# 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/T0299/ # command:# Making conformation for sequence T0299 numbered 1 through 180 Created new target T0299 from T0299.a2m # command:# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/T0299/ # command:Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0299//projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0299/manyalignments-good-all.under or /projects/compbio/experiments/protein-predict/casp7/T0299//projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0299/manyalignments-good-all.under.gz for input Trying /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0299/manyalignments-good-all.under # reading script from file /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0299/manyalignments-good-all.under # Reading fragments from alignment file # Attempting to read fragment alignments from file 1z5nA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1z5nA expands to /projects/compbio/data/pdb/1z5n.pdb.gz 1z5nA:# T0299 read from 1z5nA/merged-good-all-a2m # 1z5nA read from 1z5nA/merged-good-all-a2m # adding 1z5nA to template set # found chain 1z5nA in template set T0299 22 :AELRQELTNL 1z5nA 123 :DKLIAAAEAC # choosing archetypes in rotamer library T0299 32 :GLEKVESYINSGNIFFTSIDSKAQLVEK 1z5nA 137 :NLNAVRGLIVSGDAFINGSVGLAKIRHN T0299 68 :Y 1z5nA 165 :F T0299 70 :FIQSFSLLSLEDFEAELEN 1z5nA 166 :PQAIAVEMEATAIAHVCHN T0299 95 :RDLARKDFLFYTEGLD 1z5nA 185 :FNVPFVVVRAISDVAD T0299 111 :VDQVIATVES 1z5nA 207 :FDEFLAVAAK Number of specific fragments extracted= 6 number of extra gaps= 0 total=6 Number of alignments=1 # 1z5nA read from 1z5nA/merged-good-all-a2m # found chain 1z5nA in template set T0299 5 :ALLVRG 1z5nA 43 :VALLKS T0299 15 :GKNKVVMAELRQELTNL 1z5nA 49 :GIGKVAAALGATLLLEH T0299 35 :KVESYINSGNIFFTSID 1z5nA 67 :KPDVIINTGSAGGLAPT T0299 72 :QSFSLLS 1z5nA 87 :GDIVVSD T0299 80 :EDFEAELENLPAWWSRDLARKDFLFYTEGLDVDQVIATVESLE 1z5nA 123 :DKLIAAAEACIAELNLNAVRGLIVSGDAFINGSVGLAKIRHNF T0299 124 :K 1z5nA 166 :P T0299 132 :KLGIFW 1z5nA 167 :QAIAVE T0299 145 :YSKTAYHKYLLKVPFYR 1z5nA 173 :MEATAIAHVCHNFNVPF Number of specific fragments extracted= 8 number of extra gaps= 0 total=14 Number of alignments=2 # 1z5nA read from 1z5nA/merged-good-all-a2m # found chain 1z5nA in template set T0299 54 :AQLVEKLETFFAVH 1z5nA 123 :DKLIAAAEACIAEL T0299 68 :YPFIQSFSLLS 1z5nA 138 :LNAVRGLIVSG T0299 79 :LEDFEAELENLPA 1z5nA 155 :SVGLAKIRHNFPQ T0299 102 :FLFYTE 1z5nA 168 :AIAVEM Number of specific fragments extracted= 4 number of extra gaps= 0 total=18 Number of alignments=3 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1atg/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0299 read from 1atg/merged-good-all-a2m # 1atg read from 1atg/merged-good-all-a2m # found chain 1atg in training set T0299 55 :QLVEKLETFFAVHYPFIQSFSLLSLEDFEAELEN 1atg 13 :GTLEQLAGQFAKQTGHAVVISSGSSGPVYAQIVN T0299 89 :L 1atg 48 :A T0299 99 :RKDFLFYTEG 1atg 49 :PYNVFFSADE T0299 113 :QVIATVESLEL 1atg 59 :KSPEKLDNQGF T0299 124 :KDEVLYFGKLGIFWGKFSEESYSKTAYHK 1atg 73 :GSRFTYAIGKLVLWSAKPGLVDNQGKVLA T0299 156 :KVPFYR 1atg 102 :GNGWRH T0299 163 :ITIRN 1atg 108 :IAISN T0299 168 :AKTFDKIGQMLK 1atg 119 :GLAGTQVLTHLG Number of specific fragments extracted= 8 number of extra gaps= 0 total=26 Number of alignments=4 # 1atg read from 1atg/merged-good-all-a2m # found chain 1atg in training set T0299 55 :QLVEKLETFFAVHYPFIQSFSLLSLEDFEAEL 1atg 13 :GTLEQLAGQFAKQTGHAVVISSGSSGPVYAQI T0299 87 :ENLPA 1atg 46 :NGAPY T0299 101 :DFLFYTEG 1atg 51 :NVFFSADE T0299 113 :QVIATVESLEL 1atg 59 :KSPEKLDNQGF T0299 124 :KDEVLYFGKLGIFWGKFSEESYSKTAY 1atg 73 :GSRFTYAIGKLVLWSAKPGLVDNQGKV T0299 155 :LKVPFYRHITIRN 1atg 100 :LAGNGWRHIAISN Number of specific fragments extracted= 6 number of extra gaps= 0 total=32 Number of alignments=5 # 1atg read from 1atg/merged-good-all-a2m # found chain 1atg in training set T0299 56 :LVEKLETFFAVHYPFIQSFSLLSLEDFEAELEN 1atg 14 :TLEQLAGQFAKQTGHAVVISSGSSGPVYAQIVN T0299 98 :ARKDFLFYTEGLDVDQVIATVESLELKDEVLYFGKLGIFWGKFSEESYSKTA 1atg 47 :GAPYNVFFSADEKSPEKLDNQGFALPGSRFTYAIGKLVLWSAKPGLVDNQGK T0299 154 :LLKVPFYRHITIRN 1atg 99 :VLAGNGWRHIAISN T0299 168 :AKTFDKIGQMLK 1atg 119 :GLAGTQVLTHLG Number of specific fragments extracted= 4 number of extra gaps= 0 total=36 Number of alignments=6 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1xzoA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0299 read from 1xzoA/merged-good-all-a2m # 1xzoA read from 1xzoA/merged-good-all-a2m # found chain 1xzoA in training set Warning: unaligning (T0299)G15 because of BadResidue code BAD_PEPTIDE in next template residue (1xzoA)E46 Warning: unaligning (T0299)K16 because of BadResidue code BAD_PEPTIDE at template residue (1xzoA)E46 Warning: unaligning (T0299)M21 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1xzoA)M56 Warning: unaligning (T0299)E126 because of BadResidue code BAD_PEPTIDE in next template residue (1xzoA)D131 T0299 6 :LLVRGINVG 1xzoA 36 :WLADFIFTN T0299 17 :NKVV 1xzoA 47 :TICP T0299 22 :AELRQELTNLGLE 1xzoA 57 :TDLQKKLKAENID T0299 36 :VESYINSGN 1xzoA 70 :VRIISFSVD T0299 50 :ID 1xzoA 79 :PE T0299 78 :SLEDFEAELENLPAWWSR 1xzoA 83 :KPKQLKKFAANYPLSFDN T0299 103 :LFYTEGLDVDQVIATVES 1xzoA 101 :WDFLTGYSQSEIEEFALK T0299 124 :KD 1xzoA 128 :EG T0299 127 :VLYFGK 1xzoA 139 :FYLVGP T0299 133 :LGIFWGKFSEESYSKTAYHKYL 1xzoA 146 :GKVLKDYNGVENTPYDDIISDV Number of specific fragments extracted= 10 number of extra gaps= 3 total=46 Number of alignments=7 # 1xzoA read from 1xzoA/merged-good-all-a2m # found chain 1xzoA in training set Warning: unaligning (T0299)G15 because of BadResidue code BAD_PEPTIDE in next template residue (1xzoA)E46 Warning: unaligning (T0299)K16 because of BadResidue code BAD_PEPTIDE at template residue (1xzoA)E46 Warning: unaligning (T0299)M21 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1xzoA)M56 Warning: unaligning (T0299)D125 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1xzoA)S137 Warning: unaligning (T0299)E126 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1xzoA)S137 T0299 3 :RYALLV 1xzoA 35 :VWLADF T0299 11 :INVG 1xzoA 41 :IFTN T0299 17 :NKVV 1xzoA 47 :TICP T0299 22 :AELRQELTNLGLE 1xzoA 57 :TDLQKKLKAENID T0299 36 :VESYINSGN 1xzoA 70 :VRIISFSVD T0299 78 :SLEDFEAELENLPAWWSR 1xzoA 83 :KPKQLKKFAANYPLSFDN T0299 103 :LFYTEGLDVDQVIATVESL 1xzoA 101 :WDFLTGYSQSEIEEFALKS T0299 124 :K 1xzoA 135 :H T0299 127 :VLYF 1xzoA 138 :SFYL T0299 131 :GKLGIFWGKFSEESYSKTAYHKYLL 1xzoA 144 :PDGKVLKDYNGVENTPYDDIISDVK Number of specific fragments extracted= 10 number of extra gaps= 3 total=56 Number of alignments=8 # 1xzoA read from 1xzoA/merged-good-all-a2m # found chain 1xzoA in training set Warning: unaligning (T0299)G15 because of BadResidue code BAD_PEPTIDE in next template residue (1xzoA)E46 Warning: unaligning (T0299)K16 because of BadResidue code BAD_PEPTIDE at template residue (1xzoA)E46 Warning: unaligning (T0299)M21 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1xzoA)M56 Warning: unaligning (T0299)E126 because of BadResidue code BAD_PEPTIDE in next template residue (1xzoA)D131 Warning: unaligning (T0299)V127 because of BadResidue code BAD_PEPTIDE at template residue (1xzoA)D131 Warning: unaligning (T0299)L128 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1xzoA)Q132 Warning: unaligning (T0299)Y129 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1xzoA)V133 Warning: unaligning (T0299)K132 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1xzoA)S137 Warning: unaligning (T0299)L133 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1xzoA)S137 T0299 6 :LLVRGINVG 1xzoA 36 :WLADFIFTN T0299 17 :NKVV 1xzoA 47 :TICP T0299 22 :AELRQELTNLGLE 1xzoA 57 :TDLQKKLKAENID T0299 36 :VESYI 1xzoA 70 :VRIIS T0299 47 :FTSID 1xzoA 75 :FSVDP T0299 78 :SLEDFEAELENLPAWWSR 1xzoA 83 :KPKQLKKFAANYPLSFDN T0299 103 :LFYTEGLDVDQVIATVESL 1xzoA 101 :WDFLTGYSQSEIEEFALKS T0299 122 :ELKD 1xzoA 126 :KPEG T0299 130 :FG 1xzoA 134 :IH T0299 134 :GIFWGKFSEES 1xzoA 138 :SFYLVGPDGKV Number of specific fragments extracted= 10 number of extra gaps= 4 total=66 Number of alignments=9 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1w3iA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0299 read from 1w3iA/merged-good-all-a2m # 1w3iA read from 1w3iA/merged-good-all-a2m # found chain 1w3iA in training set Warning: unaligning (T0299)F74 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1w3iA)I70 Warning: unaligning (T0299)S75 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1w3iA)I70 Warning: unaligning (T0299)F104 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1w3iA)Y99 Warning: unaligning (T0299)Y105 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1w3iA)Y99 T0299 5 :ALLVRGINVGGKNKVVMAELRQELTNL 1w3iA 4 :IITPIITPFTKDNRIDKEKLKIHAENL T0299 32 :GL 1w3iA 34 :GI T0299 37 :ESYINSGNIFFTSIDSKAQLV 1w3iA 36 :DKLFVNGTTGLGPSLSPEEKL T0299 62 :TFFAVHYPFIQS 1w3iA 57 :ENLKAVYDVTNK T0299 76 :LL 1w3iA 71 :FQ T0299 78 :SLEDFEAELEN 1w3iA 77 :NLDDAIRLAKL T0299 94 :SRDLARKDFL 1w3iA 88 :SKDFDIVGIA T0299 106 :T 1w3iA 100 :A T0299 107 :EGLDVDQVIATVESLE 1w3iA 105 :PRMSEKHLVKYFKTLC Number of specific fragments extracted= 9 number of extra gaps= 2 total=75 Number of alignments=10 # 1w3iA read from 1w3iA/merged-good-all-a2m # found chain 1w3iA in training set Warning: unaligning (T0299)F74 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1w3iA)I70 Warning: unaligning (T0299)S75 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1w3iA)I70 Warning: unaligning (T0299)F104 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1w3iA)Y99 Warning: unaligning (T0299)Y105 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1w3iA)Y99 T0299 5 :ALLVRGINVGGKNKVVMAELR 1w3iA 4 :IITPIITPFTKDNRIDKEKLK T0299 26 :QELTNLGLEK 1w3iA 28 :ENLIRKGIDK T0299 39 :YINSGNIFFTSIDSKAQL 1w3iA 38 :LFVNGTTGLGPSLSPEEK T0299 61 :ETFFAVHYPFIQS 1w3iA 56 :LENLKAVYDVTNK T0299 76 :LL 1w3iA 71 :FQ T0299 78 :SLEDFEAELEN 1w3iA 77 :NLDDAIRLAKL T0299 94 :SRDLARKDFL 1w3iA 88 :SKDFDIVGIA T0299 106 :T 1w3iA 100 :A T0299 107 :EGLDVDQVIATVESL 1w3iA 105 :PRMSEKHLVKYFKTL Number of specific fragments extracted= 9 number of extra gaps= 2 total=84 Number of alignments=11 # 1w3iA read from 1w3iA/merged-good-all-a2m # found chain 1w3iA in training set Warning: unaligning (T0299)F74 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1w3iA)I70 Warning: unaligning (T0299)S75 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1w3iA)I70 Warning: unaligning (T0299)F104 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1w3iA)Y99 Warning: unaligning (T0299)Y105 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1w3iA)Y99 T0299 5 :ALLVRGINVGGKNKVVMAELR 1w3iA 4 :IITPIITPFTKDNRIDKEKLK T0299 26 :QELTNLGLEK 1w3iA 28 :ENLIRKGIDK T0299 39 :YINSGNIFFTSIDSKAQ 1w3iA 38 :LFVNGTTGLGPSLSPEE T0299 60 :LETFFAVHYPFIQS 1w3iA 55 :KLENLKAVYDVTNK T0299 76 :LL 1w3iA 71 :FQ T0299 78 :SLEDFEAELEN 1w3iA 77 :NLDDAIRLAKL T0299 94 :SRDLARKDFL 1w3iA 88 :SKDFDIVGIA T0299 106 :TE 1w3iA 100 :AP T0299 108 :GLDVDQVIATVESL 1w3iA 106 :RMSEKHLVKYFKTL Number of specific fragments extracted= 9 number of extra gaps= 2 total=93 Number of alignments=12 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1fp1D/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1fp1D expands to /projects/compbio/data/pdb/1fp1.pdb.gz 1fp1D:# T0299 read from 1fp1D/merged-good-all-a2m # 1fp1D read from 1fp1D/merged-good-all-a2m # adding 1fp1D to template set # found chain 1fp1D in template set T0299 23 :ELRQE 1fp1D 199 :RMLEI T0299 32 :GLEKVESYINSGN 1fp1D 206 :GFEGISTLVDVGG T0299 58 :EKLE 1fp1D 222 :RNLE T0299 63 :FFAVHYPFIQSFSLLSLE 1fp1D 226 :LIISKYPLIKGINFDLPQ T0299 85 :ELENLPAWWS 1fp1D 244 :VIENAPPLSG T0299 95 :RDLARKDFLFYTE 1fp1D 263 :ASVPQGDAMILKA T0299 108 :GLDVDQVIATVESLEL 1fp1D 279 :NWSDEKCIEFLSNCHK T0299 129 :YFGKLGIFWGKFSEESYSKTAYHKYLLK 1fp1D 297 :SPNGKVIIVEFILPEEPNTSEESKLVST T0299 157 :VPF 1fp1D 332 :TVG T0299 163 :ITIRNAKTFDKIGQMLK 1fp1D 335 :GRERTEKQYEKLSKLSG Number of specific fragments extracted= 10 number of extra gaps= 0 total=103 Number of alignments=13 # 1fp1D read from 1fp1D/merged-good-all-a2m # found chain 1fp1D in template set T0299 21 :MAELRQE 1fp1D 197 :MKRMLEI T0299 32 :GLEKVESYINSGN 1fp1D 206 :GFEGISTLVDVGG T0299 58 :EKLE 1fp1D 222 :RNLE T0299 63 :FFAVHYPFIQSFSLLSLE 1fp1D 226 :LIISKYPLIKGINFDLPQ T0299 85 :ELENLPAWWS 1fp1D 244 :VIENAPPLSG T0299 95 :RDLARKDFLFYTE 1fp1D 263 :ASVPQGDAMILKA T0299 108 :GLDVDQVIATVESLEL 1fp1D 279 :NWSDEKCIEFLSNCHK T0299 129 :YFGKLGIFWGKFSEESYSKTAYHKYLLK 1fp1D 297 :SPNGKVIIVEFILPEEPNTSEESKLVST T0299 157 :VPF 1fp1D 332 :TVG T0299 163 :ITIRNAKTFDKIGQMLK 1fp1D 335 :GRERTEKQYEKLSKLSG Number of specific fragments extracted= 10 number of extra gaps= 0 total=113 Number of alignments=14 # 1fp1D read from 1fp1D/merged-good-all-a2m # found chain 1fp1D in template set T0299 22 :AELRQE 1fp1D 198 :KRMLEI T0299 32 :GLEKVESYINSGN 1fp1D 206 :GFEGISTLVDVGG T0299 58 :EKLE 1fp1D 222 :RNLE T0299 63 :FFAVHYPFIQSFSLLSLE 1fp1D 226 :LIISKYPLIKGINFDLPQ T0299 85 :ELENLPAWWS 1fp1D 244 :VIENAPPLSG T0299 95 :RDLARKDFLFYTE 1fp1D 263 :ASVPQGDAMILKA T0299 108 :GLDVDQVIATVESLELK 1fp1D 279 :NWSDEKCIEFLSNCHKA T0299 128 :LYFGKLGIFWGK 1fp1D 296 :LSPNGKVIIVEF T0299 140 :FSEESYSKTAY 1fp1D 310 :PEEPNTSEESK T0299 151 :HKYLLKVPFYRH 1fp1D 325 :LDNLMFITVGGR T0299 165 :IRNAKTFDKIGQMLK 1fp1D 337 :ERTEKQYEKLSKLSG Number of specific fragments extracted= 11 number of extra gaps= 0 total=124 Number of alignments=15 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1t6nA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1t6nA expands to /projects/compbio/data/pdb/1t6n.pdb.gz 1t6nA:# T0299 read from 1t6nA/merged-good-all-a2m # 1t6nA read from 1t6nA/merged-good-all-a2m # adding 1t6nA to template set # found chain 1t6nA in template set T0299 4 :YALLVR 1t6nA 116 :VLVMCH T0299 20 :V 1t6nA 122 :T T0299 21 :MAELRQELTNL 1t6nA 126 :AFQISKEYERF T0299 32 :GLEKVESY 1t6nA 139 :YMPNVKVA T0299 46 :FFTSIDSKAQLVEKLET 1t6nA 147 :VFFGGLSIKKDEEVLKK T0299 70 :FIQSFSLLSLEDFEAELENL 1t6nA 164 :NCPHIVVGTPGRILALARNK T0299 94 :SRDLARKDFLFYTE 1t6nA 184 :SLNLKHIKHFILDE T0299 111 :VDQVIATVESLEL 1t6nA 204 :QLDMRRDVQEIFR T0299 124 :KDEV 1t6nA 220 :HEKQ T0299 134 :GIFWGKFSEESY 1t6nA 224 :VMMFSATLSKEI T0299 148 :TAYHKYLLKVPFY 1t6nA 236 :RPVCRKFMQDPME Number of specific fragments extracted= 11 number of extra gaps= 0 total=135 Number of alignments=16 # 1t6nA read from 1t6nA/merged-good-all-a2m # found chain 1t6nA in template set T0299 4 :YALLVR 1t6nA 116 :VLVMCH T0299 21 :MAELRQELTNL 1t6nA 126 :AFQISKEYERF T0299 32 :GLEKVESY 1t6nA 139 :YMPNVKVA T0299 46 :FFTSIDSKAQLVEKLET 1t6nA 147 :VFFGGLSIKKDEEVLKK T0299 70 :FIQSFSLLSLEDFEAELEN 1t6nA 164 :NCPHIVVGTPGRILALARN T0299 94 :SRDLARKDFLFYTE 1t6nA 184 :SLNLKHIKHFILDE T0299 112 :DQVIATVES 1t6nA 205 :LDMRRDVQE T0299 121 :LELKDEV 1t6nA 217 :MTPHEKQ T0299 134 :GIFWGKFSEESY 1t6nA 224 :VMMFSATLSKEI T0299 148 :TAYHKYLLKVPFYRH 1t6nA 236 :RPVCRKFMQDPMEIF Number of specific fragments extracted= 10 number of extra gaps= 0 total=145 Number of alignments=17 # 1t6nA read from 1t6nA/merged-good-all-a2m # found chain 1t6nA in template set T0299 21 :MAELRQELTNL 1t6nA 126 :AFQISKEYERF T0299 32 :GLEKVESY 1t6nA 139 :YMPNVKVA T0299 46 :FFTSIDSKAQLVEKLET 1t6nA 147 :VFFGGLSIKKDEEVLKK T0299 70 :FIQSFSLLSLEDFEAELENLPA 1t6nA 164 :NCPHIVVGTPGRILALARNKSL T0299 96 :DLARKDFLFYTE 1t6nA 186 :NLKHIKHFILDE T0299 110 :DVDQVIATVESLE 1t6nA 203 :EQLDMRRDVQEIF Number of specific fragments extracted= 6 number of extra gaps= 0 total=151 Number of alignments=18 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1u5tB/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1u5tB expands to /projects/compbio/data/pdb/1u5t.pdb.gz 1u5tB:# T0299 read from 1u5tB/merged-good-all-a2m # 1u5tB read from 1u5tB/merged-good-all-a2m # adding 1u5tB to template set # found chain 1u5tB in template set Warning: unaligning (T0299)H67 because of BadResidue code BAD_PEPTIDE in next template residue (1u5tB)P507 Warning: unaligning (T0299)Y68 because of BadResidue code BAD_PEPTIDE at template residue (1u5tB)P507 T0299 15 :GKNKVVMAELRQELTNL 1u5tB 451 :GTGLISPMEMREACERF T0299 32 :GLEKVESY 1u5tB 471 :GLNELKLV T0299 45 :IFFTSIDSKAQLVEKLETFFAV 1u5tB 484 :ILCVTSEKFDVVKEKLVDLIGD T0299 69 :PF 1u5tB 508 :GS T0299 78 :SLEDFEAELE 1u5tB 510 :DLLRLTQILS T0299 156 :KVPFYRHIT 1u5tB 520 :SNNSKSNWT T0299 168 :AKTFDKIGQML 1u5tB 529 :LGILMEVLQNC Number of specific fragments extracted= 7 number of extra gaps= 1 total=158 Number of alignments=19 # 1u5tB read from 1u5tB/merged-good-all-a2m # found chain 1u5tB in template set T0299 49 :SIDSKAQLVEKLETFFAVHY 1u5tB 404 :KELFLDEIAREIYEFTLSEF T0299 69 :PFIQSFSLLSLEDFEAELENLPA 1u5tB 427 :NSDTNYMIITLVDLYAMYNKSMR T0299 95 :RD 1u5tB 450 :IG T0299 106 :TEGLDVDQVIA 1u5tB 452 :TGLISPMEMRE T0299 117 :TVESLELKDEVLYFGK 1u5tB 466 :RFEHLGLNELKLVKVN T0299 133 :LGIFWGKFSE 1u5tB 484 :ILCVTSEKFD T0299 144 :SYSKTAYHKYLLKVPFYRHIT 1u5tB 508 :GSDLLRLTQILSSNNSKSNWT T0299 168 :AKTFDKIGQML 1u5tB 529 :LGILMEVLQNC Number of specific fragments extracted= 8 number of extra gaps= 0 total=166 Number of alignments=20 # 1u5tB read from 1u5tB/merged-good-all-a2m # found chain 1u5tB in template set Warning: unaligning (T0299)H67 because of BadResidue code BAD_PEPTIDE in next template residue (1u5tB)P507 Warning: unaligning (T0299)Y68 because of BadResidue code BAD_PEPTIDE at template residue (1u5tB)P507 T0299 15 :GKNKVVMAELRQELTNL 1u5tB 451 :GTGLISPMEMREACERF T0299 32 :GLEKVESYINSG 1u5tB 471 :GLNELKLVKVNK T0299 45 :IFFTSIDSKAQLVEKLETFFAV 1u5tB 484 :ILCVTSEKFDVVKEKLVDLIGD T0299 69 :PF 1u5tB 508 :GS T0299 78 :SLEDFEAELENLPAW 1u5tB 510 :DLLRLTQILSSNNSK T0299 108 :GLDVDQVIATVESL 1u5tB 525 :SNWTLGILMEVLQN T0299 122 :ELKDEVLYFGKLGIFWGKFSEES 1u5tB 541 :DEGDLLIDKQLSGIYYYKNSYWP Number of specific fragments extracted= 7 number of extra gaps= 1 total=173 Number of alignments=21 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2g40A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2g40A expands to /projects/compbio/data/pdb/2g40.pdb.gz 2g40A:Skipped atom 646, because occupancy 0.5 <= existing 0.500 in 2g40A Skipped atom 648, because occupancy 0.500 <= existing 0.500 in 2g40A Skipped atom 650, because occupancy 0.500 <= existing 0.500 in 2g40A Skipped atom 652, because occupancy 0.500 <= existing 0.500 in 2g40A Skipped atom 654, because occupancy 0.500 <= existing 0.500 in 2g40A Skipped atom 656, because occupancy 0.500 <= existing 0.500 in 2g40A Skipped atom 658, because occupancy 0.500 <= existing 0.500 in 2g40A Skipped atom 660, because occupancy 0.500 <= existing 0.500 in 2g40A Skipped atom 662, because occupancy 0.500 <= existing 0.500 in 2g40A Skipped atom 811, because occupancy 0.500 <= existing 0.500 in 2g40A Skipped atom 815, because occupancy 0.500 <= existing 0.500 in 2g40A Skipped atom 817, because occupancy 0.500 <= existing 0.500 in 2g40A Skipped atom 819, because occupancy 0.500 <= existing 0.500 in 2g40A Skipped atom 821, because occupancy 0.500 <= existing 0.500 in 2g40A # T0299 read from 2g40A/merged-good-all-a2m # 2g40A read from 2g40A/merged-good-all-a2m # adding 2g40A to template set # found chain 2g40A in template set Warning: unaligning (T0299)I50 because first residue in template chain is (2g40A)P38 T0299 51 :DSKAQLVEKLETFFAVH 2g40A 39 :LSRAEILHQFEDRILDY T0299 71 :IQSFSLLSLEDFEAELEN 2g40A 56 :GAAYTHVSAAELPGAIAK T0299 89 :LPAWWSRDLA 2g40A 83 :VPAGIPAPWL T0299 99 :RKDFLFYTEGLDVDQV 2g40A 95 :GMDVLRDEPPLSHAEL T0299 116 :ATVE 2g40A 111 :DRAD T0299 124 :KDEVLYFGKLGIFWG 2g40A 119 :GCAVAISETGTIILD T0299 140 :FSEESYSKT 2g40A 134 :HRADQGRRA Number of specific fragments extracted= 7 number of extra gaps= 0 total=180 Number of alignments=22 # 2g40A read from 2g40A/merged-good-all-a2m # found chain 2g40A in template set T0299 19 :VVMAELRQELTNL 2g40A 39 :LSRAEILHQFEDR T0299 32 :GLE 2g40A 56 :GAA T0299 47 :FT 2g40A 59 :YT T0299 49 :SIDS 2g40A 63 :SAAE T0299 60 :LETFFAVHYPFIQSFSLL 2g40A 67 :LPGAIAKALGNARRVIVP T0299 87 :ENLPAWWSRDL 2g40A 85 :AGIPAPWLTVG T0299 100 :KDFLFYTEGLDVDQVIA 2g40A 96 :MDVLRDEPPLSHAELDR T0299 121 :LE 2g40A 113 :AD T0299 124 :KDEVLYFGKLGIFWG 2g40A 119 :GCAVAISETGTIILD T0299 140 :FSEESYSK 2g40A 134 :HRADQGRR T0299 149 :AYH 2g40A 142 :ALS Number of specific fragments extracted= 11 number of extra gaps= 0 total=191 Number of alignments=23 # 2g40A read from 2g40A/merged-good-all-a2m # found chain 2g40A in template set Warning: unaligning (T0299)I50 because first residue in template chain is (2g40A)P38 T0299 51 :DSKAQLVEKLETFFAV 2g40A 39 :LSRAEILHQFEDRILD T0299 70 :FIQSFSLLSLEDFEAELEN 2g40A 55 :YGAAYTHVSAAELPGAIAK T0299 89 :LPAWWSRDL 2g40A 87 :IPAPWLTVG T0299 102 :FLFYTEGLDVD 2g40A 96 :MDVLRDEPPLS T0299 113 :QVIATVE 2g40A 108 :AELDRAD T0299 124 :KDEVLYFGKLGIFWGKFSEESYSKTA 2g40A 119 :GCAVAISETGTIILDHRADQGRRALS Number of specific fragments extracted= 6 number of extra gaps= 0 total=197 Number of alignments=24 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1zghA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1zghA expands to /projects/compbio/data/pdb/1zgh.pdb.gz 1zghA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0299 read from 1zghA/merged-good-all-a2m # 1zghA read from 1zghA/merged-good-all-a2m # adding 1zghA to template set # found chain 1zghA in template set Warning: unaligning (T0299)L128 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1zghA)I198 Warning: unaligning (T0299)Y129 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1zghA)I198 T0299 8 :VRGINVGGKN 1zghA 100 :ISAIKVDGGI T0299 41 :NSGNIFFT 1zghA 110 :DTGDIFFK T0299 49 :S 1zghA 121 :D T0299 50 :IDSKAQLVEKLETFFAVHY 1zghA 123 :YGTAEEIFMRASKIIFNDM T0299 82 :FEAELENLPAWWSRDLARKDF 1zghA 142 :IPELLTKRPVPQKQEGEATVF T0299 105 :YTEGLDVDQVIATVESLELKD 1zghA 172 :ISPDFDLEKIYDYIRMLDGEG T0299 126 :EV 1zghA 195 :RA T0299 130 :FGK 1zghA 199 :KYG T0299 133 :LGIFWGKF 1zghA 203 :YRLEFSRA Number of specific fragments extracted= 9 number of extra gaps= 1 total=206 Number of alignments=25 # 1zghA read from 1zghA/merged-good-all-a2m # found chain 1zghA in template set T0299 8 :VRGINVGGKN 1zghA 100 :ISAIKVDGGI T0299 41 :NSGNIFF 1zghA 110 :DTGDIFF T0299 49 :SIDSKAQLVEKLETFFAVHY 1zghA 122 :LYGTAEEIFMRASKIIFNDM T0299 82 :FEAELENLPAWWSRDLARKDF 1zghA 142 :IPELLTKRPVPQKQEGEATVF T0299 105 :YTEGLDVDQVIATVESLEL 1zghA 172 :ISPDFDLEKIYDYIRMLDG T0299 124 :KDEVLYFGKL 1zghA 201 :GKYRLEFSRA T0299 139 :KFSEE 1zghA 211 :SMKNG Number of specific fragments extracted= 7 number of extra gaps= 0 total=213 Number of alignments=26 # 1zghA read from 1zghA/merged-good-all-a2m # found chain 1zghA in template set Warning: unaligning (T0299)L89 because of BadResidue code BAD_PEPTIDE in next template residue (1zghA)S57 Warning: unaligning (T0299)P90 because of BadResidue code BAD_PEPTIDE at template residue (1zghA)S57 T0299 44 :NIFFTSI 1zghA 2 :NIIIATT T0299 53 :KAQLVEKLETFFAVHYPFIQSFSLL 1zghA 9 :KSWNIKNAQKFKKENESKYNTTIIT T0299 78 :SLEDFEAE 1zghA 39 :TFEKVKLI T0299 91 :AWWSRD 1zghA 58 :WIIPKE T0299 97 :LARKDFLFYTEGLDV 1zghA 66 :ENFTCVVFHMTDLPF T0299 114 :V 1zghA 86 :P T0299 117 :TVESLELKDEVL 1zghA 87 :LQNLIERGIKKT T0299 133 :LGIFWGKFSEESYSKTA 1zghA 99 :KISAIKVDGGIDTGDIF T0299 153 :YLLKVPFYRHI 1zghA 116 :FKRDLDLYGTA T0299 168 :AKTFDKIGQML 1zghA 127 :EEIFMRASKII Number of specific fragments extracted= 10 number of extra gaps= 1 total=223 Number of alignments=27 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1oxkB/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1oxkB expands to /projects/compbio/data/pdb/1oxk.pdb.gz 1oxkB:# T0299 read from 1oxkB/merged-good-all-a2m # 1oxkB read from 1oxkB/merged-good-all-a2m # adding 1oxkB to template set # found chain 1oxkB in template set T0299 5 :ALLVR 1oxkB 1090 :ILVVE T0299 16 :KNKVVMAELRQELTNLGLEKVESY 1oxkB 1095 :DNHVNQEVIKRMLNLEGIENIELA T0299 51 :DSKAQLVEKLETFFAVHYPFIQSFSLLS 1oxkB 1119 :CDGQEAFDKVKELTSKGENYNMIFMDVQ T0299 79 :LEDFEAELENLPA 1oxkB 1153 :LLSTKMIRRDLGY T0299 99 :RKDFLFYTEGLDVDQ 1oxkB 1166 :TSPIVALTAFADDSN T0299 115 :IATVESLEL 1oxkB 1181 :IKECLESGM T0299 138 :GKFSEESYSKTAYHKYLLK 1oxkB 1190 :NGFLSKPIKRPKLKTILTE Number of specific fragments extracted= 7 number of extra gaps= 0 total=230 Number of alignments=28 # 1oxkB read from 1oxkB/merged-good-all-a2m # found chain 1oxkB in template set T0299 5 :ALLVR 1oxkB 1090 :ILVVE T0299 16 :KNKVVMAELRQELTNLGLEKVESY 1oxkB 1095 :DNHVNQEVIKRMLNLEGIENIELA T0299 51 :DSKAQLVEKLETFFAVHYPFIQSFSLLS 1oxkB 1119 :CDGQEAFDKVKELTSKGENYNMIFMDVQ T0299 79 :LEDFEAELENLPA 1oxkB 1153 :LLSTKMIRRDLGY T0299 99 :RKDFLFYTEGLDVDQ 1oxkB 1166 :TSPIVALTAFADDSN T0299 115 :IATVESLELK 1oxkB 1181 :IKECLESGMN T0299 139 :KFSEESYSKTAYHKYLLK 1oxkB 1191 :GFLSKPIKRPKLKTILTE Number of specific fragments extracted= 7 number of extra gaps= 0 total=237 Number of alignments=29 # 1oxkB read from 1oxkB/merged-good-all-a2m # found chain 1oxkB in template set T0299 5 :ALLVR 1oxkB 1090 :ILVVE T0299 16 :KNKVVMAELRQELTNLGLEKVESY 1oxkB 1095 :DNHVNQEVIKRMLNLEGIENIELA T0299 51 :DSKAQLVEKLETFFAV 1oxkB 1119 :CDGQEAFDKVKELTSK T0299 69 :PFIQSFSLLS 1oxkB 1135 :GENYNMIFMD T0299 82 :FEAELE 1oxkB 1152 :GLLSTK T0299 92 :WWSRDLARKDFLFYTEGLDVDQVIATVESLE 1oxkB 1158 :MIRRDLGYTSPIVALTAFADDSNIKECLESG Number of specific fragments extracted= 6 number of extra gaps= 0 total=243 Number of alignments=30 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1eqpA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1eqpA expands to /projects/compbio/data/pdb/1eqp.pdb.gz 1eqpA:Skipped atom 466, because occupancy 0.500 <= existing 0.500 in 1eqpA Skipped atom 788, because occupancy 0.500 <= existing 0.500 in 1eqpA Skipped atom 790, because occupancy 0.500 <= existing 0.500 in 1eqpA Skipped atom 792, because occupancy 0.500 <= existing 0.500 in 1eqpA Skipped atom 1005, because occupancy 0.500 <= existing 0.500 in 1eqpA Skipped atom 1007, because occupancy 0.500 <= existing 0.500 in 1eqpA Skipped atom 1009, because occupancy 0.500 <= existing 0.500 in 1eqpA Skipped atom 1201, because occupancy 0.500 <= existing 0.500 in 1eqpA Skipped atom 1314, because occupancy 0.500 <= existing 0.500 in 1eqpA Skipped atom 1316, because occupancy 0.500 <= existing 0.500 in 1eqpA Skipped atom 1318, because occupancy 0.500 <= existing 0.500 in 1eqpA Skipped atom 1693, because occupancy 0.500 <= existing 0.500 in 1eqpA Skipped atom 2107, because occupancy 0.500 <= existing 0.500 in 1eqpA # T0299 read from 1eqpA/merged-good-all-a2m # 1eqpA read from 1eqpA/merged-good-all-a2m # adding 1eqpA to template set # found chain 1eqpA in template set T0299 3 :RYALLVRGINVGGKNK 1eqpA 129 :RVWIDLHGAPGSQNGF T0299 21 :MAELRQELTNL 1eqpA 161 :TQVTLNVLNTI T0299 32 :GLEKVESYINSGNIFFTS 1eqpA 179 :EYSDVVIGIELLNEPLGP T0299 52 :SKAQLVEKLETFFAV 1eqpA 199 :NMDKLKQFFLDGYNS T0299 67 :HYPFIQSFSLLSL 1eqpA 216 :QTGSVTPVIIHDA T0299 88 :NLPA 1eqpA 229 :FQVF T0299 95 :RDLARKDFLFYTE 1eqpA 241 :VAEGQWNVVVDHH T0299 108 :GLDVDQVIATVESL 1eqpA 264 :SRNINDHISVACNW Number of specific fragments extracted= 8 number of extra gaps= 0 total=251 Number of alignments=31 # 1eqpA read from 1eqpA/merged-good-all-a2m # found chain 1eqpA in template set T0299 4 :YALLVRGI 1eqpA 90 :FVRIPIGY T0299 12 :NVGGKNKVV 1eqpA 101 :QLLDNDPYV T0299 21 :MAELRQELTNLG 1eqpA 116 :LEKALGWARKNN T0299 36 :VESYINSGNI 1eqpA 128 :IRVWIDLHGA T0299 47 :FTSIDSKAQLVEKLETFFAVHYPFI 1eqpA 155 :FQNGDNTQVTLNVLNTIFKKYGGNE T0299 72 :QSFSL 1eqpA 184 :VIGIE T0299 77 :LSLEDFEAELEN 1eqpA 198 :LNMDKLKQFFLD T0299 91 :A 1eqpA 229 :F T0299 92 :WWS 1eqpA 231 :VFG T0299 95 :RDLARKDFLFYTE 1eqpA 241 :VAEGQWNVVVDHH T0299 108 :GLDVDQVIATVESL 1eqpA 264 :SRNINDHISVACNW Number of specific fragments extracted= 11 number of extra gaps= 0 total=262 Number of alignments=32 # 1eqpA read from 1eqpA/merged-good-all-a2m # found chain 1eqpA in template set T0299 3 :RYALLVRGINVGGKNK 1eqpA 129 :RVWIDLHGAPGSQNGF T0299 21 :MAELRQELTNL 1eqpA 161 :TQVTLNVLNTI T0299 32 :GLEKVESYINSGN 1eqpA 179 :EYSDVVIGIELLN T0299 48 :TSID 1eqpA 194 :LGPV T0299 52 :SKAQLVEKLETFFAV 1eqpA 199 :NMDKLKQFFLDGYNS T0299 67 :HYPFIQSFSLLSL 1eqpA 216 :QTGSVTPVIIHDA T0299 87 :ENLPAWWSRDLARKDFLFYTE 1eqpA 233 :GYWNNFLTVAEGQWNVVVDHH T0299 108 :GLDVDQVIATVESL 1eqpA 264 :SRNINDHISVACNW Number of specific fragments extracted= 8 number of extra gaps= 0 total=270 Number of alignments=33 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1qapA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1qapA expands to /projects/compbio/data/pdb/1qap.pdb.gz 1qapA:# T0299 read from 1qapA/merged-good-all-a2m # 1qapA read from 1qapA/merged-good-all-a2m # adding 1qapA to template set # found chain 1qapA in template set T0299 56 :LVEKLETFFAVHYPFIQSFSLLSLEDFEAELENLPA 1qapA 195 :VRQAVEKAFWLHPDVPVEVEVENLDELDDALKAGAD T0299 103 :LFYTEGLDVDQVIATVESLELKD 1qapA 231 :IIMLDNFNTDQMREAVKRVNGQA Number of specific fragments extracted= 2 number of extra gaps= 0 total=272 Number of alignments=34 # 1qapA read from 1qapA/merged-good-all-a2m # found chain 1qapA in template set T0299 56 :LVEKLETFFAVHYPFIQSFSLLSLEDFEAELE 1qapA 195 :VRQAVEKAFWLHPDVPVEVEVENLDELDDALK T0299 94 :SRD 1qapA 228 :GAD T0299 103 :LFYTEGLDVDQVIATVESLELK 1qapA 231 :IIMLDNFNTDQMREAVKRVNGQ Number of specific fragments extracted= 3 number of extra gaps= 0 total=275 Number of alignments=35 # 1qapA read from 1qapA/merged-good-all-a2m # found chain 1qapA in template set T0299 56 :LVEKLETFFAVHYPFIQSFSLLSLEDFEAELEN 1qapA 195 :VRQAVEKAFWLHPDVPVEVEVENLDELDDALKA T0299 100 :KDFLFYTEGLDVDQVIATVESLELKDE 1qapA 228 :GADIIMLDNFNTDQMREAVKRVNGQAR Number of specific fragments extracted= 2 number of extra gaps= 0 total=277 Number of alignments=36 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1wekA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1wekA expands to /projects/compbio/data/pdb/1wek.pdb.gz 1wekA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0299 read from 1wekA/merged-good-all-a2m # 1wekA read from 1wekA/merged-good-all-a2m # adding 1wekA to template set # found chain 1wekA in template set Warning: unaligning (T0299)S120 because last residue in template chain is (1wekA)A212 T0299 43 :GNIFFTSIDSKAQLVEKLETFFAVHYPFIQSFSLLSLEDFEAELENLPA 1wekA 134 :GFVFLPGGFGTLDELSEVLVLLQTEKVHRFPVFLLDRGYWEGLVRWLAF T0299 95 :RDLARKDF 1wekA 192 :EDLQLFRL T0299 106 :TE 1wekA 200 :TD T0299 110 :DVDQVIATVE 1wekA 202 :EPEEVVQALK Number of specific fragments extracted= 4 number of extra gaps= 0 total=281 Number of alignments=37 # 1wekA read from 1wekA/merged-good-all-a2m # found chain 1wekA in template set Warning: unaligning (T0299)S120 because last residue in template chain is (1wekA)A212 T0299 42 :SGNIFFTSIDSKAQLVEKLETFFAVHYPFIQSFSLLSLEDFEAELENLPA 1wekA 133 :VGFVFLPGGFGTLDELSEVLVLLQTEKVHRFPVFLLDRGYWEGLVRWLAF T0299 92 :WWSRDLARKD 1wekA 188 :AVGPEDLQLF T0299 104 :FYTE 1wekA 198 :RLTD T0299 110 :DVDQVIATVE 1wekA 202 :EPEEVVQALK Number of specific fragments extracted= 4 number of extra gaps= 0 total=285 Number of alignments=38 # 1wekA read from 1wekA/merged-good-all-a2m # found chain 1wekA in template set Warning: unaligning (T0299)S120 because last residue in template chain is (1wekA)A212 T0299 43 :GNIFFTSIDSKAQLVEKLETFFAVHYPFIQSFSLLSLEDFEAELENLPAWWSRD 1wekA 134 :GFVFLPGGFGTLDELSEVLVLLQTEKVHRFPVFLLDRGYWEGLVRWLAFLRDQK T0299 97 :LARKDFL 1wekA 194 :LQLFRLT T0299 109 :LDVDQVIATVE 1wekA 201 :DEPEEVVQALK Number of specific fragments extracted= 3 number of extra gaps= 0 total=288 Number of alignments=39 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1zavA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1zavA expands to /projects/compbio/data/pdb/1zav.pdb.gz 1zavA:Skipped atom 692, because occupancy 0.500 <= existing 0.500 in 1zavA Skipped atom 694, because occupancy 0.500 <= existing 0.500 in 1zavA Skipped atom 696, because occupancy 0.500 <= existing 0.500 in 1zavA Skipped atom 698, because occupancy 0.500 <= existing 0.500 in 1zavA Skipped atom 700, because occupancy 0.500 <= existing 0.500 in 1zavA Skipped atom 702, because occupancy 0.500 <= existing 0.500 in 1zavA Skipped atom 704, because occupancy 0.500 <= existing 0.500 in 1zavA Skipped atom 706, because occupancy 0.500 <= existing 0.500 in 1zavA # T0299 read from 1zavA/merged-good-all-a2m # 1zavA read from 1zavA/merged-good-all-a2m # adding 1zavA to template set # found chain 1zavA in template set T0299 21 :MAELRQELTN 1zavA 11 :VKEMSEIFKK T0299 42 :SGNIFFTSID 1zavA 21 :TSLILFADFL T0299 52 :SKAQLVEKLETFFAVHYPFIQSFSLLSLEDFEAELENLPAW 1zavA 32 :FTVADLTELRSRLREKYGDGARFRVVKNTLLNLALKNAEYE T0299 93 :WSRDLA 1zavA 74 :YEEFLK T0299 99 :RKDFLFYTEG 1zavA 81 :PTAVLYVTEG T0299 110 :DVDQ 1zavA 91 :DPVE T0299 114 :VIATVESLELKDEVL 1zavA 99 :IYNFYKDKKADLSRL T0299 133 :LGIFW 1zavA 114 :KGGFL T0299 142 :EESYSKTAYHKYLLKVP 1zavA 119 :EGKKFTAEEVENIAKLP Number of specific fragments extracted= 9 number of extra gaps= 0 total=297 Number of alignments=40 # 1zavA read from 1zavA/merged-good-all-a2m # found chain 1zavA in template set T0299 21 :MAELRQELTN 1zavA 11 :VKEMSEIFKK T0299 42 :SGNIFF 1zavA 21 :TSLILF T0299 48 :TSID 1zavA 28 :DFLG T0299 52 :SKA 1zavA 33 :TVA T0299 56 :LVEKLETFFAVHYPFIQSFSLLSLEDFEAELENLPA 1zavA 36 :DLTELRSRLREKYGDGARFRVVKNTLLNLALKNAEY T0299 92 :WWSR 1zavA 73 :GYEE T0299 96 :DLARKDFLFYTEG 1zavA 78 :LKGPTAVLYVTEG T0299 112 :DQVIATVESLELKDEVL 1zavA 97 :KIIYNFYKDKKADLSRL T0299 133 :LGIFW 1zavA 114 :KGGFL T0299 142 :EESYSKTAYHKYLLKVP 1zavA 119 :EGKKFTAEEVENIAKLP Number of specific fragments extracted= 10 number of extra gaps= 0 total=307 Number of alignments=41 # 1zavA read from 1zavA/merged-good-all-a2m # found chain 1zavA in template set T0299 21 :MAELRQELTN 1zavA 11 :VKEMSEIFKK T0299 42 :SGNIFFTSID 1zavA 21 :TSLILFADFL T0299 52 :SKAQ 1zavA 33 :TVAD T0299 57 :VEKLETFFAVHYPFIQSFSLLSLEDFEAELENLPAWWSRD 1zavA 37 :LTELRSRLREKYGDGARFRVVKNTLLNLALKNAEYEGYEE T0299 97 :LARKDFLFYTEGLDVDQVIATVESL 1zavA 78 :LKGPTAVLYVTEGDPVEAVKIIYNF T0299 122 :ELKD 1zavA 107 :KADL T0299 128 :LYFGKLGI 1zavA 111 :SRLKGGFL T0299 143 :ESYSKT 1zavA 119 :EGKKFT T0299 171 :FDKIGQMLK 1zavA 125 :AEEVENIAK Number of specific fragments extracted= 9 number of extra gaps= 0 total=316 Number of alignments=42 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1qtqA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1qtqA expands to /projects/compbio/data/pdb/1qtq.pdb.gz 1qtqA:# T0299 read from 1qtqA/merged-good-all-a2m # 1qtqA read from 1qtqA/merged-good-all-a2m # adding 1qtqA to template set # found chain 1qtqA in template set T0299 21 :MAELRQELTNLGLE 1qtqA 78 :VESIKNDVEWLGFH T0299 41 :NSGNIFFTS 1qtqA 92 :WSGNVRYSS T0299 51 :DSKAQLVEKLETFFAVHY 1qtqA 101 :DYFDQLHAYAIELINKGL T0299 73 :SF 1qtqA 120 :YV T0299 77 :LSLEDFEAEL 1qtqA 124 :LTPEQIREYR T0299 93 :WSRDLARKD 1qtqA 134 :GTLTQPGKN T0299 106 :TEGLDVDQVIATVESLELKD 1qtqA 145 :YRDRSVEENLALFEKMRAGG T0299 131 :GKLGIFW 1qtqA 168 :GKACLRA T0299 140 :FSE 1qtqA 175 :KID Number of specific fragments extracted= 9 number of extra gaps= 0 total=325 Number of alignments=43 # 1qtqA read from 1qtqA/merged-good-all-a2m # found chain 1qtqA in template set T0299 21 :MAELRQELTNLGLE 1qtqA 78 :VESIKNDVEWLGFH T0299 41 :NSGNIFFTSID 1qtqA 92 :WSGNVRYSSDY T0299 53 :KAQLVEKLETFFAVHY 1qtqA 103 :FDQLHAYAIELINKGL T0299 75 :SL 1qtqA 120 :YV T0299 77 :LSLEDFEAEL 1qtqA 124 :LTPEQIREYR T0299 93 :WSRDLARKD 1qtqA 134 :GTLTQPGKN T0299 106 :TEGLDVDQVIATVESLELKD 1qtqA 145 :YRDRSVEENLALFEKMRAGG T0299 131 :GKLGIFWG 1qtqA 168 :GKACLRAK T0299 141 :S 1qtqA 176 :I Number of specific fragments extracted= 9 number of extra gaps= 0 total=334 Number of alignments=44 # 1qtqA read from 1qtqA/merged-good-all-a2m # found chain 1qtqA in template set T0299 22 :AELRQELTNLGLE 1qtqA 79 :ESIKNDVEWLGFH T0299 41 :NSGNIFFTSID 1qtqA 92 :WSGNVRYSSDY T0299 53 :KAQLVEKLETFFAVHY 1qtqA 103 :FDQLHAYAIELINKGL T0299 71 :IQS 1qtqA 119 :AYV T0299 77 :LSLEDFEAEL 1qtqA 124 :LTPEQIREYR T0299 93 :WSRDLARKD 1qtqA 134 :GTLTQPGKN T0299 107 :EGLDVDQVIATVESLELKD 1qtqA 146 :RDRSVEENLALFEKMRAGG T0299 131 :GKLGIFW 1qtqA 167 :EGKACLR T0299 139 :KFSEE 1qtqA 174 :AKIDM Number of specific fragments extracted= 9 number of extra gaps= 0 total=343 Number of alignments=45 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1eqcA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1eqcA expands to /projects/compbio/data/pdb/1eqc.pdb.gz 1eqcA:Skipped atom 282, because occupancy 0.500 <= existing 0.500 in 1eqcA Skipped atom 284, because occupancy 0.500 <= existing 0.500 in 1eqcA Skipped atom 286, because occupancy 0.500 <= existing 0.500 in 1eqcA Skipped atom 625, because occupancy 0.500 <= existing 0.500 in 1eqcA Skipped atom 627, because occupancy 0.500 <= existing 0.500 in 1eqcA Skipped atom 629, because occupancy 0.500 <= existing 0.500 in 1eqcA Skipped atom 631, because occupancy 0.500 <= existing 0.500 in 1eqcA Skipped atom 796, because occupancy 0.500 <= existing 0.500 in 1eqcA Skipped atom 798, because occupancy 0.500 <= existing 0.500 in 1eqcA Skipped atom 800, because occupancy 0.500 <= existing 0.500 in 1eqcA Skipped atom 1013, because occupancy 0.500 <= existing 0.500 in 1eqcA Skipped atom 1015, because occupancy 0.500 <= existing 0.500 in 1eqcA Skipped atom 1017, because occupancy 0.500 <= existing 0.500 in 1eqcA Skipped atom 1209, because occupancy 0.500 <= existing 0.500 in 1eqcA Skipped atom 1322, because occupancy 0.500 <= existing 0.500 in 1eqcA Skipped atom 1324, because occupancy 0.500 <= existing 0.500 in 1eqcA Skipped atom 1326, because occupancy 0.500 <= existing 0.500 in 1eqcA Skipped atom 1701, because occupancy 0.500 <= existing 0.500 in 1eqcA Skipped atom 2115, because occupancy 0.500 <= existing 0.500 in 1eqcA Skipped atom 2610, because occupancy 0.500 <= existing 0.500 in 1eqcA Skipped atom 2612, because occupancy 0.500 <= existing 0.500 in 1eqcA Skipped atom 2614, because occupancy 0.500 <= existing 0.500 in 1eqcA # T0299 read from 1eqcA/merged-good-all-a2m # 1eqcA read from 1eqcA/merged-good-all-a2m # adding 1eqcA to template set # found chain 1eqcA in template set T0299 3 :RYALLVRGINVGGKNK 1eqcA 129 :RVWIDLHGAPGSQNGF T0299 21 :MAELRQELTNL 1eqcA 161 :TQVTLNVLNTI T0299 32 :GLEKVESYINSGNIFFTSI 1eqcA 179 :EYSDVVIGIELLNEPLGPV T0299 52 :SKAQLVEKLETFFAV 1eqcA 199 :NMDKLKQFFLDGYNS T0299 67 :HYPFIQSFSLLSL 1eqcA 216 :QTGSVTPVIIHDA T0299 89 :LPA 1eqcA 230 :QVF T0299 95 :RDLARKDFLFYTE 1eqcA 241 :VAEGQWNVVVDHH T0299 108 :GLDVDQVIATVESL 1eqcA 264 :SRNINDHISVACNW Number of specific fragments extracted= 8 number of extra gaps= 0 total=351 Number of alignments=46 # 1eqcA read from 1eqcA/merged-good-all-a2m # found chain 1eqcA in template set T0299 4 :YALLVRGI 1eqcA 90 :FVRIPIGY T0299 12 :NVGGKNKVV 1eqcA 101 :QLLDNDPYV T0299 21 :MAELRQELTNLG 1eqcA 116 :LEKALGWARKNN T0299 36 :VESYINSGNI 1eqcA 128 :IRVWIDLHGA T0299 47 :FTSIDSKAQLVEKLETFFAVHYPFI 1eqcA 155 :FQNGDNTQVTLNVLNTIFKKYGGNE T0299 72 :QSFSL 1eqcA 184 :VIGIE T0299 77 :LSLEDFEAELEN 1eqcA 198 :LNMDKLKQFFLD T0299 91 :A 1eqcA 229 :F T0299 92 :WWS 1eqcA 231 :VFG T0299 95 :RDLARKDFLFYTE 1eqcA 241 :VAEGQWNVVVDHH T0299 108 :GLDVDQVIATVESL 1eqcA 264 :SRNINDHISVACNW Number of specific fragments extracted= 11 number of extra gaps= 0 total=362 Number of alignments=47 # 1eqcA read from 1eqcA/merged-good-all-a2m # found chain 1eqcA in template set T0299 4 :YALLVRGINVGGKN 1eqcA 130 :VWIDLHGAPGSQNG T0299 19 :V 1eqcA 144 :F T0299 21 :MAELRQELTNL 1eqcA 161 :TQVTLNVLNTI T0299 32 :GLEKVESYINSGN 1eqcA 179 :EYSDVVIGIELLN T0299 48 :TSID 1eqcA 194 :LGPV T0299 52 :SKAQLVEKLETFFAV 1eqcA 199 :NMDKLKQFFLDGYNS T0299 67 :HYPFIQSFSLLSL 1eqcA 216 :QTGSVTPVIIHDA T0299 87 :ENLPAWWSRDLARKDFLFYTE 1eqcA 233 :GYWNNFLTVAEGQWNVVVDHH T0299 108 :GLDVDQVIATVESL 1eqcA 264 :SRNINDHISVACNW Number of specific fragments extracted= 9 number of extra gaps= 0 total=371 Number of alignments=48 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1wdjA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1wdjA expands to /projects/compbio/data/pdb/1wdj.pdb.gz 1wdjA:# T0299 read from 1wdjA/merged-good-all-a2m # 1wdjA read from 1wdjA/merged-good-all-a2m # adding 1wdjA to template set # found chain 1wdjA in template set T0299 16 :KNKVVMAELRQELTNLG 1wdjA 8 :ARPVSEEELRRLSELNP T0299 43 :GNIFFTSIDSK 1wdjA 34 :GRLWVSPTGGE T0299 54 :AQLVEKLETFFAVH 1wdjA 50 :LQLAYQLARWNEER T0299 68 :YP 1wdjA 77 :FP T0299 71 :IQSFSLLSLEDFE 1wdjA 84 :SPDAAFVERGAWE T0299 84 :AELENLPAW 1wdjA 101 :AEREGFPPL T0299 97 :LARKDFLFYTEGLDVDQVIATVESLEL 1wdjA 110 :APKAVFEVRSASQDPEELRAKMGIYLR T0299 127 :VLYFGKLGIFW 1wdjA 144 :LVDPYARAVEV T0299 140 :FSEESY 1wdjA 155 :FRPGKP Number of specific fragments extracted= 9 number of extra gaps= 0 total=380 Number of alignments=49 # 1wdjA read from 1wdjA/merged-good-all-a2m # found chain 1wdjA in template set T0299 16 :KNKVVMAELRQELTNLG 1wdjA 8 :ARPVSEEELRRLSELNP T0299 43 :GNIFFT 1wdjA 34 :GRLWVS T0299 49 :SIDSK 1wdjA 41 :TGGES T0299 54 :AQLVEKLETFFAVH 1wdjA 50 :LQLAYQLARWNEER T0299 68 :YP 1wdjA 77 :FP T0299 71 :IQSFSLLSLED 1wdjA 84 :SPDAAFVERGA T0299 86 :LENLPAWWS 1wdjA 95 :WEALSEAER T0299 95 :RDLARKDFLFYTEGLDVDQVIATVESL 1wdjA 108 :PLAPKAVFEVRSASQDPEELRAKMGIY T0299 122 :ELK 1wdjA 136 :RNG T0299 127 :VLYFGKLGIFW 1wdjA 144 :LVDPYARAVEV T0299 140 :FSEESY 1wdjA 155 :FRPGKP Number of specific fragments extracted= 11 number of extra gaps= 0 total=391 Number of alignments=50 # 1wdjA read from 1wdjA/merged-good-all-a2m # found chain 1wdjA in template set T0299 16 :KNKVVMAELRQELTNLG 1wdjA 8 :ARPVSEEELRRLSELNP T0299 43 :GNIFFTSID 1wdjA 34 :GRLWVSPTG T0299 54 :AQLVEKLETFFAVH 1wdjA 50 :LQLAYQLARWNEER T0299 68 :YP 1wdjA 77 :FP T0299 71 :IQSFSLLSLE 1wdjA 84 :SPDAAFVERG T0299 85 :ELENLPAWWSRDLARKD 1wdjA 94 :AWEALSEAEREGFPPLA T0299 102 :FLFYTE 1wdjA 113 :AVFEVR T0299 108 :GLDVDQVIATVESLELKD 1wdjA 121 :SQDPEELRAKMGIYLRNG T0299 126 :EVLYFGKLGIFWGKFSEESYS 1wdjA 143 :VLVDPYARAVEVFRPGKPPLR Number of specific fragments extracted= 9 number of extra gaps= 0 total=400 Number of alignments=51 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1vjrA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1vjrA expands to /projects/compbio/data/pdb/1vjr.pdb.gz 1vjrA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 172, because occupancy 0.330 <= existing 0.340 in 1vjrA Skipped atom 173, because occupancy 0.330 <= existing 0.340 in 1vjrA Skipped atom 177, because occupancy 0.330 <= existing 0.340 in 1vjrA Skipped atom 178, because occupancy 0.330 <= existing 0.340 in 1vjrA Skipped atom 180, because occupancy 0.330 <= existing 0.340 in 1vjrA Skipped atom 181, because occupancy 0.330 <= existing 0.340 in 1vjrA Skipped atom 183, because occupancy 0.330 <= existing 0.340 in 1vjrA Skipped atom 184, because occupancy 0.330 <= existing 0.340 in 1vjrA Skipped atom 186, because occupancy 0.330 <= existing 0.340 in 1vjrA Skipped atom 187, because occupancy 0.330 <= existing 0.340 in 1vjrA Skipped atom 237, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 241, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 243, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 245, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 247, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 249, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 271, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 275, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 277, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 279, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 281, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 283, because occupancy 0.500 <= existing 0.500 in 1vjrA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 1601, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 1605, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 1607, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 1609, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 1611, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 1613, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 1616, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 1620, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 1622, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 1624, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 1626, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 1628, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 1630, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 1632, because occupancy 0.500 <= existing 0.500 in 1vjrA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 1868, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 1872, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 1874, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 1876, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 1878, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 1880, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 1912, because occupancy 0.350 <= existing 0.650 in 1vjrA Skipped atom 1914, because occupancy 0.350 <= existing 0.650 in 1vjrA Skipped atom 1916, because occupancy 0.350 <= existing 0.650 in 1vjrA Skipped atom 1918, because occupancy 0.350 <= existing 0.650 in 1vjrA Skipped atom 1920, because occupancy 0.350 <= existing 0.650 in 1vjrA Skipped atom 1922, because occupancy 0.350 <= existing 0.650 in 1vjrA Skipped atom 1930, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 1934, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 1936, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 1938, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 1940, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 1942, because occupancy 0.500 <= existing 0.500 in 1vjrA # T0299 read from 1vjrA/merged-good-all-a2m # 1vjrA read from 1vjrA/merged-good-all-a2m # adding 1vjrA to template set # found chain 1vjrA in template set T0299 3 :RYALLVRG 1vjrA 39 :RFVFFTNN T0299 17 :NKVVMAELRQELTNLGL 1vjrA 47 :SSLGAQDYVRKLRNMGV T0299 34 :EKVES 1vjrA 68 :DAVVT T0299 63 :FFAVHYP 1vjrA 80 :HMLKRFG T0299 71 :IQSFSLLSLEDFEAELENLPAWWSRDLARKDFLFYTEGLD 1vjrA 87 :RCRIFLLGTPQLKKVFEAYGHVIDEENPDFVVLGFDKTLT T0299 112 :DQVIATVESLELKDEVLYFGK 1vjrA 127 :YERLKKACILLRKGKFYIATH T0299 138 :GKFSEESYSK 1vjrA 151 :NCPSKEGPVP T0299 148 :TAYHKYLLKVPFYRHITIRNAKTFDKIGQMLK 1vjrA 166 :MAAIEASTGRKPDLIAGKPNPLVVDVISEKFG Number of specific fragments extracted= 8 number of extra gaps= 0 total=408 Number of alignments=52 # 1vjrA read from 1vjrA/merged-good-all-a2m # found chain 1vjrA in template set T0299 21 :MAELRQELTNLGL 1vjrA 26 :SLEFLETLKEKNK T0299 37 :ESYINSGN 1vjrA 39 :RFVFFTNN T0299 49 :SIDSKAQLVEKLET 1vjrA 47 :SSLGAQDYVRKLRN T0299 63 :FFAVHYP 1vjrA 80 :HMLKRFG T0299 71 :IQSFSLLSLEDFEAELENLPAWWSRDLARKDFLFYTEGLDVDQ 1vjrA 87 :RCRIFLLGTPQLKKVFEAYGHVIDEENPDFVVLGFDKTLTYER T0299 115 :IATVESLELKDEVL 1vjrA 130 :LKKACILLRKGKFY T0299 138 :GKFSEES 1vjrA 151 :NCPSKEG T0299 146 :SKTAYHKYLLKVPFYRHITIRNAKTFDKIGQMLK 1vjrA 164 :SIMAAIEASTGRKPDLIAGKPNPLVVDVISEKFG Number of specific fragments extracted= 8 number of extra gaps= 0 total=416 Number of alignments=53 # 1vjrA read from 1vjrA/merged-good-all-a2m # found chain 1vjrA in template set T0299 3 :RYALLVR 1vjrA 39 :RFVFFTN T0299 13 :VGG 1vjrA 46 :NSS T0299 19 :VVMAELRQELTNLGL 1vjrA 49 :LGAQDYVRKLRNMGV T0299 34 :EKVES 1vjrA 68 :DAVVT T0299 63 :FFAVHYPF 1vjrA 80 :HMLKRFGR T0299 72 :QSFSLLSLEDFEAELENLPAWWSRDL 1vjrA 88 :CRIFLLGTPQLKKVFEAYGHVIDEEN T0299 99 :RKDFLFYTEGLDVDQVIATVESLELKDEVLYFGK 1vjrA 114 :PDFVVLGFDKTLTYERLKKACILLRKGKFYIATH T0299 138 :GKFSEESYS 1vjrA 151 :NCPSKEGPV T0299 147 :KTAYHKYLLKVPFYRHITIRNAKTFDKIGQMLKK 1vjrA 165 :IMAAIEASTGRKPDLIAGKPNPLVVDVISEKFGV Number of specific fragments extracted= 9 number of extra gaps= 0 total=425 Number of alignments=54 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1k68A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1k68A expands to /projects/compbio/data/pdb/1k68.pdb.gz 1k68A:Bad short name: P for alphabet: pdb_atoms Bad short name: OP1 for alphabet: pdb_atoms Bad short name: OP2 for alphabet: pdb_atoms Bad short name: OP3 for alphabet: pdb_atoms Skipped atom 719, because occupancy 0.500 <= existing 0.500 in 1k68A # T0299 read from 1k68A/merged-good-all-a2m # 1k68A read from 1k68A/merged-good-all-a2m # adding 1k68A to template set # found chain 1k68A in template set T0299 2 :TRYALLVR 1k68A 10 :HKKIFLVE T0299 52 :SKAQLVEKLETFFAVHYPFIQSFSLLSLEDFEAELENLPAWWS 1k68A 18 :DNKADIRLIQEALANSTVPHEVVTVRDGMEAMAYLRQEGEYAN T0299 95 :RDLARKDFLFYTEGLD 1k68A 89 :PTLKRIPVVVLSTSIN T0299 112 :DQVIATVESLEL 1k68A 105 :EDDIFHSYDLHV T0299 138 :GKFSEESYSKTAYHKYLL 1k68A 117 :NCYITKSANLSQLFQIVK Number of specific fragments extracted= 5 number of extra gaps= 0 total=430 Number of alignments=55 # 1k68A read from 1k68A/merged-good-all-a2m # found chain 1k68A in template set T0299 2 :TRYALLVR 1k68A 10 :HKKIFLVE T0299 52 :SKAQLVEKLETFFAVHYPFIQSFSLLSLEDFEAELENLPAWWS 1k68A 18 :DNKADIRLIQEALANSTVPHEVVTVRDGMEAMAYLRQEGEYAN T0299 95 :RDLARKDFLFYTEGLDVDQ 1k68A 89 :PTLKRIPVVVLSTSINEDD T0299 115 :IATVESLEL 1k68A 108 :IFHSYDLHV T0299 138 :GKFSEESYSKTAYHKYLL 1k68A 117 :NCYITKSANLSQLFQIVK Number of specific fragments extracted= 5 number of extra gaps= 0 total=435 Number of alignments=56 # 1k68A read from 1k68A/merged-good-all-a2m # found chain 1k68A in template set Warning: unaligning (T0299)Y105 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1k68A)L71 Warning: unaligning (T0299)E107 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1k68A)L71 T0299 46 :FFT 1k68A 14 :FLV T0299 50 :IDS 1k68A 17 :EDN T0299 54 :AQLVEKLETFFAVHYPFIQSFSLLSLEDFEAELENLPAW 1k68A 20 :KADIRLIQEALANSTVPHEVVTVRDGMEAMAYLRQEGEY T0299 95 :RDLARKDFLF 1k68A 59 :ANASRPDLIL T0299 108 :GLDVDQVIATVESLELKD 1k68A 72 :NLPKKDGREVLAEIKSDP Number of specific fragments extracted= 5 number of extra gaps= 0 total=440 Number of alignments=57 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1jysA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1jysA expands to /projects/compbio/data/pdb/1jys.pdb.gz 1jysA:# T0299 read from 1jysA/merged-good-all-a2m # 1jysA read from 1jysA/merged-good-all-a2m # adding 1jysA to template set # found chain 1jysA in template set Warning: unaligning (T0299)D110 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1jysA)S206 T0299 21 :MAELRQELTNLGLEKVESYINSGNIFFTSIDSKAQLVEK 1jysA 126 :IAAAEACIAELNLNAVRGLIVSGDAFINGSVGLAKIRHN T0299 68 :YP 1jysA 165 :FP T0299 71 :IQSFSLLSLEDFEAELEN 1jysA 167 :QAIAVEMEATAIAHVCHN T0299 95 :RDLARKDFLFYTE 1jysA 185 :FNVPFVVVRAISD T0299 111 :VDQVIATVES 1jysA 207 :FDEFLAVAAK Number of specific fragments extracted= 5 number of extra gaps= 0 total=445 Number of alignments=58 # 1jysA read from 1jysA/merged-good-all-a2m # found chain 1jysA in template set Warning: unaligning (T0299)D110 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1jysA)S206 T0299 21 :MAELRQELTNLGLEKVESYINSGNIFFTSIDSKAQLVEK 1jysA 126 :IAAAEACIAELNLNAVRGLIVSGDAFINGSVGLAKIRHN T0299 68 :YPF 1jysA 165 :FPQ T0299 72 :QSFSLLSLEDFEAEL 1jysA 168 :AIAVEMEATAIAHVC T0299 93 :WSRDLARKDFLFYTE 1jysA 183 :HNFNVPFVVVRAISD T0299 111 :VDQVIATVES 1jysA 207 :FDEFLAVAAK Number of specific fragments extracted= 5 number of extra gaps= 0 total=450 Number of alignments=59 # 1jysA read from 1jysA/merged-good-all-a2m # found chain 1jysA in template set T0299 21 :MAELRQELTNLGLEKVESYINSGN 1jysA 126 :IAAAEACIAELNLNAVRGLIVSGD T0299 50 :ID 1jysA 150 :AF T0299 52 :SKAQ 1jysA 154 :GSVG T0299 57 :VEKLETF 1jysA 158 :LAKIRHN T0299 68 :YP 1jysA 165 :FP T0299 71 :IQSFSLLSLEDFEAELENL 1jysA 167 :QAIAVEMEATAIAHVCHNF Number of specific fragments extracted= 6 number of extra gaps= 0 total=456 Number of alignments=60 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ccwA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0299 read from 1ccwA/merged-good-all-a2m # 1ccwA read from 1ccwA/merged-good-all-a2m # found chain 1ccwA in training set Warning: unaligning (T0299)T2 because of BadResidue code BAD_PEPTIDE in next template residue (1ccwA)K4 Warning: unaligning (T0299)R3 because of BadResidue code BAD_PEPTIDE at template residue (1ccwA)K4 Warning: unaligning (T0299)F70 because of BadResidue code BAD_PEPTIDE in next template residue (1ccwA)D56 Warning: unaligning (T0299)Q72 because of BadResidue code BAD_PEPTIDE at template residue (1ccwA)D56 Warning: unaligning (T0299)E107 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1ccwA)I94 T0299 4 :YALL 1ccwA 5 :TIVL T0299 10 :GINVGGKNKVVMAELRQELTNLGL 1ccwA 9 :GVIGSDCHAVGNKILDHAFTNAGF T0299 35 :KVESY 1ccwA 33 :NVVNI T0299 40 :IN 1ccwA 39 :VL T0299 52 :SKAQLVEKLETF 1ccwA 42 :PQELFIKAAIET T0299 69 :P 1ccwA 54 :K T0299 73 :SFSLLS 1ccwA 57 :AILVSS T0299 82 :FEAELENL 1ccwA 74 :LRQKCDEA T0299 96 :DLARKDFLFYT 1ccwA 82 :GLEGILLYVGG T0299 108 :GLDVDQVIATVESLEL 1ccwA 98 :KQHWPDVEKRFKDMGY T0299 138 :GKFSEESYSKTAYHKYLLK 1ccwA 114 :DRVYAPGTPPEVGIADLKK Number of specific fragments extracted= 11 number of extra gaps= 3 total=467 Number of alignments=61 # 1ccwA read from 1ccwA/merged-good-all-a2m # found chain 1ccwA in training set Warning: unaligning (T0299)T2 because of BadResidue code BAD_PEPTIDE in next template residue (1ccwA)K4 Warning: unaligning (T0299)R3 because of BadResidue code BAD_PEPTIDE at template residue (1ccwA)K4 Warning: unaligning (T0299)F70 because of BadResidue code BAD_PEPTIDE in next template residue (1ccwA)D56 Warning: unaligning (T0299)I71 because of BadResidue code BAD_PEPTIDE at template residue (1ccwA)D56 T0299 4 :YALL 1ccwA 5 :TIVL T0299 10 :GINVGGKNKVVMAELRQELTNLGLE 1ccwA 9 :GVIGSDCHAVGNKILDHAFTNAGFN T0299 36 :VESY 1ccwA 34 :VVNI T0299 44 :N 1ccwA 39 :V T0299 52 :SKAQLVEKLETF 1ccwA 42 :PQELFIKAAIET T0299 69 :P 1ccwA 54 :K T0299 72 :QSFSLLS 1ccwA 57 :AILVSSL T0299 82 :FEAELENL 1ccwA 74 :LRQKCDEA T0299 96 :DLARKDFLFY 1ccwA 82 :GLEGILLYVG T0299 106 :TEGLDVDQVIATVESLEL 1ccwA 96 :VGKQHWPDVEKRFKDMGY T0299 138 :GKFSEESYSKTAYHKYLLKV 1ccwA 114 :DRVYAPGTPPEVGIADLKKD Number of specific fragments extracted= 11 number of extra gaps= 2 total=478 Number of alignments=62 # 1ccwA read from 1ccwA/merged-good-all-a2m # found chain 1ccwA in training set Warning: unaligning (T0299)R3 because of BadResidue code BAD_PEPTIDE at template residue (1ccwA)K4 Warning: unaligning (T0299)F70 because of BadResidue code BAD_PEPTIDE in next template residue (1ccwA)D56 Warning: unaligning (T0299)Q72 because of BadResidue code BAD_PEPTIDE at template residue (1ccwA)D56 Warning: unaligning (T0299)E107 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1ccwA)I94 T0299 4 :YALL 1ccwA 5 :TIVL T0299 10 :GINVGGKNKVVMAELRQELTNLGL 1ccwA 9 :GVIGSDCHAVGNKILDHAFTNAGF T0299 35 :KVESY 1ccwA 33 :NVVNI T0299 52 :SKAQLVEKLETF 1ccwA 42 :PQELFIKAAIET T0299 69 :P 1ccwA 54 :K T0299 73 :SFSLLS 1ccwA 57 :AILVSS T0299 82 :FEAELENL 1ccwA 74 :LRQKCDEA T0299 96 :DLARKDFLFYT 1ccwA 82 :GLEGILLYVGG T0299 108 :GLDVDQVIATVESLELKD 1ccwA 98 :KQHWPDVEKRFKDMGYDR T0299 140 :FSEESYSKTA 1ccwA 116 :VYAPGTPPEV T0299 170 :TFDKIGQMLKK 1ccwA 126 :GIADLKKDLNI Number of specific fragments extracted= 11 number of extra gaps= 3 total=489 Number of alignments=63 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1u0sA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1u0sA expands to /projects/compbio/data/pdb/1u0s.pdb.gz 1u0sA:Skipped atom 1009, because occupancy 0.500 <= existing 0.500 in 1u0sA Skipped atom 1011, because occupancy 0.500 <= existing 0.500 in 1u0sA Skipped atom 1013, because occupancy 0.500 <= existing 0.500 in 1u0sA Skipped atom 1015, because occupancy 0.500 <= existing 0.500 in 1u0sA Skipped atom 1017, because occupancy 0.500 <= existing 0.500 in 1u0sA Skipped atom 1019, because occupancy 0.500 <= existing 0.500 in 1u0sA Skipped atom 1021, because occupancy 0.500 <= existing 0.500 in 1u0sA Skipped atom 1023, because occupancy 0.500 <= existing 0.500 in 1u0sA Skipped atom 1025, because occupancy 0.500 <= existing 0.500 in 1u0sA # T0299 read from 1u0sA/merged-good-all-a2m # 1u0sA read from 1u0sA/merged-good-all-a2m # adding 1u0sA to template set # found chain 1u0sA in template set T0299 45 :IFFT 1u0sA 183 :VILK T0299 49 :SIDSKAQLVEKLETFFAV 1u0sA 188 :GTQLKSARIYLVFHKLEE T0299 68 :YPFIQSFSLLSLEDFE 1u0sA 206 :LKCEVVRTIPSVEEIE T0299 94 :SRDLARKDFLFYTEGLDVDQVIATVESLE 1u0sA 222 :EEKFENEVELFVISPVDLEKLSEALSSIA T0299 124 :KDEVLYFGK 1u0sA 251 :DIERVIIKE Number of specific fragments extracted= 5 number of extra gaps= 0 total=494 Number of alignments=64 # 1u0sA read from 1u0sA/merged-good-all-a2m # found chain 1u0sA in template set T0299 45 :IFFT 1u0sA 183 :VILK T0299 49 :SIDSKAQL 1u0sA 189 :TQLKSARI T0299 58 :EKLETFFAV 1u0sA 197 :YLVFHKLEE T0299 68 :YPFIQSFSLLSLEDFE 1u0sA 206 :LKCEVVRTIPSVEEIE T0299 94 :SRDLARKDFLFYTEGLDVDQVIATVESLE 1u0sA 222 :EEKFENEVELFVISPVDLEKLSEALSSIA T0299 124 :KDEVLYFGK 1u0sA 251 :DIERVIIKE Number of specific fragments extracted= 6 number of extra gaps= 0 total=500 Number of alignments=65 # 1u0sA read from 1u0sA/merged-good-all-a2m # found chain 1u0sA in template set T0299 22 :AELRQELTNLGLE 1u0sA 197 :YLVFHKLEELKCE T0299 46 :FFTSIDSKAQLV 1u0sA 210 :VVRTIPSVEEIE T0299 65 :AVHYPFIQSFSL 1u0sA 222 :EEKFENEVELFV T0299 78 :SLEDFEAELENLPAW 1u0sA 238 :DLEKLSEALSSIADI T0299 126 :E 1u0sA 253 :E Number of specific fragments extracted= 5 number of extra gaps= 0 total=505 Number of alignments=66 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1yqgA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1yqgA expands to /projects/compbio/data/pdb/1yqg.pdb.gz 1yqgA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0299 read from 1yqgA/merged-good-all-a2m # 1yqgA read from 1yqgA/merged-good-all-a2m # adding 1yqgA to template set # found chain 1yqgA in template set T0299 4 :YALLVRG 1yqgA 2 :NVYFLGG T0299 21 :MAELRQELTNL 1yqgA 12 :AAAVAGGLVKQ T0299 34 :EKVESYINS 1yqgA 23 :GGYRIYIAN T0299 51 :DSKAQ 1yqgA 32 :RGAEK T0299 61 :ETFFAVHYPFIQS 1yqgA 37 :RERLEKELGVETS T0299 74 :FSLLSLEDFEAELENL 1yqgA 62 :ILAVKPQDMEAACKNI T0299 96 :DLARKDFLFYTEGLDVDQVIATVESLE 1yqgA 78 :RTNGALVLSVAAGLSVGTLSRYLGGTR T0299 126 :EVLYFGK 1yqgA 105 :RIVRVMP T0299 134 :GIFW 1yqgA 121 :VSGM T0299 140 :FSEESYSKTAYH 1yqgA 125 :YAEAEVSETDRR Number of specific fragments extracted= 10 number of extra gaps= 0 total=515 Number of alignments=67 # 1yqgA read from 1yqgA/merged-good-all-a2m # found chain 1yqgA in template set T0299 4 :YALLVRG 1yqgA 2 :NVYFLGG T0299 21 :MAELRQELTNL 1yqgA 12 :AAAVAGGLVKQ T0299 34 :EKVESYINS 1yqgA 23 :GGYRIYIAN T0299 51 :DSKAQL 1yqgA 32 :RGAEKR T0299 62 :TFFAVHYPFIQS 1yqgA 38 :ERLEKELGVETS T0299 74 :FSLLSLEDFEAELENL 1yqgA 62 :ILAVKPQDMEAACKNI T0299 96 :DLARKDFLFYTEGLDVDQVIATVESLEL 1yqgA 78 :RTNGALVLSVAAGLSVGTLSRYLGGTRR T0299 134 :GIFW 1yqgA 121 :VSGM T0299 140 :FSEESYSKT 1yqgA 125 :YAEAEVSET T0299 149 :AYHKYLL 1yqgA 136 :RIADRIM Number of specific fragments extracted= 10 number of extra gaps= 0 total=525 Number of alignments=68 # 1yqgA read from 1yqgA/merged-good-all-a2m # found chain 1yqgA in template set T0299 4 :YALLVRG 1yqgA 2 :NVYFLGG T0299 21 :MAELRQELTNL 1yqgA 12 :AAAVAGGLVKQ T0299 34 :EKVESYINS 1yqgA 23 :GGYRIYIAN T0299 51 :DSKAQ 1yqgA 32 :RGAEK T0299 61 :ETFFAVHYPFIQS 1yqgA 37 :RERLEKELGVETS T0299 74 :FSLLSLEDFEAELENL 1yqgA 62 :ILAVKPQDMEAACKNI T0299 96 :DLARKDFLFYTEGLDVDQVIATVESLEL 1yqgA 78 :RTNGALVLSVAAGLSVGTLSRYLGGTRR Number of specific fragments extracted= 7 number of extra gaps= 0 total=532 Number of alignments=69 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1bqcA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0299 read from 1bqcA/merged-good-all-a2m # 1bqcA read from 1bqcA/merged-good-all-a2m # found chain 1bqcA in training set T0299 5 :ALLVRG 1bqcA 80 :ICMLEV T0299 14 :GGKNKVVMAELRQELTNL 1bqcA 93 :EQSGASTLDQAVDYWIEL T0299 32 :GLEK 1bqcA 116 :GEED T0299 37 :ESYINSGNIFFT 1bqcA 120 :YVLINIGNEPYG T0299 49 :SIDSKAQLVEKLETFFAV 1bqcA 133 :DSATVAAWATDTSAAIQR T0299 67 :HYPFIQSFSLLS 1bqcA 153 :AAGFEHTLVVDA T0299 79 :LEDFEAELENLPA 1bqcA 176 :RNNADQVYASDPT T0299 98 :ARKDFLFYTEG 1bqcA 189 :GNTVFSIHMYG T0299 109 :LDVDQVIATVESLELKD 1bqcA 202 :SQASTITSYLEHFVNAG T0299 133 :LGIFWGKFSEES 1bqcA 219 :LPLIIGEFGHDH Number of specific fragments extracted= 10 number of extra gaps= 0 total=542 Number of alignments=70 # 1bqcA read from 1bqcA/merged-good-all-a2m # found chain 1bqcA in training set T0299 5 :ALLVR 1bqcA 80 :ICMLE T0299 14 :GGKNKVVMAELRQELTNL 1bqcA 93 :EQSGASTLDQAVDYWIEL T0299 32 :GLE 1bqcA 116 :GEE T0299 38 :SYINSGNIFFT 1bqcA 121 :VLINIGNEPYG T0299 49 :SIDSKAQLVEKLETFFAV 1bqcA 133 :DSATVAAWATDTSAAIQR T0299 67 :HYPFIQSFSLLS 1bqcA 153 :AAGFEHTLVVDA T0299 79 :LEDFEAELENLPA 1bqcA 176 :RNNADQVYASDPT T0299 98 :ARKDFLFYTEG 1bqcA 189 :GNTVFSIHMYG T0299 109 :LDVDQVIATVESLEL 1bqcA 202 :SQASTITSYLEHFVN T0299 125 :DE 1bqcA 218 :GL T0299 133 :LGIFWGKFSEE 1bqcA 220 :PLIIGEFGHDH T0299 144 :SYSKTAYHKYLLKVPFY 1bqcA 234 :NPDEDTIMAEAERLKLG Number of specific fragments extracted= 12 number of extra gaps= 0 total=554 Number of alignments=71 # 1bqcA read from 1bqcA/merged-good-all-a2m # found chain 1bqcA in training set T0299 5 :ALLVR 1bqcA 80 :ICMLE T0299 13 :VGGKNKVVMAELRQELTNL 1bqcA 92 :GEQSGASTLDQAVDYWIEL T0299 32 :GLEK 1bqcA 116 :GEED T0299 37 :ESYINSGNIFFTSID 1bqcA 120 :YVLINIGNEPYGNDS T0299 52 :SKAQLVEKLETFFAV 1bqcA 136 :TVAAWATDTSAAIQR T0299 67 :HYPFIQSFSLLS 1bqcA 153 :AAGFEHTLVVDA T0299 79 :LEDFEAELENLPAW 1bqcA 176 :RNNADQVYASDPTG T0299 100 :KDFLFYTEG 1bqcA 190 :NTVFSIHMY T0299 109 :LDVDQVIATVE 1bqcA 202 :SQASTITSYLE Number of specific fragments extracted= 9 number of extra gaps= 0 total=563 Number of alignments=72 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1fxlA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0299 read from 1fxlA/merged-good-all-a2m # 1fxlA read from 1fxlA/merged-good-all-a2m # found chain 1fxlA in training set T0299 11 :INVGGKN 1fxlA 43 :VNYLPQN T0299 19 :VVMAELRQELTNL 1fxlA 50 :MTQEEFRSLFGSI T0299 32 :GLEKVESYI 1fxlA 64 :EIESCKLVR T0299 41 :NSGNIFFTS 1fxlA 79 :SLGYGFVNY T0299 51 :DSKA 1fxlA 88 :IDPK T0299 59 :KLETFFAVHYPFIQ 1fxlA 92 :DAEKAINTLNGLRL T0299 73 :SFSLLSL 1fxlA 109 :TIKVSYA T0299 89 :LPA 1fxlA 116 :RPS T0299 94 :SRDLARKDFLF 1fxlA 119 :SASIRDANLYV T0299 105 :YTEGLDVDQVIATVESLEL 1fxlA 132 :LPKTMTQKELEQLFSQYGR T0299 124 :KDEVLYFGK 1fxlA 152 :ITSRILVDQ T0299 133 :LGIFW 1fxlA 167 :GVGFI T0299 140 :FSEESYSKTAYHKYLLKVPF 1fxlA 172 :RFDKRIEAEEAIKGLNGQKP Number of specific fragments extracted= 13 number of extra gaps= 0 total=576 Number of alignments=73 # 1fxlA read from 1fxlA/merged-good-all-a2m # found chain 1fxlA in training set T0299 12 :NVGGKN 1fxlA 44 :NYLPQN T0299 19 :VVMAELRQELTNL 1fxlA 50 :MTQEEFRSLFGSI T0299 32 :GLEKVESYI 1fxlA 64 :EIESCKLVR T0299 41 :NSGNIFFTSIDSK 1fxlA 79 :SLGYGFVNYIDPK T0299 59 :KLETFFAVHYPFIQ 1fxlA 92 :DAEKAINTLNGLRL T0299 73 :SFSLLS 1fxlA 109 :TIKVSY T0299 89 :LPAWWSRDLARKDFLFYTEGLDVDQVIATVESLEL 1fxlA 116 :RPSSASIRDANLYVSGLPKTMTQKELEQLFSQYGR T0299 124 :KDEVLYFGK 1fxlA 152 :ITSRILVDQ T0299 133 :LGIFW 1fxlA 167 :GVGFI T0299 140 :FSEESYSKTAYHKYLLKVPF 1fxlA 172 :RFDKRIEAEEAIKGLNGQKP Number of specific fragments extracted= 10 number of extra gaps= 0 total=586 Number of alignments=74 # 1fxlA read from 1fxlA/merged-good-all-a2m # found chain 1fxlA in training set T0299 11 :INVGGKN 1fxlA 43 :VNYLPQN T0299 19 :VVMAELRQELTNLG 1fxlA 50 :MTQEEFRSLFGSIG T0299 33 :LEKVESYI 1fxlA 65 :IESCKLVR T0299 41 :NSGNIFFTSIDSK 1fxlA 79 :SLGYGFVNYIDPK T0299 59 :KLETFFAVHYPFIQ 1fxlA 92 :DAEKAINTLNGLRL T0299 73 :SFSLLSL 1fxlA 109 :TIKVSYA T0299 89 :LPAW 1fxlA 116 :RPSS T0299 95 :RDLARKDFLF 1fxlA 120 :ASIRDANLYV T0299 105 :YTEGLDVDQVIATVESLELKDEVLYFG 1fxlA 132 :LPKTMTQKELEQLFSQYGRIITSRILV T0299 132 :KLGIFWGKFSEE 1fxlA 166 :RGVGFIRFDKRI Number of specific fragments extracted= 10 number of extra gaps= 0 total=596 Number of alignments=75 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ispA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0299 read from 1ispA/merged-good-all-a2m # 1ispA read from 1ispA/merged-good-all-a2m # found chain 1ispA in training set T0299 5 :ALLVRGI 1ispA 6 :VVMVHGI T0299 14 :GGKN 1ispA 13 :GGAS T0299 21 :MAELRQELTNLGLEKVESYI 1ispA 19 :FAGIKSYLVSQGWSRDKLYA T0299 45 :IFFTSID 1ispA 39 :VDFWDKT T0299 52 :SK 1ispA 47 :TN T0299 54 :AQLVEKLETFFAVHYPFIQSFSLLSL 1ispA 53 :PVLSRFVQKVLDETGAKKVDIVAHSM T0299 82 :FEAELENLPAWWS 1ispA 83 :TLYYIKNLDGGNK T0299 101 :DFLFY 1ispA 98 :NVVTL Number of specific fragments extracted= 8 number of extra gaps= 0 total=604 Number of alignments=76 # 1ispA read from 1ispA/merged-good-all-a2m # found chain 1ispA in training set T0299 5 :ALLVRGINVGGKN 1ispA 6 :VVMVHGIGGASFN T0299 21 :MAELRQELTNLGLEKVESYI 1ispA 19 :FAGIKSYLVSQGWSRDKLYA T0299 45 :IFFTSID 1ispA 39 :VDFWDKT T0299 53 :KAQLVEKLETFFAVHYPFIQSFSLLSL 1ispA 52 :GPVLSRFVQKVLDETGAKKVDIVAHSM T0299 85 :ELENLPAWWS 1ispA 86 :YIKNLDGGNK T0299 95 :RDLARKDFLFYTEG 1ispA 118 :DPNQKILYTSIYSS T0299 109 :LDVDQ 1ispA 136 :VMNYL T0299 121 :LELKDEVL 1ispA 141 :SRLDGARN T0299 140 :FSEESYSKTAYHK 1ispA 149 :VQIHGVGHIGLLY T0299 167 :NAKTFDKIGQMLK 1ispA 162 :SSQVNSLIKEGLN Number of specific fragments extracted= 10 number of extra gaps= 0 total=614 Number of alignments=77 # 1ispA read from 1ispA/merged-good-all-a2m # found chain 1ispA in training set T0299 5 :ALLVRGINVGGKN 1ispA 6 :VVMVHGIGGASFN T0299 21 :MAELRQELTNLGLEKVESYIN 1ispA 19 :FAGIKSYLVSQGWSRDKLYAV T0299 46 :FFTSID 1ispA 40 :DFWDKT T0299 52 :SKAQ 1ispA 47 :TNYN T0299 56 :LVEKLETFFAVHYPFIQSFSLLSL 1ispA 55 :LSRFVQKVLDETGAKKVDIVAHSM T0299 82 :FEAELENL 1ispA 83 :TLYYIKNL T0299 96 :DLARKDFLFYTEG 1ispA 91 :DGGNKVANVVTLG Number of specific fragments extracted= 7 number of extra gaps= 0 total=621 Number of alignments=78 # command:Using radius: 8.0000 Alignment mode NUMB_ALIGNS: 78 Adding 3212 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: -312.1383, CN propb: -312.1383 weights: 0.2157 constraints: 703 # command:Found ConstraintSet # PrintContacts align.constraints_v3 Number of constraints in align.constraints 703 # command:Found ConstraintSet # PrintContacts align_bonus.constraints_v3 Number of constraints in align.constraints.bonus 703 # command:Found ConstraintSet # PrintContacts rejected.constraints_v3 Number of constraints in rejected.constraints 2509 # command:Found ConstraintSet # PrintContacts rejected_bonus.constraints_v3 Number of constraints in rejected.constraints.bonus 2509 # 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 3212 # command: