parameters: 0.6 1.3 0.5 200 50 # 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/T0332/ # command:# Making conformation for sequence T0332 numbered 1 through 159 Created new target T0332 from T0332.a2m # command:# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/T0332/ # command:Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0332//projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0332/manyalignments-good-all.under or /projects/compbio/experiments/protein-predict/casp7/T0332//projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0332/manyalignments-good-all.under.gz for input Trying /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0332/manyalignments-good-all.under # reading script from file /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0332/manyalignments-good-all.under # Reading fragments from alignment file # Attempting to read fragment alignments from file 1vbuA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1vbuA expands to /projects/compbio/data/pdb/1vbu.pdb.gz 1vbuA:# T0332 read from 1vbuA/merged-good-all-a2m # 1vbuA read from 1vbuA/merged-good-all-a2m # adding 1vbuA to template set # found chain 1vbuA in template set T0332 4 :SISRLIVVASLID 1vbuA 637 :GRVKIWDVVNEAV # choosing archetypes in rotamer library T0332 17 :KPTNLGGLCRTCEVF 1vbuA 665 :GPEYIEKAFRWAKEA T0332 32 :GA 1vbuA 682 :DA T0332 35 :VLVVGSLQC 1vbuA 684 :ILIYNDYSI T0332 44 :ISDKQFQHLSVSAEQ 1vbuA 694 :EINAKSNFVYNMIKE T0332 59 :WLPLVEVKPPQLIDYLQQKKTEGYTIIGVEQ 1vbuA 724 :HIDYRGLNYDSFRRNLERFAKLGLQIYITEM T0332 127 :CVEIPQQGI 1vbuA 755 :DVRIPLSGS T0332 141 :VHVSGALLIW 1vbuA 768 :LKKQAEVCAK Number of specific fragments extracted= 8 number of extra gaps= 0 total=8 Number of alignments=1 # 1vbuA read from 1vbuA/merged-good-all-a2m # found chain 1vbuA in template set T0332 4 :SISRLIVVASLID 1vbuA 637 :GRVKIWDVVNEAV T0332 17 :KPTNLGGLCRTCEVF 1vbuA 665 :GPEYIEKAFRWAKEA T0332 32 :GASVLVVGSLQCISDKQ 1vbuA 682 :DAILIYNDYSIEEINAK T0332 49 :FQHLSVSAEQ 1vbuA 702 :VYNMIKELKE T0332 59 :WLPLVEVKPPQLIDYLQQKKTEGYTIIGVEQ 1vbuA 724 :HIDYRGLNYDSFRRNLERFAKLGLQIYITEM T0332 127 :CVEIPQQGI 1vbuA 755 :DVRIPLSGS Number of specific fragments extracted= 6 number of extra gaps= 0 total=14 Number of alignments=2 # 1vbuA read from 1vbuA/merged-good-all-a2m # found chain 1vbuA in template set T0332 4 :SISRLIVVASLIDKPT 1vbuA 637 :GRVKIWDVVNEAVSDS T0332 21 :LGGLCRTCEVF 1vbuA 669 :IEKAFRWAKEA T0332 32 :GASVLVVG 1vbuA 682 :DAILIYND T0332 41 :LQCISDKQFQHLSVSA 1vbuA 690 :YSIEEINAKSNFVYNM T0332 57 :EQWL 1vbuA 713 :GVPV T0332 62 :LVEVKPPQ 1vbuA 722 :QMHIDYRG T0332 70 :LIDYLQQKKTEGYTIIGVE 1vbuA 735 :FRRNLERFAKLGLQIYITE T0332 126 :VCVEIPQQGI 1vbuA 754 :MDVRIPLSGS Number of specific fragments extracted= 8 number of extra gaps= 0 total=22 Number of alignments=3 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1v6zA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1v6zA expands to /projects/compbio/data/pdb/1v6z.pdb.gz 1v6zA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0332 read from 1v6zA/merged-good-all-a2m # 1v6zA read from 1v6zA/merged-good-all-a2m # adding 1v6zA to template set # found chain 1v6zA in template set T0332 5 :ISRLIVVASLIDK 1v6zA 70 :GVEVVLYVALLKG T0332 19 :TNLGGLCRTCEVFGASVL 1v6zA 83 :DKLAEVVRAATELGATRI T0332 37 :VVGSLQC 1v6zA 102 :PLVTRHS T0332 44 :ISDKQFQH 1v6zA 112 :EMGEGKLR T0332 69 :QLIDYLQQK 1v6zA 120 :RLRAVALEA T0332 85 :IGVEQTAKSLDLTQYCFPE 1v6zA 155 :GLVAHVGATARVREVLDPE T0332 104 :KSLLLLGNER 1v6zA 175 :PLALAVGPEG T0332 115 :GIPANLIQQL 1v6zA 185 :GFAEEEVALL T0332 127 :CVEIPQQGI 1v6zA 199 :FTPVSLGRR T0332 136 :IRSLNVHVSGA 1v6zA 209 :LRAETAALALL Number of specific fragments extracted= 10 number of extra gaps= 0 total=32 Number of alignments=4 # 1v6zA read from 1v6zA/merged-good-all-a2m # found chain 1v6zA in template set T0332 5 :ISRLIVVASLIDK 1v6zA 70 :GVEVVLYVALLKG T0332 19 :TNLGGLCRTCEVFGASVLVVGSLQ 1v6zA 83 :DKLAEVVRAATELGATRIQPLVTR T0332 45 :S 1v6zA 110 :P T0332 46 :DKQFQH 1v6zA 114 :GEGKLR T0332 69 :QLIDYLQQK 1v6zA 120 :RLRAVALEA T0332 83 :TIIGVE 1v6zA 154 :QGLVAH T0332 90 :TAKSLDLTQY 1v6zA 160 :VGATARVREV T0332 100 :CFPEKSLLLLGNER 1v6zA 171 :DPEKPLALAVGPEG T0332 115 :GIPANLIQQL 1v6zA 185 :GFAEEEVALL T0332 127 :CVEIPQQGI 1v6zA 199 :FTPVSLGRR T0332 136 :IR 1v6zA 209 :LR T0332 141 :VHVSGALLIW 1v6zA 211 :AETAALALLA Number of specific fragments extracted= 12 number of extra gaps= 0 total=44 Number of alignments=5 # 1v6zA read from 1v6zA/merged-good-all-a2m # found chain 1v6zA in template set T0332 4 :SISRLIVVASLIDKPT 1v6zA 69 :VGVEVVLYVALLKGDK T0332 21 :LGGLCRTCEVFGASVLVVGSLQ 1v6zA 85 :LAEVVRAATELGATRIQPLVTR T0332 43 :CISD 1v6zA 108 :SVPK T0332 47 :KQFQHL 1v6zA 115 :EGKLRR T0332 70 :LIDYLQQK 1v6zA 121 :LRAVALEA T0332 78 :KTEGY 1v6zA 130 :KQSGR T0332 83 :TIIGVE 1v6zA 154 :QGLVAH T0332 90 :TAKSLDLTQY 1v6zA 160 :VGATARVREV T0332 100 :CFPEKSLLLLGNER 1v6zA 171 :DPEKPLALAVGPEG T0332 115 :GIPANLIQQL 1v6zA 185 :GFAEEEVALL T0332 125 :DVCVEIPQQG 1v6zA 197 :RGFTPVSLGR T0332 135 :IIRSLNVHVSGAL 1v6zA 208 :ILRAETAALALLA Number of specific fragments extracted= 12 number of extra gaps= 0 total=56 Number of alignments=6 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1mxiA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0332 read from 1mxiA/merged-good-all-a2m # 1mxiA read from 1mxiA/merged-good-all-a2m # found chain 1mxiA in training set Warning: unaligning (T0332)R7 because first residue in template chain is (1mxiA)M1 T0332 8 :LIVVASLIDKPTNLGGLCRTCEVFGASVLVVGSLQC 1mxiA 2 :LDIVLYEPEIPQNTGNIIRLCANTGFRLHLIEPLGF T0332 44 :ISDKQFQHLSVSAEQWLPLVEVK 1mxiA 39 :WDDKRLRRSGLDYHEFAEIKRHK T0332 69 :QLIDYLQQK 1mxiA 62 :TFEAFLESE T0332 78 :KT 1mxiA 72 :PK T0332 83 :TIIGVE 1mxiA 74 :RLFALT T0332 90 :TAKSLDLTQYCFPEKSLLLLGNEREGIPANLIQQL 1mxiA 80 :TKGCPAHSQVKFKLGDYLMFGPETRGIPMSILNEM T0332 125 :DVCVEIPQQGIIRSLNVHVSGALLIWEYTRQQLL 1mxiA 117 :EQKIRIPMTANSRSMNLSNSVAVTVYEAWRQLGY Number of specific fragments extracted= 7 number of extra gaps= 0 total=63 Number of alignments=7 # 1mxiA read from 1mxiA/merged-good-all-a2m # found chain 1mxiA in training set Warning: unaligning (T0332)R7 because first residue in template chain is (1mxiA)M1 T0332 8 :LIVVASLIDKPTNLGGLCRTCEVFGASVLVVGSLQCIS 1mxiA 2 :LDIVLYEPEIPQNTGNIIRLCANTGFRLHLIEPLGFTW T0332 46 :DKQFQHLSVSAEQWLPLVEVK 1mxiA 41 :DKRLRRSGLDYHEFAEIKRHK T0332 69 :QLIDYLQQK 1mxiA 62 :TFEAFLESE T0332 79 :T 1mxiA 73 :K T0332 83 :TIIGVE 1mxiA 74 :RLFALT T0332 90 :TAKSLDLTQYCFPEKSLLLLGNEREGIPANLIQQL 1mxiA 80 :TKGCPAHSQVKFKLGDYLMFGPETRGIPMSILNEM T0332 125 :DVCVEIPQQGIIRSLNVHVSGALLIWEYTRQQLL 1mxiA 117 :EQKIRIPMTANSRSMNLSNSVAVTVYEAWRQLGY Number of specific fragments extracted= 7 number of extra gaps= 0 total=70 Number of alignments=8 # 1mxiA read from 1mxiA/merged-good-all-a2m # found chain 1mxiA in training set T0332 8 :LIVVASLIDKPTNLGGLCRTCEVFGASVLVVGSLQCISDKQFQHL 1mxiA 2 :LDIVLYEPEIPQNTGNIIRLCANTGFRLHLIEPLGFTWDDKRLRR T0332 54 :VSAEQWLPLVEVKPPQLIDYLQQK 1mxiA 47 :SGLDYHEFAEIKRHKTFEAFLESE T0332 83 :TIIGVE 1mxiA 74 :RLFALT T0332 90 :TAKSLDLTQYCFPEKSLLLLGNEREGIPANLIQQL 1mxiA 80 :TKGCPAHSQVKFKLGDYLMFGPETRGIPMSILNEM T0332 125 :DVCVEIPQQGIIRSLNVHVSGALLIWEYTRQQL 1mxiA 117 :EQKIRIPMTANSRSMNLSNSVAVTVYEAWRQLG Number of specific fragments extracted= 5 number of extra gaps= 0 total=75 Number of alignments=9 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1z85A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1z85A expands to /projects/compbio/data/pdb/1z85.pdb.gz 1z85A:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 1584, because occupancy 0.35 <= existing 0.650 in 1z85A Skipped atom 1586, because occupancy 0.350 <= existing 0.650 in 1z85A Skipped atom 1588, because occupancy 0.350 <= existing 0.650 in 1z85A # T0332 read from 1z85A/merged-good-all-a2m # 1z85A read from 1z85A/merged-good-all-a2m # adding 1z85A to template set # found chain 1z85A in template set Warning: unaligning (T0332)T90 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1z85A)Q159 Warning: unaligning (T0332)L94 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1z85A)Q159 Warning: unaligning (T0332)D95 because of BadResidue code TOO_FEW_ATOMS+NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1z85A)N160 Warning: unaligning (T0332)L96 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1z85A)L161 T0332 2 :GKSISRLIVV 1z85A 69 :KEPTEKLSVV T0332 13 :SLIDKPTNLGGLCRTCEVFGASVLVVGSLQCISDK 1z85A 79 :VPIGRWERTRFLIEKCVELGVDEIFFHKFERSQHE T0332 65 :VKPPQLIDYLQQK 1z85A 114 :ISLDKAKIVVREA T0332 79 :TEGYTIIGVE 1z85A 145 :EFSGNVITLD T0332 97 :TQYCFPEKSLLLLGNER 1z85A 162 :LDANLEGSITVVVGPEG T0332 115 :GIPANLIQQLD 1z85A 179 :GFSEKERELLR Number of specific fragments extracted= 6 number of extra gaps= 0 total=81 Number of alignments=10 # 1z85A read from 1z85A/merged-good-all-a2m # found chain 1z85A in template set Warning: unaligning (T0332)T90 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1z85A)Q159 Warning: unaligning (T0332)L94 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1z85A)Q159 Warning: unaligning (T0332)D95 because of BadResidue code TOO_FEW_ATOMS+NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1z85A)N160 Warning: unaligning (T0332)L96 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1z85A)L161 Warning: unaligning (T0332)V128 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1z85A)L202 T0332 2 :GKSISRLIVV 1z85A 69 :KEPTEKLSVV T0332 13 :SLIDKPTNLGGLCRTCEVFGASVLVVGSLQCISD 1z85A 79 :VPIGRWERTRFLIEKCVELGVDEIFFHKFERSQH T0332 47 :KQFQHLSVSAE 1z85A 117 :DKAKIVVREAA T0332 58 :QWLPLVEVK 1z85A 134 :LFPKVSFLE T0332 69 :QL 1z85A 143 :KL T0332 79 :TEGYTIIGVE 1z85A 145 :EFSGNVITLD T0332 97 :TQYCFPEKSLLLLGNER 1z85A 162 :LDANLEGSITVVVGPEG T0332 115 :GIPANLIQQL 1z85A 179 :GFSEKERELL T0332 125 :DVC 1z85A 192 :TTI Number of specific fragments extracted= 9 number of extra gaps= 0 total=90 Number of alignments=11 # 1z85A read from 1z85A/merged-good-all-a2m # found chain 1z85A in template set Warning: unaligning (T0332)T90 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1z85A)Q159 Warning: unaligning (T0332)L94 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1z85A)Q159 Warning: unaligning (T0332)D95 because of BadResidue code TOO_FEW_ATOMS+NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1z85A)N160 Warning: unaligning (T0332)L96 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1z85A)L161 Warning: unaligning (T0332)P131 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1z85A)L202 T0332 2 :GKSISRLIVVASLID 1z85A 69 :KEPTEKLSVVVPIGR T0332 21 :LGGLCRTCEVFGASVLVVGSLQCISDK 1z85A 87 :TRFLIEKCVELGVDEIFFHKFERSQHE T0332 48 :QFQHLSVS 1z85A 120 :KIVVREAA T0332 56 :AEQWLPLVEVKPPQL 1z85A 130 :CKRYLFPKVSFLEKL T0332 80 :EGYTIIGVE 1z85A 146 :FSGNVITLD T0332 97 :TQYCFPEKSLLLLGNER 1z85A 162 :LDANLEGSITVVVGPEG T0332 115 :GIPANLIQQLDVCVEI 1z85A 179 :GFSEKERELLRSSTTI Number of specific fragments extracted= 7 number of extra gaps= 0 total=97 Number of alignments=12 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ualA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0332 read from 1ualA/merged-good-all-a2m # 1ualA read from 1ualA/merged-good-all-a2m # found chain 1ualA in training set Warning: unaligning (T0332)S6 because first residue in template chain is (1ualA)S-1 T0332 7 :RLIVVASLID 1ualA 0 :HMWIGVISLF T0332 17 :KPTNLG 1ualA 18 :EFGVTG T0332 26 :R 1ualA 24 :R T0332 28 :CEVFGASVLVVGSLQC 1ualA 25 :AVKHNLLKVECWNPRD T0332 44 :ISDKQ 1ualA 42 :TFDKH T0332 61 :PLVEVKPPQLIDYLQQK 1ualA 58 :PGMLMMVQPLRDAIHTA T0332 78 :KTEGYTIIGVEQT 1ualA 78 :AGEGAKVIYLSPQ T0332 93 :SL 1ualA 91 :GR T0332 100 :CFP 1ualA 93 :KLD T0332 103 :EKSLLLLGN 1ualA 106 :QKLILVCGR T0332 113 :REGIPANLIQ 1ualA 115 :YEGIDERLIQ T0332 123 :QLDVCVEIPQQGIIRS 1ualA 126 :EIDEEWSIGDYVLTGG T0332 142 :HVSGALLIWE 1ualA 142 :ELPAMTLIDA Number of specific fragments extracted= 13 number of extra gaps= 0 total=110 Number of alignments=13 # 1ualA read from 1ualA/merged-good-all-a2m # found chain 1ualA in training set Warning: unaligning (T0332)S6 because first residue in template chain is (1ualA)S-1 T0332 7 :RLIVVASLIDKPT 1ualA 0 :HMWIGVISLFPEM T0332 20 :NLG 1ualA 21 :VTG T0332 26 :R 1ualA 24 :R T0332 28 :CEVFGASVLVVGSLQ 1ualA 25 :AVKHNLLKVECWNPR T0332 43 :CISDKQ 1ualA 41 :FTFDKH T0332 61 :PLVEVKPPQLIDYLQQKKT 1ualA 58 :PGMLMMVQPLRDAIHTAKA T0332 80 :EGYTIIGVEQ 1ualA 80 :EGAKVIYLSP T0332 92 :KSLDLTQ 1ualA 90 :QGRKLDQ T0332 99 :YCFPEKSLLLLGN 1ualA 102 :LAQNQKLILVCGR T0332 113 :REGIPANLIQ 1ualA 115 :YEGIDERLIQ T0332 123 :QLDVCVEIPQQGI 1ualA 126 :EIDEEWSIGDYVL T0332 142 :HVSGALLIWEYT 1ualA 142 :ELPAMTLIDAVA Number of specific fragments extracted= 12 number of extra gaps= 0 total=122 Number of alignments=14 # 1ualA read from 1ualA/merged-good-all-a2m # found chain 1ualA in training set Warning: unaligning (T0332)S6 because first residue in template chain is (1ualA)S-1 T0332 7 :RLIVVASLIDKPT 1ualA 0 :HMWIGVISLFPEM T0332 24 :LC 1ualA 22 :TG T0332 27 :TCEVFGASVLVVGSLQCISDKQFQHL 1ualA 24 :RAVKHNLLKVECWNPRDFTFDKHKTV T0332 63 :VE 1ualA 50 :DD T0332 70 :LIDYLQQKKT 1ualA 67 :LRDAIHTAKA T0332 80 :EGYTIIGVEQTAKSLD 1ualA 80 :EGAKVIYLSPQGRKLD T0332 96 :LTQYCFPEKSLLLLGNE 1ualA 99 :VTELAQNQKLILVCGRY T0332 114 :EGIPANLIQ 1ualA 116 :EGIDERLIQ T0332 123 :QLDVCVEIPQQGIIRS 1ualA 126 :EIDEEWSIGDYVLTGG T0332 144 :SGALLIWEYT 1ualA 143 :LPAMTLIDAV Number of specific fragments extracted= 10 number of extra gaps= 0 total=132 Number of alignments=15 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1qwgA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0332 read from 1qwgA/merged-good-all-a2m # 1qwgA read from 1qwgA/merged-good-all-a2m # found chain 1qwgA in training set Warning: unaligning (T0332)Y82 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1qwgA)M129 Warning: unaligning (T0332)T83 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1qwgA)M129 T0332 2 :GK 1qwgA 10 :DF T0332 5 :ISRLIVVASLIDKPTNLGGLCRTCE 1qwgA 12 :QRGLTVVLDKGLPPKFVEDYLKVCG T0332 33 :ASVLVVGSLQC 1qwgA 39 :IDFVKFGWGTS T0332 44 :ISDKQFQHLSVSAEQW 1qwgA 52 :IDRDVVKEKINYYKDW T0332 60 :LPLVEV 1qwgA 69 :IKVYPG T0332 66 :KPPQLIDYLQQK 1qwgA 86 :KFDEFLNECEKL T0332 78 :KTEG 1qwgA 124 :KDNG T0332 84 :IIGVEQTAK 1qwgA 130 :VLTEVGKKM T0332 104 :KSLLLLGNER 1qwgA 163 :DYVIIEGRES T0332 114 :EG 1qwgA 182 :EG T0332 116 :IPANLIQQL 1qwgA 185 :VKENELDVL Number of specific fragments extracted= 11 number of extra gaps= 1 total=143 Number of alignments=16 # 1qwgA read from 1qwgA/merged-good-all-a2m # found chain 1qwgA in training set Warning: unaligning (T0332)Y82 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1qwgA)M129 Warning: unaligning (T0332)T83 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1qwgA)M129 T0332 2 :GKSISRLIVVASLIDKPTNLGGLCR 1qwgA 9 :EDFQRGLTVVLDKGLPPKFVEDYLK T0332 33 :ASVLVVGSLQCIS 1qwgA 39 :IDFVKFGWGTSAV T0332 46 :DKQFQHLSVSAEQW 1qwgA 54 :RDVVKEKINYYKDW T0332 60 :LPLVEV 1qwgA 69 :IKVYPG T0332 67 :PPQLIDYLQQK 1qwgA 84 :KGKFDEFLNEC T0332 78 :KTEG 1qwgA 124 :KDNG T0332 84 :IIGVEQTA 1qwgA 130 :VLTEVGKK T0332 92 :KSLDLTQ 1qwgA 143 :KQLTIDD T0332 103 :EKSLLLLGNER 1qwgA 162 :ADYVIIEGRES T0332 114 :EG 1qwgA 182 :EG T0332 116 :IPANLIQQL 1qwgA 185 :VKENELDVL T0332 125 :DVCVEIPQ 1qwgA 201 :KVIFEAPQ T0332 141 :VHVSGA 1qwgA 211 :QQVAFI Number of specific fragments extracted= 13 number of extra gaps= 1 total=156 Number of alignments=17 # 1qwgA read from 1qwgA/merged-good-all-a2m # found chain 1qwgA in training set Warning: unaligning (T0332)Y82 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1qwgA)M129 Warning: unaligning (T0332)T83 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1qwgA)M129 T0332 3 :KSISRLIVVASLIDKPTNLGGLCRT 1qwgA 10 :DFQRGLTVVLDKGLPPKFVEDYLKV T0332 33 :ASVLVVGSLQCISDKQFQHL 1qwgA 39 :IDFVKFGWGTSAVIDRDVVK T0332 54 :VSAEQW 1qwgA 59 :EKINYY T0332 60 :LPLVEVK 1qwgA 67 :WGIKVYP T0332 68 :PQLIDYLQQK 1qwgA 85 :GKFDEFLNEC T0332 78 :KTEG 1qwgA 124 :KDNG T0332 84 :IIGVEQTAK 1qwgA 130 :VLTEVGKKM T0332 102 :PEKSLLLLGNER 1qwgA 161 :GADYVIIEGRES T0332 114 :EGIPANLIQQL 1qwgA 183 :GKVKENELDVL Number of specific fragments extracted= 9 number of extra gaps= 1 total=165 Number of alignments=18 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2as0A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2as0A expands to /projects/compbio/data/pdb/2as0.pdb.gz 2as0A:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0332 read from 2as0A/merged-good-all-a2m # 2as0A read from 2as0A/merged-good-all-a2m # adding 2as0A to template set # found chain 2as0A in template set T0332 2 :GK 2as0A 216 :QP T0332 7 :RLIVVASLIDKP 2as0A 218 :GDRVLDVFTYTG T0332 22 :G 2as0A 230 :G T0332 24 :LCRTCEVFGASVLVVGSLQ 2as0A 231 :FAIHAAIAGADEVIGIDKS T0332 47 :KQFQHLSVSA 2as0A 250 :PRAIETAKEN T0332 57 :EQWLPLVEVK 2as0A 266 :EDRMKFIVGS T0332 70 :LIDYLQQKKTEG 2as0A 276 :AFEEMEKLQKKG T0332 82 :YTIIGVEQTAKSLDLTQY 2as0A 290 :FDIVVLDPPAFVQHEKDL T0332 118 :ANLIQQL 2as0A 308 :KAGLRAY T0332 139 :LNVHVSGA 2as0A 315 :FNVNFAGL Number of specific fragments extracted= 10 number of extra gaps= 0 total=175 Number of alignments=19 # 2as0A read from 2as0A/merged-good-all-a2m # found chain 2as0A in template set T0332 5 :ISRLIVVASLID 2as0A 216 :QPGDRVLDVFTY T0332 21 :LGGLCRTCEVFGASVLVVGSL 2as0A 228 :TGGFAIHAAIAGADEVIGIDK T0332 46 :DKQFQHLSVSA 2as0A 249 :SPRAIETAKEN T0332 57 :EQWLPLVEV 2as0A 266 :EDRMKFIVG T0332 69 :QLIDYLQQKKTEG 2as0A 275 :SAFEEMEKLQKKG T0332 82 :YTIIGVEQTAKSLDLTQ 2as0A 290 :FDIVVLDPPAFVQHEKD T0332 118 :ANLIQQL 2as0A 308 :KAGLRAY T0332 139 :LNVHVSGA 2as0A 315 :FNVNFAGL Number of specific fragments extracted= 8 number of extra gaps= 0 total=183 Number of alignments=20 # 2as0A read from 2as0A/merged-good-all-a2m # found chain 2as0A in template set T0332 4 :SISRLIVVASLID 2as0A 215 :VQPGDRVLDVFTY T0332 21 :LGGLCRTCEVFGASVLVVGSLQ 2as0A 228 :TGGFAIHAAIAGADEVIGIDKS T0332 47 :KQFQHL 2as0A 250 :PRAIET T0332 53 :SVSAEQWLPLVEVKPPQLIDYLQQKKTEG 2as0A 259 :NAKLNGVEDRMKFIVGSAFEEMEKLQKKG T0332 82 :YTIIGVEQTAKSLDLTQY 2as0A 290 :FDIVVLDPPAFVQHEKDL T0332 118 :ANLIQQL 2as0A 308 :KAGLRAY T0332 139 :LNVHVSG 2as0A 315 :FNVNFAG Number of specific fragments extracted= 7 number of extra gaps= 0 total=190 Number of alignments=21 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1zxxA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1zxxA expands to /projects/compbio/data/pdb/1zxx.pdb.gz 1zxxA:# T0332 read from 1zxxA/merged-good-all-a2m # 1zxxA read from 1zxxA/merged-good-all-a2m # adding 1zxxA to template set # found chain 1zxxA in template set T0332 6 :SRLIVVASLIDKPTNL 1zxxA 161 :HRVFIVNVMGRNCGDI T0332 24 :LCRTCEVFGASVLVVGSLQ 1zxxA 177 :AMRVGVACGADAIVIPERP T0332 65 :VKPPQLIDYLQQKKTEGY 1zxxA 196 :YDVEEIANRLKQAQESGK T0332 83 :TIIGVE 1zxxA 216 :GLVVVA T0332 91 :AKSLDL 1zxxA 222 :EGVMTA Number of specific fragments extracted= 5 number of extra gaps= 0 total=195 Number of alignments=22 # 1zxxA read from 1zxxA/merged-good-all-a2m # found chain 1zxxA in template set T0332 6 :SRLIVVASLIDKPTNL 1zxxA 161 :HRVFIVNVMGRNCGDI T0332 24 :LCRTCEVFGASVLVVGSLQCI 1zxxA 177 :AMRVGVACGADAIVIPERPYD T0332 67 :PPQLIDYLQQKKTEG 1zxxA 198 :VEEIANRLKQAQESG T0332 82 :YTIIGV 1zxxA 215 :HGLVVV T0332 90 :TAKSLDLTQ 1zxxA 221 :AEGVMTADQ T0332 119 :NLIQQ 1zxxA 233 :ELKKY T0332 124 :LD 1zxxA 240 :FD T0332 128 :VEIPQQG 1zxxA 242 :VRANVLG Number of specific fragments extracted= 8 number of extra gaps= 0 total=203 Number of alignments=23 # 1zxxA read from 1zxxA/merged-good-all-a2m # found chain 1zxxA in template set T0332 6 :SRLIVVASLIDKPTN 1zxxA 161 :HRVFIVNVMGRNCGD T0332 23 :GLCRTCEVFGASVLVVGSLQCISDK 1zxxA 176 :IAMRVGVACGADAIVIPERPYDVEE T0332 70 :LIDYLQQKKTEGY 1zxxA 201 :IANRLKQAQESGK T0332 83 :TIIGVE 1zxxA 216 :GLVVVA T0332 91 :AKSLD 1zxxA 222 :EGVMT Number of specific fragments extracted= 5 number of extra gaps= 0 total=208 Number of alignments=24 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1eny/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1eny expands to /projects/compbio/data/pdb/1eny.pdb.gz 1eny:Warning: there is no chain 1eny will retry with 1enyA # T0332 read from 1eny/merged-good-all-a2m # 1eny read from 1eny/merged-good-all-a2m # adding 1eny to template set # found chain 1eny in template set Warning: unaligning (T0332)A12 because of BadResidue code BAD_PEPTIDE in next template residue (1eny)S13 Warning: unaligning (T0332)S13 because of BadResidue code BAD_PEPTIDE at template residue (1eny)S13 Warning: unaligning (T0332)S40 because of BadResidue code BAD_PEPTIDE in next template residue (1eny)D42 Warning: unaligning (T0332)L41 because of BadResidue code BAD_PEPTIDE at template residue (1eny)D42 Warning: unaligning (T0332)S93 because of BadResidue code BAD_PEPTIDE in next template residue (1eny)M103 T0332 7 :RLIVV 1eny 7 :GKRIL T0332 14 :LIDKPTNLG 1eny 14 :GIITDSSIA T0332 23 :GLCRTCEVFGASVLVVG 1eny 24 :HIARVAQEQGAQLVLTG T0332 42 :Q 1eny 43 :R T0332 46 :DKQFQHLSVSAEQWLPLVEVK 1eny 44 :LRLIQRITDRLPAKAPLLELD T0332 67 :PPQLIDYLQQKKTEGYTIIGV 1eny 71 :LASLAGRVTEAIGAGNKLDGV T0332 88 :E 1eny 94 :S T0332 89 :QTAK 1eny 98 :MPQT T0332 94 :LDLTQY 1eny 106 :NPFFDA T0332 102 :P 1eny 112 :P T0332 103 :EKSLLLLGN 1eny 141 :GGSIVGMDF T0332 131 :PQQGIIRSLNVHVSGALLIWEYTRQQ 1eny 150 :DPSRAMPAYNWMTVAKSALESVNRFV Number of specific fragments extracted= 12 number of extra gaps= 3 total=220 Number of alignments=25 # 1eny read from 1eny/merged-good-all-a2m # found chain 1eny in template set Warning: unaligning (T0332)A12 because of BadResidue code BAD_PEPTIDE in next template residue (1eny)S13 Warning: unaligning (T0332)S13 because of BadResidue code BAD_PEPTIDE at template residue (1eny)S13 Warning: unaligning (T0332)S40 because of BadResidue code BAD_PEPTIDE in next template residue (1eny)D42 Warning: unaligning (T0332)I44 because of BadResidue code BAD_PEPTIDE at template residue (1eny)D42 Warning: unaligning (T0332)S93 because of BadResidue code BAD_PEPTIDE in next template residue (1eny)M103 T0332 6 :SRLIVV 1eny 6 :DGKRIL T0332 14 :LIDKPTNLG 1eny 14 :GIITDSSIA T0332 23 :GLCRTCEVFGASVLVVG 1eny 24 :HIARVAQEQGAQLVLTG T0332 45 :SDKQFQHLSVSAEQWLPLVEVK 1eny 43 :RLRLIQRITDRLPAKAPLLELD T0332 67 :PPQLIDYLQQKKTEGYTIIGV 1eny 71 :LASLAGRVTEAIGAGNKLDGV T0332 89 :QTAK 1eny 98 :MPQT T0332 94 :LDLTQ 1eny 106 :NPFFD T0332 99 :YCFPEKSLLLLGN 1eny 137 :IMNPGGSIVGMDF T0332 131 :PQQGIIRSLNVHVSGALLIWEYTRQQ 1eny 150 :DPSRAMPAYNWMTVAKSALESVNRFV Number of specific fragments extracted= 9 number of extra gaps= 3 total=229 Number of alignments=26 # 1eny read from 1eny/merged-good-all-a2m # found chain 1eny in template set Warning: unaligning (T0332)A12 because of BadResidue code BAD_PEPTIDE in next template residue (1eny)S13 Warning: unaligning (T0332)S13 because of BadResidue code BAD_PEPTIDE at template residue (1eny)S13 Warning: unaligning (T0332)S40 because of BadResidue code BAD_PEPTIDE in next template residue (1eny)D42 Warning: unaligning (T0332)L41 because of BadResidue code BAD_PEPTIDE at template residue (1eny)D42 Warning: unaligning (T0332)S93 because of BadResidue code BAD_PEPTIDE in next template residue (1eny)M103 T0332 7 :RLIVV 1eny 7 :GKRIL T0332 14 :LIDKPTNLG 1eny 14 :GIITDSSIA T0332 23 :GLCRTCEVFGASVLVVG 1eny 24 :HIARVAQEQGAQLVLTG T0332 46 :DKQFQHL 1eny 43 :RLRLIQR T0332 54 :VSAEQWLPLVEVKPP 1eny 50 :ITDRLPAKAPLLELD T0332 69 :QLIDYLQQKKTEG 1eny 73 :SLAGRVTEAIGAG T0332 82 :YTIIGVEQ 1eny 88 :LDGVVHSI T0332 90 :TAK 1eny 99 :PQT T0332 94 :LDLTQYCF 1eny 106 :NPFFDAPY T0332 102 :PEKSLLLLGN 1eny 140 :PGGSIVGMDF T0332 131 :PQQGIIRSLNVHVSGALLIWEYTR 1eny 150 :DPSRAMPAYNWMTVAKSALESVNR Number of specific fragments extracted= 11 number of extra gaps= 3 total=240 Number of alignments=27 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1k3rA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1k3rA expands to /projects/compbio/data/pdb/1k3r.pdb.gz 1k3rA:# T0332 read from 1k3rA/merged-good-all-a2m # 1k3rA read from 1k3rA/merged-good-all-a2m # adding 1k3rA to template set # found chain 1k3rA in template set T0332 4 :SISRLIVVASL 1k3rA 2 :NRVDLSLFIPD T0332 15 :IDK 1k3rA 18 :TGD T0332 18 :PTNLGGLCRTCEVFGASVLVVGSLQC 1k3rA 25 :TYKVVLIARAASIFGVKRIVIYHDDA T0332 44 :ISDK 1k3rA 52 :GEAR T0332 69 :QLIDYLQQK 1k3rA 56 :FIRDILTYM T0332 78 :K 1k3rA 183 :A T0332 83 :TIIGVE 1k3rA 184 :DVVVAT T0332 90 :TAKSLDLTQY 1k3rA 190 :SRNASPITSI T0332 100 :CFPEKSLLLLGNEREGIPA 1k3rA 208 :RGAREAAILFGGPYKGLPE T0332 124 :LDVC 1k3rA 229 :ADIW T0332 130 :IPQQGI 1k3rA 233 :VNTLPG T0332 136 :IR 1k3rA 244 :VR T0332 141 :VHVSGALLIWEYTRQ 1k3rA 246 :TEEAVLATLSVFNML Number of specific fragments extracted= 13 number of extra gaps= 0 total=253 Number of alignments=28 # 1k3rA read from 1k3rA/merged-good-all-a2m # found chain 1k3rA in template set T0332 4 :SISRLIVVASL 1k3rA 2 :NRVDLSLFIPD T0332 19 :TNLGGLCRTCEVFGASVLVVGSLQCISD 1k3rA 26 :YKVVLIARAASIFGVKRIVIYHDDADGE T0332 67 :PPQLIDYLQQK 1k3rA 54 :ARFIRDILTYM T0332 81 :GYTIIGVE 1k3rA 182 :GADVVVAT T0332 90 :TAKSLDLTQ 1k3rA 190 :SRNASPITS T0332 99 :YCFPEKSLLLLGNEREGIPA 1k3rA 207 :MRGAREAAILFGGPYKGLPE T0332 124 :LDV 1k3rA 229 :ADI T0332 129 :EIPQQGI 1k3rA 232 :WVNTLPG T0332 136 :IR 1k3rA 244 :VR T0332 141 :VHVSGALLIWEYTRQ 1k3rA 246 :TEEAVLATLSVFNML Number of specific fragments extracted= 10 number of extra gaps= 0 total=263 Number of alignments=29 # 1k3rA read from 1k3rA/merged-good-all-a2m # found chain 1k3rA in template set T0332 4 :SISRLIVVASL 1k3rA 2 :NRVDLSLFIPD T0332 15 :IDK 1k3rA 18 :TGD T0332 21 :LGGLCRTCEVFGASVLVVGSLQCISDKQFQHL 1k3rA 28 :VVLIARAASIFGVKRIVIYHDDADGEARFIRD T0332 73 :YLQQK 1k3rA 60 :ILTYM T0332 80 :EGYTIIGVE 1k3rA 181 :VGADVVVAT T0332 90 :TAKSLDLTQY 1k3rA 190 :SRNASPITSI T0332 100 :CFPEKSLLLLGNEREGIPA 1k3rA 208 :RGAREAAILFGGPYKGLPE T0332 124 :LDVCVEIPQQG 1k3rA 227 :IDADIWVNTLP T0332 135 :IIRSLNVHVSGALLIW 1k3rA 243 :TVRTEEAVLATLSVFN Number of specific fragments extracted= 9 number of extra gaps= 0 total=272 Number of alignments=30 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1gci/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0332 read from 1gci/merged-good-all-a2m # 1gci read from 1gci/merged-good-all-a2m # found chain 1gci in training set T0332 7 :RLIVVASLID 1gci 89 :ELYAVKVLGA T0332 17 :KPTNLGGLCRTCEVFGASVLVVGSLQCIS 1gci 103 :SVSSIAQGLEWAGNNGMHVANLSLGSPSP T0332 67 :PPQLIDYLQQKKTEGYTIIGVEQTAKSLDLTQYCFPEKSLLLLG 1gci 132 :SATLEQAVNSATSRGVLVVAASGNSGAGSISYPARYANAMAVGA T0332 111 :NEREGI 1gci 191 :QYGAGL T0332 127 :CVEIPQQG 1gci 197 :DIVAPGVN T0332 136 :IRSLNVHVSGALLIWEYTRQQ 1gci 217 :LNGTSMATPHVAGAAALVKQK Number of specific fragments extracted= 6 number of extra gaps= 0 total=278 Number of alignments=31 # 1gci read from 1gci/merged-good-all-a2m # found chain 1gci in training set T0332 7 :RLIVVASLID 1gci 89 :ELYAVKVLGA T0332 17 :KPTNLGGLCRTCEVFGASVLVVGSLQCIS 1gci 103 :SVSSIAQGLEWAGNNGMHVANLSLGSPSP T0332 67 :PPQLIDYLQQKKTEGYTIIGVEQTAKSLDLTQYCFPEKSLLLLG 1gci 132 :SATLEQAVNSATSRGVLVVAASGNSGAGSISYPARYANAMAVGA T0332 111 :NEREG 1gci 191 :QYGAG T0332 126 :VCVEIPQQGI 1gci 196 :LDIVAPGVNV T0332 136 :IRSLNVHVSGALLIWEY 1gci 220 :TSMATPHVAGAAALVKQ Number of specific fragments extracted= 6 number of extra gaps= 0 total=284 Number of alignments=32 # 1gci read from 1gci/merged-good-all-a2m # found chain 1gci in training set T0332 5 :ISRLIVVASLIDKPT 1gci 87 :SAELYAVKVLGASGS T0332 21 :LGGLCRTCEVFGASVLVVGSLQCISDK 1gci 107 :IAQGLEWAGNNGMHVANLSLGSPSPSA T0332 51 :H 1gci 134 :T T0332 70 :LIDYLQQKKTEGYTIIGVEQTAKSLDLTQYCFPEKSLLLLG 1gci 135 :LEQAVNSATSRGVLVVAASGNSGAGSISYPARYANAMAVGA T0332 111 :NEREGI 1gci 191 :QYGAGL T0332 127 :CVEIPQQG 1gci 197 :DIVAPGVN T0332 135 :IIRSLNVHVSGALLIWEYTRQQ 1gci 216 :SLNGTSMATPHVAGAAALVKQK Number of specific fragments extracted= 7 number of extra gaps= 0 total=291 Number of alignments=33 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1x7oA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1x7oA expands to /projects/compbio/data/pdb/1x7o.pdb.gz 1x7oA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0332 read from 1x7oA/merged-good-all-a2m # 1x7oA read from 1x7oA/merged-good-all-a2m # adding 1x7oA to template set # found chain 1x7oA in template set T0332 1 :LGKSISRLIVVASLIDKPTNLGGLCRTCEVFGASVLVVGSLQC 1x7oA 120 :IPVREDFLGVLFDRPTSPGNIGSIIRSADALGAHGLIVAGHAA T0332 44 :ISDKQFQHLSVSAEQWLPLVEVK 1x7oA 164 :VYDPKSVRSSTGSLFSLPAVRVP T0332 67 :PPQLIDYLQQKKTEG 1x7oA 188 :PGEVMDWVEARRAAG T0332 82 :YTIIGVE 1x7oA 205 :IVLVGTD T0332 90 :TAKSLDLTQYCFPEKSLLLLGNEREGIPANLIQQLDVCVEIPQQGIIRSLNVHVSGALLIWEYTRQQLL 1x7oA 212 :EHGDCDVFDFDFTQPTLLLIGNETAGLSNAWRTLCDYTVSIPMAGSASSLNAANAATAILYEAVRQRIS Number of specific fragments extracted= 5 number of extra gaps= 0 total=296 Number of alignments=34 # 1x7oA read from 1x7oA/merged-good-all-a2m # found chain 1x7oA in template set T0332 2 :GKSISRLIVVASLIDKPTNLGGLCRTCEVFGASVLVVGSLQCIS 1x7oA 121 :PVREDFLGVLFDRPTSPGNIGSIIRSADALGAHGLIVAGHAADV T0332 46 :DKQFQHLSVSAEQWLPLVEVK 1x7oA 166 :DPKSVRSSTGSLFSLPAVRVP T0332 67 :PPQLIDYLQQKKTEG 1x7oA 188 :PGEVMDWVEARRAAG T0332 82 :YTIIGVE 1x7oA 205 :IVLVGTD T0332 90 :TAKSLDLTQYCFPEKSLLLLGNEREGIPANLIQQLDVCVEIPQQGIIRSLNVHVSGALLIWEYTRQQLLS 1x7oA 212 :EHGDCDVFDFDFTQPTLLLIGNETAGLSNAWRTLCDYTVSIPMAGSASSLNAANAATAILYEAVRQRISG Number of specific fragments extracted= 5 number of extra gaps= 0 total=301 Number of alignments=35 # 1x7oA read from 1x7oA/merged-good-all-a2m # found chain 1x7oA in template set T0332 2 :GKSISRLIVVASLIDKPTNLGGLCRTCEVFGASVLVVGSLQCISDKQFQHL 1x7oA 121 :PVREDFLGVLFDRPTSPGNIGSIIRSADALGAHGLIVAGHAADVYDPKSVR T0332 54 :VSAEQWLPLVEVKPPQ 1x7oA 172 :SSTGSLFSLPAVRVPS T0332 70 :LIDYLQQKKTEG 1x7oA 191 :VMDWVEARRAAG T0332 82 :YTIIGVE 1x7oA 205 :IVLVGTD T0332 90 :TAKSLDLTQYCFPEKSLLLLGNEREGIPANLIQQLDVCVEIPQQGIIRSLNVHVSGALLIWEYTRQQ 1x7oA 212 :EHGDCDVFDFDFTQPTLLLIGNETAGLSNAWRTLCDYTVSIPMAGSASSLNAANAATAILYEAVRQR Number of specific fragments extracted= 5 number of extra gaps= 0 total=306 Number of alignments=36 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1gz0A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1gz0A expands to /projects/compbio/data/pdb/1gz0.pdb.gz 1gz0A:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0332 read from 1gz0A/merged-good-all-a2m # 1gz0A read from 1gz0A/merged-good-all-a2m # adding 1gz0A to template set # found chain 1gz0A in template set T0332 6 :SRLIVVASLIDKPTNLGGLCRTCEVFGASVLVVGSLQC 1gz0A 94 :QPFLLILDGVTDPHNLGACLRSADAAGVHAVIVPKDRS T0332 44 :ISDKQFQHLSVSAEQWLPLVEVK 1gz0A 133 :QLNATAKKVACGAAESVPLIRVT T0332 69 :QLIDYLQQKKTEGYTIIGVE 1gz0A 156 :NLARTMRMLQEENIWIVGTA T0332 90 :TAKSLDLTQYCFPEKSLLLLGNEREGIPANLIQQLDVCVEIPQQGIIRSLNVHVSGALLIWEYTRQQ 1gz0A 176 :GEADHTLYQSKMTGRLALVMGAEGEGMRRLTREHCDELISIPMAGSVSSLNVSVATGICLFEAVRQR Number of specific fragments extracted= 4 number of extra gaps= 0 total=310 Number of alignments=37 # 1gz0A read from 1gz0A/merged-good-all-a2m # found chain 1gz0A in template set T0332 6 :SRLIVVASLIDKPTNLGGLCRTCEVFGASVLVVGSLQCIS 1gz0A 94 :QPFLLILDGVTDPHNLGACLRSADAAGVHAVIVPKDRSAQ T0332 46 :DKQFQHLSVSAEQWLPLVEVK 1gz0A 135 :NATAKKVACGAAESVPLIRVT T0332 69 :QLIDYLQQKKTEGYTIIGVE 1gz0A 156 :NLARTMRMLQEENIWIVGTA T0332 90 :TAKSLDLTQYCFPEKSLLLLGNEREGIPANLIQQLDVCVEIPQQGIIRSLNVHVSGALLIWEYTRQQ 1gz0A 176 :GEADHTLYQSKMTGRLALVMGAEGEGMRRLTREHCDELISIPMAGSVSSLNVSVATGICLFEAVRQR Number of specific fragments extracted= 4 number of extra gaps= 0 total=314 Number of alignments=38 # 1gz0A read from 1gz0A/merged-good-all-a2m # found chain 1gz0A in template set T0332 5 :ISRLIVVASLIDKPTNLGGLCRTCEVFGASVLVVGSLQCISDKQFQHL 1gz0A 93 :DQPFLLILDGVTDPHNLGACLRSADAAGVHAVIVPKDRSAQLNATAKK T0332 54 :VSAEQWLPLVEVKPPQLIDYLQQKKTEGYTIIGVE 1gz0A 141 :VACGAAESVPLIRVTNLARTMRMLQEENIWIVGTA T0332 90 :TAKSLDLTQYCFPEKSLLLLGNEREGIPANLIQQLDVCVEIPQQGIIRSLNVHVSGALLIWEYTRQQ 1gz0A 176 :GEADHTLYQSKMTGRLALVMGAEGEGMRRLTREHCDELISIPMAGSVSSLNVSVATGICLFEAVRQR Number of specific fragments extracted= 3 number of extra gaps= 0 total=317 Number of alignments=39 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1d2nA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0332 read from 1d2nA/merged-good-all-a2m # 1d2nA read from 1d2nA/merged-good-all-a2m # found chain 1d2nA in training set T0332 2 :GKSISRLIVVASLIDKPTNLGGLCRTCEVFGASVLVVGSLQC 1d2nA 539 :SDRTPLVSVLLEGPPHSGKTALAAKIAEESNFPFIKICSPDK T0332 44 :ISDKQFQH 1d2nA 584 :FSETAKCQ T0332 69 :QLIDYLQQKKTEGYTIIGVE 1d2nA 592 :AMKKIFDDAYKSQLSCVVVD T0332 89 :QTAKSLD 1d2nA 619 :YVPIGPR T0332 96 :LTQYCFPEKSLLLLGNER 1d2nA 638 :LKKAPPQGRKLLIIGTTS T0332 117 :PANLIQ 1d2nA 656 :RKDVLQ T0332 123 :QLDVCVEIPQQGIIR 1d2nA 668 :AFSTTIHVPNIATGE T0332 148 :LIWEYTRQQLL 1d2nA 683 :QLLEALELLGN Number of specific fragments extracted= 8 number of extra gaps= 0 total=325 Number of alignments=40 # 1d2nA read from 1d2nA/merged-good-all-a2m # found chain 1d2nA in training set T0332 2 :GKSISRLIVVASLIDKPTNLGGLCRTCEVFGASVLVVGSLQCIS 1d2nA 539 :SDRTPLVSVLLEGPPHSGKTALAAKIAEESNFPFIKICSPDKMI T0332 46 :DKQFQH 1d2nA 586 :ETAKCQ T0332 69 :QLIDYLQQKKTEGYTIIGVE 1d2nA 592 :AMKKIFDDAYKSQLSCVVVD T0332 89 :QTAKSLDLTQ 1d2nA 619 :YVPIGPRFSN T0332 99 :YCFPEKSLLLLGNER 1d2nA 641 :APPQGRKLLIIGTTS T0332 117 :PANLIQ 1d2nA 656 :RKDVLQ T0332 123 :QLDVCVEIPQQGIIR 1d2nA 668 :AFSTTIHVPNIATGE T0332 148 :LIWEYTRQQLL 1d2nA 683 :QLLEALELLGN Number of specific fragments extracted= 8 number of extra gaps= 0 total=333 Number of alignments=41 # 1d2nA read from 1d2nA/merged-good-all-a2m # found chain 1d2nA in training set T0332 3 :KSISRLIVVASLIDKPTNLGGLCRTCEVFGASVLVVGSLQCISDKQFQHLSVS 1d2nA 540 :DRTPLVSVLLEGPPHSGKTALAAKIAEESNFPFIKICSPDKMIGFSETAKCQA T0332 70 :LIDYLQQKKTEGYTIIGVEQ 1d2nA 593 :MKKIFDDAYKSQLSCVVVDD T0332 90 :TAKS 1d2nA 620 :VPIG T0332 96 :LTQYCFPEKSLLLLGNER 1d2nA 638 :LKKAPPQGRKLLIIGTTS T0332 117 :PANLIQ 1d2nA 656 :RKDVLQ T0332 123 :QLDVCVEIPQ 1d2nA 668 :AFSTTIHVPN Number of specific fragments extracted= 6 number of extra gaps= 0 total=339 Number of alignments=42 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1nxzA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1nxzA expands to /projects/compbio/data/pdb/1nxz.pdb.gz 1nxzA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0332 read from 1nxzA/merged-good-all-a2m # 1nxzA read from 1nxzA/merged-good-all-a2m # adding 1nxzA to template set # found chain 1nxzA in template set T0332 6 :SRLIVVASLIDKPTNLGGLCR 1nxzA 78 :LKIHLGQVISRGERMEFTIQK T0332 28 :CEVFGASVLV 1nxzA 99 :SVELGVNVIT T0332 38 :VGSLQC 1nxzA 110 :LWSERC T0332 44 :ISDKQFQHLSVSAEQ 1nxzA 119 :LDAERMDKKIQQWQK T0332 59 :WLPLVEVK 1nxzA 147 :VPEIRPLM T0332 69 :QLIDYLQ 1nxzA 155 :KLQDWCA T0332 78 :KTEGYTIIGVE 1nxzA 162 :ENDGALKLNLH T0332 90 :TAKSLDLTQY 1nxzA 173 :PRAHYSIKTL T0332 100 :CF 1nxzA 184 :TI T0332 102 :PEKSLLLLGNER 1nxzA 187 :AGGVRLLIGSEG T0332 115 :GIPANLIQQLDV 1nxzA 199 :GLSAQEIAQTEQ T0332 128 :VEIPQQGI 1nxzA 214 :TEILLGKR T0332 136 :IRSLNVHVSGALLI 1nxzA 223 :LRTETASLAAISAL T0332 153 :TRQ 1nxzA 237 :QIC Number of specific fragments extracted= 14 number of extra gaps= 0 total=353 Number of alignments=43 # 1nxzA read from 1nxzA/merged-good-all-a2m # found chain 1nxzA in template set T0332 5 :ISRLIVVASLIDKPTNLGGLCRTCE 1nxzA 77 :HLKIHLGQVISRGERMEFTIQKSVE T0332 31 :FGASVLVVGSLQ 1nxzA 102 :LGVNVITPLWSE T0332 43 :CIS 1nxzA 115 :CGV T0332 46 :DKQ 1nxzA 120 :DAE T0332 49 :FQHLSVSAEQW 1nxzA 124 :MDKKIQQWQKI T0332 60 :LPLVEVK 1nxzA 148 :PEIRPLM T0332 69 :QLIDYLQ 1nxzA 155 :KLQDWCA T0332 78 :KTEGYTIIGVE 1nxzA 162 :ENDGALKLNLH T0332 90 :TAKSLDLTQYC 1nxzA 173 :PRAHYSIKTLP T0332 101 :F 1nxzA 185 :I T0332 102 :PEKSLLLLGNER 1nxzA 187 :AGGVRLLIGSEG T0332 115 :GIPANLIQQL 1nxzA 199 :GLSAQEIAQT T0332 126 :V 1nxzA 214 :T T0332 129 :EIPQQGI 1nxzA 215 :EILLGKR T0332 136 :IRSLNVHVSGALLIWEY 1nxzA 223 :LRTETASLAAISALQIC Number of specific fragments extracted= 15 number of extra gaps= 0 total=368 Number of alignments=44 # 1nxzA read from 1nxzA/merged-good-all-a2m # found chain 1nxzA in template set T0332 3 :KSISRLIVVASLIDKPT 1nxzA 75 :ESHLKIHLGQVISRGER T0332 23 :GLCRTCEVFGASVLVVGS 1nxzA 94 :FTIQKSVELGVNVITPLW T0332 41 :LQCISDKQFQHL 1nxzA 115 :CGVKLDAERMDK T0332 53 :SVSAEQWLPLVEVKPPQLIDYLQQ 1nxzA 139 :CEQCGRNIVPEIRPLMKLQDWCAE T0332 79 :TEGYTIIGVE 1nxzA 163 :NDGALKLNLH T0332 90 :TAKSLDLTQY 1nxzA 173 :PRAHYSIKTL T0332 102 :PEKSLLLLGNER 1nxzA 187 :AGGVRLLIGSEG T0332 115 :GIPANLIQQL 1nxzA 199 :GLSAQEIAQT T0332 125 :DVCVEIPQQG 1nxzA 211 :QGFTEILLGK T0332 135 :IIRSLNVHVSGALLIWEY 1nxzA 222 :VLRTETASLAAISALQIC Number of specific fragments extracted= 10 number of extra gaps= 0 total=378 Number of alignments=45 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1h1yA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1h1yA expands to /projects/compbio/data/pdb/1h1y.pdb.gz 1h1yA:# T0332 read from 1h1yA/merged-good-all-a2m # 1h1yA read from 1h1yA/merged-good-all-a2m # adding 1h1yA to template set # found chain 1h1yA in template set T0332 6 :SRLIVVASLIDKPTN 1h1yA 63 :KAYLDCHLMVTNPSD T0332 28 :CEVFGASVLVVG 1h1yA 82 :LAKAGASGFTFH T0332 57 :EQWL 1h1yA 94 :IEVS T0332 67 :PPQLIDYLQQKKTEGYTIIGVEQ 1h1yA 98 :RDNWQELIQSIKAKGMRPGVSLR T0332 92 :KSLDLTQY 1h1yA 121 :PGTPVEEV T0332 100 :CFPE 1h1yA 133 :EAEN T0332 104 :KSLLLL 1h1yA 139 :ELVLVM Number of specific fragments extracted= 7 number of extra gaps= 0 total=385 Number of alignments=46 # 1h1yA read from 1h1yA/merged-good-all-a2m # found chain 1h1yA in template set T0332 6 :SRL 1h1yA 64 :AYL T0332 10 :VVASLIDKPTN 1h1yA 67 :DCHLMVTNPSD T0332 21 :LGG 1h1yA 79 :VEP T0332 28 :CEVFGASVLVVG 1h1yA 82 :LAKAGASGFTFH T0332 57 :EQWL 1h1yA 94 :IEVS T0332 67 :PPQLIDYLQQKKTEGYTIIGVEQ 1h1yA 98 :RDNWQELIQSIKAKGMRPGVSLR T0332 92 :KSLDLTQ 1h1yA 121 :PGTPVEE T0332 100 :CFPEKSLLLLGNEREGIPANLIQQ 1h1yA 169 :KYPSLDIEVDGGLGPSTIDVAASA T0332 124 :LDVCV 1h1yA 194 :ANCIV Number of specific fragments extracted= 9 number of extra gaps= 0 total=394 Number of alignments=47 # 1h1yA read from 1h1yA/merged-good-all-a2m # found chain 1h1yA in template set T0332 4 :SISRLIVVAS 1h1yA 62 :TKAYLDCHLM T0332 15 :IDKPT 1h1yA 72 :VTNPS T0332 27 :TCEVFGASVLVVGSLQCI 1h1yA 81 :PLAKAGASGFTFHIEVSR T0332 68 :PQLIDYLQQKKTEGYTIIGVEQTA 1h1yA 99 :DNWQELIQSIKAKGMRPGVSLRPG T0332 94 :LDLTQY 1h1yA 123 :TPVEEV T0332 100 :CFPE 1h1yA 133 :EAEN T0332 104 :KSLLLLG 1h1yA 139 :ELVLVMT Number of specific fragments extracted= 7 number of extra gaps= 0 total=401 Number of alignments=48 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1v2xA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0332 read from 1v2xA/merged-good-all-a2m # 1v2xA read from 1v2xA/merged-good-all-a2m # found chain 1v2xA in training set T0332 5 :ISRLIVVASLIDKPTNLGGLCRTCEVFGASVLVVGSLQC 1v2xA 20 :QPDLTVLLENVHKPHNLSAILRTCDAVGVLEAHAVNPTG T0332 44 :ISD 1v2xA 60 :VPT T0332 52 :LSVSAEQWLPLVEVK 1v2xA 66 :TSGGSHKWVYLRVHP T0332 69 :QLIDYLQQKKTEGYTIIGVEQTAKSLDLTQYCFPEKSLLLLGNEREGIPANLIQQLDVCVEIPQQGIIRSLNVHVSGALLIWEYTRQQL 1v2xA 81 :DLHEAFRFLKERGFTVYATALREDARDFREVDYTKPTAVLFGAEKWGVSEEALALADGAIKIPMLGMVQSLNVSVAAAVILFEAQRQRL Number of specific fragments extracted= 4 number of extra gaps= 0 total=405 Number of alignments=49 # 1v2xA read from 1v2xA/merged-good-all-a2m # found chain 1v2xA in training set T0332 5 :ISRLIVVASLIDKPTNLGGLCRTCEVFGASVLVVGSLQ 1v2xA 20 :QPDLTVLLENVHKPHNLSAILRTCDAVGVLEAHAVNPT T0332 43 :CISDK 1v2xA 61 :PTFNE T0332 52 :LSVSAEQWLPLVEVK 1v2xA 66 :TSGGSHKWVYLRVHP T0332 69 :QLIDYLQQKKTEGYTIIGVEQTAKSLDLTQYCFPEKSLLLLGNEREGIPANLIQQLDVCVEIPQQGIIRSLNVHVSGALLIWEYTRQQL 1v2xA 81 :DLHEAFRFLKERGFTVYATALREDARDFREVDYTKPTAVLFGAEKWGVSEEALALADGAIKIPMLGMVQSLNVSVAAAVILFEAQRQRL Number of specific fragments extracted= 4 number of extra gaps= 0 total=409 Number of alignments=50 # 1v2xA read from 1v2xA/merged-good-all-a2m # found chain 1v2xA in training set T0332 2 :GKSISRLIVVASLIDKPTNLGGLCRTCEVFGASVLVVGSLQCISDK 1v2xA 17 :RRRQPDLTVLLENVHKPHNLSAILRTCDAVGVLEAHAVNPTGGVPT T0332 51 :HL 1v2xA 64 :NE T0332 54 :VSAEQWLPLVEVKPPQLIDYLQQKKTEGYTIIGVEQTAKSLDLTQYCFPEKSLLLLGNEREGIPANLIQQLDVCVEIPQQGIIRSLNVHVSGALLIWEYTRQQ 1v2xA 66 :TSGGSHKWVYLRVHPDLHEAFRFLKERGFTVYATALREDARDFREVDYTKPTAVLFGAEKWGVSEEALALADGAIKIPMLGMVQSLNVSVAAAVILFEAQRQR Number of specific fragments extracted= 3 number of extra gaps= 0 total=412 Number of alignments=51 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ipaA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1ipaA expands to /projects/compbio/data/pdb/1ipa.pdb.gz 1ipaA:# T0332 read from 1ipaA/merged-good-all-a2m # 1ipaA read from 1ipaA/merged-good-all-a2m # adding 1ipaA to template set # found chain 1ipaA in template set Warning: unaligning (T0332)L158 because last residue in template chain is (1ipaA)L263 T0332 3 :KSISRLIVVASLIDKPTNLGGLCRTCEVFGASVLVVGSLQCISDKQFQHLSVSAEQWLPLVEVKPPQLIDYLQ 1ipaA 112 :PSPDALILVAVGLEKPGNLGAVLRSADAAGAEAVLVAGGVDLYSPQVIRNSTGVVFSLRTLAASESEVLDWIK T0332 79 :TEGYTIIGVE 1ipaA 185 :QHNLPLVATT T0332 90 :TAKSLDLTQYCFPEKSLLLLGNEREGIPANLIQQLDVCVEIPQQGIIRSLNVHVSGALLIWEYTRQQL 1ipaA 195 :PHAEALYWEANLRPPVAIAVGPEHEGLRAAWLEAAQTQVRIPMQGQADSLNVSVSAALLLYEALRQRL Number of specific fragments extracted= 3 number of extra gaps= 0 total=415 Number of alignments=52 # 1ipaA read from 1ipaA/merged-good-all-a2m # found chain 1ipaA in template set Warning: unaligning (T0332)L158 because last residue in template chain is (1ipaA)L263 T0332 2 :GKSISRLIVVASLIDKPTNLGGLCRTCEVFGASVLVVGSLQCISDKQFQHLSVSAEQWLPLVEVKPPQLIDYL 1ipaA 111 :RPSPDALILVAVGLEKPGNLGAVLRSADAAGAEAVLVAGGVDLYSPQVIRNSTGVVFSLRTLAASESEVLDWI T0332 78 :KTEGYTIIGVE 1ipaA 184 :KQHNLPLVATT T0332 90 :TAKSLDLTQYCFPEKSLLLLGNEREGIPANLIQQLDVCVEIPQQGIIRSLNVHVSGALLIWEYTRQQL 1ipaA 195 :PHAEALYWEANLRPPVAIAVGPEHEGLRAAWLEAAQTQVRIPMQGQADSLNVSVSAALLLYEALRQRL Number of specific fragments extracted= 3 number of extra gaps= 0 total=418 Number of alignments=53 # 1ipaA read from 1ipaA/merged-good-all-a2m # found chain 1ipaA in template set Warning: unaligning (T0332)L158 because last residue in template chain is (1ipaA)L263 T0332 3 :KSISRLIVVASLIDKPTNLGGLCRTCEVFGASVLVVGS 1ipaA 112 :PSPDALILVAVGLEKPGNLGAVLRSADAAGAEAVLVAG T0332 42 :QCISDKQFQHL 1ipaA 150 :GVDLYSPQVIR T0332 54 :VSAEQWLPLVEVKP 1ipaA 161 :NSTGVVFSLRTLAA T0332 69 :QLIDYLQQKKTEGYTIIGVE 1ipaA 175 :SESEVLDWIKQHNLPLVATT T0332 90 :TAKSLDLTQYCFPEKSLLLLGNEREGIPANLIQQLDVCVEIPQQGIIRSLNVHVSGALLIWEYTRQQL 1ipaA 195 :PHAEALYWEANLRPPVAIAVGPEHEGLRAAWLEAAQTQVRIPMQGQADSLNVSVSAALLLYEALRQRL Number of specific fragments extracted= 5 number of extra gaps= 0 total=423 Number of alignments=54 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2aq8A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2aq8A expands to /projects/compbio/data/pdb/2aq8.pdb.gz 2aq8A:# T0332 read from 2aq8A/merged-good-all-a2m # 2aq8A read from 2aq8A/merged-good-all-a2m # adding 2aq8A to template set # found chain 2aq8A in template set Warning: unaligning (T0332)V35 because of BadResidue code BAD_PEPTIDE in next template residue (2aq8A)V37 Warning: unaligning (T0332)L36 because of BadResidue code BAD_PEPTIDE at template residue (2aq8A)V37 T0332 7 :RLIVVASLIDKPTNLG 2aq8A 7 :GKRILVSGIITDSSIA T0332 23 :GLCRTCEVFGAS 2aq8A 24 :HIARVAQEQGAQ T0332 37 :VVGSLQ 2aq8A 38 :LTGFDR T0332 46 :DKQFQHLSVSAEQWLPLVEVK 2aq8A 44 :LRLIQRITDRLPAKAPLLELD T0332 67 :PPQLIDYLQQKKTEGYTIIGV 2aq8A 71 :LASLAGRVTEAIGAGNKLDGV T0332 88 :EQTAKS 2aq8A 97 :FMPQTG T0332 94 :LDLTQY 2aq8A 106 :NPFFDA T0332 102 :P 2aq8A 112 :P T0332 103 :EKSLLLLGN 2aq8A 141 :GGSIVGMDF T0332 131 :PQQGIIRSLNVHVSGALLIWEYTRQ 2aq8A 150 :DPSRAMPAYNWMTVAKSALESVNRF Number of specific fragments extracted= 10 number of extra gaps= 1 total=433 Number of alignments=55 # 2aq8A read from 2aq8A/merged-good-all-a2m # found chain 2aq8A in template set Warning: unaligning (T0332)V35 because of BadResidue code BAD_PEPTIDE in next template residue (2aq8A)V37 Warning: unaligning (T0332)L36 because of BadResidue code BAD_PEPTIDE at template residue (2aq8A)V37 T0332 7 :RLIVVASLIDKPTNLG 2aq8A 7 :GKRILVSGIITDSSIA T0332 23 :GLCRTCEVFGAS 2aq8A 24 :HIARVAQEQGAQ T0332 37 :VVG 2aq8A 38 :LTG T0332 43 :CISDKQFQHLSVSAEQWLPLVEVK 2aq8A 41 :FDRLRLIQRITDRLPAKAPLLELD T0332 68 :PQLIDYLQQKKTEGYTIIGV 2aq8A 72 :ASLAGRVTEAIGAGNKLDGV T0332 88 :EQTAKS 2aq8A 97 :FMPQTG T0332 94 :LDLTQ 2aq8A 106 :NPFFD T0332 99 :YCFPEKSLLLLGN 2aq8A 137 :IMNPGGSIVGMDF T0332 131 :PQQGIIRSLNVHVSGALLIWEYTRQ 2aq8A 150 :DPSRAMPAYNWMTVAKSALESVNRF Number of specific fragments extracted= 9 number of extra gaps= 1 total=442 Number of alignments=56 # 2aq8A read from 2aq8A/merged-good-all-a2m # found chain 2aq8A in template set Warning: unaligning (T0332)V35 because of BadResidue code BAD_PEPTIDE in next template residue (2aq8A)V37 Warning: unaligning (T0332)L36 because of BadResidue code BAD_PEPTIDE at template residue (2aq8A)V37 T0332 7 :RLIVVASLIDKPTNLG 2aq8A 7 :GKRILVSGIITDSSIA T0332 23 :GLCRTCEVFGAS 2aq8A 24 :HIARVAQEQGAQ T0332 37 :VVGS 2aq8A 38 :LTGF T0332 45 :SDKQFQHL 2aq8A 42 :DRLRLIQR T0332 54 :VSAEQWLPLVEVKPP 2aq8A 50 :ITDRLPAKAPLLELD T0332 70 :LIDYLQQKKTEGYTIIGVEQ 2aq8A 74 :LAGRVTEAIGAGNKLDGVVH T0332 90 :TAKS 2aq8A 99 :PQTG T0332 94 :LDLTQYCF 2aq8A 106 :NPFFDAPY T0332 102 :PEKSLLLLGN 2aq8A 140 :PGGSIVGMDF T0332 131 :PQQGIIRSLNVHVSGALLIWEYTR 2aq8A 150 :DPSRAMPAYNWMTVAKSALESVNR Number of specific fragments extracted= 10 number of extra gaps= 1 total=452 Number of alignments=57 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1zjrA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1zjrA expands to /projects/compbio/data/pdb/1zjr.pdb.gz 1zjrA:# T0332 read from 1zjrA/merged-good-all-a2m # 1zjrA read from 1zjrA/merged-good-all-a2m # adding 1zjrA to template set # found chain 1zjrA in template set T0332 6 :SRLIVVASLIDKPTNLGGLCRTCEVFGASVLVVGSL 1zjrA 24 :KDLIVFADNVKNEHNFSAIVRTCDAVGVLYLYYYHA T0332 42 :QC 1zjrA 63 :KA T0332 44 :ISDKQ 1zjrA 66 :INEGI T0332 53 :SVSAEQWLPLVEVK 1zjrA 71 :TQGSHKWVFIEKVD T0332 69 :QLIDYLQQKKTEGYTIIGVEQTAKSLDLTQYCFPEKSLLLLGNEREGIPANLIQQLDVCVEIPQQGIIRSLNVHVSGALLIWEYTRQQL 1zjrA 85 :NPVQKLLEFKNRGFQIVATWLSKESVNFREVDYTKPTVLVVGNELQGVSPEIVEIADKKIVIPMYGMAQSLNVSVATGIILYEAQRQRE Number of specific fragments extracted= 5 number of extra gaps= 0 total=457 Number of alignments=58 # 1zjrA read from 1zjrA/merged-good-all-a2m # found chain 1zjrA in template set T0332 6 :SRLIVVASLIDKPTNLGGLCRTCEVFGASVLVVG 1zjrA 24 :KDLIVFADNVKNEHNFSAIVRTCDAVGVLYLYYY T0332 40 :SLQCISDKQ 1zjrA 61 :GKKAKINEG T0332 52 :LSVSAEQWLPLVEVK 1zjrA 70 :ITQGSHKWVFIEKVD T0332 69 :QLIDYLQQKKTEGYTIIGVEQTAKSLDLTQYCFPEKSLLLLGNEREGIPANLIQQLDVCVEIPQQGIIRSLNVHVSGALLIWEYTRQQL 1zjrA 85 :NPVQKLLEFKNRGFQIVATWLSKESVNFREVDYTKPTVLVVGNELQGVSPEIVEIADKKIVIPMYGMAQSLNVSVATGIILYEAQRQRE Number of specific fragments extracted= 4 number of extra gaps= 0 total=461 Number of alignments=59 # 1zjrA read from 1zjrA/merged-good-all-a2m # found chain 1zjrA in template set T0332 2 :GKSISRLIVVASLIDKPTNLGGLCRTCEVFGASVLVVG 1zjrA 20 :EKRQKDLIVFADNVKNEHNFSAIVRTCDAVGVLYLYYY T0332 40 :SLQCISDKQ 1zjrA 61 :GKKAKINEG T0332 54 :VSAEQWLPLVEVKPPQLIDYLQQKKTEGYTIIGVEQTAKSLDLTQYCFPEKSLLLLGNEREGIPANLIQQLDVCVEIPQQGIIRSLNVHVSGALLIWEYTRQQ 1zjrA 70 :ITQGSHKWVFIEKVDNPVQKLLEFKNRGFQIVATWLSKESVNFREVDYTKPTVLVVGNELQGVSPEIVEIADKKIVIPMYGMAQSLNVSVATGIILYEAQRQR Number of specific fragments extracted= 3 number of extra gaps= 0 total=464 Number of alignments=60 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1dbiA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1dbiA expands to /projects/compbio/data/pdb/1dbi.pdb.gz 1dbiA:Skipped atom 258, because occupancy 1.000 <= existing 1.000 in 1dbiA Skipped atom 1059, because occupancy 1.000 <= existing 1.000 in 1dbiA Skipped atom 1061, because occupancy 1.000 <= existing 1.000 in 1dbiA Skipped atom 1591, because occupancy 1.000 <= existing 1.000 in 1dbiA Skipped atom 1673, because occupancy 1.000 <= existing 1.000 in 1dbiA Skipped atom 1675, because occupancy 1.000 <= existing 1.000 in 1dbiA Skipped atom 1677, because occupancy 1.000 <= existing 1.000 in 1dbiA Skipped atom 1702, because occupancy 1.000 <= existing 1.000 in 1dbiA Skipped atom 1704, because occupancy 1.000 <= existing 1.000 in 1dbiA Skipped atom 1706, because occupancy 1.000 <= existing 1.000 in 1dbiA # T0332 read from 1dbiA/merged-good-all-a2m # 1dbiA read from 1dbiA/merged-good-all-a2m # adding 1dbiA to template set # found chain 1dbiA in template set Warning: unaligning (T0332)A91 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1dbiA)S175 Warning: unaligning (T0332)F101 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1dbiA)S175 T0332 6 :SRLIVVASLIDKP 1dbiA 95 :PNTRILAVRALDR T0332 19 :TNLGGLCRTCEVFGASVLVVGSLQCISDK 1dbiA 114 :SDIADAIIYAADSGAEVINLSLGCDCHTT T0332 69 :QLIDYLQQKKTEGYTIIGVEQT 1dbiA 143 :TLENAVNYAWNKGSVVVAAAGN T0332 102 :PEKSLLLLG 1dbiA 176 :YENVIAVGA T0332 111 :NEREGIPA 1dbiA 186 :DQYDRLAS T0332 123 :QLDV 1dbiA 194 :FSNY T0332 127 :CVEIPQQG 1dbiA 202 :DVVAPGVD T0332 136 :IRSLNVHVSGALLIWEYTRQQLLS 1dbiA 222 :MSGTSMASPHVAGLAALLASQGRN Number of specific fragments extracted= 8 number of extra gaps= 0 total=472 Number of alignments=61 # 1dbiA read from 1dbiA/merged-good-all-a2m # found chain 1dbiA in template set Warning: unaligning (T0332)A91 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1dbiA)S175 Warning: unaligning (T0332)F101 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1dbiA)S175 T0332 6 :SRLIVVASLIDKPT 1dbiA 95 :PNTRILAVRALDRN T0332 20 :NLGGLCRTCEVFGASVLVVGSLQCIS 1dbiA 115 :DIADAIIYAADSGAEVINLSLGCDCH T0332 67 :PPQLIDYLQQKKTEGYTIIGVEQT 1dbiA 141 :TTTLENAVNYAWNKGSVVVAAAGN T0332 102 :PEKSLLLLGNEREG 1dbiA 176 :YENVIAVGAVDQYD T0332 116 :IPA 1dbiA 191 :LAS T0332 123 :QLDV 1dbiA 194 :FSNY T0332 127 :CVEIPQQGI 1dbiA 202 :DVVAPGVDI T0332 136 :IRSLNVHVSGALLIWEYTRQQLL 1dbiA 222 :MSGTSMASPHVAGLAALLASQGR Number of specific fragments extracted= 8 number of extra gaps= 0 total=480 Number of alignments=62 # 1dbiA read from 1dbiA/merged-good-all-a2m # found chain 1dbiA in template set Warning: unaligning (T0332)A91 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1dbiA)S175 Warning: unaligning (T0332)C100 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1dbiA)S175 T0332 6 :SRLIVVASLIDKPT 1dbiA 95 :PNTRILAVRALDRN T0332 20 :NLGGLCRTCEVFGASVLVVGSLQCISDKQ 1dbiA 115 :DIADAIIYAADSGAEVINLSLGCDCHTTT T0332 70 :LIDYLQQKKTEGYTIIGVEQT 1dbiA 144 :LENAVNYAWNKGSVVVAAAGN T0332 101 :FPEKSLLLLGNEREGIPA 1dbiA 176 :YENVIAVGAVDQYDRLAS T0332 123 :QLDV 1dbiA 194 :FSNY T0332 127 :CVEIPQQG 1dbiA 202 :DVVAPGVD T0332 135 :IIRSLNVHVSGALLIWEYTRQQLLS 1dbiA 221 :YMSGTSMASPHVAGLAALLASQGRN Number of specific fragments extracted= 7 number of extra gaps= 0 total=487 Number of alignments=63 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1vhyA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1vhyA expands to /projects/compbio/data/pdb/1vhy.pdb.gz 1vhyA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 679, because occupancy 0.350 <= existing 0.650 in 1vhyA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 681, because occupancy 0.350 <= existing 0.650 in 1vhyA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 683, because occupancy 0.350 <= existing 0.650 in 1vhyA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 685, because occupancy 0.350 <= existing 0.650 in 1vhyA Skipped atom 778, because occupancy 0.350 <= existing 0.650 in 1vhyA Skipped atom 780, because occupancy 0.350 <= existing 0.650 in 1vhyA Skipped atom 782, because occupancy 0.350 <= existing 0.650 in 1vhyA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 1831, because occupancy 0.350 <= existing 0.650 in 1vhyA Skipped atom 1833, because occupancy 0.350 <= existing 0.650 in 1vhyA Skipped atom 1835, because occupancy 0.350 <= existing 0.650 in 1vhyA Skipped atom 1837, because occupancy 0.350 <= existing 0.650 in 1vhyA Skipped atom 1839, because occupancy 0.350 <= existing 0.650 in 1vhyA # T0332 read from 1vhyA/merged-good-all-a2m # 1vhyA read from 1vhyA/merged-good-all-a2m # adding 1vhyA to template set # found chain 1vhyA in template set Warning: unaligning (T0332)L14 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1vhyA)R91 Warning: unaligning (T0332)T19 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1vhyA)R91 T0332 6 :SRLIVVAS 1vhyA 78 :LKIHLGQV T0332 20 :NLGGLC 1vhyA 92 :MEFTIQ T0332 27 :TCEVFGASVLVVGSL 1vhyA 98 :KSVELGVNVITPLWS T0332 42 :QC 1vhyA 114 :RC T0332 44 :ISDKQF 1vhyA 119 :LDAERM T0332 50 :QHLSVSAE 1vhyA 132 :QKIAIAAC T0332 58 :QWLPLVEVK 1vhyA 146 :IVPEIRPLM T0332 69 :QLIDYLQ 1vhyA 155 :KLQDWCA T0332 78 :KTEGYTIIGVE 1vhyA 162 :ENDGALKLNLH T0332 90 :TAKSLDLTQY 1vhyA 173 :PRAHYSIKTL T0332 100 :CFPEKSLLLLGNE 1vhyA 185 :IPAGGVRLLIGSE T0332 114 :EGIPANLIQQL 1vhyA 198 :GGLSAQEIAQT T0332 128 :VEIPQQGI 1vhyA 214 :TEILLGKR T0332 136 :IRSLNVHVSGALLIWE 1vhyA 223 :LRTETASLAAISALQI Number of specific fragments extracted= 14 number of extra gaps= 0 total=501 Number of alignments=64 # 1vhyA read from 1vhyA/merged-good-all-a2m # found chain 1vhyA in template set Warning: unaligning (T0332)L14 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1vhyA)R91 Warning: unaligning (T0332)T19 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1vhyA)R91 T0332 5 :ISRLIVVAS 1vhyA 77 :HLKIHLGQV T0332 20 :NLGGLCRTCE 1vhyA 92 :MEFTIQKSVE T0332 31 :FGASVLVVG 1vhyA 102 :LGVNVITPL T0332 40 :SLQCISDKQ 1vhyA 114 :RCGVKLDAE T0332 49 :FQHLSVSAE 1vhyA 131 :WQKIAIAAC T0332 58 :QWLPLVEVK 1vhyA 146 :IVPEIRPLM T0332 69 :QLIDYLQ 1vhyA 155 :KLQDWCA T0332 78 :KTEGYTIIGVE 1vhyA 162 :ENDGALKLNLH T0332 90 :TAKSLDLTQYC 1vhyA 173 :PRAHYSIKTLP T0332 101 :FPEKSLLLLGNER 1vhyA 186 :PAGGVRLLIGSEG T0332 115 :GIPANLIQQL 1vhyA 199 :GLSAQEIAQT T0332 126 :VCVEIP 1vhyA 214 :TEILLG T0332 133 :QGIIRSLNVHVSGALLIWEYT 1vhyA 220 :KRVLRTETASLAAISALQICF Number of specific fragments extracted= 13 number of extra gaps= 0 total=514 Number of alignments=65 # 1vhyA read from 1vhyA/merged-good-all-a2m # found chain 1vhyA in template set Warning: unaligning (T0332)L14 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1vhyA)R91 Warning: unaligning (T0332)T19 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1vhyA)R91 T0332 3 :KSISRLIVVAS 1vhyA 75 :ESHLKIHLGQV T0332 20 :NLGGL 1vhyA 92 :MEFTI T0332 26 :RTCEVFGASVLVVGSLQCISDK 1vhyA 97 :QKSVELGVNVITPLWSERCGVK T0332 48 :QFQ 1vhyA 122 :ERM T0332 51 :HLSVSAEQWLPLVEVKPPQLIDYLQQ 1vhyA 137 :AACEQCGRNIVPEIRPLMKLQDWCAE T0332 79 :TEGYTIIGVE 1vhyA 163 :NDGALKLNLH T0332 90 :TAKSLDLTQY 1vhyA 173 :PRAHYSIKTL T0332 100 :CFPEKSLLLLGNER 1vhyA 185 :IPAGGVRLLIGSEG T0332 115 :GIPANLIQQL 1vhyA 199 :GLSAQEIAQT T0332 125 :DVCVEIPQQG 1vhyA 211 :QGFTEILLGK T0332 135 :IIRSLNVHVSGALLIWE 1vhyA 222 :VLRTETASLAAISALQI Number of specific fragments extracted= 11 number of extra gaps= 0 total=525 Number of alignments=66 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1o6dA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0332 read from 1o6dA/merged-good-all-a2m # 1o6dA read from 1o6dA/merged-good-all-a2m # found chain 1o6dA in training set Warning: unaligning (T0332)S6 because first residue in template chain is (1o6dA)L1 T0332 7 :RLIVVASLIDKPTNLGGLCRTCEVFG 1o6dA 2 :RVRIAVIGKLDGFIKEGIKHYEKFLR T0332 34 :S 1o6dA 31 :K T0332 35 :VLVVGSLQC 1o6dA 33 :EVLEIKRVH T0332 44 :ISDKQFQHLSVSAEQWL 1o6dA 44 :SIEEIVRKETEDLTNRI T0332 61 :PLVEVKPPQLIDYLQQKKTEG 1o6dA 72 :RGEEVSSEEFADFLKDLEMKG T0332 103 :EKSLLLLGN 1o6dA 93 :KDITILIGG T0332 113 :REGIPANLIQQLDVCVEIPQQGI 1o6dA 102 :PYGLNEEIFAKAHRVFSLSKMTF T0332 141 :VHVSGALLIWEYTRQQLL 1o6dA 126 :HGMTVLIVLEQIFRAFKI Number of specific fragments extracted= 8 number of extra gaps= 0 total=533 Number of alignments=67 # 1o6dA read from 1o6dA/merged-good-all-a2m # found chain 1o6dA in training set Warning: unaligning (T0332)S6 because first residue in template chain is (1o6dA)L1 T0332 7 :RLIVVASLI 1o6dA 2 :RVRIAVIGK T0332 45 :SDKQFQHLSVSAEQW 1o6dA 11 :LDGFIKEGIKHYEKF T0332 60 :LPLVEVK 1o6dA 32 :PEVLEIK T0332 67 :PPQLID 1o6dA 45 :IEEIVR T0332 73 :YLQQKKTE 1o6dA 52 :ETEDLTNR T0332 81 :GYTIIGVEQTAKSLDLTQ 1o6dA 63 :GSFVMVMDKRGEEVSSEE T0332 102 :PEKSLLLLGN 1o6dA 92 :GKDITILIGG T0332 113 :REGIPANLIQQLDVCVEIPQQGI 1o6dA 102 :PYGLNEEIFAKAHRVFSLSKMTF T0332 141 :VHVSGALLIWEYTRQQLL 1o6dA 126 :HGMTVLIVLEQIFRAFKI Number of specific fragments extracted= 9 number of extra gaps= 0 total=542 Number of alignments=68 # 1o6dA read from 1o6dA/merged-good-all-a2m # found chain 1o6dA in training set T0332 8 :LIVVA 1o6dA 3 :VRIAV T0332 38 :VGSLQCISDKQFQHLSVSAEQWLPLVEVKPPQ 1o6dA 8 :IGKLDGFIKEGIKHYEKFLRRFCKPEVLEIKR T0332 70 :LIDYLQQKKTE 1o6dA 49 :VRKETEDLTNR T0332 81 :GYTIIGVEQTAKSLDLTQY 1o6dA 63 :GSFVMVMDKRGEEVSSEEF T0332 102 :PEKSLLLLGN 1o6dA 92 :GKDITILIGG T0332 113 :REGIPANLIQQLDVCVEIPQQG 1o6dA 102 :PYGLNEEIFAKAHRVFSLSKMT T0332 141 :VHVSGALLIWEYTRQQ 1o6dA 126 :HGMTVLIVLEQIFRAF Number of specific fragments extracted= 7 number of extra gaps= 0 total=549 Number of alignments=69 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ns5A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0332 read from 1ns5A/merged-good-all-a2m # 1ns5A read from 1ns5A/merged-good-all-a2m # found chain 1ns5A in training set T0332 7 :RLIVVASL 1ns5A 2 :KLQLVAVG T0332 41 :LQ 1ns5A 10 :TK T0332 45 :SDKQFQHLSVSAEQWLP 1ns5A 12 :MPDWVQTGFTEYLRRFP T0332 62 :LVEVK 1ns5A 35 :LIEIP T0332 67 :PPQLIDYLQQKK 1ns5A 53 :LDKEGEQMLAAA T0332 80 :EGYTIIGVEQTA 1ns5A 65 :GKNRIVTLDIPG T0332 99 :YCFP 1ns5A 77 :KPWD T0332 103 :EKSLLLLGN 1ns5A 96 :RDVSLLIGG T0332 113 :REGIPANLIQQLDVCVEIPQQG 1ns5A 105 :PEGLSPACKAAAEQSWSLSALT T0332 136 :IRSLNVHVSGALLIWEYTRQQLL 1ns5A 127 :LPHPLVRVLVAESLYRAWSITTN Number of specific fragments extracted= 10 number of extra gaps= 0 total=559 Number of alignments=70 # 1ns5A read from 1ns5A/merged-good-all-a2m # found chain 1ns5A in training set T0332 7 :RLIVVASLI 1ns5A 2 :KLQLVAVGT T0332 44 :ISDKQFQHLSVSAEQW 1ns5A 11 :KMPDWVQTGFTEYLRR T0332 60 :LPLVEVK 1ns5A 33 :FELIEIP T0332 70 :LIDYLQQKKT 1ns5A 53 :LDKEGEQMLA T0332 80 :EGYTIIGVEQTAKSLDLTQ 1ns5A 65 :GKNRIVTLDIPGKPWDTPQ T0332 102 :PEKSLLLLGN 1ns5A 95 :GRDVSLLIGG T0332 113 :REGIPANLIQQLDVCVEIPQQGIIRSL 1ns5A 105 :PEGLSPACKAAAEQSWSLSALTLPHPL T0332 141 :VHVSGALLIWEYTRQQLL 1ns5A 132 :VRVLVAESLYRAWSITTN Number of specific fragments extracted= 8 number of extra gaps= 0 total=567 Number of alignments=71 # 1ns5A read from 1ns5A/merged-good-all-a2m # found chain 1ns5A in training set T0332 35 :VLVVGSLQCISDKQFQ 1ns5A 4 :QLVAVGTKMPDWVQTG T0332 52 :LSVSAEQWL 1ns5A 20 :FTEYLRRFP T0332 61 :PLVEVKPPQ 1ns5A 32 :PFELIEIPA T0332 70 :LIDYLQQKKT 1ns5A 53 :LDKEGEQMLA T0332 80 :EGYTIIGVEQTAKSLDLTQY 1ns5A 65 :GKNRIVTLDIPGKPWDTPQL T0332 102 :PEKSLLLLGN 1ns5A 95 :GRDVSLLIGG T0332 113 :REGIPANLIQQLDVCVEIPQQGIIRSL 1ns5A 105 :PEGLSPACKAAAEQSWSLSALTLPHPL T0332 141 :VHVSGALLIWEYTR 1ns5A 132 :VRVLVAESLYRAWS Number of specific fragments extracted= 8 number of extra gaps= 0 total=575 Number of alignments=72 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1nsf/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1nsf expands to /projects/compbio/data/pdb/1nsf.pdb.gz 1nsf:Warning: there is no chain 1nsf will retry with 1nsfA # T0332 read from 1nsf/merged-good-all-a2m # 1nsf read from 1nsf/merged-good-all-a2m # adding 1nsf to template set # found chain 1nsf in template set T0332 2 :GKSISRLIVVASLIDKPTNLGGLCRTCEVFGASVLVVGSLQC 1nsf 531 :SDRTPLVSVLLEGPPHSGKTALAAKIAEESNFPFIKICSPDK T0332 44 :ISDKQFQH 1nsf 576 :FSETAKCQ T0332 69 :QLIDYLQQKKTEGYTIIGVE 1nsf 584 :AMKKIFDDAYKSQLSCVVVD T0332 89 :QTAKSLDLT 1nsf 611 :YVPIGPRFS T0332 103 :EKSLLLLGNERE 1nsf 637 :GRKLLIIGTTSR T0332 118 :ANLIQ 1nsf 649 :KDVLQ T0332 123 :QLDVCVEIPQQGIIR 1nsf 660 :AFSTTIHVPNIATGE T0332 148 :LIWEYTRQQLL 1nsf 675 :QLLEALELLGN Number of specific fragments extracted= 8 number of extra gaps= 0 total=583 Number of alignments=73 # 1nsf read from 1nsf/merged-good-all-a2m # found chain 1nsf in template set T0332 2 :GKSISRLIVVASLIDKPTNLGGLCRTCEVFGASVLVVGSLQCIS 1nsf 531 :SDRTPLVSVLLEGPPHSGKTALAAKIAEESNFPFIKICSPDKMI T0332 46 :DKQFQH 1nsf 578 :ETAKCQ T0332 69 :QLIDYLQQKKTEGYTIIGVE 1nsf 584 :AMKKIFDDAYKSQLSCVVVD T0332 89 :QTAKSLDLTQ 1nsf 611 :YVPIGPRFSN T0332 99 :YCFPEKSLLLLGNER 1nsf 633 :APPQGRKLLIIGTTS T0332 117 :PANLIQ 1nsf 648 :RKDVLQ T0332 123 :QLDVCVEIPQQGIIR 1nsf 660 :AFSTTIHVPNIATGE T0332 148 :LIWEYTRQQLL 1nsf 675 :QLLEALELLGN Number of specific fragments extracted= 8 number of extra gaps= 0 total=591 Number of alignments=74 # 1nsf read from 1nsf/merged-good-all-a2m # found chain 1nsf in template set T0332 3 :KSISRLIVVASLIDKPTNLGGLCRTCEVFGASVLVVGSLQCISDKQFQHLSVS 1nsf 532 :DRTPLVSVLLEGPPHSGKTALAAKIAEESNFPFIKICSPDKMIGFSETAKCQA T0332 70 :LIDYLQQKKTEGYTIIGVEQ 1nsf 585 :MKKIFDDAYKSQLSCVVVDD T0332 90 :TAKS 1nsf 612 :VPIG T0332 96 :LTQYCFPEKSLLLLGNERE 1nsf 630 :LKKAPPQGRKLLIIGTTSR T0332 119 :NLIQQLDVCVEIP 1nsf 656 :EMLNAFSTTIHVP Number of specific fragments extracted= 5 number of extra gaps= 0 total=596 Number of alignments=75 # command:# PrintAlignmentsContacts allconstraints.under Using radius: 8.0000 NUMB_ALIGNS: 75 Done printing distance constraints # command: