# 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:Using radius: 8.0000 Alignment mode NUMB_ALIGNS: 102 Adding 1033 constraints to all.constraints Done adding distance constraints # command:Reading probabilities from probabilities.dat Reading constraints from ConstraintSet all.constraints maxweight: 1.0000 Optimizing... Probability sum: -277.9731, CN propb: -277.9731 weights: 0.4483 constraints: 389 # command:Found ConstraintSet # PrintContacts align.constraints_v3 Number of constraints in align.constraints 389 # command:Found ConstraintSet # PrintContacts align_bonus.constraints_v3 Number of constraints in align.constraints.bonus 389 # command:Found ConstraintSet # PrintContacts rejected.constraints_v3 Number of constraints in rejected.constraints 644 # command:Found ConstraintSet # PrintContacts rejected_bonus.constraints_v3 Number of constraints in rejected.constraints.bonus 644 # command:Found ConstraintSet # PrintContacts non_contacts.constraints_v3 Number of constraints in noncontact.constraints 0 # command:Found ConstraintSet # PrintContacts non_contacts_bonus.constraints_v3 Number of constraints in noncontact.constraints.bonus 0 # command:Found ConstraintSet # PrintContacts all.constraints_v3 Number of constraints in all.constraints 1033 # command: