 T0362 can't currently be optimized by undertaker # naming current conformation UNI-EID_sfst_AL2 # ReadConformPDB reading from PDB file servers/UNI-EID_sfst_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0362 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 T0362 can't currently be optimized by undertaker # naming current conformation UNI-EID_sfst_AL4 # ReadConformPDB reading from PDB file servers/UNI-EID_sfst_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0362 can't currently be optimized by undertaker # naming current conformation UNI-EID_sfst_AL5 # ReadConformPDB reading from PDB file servers/Zhang-Server_TS1.pdb.gz looking for model 1 # Found a chain break before 144 # 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 104 # 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 61 # 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 147 # 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 57 # 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 T0362 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 T0362 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 T0362 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 T0362 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 T0362 can't currently be optimized by undertaker # naming current conformation forecast-s_AL3 # ReadConformPDB reading from PDB file servers/forecast-s_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0362 can't currently be optimized by undertaker # naming current conformation forecast-s_AL5 # ReadConformPDB reading from PDB file servers/karypis.srv.2_TS1.pdb.gz looking for model 1 # Found a chain break before 105 # 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 116 # copying to AlignedFragments data structure # naming current conformation karypis.srv.2_TS2 # ReadConformPDB reading from PDB file servers/karypis.srv.2_TS3.pdb.gz looking for model 1 # Found a chain break before 105 # copying to AlignedFragments data structure # naming current conformation karypis.srv.2_TS3 # ReadConformPDB reading from PDB file servers/karypis.srv.2_TS4.pdb.gz looking for model 1 # Found a chain break before 119 # 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 105 # copying to AlignedFragments data structure # naming current conformation karypis.srv.2_TS5 # ReadConformPDB reading from PDB file servers/karypis.srv.4_TS1.pdb.gz looking for model 1 # Found a chain break before 148 # 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 150 # 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 150 # 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 149 # 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 148 # 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 T0362 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 T0362 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 T0362 can't currently be optimized by undertaker # naming current conformation karypis.srv_TS3 # ReadConformPDB reading from PDB file servers/karypis.srv_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0362 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 # 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 52 # 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 # 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 117 # 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 # naming current conformation keasar-server_TS5 # ReadConformPDB reading from PDB file servers/mGen-3D_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0362 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 T0362 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 T0362 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 T0362 can't currently be optimized by undertaker # naming current conformation nFOLD_TS3 # ReadConformPDB reading from PDB file servers/nFOLD_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0362 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 T0362 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: atoms too close: (T0362)D50.N and (T0362)I51.N only 0.000 apart, marking (T0362)I51.N as missing WARNING: atoms too close: (T0362)D50.CA and (T0362)I51.CA only 0.000 apart, marking (T0362)I51.CA as missing WARNING: atoms too close: (T0362)D50.CB and (T0362)I51.CB only 0.000 apart, marking (T0362)I51.CB as missing WARNING: atoms too close: (T0362)D50.O and (T0362)I51.O only 0.000 apart, marking (T0362)I51.O as missing WARNING: atoms too close: (T0362)D50.C and (T0362)I51.C only 0.000 apart, marking (T0362)I51.C as missing WARNING: atoms too close: (T0362)I51.N and (T0362)F52.N only 0.000 apart, marking (T0362)I51.N as missing WARNING: atoms too close: (T0362)D50.N and (T0362)F52.N only 0.000 apart, marking (T0362)F52.N as missing WARNING: atoms too close: (T0362)I51.CA and (T0362)F52.CA only 0.000 apart, marking (T0362)F52.CA as missing WARNING: atoms too close: (T0362)D50.CA and (T0362)F52.CA only 0.000 apart, marking (T0362)F52.CA as missing WARNING: atoms too close: (T0362)I51.CB and (T0362)F52.CB only 0.000 apart, marking (T0362)F52.CB as missing WARNING: atoms too close: (T0362)D50.CB and (T0362)F52.CB only 0.000 apart, marking (T0362)F52.CB as missing WARNING: atoms too close: (T0362)I51.O and (T0362)F52.O only 0.000 apart, marking (T0362)F52.O as missing WARNING: atoms too close: (T0362)D50.O and (T0362)F52.O only 0.000 apart, marking (T0362)F52.O as missing WARNING: atoms too close: (T0362)I51.C and (T0362)F52.C only 0.000 apart, marking (T0362)F52.C as missing WARNING: atoms too close: (T0362)D50.C and (T0362)F52.C only 0.000 apart, marking (T0362)F52.C as missing WARNING: atoms too close: (T0362)F52.N and (T0362)P53.N only 0.000 apart, marking (T0362)F52.N as missing WARNING: atoms too close: (T0362)I51.N and (T0362)P53.N only 0.000 apart, marking (T0362)I51.N as missing WARNING: atoms too close: (T0362)D50.N and (T0362)P53.N only 0.000 apart, marking (T0362)P53.N as missing WARNING: atoms too close: (T0362)F52.CA and (T0362)P53.CA only 0.000 apart, marking (T0362)P53.CA as missing WARNING: atoms too close: (T0362)I51.CA and (T0362)P53.CA only 0.000 apart, marking (T0362)P53.CA as missing WARNING: atoms too close: (T0362)D50.CA and (T0362)P53.CA only 0.000 apart, marking (T0362)P53.CA as missing WARNING: atoms too close: (T0362)F52.CB and (T0362)P53.CB only 0.000 apart, marking (T0362)P53.CB as missing WARNING: atoms too close: (T0362)I51.CB and (T0362)P53.CB only 0.000 apart, marking (T0362)P53.CB as missing WARNING: atoms too close: (T0362)D50.CB and (T0362)P53.CB only 0.000 apart, marking (T0362)P53.CB as missing WARNING: atoms too close: (T0362)F52.O and (T0362)P53.O only 0.000 apart, marking (T0362)P53.O as missing WARNING: atoms too close: (T0362)I51.O and (T0362)P53.O only 0.000 apart, marking (T0362)P53.O as missing WARNING: atoms too close: (T0362)D50.O and (T0362)P53.O only 0.000 apart, marking (T0362)P53.O as missing WARNING: atoms too close: (T0362)F52.C and (T0362)P53.C only 0.000 apart, marking (T0362)P53.C as missing WARNING: atoms too close: (T0362)I51.C and (T0362)P53.C only 0.000 apart, marking (T0362)P53.C as missing WARNING: atoms too close: (T0362)D50.C and (T0362)P53.C only 0.000 apart, marking (T0362)P53.C as missing WARNING: atoms too close: (T0362)P53.N and (T0362)G54.N only 0.000 apart, marking (T0362)P53.N as missing WARNING: atoms too close: (T0362)F52.N and (T0362)G54.N only 0.000 apart, marking (T0362)F52.N as missing WARNING: atoms too close: (T0362)I51.N and (T0362)G54.N only 0.000 apart, marking (T0362)I51.N as missing WARNING: atoms too close: (T0362)D50.N and (T0362)G54.N only 0.000 apart, marking (T0362)G54.N as missing WARNING: atoms too close: (T0362)P53.CA and (T0362)G54.CA only 0.000 apart, marking (T0362)G54.CA as missing WARNING: atoms too close: (T0362)F52.CA and (T0362)G54.CA only 0.000 apart, marking (T0362)G54.CA as missing WARNING: atoms too close: (T0362)I51.CA and (T0362)G54.CA only 0.000 apart, marking (T0362)G54.CA as missing WARNING: atoms too close: (T0362)D50.CA and (T0362)G54.CA only 0.000 apart, marking (T0362)G54.CA as missing WARNING: atoms too close: (T0362)P53.O and (T0362)G54.O only 0.000 apart, marking (T0362)G54.O as missing WARNING: atoms too close: (T0362)F52.O and (T0362)G54.O only 0.000 apart, marking (T0362)G54.O as missing WARNING: atoms too close: (T0362)I51.O and (T0362)G54.O only 0.000 apart, marking (T0362)G54.O as missing WARNING: atoms too close: (T0362)D50.O and (T0362)G54.O only 0.000 apart, marking (T0362)G54.O as missing WARNING: atoms too close: (T0362)P53.C and (T0362)G54.C only 0.000 apart, marking (T0362)G54.C as missing WARNING: atoms too close: (T0362)F52.C and (T0362)G54.C only 0.000 apart, marking (T0362)G54.C as missing WARNING: atoms too close: (T0362)I51.C and (T0362)G54.C only 0.000 apart, marking (T0362)G54.C as missing WARNING: atoms too close: (T0362)D50.C and (T0362)G54.C only 0.000 apart, marking (T0362)G54.C as missing WARNING: atoms too close: (T0362)G54.N and (T0362)S55.N only 0.000 apart, marking (T0362)G54.N as missing WARNING: atoms too close: (T0362)P53.N and (T0362)S55.N only 0.000 apart, marking (T0362)P53.N as missing WARNING: atoms too close: (T0362)F52.N and (T0362)S55.N only 0.000 apart, marking (T0362)F52.N as missing WARNING: atoms too close: (T0362)I51.N and (T0362)S55.N only 0.000 apart, marking (T0362)I51.N as missing WARNING: atoms too close: (T0362)D50.N and (T0362)S55.N only 0.000 apart, marking (T0362)S55.N as missing WARNING: atoms too close: (T0362)G54.CA and (T0362)S55.CA only 0.000 apart, marking (T0362)S55.CA as missing WARNING: atoms too close: (T0362)P53.CA and (T0362)S55.CA only 0.000 apart, marking (T0362)S55.CA as missing WARNING: atoms too close: (T0362)F52.CA and (T0362)S55.CA only 0.000 apart, marking (T0362)S55.CA as missing WARNING: atoms too close: (T0362)I51.CA and (T0362)S55.CA only 0.000 apart, marking (T0362)S55.CA as missing WARNING: atoms too close: (T0362)D50.CA and (T0362)S55.CA only 0.000 apart, marking (T0362)S55.CA as missing WARNING: atoms too close: (T0362)P53.CB and (T0362)S55.CB only 0.000 apart, marking (T0362)S55.CB as missing WARNING: atoms too close: (T0362)F52.CB and (T0362)S55.CB only 0.000 apart, marking (T0362)S55.CB as missing WARNING: atoms too close: (T0362)I51.CB and (T0362)S55.CB only 0.000 apart, marking (T0362)S55.CB as missing WARNING: atoms too close: (T0362)D50.CB and (T0362)S55.CB only 0.000 apart, marking (T0362)S55.CB as missing WARNING: atoms too close: (T0362)G54.O and (T0362)S55.O only 0.000 apart, marking (T0362)S55.O as missing WARNING: atoms too close: (T0362)P53.O and (T0362)S55.O only 0.000 apart, marking (T0362)S55.O as missing WARNING: atoms too close: (T0362)F52.O and (T0362)S55.O only 0.000 apart, marking (T0362)S55.O as missing WARNING: atoms too close: (T0362)I51.O and (T0362)S55.O only 0.000 apart, marking (T0362)S55.O as missing WARNING: atoms too close: (T0362)D50.O and (T0362)S55.O only 0.000 apart, marking (T0362)S55.O as missing WARNING: atoms too close: (T0362)G54.C and (T0362)S55.C only 0.000 apart, marking (T0362)S55.C as missing WARNING: atoms too close: (T0362)P53.C and (T0362)S55.C only 0.000 apart, marking (T0362)S55.C as missing WARNING: atoms too close: (T0362)F52.C and (T0362)S55.C only 0.000 apart, marking (T0362)S55.C as missing WARNING: atoms too close: (T0362)I51.C and (T0362)S55.C only 0.000 apart, marking (T0362)S55.C as missing WARNING: atoms too close: (T0362)D50.C and (T0362)S55.C only 0.000 apart, marking (T0362)S55.C as missing # WARNING: incomplete conformation T0362 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 T0362 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 -0.6066 model score -0.6131 model score -0.6098 model score -0.6146 model score -0.6146 model score -0.4819 model score -0.5523 model score -0.3275 model score -0.1824 model score -0.2351 model score -0.2439 model score -0.5279 model score -0.5194 model score -0.2377 model score -0.2550 model score 0.0102 model score -0.2700 model score -0.3168 model score -0.3384 model score -0.3432 model score -0.6430 model score -0.6181 model score -0.5410 model score -0.4505 model score -0.5551 model score 1.2953 model score 1.2247 model score 1.3636 model score 1.3207 model score 1.3694 model score -0.6459 model score -0.6509 model score -0.4600 model score -0.5338 model score -0.6103 model score -0.4781 model score -0.5435 model score -0.5294 model score -0.5508 model score -0.4129 model score -0.6333 model score -0.2601 model score -0.5324 model score -0.4968 model score -0.6553 model score -0.6357 model score -0.5641 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score -0.5229 model score -0.4980 model score -0.5016 model score -0.6333 model score -0.4995 model score -0.3687 model score -0.5435 model score -0.5508 model score -0.5294 model score -0.4994 model score -0.5869 model score -0.5935 model score -0.4863 model score -0.5469 model score -0.4540 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 2.1872 model score 2.2865 model score 2.1840 model score 2.3071 model score 1.8939 model score -0.5355 model score -0.5816 model score -0.5381 model score -0.3931 model score -0.1986 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score -0.4637 model score -0.5145 model score -0.5325 model score -0.5362 model score -0.4994 model score -0.6301 model score -0.5843 model score -0.5203 model score -0.5547 model score -0.5788 model score -0.5456 model score -0.6476 model score -0.6476 model score -0.5106 model score -0.3848 model score -0.6305 model score -0.3790 model score -0.6033 model score -0.4583 model score -0.3755 model score -0.5095 model score -0.5695 model score -0.4308 model score 1.2771 model score -0.6615 model score -0.6225 model score -0.4897 model score -0.5884 model score -0.5718 model score -0.6225 model score -0.5263 model score -0.5384 model score -0.5430 model score -0.5903 model score -0.4913 model score -0.6675 model score -0.6239 model score -0.5277 model score -0.6339 model score -0.4583 model score -0.6136 model score -0.6176 model score -0.6188 model score -0.6225 model score -0.6147 model score -0.6268 model score -0.6136 model score -0.5758 model score -0.6225 model score -0.6130 model score -0.6451 model score -0.6355 model score -0.5888 model score -0.6173 model score -0.5341 model score -0.6560 model score -0.6444 model score -0.6415 model score -0.6425 model score -0.6427 model score -0.6419 model score -0.5532 model score -0.5703 model score -0.6106 model score -0.6548 model score -0.5424 model score -0.5886 model score -0.6587 model score -0.5296 model score -0.5927 model score -0.6016 model score -0.5680 model score -0.5508 model score -0.5605 model score -0.5397 model score -0.4668 model score -0.6476 model score -0.6450 model score -0.5853 model score -0.6627 model score -0.5632 model score -0.5532 model score -0.5453 model score -0.5573 model score -0.5424 model score -0.5703 model score -0.6362 model score -0.5351 model score -0.4700 model score -0.5251 model score -0.5754 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score -0.6443 model score -0.6498 model score -0.6350 model score -0.6175 model score 0.1285 model score -0.6466 model score -0.5631 model score -0.5724 model score -0.5317 model score -0.5137 model score -0.5763 model score -0.6502 model score -0.5501 model score -0.5295 model score -0.5415 model score -0.6466 model score -0.5631 model score -0.5351 model score -0.5228 model score -0.5283 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score -0.6457 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score -0.6388 model score -0.6279 model score -0.6347 model score -0.6131 model score -0.6285 model score 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USE_EVALUE, weight: 0.9999 eval: 0.0000 min: 0.0000 max: 0.1435 USE_EVALUE, weight: 0.9999 eval: 0.0000 min: 0.0000 max: 0.1435 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.1435 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.1435 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.1435 USE_EVALUE, weight: 0.9943 eval: 0.0009 min: 0.0000 max: 0.1435 USE_EVALUE, weight: 0.9943 eval: 0.0009 min: 0.0000 max: 0.1435 USE_EVALUE, weight: 0.9943 eval: 0.0009 min: 0.0000 max: 0.1435 USE_EVALUE, weight: 0.9701 eval: 0.0048 min: 0.0000 max: 0.1435 USE_EVALUE, weight: 0.9701 eval: 0.0048 min: 0.0000 max: 0.1435 USE_EVALUE, weight: 0.9701 eval: 0.0048 min: 0.0000 max: 0.1435 USE_EVALUE, weight: 0.9956 eval: 0.0007 min: 0.0000 max: 0.1435 USE_EVALUE, weight: 0.9956 eval: 0.0007 min: 0.0000 max: 0.1435 USE_EVALUE, weight: 0.9956 eval: 0.0007 min: 0.0000 max: 0.1435 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.1435 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.1435 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.1435 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.1435 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.1435 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.1435 USE_EVALUE, weight: 0.9942 eval: 0.0009 min: 0.0000 max: 0.1435 USE_EVALUE, weight: 0.9942 eval: 0.0009 min: 0.0000 max: 0.1435 USE_EVALUE, weight: 0.9942 eval: 0.0009 min: 0.0000 max: 0.1435 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.1435 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.1435 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.1435 USE_EVALUE, weight: 0.9911 eval: 0.0014 min: 0.0000 max: 0.1435 USE_EVALUE, weight: 0.9911 eval: 0.0014 min: 0.0000 max: 0.1435 USE_EVALUE, weight: 0.9911 eval: 0.0014 min: 0.0000 max: 0.1435 Number of contacts in models: 261 Number of contacts in alignments: 102 NUMB_ALIGNS: 102 Adding 4193 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: -263.4046, CN propb: -263.4046 weights: 0.3680 constraints: 520 # command:Found ConstraintSet # PrintContacts align.constraints_meta03 Number of constraints in align3.constraints 520 # command:Found ConstraintSet # PrintContacts align_bonus.constraints_meta03 Number of constraints in align3.constraints.bonus 520 # command:Found ConstraintSet # PrintContacts rejected.constraints_meta03 Number of constraints in rejected3.constraints 3673 # command:Found ConstraintSet # PrintContacts rejected_bonus.constraints_meta03 Number of constraints in rejected3.constraints.bonus 3673 # 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 4193 # command: