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/T0345/ # command:# Making conformation for sequence T0345 numbered 1 through 185 Created new target T0345 from T0345.a2m # command:# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/T0345/ # command:Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0345//projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0345/manyalignments-good-all.under or /projects/compbio/experiments/protein-predict/casp7/T0345//projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0345/manyalignments-good-all.under.gz for input Trying /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0345/manyalignments-good-all.under # reading script from file /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0345/manyalignments-good-all.under # Reading fragments from alignment file # Attempting to read fragment alignments from file 1o8xA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0345 read from 1o8xA/merged-good-all-a2m # 1o8xA read from 1o8xA/merged-good-all-a2m # found chain 1o8xA in training set Warning: unaligning (T0345)R27 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1o8xA)L30 Warning: unaligning (T0345)A28 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1o8xA)L30 Warning: unaligning (T0345)R54 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (1o8xA)F57 Warning: unaligning (T0345)F55 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (1o8xA)F57 T0345 11 :AINLDGEKVDFNTFRG 1o8xA 13 :KLRRGDGEVEVKSLAG # choosing archetypes in rotamer library T0345 29 :VLIENVASLCGTTTRDFTQLNELQC 1o8xA 31 :VFFYFSASWCPPARGFTPQLIEFYD T0345 56 :PRRLVVLGFP 1o8xA 60 :SKNFEVVFCT T0345 73 :ENCQNEEILNSLK 1o8xA 70 :WDEEEDGFAGYFA T0345 92 :GYQPTFTL 1o8xA 83 :KMPWLAVP T0345 108 :QNEHPVFAYLKDKLPYP 1o8xA 91 :FAQSEAVQKLSKHFNVE T0345 146 :SDVA 1o8xA 108 :SIPT T0345 154 :KFLIG 1o8xA 112 :LIGVD T0345 159 :PEGEPFR 1o8xA 118 :DSGDVVT Number of specific fragments extracted= 9 number of extra gaps= 2 total=9 Number of alignments=1 # 1o8xA read from 1o8xA/merged-good-all-a2m # found chain 1o8xA in training set Warning: unaligning (T0345)R27 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1o8xA)L30 Warning: unaligning (T0345)A28 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1o8xA)L30 Warning: unaligning (T0345)R54 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (1o8xA)F57 Warning: unaligning (T0345)F55 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (1o8xA)F57 T0345 11 :AINLDGEKVDFNTFRG 1o8xA 13 :KLRRGDGEVEVKSLAG T0345 29 :VLIENVASLCGTTTRDFTQLNELQC 1o8xA 31 :VFFYFSASWCPPARGFTPQLIEFYD T0345 56 :PRRLVVLGFPC 1o8xA 60 :SKNFEVVFCTW T0345 74 :NCQNEEILNSLK 1o8xA 71 :DEEEDGFAGYFA T0345 92 :GYQPTFTLV 1o8xA 83 :KMPWLAVPF T0345 109 :NEHPVFAYLKDKLPYP 1o8xA 92 :AQSEAVQKLSKHFNVE T0345 146 :SDVAWNF 1o8xA 108 :SIPTLIG T0345 156 :LIGPEGEPFR 1o8xA 115 :VDADSGDVVT Number of specific fragments extracted= 8 number of extra gaps= 2 total=17 Number of alignments=2 # 1o8xA read from 1o8xA/merged-good-all-a2m # found chain 1o8xA in training set Warning: unaligning (T0345)R27 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1o8xA)L30 Warning: unaligning (T0345)A28 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1o8xA)L30 Warning: unaligning (T0345)C53 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (1o8xA)F57 Warning: unaligning (T0345)R54 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (1o8xA)F57 T0345 15 :DGEKVDFNTFRG 1o8xA 17 :GDGEVEVKSLAG T0345 29 :VLIENVASLCGTTT 1o8xA 31 :VFFYFSASWCPPAR T0345 43 :RDFTQLNELQ 1o8xA 46 :FTPQLIEFYD T0345 55 :FP 1o8xA 58 :HE T0345 57 :RRLVVLGFP 1o8xA 61 :KNFEVVFCT T0345 73 :ENCQNEEILNSLK 1o8xA 70 :WDEEEDGFAGYFA T0345 92 :G 1o8xA 83 :K T0345 95 :PTFTLVQK 1o8xA 84 :MPWLAVPF T0345 109 :NEHPVFAYLKDKLPYPYD 1o8xA 92 :AQSEAVQKLSKHFNVESI T0345 152 :FEKFLIG 1o8xA 110 :PTLIGVD T0345 159 :PEGEPFR 1o8xA 118 :DSGDVVT Number of specific fragments extracted= 11 number of extra gaps= 2 total=28 Number of alignments=3 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1q98A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1q98A expands to /projects/compbio/data/pdb/1q98.pdb.gz 1q98A:# T0345 read from 1q98A/merged-good-all-a2m # 1q98A read from 1q98A/merged-good-all-a2m # adding 1q98A to template set # found chain 1q98A in template set T0345 3 :AKSFYDLSAINLDGEKVDFNTFRGRAVLIENVASL 1q98A 20 :GEIVENFILVGNDLADVALNDFASKRKVLNIFPSI T0345 38 :CGTTT 1q98A 56 :TGVCA T0345 46 :TQLNELQCRF 1q98A 61 :TSVRKFNQQA T0345 56 :PRRLVVLGFPC 1q98A 73 :LSNTIVLCISA T0345 75 :CQNEEILNS 1q98A 84 :DLPFAQARF T0345 88 :RPGGGYQ 1q98A 93 :CGAEGIE T0345 99 :LVQKC 1q98A 100 :NAKTV T0345 106 :NGQNEHPVFAYLK 1q98A 105 :STFRNHALHSQLG T0345 137 :LIIWSPVRRSDV 1q98A 118 :VDIQTGPLAGLT T0345 151 :NFEKFLIGPEGEPFRRY 1q98A 130 :SRAVIVLDEQNNVLHSQ T0345 168 :SRTFP 1q98A 152 :KEEPN T0345 177 :EPDIKRLLK 1q98A 157 :YEAALAVLA Number of specific fragments extracted= 12 number of extra gaps= 0 total=40 Number of alignments=4 # 1q98A read from 1q98A/merged-good-all-a2m # found chain 1q98A in template set T0345 3 :AKSFYDLSAINLDGEKVDFNTFRGRAVLIENVASLC 1q98A 20 :GEIVENFILVGNDLADVALNDFASKRKVLNIFPSID T0345 41 :TTRDFTQLNELQCRF 1q98A 56 :TGVCATSVRKFNQQA T0345 56 :PRRLVVLGFPC 1q98A 73 :LSNTIVLCISA T0345 75 :CQNEEILNSLK 1q98A 84 :DLPFAQARFCG T0345 90 :GGGY 1q98A 95 :AEGI T0345 98 :TLVQK 1q98A 99 :ENAKT T0345 105 :VNGQNEHPVFAYLK 1q98A 104 :VSTFRNHALHSQLG T0345 137 :LIIWSPVRRSDVAW 1q98A 118 :VDIQTGPLAGLTSR T0345 153 :EKFLIGPEGEPFRRYSRT 1q98A 132 :AVIVLDEQNNVLHSQLVE T0345 171 :FPT 1q98A 153 :EEP T0345 177 :EPDIKRLLK 1q98A 157 :YEAALAVLA Number of specific fragments extracted= 11 number of extra gaps= 0 total=51 Number of alignments=5 # 1q98A read from 1q98A/merged-good-all-a2m # found chain 1q98A in template set T0345 3 :AKSFYDLSAINLDGEKVDFNTFRGRAVLIENVASL 1q98A 20 :GEIVENFILVGNDLADVALNDFASKRKVLNIFPSI T0345 38 :CGT 1q98A 56 :TGV T0345 43 :RDFTQLNELQCRFP 1q98A 59 :CATSVRKFNQQAAK T0345 57 :RRLVVLGFPC 1q98A 74 :SNTIVLCISA T0345 75 :CQNEEILNSLK 1q98A 84 :DLPFAQARFCG T0345 88 :RPGGGY 1q98A 95 :AEGIEN T0345 94 :QP 1q98A 102 :KT T0345 105 :VNGQNEHPVFAYLK 1q98A 104 :VSTFRNHALHSQLG T0345 140 :WSPVRRSDVAW 1q98A 121 :QTGPLAGLTSR T0345 153 :EKFLIGPEGEPFRRYS 1q98A 132 :AVIVLDEQNNVLHSQL T0345 169 :RTFPTI 1q98A 153 :EEPNYE T0345 179 :DIKRLL 1q98A 159 :AALAVL Number of specific fragments extracted= 12 number of extra gaps= 0 total=63 Number of alignments=6 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2fy6A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2fy6A expands to /projects/compbio/data/pdb/2fy6.pdb.gz 2fy6A:# T0345 read from 2fy6A/merged-good-all-a2m # 2fy6A read from 2fy6A/merged-good-all-a2m # adding 2fy6A to template set # found chain 2fy6A in template set T0345 11 :AINLDGEK 2fy6A 40 :LKTADNRP T0345 21 :FNTF 2fy6A 48 :ASVY T0345 25 :RGRAVLIENVASLCGTTTRDFTQLNELQC 2fy6A 54 :KDKPTLIKFWASWCPLCLSELGQTEKWAQ T0345 57 :RRLVVLGFPCNQFGHQE 2fy6A 87 :SSANLITVASPGFLHEK T0345 76 :QNEEILNSLKYVRPGG 2fy6A 104 :KDGDFQKWYAGLNYPK T0345 93 :YQ 2fy6A 120 :LP T0345 99 :LV 2fy6A 122 :VV T0345 104 :E 2fy6A 124 :T T0345 108 :QNEHPVFAYL 2fy6A 125 :DNGGTIAQSL T0345 147 :DVAWNFEKFLIGPEGEPFRRYSRTFP 2fy6A 135 :NISVYPSWALIGKDGDVQRIVKGSIN T0345 177 :EPDIKRLLK 2fy6A 161 :EAQALALIR Number of specific fragments extracted= 11 number of extra gaps= 0 total=74 Number of alignments=7 # 2fy6A read from 2fy6A/merged-good-all-a2m # found chain 2fy6A in template set T0345 11 :AINLDGEK 2fy6A 40 :LKTADNRP T0345 21 :FNTF 2fy6A 48 :ASVY T0345 25 :RGRAVLIENVASLCGTTTRDFTQLNELQC 2fy6A 54 :KDKPTLIKFWASWCPLCLSELGQTEKWAQ T0345 54 :RF 2fy6A 85 :KF T0345 56 :PRRLVVLGFP 2fy6A 88 :SANLITVASP T0345 68 :QFGHQE 2fy6A 98 :GFLHEK T0345 76 :QNEEILNSLKYVRPGG 2fy6A 104 :KDGDFQKWYAGLNYPK T0345 93 :YQP 2fy6A 120 :LPV T0345 100 :V 2fy6A 123 :V T0345 109 :NEHPVFAYL 2fy6A 126 :NGGTIAQSL T0345 120 :K 2fy6A 135 :N T0345 148 :VAWNFEKFLIGPEGEPFRRYSRTFPTINIEPDIK 2fy6A 136 :ISVYPSWALIGKDGDVQRIVKGSINEAQALALIR Number of specific fragments extracted= 12 number of extra gaps= 0 total=86 Number of alignments=8 # 2fy6A read from 2fy6A/merged-good-all-a2m # found chain 2fy6A in template set T0345 11 :AINLDGEK 2fy6A 40 :LKTADNRP T0345 21 :FNTF 2fy6A 48 :ASVY T0345 25 :RGRAVLIENVASLCGTTT 2fy6A 54 :KDKPTLIKFWASWCPLCL T0345 43 :RDFTQLNELQCRFPRRLVVLGFPCNQFGHQEN 2fy6A 73 :ELGQTEKWAQDAKFSSANLITVASPGFLHEKK T0345 77 :NEEILNSLKYVRPG 2fy6A 105 :DGDFQKWYAGLNYP T0345 96 :TFTLVQK 2fy6A 119 :KLPVVTD T0345 109 :NEHPVFAYL 2fy6A 126 :NGGTIAQSL T0345 147 :DVAWNFEKFLIGPEGEPFRRYSRTFPTINIEPDIK 2fy6A 135 :NISVYPSWALIGKDGDVQRIVKGSINEAQALALIR Number of specific fragments extracted= 8 number of extra gaps= 0 total=94 Number of alignments=9 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2f9sA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2f9sA expands to /projects/compbio/data/pdb/2f9s.pdb.gz 2f9sA:Skipped atom 182, because occupancy 0.5 <= existing 0.500 in 2f9sA Skipped atom 184, because occupancy 0.500 <= existing 0.500 in 2f9sA Skipped atom 186, because occupancy 0.500 <= existing 0.500 in 2f9sA Skipped atom 188, because occupancy 0.500 <= existing 0.500 in 2f9sA Skipped atom 190, because occupancy 0.500 <= existing 0.500 in 2f9sA Skipped atom 201, because occupancy 0.500 <= existing 0.500 in 2f9sA Skipped atom 203, because occupancy 0.500 <= existing 0.500 in 2f9sA Skipped atom 205, because occupancy 0.000 <= existing 0.000 in 2f9sA Skipped atom 207, because occupancy 0.000 <= existing 0.000 in 2f9sA Skipped atom 284, because occupancy 0.500 <= existing 0.500 in 2f9sA Skipped atom 288, because occupancy 0.500 <= existing 0.500 in 2f9sA Skipped atom 290, because occupancy 0.500 <= existing 0.500 in 2f9sA Skipped atom 292, because occupancy 0.500 <= existing 0.500 in 2f9sA Skipped atom 294, because occupancy 0.500 <= existing 0.500 in 2f9sA Skipped atom 296, because occupancy 0.500 <= existing 0.500 in 2f9sA Skipped atom 298, because occupancy 0.500 <= existing 0.500 in 2f9sA Skipped atom 300, because occupancy 0.500 <= existing 0.500 in 2f9sA Skipped atom 302, because occupancy 0.500 <= existing 0.500 in 2f9sA Skipped atom 304, because occupancy 0.500 <= existing 0.500 in 2f9sA Skipped atom 306, because occupancy 0.500 <= existing 0.500 in 2f9sA Skipped atom 312, because occupancy 0.300 <= existing 0.700 in 2f9sA Skipped atom 314, because occupancy 0.300 <= existing 0.700 in 2f9sA Skipped atom 320, because occupancy 0.000 <= existing 1.000 in 2f9sA Skipped atom 322, because occupancy 0.000 <= existing 1.000 in 2f9sA Skipped atom 324, because occupancy 0.000 <= existing 1.000 in 2f9sA Skipped atom 326, because occupancy 0.000 <= existing 1.000 in 2f9sA Skipped atom 328, because occupancy 0.000 <= existing 1.000 in 2f9sA Skipped atom 357, because occupancy 0.500 <= existing 0.500 in 2f9sA Skipped atom 359, because occupancy 0.500 <= existing 0.500 in 2f9sA Skipped atom 361, because occupancy 0.500 <= existing 0.500 in 2f9sA Skipped atom 363, because occupancy 0.500 <= existing 0.500 in 2f9sA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 424, because occupancy 0.200 <= existing 0.800 in 2f9sA Skipped atom 426, because occupancy 0.200 <= existing 0.800 in 2f9sA Skipped atom 428, because occupancy 0.200 <= existing 0.800 in 2f9sA Skipped atom 430, because occupancy 0.200 <= existing 0.800 in 2f9sA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 749, because occupancy 0.400 <= existing 0.600 in 2f9sA Skipped atom 751, because occupancy 0.400 <= existing 0.600 in 2f9sA Skipped atom 753, because occupancy 0.400 <= existing 0.600 in 2f9sA Skipped atom 755, because occupancy 0.400 <= existing 0.600 in 2f9sA Skipped atom 770, because occupancy 0.500 <= existing 0.500 in 2f9sA Skipped atom 772, because occupancy 0.500 <= existing 0.500 in 2f9sA Skipped atom 778, because occupancy 0.500 <= existing 0.500 in 2f9sA Skipped atom 780, because occupancy 0.500 <= existing 0.500 in 2f9sA Skipped atom 782, because occupancy 0.500 <= existing 0.500 in 2f9sA Skipped atom 784, because occupancy 0.500 <= existing 0.500 in 2f9sA Skipped atom 865, because occupancy 0.500 <= existing 0.500 in 2f9sA Skipped atom 867, because occupancy 0.500 <= existing 0.500 in 2f9sA Skipped atom 951, because occupancy 0.000 <= existing 1.000 in 2f9sA Skipped atom 953, because occupancy 0.000 <= existing 1.000 in 2f9sA Skipped atom 955, because occupancy 0.000 <= existing 1.000 in 2f9sA Skipped atom 957, because occupancy 0.000 <= existing 1.000 in 2f9sA Skipped atom 959, because occupancy 0.000 <= existing 1.000 in 2f9sA Skipped atom 970, because occupancy 0.500 <= existing 0.500 in 2f9sA Skipped atom 972, because occupancy 0.500 <= existing 0.500 in 2f9sA Skipped atom 974, because occupancy 0.000 <= existing 0.000 in 2f9sA Skipped atom 976, because occupancy 0.000 <= existing 0.000 in 2f9sA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 1038, because occupancy 0.000 <= existing 1.000 in 2f9sA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1040, because occupancy 0.000 <= existing 1.000 in 2f9sA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1042, because occupancy 0.000 <= existing 1.000 in 2f9sA Skipped atom 1064, because occupancy 0.500 <= existing 0.500 in 2f9sA Skipped atom 1066, because occupancy 0.500 <= existing 0.500 in 2f9sA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 1119, because occupancy 0.000 <= existing 1.000 in 2f9sA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1121, because occupancy 0.000 <= existing 1.000 in 2f9sA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1123, because occupancy 0.000 <= existing 1.000 in 2f9sA # T0345 read from 2f9sA/merged-good-all-a2m # 2f9sA read from 2f9sA/merged-good-all-a2m # adding 2f9sA to template set # found chain 2f9sA in template set T0345 3 :AKSFYDLSAINLDGEKVDFNTFRGRAVLIENVASLCGTTTRDFTQLNELQCRF 2f9sA 39 :GSDAPNFVLEDTNGKRIELSDLKGKGVFLNFWGTWCEPCKKEFPYMANQYKHF T0345 56 :PRRLVVLGFPC 2f9sA 93 :SQGVEIVAVNV T0345 74 :NCQNEEILNSLKY 2f9sA 104 :GESKIAVHNFMKS T0345 93 :YQPTFTLVQK 2f9sA 117 :YGVNFPVVLD T0345 109 :NEHPVFA 2f9sA 127 :TDRQVLD T0345 120 :KLPYPY 2f9sA 134 :AYDVSP T0345 151 :NFEKFLIGPEGEPFRRYSRTFP 2f9sA 140 :LPTTFLINPEGKVVKVVTGTMT T0345 177 :EPDIKRLLK 2f9sA 162 :ESMIHDYMN Number of specific fragments extracted= 8 number of extra gaps= 0 total=102 Number of alignments=10 # 2f9sA read from 2f9sA/merged-good-all-a2m # found chain 2f9sA in template set Warning: unaligning (T0345)I2 because first residue in template chain is (2f9sA)E38 T0345 3 :AKSFYDLSAINLDGEKVDFNTFRGRAVLIENVASLCGTTTRDFTQLNELQCRF 2f9sA 39 :GSDAPNFVLEDTNGKRIELSDLKGKGVFLNFWGTWCEPCKKEFPYMANQYKHF T0345 56 :PRRLVVLGF 2f9sA 93 :SQGVEIVAV T0345 74 :NCQNEEILNSLKY 2f9sA 104 :GESKIAVHNFMKS T0345 93 :YQPTFTLV 2f9sA 117 :YGVNFPVV T0345 109 :NEHPV 2f9sA 127 :TDRQV T0345 118 :KDKLPYPY 2f9sA 132 :LDAYDVSP T0345 151 :NFEKFLIGPEGEPFRRYSRTFP 2f9sA 140 :LPTTFLINPEGKVVKVVTGTMT T0345 177 :EPDIKRLLK 2f9sA 162 :ESMIHDYMN Number of specific fragments extracted= 8 number of extra gaps= 0 total=110 Number of alignments=11 # 2f9sA read from 2f9sA/merged-good-all-a2m # found chain 2f9sA in template set T0345 4 :KSFYDLSAINLDGEKVDFNTFRGRAVLIENVASLCGTTT 2f9sA 40 :SDAPNFVLEDTNGKRIELSDLKGKGVFLNFWGTWCEPCK T0345 43 :RDFTQLNELQCRFPRRLVVLGFPC 2f9sA 80 :EFPYMANQYKHFKSQGVEIVAVNV T0345 74 :NCQNEEILNSLK 2f9sA 104 :GESKIAVHNFMK T0345 92 :GYQPTFTLVQKC 2f9sA 116 :SYGVNFPVVLDT T0345 108 :QN 2f9sA 128 :DR T0345 116 :YLKDKLPYPY 2f9sA 130 :QVLDAYDVSP T0345 151 :NFEKFLIGPEGEPFRRYSRTFPTINIEPDIK 2f9sA 140 :LPTTFLINPEGKVVKVVTGTMTESMIHDYMN Number of specific fragments extracted= 7 number of extra gaps= 0 total=117 Number of alignments=12 # 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 # T0345 read from 1xzoA/merged-good-all-a2m # 1xzoA read from 1xzoA/merged-good-all-a2m # found chain 1xzoA in training set Warning: unaligning (T0345)C38 because of BadResidue code BAD_PEPTIDE in next template residue (1xzoA)E46 Warning: unaligning (T0345)G39 because of BadResidue code BAD_PEPTIDE at template residue (1xzoA)E46 Warning: unaligning (T0345)Q47 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1xzoA)M56 Warning: unaligning (T0345)L48 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1xzoA)M56 Warning: unaligning (T0345)R145 because of BadResidue code BAD_PEPTIDE in next template residue (1xzoA)D131 Warning: unaligning (T0345)S146 because of BadResidue code BAD_PEPTIDE at template residue (1xzoA)D131 Warning: unaligning (T0345)D147 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1xzoA)Q132 Warning: unaligning (T0345)V148 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1xzoA)V133 Warning: unaligning (T0345)N151 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1xzoA)S137 Warning: unaligning (T0345)F152 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1xzoA)S137 T0345 2 :IAKSFYDLSAINLDGEKVDFNTFRGRAVLIENVASL 1xzoA 9 :LNYEVEPFTFQNQDGKNVSLESLKGEVWLADFIFTN T0345 40 :TTTRDFT 1xzoA 48 :ICPPMTA T0345 49 :NELQCRF 1xzoA 57 :TDLQKKL T0345 56 :PRRLVVLGFP 1xzoA 67 :NIDVRIISFS T0345 70 :GHQENCQNEEILNSLK 1xzoA 77 :VDPENDKPKQLKKFAA T0345 92 :GYQPTFTLVQKC 1xzoA 93 :NYPLSFDNWDFL T0345 106 :NGQNEHPVFAYLKDKLPYPYDD 1xzoA 105 :TGYSQSEIEEFALKSFKAIVKK T0345 142 :PVR 1xzoA 127 :PEG T0345 149 :AW 1xzoA 134 :IH T0345 153 :EKFLIGPEGEPFRRYS 1xzoA 138 :SFYLVGPDGKVLKDYN T0345 169 :RTFPTINIEPDIKR 1xzoA 156 :ENTPYDDIISDVKS Number of specific fragments extracted= 11 number of extra gaps= 4 total=128 Number of alignments=13 # 1xzoA read from 1xzoA/merged-good-all-a2m # found chain 1xzoA in training set Warning: unaligning (T0345)C38 because of BadResidue code BAD_PEPTIDE in next template residue (1xzoA)E46 Warning: unaligning (T0345)G39 because of BadResidue code BAD_PEPTIDE at template residue (1xzoA)E46 Warning: unaligning (T0345)Q47 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1xzoA)M56 Warning: unaligning (T0345)L48 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1xzoA)M56 Warning: unaligning (T0345)R145 because of BadResidue code BAD_PEPTIDE in next template residue (1xzoA)D131 Warning: unaligning (T0345)S146 because of BadResidue code BAD_PEPTIDE at template residue (1xzoA)D131 Warning: unaligning (T0345)D147 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1xzoA)Q132 Warning: unaligning (T0345)V148 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1xzoA)V133 Warning: unaligning (T0345)N151 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1xzoA)S137 Warning: unaligning (T0345)F152 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1xzoA)S137 T0345 2 :IAKSFYDLSAINLDGEKVDFNTFRGRAVLIENVASL 1xzoA 9 :LNYEVEPFTFQNQDGKNVSLESLKGEVWLADFIFTN T0345 40 :TTTRD 1xzoA 47 :TICPP T0345 45 :FT 1xzoA 53 :TA T0345 49 :NELQCRF 1xzoA 57 :TDLQKKL T0345 56 :PRRLVVLGFP 1xzoA 67 :NIDVRIISFS T0345 70 :GHQENCQNEEILNSLK 1xzoA 77 :VDPENDKPKQLKKFAA T0345 92 :GYQPTFTLVQK 1xzoA 93 :NYPLSFDNWDF T0345 105 :VNGQNEHPVFAYLKDKLPYPYDD 1xzoA 104 :LTGYSQSEIEEFALKSFKAIVKK T0345 142 :PVR 1xzoA 127 :PEG T0345 149 :AW 1xzoA 134 :IH T0345 153 :EKFLIGPEGEPFRRYS 1xzoA 138 :SFYLVGPDGKVLKDYN T0345 169 :RTFPTINIEPDIKRL 1xzoA 156 :ENTPYDDIISDVKSA Number of specific fragments extracted= 12 number of extra gaps= 4 total=140 Number of alignments=14 # 1xzoA read from 1xzoA/merged-good-all-a2m # found chain 1xzoA in training set Warning: unaligning (T0345)C38 because of BadResidue code BAD_PEPTIDE in next template residue (1xzoA)E46 Warning: unaligning (T0345)G39 because of BadResidue code BAD_PEPTIDE at template residue (1xzoA)E46 Warning: unaligning (T0345)T46 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1xzoA)M56 Warning: unaligning (T0345)Q47 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1xzoA)M56 Warning: unaligning (T0345)R145 because of BadResidue code BAD_PEPTIDE in next template residue (1xzoA)D131 Warning: unaligning (T0345)S146 because of BadResidue code BAD_PEPTIDE at template residue (1xzoA)D131 Warning: unaligning (T0345)D147 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1xzoA)Q132 Warning: unaligning (T0345)V148 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1xzoA)V133 Warning: unaligning (T0345)N151 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1xzoA)S137 Warning: unaligning (T0345)F152 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1xzoA)S137 T0345 2 :IAKSFYDLSAINLDGEKVDFNTFRGRAVLIENVASL 1xzoA 9 :LNYEVEPFTFQNQDGKNVSLESLKGEVWLADFIFTN T0345 40 :TTT 1xzoA 47 :TIC T0345 43 :RDF 1xzoA 52 :MTA T0345 48 :LNELQCRFPRR 1xzoA 57 :TDLQKKLKAEN T0345 59 :LVVLGFPCN 1xzoA 70 :VRIISFSVD T0345 72 :QENCQNEEILNSLK 1xzoA 79 :PENDKPKQLKKFAA T0345 92 :GYQPTFTLVQKC 1xzoA 93 :NYPLSFDNWDFL T0345 106 :NGQNEHPVFAYLKDKLPYPYD 1xzoA 105 :TGYSQSEIEEFALKSFKAIVK T0345 141 :SPVR 1xzoA 126 :KPEG T0345 149 :AW 1xzoA 134 :IH T0345 153 :EKFLIGPEGEPFRRYS 1xzoA 138 :SFYLVGPDGKVLKDYN T0345 169 :RTFPTINIEPDIKR 1xzoA 156 :ENTPYDDIISDVKS Number of specific fragments extracted= 12 number of extra gaps= 4 total=152 Number of alignments=15 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1v98A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1v98A expands to /projects/compbio/data/pdb/1v98.pdb.gz 1v98A:# T0345 read from 1v98A/merged-good-all-a2m # 1v98A read from 1v98A/merged-good-all-a2m # adding 1v98A to template set # found chain 1v98A in template set T0345 27 :RAVLIENVASLCGTTTRDFTQLNELQCRFPRRLVVLGFPCN 1v98A 51 :PLTLVDFFAPWCGPCRLVSPILEELARDHAGRLKVVKVNVD T0345 75 :CQNEEILNS 1v98A 92 :EHPGLAARY T0345 92 :GYQ 1v98A 101 :GVR T0345 146 :SD 1v98A 104 :SV T0345 152 :FEKFLIGP 1v98A 106 :PTLVLFRR T0345 161 :GEPFRRYSRTFPTINIEPDIKRLLK 1v98A 114 :GAPVATWVGASPRRVLEERLRPYLE Number of specific fragments extracted= 6 number of extra gaps= 0 total=158 Number of alignments=16 # 1v98A read from 1v98A/merged-good-all-a2m # found chain 1v98A in template set T0345 27 :RAVLIENVASLCGTTTRDFTQLNELQCRFPRRLVVLGFPCN 1v98A 51 :PLTLVDFFAPWCGPCRLVSPILEELARDHAGRLKVVKVNVD T0345 75 :CQNEEILNS 1v98A 92 :EHPGLAARY T0345 92 :GYQ 1v98A 101 :GVR T0345 146 :SDVA 1v98A 104 :SVPT T0345 155 :FLIGPEGEPFRRYSRTFPTINIEPDIKRLLK 1v98A 108 :LVLFRRGAPVATWVGASPRRVLEERLRPYLE Number of specific fragments extracted= 5 number of extra gaps= 0 total=163 Number of alignments=17 # 1v98A read from 1v98A/merged-good-all-a2m # found chain 1v98A in template set T0345 27 :RAVLIENVASLCGTTTRDFTQLNELQCRFPRRLVVLGFPC 1v98A 51 :PLTLVDFFAPWCGPCRLVSPILEELARDHAGRLKVVKVNV T0345 74 :NCQNEEILNS 1v98A 91 :DEHPGLAARY T0345 147 :DVAWNFEKFLIGP 1v98A 101 :GVRSVPTLVLFRR T0345 161 :GEPFRRYSRTFPTINIEPDIKRLLK 1v98A 114 :GAPVATWVGASPRRVLEERLRPYLE Number of specific fragments extracted= 4 number of extra gaps= 0 total=167 Number of alignments=18 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1kebA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1kebA expands to /projects/compbio/data/pdb/1keb.pdb.gz 1kebA:# T0345 read from 1kebA/merged-good-all-a2m # 1kebA read from 1kebA/merged-good-all-a2m # adding 1kebA to template set # found chain 1kebA in template set T0345 27 :RAVLIENVASLCGTTTRDFTQLNELQCRFPRRLVVLGFPCNQFGHQEN 1kebA 21 :GAILVDFWAEWCGPCKLIASILDEIADEYQGKLTVAKLNIDQNPGTAP T0345 92 :GYQ 1kebA 69 :KYG T0345 105 :VNG 1kebA 72 :IRG T0345 152 :FEKFLIGPEGEPFRRYSRTFPTINIEPDIKRLL 1kebA 75 :IPTLLLFKNGEVAATKVGALSKGQLKEFLDANL Number of specific fragments extracted= 4 number of extra gaps= 0 total=171 Number of alignments=19 # 1kebA read from 1kebA/merged-good-all-a2m # found chain 1kebA in template set T0345 26 :GRAVLIENVASLCGTTTRDFTQLNELQCRFPRRLVVLGFPCNQFGHQE 1kebA 20 :DGAILVDFWAEWCGPCKLIASILDEIADEYQGKLTVAKLNIDQNPGTA T0345 101 :QKC 1kebA 68 :PKY T0345 120 :KLPYP 1kebA 71 :GIRGI T0345 153 :EKFLIGPEGEPFRRYSRTFPTINIEPDIKRLL 1kebA 76 :PTLLLFKNGEVAATKVGALSKGQLKEFLDANL Number of specific fragments extracted= 4 number of extra gaps= 0 total=175 Number of alignments=20 # 1kebA read from 1kebA/merged-good-all-a2m # found chain 1kebA in template set T0345 27 :RAVLIENVASLCGTTTRDFTQLNELQCRFPRRLVVLGFPCN 1kebA 21 :GAILVDFWAEWCGPCKLIASILDEIADEYQGKLTVAKLNID T0345 120 :KLPYPYD 1kebA 62 :QNPGTAP T0345 145 :RSDVAWNFEKFLI 1kebA 69 :KYGIRGIPTLLLF T0345 159 :PEGEPFRRYSRTFPTINIEPDIKRLL 1kebA 82 :KNGEVAATKVGALSKGQLKEFLDANL Number of specific fragments extracted= 4 number of extra gaps= 0 total=179 Number of alignments=21 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1qxhA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1qxhA expands to /projects/compbio/data/pdb/1qxh.pdb.gz 1qxhA:# T0345 read from 1qxhA/merged-good-all-a2m # 1qxhA read from 1qxhA/merged-good-all-a2m # adding 1qxhA to template set # found chain 1qxhA in template set T0345 2 :IAKSFYDLSAINLDGEKVDFNTFRGRAVLIENVASLC 1qxhA 21 :AGSKAQTFTLVAKDLSDVTLGQFAGKRKVLNIFPSID T0345 41 :TTRDFTQLNELQCRF 1qxhA 58 :TGVCAASVRKFNQLA T0345 56 :P 1qxhA 74 :E T0345 57 :RRLVVLGFPC 1qxhA 76 :DNTVVLCISA T0345 75 :CQNEEILNS 1qxhA 86 :DLPFAQSRF T0345 86 :YVRPGGGY 1qxhA 95 :CGAEGLNN T0345 100 :VQKC 1qxhA 103 :VITL T0345 106 :NGQNEHPVFAYL 1qxhA 107 :STFRNAEFLQAY T0345 136 :KLIIWSPVRRSDVA 1qxhA 119 :GVAIADGPLKGLAA T0345 152 :FEKFLIGPEGEPFRR 1qxhA 133 :RAVVVIDENDNVIFS Number of specific fragments extracted= 10 number of extra gaps= 0 total=189 Number of alignments=22 # 1qxhA read from 1qxhA/merged-good-all-a2m # found chain 1qxhA in template set T0345 3 :AKSFYDLSAINLDGEKVDFNTFRGRAVLIENVASLCGTTTR 1qxhA 22 :GSKAQTFTLVAKDLSDVTLGQFAGKRKVLNIFPSIDTGVCA T0345 46 :TQLNELQCRF 1qxhA 63 :ASVRKFNQLA T0345 56 :P 1qxhA 74 :E T0345 57 :RRLVVLGFPC 1qxhA 76 :DNTVVLCISA T0345 75 :CQNEEILNS 1qxhA 86 :DLPFAQSRF T0345 86 :YVRPGGGY 1qxhA 95 :CGAEGLNN T0345 103 :CEVNGQNEHPVFAYL 1qxhA 104 :ITLSTFRNAEFLQAY T0345 136 :KLIIWSPVRRSDVAW 1qxhA 119 :GVAIADGPLKGLAAR T0345 153 :EKFLIGPEGEPFRRY 1qxhA 134 :AVVVIDENDNVIFSQ Number of specific fragments extracted= 9 number of extra gaps= 0 total=198 Number of alignments=23 # 1qxhA read from 1qxhA/merged-good-all-a2m # found chain 1qxhA in template set T0345 3 :AKSFYDLSAINLDGEKVDFNTFRGRAVLIENVASLCGTT 1qxhA 22 :GSKAQTFTLVAKDLSDVTLGQFAGKRKVLNIFPSIDTGV T0345 43 :RDFTQLNELQCRFP 1qxhA 61 :CAASVRKFNQLATE T0345 57 :RRLVVLGFPC 1qxhA 76 :DNTVVLCISA T0345 75 :CQNEEILNSLK 1qxhA 86 :DLPFAQSRFCG T0345 88 :RPGGGYQPTFTLV 1qxhA 97 :AEGLNNVITLSTF T0345 109 :NEH 1qxhA 110 :RNA T0345 130 :SLMTDPKLIIWSPVRRSDVAW 1qxhA 113 :EFLQAYGVAIADGPLKGLAAR T0345 153 :EKFLIGPEGEPFRRYS 1qxhA 134 :AVVVIDENDNVIFSQL Number of specific fragments extracted= 8 number of extra gaps= 0 total=206 Number of alignments=24 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1faaA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1faaA expands to /projects/compbio/data/pdb/1faa.pdb.gz 1faaA:# T0345 read from 1faaA/merged-good-all-a2m # 1faaA read from 1faaA/merged-good-all-a2m # adding 1faaA to template set # found chain 1faaA in template set T0345 25 :RGRAVLIENVASLCGTTTRDFTQLNELQCRF 1faaA 33 :GDKPVVLDMFTQWCGPCKAMAPKYEKLAEEY T0345 58 :RLVVLGFPCN 1faaA 65 :DVIFLKLDCN T0345 72 :QEN 1faaA 75 :QEN T0345 77 :NEEILNS 1faaA 78 :KTLAKEL T0345 92 :GYQPTFTLVQ 1faaA 87 :RVVPTFKILK T0345 160 :EGEPFRRYSR 1faaA 97 :ENSVVGEVTG T0345 171 :FPTINIEPDIKR 1faaA 107 :AKYDKLLEAIQA Number of specific fragments extracted= 7 number of extra gaps= 0 total=213 Number of alignments=25 # 1faaA read from 1faaA/merged-good-all-a2m # found chain 1faaA in template set T0345 24 :FRGRAVLIENVASLCGTTTRDFTQLNELQCRF 1faaA 32 :AGDKPVVLDMFTQWCGPCKAMAPKYEKLAEEY T0345 58 :RLVVLGFPCNQ 1faaA 65 :DVIFLKLDCNQ T0345 109 :NEHPVFAYL 1faaA 76 :ENKTLAKEL T0345 122 :PYPYDD 1faaA 85 :GIRVVP T0345 153 :EKFLIG 1faaA 91 :TFKILK T0345 160 :EGEPFRRYSR 1faaA 97 :ENSVVGEVTG T0345 171 :FPTINIEPDIKRL 1faaA 107 :AKYDKLLEAIQAA Number of specific fragments extracted= 7 number of extra gaps= 0 total=220 Number of alignments=26 # 1faaA read from 1faaA/merged-good-all-a2m # found chain 1faaA in template set T0345 24 :FRGRAVLIENVASLCGTT 1faaA 32 :AGDKPVVLDMFTQWCGPC T0345 45 :FTQLNELQCRFP 1faaA 50 :KAMAPKYEKLAE T0345 57 :RRLVVLGFPCNQ 1faaA 64 :LDVIFLKLDCNQ T0345 74 :NC 1faaA 76 :EN T0345 77 :NE 1faaA 78 :KT T0345 117 :LKDKLPYPYD 1faaA 80 :LAKELGIRVV T0345 152 :FEKFLIGPE 1faaA 90 :PTFKILKEN T0345 162 :EPFRRYSRT 1faaA 99 :SVVGEVTGA T0345 172 :PTINIEPDIKR 1faaA 108 :KYDKLLEAIQA Number of specific fragments extracted= 9 number of extra gaps= 0 total=229 Number of alignments=27 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2f8aA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2f8aA expands to /projects/compbio/data/pdb/2f8a.pdb.gz 2f8aA:Skipped atom 64, because occupancy 0.500 <= existing 0.500 in 2f8aA Skipped atom 68, because occupancy 0.500 <= existing 0.500 in 2f8aA Skipped atom 70, because occupancy 0.500 <= existing 0.500 in 2f8aA Skipped atom 141, because occupancy 0.500 <= existing 0.500 in 2f8aA Skipped atom 145, because occupancy 0.500 <= existing 0.500 in 2f8aA Skipped atom 147, because occupancy 0.500 <= existing 0.500 in 2f8aA Skipped atom 149, because occupancy 0.500 <= existing 0.500 in 2f8aA Skipped atom 151, because occupancy 0.500 <= existing 0.500 in 2f8aA Skipped atom 365, because occupancy 0.500 <= existing 0.500 in 2f8aA Skipped atom 369, because occupancy 0.500 <= existing 0.500 in 2f8aA Skipped atom 371, because occupancy 0.500 <= existing 0.500 in 2f8aA Skipped atom 373, because occupancy 0.500 <= existing 0.500 in 2f8aA Skipped atom 375, because occupancy 0.500 <= existing 0.500 in 2f8aA Skipped atom 377, because occupancy 0.500 <= existing 0.500 in 2f8aA Skipped atom 797, because occupancy 0.500 <= existing 0.500 in 2f8aA Skipped atom 801, because occupancy 0.500 <= existing 0.500 in 2f8aA Skipped atom 803, because occupancy 0.500 <= existing 0.500 in 2f8aA Skipped atom 805, because occupancy 0.500 <= existing 0.500 in 2f8aA Skipped atom 807, because occupancy 0.500 <= existing 0.500 in 2f8aA Skipped atom 809, because occupancy 0.500 <= existing 0.500 in 2f8aA Skipped atom 999, because occupancy 0.250 <= existing 0.250 in 2f8aA Skipped atom 1004, because occupancy 0.250 <= existing 0.250 in 2f8aA Skipped atom 1007, because occupancy 0.250 <= existing 0.250 in 2f8aA Skipped atom 1010, because occupancy 0.250 <= existing 0.250 in 2f8aA Skipped atom 1103, because occupancy 0.500 <= existing 0.500 in 2f8aA Skipped atom 1107, because occupancy 0.500 <= existing 0.500 in 2f8aA Skipped atom 1109, because occupancy 0.500 <= existing 0.500 in 2f8aA Skipped atom 1344, because occupancy 0.300 <= existing 0.700 in 2f8aA Skipped atom 1348, because occupancy 0.300 <= existing 0.700 in 2f8aA Skipped atom 1350, because occupancy 0.300 <= existing 0.700 in 2f8aA Skipped atom 1352, because occupancy 0.300 <= existing 0.700 in 2f8aA Skipped atom 1354, because occupancy 0.300 <= existing 0.700 in 2f8aA Skipped atom 1356, because occupancy 0.300 <= existing 0.700 in 2f8aA Skipped atom 1358, because occupancy 0.300 <= existing 0.700 in 2f8aA Skipped atom 1360, because occupancy 0.300 <= existing 0.700 in 2f8aA Skipped atom 1414, because occupancy 0.500 <= existing 0.500 in 2f8aA Skipped atom 1418, because occupancy 0.500 <= existing 0.500 in 2f8aA Skipped atom 1420, because occupancy 0.500 <= existing 0.500 in 2f8aA Skipped atom 1422, because occupancy 0.500 <= existing 0.500 in 2f8aA Skipped atom 1424, because occupancy 0.500 <= existing 0.500 in 2f8aA Skipped atom 1426, because occupancy 0.500 <= existing 0.500 in 2f8aA # T0345 read from 2f8aA/merged-good-all-a2m # 2f8aA read from 2f8aA/merged-good-all-a2m # adding 2f8aA to template set # found chain 2f8aA in template set Warning: unaligning (T0345)I2 because first residue in template chain is (2f8aA)S-1 Warning: unaligning (T0345)F152 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2f8aA)E163 Warning: unaligning (T0345)E153 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2f8aA)E163 T0345 3 :AKSFYDLSAINLD 2f8aA 0 :MQSVYAFSARPLA T0345 16 :GEKVDFNTFRGRAVLIENVASLCGTTTRDFTQLNELQCRF 2f8aA 25 :GEPVSLGSLRGKVLLIENVASLGGTTVRDYTQMNELQRRL T0345 56 :PRRLVVLGFPCNQFGHQENCQNEEILNSLKYVRPGGGYQPTFTLVQKCEVNGQNEHPVFAYLKDKLPYPYDDPFSLMTDPKLIIWSPVRRSDVAWN 2f8aA 66 :PRGLVVLGFPCNQFGHQENAKNEEILNSLKYVRPGGGFEPNFMLFEKCEVNGAGAHPLFAFLREALPAPSDDATALMTDPKLITWSPVCRNDVAWN T0345 154 :KFLIGPEGEPFRRYSRTFPTINIEPDIKRLLK 2f8aA 164 :KFLVGPDGVPLRRYSRRFQTIDIEPDIEALLS Number of specific fragments extracted= 4 number of extra gaps= 1 total=233 Number of alignments=28 # 2f8aA read from 2f8aA/merged-good-all-a2m # found chain 2f8aA in template set Warning: unaligning (T0345)I2 because first residue in template chain is (2f8aA)S-1 Warning: unaligning (T0345)F152 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2f8aA)E163 Warning: unaligning (T0345)E153 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2f8aA)E163 T0345 3 :AKSFYDLSAINLD 2f8aA 0 :MQSVYAFSARPLA T0345 16 :GEKVDFNTFRGRAVLIENVASLCGTTTRDFTQLNELQCRF 2f8aA 25 :GEPVSLGSLRGKVLLIENVASLGGTTVRDYTQMNELQRRL T0345 56 :PRRLVVLGFPCNQFGHQENCQNEEILNSLKYVRPGGGYQPTFTLVQKCEVNGQNEHPVFAYLKDKLPYPYDDPFSLMTDPKLIIWSPVRRSDVAWN 2f8aA 66 :PRGLVVLGFPCNQFGHQENAKNEEILNSLKYVRPGGGFEPNFMLFEKCEVNGAGAHPLFAFLREALPAPSDDATALMTDPKLITWSPVCRNDVAWN T0345 154 :KFLIGPEGEPFRRYSRTFPTINIEPDIKRLLK 2f8aA 164 :KFLVGPDGVPLRRYSRRFQTIDIEPDIEALLS Number of specific fragments extracted= 4 number of extra gaps= 1 total=237 Number of alignments=29 # 2f8aA read from 2f8aA/merged-good-all-a2m # found chain 2f8aA in template set Warning: unaligning (T0345)F152 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2f8aA)E163 Warning: unaligning (T0345)E153 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2f8aA)E163 T0345 3 :AKSFYDLSAINLD 2f8aA 0 :MQSVYAFSARPLA T0345 16 :GEKVDFNTFRGRAVLIENVASLCGTTT 2f8aA 25 :GEPVSLGSLRGKVLLIENVASLGGTTV T0345 43 :RDFTQLNELQCRFPRRLVVLGFPCNQFGHQENCQNEEILNSLKYVRPGGGYQPTFTLVQKCEVNGQNEHPVFAYLKDKLPYPYDDPFSLMTDPKLIIWSPVRRSDVAWN 2f8aA 53 :DYTQMNELQRRLGPRGLVVLGFPCNQFGHQENAKNEEILNSLKYVRPGGGFEPNFMLFEKCEVNGAGAHPLFAFLREALPAPSDDATALMTDPKLITWSPVCRNDVAWN T0345 154 :KFLIGPEGEPFRRYSRTFPTINIEPDIKRLLK 2f8aA 164 :KFLVGPDGVPLRRYSRRFQTIDIEPDIEALLS Number of specific fragments extracted= 4 number of extra gaps= 1 total=241 Number of alignments=30 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1gp1A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1gp1A expands to /projects/compbio/data/pdb/1gp1.pdb.gz 1gp1A:# T0345 read from 1gp1A/merged-good-all-a2m # 1gp1A read from 1gp1A/merged-good-all-a2m # adding 1gp1A to template set # found chain 1gp1A in template set Warning: unaligning (T0345)K4 because first residue in template chain is (1gp1A)R10 Warning: unaligning (T0345)G16 because of BadResidue code BAD_PEPTIDE in next template residue (1gp1A)G23 Warning: unaligning (T0345)E17 because of BadResidue code BAD_PEPTIDE at template residue (1gp1A)E24 Warning: unaligning (T0345)L37 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1gp1A)G46 Warning: unaligning (T0345)G39 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1gp1A)G46 Warning: unaligning (T0345)F152 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1gp1A)E161 Warning: unaligning (T0345)E153 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1gp1A)E161 T0345 5 :SFYDLSAINLD 1gp1A 11 :TVYAFSARPLA T0345 18 :KVDFNTFRGRAVLIENVAS 1gp1A 25 :PFNLSSLRGKVLLIENVAS T0345 40 :TTTRDFTQLNELQCRF 1gp1A 47 :TTVRDYTQMNDLQRRL T0345 56 :PRRLVVLGFPCNQFGHQENCQNEEILNSLKYVRPGGGYQPTFTLVQKCEVNGQNEHPVFAYLKDKLPYPYDDPFSLMTDPKLIIWSPVRRSDVAWN 1gp1A 64 :PRGLVVLGFPCNQFGHQENAKNEEILNCLKYVRPGGGFEPNFMLFEKCEVNGEKAHPLFAFLREVLPTPSDDATALMTDPKFITWSPVCRNDVSWN T0345 154 :KFLIGPEGEPFRRYSRTFPTINIEPDIKRLLK 1gp1A 162 :KFLVGPDGVPVRRYSRRFLTIDIEPDIETLLS Number of specific fragments extracted= 5 number of extra gaps= 3 total=246 Number of alignments=31 # 1gp1A read from 1gp1A/merged-good-all-a2m # found chain 1gp1A in template set Warning: unaligning (T0345)K4 because first residue in template chain is (1gp1A)R10 Warning: unaligning (T0345)G16 because of BadResidue code BAD_PEPTIDE in next template residue (1gp1A)G23 Warning: unaligning (T0345)E17 because of BadResidue code BAD_PEPTIDE at template residue (1gp1A)E24 Warning: unaligning (T0345)L37 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1gp1A)G46 Warning: unaligning (T0345)G39 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1gp1A)G46 Warning: unaligning (T0345)F152 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1gp1A)E161 Warning: unaligning (T0345)E153 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1gp1A)E161 T0345 5 :SFYDLSAINLD 1gp1A 11 :TVYAFSARPLA T0345 18 :KVDFNTFRGRAVLIENVAS 1gp1A 25 :PFNLSSLRGKVLLIENVAS T0345 40 :TTTRDFTQLNELQCRF 1gp1A 47 :TTVRDYTQMNDLQRRL T0345 56 :PRRLVVLGFPCNQFGHQENCQNEEILNSLKYVRPGGGYQPTFTLVQKCEVNGQNEHPVFAYLKDKLPYPYDDPFSLMTDPKLIIWSPVRRSDVAWN 1gp1A 64 :PRGLVVLGFPCNQFGHQENAKNEEILNCLKYVRPGGGFEPNFMLFEKCEVNGEKAHPLFAFLREVLPTPSDDATALMTDPKFITWSPVCRNDVSWN T0345 154 :KFLIGPEGEPFRRYSRTFPTINIEPDIKRLLK 1gp1A 162 :KFLVGPDGVPVRRYSRRFLTIDIEPDIETLLS Number of specific fragments extracted= 5 number of extra gaps= 3 total=251 Number of alignments=32 # 1gp1A read from 1gp1A/merged-good-all-a2m # found chain 1gp1A in template set Warning: unaligning (T0345)K4 because first residue in template chain is (1gp1A)R10 Warning: unaligning (T0345)G16 because of BadResidue code BAD_PEPTIDE in next template residue (1gp1A)G23 Warning: unaligning (T0345)E17 because of BadResidue code BAD_PEPTIDE at template residue (1gp1A)G23 Warning: unaligning (T0345)K18 because of BadResidue code BAD_PEPTIDE at template residue (1gp1A)E24 Warning: unaligning (T0345)L37 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1gp1A)G46 Warning: unaligning (T0345)G39 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1gp1A)G46 Warning: unaligning (T0345)F152 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1gp1A)E161 Warning: unaligning (T0345)E153 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1gp1A)E161 T0345 5 :SFYDLSAINLD 1gp1A 11 :TVYAFSARPLA T0345 19 :VDFNTFRGRAVLIENVAS 1gp1A 26 :FNLSSLRGKVLLIENVAS T0345 40 :TTT 1gp1A 47 :TTV T0345 43 :RDFTQLNELQCRFPRRLVVLGFPCNQFGHQENCQNEEILNSLKYVRPGGGYQPTFTLVQKCEVNGQNEHPVFAYLKDKLPYPYDDPFSLMTDPKLIIWSPVRRSDVAWN 1gp1A 51 :DYTQMNDLQRRLGPRGLVVLGFPCNQFGHQENAKNEEILNCLKYVRPGGGFEPNFMLFEKCEVNGEKAHPLFAFLREVLPTPSDDATALMTDPKFITWSPVCRNDVSWN T0345 154 :KFLIGPEGEPFRRYSRTFPTINIEPDIKRLLK 1gp1A 162 :KFLVGPDGVPVRRYSRRFLTIDIEPDIETLLS Number of specific fragments extracted= 5 number of extra gaps= 2 total=256 Number of alignments=33 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1qq2A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1qq2A expands to /projects/compbio/data/pdb/1qq2.pdb.gz 1qq2A:# T0345 read from 1qq2A/merged-good-all-a2m # 1qq2A read from 1qq2A/merged-good-all-a2m # adding 1qq2A to template set # found chain 1qq2A in template set T0345 7 :YDLSAINLDGEK 1qq2A 15 :FKATAVMPDGQF T0345 19 :VDFNTFRGRAVLIENVA 1qq2A 29 :ISLSDYKGKYVVFFFYP T0345 36 :SLCGTTT 1qq2A 47 :DFTFVCP T0345 44 :DFTQLNEL 1qq2A 62 :RAEEFKKL T0345 58 :RLVVLGFPC 1qq2A 70 :NCQVIGASV T0345 75 :CQNEEILNSLKYVRPGGGY 1qq2A 79 :DSHFSHLAWINTPKKQGGL T0345 94 :QPTFTLVQ 1qq2A 99 :PMNIPLVS T0345 108 :QNEHPVFA 1qq2A 107 :DPKRTIAQ T0345 120 :KLPYPYDDP 1qq2A 115 :DYGVLKADE T0345 146 :SDVAWN 1qq2A 124 :GISFRG T0345 154 :KFLIGPEGEPFR 1qq2A 130 :LFIIDDKGILRQ T0345 166 :RYSRTFPTINIEPDIKRL 1qq2A 146 :DLPVGRSVDEILRLVQAF Number of specific fragments extracted= 12 number of extra gaps= 0 total=268 Number of alignments=34 # 1qq2A read from 1qq2A/merged-good-all-a2m # found chain 1qq2A in template set T0345 7 :YDLSAINLDGEK 1qq2A 15 :FKATAVMPDGQF T0345 19 :VDFNTFRGRAVLIENVASLCGTTTR 1qq2A 29 :ISLSDYKGKYVVFFFYPLDFTFVCP T0345 44 :DFTQLNEL 1qq2A 62 :RAEEFKKL T0345 58 :RLVVLGFPC 1qq2A 70 :NCQVIGASV T0345 75 :CQNEEILNSLKYVRPGGGY 1qq2A 79 :DSHFSHLAWINTPKKQGGL T0345 94 :QPTFTLVQ 1qq2A 99 :PMNIPLVS T0345 108 :QNEHPVF 1qq2A 107 :DPKRTIA T0345 119 :DKLPYPYDDP 1qq2A 114 :QDYGVLKADE T0345 146 :SDVAWN 1qq2A 124 :GISFRG T0345 154 :KFLIGPEGEPFRRY 1qq2A 130 :LFIIDDKGILRQIT T0345 168 :SRTFPTINIEPDIKRL 1qq2A 148 :PVGRSVDEILRLVQAF Number of specific fragments extracted= 11 number of extra gaps= 0 total=279 Number of alignments=35 # 1qq2A read from 1qq2A/merged-good-all-a2m # found chain 1qq2A in template set T0345 7 :YDLSAINLDGEK 1qq2A 15 :FKATAVMPDGQF T0345 19 :VDFNTFRGRAVLIENVASL 1qq2A 29 :ISLSDYKGKYVVFFFYPLD T0345 38 :CGTTT 1qq2A 49 :TFVCP T0345 43 :RDFTQLNELQCRFPRRLVVLGFPC 1qq2A 55 :EIIAFSDRAEEFKKLNCQVIGASV T0345 75 :CQNEEILNSLKYVRPGGGYQ 1qq2A 79 :DSHFSHLAWINTPKKQGGLG T0345 95 :PTFTLVQK 1qq2A 100 :MNIPLVSD T0345 109 :NEH 1qq2A 108 :PKR T0345 116 :YLKDKLPYPYDDP 1qq2A 111 :TIAQDYGVLKADE T0345 146 :SD 1qq2A 124 :GI T0345 150 :WNFEKFLIGPEGEPFRRY 1qq2A 126 :SFRGLFIIDDKGILRQIT T0345 168 :SRTFPTINIEPDIKRL 1qq2A 148 :PVGRSVDEILRLVQAF Number of specific fragments extracted= 11 number of extra gaps= 0 total=290 Number of alignments=36 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2b7kA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2b7kA expands to /projects/compbio/data/pdb/2b7k.pdb.gz 2b7kA:# T0345 read from 2b7kA/merged-good-all-a2m # 2b7kA read from 2b7kA/merged-good-all-a2m # adding 2b7kA to template set # found chain 2b7kA in template set Warning: unaligning (T0345)Y123 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2b7kA)L236 Warning: unaligning (T0345)R144 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2b7kA)L236 T0345 3 :AKSF 2b7kA 112 :KPSL T0345 7 :YDLSAINLDGEKVDFNTFRGRAVLIENVASLCGT 2b7kA 117 :GPFHLEDMYGNEFTEKNLLGKFSIIYFGFSNCPD T0345 41 :TTRDFTQLNELQC 2b7kA 152 :CPDELDKLGLWLN T0345 54 :RFPRRLVVLGFPC 2b7kA 169 :KYGITLQPLFITC T0345 71 :HQENCQNEEILNSLK 2b7kA 182 :DPARDSPAVLKEYLS T0345 92 :GYQPTFTLVQ 2b7kA 197 :DFHPSILGLT T0345 109 :NEHPVFAYLKDKLP 2b7kA 207 :GTFDEVKNACKKYR T0345 145 :RSDVA 2b7kA 237 :VDHSI T0345 153 :EKFLIGPEGEPFRRYSRTFPTINIEPDIKRLLK 2b7kA 242 :FFYLMDPEGQFVDALGRNYDEKTGVDKIVEHVK Number of specific fragments extracted= 9 number of extra gaps= 0 total=299 Number of alignments=37 # 2b7kA read from 2b7kA/merged-good-all-a2m # found chain 2b7kA in template set Warning: unaligning (T0345)Y123 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2b7kA)L236 Warning: unaligning (T0345)R144 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2b7kA)L236 T0345 2 :IAKSFYDLSAINLDGEKVDFNTFRGRAVLIENVASLCGT 2b7kA 112 :KPSLGGPFHLEDMYGNEFTEKNLLGKFSIIYFGFSNCPD T0345 41 :TTRDFTQLNELQC 2b7kA 152 :CPDELDKLGLWLN T0345 54 :RFPRRLVVLGFPCN 2b7kA 169 :KYGITLQPLFITCD T0345 72 :QENCQNEEILNSLK 2b7kA 183 :PARDSPAVLKEYLS T0345 92 :GYQPTFTLVQ 2b7kA 197 :DFHPSILGLT T0345 107 :G 2b7kA 207 :G T0345 110 :EHPVFAYLKDKLP 2b7kA 208 :TFDEVKNACKKYR T0345 145 :RSDVA 2b7kA 237 :VDHSI T0345 153 :EKFLIGPEGEPFRRYSRTFPTINIEPDIKRLL 2b7kA 242 :FFYLMDPEGQFVDALGRNYDEKTGVDKIVEHV Number of specific fragments extracted= 9 number of extra gaps= 0 total=308 Number of alignments=38 # 2b7kA read from 2b7kA/merged-good-all-a2m # found chain 2b7kA in template set Warning: unaligning (T0345)Y123 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2b7kA)L236 Warning: unaligning (T0345)R144 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2b7kA)L236 T0345 7 :YDLSAINLDGEKVDFNTFRGRAVLIENVASLCGT 2b7kA 117 :GPFHLEDMYGNEFTEKNLLGKFSIIYFGFSNCPD T0345 41 :TT 2b7kA 152 :CP T0345 43 :RDFTQLNELQCRFPRRLVVLGFPCN 2b7kA 158 :KLGLWLNTLSSKYGITLQPLFITCD T0345 72 :QENCQNEEILNSLKYVRPGG 2b7kA 183 :PARDSPAVLKEYLSDFHPSI T0345 98 :TLVQ 2b7kA 203 :LGLT T0345 109 :NEHPVFAYLKDKLP 2b7kA 207 :GTFDEVKNACKKYR T0345 145 :RSDVA 2b7kA 237 :VDHSI T0345 153 :EKFLIGPEGEPFRRYSRTFPTINIEPDIKRLL 2b7kA 242 :FFYLMDPEGQFVDALGRNYDEKTGVDKIVEHV Number of specific fragments extracted= 8 number of extra gaps= 0 total=316 Number of alignments=39 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1w4vA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1w4vA expands to /projects/compbio/data/pdb/1w4v.pdb.gz 1w4vA:# T0345 read from 1w4vA/merged-good-all-a2m # 1w4vA read from 1w4vA/merged-good-all-a2m # adding 1w4vA to template set # found chain 1w4vA in template set T0345 27 :RAVLIENVASLCGTTTRDFTQLNELQCRFPRRLVVLGFPCNQF 1w4vA 20 :TPVVVDFHAQWCGPCKILGPRLEKMVAKQHGKVVMAKVDIDDH T0345 81 :LNSLKY 1w4vA 63 :TDLAIE T0345 93 :YQPT 1w4vA 69 :YEVS T0345 125 :Y 1w4vA 73 :A T0345 147 :D 1w4vA 74 :V T0345 152 :FE 1w4vA 75 :PT T0345 155 :FLIGPEGEPFRRYSRTFPTINIEPDIKRLLK 1w4vA 77 :VLAMKNGDVVDKFVGIKDEDQLEAFLKKLIG Number of specific fragments extracted= 7 number of extra gaps= 0 total=323 Number of alignments=40 # 1w4vA read from 1w4vA/merged-good-all-a2m # found chain 1w4vA in template set T0345 26 :GRAVLIENVASLCGTTTRDFTQLNELQCRFPRRLVVLGFPCNQF 1w4vA 19 :ETPVVVDFHAQWCGPCKILGPRLEKMVAKQHGKVVMAKVDIDDH T0345 81 :LNSL 1w4vA 63 :TDLA T0345 119 :DKLPYPYD 1w4vA 67 :IEYEVSAV T0345 153 :EKFLIGPEGEPFRRYSRTFPTINIEPDIKRLLK 1w4vA 75 :PTVLAMKNGDVVDKFVGIKDEDQLEAFLKKLIG Number of specific fragments extracted= 4 number of extra gaps= 0 total=327 Number of alignments=41 # 1w4vA read from 1w4vA/merged-good-all-a2m # found chain 1w4vA in template set T0345 27 :RAVLIENVASLCGTTT 1w4vA 20 :TPVVVDFHAQWCGPCK T0345 43 :RDFTQLNELQCR 1w4vA 37 :LGPRLEKMVAKQ T0345 56 :PRRLVVLGFPCNQF 1w4vA 49 :HGKVVMAKVDIDDH T0345 115 :AYLKDKLPYPYD 1w4vA 63 :TDLAIEYEVSAV T0345 152 :FE 1w4vA 75 :PT T0345 155 :FLIGPEGEPFRRYSRTFPTINIEPDIKRLLK 1w4vA 77 :VLAMKNGDVVDKFVGIKDEDQLEAFLKKLIG Number of specific fragments extracted= 6 number of extra gaps= 0 total=333 Number of alignments=42 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1jfuA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0345 read from 1jfuA/merged-good-all-a2m # 1jfuA read from 1jfuA/merged-good-all-a2m # found chain 1jfuA in training set T0345 3 :AKSFYDLSAINLDGEKVDFNTFRGRAVLIENVASLCGTTTRDFTQLNELQCRF 1jfuA 37 :PLKLPDLAFEDADGKPKKLSDFRGKTLLVNLWATWCVPCRKEMPALDELQGKL T0345 56 :PRRLVVLGFP 1jfuA 91 :GPNFEVVAIN T0345 72 :QENCQNEEILNSLKYV 1jfuA 101 :IDTRDPEKPKTFLKEA T0345 92 :GYQ 1jfuA 117 :NLT T0345 96 :TFTLVQ 1jfuA 120 :RLGYFN T0345 108 :QNEHPVFAYLKD 1jfuA 126 :DQKAKVFQDLKA T0345 121 :LPYPYD 1jfuA 138 :IGRALG T0345 151 :NFEKFLIGPEGEPFRRYSRTFPTIN 1jfuA 144 :MPTSVLVDPQGCEIATIAGPAEWAS T0345 178 :PDIKRLLK 1jfuA 169 :EDALKLIR Number of specific fragments extracted= 9 number of extra gaps= 0 total=342 Number of alignments=43 # 1jfuA read from 1jfuA/merged-good-all-a2m # found chain 1jfuA in training set T0345 2 :IAKSFYDLSAINLDGEKVDFNTFRGRAVLIENVASLCGTTTRDFTQLNELQCRF 1jfuA 36 :APLKLPDLAFEDADGKPKKLSDFRGKTLLVNLWATWCVPCRKEMPALDELQGKL T0345 56 :PRRLVVLGF 1jfuA 91 :GPNFEVVAI T0345 71 :HQENCQNEEILNSLKY 1jfuA 100 :NIDTRDPEKPKTFLKE T0345 95 :PTFTLVQKCE 1jfuA 116 :ANLTRLGYFN T0345 108 :QNEHPVFAYLKDK 1jfuA 126 :DQKAKVFQDLKAI T0345 122 :PYPYDD 1jfuA 139 :GRALGM T0345 152 :FEKFLIGPEGEPFRRYSRTFPTIN 1jfuA 145 :PTSVLVDPQGCEIATIAGPAEWAS T0345 178 :PDIKRLL 1jfuA 169 :EDALKLI Number of specific fragments extracted= 8 number of extra gaps= 0 total=350 Number of alignments=44 # 1jfuA read from 1jfuA/merged-good-all-a2m # found chain 1jfuA in training set T0345 3 :AKSFYDLSAINLDGEKVDFNTFRGRAVLIENVASLCGTTT 1jfuA 37 :PLKLPDLAFEDADGKPKKLSDFRGKTLLVNLWATWCVPCR T0345 43 :RDFTQLNELQCRFPRRLVVLGFPC 1jfuA 78 :EMPALDELQGKLSGPNFEVVAINI T0345 73 :ENCQNEEILNSLKYV 1jfuA 102 :DTRDPEKPKTFLKEA T0345 92 :GYQ 1jfuA 117 :NLT T0345 96 :TFTLVQK 1jfuA 120 :RLGYFND T0345 109 :NEHPVFAYLKD 1jfuA 127 :QKAKVFQDLKA T0345 145 :RSDVAWNFEKFLIGPEGEPFRRYSRTFPTIN 1jfuA 138 :IGRALGMPTSVLVDPQGCEIATIAGPAEWAS T0345 178 :PDIKRLL 1jfuA 169 :EDALKLI Number of specific fragments extracted= 8 number of extra gaps= 0 total=358 Number of alignments=45 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1t00A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1t00A expands to /projects/compbio/data/pdb/1t00.pdb.gz 1t00A:Skipped atom 440, because occupancy 0.500 <= existing 0.500 in 1t00A Skipped atom 442, because occupancy 0.500 <= existing 0.500 in 1t00A Skipped atom 444, because occupancy 0.500 <= existing 0.500 in 1t00A Skipped atom 446, because occupancy 0.500 <= existing 0.500 in 1t00A Skipped atom 448, because occupancy 0.500 <= existing 0.500 in 1t00A Skipped atom 544, because occupancy 0.500 <= existing 0.500 in 1t00A Skipped atom 546, because occupancy 0.500 <= existing 0.500 in 1t00A Skipped atom 548, because occupancy 0.500 <= existing 0.500 in 1t00A Skipped atom 550, because occupancy 0.500 <= existing 0.500 in 1t00A Skipped atom 552, because occupancy 0.500 <= existing 0.500 in 1t00A Skipped atom 554, because occupancy 0.500 <= existing 0.500 in 1t00A # T0345 read from 1t00A/merged-good-all-a2m # 1t00A read from 1t00A/merged-good-all-a2m # adding 1t00A to template set # found chain 1t00A in template set Warning: unaligning (T0345)R27 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1t00A)P23 Warning: unaligning (T0345)A28 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1t00A)P23 Warning: unaligning (T0345)L81 because of BadResidue code BAD_PEPTIDE in next template residue (1t00A)G66 Warning: unaligning (T0345)N82 because of BadResidue code BAD_PEPTIDE at template residue (1t00A)G66 T0345 26 :G 1t00A 21 :D T0345 29 :VLIENVASLCGTTTRDFTQLNELQCRFPRRLVVLGFPCNQF 1t00A 24 :VLVDFWAAWCGPCRQIAPSLEAIAAEYGDKIEIVKLNIDEN T0345 83 :SLKY 1t00A 67 :TAAK T0345 121 :LPYP 1t00A 71 :YGVM T0345 146 :SD 1t00A 75 :SI T0345 152 :FEKFLIG 1t00A 77 :PTLNVYQ T0345 160 :EGEPFRRYSRTFPTINIEPDIKRLLK 1t00A 84 :GGEVAKTIVGAKPKAAIVRDLEDFIA Number of specific fragments extracted= 7 number of extra gaps= 2 total=365 Number of alignments=46 # 1t00A read from 1t00A/merged-good-all-a2m # found chain 1t00A in template set Warning: unaligning (T0345)R27 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1t00A)P23 Warning: unaligning (T0345)A28 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1t00A)P23 Warning: unaligning (T0345)Q76 because of BadResidue code BAD_PEPTIDE in next template residue (1t00A)G66 Warning: unaligning (T0345)N82 because of BadResidue code BAD_PEPTIDE at template residue (1t00A)G66 T0345 26 :G 1t00A 21 :D T0345 29 :VLIENVASLCGTTTRDFTQLNELQCRFPRRLVVLGFPCNQF 1t00A 24 :VLVDFWAAWCGPCRQIAPSLEAIAAEYGDKIEIVKLNIDEN T0345 117 :LKDKLPYP 1t00A 67 :TAAKYGVM T0345 146 :SDVAWNFEK 1t00A 75 :SIPTLNVYQ T0345 160 :EGEPFRRYSRTFPTINIEPDIKRLLK 1t00A 84 :GGEVAKTIVGAKPKAAIVRDLEDFIA Number of specific fragments extracted= 5 number of extra gaps= 2 total=370 Number of alignments=47 # 1t00A read from 1t00A/merged-good-all-a2m # found chain 1t00A in template set Warning: unaligning (T0345)R27 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1t00A)P23 Warning: unaligning (T0345)A28 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1t00A)P23 Warning: unaligning (T0345)Q76 because of BadResidue code BAD_PEPTIDE in next template residue (1t00A)G66 Warning: unaligning (T0345)E79 because of BadResidue code BAD_PEPTIDE at template residue (1t00A)G66 T0345 26 :G 1t00A 21 :D T0345 29 :VLIENVASLCGTTTRDFTQLNELQCRFPRRLVVLGFPCNQF 1t00A 24 :VLVDFWAAWCGPCRQIAPSLEAIAAEYGDKIEIVKLNIDEN T0345 117 :LKDKLP 1t00A 67 :TAAKYG T0345 148 :VAWNFEKFLIG 1t00A 73 :VMSIPTLNVYQ T0345 160 :EGEPFRRYSRTFPTINIEPDIKRLLK 1t00A 84 :GGEVAKTIVGAKPKAAIVRDLEDFIA Number of specific fragments extracted= 5 number of extra gaps= 2 total=375 Number of alignments=48 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1prxA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1prxA expands to /projects/compbio/data/pdb/1prx.pdb.gz 1prxA:Bad short name: OD for alphabet: pdb_atoms # T0345 read from 1prxA/merged-good-all-a2m # 1prxA read from 1prxA/merged-good-all-a2m # adding 1prxA to template set # found chain 1prxA in template set Warning: unaligning (T0345)R43 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1prxA)T48 Warning: unaligning (T0345)F45 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1prxA)T48 T0345 1 :MIAKSFYDLSAINLD 1prxA 6 :LLGDVAPNFEANTTV T0345 17 :EKVDFNT 1prxA 21 :GRIRFHD T0345 24 :FRGRAVLIENVA 1prxA 29 :LGDSWGILFSHP T0345 38 :CGTTT 1prxA 41 :RDFTP T0345 46 :TQLNELQC 1prxA 49 :TELGRAAK T0345 54 :RF 1prxA 60 :EF T0345 56 :PRRLVVLGFPC 1prxA 63 :KRNVKLIALSI T0345 75 :CQNEEILNSLKYVR 1prxA 74 :DSVEDHLAWSKDIN T0345 89 :PGGGYQPTFTLVQ 1prxA 92 :EEPTEKLPFPIID T0345 108 :QNEHPVFAYL 1prxA 105 :DRNRELAILL T0345 119 :DKLPYPYDDPF 1prxA 115 :GMLDPAEKDEK T0345 146 :SDVAWNFEKFLIGPEGEPFR 1prxA 126 :GMPVTARVVFVFGPDKKLKL T0345 166 :RYSRT 1prxA 148 :LYPAT T0345 171 :FPTINIEPDIK 1prxA 155 :RNFDEILRVVI Number of specific fragments extracted= 14 number of extra gaps= 0 total=389 Number of alignments=49 # 1prxA read from 1prxA/merged-good-all-a2m # found chain 1prxA in template set Warning: unaligning (T0345)R43 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1prxA)T48 Warning: unaligning (T0345)F45 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1prxA)T48 T0345 1 :MIAKSFYDLSAINL 1prxA 6 :LLGDVAPNFEANTT T0345 16 :GEKVDFNTF 1prxA 20 :VGRIRFHDF T0345 25 :RGRAVLIENV 1prxA 30 :GDSWGILFSH T0345 37 :LCGTTT 1prxA 40 :PRDFTP T0345 46 :TQLNELQC 1prxA 49 :TELGRAAK T0345 54 :RFPRRLVVLGF 1prxA 63 :KRNVKLIALSI T0345 75 :CQNEEILNSLKYV 1prxA 74 :DSVEDHLAWSKDI T0345 89 :PGGGYQPTFTLVQ 1prxA 92 :EEPTEKLPFPIID T0345 108 :QNEHPVFAYL 1prxA 105 :DRNRELAILL T0345 119 :DKLPYPYDDPFSLM 1prxA 115 :GMLDPAEKDEKGMP T0345 149 :AWNFEKFLIGPEGEPFR 1prxA 129 :VTARVVFVFGPDKKLKL T0345 166 :RYSRT 1prxA 148 :LYPAT T0345 171 :FPTINIEPDIKR 1prxA 155 :RNFDEILRVVIS Number of specific fragments extracted= 13 number of extra gaps= 0 total=402 Number of alignments=50 # 1prxA read from 1prxA/merged-good-all-a2m # found chain 1prxA in template set T0345 3 :AKSFYDLSAINLDG 1prxA 8 :GDVAPNFEANTTVG T0345 18 :KVDFNTF 1prxA 22 :RIRFHDF T0345 25 :RGRAVLIENV 1prxA 30 :GDSWGILFSH T0345 37 :LCGTTT 1prxA 40 :PRDFTP T0345 43 :RDFTQLNELQCRFPRRLVVLGFPC 1prxA 50 :ELGRAAKLAPEFAKRNVKLIALSI T0345 75 :CQNEEILNSLK 1prxA 74 :DSVEDHLAWSK T0345 86 :YVRPGGGYQPTFTLVQK 1prxA 89 :YNSEEPTEKLPFPIIDD T0345 109 :NEHPVFAYL 1prxA 106 :RNRELAILL T0345 119 :DKLPYPYDDPF 1prxA 115 :GMLDPAEKDEK T0345 146 :SDVAWNFEKFLIGPEGEPFR 1prxA 126 :GMPVTARVVFVFGPDKKLKL T0345 166 :RYSRT 1prxA 148 :LYPAT T0345 171 :FPTINIEPDIKRL 1prxA 155 :RNFDEILRVVISL Number of specific fragments extracted= 12 number of extra gaps= 0 total=414 Number of alignments=51 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1qk8A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1qk8A expands to /projects/compbio/data/pdb/1qk8.pdb.gz 1qk8A:Skipped atom 842, because occupancy 0.300 <= existing 0.700 in 1qk8A Skipped atom 844, because occupancy 0.300 <= existing 0.700 in 1qk8A Skipped atom 846, because occupancy 0.300 <= existing 0.700 in 1qk8A # T0345 read from 1qk8A/merged-good-all-a2m # 1qk8A read from 1qk8A/merged-good-all-a2m # adding 1qk8A to template set # found chain 1qk8A in template set Warning: unaligning (T0345)D126 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1qk8A)P110 Warning: unaligning (T0345)F152 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1qk8A)P110 T0345 5 :SFYDL 1qk8A 10 :GIEKL T0345 13 :NLDGEKVDFNTFRGRAVLIENVASLCGTTTRDFTQLNELQCRF 1qk8A 15 :RRGDGEVEVKSLAGKLVFFYFSASWCPPCRGFTPQLIEFYDKF T0345 56 :PRRLVVLGFPC 1qk8A 60 :SKNFEVVFCTW T0345 74 :NCQNEEILNSLK 1qk8A 71 :DEEEDGFAGYFA T0345 92 :GYQPTF 1qk8A 83 :KMPWLA T0345 100 :VQ 1qk8A 89 :VP T0345 108 :QNEHPVFAYLKDKLPYPY 1qk8A 91 :FAQSEAVQKLSKHFNVES T0345 153 :EKFLIG 1qk8A 111 :TLIGVD T0345 159 :PEGEPFRR 1qk8A 118 :DSGDVVTT Number of specific fragments extracted= 9 number of extra gaps= 1 total=423 Number of alignments=52 # 1qk8A read from 1qk8A/merged-good-all-a2m # found chain 1qk8A in template set Warning: unaligning (T0345)D126 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1qk8A)P110 Warning: unaligning (T0345)V148 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1qk8A)P110 T0345 9 :LSAINLDGEKVDFNTFRGRAVLIENVASLCGTTTRDFTQLNELQCRF 1qk8A 11 :IEKLRRGDGEVEVKSLAGKLVFFYFSASWCPPCRGFTPQLIEFYDKF T0345 56 :PRRLVVLGFPC 1qk8A 60 :SKNFEVVFCTW T0345 74 :NCQNEEILNSLK 1qk8A 71 :DEEEDGFAGYFA T0345 92 :GYQPTFTL 1qk8A 83 :KMPWLAVP T0345 108 :QNEHPVFAYLKDKLPYPY 1qk8A 91 :FAQSEAVQKLSKHFNVES T0345 149 :AW 1qk8A 111 :TL T0345 155 :FLIG 1qk8A 113 :IGVD T0345 159 :PEGEPFR 1qk8A 118 :DSGDVVT Number of specific fragments extracted= 8 number of extra gaps= 1 total=431 Number of alignments=53 # 1qk8A read from 1qk8A/merged-good-all-a2m # found chain 1qk8A in template set Warning: unaligning (T0345)D126 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1qk8A)P110 Warning: unaligning (T0345)F152 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1qk8A)P110 T0345 15 :DGEKVDFNTFRGRAVLIENVASLCGTTT 1qk8A 17 :GDGEVEVKSLAGKLVFFYFSASWCPPCR T0345 43 :RDFTQLNELQCRFP 1qk8A 46 :FTPQLIEFYDKFHE T0345 57 :RRLVVLGFP 1qk8A 61 :KNFEVVFCT T0345 73 :ENCQNEEILNSLK 1qk8A 70 :WDEEEDGFAGYFA T0345 94 :QPTFTLVQK 1qk8A 83 :KMPWLAVPF T0345 109 :NEHPVFAYLKDKLPYPY 1qk8A 92 :AQSEAVQKLSKHFNVES T0345 153 :EKFLIG 1qk8A 111 :TLIGVD T0345 159 :PEGEPFRR 1qk8A 118 :DSGDVVTT Number of specific fragments extracted= 8 number of extra gaps= 1 total=439 Number of alignments=54 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1aiu/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1aiu expands to /projects/compbio/data/pdb/1aiu.pdb.gz 1aiu:Warning: there is no chain 1aiu will retry with 1aiuA # T0345 read from 1aiu/merged-good-all-a2m # 1aiu read from 1aiu/merged-good-all-a2m # adding 1aiu to template set # found chain 1aiu in template set T0345 24 :FRGRAVLIENVASLCGTTTRDFTQLNELQCRF 1aiu 18 :AGDKLVVVDFSATWCGPCKMIKPFFHSLSEKY T0345 58 :RLVVLGFPCNQF 1aiu 51 :NVIFLEVDVNDC T0345 78 :EEILNSLKY 1aiu 63 :QDVASECEV T0345 92 :GYQPTFTLVQ 1aiu 72 :KCMPTFQFFK T0345 160 :EGEPFRRYSR 1aiu 82 :KGQKVGEFSG T0345 171 :FPTINIEPDIKRL 1aiu 92 :ANKEKLEATINEL Number of specific fragments extracted= 6 number of extra gaps= 0 total=445 Number of alignments=55 # 1aiu read from 1aiu/merged-good-all-a2m # found chain 1aiu in template set Warning: unaligning (T0345)L184 because last residue in template chain is (1aiu)V105 T0345 23 :TFRGRAVLIENVASLCGTTTRDFTQLNELQCRF 1aiu 17 :AAGDKLVVVDFSATWCGPCKMIKPFFHSLSEKY T0345 58 :RLVVLGFPCNQF 1aiu 51 :NVIFLEVDVNDC T0345 78 :EEILNSLKY 1aiu 63 :QDVASECEV T0345 92 :G 1aiu 72 :K T0345 146 :SDVAWNFEK 1aiu 73 :CMPTFQFFK T0345 160 :EGEPFRRYSR 1aiu 82 :KGQKVGEFSG T0345 171 :FPTINIEPDIKRL 1aiu 92 :ANKEKLEATINEL Number of specific fragments extracted= 7 number of extra gaps= 0 total=452 Number of alignments=56 # 1aiu read from 1aiu/merged-good-all-a2m # found chain 1aiu in template set Warning: unaligning (T0345)L184 because last residue in template chain is (1aiu)V105 T0345 22 :NTFRGRAVLIENVASLCGTTT 1aiu 16 :DAAGDKLVVVDFSATWCGPCK T0345 43 :RDFTQLNELQCR 1aiu 38 :IKPFFHSLSEKY T0345 57 :RRLVVLGFPCNQF 1aiu 50 :SNVIFLEVDVNDC T0345 78 :EEILNSLK 1aiu 63 :QDVASECE T0345 91 :GGYQPTFTLVQ 1aiu 71 :VKCMPTFQFFK T0345 160 :EGEPFRRYSR 1aiu 82 :KGQKVGEFSG T0345 171 :FPTINIEPDIKRL 1aiu 92 :ANKEKLEATINEL Number of specific fragments extracted= 7 number of extra gaps= 0 total=459 Number of alignments=57 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2trxA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2trxA expands to /projects/compbio/data/pdb/2trx.pdb.gz 2trxA:Skipped atom 35, because occupancy 0.500 <= existing 0.500 in 2trxA Skipped atom 37, because occupancy 0.500 <= existing 0.500 in 2trxA Skipped atom 43, because occupancy 0.500 <= existing 0.500 in 2trxA Skipped atom 45, because occupancy 0.500 <= existing 0.500 in 2trxA Skipped atom 47, because occupancy 0.500 <= existing 0.500 in 2trxA Skipped atom 49, because occupancy 0.500 <= existing 0.500 in 2trxA Skipped atom 51, because occupancy 0.500 <= existing 0.500 in 2trxA Skipped atom 53, because occupancy 0.500 <= existing 0.500 in 2trxA Skipped atom 55, because occupancy 0.500 <= existing 0.500 in 2trxA Skipped atom 57, because occupancy 0.500 <= existing 0.500 in 2trxA Skipped atom 59, because occupancy 0.500 <= existing 0.500 in 2trxA Skipped atom 61, because occupancy 0.500 <= existing 0.500 in 2trxA Skipped atom 63, because occupancy 0.500 <= existing 0.500 in 2trxA Skipped atom 186, because occupancy 0.500 <= existing 0.500 in 2trxA Skipped atom 188, because occupancy 0.500 <= existing 0.500 in 2trxA Skipped atom 190, because occupancy 0.500 <= existing 0.500 in 2trxA Skipped atom 379, because occupancy 0.500 <= existing 0.500 in 2trxA Skipped atom 381, because occupancy 0.500 <= existing 0.500 in 2trxA Skipped atom 383, because occupancy 0.500 <= existing 0.500 in 2trxA Skipped atom 390, because occupancy 0.500 <= existing 0.500 in 2trxA Skipped atom 392, because occupancy 0.500 <= existing 0.500 in 2trxA Skipped atom 394, because occupancy 0.500 <= existing 0.500 in 2trxA Skipped atom 396, because occupancy 0.500 <= existing 0.500 in 2trxA Skipped atom 474, because occupancy 0.500 <= existing 0.500 in 2trxA Skipped atom 476, because occupancy 0.500 <= existing 0.500 in 2trxA Skipped atom 641, because occupancy 0.500 <= existing 0.500 in 2trxA Skipped atom 643, because occupancy 0.500 <= existing 0.500 in 2trxA # T0345 read from 2trxA/merged-good-all-a2m # 2trxA read from 2trxA/merged-good-all-a2m # adding 2trxA to template set # found chain 2trxA in template set Warning: unaligning (T0345)L184 because of BadResidue code HAS_OXT+BAD_PEPTIDE in next template residue (2trxA)A108 Warning: unaligning (T0345)K185 because of BadResidue code HAS_OXT+BAD_PEPTIDE at template residue (2trxA)A108 T0345 26 :GRAVLIENVASLCGTTTRDFTQLNELQCRFPRRLVVLGFPCNQFGH 2trxA 20 :DGAILVDFWAEWCGPCKMIAPILDEIADEYQGKLTVAKLNIDQNPG T0345 83 :SLKY 2trxA 66 :TAPK T0345 93 :YQPT 2trxA 70 :YGIR T0345 107 :G 2trxA 74 :G T0345 151 :NFEKFLIG 2trxA 75 :IPTLLLFK T0345 160 :EGEPFRRYSRTFPTINIEPDIKRL 2trxA 83 :NGEVAATKVGALSKGQLKEFLDAN Number of specific fragments extracted= 6 number of extra gaps= 1 total=465 Number of alignments=58 # 2trxA read from 2trxA/merged-good-all-a2m # found chain 2trxA in template set Warning: unaligning (T0345)L184 because of BadResidue code HAS_OXT+BAD_PEPTIDE in next template residue (2trxA)A108 Warning: unaligning (T0345)K185 because of BadResidue code HAS_OXT+BAD_PEPTIDE at template residue (2trxA)A108 T0345 26 :GRAVLIENVASLCGTTTRDFTQLNELQCRFPRRLVVLGFPCNQF 2trxA 20 :DGAILVDFWAEWCGPCKMIAPILDEIADEYQGKLTVAKLNIDQN T0345 108 :QNEHP 2trxA 64 :PGTAP T0345 120 :KLPYP 2trxA 69 :KYGIR T0345 146 :SD 2trxA 74 :GI T0345 152 :FE 2trxA 76 :PT T0345 155 :FLIGPEGEPFRRYSRTFPTINIEPDIKRL 2trxA 78 :LLLFKNGEVAATKVGALSKGQLKEFLDAN Number of specific fragments extracted= 6 number of extra gaps= 1 total=471 Number of alignments=59 # 2trxA read from 2trxA/merged-good-all-a2m # found chain 2trxA in template set Warning: unaligning (T0345)L184 because of BadResidue code HAS_OXT+BAD_PEPTIDE in next template residue (2trxA)A108 Warning: unaligning (T0345)K185 because of BadResidue code HAS_OXT+BAD_PEPTIDE at template residue (2trxA)A108 T0345 26 :GRAVLIENVASLCGTTTRDFTQLNELQCRFPRRLVVLGFPCNQF 2trxA 20 :DGAILVDFWAEWCGPCKMIAPILDEIADEYQGKLTVAKLNIDQN T0345 74 :NC 2trxA 64 :PG T0345 117 :LKDKLP 2trxA 66 :TAPKYG T0345 148 :VAWNFEKFLIG 2trxA 72 :IRGIPTLLLFK T0345 160 :EGEPFRRYSRTFPTINIEPDIKRL 2trxA 83 :NGEVAATKVGALSKGQLKEFLDAN Number of specific fragments extracted= 5 number of extra gaps= 1 total=476 Number of alignments=60 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1st9A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0345 read from 1st9A/merged-good-all-a2m # 1st9A read from 1st9A/merged-good-all-a2m # found chain 1st9A in training set Warning: unaligning (T0345)I12 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (1st9A)D48 Warning: unaligning (T0345)N13 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (1st9A)D48 T0345 3 :AKSFYDLSA 1st9A 38 :GSDAPNFVL T0345 14 :LDGEKVDFNTFRGRAVLIENVASLCGTTTRDFTQLNELQCRF 1st9A 49 :TNGKRIELSDLKGKGVFLNFWGTWCEPCKKEFPYMANQYKHF T0345 56 :PRRLVVLGFPC 1st9A 92 :SQGVEIVAVNV T0345 74 :NCQNEEILNSLKY 1st9A 103 :GESKIAVHNFMKS T0345 93 :YQPTFTLVQK 1st9A 116 :YGVNFPVVLD T0345 108 :Q 1st9A 126 :T T0345 110 :EHPVFAYL 1st9A 127 :DRQVLDAY T0345 120 :KLPY 1st9A 135 :DVSP T0345 151 :NFEKFLIGPEGEPFRRYSRTFP 1st9A 139 :LPTTFLINPEGKVVKVVTGTMT T0345 177 :EPDIKRLLK 1st9A 161 :ESMIHDYMN Number of specific fragments extracted= 10 number of extra gaps= 1 total=486 Number of alignments=61 # 1st9A read from 1st9A/merged-good-all-a2m # found chain 1st9A in training set Warning: unaligning (T0345)I2 because first residue in template chain is (1st9A)E37 Warning: unaligning (T0345)I12 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (1st9A)D48 Warning: unaligning (T0345)N13 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (1st9A)D48 T0345 3 :AKSFYDLSA 1st9A 38 :GSDAPNFVL T0345 14 :LDGEKVDFNTFRGRAVLIENVASLCGTTTRDFTQLNELQCRF 1st9A 49 :TNGKRIELSDLKGKGVFLNFWGTWCEPCKKEFPYMANQYKHF T0345 56 :PRRLVVLGFPC 1st9A 92 :SQGVEIVAVNV T0345 74 :NCQNEEILNSLKY 1st9A 103 :GESKIAVHNFMKS T0345 93 :YQPTFTLV 1st9A 116 :YGVNFPVV T0345 109 :NEHPVFAYL 1st9A 126 :TDRQVLDAY T0345 120 :KLPYP 1st9A 135 :DVSPL T0345 152 :FEKFLIGPEGEPFRRYSRTFP 1st9A 140 :PTTFLINPEGKVVKVVTGTMT T0345 177 :EPDIKRLLK 1st9A 161 :ESMIHDYMN Number of specific fragments extracted= 9 number of extra gaps= 1 total=495 Number of alignments=62 # 1st9A read from 1st9A/merged-good-all-a2m # found chain 1st9A in training set Warning: unaligning (T0345)I12 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (1st9A)D48 Warning: unaligning (T0345)N13 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (1st9A)D48 T0345 4 :KSFYDLSA 1st9A 39 :SDAPNFVL T0345 14 :LDGEKVDFNTFRGRAVLIENVASLCGTTT 1st9A 49 :TNGKRIELSDLKGKGVFLNFWGTWCEPCK T0345 43 :RDFTQLNELQCRFPRRLVVLGFPC 1st9A 79 :EFPYMANQYKHFKSQGVEIVAVNV T0345 74 :NCQNEEILNSLK 1st9A 103 :GESKIAVHNFMK T0345 92 :GYQPTFTLVQK 1st9A 115 :SYGVNFPVVLD T0345 117 :LKDKLPYPYD 1st9A 130 :VLDAYDVSPL T0345 152 :FEKFLIGPEGEPFRRYSRTFPTINIEPDIK 1st9A 140 :PTTFLINPEGKVVKVVTGTMTESMIHDYMN Number of specific fragments extracted= 7 number of extra gaps= 1 total=502 Number of alignments=63 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1n8jA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1n8jA expands to /projects/compbio/data/pdb/1n8j.pdb.gz 1n8jA:# T0345 read from 1n8jA/merged-good-all-a2m # 1n8jA read from 1n8jA/merged-good-all-a2m # adding 1n8jA to template set # found chain 1n8jA in template set T0345 7 :YDLSAI 1n8jA 10 :FKNQAF T0345 14 :LDGEKVDFNT 1n8jA 16 :KNGEFIEVTE T0345 24 :FRGRAVLIENVAS 1n8jA 28 :TEGRWSVFFFYPA T0345 39 :GTTTRDFTQLNELQCRF 1n8jA 41 :DFTFVSPTELGDVADHY T0345 56 :PRRLVVLGFPC 1n8jA 62 :KLGVDVYSVST T0345 75 :CQNEEILNSLKY 1n8jA 73 :DTHFTHKAWHSS T0345 97 :FTLVQKCEVN 1n8jA 85 :SETIAKIKYA T0345 107 :GQNEHPVFAYL 1n8jA 97 :GDPTGALTRNF T0345 141 :SPVRRSDVAWNFEKFLIGPEGEPFR 1n8jA 108 :DNMREDEGLADRATFVVDPQGIIQA T0345 167 :YSRT 1n8jA 136 :TAEG T0345 171 :FPTINIEPDIKR 1n8jA 142 :RDASDLLRKIKA Number of specific fragments extracted= 11 number of extra gaps= 0 total=513 Number of alignments=64 # 1n8jA read from 1n8jA/merged-good-all-a2m # found chain 1n8jA in template set T0345 6 :FYDLSAI 1n8jA 9 :PFKNQAF T0345 14 :LDGEKVDFNT 1n8jA 16 :KNGEFIEVTE T0345 24 :FRGRAVLIENVASL 1n8jA 28 :TEGRWSVFFFYPAD T0345 40 :TTTRDFTQLNELQCRF 1n8jA 42 :FTFVSPTELGDVADHY T0345 56 :PRRLVVLGFPC 1n8jA 62 :KLGVDVYSVST T0345 75 :CQNEEILNSLKY 1n8jA 73 :DTHFTHKAWHSS T0345 97 :FTLVQKCE 1n8jA 85 :SETIAKIK T0345 107 :GQNEHPVFAYL 1n8jA 97 :GDPTGALTRNF T0345 122 :PYPYD 1n8jA 108 :DNMRE T0345 146 :SDVAWNFEKFLIGPEGEPFRRY 1n8jA 113 :DEGLADRATFVVDPQGIIQAIE T0345 168 :SR 1n8jA 138 :EG T0345 171 :FPTINIEPDIKRL 1n8jA 142 :RDASDLLRKIKAA Number of specific fragments extracted= 12 number of extra gaps= 0 total=525 Number of alignments=65 # 1n8jA read from 1n8jA/merged-good-all-a2m # found chain 1n8jA in template set T0345 6 :FYDLSAI 1n8jA 7 :IKPFKNQ T0345 14 :LDGEK 1n8jA 16 :KNGEF T0345 19 :VDFNTFRGRAVLIENV 1n8jA 23 :VTEKDTEGRWSVFFFY T0345 37 :LCGTTT 1n8jA 39 :PADFTF T0345 43 :RDFTQLNELQCRFPRRLVVLGFPC 1n8jA 49 :ELGDVADHYEELQKLGVDVYSVST T0345 75 :CQNEEILNSLKYVRPGGGYQP 1n8jA 73 :DTHFTHKAWHSSSETIAKIKY T0345 98 :TLVQK 1n8jA 94 :AMIGD T0345 109 :NEHP 1n8jA 99 :PTGA T0345 117 :LKDKLPYPYD 1n8jA 103 :LTRNFDNMRE T0345 144 :RRSDVAW 1n8jA 113 :DEGLADR T0345 153 :EKFLIGPEGEPFR 1n8jA 120 :ATFVVDPQGIIQA T0345 166 :RYSRT 1n8jA 135 :VTAEG T0345 171 :FPTINIEPDIKR 1n8jA 142 :RDASDLLRKIKA Number of specific fragments extracted= 13 number of extra gaps= 0 total=538 Number of alignments=66 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1thx/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0345 read from 1thx/merged-good-all-a2m # 1thx read from 1thx/merged-good-all-a2m # found chain 1thx in training set T0345 27 :RAVLIENVASLCGTTTRDFTQLNELQCRFPRRLVVLGF 1thx 21 :QPVLVYFWASWCGPCQLMSPLINLAANTYSDRLKVVKL T0345 71 :HQENCQN 1thx 59 :EIDPNPT T0345 80 :ILNSL 1thx 66 :TVKKY T0345 104 :EVNGQ 1thx 71 :KVEGV T0345 152 :FEKFLIGPE 1thx 76 :PALRLVKGE T0345 162 :EPFRRYSRTFPTINIEPDIKRLLK 1thx 85 :QILDSTEGVISKDKLLSFLDTHLN Number of specific fragments extracted= 6 number of extra gaps= 0 total=544 Number of alignments=67 # 1thx read from 1thx/merged-good-all-a2m # found chain 1thx in training set T0345 26 :GRAVLIENVASLCGTTTRDFTQLNELQCRFPRRLVVLGFP 1thx 20 :EQPVLVYFWASWCGPCQLMSPLINLAANTYSDRLKVVKLE T0345 72 :QENCQ 1thx 60 :IDPNP T0345 79 :EILNSLK 1thx 65 :TTVKKYK T0345 105 :VNG 1thx 72 :VEG T0345 124 :P 1thx 75 :V T0345 152 :FEKFLIGPE 1thx 76 :PALRLVKGE T0345 162 :EPFRRYSRTFPTINIEPDIKRLLK 1thx 85 :QILDSTEGVISKDKLLSFLDTHLN Number of specific fragments extracted= 7 number of extra gaps= 0 total=551 Number of alignments=68 # 1thx read from 1thx/merged-good-all-a2m # found chain 1thx in training set T0345 26 :GRAVLIENVASLCGTTTRDFTQLNELQCRFPRRLVVLGF 1thx 20 :EQPVLVYFWASWCGPCQLMSPLINLAANTYSDRLKVVKL T0345 71 :HQENCQ 1thx 59 :EIDPNP T0345 79 :EILNSLK 1thx 65 :TTVKKYK T0345 105 :VNG 1thx 72 :VEG T0345 151 :NFEKFLIGPE 1thx 75 :VPALRLVKGE T0345 162 :EPFRRYSRTFPTINIEPDIKRLLK 1thx 85 :QILDSTEGVISKDKLLSFLDTHLN Number of specific fragments extracted= 6 number of extra gaps= 0 total=557 Number of alignments=69 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1zzoA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1zzoA expands to /projects/compbio/data/pdb/1zzo.pdb.gz 1zzoA:# T0345 read from 1zzoA/merged-good-all-a2m # 1zzoA read from 1zzoA/merged-good-all-a2m # adding 1zzoA to template set # found chain 1zzoA in template set T0345 3 :AKSFYDLSAINLDGEKVDFNTFRGRAVLIENVASLCGTTTRDFTQLNELQCRF 1zzoA 46 :VPAQLQFSAKTLDGHDFHGESLLGKPAVLWFWAPWCPTCQGEAPVVGQVAASH T0345 58 :RLVVLGFP 1zzoA 100 :EVTFVGVA T0345 73 :ENCQNEEILNSLKY 1zzoA 108 :GLDQVPAMQEFVNK T0345 93 :YQP 1zzoA 122 :YPV T0345 98 :TLVQKCEVN 1zzoA 125 :KTFTQLADT T0345 110 :EHPVFAY 1zzoA 134 :DGSVWAN T0345 121 :LPYPYD 1zzoA 141 :FGVTQQ T0345 152 :FEKFLIGPEGEP 1zzoA 147 :PAYAFVDPHGNV T0345 165 :RRYSRTFPTINIEPDIKRL 1zzoA 159 :DVVRGRMSQDELTRRVTAL Number of specific fragments extracted= 9 number of extra gaps= 0 total=566 Number of alignments=70 # 1zzoA read from 1zzoA/merged-good-all-a2m # found chain 1zzoA in template set Warning: unaligning (T0345)I2 because first residue in template chain is (1zzoA)T45 T0345 3 :AKSFYDLSAINLDGEKVDFNTFRGRAVLIENVASLCGTTTRDFTQLNELQCRF 1zzoA 46 :VPAQLQFSAKTLDGHDFHGESLLGKPAVLWFWAPWCPTCQGEAPVVGQVAASH T0345 56 :PRRLVVLGF 1zzoA 100 :EVTFVGVAG T0345 74 :NCQNEEILNSLKY 1zzoA 109 :LDQVPAMQEFVNK T0345 93 :YQP 1zzoA 122 :YPV T0345 98 :TLVQKCEV 1zzoA 125 :KTFTQLAD T0345 109 :NEHPVFAY 1zzoA 133 :TDGSVWAN T0345 121 :LPYPYDD 1zzoA 141 :FGVTQQP T0345 153 :EKFLIGPEGEP 1zzoA 148 :AYAFVDPHGNV T0345 165 :RRYSRTFPTINIEPDIKRL 1zzoA 159 :DVVRGRMSQDELTRRVTAL Number of specific fragments extracted= 9 number of extra gaps= 0 total=575 Number of alignments=71 # 1zzoA read from 1zzoA/merged-good-all-a2m # found chain 1zzoA in template set T0345 4 :KSFYDLSAINLDGEKVDFNTFRGRAVLIENVASLCG 1zzoA 47 :PAQLQFSAKTLDGHDFHGESLLGKPAVLWFWAPWCP T0345 43 :RDFTQLNELQCRFP 1zzoA 83 :TCQGEAPVVGQVAA T0345 57 :RRLVVLGFP 1zzoA 99 :PEVTFVGVA T0345 73 :ENCQNEEILNSLK 1zzoA 108 :GLDQVPAMQEFVN T0345 92 :GYQP 1zzoA 121 :KYPV T0345 96 :TFTLVQK 1zzoA 126 :TFTQLAD T0345 106 :N 1zzoA 133 :T T0345 110 :EH 1zzoA 134 :DG T0345 116 :YLKDKLPYPYD 1zzoA 136 :SVWANFGVTQQ T0345 152 :FEKFLIGPEGEP 1zzoA 147 :PAYAFVDPHGNV T0345 165 :RRYSRTFPTINIEPDIKRL 1zzoA 159 :DVVRGRMSQDELTRRVTAL Number of specific fragments extracted= 11 number of extra gaps= 0 total=586 Number of alignments=72 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1erv/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0345 read from 1erv/merged-good-all-a2m # 1erv read from 1erv/merged-good-all-a2m # found chain 1erv in training set T0345 23 :TFRGRAVLIENVASLCGTTTRDFTQLNELQCRFP 1erv 17 :AAGDKLVVVDFSATWCGPCKMIKPFFHSLSEKYS T0345 58 :RLVVLGFPCNQF 1erv 51 :NVIFLEVDVDDC T0345 78 :EEILNSLKY 1erv 63 :QDVASECEV T0345 92 :GYQPTFTLVQ 1erv 72 :KSMPTFQFFK T0345 160 :EGEPFRRYSR 1erv 82 :KGQKVGEFSG T0345 171 :FPTINIEPDIKRL 1erv 92 :ANKEKLEATINEL Number of specific fragments extracted= 6 number of extra gaps= 0 total=592 Number of alignments=73 # 1erv read from 1erv/merged-good-all-a2m # found chain 1erv in training set Warning: unaligning (T0345)L184 because last residue in template chain is (1erv)V105 T0345 22 :NTFRGRAVLIENVASLCGTTTRDFTQLNELQCRFP 1erv 16 :DAAGDKLVVVDFSATWCGPCKMIKPFFHSLSEKYS T0345 58 :RLVVLGFPCNQF 1erv 51 :NVIFLEVDVDDC T0345 78 :EEILNSLKY 1erv 63 :QDVASECEV T0345 122 :P 1erv 72 :K T0345 146 :SDVAWNFEK 1erv 73 :SMPTFQFFK T0345 160 :EGEPFRRYSR 1erv 82 :KGQKVGEFSG T0345 171 :FPTINIEPDIKRL 1erv 92 :ANKEKLEATINEL Number of specific fragments extracted= 7 number of extra gaps= 0 total=599 Number of alignments=74 # 1erv read from 1erv/merged-good-all-a2m # found chain 1erv in training set Warning: unaligning (T0345)L184 because last residue in template chain is (1erv)V105 T0345 22 :NTFRGRAVLIENVASLCGTTT 1erv 16 :DAAGDKLVVVDFSATWCGPCK T0345 43 :RDFTQLNELQCR 1erv 38 :IKPFFHSLSEKY T0345 57 :RRLVVLGFPCNQF 1erv 50 :SNVIFLEVDVDDC T0345 78 :EEILNSLK 1erv 63 :QDVASECE T0345 91 :G 1erv 71 :V T0345 149 :AWNFEKFLI 1erv 72 :KSMPTFQFF T0345 159 :PEGEPFRRYSR 1erv 81 :KKGQKVGEFSG T0345 171 :FPTINIEPDIKRL 1erv 92 :ANKEKLEATINEL Number of specific fragments extracted= 8 number of extra gaps= 0 total=607 Number of alignments=75 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1erw/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1erw expands to /projects/compbio/data/pdb/1erw.pdb.gz 1erw:Warning: there is no chain 1erw will retry with 1erwA Skipped atom 331, because occupancy 0.500 <= existing 0.500 in 1erw Skipped atom 333, because occupancy 0.500 <= existing 0.500 in 1erw Skipped atom 335, because occupancy 0.500 <= existing 0.500 in 1erw Skipped atom 337, because occupancy 0.500 <= existing 0.500 in 1erw Skipped atom 339, because occupancy 0.500 <= existing 0.500 in 1erw # T0345 read from 1erw/merged-good-all-a2m # 1erw read from 1erw/merged-good-all-a2m # adding 1erw to template set # found chain 1erw in template set T0345 24 :FRGRAVLIENVASLCGTTTRDFTQLNELQCRFP 1erw 18 :AGDKLVVVDFSATWSGPSKMIKPFFHSLSEKYS T0345 58 :RLVVLGFPCNQF 1erw 51 :NVIFLEVDVDDC T0345 78 :EEILNSLKY 1erw 63 :QDVASECEV T0345 92 :GYQPTFTLVQ 1erw 72 :KCMPTFQFFK T0345 160 :EGEPFRRYSR 1erw 82 :KGQKVGEFSG T0345 171 :FPTINIEPDIKRL 1erw 92 :ANKEKLEATINEL Number of specific fragments extracted= 6 number of extra gaps= 0 total=613 Number of alignments=76 # 1erw read from 1erw/merged-good-all-a2m # found chain 1erw in template set Warning: unaligning (T0345)L184 because last residue in template chain is (1erw)V105 T0345 24 :FRGRAVLIENVASLCGTTTRDFTQLNELQCRFP 1erw 18 :AGDKLVVVDFSATWSGPSKMIKPFFHSLSEKYS T0345 58 :RLVVLGFPCNQF 1erw 51 :NVIFLEVDVDDC T0345 78 :EEILNSLKY 1erw 63 :QDVASECEV T0345 92 :GYQPTF 1erw 72 :KCMPTF T0345 151 :NFEK 1erw 78 :QFFK T0345 160 :EGEPFRRYSR 1erw 82 :KGQKVGEFSG T0345 171 :FPTINIEPDIKRL 1erw 92 :ANKEKLEATINEL Number of specific fragments extracted= 7 number of extra gaps= 0 total=620 Number of alignments=77 # 1erw read from 1erw/merged-good-all-a2m # found chain 1erw in template set Warning: unaligning (T0345)L184 because last residue in template chain is (1erw)V105 T0345 23 :TFRGRAVLIENVASLCG 1erw 17 :AAGDKLVVVDFSATWSG T0345 43 :RDFTQLNELQCRFP 1erw 34 :PSKMIKPFFHSLSE T0345 57 :RRLVVLGFPCNQF 1erw 50 :SNVIFLEVDVDDC T0345 78 :EEILNSLK 1erw 63 :QDVASECE T0345 91 :GGYQPTFTLVQ 1erw 71 :VKCMPTFQFFK T0345 160 :EGEPFRRYSR 1erw 82 :KGQKVGEFSG T0345 171 :FPTINIEPDIKRL 1erw 92 :ANKEKLEATINEL Number of specific fragments extracted= 7 number of extra gaps= 0 total=627 Number of alignments=78 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2cvbA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2cvbA expands to /projects/compbio/data/pdb/2cvb.pdb.gz 2cvbA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0345 read from 2cvbA/merged-good-all-a2m # 2cvbA read from 2cvbA/merged-good-all-a2m # adding 2cvbA to template set # found chain 2cvbA in template set T0345 2 :IAKSFYDLSAINLDGEKVDFNTFRGRAVLIENVASLCGTTTRDFTQLNELQCRFPRRLVVLGFPCNQFGHQENCQNEEILNSLKYV 2cvbA 9 :LESPLIDAELPDPRGGRYRLSQFHEPLLAVVFMCNHCPYVKGSIGELVALAERYRGKVAFVGINANDYEKYPEDAPEKMAAFAEEH T0345 92 :GYQPTFTLV 2cvbA 95 :GIFFPYLLD T0345 109 :NEHPVFAYL 2cvbA 104 :ETQEVAKAY T0345 147 :DVAWNFEKFLIGPEGEPFRRY 2cvbA 113 :RALRTPEVFLFDERRLLRYHG T0345 168 :SRTFPTIN 2cvbA 137 :DNPKDPSK T0345 176 :IEPDIKRLLK 2cvbA 150 :LEAAIEALLR Number of specific fragments extracted= 6 number of extra gaps= 0 total=633 Number of alignments=79 # 2cvbA read from 2cvbA/merged-good-all-a2m # found chain 2cvbA in template set T0345 2 :IAKSFYDLSAINLDGEKVDFNTFRGRAVLIENVASLCGTTTRDFTQLNELQCRFPRRLVVLGFPCNQFGHQENCQNEEILNSLKYV 2cvbA 9 :LESPLIDAELPDPRGGRYRLSQFHEPLLAVVFMCNHCPYVKGSIGELVALAERYRGKVAFVGINANDYEKYPEDAPEKMAAFAEEH T0345 92 :GYQPTFTLV 2cvbA 95 :GIFFPYLLD T0345 109 :NEHPVFAYL 2cvbA 104 :ETQEVAKAY T0345 147 :DVAWNFEKFLIGPEGEPFRRY 2cvbA 113 :RALRTPEVFLFDERRLLRYHG T0345 168 :SRTFPTIN 2cvbA 137 :DNPKDPSK T0345 176 :IEPDIKRLL 2cvbA 150 :LEAAIEALL Number of specific fragments extracted= 6 number of extra gaps= 0 total=639 Number of alignments=80 # 2cvbA read from 2cvbA/merged-good-all-a2m # found chain 2cvbA in template set T0345 3 :AKSFYDLSAINLDGEKVDFNTFRGRAVLIENVASLCGTTT 2cvbA 10 :ESPLIDAELPDPRGGRYRLSQFHEPLLAVVFMCNHCPYVK T0345 43 :RDFTQLNELQCRFP 2cvbA 51 :SIGELVALAERYRG T0345 58 :RLVVLGFPCNQFGHQENCQNEEILNSLK 2cvbA 65 :KVAFVGINANDYEKYPEDAPEKMAAFAE T0345 92 :GYQPTFTLVQK 2cvbA 93 :EHGIFFPYLLD T0345 109 :NEHPVFAYL 2cvbA 104 :ETQEVAKAY T0345 147 :DVAWNFEKFLIGPEGEPFRRYS 2cvbA 113 :RALRTPEVFLFDERRLLRYHGR T0345 172 :PTIN 2cvbA 141 :DPSK T0345 176 :IEPDIKRLL 2cvbA 150 :LEAAIEALL Number of specific fragments extracted= 8 number of extra gaps= 0 total=647 Number of alignments=81 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2gs3A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0345/2gs3A/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0345/2gs3A/merged-good-all-a2m.gz for input Trying 2gs3A/merged-good-all-a2m Error: Couldn't open file 2gs3A/merged-good-all-a2m or 2gs3A/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1lu4A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0345 read from 1lu4A/merged-good-all-a2m # 1lu4A read from 1lu4A/merged-good-all-a2m # found chain 1lu4A in training set Warning: unaligning (T0345)A3 because first residue in template chain is (1lu4A)A1001 Warning: unaligning (T0345)S5 because of BadResidue code BAD_PEPTIDE in next template residue (1lu4A)R1004 Warning: unaligning (T0345)F6 because of BadResidue code BAD_PEPTIDE at template residue (1lu4A)R1004 Warning: unaligning (T0345)F114 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1lu4A)A1093 Warning: unaligning (T0345)A115 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1lu4A)A1093 Warning: unaligning (T0345)P122 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1lu4A)V1097 Warning: unaligning (T0345)Y123 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1lu4A)V1097 Warning: unaligning (T0345)P124 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1lu4A)P1098 Warning: unaligning (T0345)Y125 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1lu4A)W1099 Warning: unaligning (T0345)D126 because of BadResidue code BAD_PEPTIDE at template residue (1lu4A)Q1100 T0345 4 :K 1lu4A 1002 :D T0345 7 :YDLSAINLDGEKVDFNTFRGRAVLIENVASLCGTTTRDFTQLNELQCRF 1lu4A 1005 :LQFTATTLSGAPFDGASLQGKPAVLWFWTPWCPFCNAEAPSLSQVAAAN T0345 56 :PRRLVVLGF 1lu4A 1055 :AVTFVGIAT T0345 74 :NCQNEEILNSLKYV 1lu4A 1064 :RADVGAMQSFVSKY T0345 92 :GYQ 1lu4A 1078 :NLN T0345 97 :FTLVQ 1lu4A 1081 :FTNLN T0345 107 :GQN 1lu4A 1086 :DAD T0345 111 :HPV 1lu4A 1089 :GVI T0345 116 :Y 1lu4A 1094 :R T0345 121 :L 1lu4A 1095 :Y T0345 152 :FEKFLIGPEGEPFRRYSRT 1lu4A 1101 :PAFVFYRADGTSTFVNNPT T0345 171 :FPTINIEPDIKR 1lu4A 1122 :MSQDELSGRVAA Number of specific fragments extracted= 12 number of extra gaps= 3 total=659 Number of alignments=82 # 1lu4A read from 1lu4A/merged-good-all-a2m # found chain 1lu4A in training set Warning: unaligning (T0345)S5 because of BadResidue code BAD_PEPTIDE in next template residue (1lu4A)R1004 Warning: unaligning (T0345)F6 because of BadResidue code BAD_PEPTIDE at template residue (1lu4A)R1004 Warning: unaligning (T0345)F114 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1lu4A)A1093 Warning: unaligning (T0345)A115 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1lu4A)A1093 Warning: unaligning (T0345)P122 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1lu4A)V1097 Warning: unaligning (T0345)Y123 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1lu4A)V1097 Warning: unaligning (T0345)P124 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1lu4A)P1098 Warning: unaligning (T0345)Y125 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1lu4A)W1099 Warning: unaligning (T0345)D126 because of BadResidue code BAD_PEPTIDE at template residue (1lu4A)Q1100 T0345 4 :K 1lu4A 1002 :D T0345 7 :YDLSAINLDGEKVDFNTFRGRAVLIENVASLCGTTTRDFTQLNELQCRF 1lu4A 1005 :LQFTATTLSGAPFDGASLQGKPAVLWFWTPWCPFCNAEAPSLSQVAAAN T0345 56 :PRRLVVLGF 1lu4A 1055 :AVTFVGIAT T0345 74 :NCQNEEILNSLKYV 1lu4A 1064 :RADVGAMQSFVSKY T0345 92 :GYQPT 1lu4A 1078 :NLNFT T0345 99 :LVQ 1lu4A 1083 :NLN T0345 107 :GQ 1lu4A 1086 :DA T0345 110 :EHPV 1lu4A 1088 :DGVI T0345 116 :YL 1lu4A 1094 :RY T0345 127 :D 1lu4A 1101 :P T0345 153 :EKFLIGPEGEPFRRYSRT 1lu4A 1102 :AFVFYRADGTSTFVNNPT T0345 171 :FPTINIEPDIKR 1lu4A 1122 :MSQDELSGRVAA Number of specific fragments extracted= 12 number of extra gaps= 3 total=671 Number of alignments=83 # 1lu4A read from 1lu4A/merged-good-all-a2m # found chain 1lu4A in training set Warning: unaligning (T0345)S5 because of BadResidue code BAD_PEPTIDE in next template residue (1lu4A)R1004 Warning: unaligning (T0345)F6 because of BadResidue code BAD_PEPTIDE at template residue (1lu4A)R1004 Warning: unaligning (T0345)K118 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1lu4A)A1093 Warning: unaligning (T0345)D119 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1lu4A)A1093 Warning: unaligning (T0345)P122 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1lu4A)V1097 Warning: unaligning (T0345)Y123 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1lu4A)V1097 Warning: unaligning (T0345)P124 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1lu4A)P1098 Warning: unaligning (T0345)Y125 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1lu4A)W1099 Warning: unaligning (T0345)D126 because of BadResidue code BAD_PEPTIDE at template residue (1lu4A)Q1100 T0345 4 :K 1lu4A 1002 :D T0345 7 :YDLSAINLDGEKVDFNTFRGRAVLIENVASLCGTTT 1lu4A 1005 :LQFTATTLSGAPFDGASLQGKPAVLWFWTPWCPFCN T0345 43 :RDFTQLNELQCRFPRRLVVLG 1lu4A 1042 :EAPSLSQVAAANPAVTFVGIA T0345 73 :ENCQNEEILNSLK 1lu4A 1063 :TRADVGAMQSFVS T0345 92 :GYQPTFTLVQK 1lu4A 1076 :KYNLNFTNLND T0345 108 :QNE 1lu4A 1087 :ADG T0345 116 :YL 1lu4A 1090 :VI T0345 120 :KL 1lu4A 1094 :RY T0345 152 :FEKFLIGPEGEPFRRYSRT 1lu4A 1101 :PAFVFYRADGTSTFVNNPT T0345 171 :FPTINIEPDIKR 1lu4A 1122 :MSQDELSGRVAA Number of specific fragments extracted= 10 number of extra gaps= 3 total=681 Number of alignments=84 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1nw2A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1nw2A expands to /projects/compbio/data/pdb/1nw2.pdb.gz 1nw2A:# T0345 read from 1nw2A/merged-good-all-a2m # 1nw2A read from 1nw2A/merged-good-all-a2m # adding 1nw2A to template set # found chain 1nw2A in template set Warning: unaligning (T0345)D126 because of BadResidue code BAD_PEPTIDE in next template residue (1nw2A)P73 Warning: unaligning (T0345)F152 because of BadResidue code BAD_PEPTIDE at template residue (1nw2A)P73 T0345 26 :GRAVLIENVASLCGTTTRDFTQLNELQCRFPRRLVVLGFPCN 1nw2A 17 :DKPVLVDFWAAWCGPCRMMAPVLEEFAEAHADKVTVAKLNVD T0345 110 :EHP 1nw2A 59 :ENP T0345 116 :YLKDKLPYPY 1nw2A 62 :ETTSQFGIMS T0345 153 :EKFLIG 1nw2A 74 :TLILFK T0345 160 :EGEPFRRYSRTFP 1nw2A 80 :GGEPVKQLIGYQP T0345 177 :EPDIKRLLK 1nw2A 93 :KEQLEAQLA Number of specific fragments extracted= 6 number of extra gaps= 1 total=687 Number of alignments=85 # 1nw2A read from 1nw2A/merged-good-all-a2m # found chain 1nw2A in template set Warning: unaligning (T0345)D126 because of BadResidue code BAD_PEPTIDE in next template residue (1nw2A)P73 Warning: unaligning (T0345)F152 because of BadResidue code BAD_PEPTIDE at template residue (1nw2A)P73 T0345 26 :GRAVLIENVASLCGTTTRDFTQLNELQCRFPRRLVVLGFPCNQ 1nw2A 17 :DKPVLVDFWAAWCGPCRMMAPVLEEFAEAHADKVTVAKLNVDE T0345 77 :NEE 1nw2A 60 :NPE T0345 117 :LKDKLPYPY 1nw2A 63 :TTSQFGIMS T0345 153 :EKFLIG 1nw2A 74 :TLILFK T0345 160 :EGEPFRRYSRTFP 1nw2A 80 :GGEPVKQLIGYQP T0345 177 :EPDIKRLLK 1nw2A 93 :KEQLEAQLA Number of specific fragments extracted= 6 number of extra gaps= 1 total=693 Number of alignments=86 # 1nw2A read from 1nw2A/merged-good-all-a2m # found chain 1nw2A in template set Warning: unaligning (T0345)D126 because of BadResidue code BAD_PEPTIDE in next template residue (1nw2A)P73 Warning: unaligning (T0345)F152 because of BadResidue code BAD_PEPTIDE at template residue (1nw2A)P73 T0345 26 :GRAVLIENVASLCGTTTRDFTQLNELQCRFPRRLVVLGFPCN 1nw2A 17 :DKPVLVDFWAAWCGPCRMMAPVLEEFAEAHADKVTVAKLNVD T0345 74 :NCQ 1nw2A 59 :ENP T0345 79 :E 1nw2A 62 :E T0345 117 :LKDKLPYPY 1nw2A 63 :TTSQFGIMS T0345 153 :EKFLIG 1nw2A 74 :TLILFK T0345 160 :EGEPFRRYSRTFPTIN 1nw2A 80 :GGEPVKQLIGYQPKEQ T0345 180 :IKRLLK 1nw2A 96 :LEAQLA Number of specific fragments extracted= 7 number of extra gaps= 1 total=700 Number of alignments=87 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1nswA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1nswA expands to /projects/compbio/data/pdb/1nsw.pdb.gz 1nswA:# T0345 read from 1nswA/merged-good-all-a2m # 1nswA read from 1nswA/merged-good-all-a2m # adding 1nswA to template set # found chain 1nswA in template set T0345 26 :GRAVLIENVASLCGTTTRDFTQLNELQCRFPRRLVVLGFPCN 1nswA 17 :DGPVLVDFWAAWCGPCRMMAPVLEEFAEAHADKVTVAKLNVD T0345 110 :EHP 1nswA 59 :ENP T0345 116 :YLKDKLPYP 1nswA 62 :ETTSQFGIM T0345 150 :WNFEKFLIG 1nswA 71 :SIPTLILFK T0345 160 :EGEPFRRYSRTFP 1nswA 80 :GGRPVKQLIGYQP T0345 177 :EPDIKRLLK 1nswA 93 :KEQLEAQLA Number of specific fragments extracted= 6 number of extra gaps= 0 total=706 Number of alignments=88 # 1nswA read from 1nswA/merged-good-all-a2m # found chain 1nswA in template set T0345 25 :RGRAVLIENVASLCGTTTRDFTQLNELQCRFPRRLVVLGFPCN 1nswA 16 :GDGPVLVDFWAAWCGPCRMMAPVLEEFAEAHADKVTVAKLNVD T0345 76 :QNEEILNSL 1nswA 59 :ENPETTSQF T0345 122 :PYPY 1nswA 68 :GIMS T0345 151 :NFEKFLIG 1nswA 72 :IPTLILFK T0345 160 :EGEPFRRYSRTFP 1nswA 80 :GGRPVKQLIGYQP T0345 177 :EPDIKRLLK 1nswA 93 :KEQLEAQLA Number of specific fragments extracted= 6 number of extra gaps= 0 total=712 Number of alignments=89 # 1nswA read from 1nswA/merged-good-all-a2m # found chain 1nswA in template set T0345 26 :GRAVLIENVASLCGTTTRDFTQLNELQCRFPRRLVVLGFPC 1nswA 17 :DGPVLVDFWAAWCGPCRMMAPVLEEFAEAHADKVTVAKLNV T0345 75 :CQNEEILNS 1nswA 58 :DENPETTSQ T0345 121 :LP 1nswA 67 :FG T0345 148 :VAWNFEKFLIG 1nswA 69 :IMSIPTLILFK T0345 160 :EGEPFRRYSRTFPTINIEPDIKRLL 1nswA 80 :GGRPVKQLIGYQPKEQLEAQLADVL Number of specific fragments extracted= 5 number of extra gaps= 0 total=717 Number of alignments=90 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ewxA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1ewxA expands to /projects/compbio/data/pdb/1ewx.pdb.gz 1ewxA:# T0345 read from 1ewxA/merged-good-all-a2m # 1ewxA read from 1ewxA/merged-good-all-a2m # adding 1ewxA to template set # found chain 1ewxA in template set T0345 6 :FYDL 1ewxA 11 :IEKL T0345 13 :NLDGEKVDFNTFRGRAVLIENVASLCGTTTRDFTQLNELQCRF 1ewxA 15 :RRGDGEVEVKSLAGKLVFFYFSASWCPPCRGFTPQLIEFYDKF T0345 56 :PRRLVVLGFP 1ewxA 60 :SKNFEVVFCT T0345 73 :ENCQNEEILNSLK 1ewxA 70 :WDEEEDGFAGYFA T0345 92 :GYQPTF 1ewxA 83 :KMPWLA T0345 100 :VQ 1ewxA 89 :VP T0345 108 :QNEHPVFAYLKDKLPYPYD 1ewxA 91 :FAQSEAVQKLSKHFNVESI T0345 152 :FEKFLIG 1ewxA 110 :PTLIGVD T0345 159 :PEGEPFRR 1ewxA 118 :DSGDVVTT T0345 175 :NIEPDIKR 1ewxA 126 :RARATLVK Number of specific fragments extracted= 10 number of extra gaps= 0 total=727 Number of alignments=91 # 1ewxA read from 1ewxA/merged-good-all-a2m # found chain 1ewxA in template set T0345 9 :LSAINLDGEKVDFNTFRGRAVLIENVASLCGTTTRDFTQLNELQCRF 1ewxA 11 :IEKLRRGDGEVEVKSLAGKLVFFYFSASWCPPCRGFTPQLIEFYDKF T0345 56 :PRRLVVLGFPC 1ewxA 60 :SKNFEVVFCTW T0345 74 :NCQNEEILNSLKY 1ewxA 71 :DEEEDGFAGYFAK T0345 93 :YQPTFTL 1ewxA 84 :MPWLAVP T0345 108 :QNEHPVFAYLKDKLPYPYD 1ewxA 91 :FAQSEAVQKLSKHFNVESI T0345 146 :S 1ewxA 110 :P T0345 153 :EKFLIG 1ewxA 111 :TLIGVD T0345 159 :PEGEPFR 1ewxA 118 :DSGDVVT Number of specific fragments extracted= 8 number of extra gaps= 0 total=735 Number of alignments=92 # 1ewxA read from 1ewxA/merged-good-all-a2m # found chain 1ewxA in template set T0345 15 :DGEKVDFNTFRGRAVLIENVASLCGTTT 1ewxA 17 :GDGEVEVKSLAGKLVFFYFSASWCPPCR T0345 43 :RDFTQLNELQCRFP 1ewxA 46 :FTPQLIEFYDKFHE T0345 57 :RRLVVLGFP 1ewxA 61 :KNFEVVFCT T0345 73 :ENCQNEEILNSLK 1ewxA 70 :WDEEEDGFAGYFA T0345 94 :QPTFTLVQK 1ewxA 83 :KMPWLAVPF T0345 109 :NEHPVFAYLKDKLPYPYD 1ewxA 92 :AQSEAVQKLSKHFNVESI T0345 152 :FEKFLIG 1ewxA 110 :PTLIGVD T0345 159 :PEGEPFRR 1ewxA 118 :DSGDVVTT T0345 175 :NIEPDIKR 1ewxA 126 :RARATLVK Number of specific fragments extracted= 9 number of extra gaps= 0 total=744 Number of alignments=93 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1xvqA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0345 read from 1xvqA/merged-good-all-a2m # 1xvqA read from 1xvqA/merged-good-all-a2m # found chain 1xvqA in training set Warning: unaligning (T0345)L62 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1xvqA)V81 Warning: unaligning (T0345)F64 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1xvqA)V81 Warning: unaligning (T0345)L84 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1xvqA)N100 Warning: unaligning (T0345)T96 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1xvqA)N100 T0345 1 :MIAKSFYDLSAINLDGEKVDFNTFRGRAVLIENVASLCGTTTR 1xvqA 19 :AVGSPAPAFTLTGGDLGVISSDQFRGKSVLLNIFPSVDTPVCA T0345 46 :TQLNELQCRF 1xvqA 62 :TSVRTFDERA T0345 56 :PRRLVV 1xvqA 73 :ASGATV T0345 65 :P 1xvqA 82 :S T0345 74 :NCQNEEILNS 1xvqA 83 :KDLPFAQKRF T0345 100 :VQKCEVNGQN 1xvqA 101 :VMPASAFRDS T0345 117 :LKDKLPYPYDDPFS 1xvqA 111 :FGEDYGVTIADGPM T0345 145 :RSDVAWN 1xvqA 125 :AGLLARA T0345 154 :KFLIGPEGEPFRRY 1xvqA 132 :IVVIGADGNVAYTE T0345 168 :SRTFPTINIEPDIKRL 1xvqA 151 :AQEPNYEAALAALGAT Number of specific fragments extracted= 10 number of extra gaps= 0 total=754 Number of alignments=94 # 1xvqA read from 1xvqA/merged-good-all-a2m # found chain 1xvqA in training set Warning: unaligning (T0345)L62 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1xvqA)V81 Warning: unaligning (T0345)F64 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1xvqA)V81 Warning: unaligning (T0345)L84 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1xvqA)N100 Warning: unaligning (T0345)T96 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1xvqA)N100 T0345 2 :IAKSFYDLSAINLDGEKVDFNTFRGRAVLIENVASLCGTTTR 1xvqA 20 :VGSPAPAFTLTGGDLGVISSDQFRGKSVLLNIFPSVDTPVCA T0345 46 :TQLNELQCRF 1xvqA 62 :TSVRTFDERA T0345 56 :PRRLVV 1xvqA 73 :ASGATV T0345 65 :P 1xvqA 82 :S T0345 74 :NCQNEEILNS 1xvqA 83 :KDLPFAQKRF T0345 100 :VQKCEVNGQN 1xvqA 101 :VMPASAFRDS T0345 117 :LKDKLPYPYDD 1xvqA 111 :FGEDYGVTIAD T0345 142 :PVRRSDVAW 1xvqA 122 :GPMAGLLAR T0345 153 :EKFLIGPEGEPFRRY 1xvqA 131 :AIVVIGADGNVAYTE T0345 168 :SRTFPTINIEPDIKRL 1xvqA 151 :AQEPNYEAALAALGAT Number of specific fragments extracted= 10 number of extra gaps= 0 total=764 Number of alignments=95 # 1xvqA read from 1xvqA/merged-good-all-a2m # found chain 1xvqA in training set Warning: unaligning (T0345)L62 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1xvqA)V81 Warning: unaligning (T0345)F64 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1xvqA)V81 Warning: unaligning (T0345)L84 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1xvqA)N100 Warning: unaligning (T0345)T96 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1xvqA)N100 T0345 2 :IAKSFYDLSAINLDGEKVDFNTFRGRAVLIENVASLCGT 1xvqA 20 :VGSPAPAFTLTGGDLGVISSDQFRGKSVLLNIFPSVDTP T0345 43 :RDFTQLNELQCRFPRRLVV 1xvqA 60 :CATSVRTFDERAAASGATV T0345 65 :PC 1xvqA 82 :SK T0345 75 :CQNEEILNS 1xvqA 84 :DLPFAQKRF T0345 97 :FTLVQK 1xvqA 101 :VMPASA T0345 127 :DPFSLMTDPKLIIWSPVRRSDVAWN 1xvqA 107 :FRDSFGEDYGVTIADGPMAGLLARA T0345 154 :KFLIGPEGEPFRRYS 1xvqA 132 :IVVIGADGNVAYTEL T0345 169 :RTFPTINIEPDIKRL 1xvqA 152 :QEPNYEAALAALGAT Number of specific fragments extracted= 8 number of extra gaps= 0 total=772 Number of alignments=96 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1i5gA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1i5gA expands to /projects/compbio/data/pdb/1i5g.pdb.gz 1i5gA:# T0345 read from 1i5gA/merged-good-all-a2m # 1i5gA read from 1i5gA/merged-good-all-a2m # adding 1i5gA to template set # found chain 1i5gA in template set Warning: unaligning (T0345)R27 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1i5gA)T31 Warning: unaligning (T0345)A28 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1i5gA)T31 T0345 14 :LDGEK 1i5gA 16 :KGAAA T0345 19 :VDFNTFRG 1i5gA 22 :IALPSLAG T0345 29 :VLIENVASLCGTTTRDFTQLNELQCRF 1i5gA 32 :VFFYFSASWCPPSRAFTPQLIDFYKAH T0345 56 :PRRLVVLGFPC 1i5gA 61 :KKNFEVMLISW T0345 74 :NCQNEEILNSLK 1i5gA 72 :DESAEDFKDYYA T0345 92 :GYQPTF 1i5gA 84 :KMPWLA T0345 100 :VQ 1i5gA 90 :LP T0345 108 :QNEHPVFAYLKDKLPYP 1i5gA 92 :FEDRKGMEFLTTGFDVK T0345 146 :SDVAWNF 1i5gA 109 :SIPTLVG T0345 156 :LIGPEGEPFRR 1i5gA 116 :VEADSGNIITT Number of specific fragments extracted= 10 number of extra gaps= 1 total=782 Number of alignments=97 # 1i5gA read from 1i5gA/merged-good-all-a2m # found chain 1i5gA in template set Warning: unaligning (T0345)R27 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1i5gA)T31 Warning: unaligning (T0345)A28 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1i5gA)T31 T0345 14 :LDGEK 1i5gA 16 :KGAAA T0345 19 :VDFNTFRG 1i5gA 22 :IALPSLAG T0345 29 :VLIENVASLCGTTTRDFTQLNELQCRF 1i5gA 32 :VFFYFSASWCPPSRAFTPQLIDFYKAH T0345 56 :PRRLVVLGFPC 1i5gA 61 :KKNFEVMLISW T0345 74 :NCQNEEILNSLK 1i5gA 72 :DESAEDFKDYYA T0345 92 :GYQPTF 1i5gA 84 :KMPWLA T0345 99 :L 1i5gA 91 :P T0345 108 :QNEHPVFAYLKDKLPYP 1i5gA 92 :FEDRKGMEFLTTGFDVK T0345 146 :SDVAWN 1i5gA 109 :SIPTLV T0345 155 :FLIGPEGEPFR 1i5gA 115 :GVEADSGNIIT Number of specific fragments extracted= 10 number of extra gaps= 1 total=792 Number of alignments=98 # 1i5gA read from 1i5gA/merged-good-all-a2m # found chain 1i5gA in template set Warning: unaligning (T0345)R27 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1i5gA)T31 Warning: unaligning (T0345)A28 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1i5gA)T31 T0345 18 :KVDFNTFRG 1i5gA 21 :DIALPSLAG T0345 29 :VLIENVASLCGTTT 1i5gA 32 :VFFYFSASWCPPSR T0345 43 :RDFTQLNELQCRFPR 1i5gA 47 :FTPQLIDFYKAHAEK T0345 58 :RLVVLGFPC 1i5gA 63 :NFEVMLISW T0345 74 :NCQNEEILNSLK 1i5gA 72 :DESAEDFKDYYA T0345 94 :QPTFTLVQ 1i5gA 84 :KMPWLALP T0345 108 :QNEHPVFAYLKDKLPYPYD 1i5gA 92 :FEDRKGMEFLTTGFDVKSI T0345 152 :FEKFLIG 1i5gA 111 :PTLVGVE T0345 159 :PEGEPFRR 1i5gA 119 :DSGNIITT Number of specific fragments extracted= 9 number of extra gaps= 1 total=801 Number of alignments=99 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1xccA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1xccA expands to /projects/compbio/data/pdb/1xcc.pdb.gz 1xccA:# T0345 read from 1xccA/merged-good-all-a2m # 1xccA read from 1xccA/merged-good-all-a2m # adding 1xccA to template set # found chain 1xccA in template set Warning: unaligning (T0345)R27 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1xccA)W33 Warning: unaligning (T0345)A28 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1xccA)W33 Warning: unaligning (T0345)F64 because of BadResidue code BAD_PEPTIDE in next template residue (1xccA)S72 Warning: unaligning (T0345)P65 because of BadResidue code BAD_PEPTIDE at template residue (1xccA)S72 Warning: unaligning (T0345)E153 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1xccA)L131 Warning: unaligning (T0345)K154 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1xccA)L131 T0345 2 :IAKSFYDLSAINLD 1xccA 5 :LGATFPNFTAKASG T0345 16 :GEKVDFNTF 1xccA 20 :DGDFELYKY T0345 25 :RG 1xccA 30 :EN T0345 29 :VLIENV 1xccA 34 :AILFSH T0345 37 :LCGTTTRDFTQLNELQCRF 1xccA 40 :PNDFTPVCTTELAELGKMH T0345 56 :PRRLVVLG 1xccA 63 :KLNCKLIG T0345 66 :CN 1xccA 73 :CN T0345 76 :QNEEILNS 1xccA 75 :SKESHDKW T0345 84 :LKYVRPGGGYQPTFTLV 1xccA 86 :IKYYGKLNKWEIPIVCD T0345 109 :NEHPVFAYLK 1xccA 103 :ESRELANKLK T0345 138 :IIWSPVR 1xccA 113 :IMDEQEK T0345 145 :RSDVAWNF 1xccA 122 :TGLPLTCR T0345 155 :FLIGPEGEPFR 1xccA 132 :FFISPEKKIKA T0345 166 :RYSRT 1xccA 145 :LYPAT T0345 171 :FPTINIEPDIKRL 1xccA 152 :RNAHEILRVLKSL Number of specific fragments extracted= 15 number of extra gaps= 3 total=816 Number of alignments=100 # 1xccA read from 1xccA/merged-good-all-a2m # found chain 1xccA in template set Warning: unaligning (T0345)R27 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1xccA)W33 Warning: unaligning (T0345)A28 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1xccA)W33 Warning: unaligning (T0345)F64 because of BadResidue code BAD_PEPTIDE in next template residue (1xccA)S72 Warning: unaligning (T0345)P65 because of BadResidue code BAD_PEPTIDE at template residue (1xccA)S72 Warning: unaligning (T0345)E153 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1xccA)L131 Warning: unaligning (T0345)K154 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1xccA)L131 T0345 3 :AKSFYDLSAINLD 1xccA 6 :GATFPNFTAKASG T0345 16 :GEKVDFNTF 1xccA 20 :DGDFELYKY T0345 25 :RG 1xccA 30 :EN T0345 29 :VLIENV 1xccA 34 :AILFSH T0345 37 :LCGTTTRDFTQLNELQCRF 1xccA 40 :PNDFTPVCTTELAELGKMH T0345 56 :PRRLVVLG 1xccA 63 :KLNCKLIG T0345 66 :CN 1xccA 73 :CN T0345 76 :QNEEILNSL 1xccA 75 :SKESHDKWI T0345 85 :KYVRPGGGYQPTFTLV 1xccA 87 :KYYGKLNKWEIPIVCD T0345 109 :NEHPVFAYLK 1xccA 103 :ESRELANKLK T0345 123 :YP 1xccA 113 :IM T0345 138 :IIWSPVRRSDVAWNF 1xccA 115 :DEQEKDITGLPLTCR T0345 155 :FLIGPEGEPFRR 1xccA 132 :FFISPEKKIKAT T0345 167 :Y 1xccA 146 :Y T0345 168 :SRTFPTINIEPDIKRL 1xccA 149 :TTGRNAHEILRVLKSL Number of specific fragments extracted= 15 number of extra gaps= 3 total=831 Number of alignments=101 # 1xccA read from 1xccA/merged-good-all-a2m # found chain 1xccA in template set Warning: unaligning (T0345)R27 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1xccA)W33 Warning: unaligning (T0345)A28 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1xccA)W33 Warning: unaligning (T0345)F64 because of BadResidue code BAD_PEPTIDE in next template residue (1xccA)S72 Warning: unaligning (T0345)P65 because of BadResidue code BAD_PEPTIDE at template residue (1xccA)S72 Warning: unaligning (T0345)E153 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1xccA)L131 Warning: unaligning (T0345)K154 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1xccA)L131 T0345 3 :AKSFYDLSAINLD 1xccA 6 :GATFPNFTAKASG T0345 16 :GEKVDFNTF 1xccA 20 :DGDFELYKY T0345 25 :RG 1xccA 30 :EN T0345 29 :VLIEN 1xccA 34 :AILFS T0345 36 :SLCGTTT 1xccA 39 :HPNDFTP T0345 43 :RDFTQLNELQCRFPRRLVVLG 1xccA 50 :ELAELGKMHEDFLKLNCKLIG T0345 66 :C 1xccA 73 :C T0345 75 :CQNEEILNSLKY 1xccA 74 :NSKESHDKWIED T0345 91 :GGYQPTFTLVQK 1xccA 91 :KLNKWEIPIVCD T0345 109 :NEHPVFAYLK 1xccA 103 :ESRELANKLK T0345 140 :WSPVRRSDVAWNF 1xccA 117 :QEKDITGLPLTCR T0345 155 :FLIGPEGEPFR 1xccA 132 :FFISPEKKIKA T0345 166 :RYSRT 1xccA 145 :LYPAT T0345 171 :FPTINIEPDIKRL 1xccA 152 :RNAHEILRVLKSL Number of specific fragments extracted= 14 number of extra gaps= 3 total=845 Number of alignments=102 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1qmvA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0345 read from 1qmvA/merged-good-all-a2m # 1qmvA read from 1qmvA/merged-good-all-a2m # found chain 1qmvA in training set Warning: unaligning (T0345)T41 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (1qmvA)F49 Warning: unaligning (T0345)T42 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (1qmvA)F49 Warning: unaligning (T0345)R43 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1qmvA)P52 Warning: unaligning (T0345)F45 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1qmvA)P52 T0345 2 :IAKSFYDLSAIN 1qmvA 8 :IGKPAPDFKATA T0345 14 :LDGEK 1qmvA 21 :VDGAF T0345 19 :VDFNTFRGRAVLIENVA 1qmvA 28 :VKLSDYKGKYVVLFFYP T0345 38 :CGT 1qmvA 45 :LDF T0345 46 :TQLNELQCRF 1qmvA 53 :TEIIAFSNRA T0345 56 :PRRLVVLGFPC 1qmvA 67 :KLGCEVLGVSV T0345 75 :CQNEEILNSLKYVRPGGGY 1qmvA 78 :DSQFTHLAWINTPRKEGGL T0345 94 :QPTFTLVQK 1qmvA 98 :PLNIPLLAD T0345 109 :NEHPVFAYL 1qmvA 107 :VTRRLSEDY T0345 130 :SLMTDPK 1qmvA 116 :GVLKTDE T0345 146 :SDVAWNF 1qmvA 123 :GIAYRGL T0345 155 :FLIGPEGEPFRR 1qmvA 130 :FIIDGKGVLRQI T0345 168 :SRT 1qmvA 146 :LPV T0345 171 :FPTINIEPDIKR 1qmvA 150 :RSVDEALRLVQA Number of specific fragments extracted= 14 number of extra gaps= 1 total=859 Number of alignments=103 # 1qmvA read from 1qmvA/merged-good-all-a2m # found chain 1qmvA in training set Warning: unaligning (T0345)T41 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (1qmvA)F49 Warning: unaligning (T0345)T42 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (1qmvA)F49 Warning: unaligning (T0345)R43 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1qmvA)P52 Warning: unaligning (T0345)F45 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1qmvA)P52 T0345 3 :AKSFYDLSAIN 1qmvA 9 :GKPAPDFKATA T0345 14 :LDGEK 1qmvA 21 :VDGAF T0345 19 :VDFNTFRGRAVLIENVA 1qmvA 28 :VKLSDYKGKYVVLFFYP T0345 38 :CGT 1qmvA 45 :LDF T0345 46 :TQLNELQCRF 1qmvA 53 :TEIIAFSNRA T0345 56 :PRRLVVLGFPC 1qmvA 67 :KLGCEVLGVSV T0345 75 :CQNEEILNSLKYVRPGGGY 1qmvA 78 :DSQFTHLAWINTPRKEGGL T0345 94 :QPTFTLVQK 1qmvA 98 :PLNIPLLAD T0345 109 :NEHPVFAYL 1qmvA 107 :VTRRLSEDY T0345 122 :PYPYDD 1qmvA 116 :GVLKTD T0345 145 :RSDVAWNF 1qmvA 122 :EGIAYRGL T0345 155 :FLIGPEGEPFRRY 1qmvA 130 :FIIDGKGVLRQIT T0345 168 :SRTFPTINIEPDIKR 1qmvA 147 :PVGRSVDEALRLVQA Number of specific fragments extracted= 13 number of extra gaps= 1 total=872 Number of alignments=104 # 1qmvA read from 1qmvA/merged-good-all-a2m # found chain 1qmvA in training set Warning: unaligning (T0345)T41 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (1qmvA)F49 Warning: unaligning (T0345)T42 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (1qmvA)F49 T0345 3 :AKSFYDLSAI 1qmvA 9 :GKPAPDFKAT T0345 15 :DGEK 1qmvA 22 :DGAF T0345 19 :VDFNTFRGRAVLIENVAS 1qmvA 28 :VKLSDYKGKYVVLFFYPL T0345 39 :GT 1qmvA 46 :DF T0345 43 :RDFTQLNELQCRFPRRLVVLGFPC 1qmvA 54 :EIIAFSNRAEDFRKLGCEVLGVSV T0345 75 :CQNEEILNSLKYVRPGGGYQ 1qmvA 78 :DSQFTHLAWINTPRKEGGLG T0345 95 :PTFTLVQK 1qmvA 99 :LNIPLLAD T0345 109 :NEHPVF 1qmvA 107 :VTRRLS T0345 119 :DKLPYPYD 1qmvA 113 :EDYGVLKT T0345 144 :RRSDVAWN 1qmvA 121 :DEGIAYRG T0345 154 :KFLIGPEGEPFRRY 1qmvA 129 :LFIIDGKGVLRQIT T0345 168 :SRT 1qmvA 146 :LPV T0345 171 :FPTINIEPDIKRL 1qmvA 150 :RSVDEALRLVQAF Number of specific fragments extracted= 13 number of extra gaps= 1 total=885 Number of alignments=105 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1r26A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0345 read from 1r26A/merged-good-all-a2m # 1r26A read from 1r26A/merged-good-all-a2m # found chain 1r26A in training set T0345 44 :DFTQLNELQCR 1r26A 7 :SVEQFRNIMSE T0345 57 :RRLVVLGFPC 1r26A 18 :DILTVAWFTA T0345 73 :ENC 1r26A 28 :VWC T0345 77 :NEEILNSLKY 1r26A 37 :ERPMEKIAYE T0345 97 :FTLVQKCEVNGQNEHPVFA 1r26A 47 :FPTVKFAKVDADNNSEIVS T0345 120 :KLPYPYD 1r26A 66 :KCRVLQL T0345 148 :VA 1r26A 73 :PT T0345 155 :FLIGPEGEPFRRYS 1r26A 75 :FIIARSGKMLGHVI T0345 170 :TFPTINIEPDIKRLLK 1r26A 89 :GANPGMLRQKLRDIIK Number of specific fragments extracted= 9 number of extra gaps= 0 total=894 Number of alignments=106 # 1r26A read from 1r26A/merged-good-all-a2m # found chain 1r26A in training set T0345 25 :RGRAVLIENVASLCGTTTRDFTQLNELQCRF 1r26A 17 :EDILTVAWFTAVWCGPCKTIERPMEKIAYEF T0345 58 :RLVVLGFPCNQ 1r26A 49 :TVKFAKVDADN T0345 77 :NEEILNSLK 1r26A 60 :NSEIVSKCR T0345 93 :Y 1r26A 69 :V T0345 124 :P 1r26A 70 :L T0345 146 :SDV 1r26A 71 :QLP T0345 154 :KFLIGPEGEPFRRYSR 1r26A 74 :TFIIARSGKMLGHVIG T0345 171 :FPTINIEPDIKRLLK 1r26A 90 :ANPGMLRQKLRDIIK Number of specific fragments extracted= 8 number of extra gaps= 0 total=902 Number of alignments=107 # 1r26A read from 1r26A/merged-good-all-a2m # found chain 1r26A in training set T0345 25 :RGRAVLIENVASLCGTTT 1r26A 17 :EDILTVAWFTAVWCGPCK T0345 43 :RDFTQLNELQCRF 1r26A 36 :IERPMEKIAYEFP T0345 58 :RLVVLGFPCN 1r26A 49 :TVKFAKVDAD T0345 76 :QNEEILNSLK 1r26A 59 :NNSEIVSKCR T0345 123 :YPYD 1r26A 69 :VLQL T0345 153 :EKFLIGPEGEPFRRYSRT 1r26A 73 :PTFIIARSGKMLGHVIGA T0345 172 :PTINIEPDIKRLLK 1r26A 91 :NPGMLRQKLRDIIK Number of specific fragments extracted= 7 number of extra gaps= 0 total=909 Number of alignments=108 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1dbyA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1dbyA expands to /projects/compbio/data/pdb/1dby.pdb.gz 1dbyA:# T0345 read from 1dbyA/merged-good-all-a2m # 1dbyA read from 1dbyA/merged-good-all-a2m # adding 1dbyA to template set # found chain 1dbyA in template set T0345 28 :AVLIENVASLCGTTTRDFTQLNELQCRFPRRLVVLGFPCNQF 1dbyA 21 :PVLVDFWAPWCGPCRIIAPVVDEIAGEYKDKLKCVKLNTDES T0345 81 :LNSLKYV 1dbyA 63 :PNVASEY T0345 92 :GY 1dbyA 70 :GI T0345 126 :DD 1dbyA 72 :RS T0345 147 :D 1dbyA 74 :I T0345 152 :FE 1dbyA 75 :PT T0345 155 :FLIGPEGEPFRRYSRTFPTINIEPDIKRLLK 1dbyA 77 :IMVFKGGKKCETIIGAVPKATIVQTVEKYLN Number of specific fragments extracted= 7 number of extra gaps= 0 total=916 Number of alignments=109 # 1dbyA read from 1dbyA/merged-good-all-a2m # found chain 1dbyA in template set T0345 26 :GRAVLIENVASLCGTTTRDFTQLNELQCRFPRRLVVLGFPCNQF 1dbyA 19 :SVPVLVDFWAPWCGPCRIIAPVVDEIAGEYKDKLKCVKLNTDES T0345 81 :LNSLKY 1dbyA 63 :PNVASE T0345 117 :L 1dbyA 69 :Y T0345 120 :KLPYP 1dbyA 70 :GIRSI T0345 148 :V 1dbyA 75 :P T0345 154 :KFLIGPEGEPFRRYSRTFPTINIEPDIKRLLK 1dbyA 76 :TIMVFKGGKKCETIIGAVPKATIVQTVEKYLN Number of specific fragments extracted= 6 number of extra gaps= 0 total=922 Number of alignments=110 # 1dbyA read from 1dbyA/merged-good-all-a2m # found chain 1dbyA in template set T0345 27 :RAVLIENVASLCGTTT 1dbyA 20 :VPVLVDFWAPWCGPCR T0345 43 :RDFTQLNELQCRFP 1dbyA 37 :IAPVVDEIAGEYKD T0345 58 :RLVVLGFPCNQ 1dbyA 51 :KLKCVKLNTDE T0345 75 :C 1dbyA 62 :S T0345 81 :L 1dbyA 63 :P T0345 116 :YLKDKLPYPYD 1dbyA 64 :NVASEYGIRSI T0345 152 :FE 1dbyA 75 :PT T0345 155 :FLIGPEGEPFRRYSRTFPTINIEPDIKRLLK 1dbyA 77 :IMVFKGGKKCETIIGAVPKATIVQTVEKYLN Number of specific fragments extracted= 8 number of extra gaps= 0 total=930 Number of alignments=111 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2a4vA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2a4vA expands to /projects/compbio/data/pdb/2a4v.pdb.gz 2a4vA:# T0345 read from 2a4vA/merged-good-all-a2m # 2a4vA read from 2a4vA/merged-good-all-a2m # adding 2a4vA to template set # found chain 2a4vA in template set T0345 2 :IAKSFYDLSAINLDGEKVDFNTF 2a4vA 65 :IGDPIPDLSLLNEDNDSISLKKI T0345 26 :GRAVLIENV 2a4vA 91 :NRVVVFFVY T0345 35 :ASL 2a4vA 102 :AST T0345 42 :TR 2a4vA 109 :RQ T0345 45 :FTQLNELQCRFPRRLVVLGFPC 2a4vA 111 :ASGFRDNYQELKEYAAVFGLSA T0345 75 :CQNEEILNSLKYV 2a4vA 133 :DSVTSQKKFQSKQ T0345 94 :QPTFTLVQ 2a4vA 146 :NLPYHLLS T0345 108 :QNEHPVFAYLKDKLPYP 2a4vA 154 :DPKREFIGLLGAKKTPL T0345 146 :SDVAWNFEKFL 2a4vA 171 :SGSIRSHFIFV T0345 160 :EGEPFRRYS 2a4vA 182 :DGKLKFKRV T0345 170 :TFPTINIEPDIKRLL 2a4vA 191 :KISPEVSVNDAKKEV Number of specific fragments extracted= 11 number of extra gaps= 0 total=941 Number of alignments=112 # 2a4vA read from 2a4vA/merged-good-all-a2m # found chain 2a4vA in template set T0345 3 :AKSFYDLSAINLDGEKVDFNTF 2a4vA 66 :GDPIPDLSLLNEDNDSISLKKI T0345 25 :RGRAVLIENV 2a4vA 90 :NNRVVVFFVY T0345 35 :ASLCGTTTR 2a4vA 102 :ASTPGSTRQ T0345 45 :FTQLNELQCRFPRRLVVLGFPC 2a4vA 111 :ASGFRDNYQELKEYAAVFGLSA T0345 75 :CQNEEILNSLKYV 2a4vA 133 :DSVTSQKKFQSKQ T0345 92 :GYQPT 2a4vA 146 :NLPYH T0345 99 :LVQ 2a4vA 151 :LLS T0345 108 :QNEHPVFAYLKDKLPYP 2a4vA 154 :DPKREFIGLLGAKKTPL T0345 146 :SDVAWNFEKFL 2a4vA 171 :SGSIRSHFIFV T0345 160 :EGEPFRRYS 2a4vA 182 :DGKLKFKRV T0345 170 :TFPTINIEPDIKRLL 2a4vA 191 :KISPEVSVNDAKKEV Number of specific fragments extracted= 11 number of extra gaps= 0 total=952 Number of alignments=113 # 2a4vA read from 2a4vA/merged-good-all-a2m # found chain 2a4vA in template set T0345 3 :AKSFYDLSAINLDGEKVDFNTF 2a4vA 66 :GDPIPDLSLLNEDNDSISLKKI T0345 25 :RGRAVLIENV 2a4vA 90 :NNRVVVFFVY T0345 39 :GTTTRDFTQLNELQCRFP 2a4vA 102 :ASTPGSTRQASGFRDNYQ T0345 57 :RRLVVLGFPC 2a4vA 123 :EYAAVFGLSA T0345 75 :CQNEEILNSLK 2a4vA 133 :DSVTSQKKFQS T0345 92 :GYQPTFTLVQK 2a4vA 144 :KQNLPYHLLSD T0345 109 :NEHPVFAYLKDKLPY 2a4vA 155 :PKREFIGLLGAKKTP T0345 145 :RSDVAWNFEKFL 2a4vA 170 :LSGSIRSHFIFV T0345 160 :EGEPFRRYSR 2a4vA 182 :DGKLKFKRVK T0345 171 :FPTINIEPDIKRLL 2a4vA 192 :ISPEVSVNDAKKEV Number of specific fragments extracted= 10 number of extra gaps= 0 total=962 Number of alignments=114 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1uvzA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1uvzA expands to /projects/compbio/data/pdb/1uvz.pdb.gz 1uvzA:# T0345 read from 1uvzA/merged-good-all-a2m # 1uvzA read from 1uvzA/merged-good-all-a2m # adding 1uvzA to template set # found chain 1uvzA in template set T0345 27 :RAVLIENVASLCGTTTRDFTQLNELQCRFPRRLVVLGFPCNQF 1uvzA 20 :TPVVVDFHAQWCGPCKILGPRLEKMVAKQHGKVVMAKVDIDDH T0345 81 :LNSLK 1uvzA 63 :TDLAI T0345 120 :KLPYPYD 1uvzA 68 :EYEVSAV T0345 152 :FE 1uvzA 75 :PT T0345 155 :FLIGPEGEPFRRYSRTFPTINIEPDIKRLLK 1uvzA 77 :VLAMKNGDVVDKFVGIKDEDQLEAFLKKLIG Number of specific fragments extracted= 5 number of extra gaps= 0 total=967 Number of alignments=115 # 1uvzA read from 1uvzA/merged-good-all-a2m # found chain 1uvzA in template set T0345 26 :GRAVLIENVASLCGTTTRDFTQLNELQCRFPRRLVVLGFPCNQF 1uvzA 19 :ETPVVVDFHAQWCGPCKILGPRLEKMVAKQHGKVVMAKVDIDDH T0345 78 :EE 1uvzA 63 :TD T0345 117 :LKDKLPYPYD 1uvzA 65 :LAIEYEVSAV T0345 153 :EKFLIGPEGEPFRRYSRTFPTINIEPDIKRLLK 1uvzA 75 :PTVLAMKNGDVVDKFVGIKDEDQLEAFLKKLIG Number of specific fragments extracted= 4 number of extra gaps= 0 total=971 Number of alignments=116 # 1uvzA read from 1uvzA/merged-good-all-a2m # found chain 1uvzA in template set T0345 27 :RAVLIENVASLCGTTT 1uvzA 20 :TPVVVDFHAQWCGPCK T0345 43 :RDFTQLNELQCR 1uvzA 37 :LGPRLEKMVAKQ T0345 56 :PRRLVVLGFPCNQF 1uvzA 49 :HGKVVMAKVDIDDH T0345 78 :EE 1uvzA 63 :TD T0345 117 :LKDKLPYPYD 1uvzA 65 :LAIEYEVSAV T0345 152 :FE 1uvzA 75 :PT T0345 155 :FLIGPEGEPFRRYSRTFPTINIEPDIKRLLK 1uvzA 77 :VLAMKNGDVVDKFVGIKDEDQLEAFLKKLIG Number of specific fragments extracted= 7 number of extra gaps= 0 total=978 Number of alignments=117 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1fb6A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1fb6A expands to /projects/compbio/data/pdb/1fb6.pdb.gz 1fb6A:# T0345 read from 1fb6A/merged-good-all-a2m # 1fb6A read from 1fb6A/merged-good-all-a2m # adding 1fb6A to template set # found chain 1fb6A in template set Warning: unaligning (T0345)L184 because last residue in template chain is (1fb6A)L112 T0345 28 :AVLIENVASLCGTTTRDFTQLNELQCRFPRRLVVLGF 1fb6A 27 :PVMVDFWAPWCGPCKLIAPVIDELAKEYSGKIAVYKL T0345 106 :NGQNEHPVFAYL 1fb6A 64 :NTDEAPGIATQY T0345 122 :PY 1fb6A 76 :NI T0345 126 :DD 1fb6A 78 :RS T0345 152 :FEKFLIGPEGEPFRRYSRTFPTINIEPDIKRL 1fb6A 80 :IPTVLFFKNGERKESIIGAVPKSTLTDSIEKY Number of specific fragments extracted= 5 number of extra gaps= 0 total=983 Number of alignments=118 # 1fb6A read from 1fb6A/merged-good-all-a2m # found chain 1fb6A in template set Warning: unaligning (T0345)L184 because last residue in template chain is (1fb6A)L112 T0345 26 :GRAVLIENVASLCGTTTRDFTQLNELQCRFPRRLVVLGFP 1fb6A 25 :EVPVMVDFWAPWCGPCKLIAPVIDELAKEYSGKIAVYKLN T0345 107 :GQNEHPVFAYL 1fb6A 65 :TDEAPGIATQY T0345 120 :KLPY 1fb6A 76 :NIRS T0345 148 :V 1fb6A 80 :I T0345 153 :EKFLIGPEGEPFRRYSRTFPTINIEPDIKRL 1fb6A 81 :PTVLFFKNGERKESIIGAVPKSTLTDSIEKY Number of specific fragments extracted= 5 number of extra gaps= 0 total=988 Number of alignments=119 # 1fb6A read from 1fb6A/merged-good-all-a2m # found chain 1fb6A in template set Warning: unaligning (T0345)L184 because last residue in template chain is (1fb6A)L112 T0345 27 :RAVLIENVASLCGTTTRDFTQLNELQCRFPRRLVVLGFP 1fb6A 26 :VPVMVDFWAPWCGPCKLIAPVIDELAKEYSGKIAVYKLN T0345 107 :GQNEHP 1fb6A 65 :TDEAPG T0345 117 :LKDKLPY 1fb6A 71 :IATQYNI T0345 149 :AWNFEKFLI 1fb6A 78 :RSIPTVLFF T0345 159 :PEGEPFRRYSRTFPTINIEPDIKRL 1fb6A 87 :KNGERKESIIGAVPKSTLTDSIEKY Number of specific fragments extracted= 5 number of extra gaps= 0 total=993 Number of alignments=120 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1zyeA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1zyeA expands to /projects/compbio/data/pdb/1zye.pdb.gz 1zyeA:# T0345 read from 1zyeA/merged-good-all-a2m # 1zyeA read from 1zyeA/merged-good-all-a2m # adding 1zyeA to template set # found chain 1zyeA in template set Warning: unaligning (T0345)A3 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1zyeA)T5 Warning: unaligning (T0345)D44 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1zyeA)P48 Warning: unaligning (T0345)F45 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1zyeA)P48 T0345 4 :KSF 1zyeA 6 :QHA T0345 7 :YDLSAINLDG 1zyeA 11 :FKGTAVVSGE T0345 17 :EKVDFNTFRGRAVLIENVA 1zyeA 22 :KEISLDDFKGKYLVLFFYP T0345 38 :CGTTTR 1zyeA 41 :LDFTFV T0345 46 :TQLNELQCRF 1zyeA 49 :TEIIAFSDKA T0345 56 :PRRLVVLGFPC 1zyeA 63 :DVNCEVVAVSV T0345 75 :CQNEEILNSLKYVRPGGGY 1zyeA 74 :DSHFSHLAWINTPRKNGGL T0345 94 :QPTFTLVQK 1zyeA 94 :HMNIALLSD T0345 109 :NEHPVFAYL 1zyeA 103 :LTKQISRDY T0345 122 :PYPYDDP 1zyeA 112 :GVLLEGP T0345 146 :SDVAWNF 1zyeA 119 :GLALRGL T0345 155 :FLIGPEGEPFR 1zyeA 126 :FIIDPNGVIKH T0345 167 :YSRTFPTINIEPDIKRL 1zyeA 142 :LPVGRSVEETLRLVKAF Number of specific fragments extracted= 13 number of extra gaps= 2 total=1006 Number of alignments=121 # 1zyeA read from 1zyeA/merged-good-all-a2m # found chain 1zyeA in template set Warning: unaligning (T0345)D44 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1zyeA)P48 Warning: unaligning (T0345)F45 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1zyeA)P48 T0345 5 :SFYDLSAINLDG 1zyeA 9 :PYFKGTAVVSGE T0345 17 :EKVDFNTFRGRAVLIENVA 1zyeA 22 :KEISLDDFKGKYLVLFFYP T0345 38 :CGTTTR 1zyeA 41 :LDFTFV T0345 46 :TQLNELQCRF 1zyeA 49 :TEIIAFSDKA T0345 56 :PRRLVVLGFPC 1zyeA 63 :DVNCEVVAVSV T0345 75 :CQNEEILNSLKYVRPGGGYQ 1zyeA 74 :DSHFSHLAWINTPRKNGGLG T0345 95 :PTFTLVQ 1zyeA 95 :MNIALLS T0345 109 :NEHPVFAY 1zyeA 103 :LTKQISRD T0345 121 :LPYPYDDP 1zyeA 111 :YGVLLEGP T0345 146 :SDVAWNF 1zyeA 119 :GLALRGL T0345 155 :FLIGPEGEPFRRY 1zyeA 126 :FIIDPNGVIKHLS T0345 168 :SRTFPTINIEPDIKRL 1zyeA 143 :PVGRSVEETLRLVKAF Number of specific fragments extracted= 12 number of extra gaps= 1 total=1018 Number of alignments=122 # 1zyeA read from 1zyeA/merged-good-all-a2m # found chain 1zyeA in template set Warning: unaligning (T0345)A3 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1zyeA)T5 Warning: unaligning (T0345)T41 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1zyeA)P48 Warning: unaligning (T0345)T42 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1zyeA)P48 T0345 4 :KSFYDLSAI 1zyeA 6 :QHAPYFKGT T0345 13 :NLDGEKVDFNTFRGRAVLIENVA 1zyeA 18 :SGEFKEISLDDFKGKYLVLFFYP T0345 36 :SLCGT 1zyeA 42 :DFTFV T0345 43 :RDFTQLNELQCRFPRRLVVLGFPC 1zyeA 50 :EIIAFSDKASEFHDVNCEVVAVSV T0345 75 :CQNEEILNSLKYVRPGGGYQ 1zyeA 74 :DSHFSHLAWINTPRKNGGLG T0345 95 :PTFTLVQK 1zyeA 95 :MNIALLSD T0345 109 :NEHP 1zyeA 103 :LTKQ T0345 117 :LKDKLPYPYDD 1zyeA 107 :ISRDYGVLLEG T0345 145 :RSDVAWN 1zyeA 118 :PGLALRG T0345 154 :KFLIGPEGEPFRRY 1zyeA 125 :LFIIDPNGVIKHLS T0345 168 :SRTFPTINIEPDIKRL 1zyeA 143 :PVGRSVEETLRLVKAF Number of specific fragments extracted= 11 number of extra gaps= 2 total=1029 Number of alignments=123 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1on4A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0345/1on4A/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0345/1on4A/merged-good-all-a2m.gz for input Trying 1on4A/merged-good-all-a2m Error: Couldn't open file 1on4A/merged-good-all-a2m or 1on4A/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1z5yE/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1z5yE expands to /projects/compbio/data/pdb/1z5y.pdb.gz 1z5yE:Skipped atom 1212, because occupancy 0.500 <= existing 0.500 in 1z5yE Skipped atom 1214, because occupancy 0.500 <= existing 0.500 in 1z5yE Skipped atom 1216, because occupancy 0.500 <= existing 0.500 in 1z5yE Skipped atom 1218, because occupancy 0.500 <= existing 0.500 in 1z5yE Skipped atom 1220, because occupancy 0.500 <= existing 0.500 in 1z5yE Skipped atom 1222, because occupancy 0.500 <= existing 0.500 in 1z5yE Skipped atom 1224, because occupancy 0.500 <= existing 0.500 in 1z5yE Skipped atom 1226, because occupancy 0.500 <= existing 0.500 in 1z5yE Skipped atom 1409, because occupancy 0.500 <= existing 0.500 in 1z5yE Skipped atom 1411, because occupancy 0.500 <= existing 0.500 in 1z5yE Skipped atom 1413, because occupancy 0.500 <= existing 0.500 in 1z5yE Skipped atom 1415, because occupancy 0.500 <= existing 0.500 in 1z5yE Skipped atom 1417, because occupancy 0.500 <= existing 0.500 in 1z5yE Skipped atom 1419, because occupancy 0.500 <= existing 0.500 in 1z5yE Skipped atom 1421, because occupancy 0.500 <= existing 0.500 in 1z5yE Skipped atom 1423, because occupancy 0.500 <= existing 0.500 in 1z5yE Skipped atom 1425, because occupancy 0.500 <= existing 0.500 in 1z5yE Skipped atom 1541, because occupancy 0.500 <= existing 0.500 in 1z5yE Skipped atom 1543, because occupancy 0.500 <= existing 0.500 in 1z5yE Skipped atom 1545, because occupancy 0.500 <= existing 0.500 in 1z5yE Skipped atom 1547, because occupancy 0.500 <= existing 0.500 in 1z5yE Skipped atom 1549, because occupancy 0.500 <= existing 0.500 in 1z5yE Skipped atom 1551, because occupancy 0.500 <= existing 0.500 in 1z5yE Skipped atom 1553, because occupancy 0.500 <= existing 0.500 in 1z5yE Skipped atom 1555, because occupancy 0.500 <= existing 0.500 in 1z5yE Skipped atom 1557, because occupancy 0.500 <= existing 0.500 in 1z5yE Skipped atom 1670, because occupancy 0.500 <= existing 0.500 in 1z5yE Skipped atom 1672, because occupancy 0.500 <= existing 0.500 in 1z5yE Skipped atom 1674, because occupancy 0.500 <= existing 0.500 in 1z5yE Skipped atom 1676, because occupancy 0.500 <= existing 0.500 in 1z5yE Skipped atom 1678, because occupancy 0.500 <= existing 0.500 in 1z5yE Skipped atom 1680, because occupancy 0.500 <= existing 0.500 in 1z5yE Skipped atom 1713, because occupancy 0.500 <= existing 0.500 in 1z5yE Skipped atom 1715, because occupancy 0.500 <= existing 0.500 in 1z5yE Skipped atom 1717, because occupancy 0.500 <= existing 0.500 in 1z5yE Skipped atom 1719, because occupancy 0.500 <= existing 0.500 in 1z5yE Skipped atom 1721, because occupancy 0.500 <= existing 0.500 in 1z5yE Skipped atom 1723, because occupancy 0.500 <= existing 0.500 in 1z5yE Skipped atom 1725, because occupancy 0.500 <= existing 0.500 in 1z5yE Skipped atom 1727, because occupancy 0.500 <= existing 0.500 in 1z5yE # T0345 read from 1z5yE/merged-good-all-a2m # 1z5yE read from 1z5yE/merged-good-all-a2m # adding 1z5yE to template set # found chain 1z5yE in template set Warning: unaligning (T0345)S10 because first residue in template chain is (1z5yE)R49 T0345 11 :AINL 1z5yE 50 :LESL T0345 15 :DGEKVDFNT 1z5yE 56 :PGQFYQADV T0345 24 :FRGRAVLIENVASLCGTTTRDFTQLNELQCR 1z5yE 66 :TQGKPVLLNVWATWCPTSRAEHQYLNQLSAQ T0345 58 :RLVVLGFPC 1z5yE 97 :GIRVVGMNY T0345 74 :NCQNEEILNSLKYV 1z5yE 106 :KDDRQKAISWLKEL T0345 92 :GYQPTFTLVQ 1z5yE 120 :GNPYALSLFD T0345 109 :NEHPVFAYL 1z5yE 130 :GDGMLGLDL T0345 122 :PYPY 1z5yE 139 :GVYG T0345 151 :NFEKFLIGPEGEPFRRYSRTFPTINIEPDIKRLLK 1z5yE 143 :APETFLIDGNGIIRYRHAGDLNPRVWEEEIKPLWE Number of specific fragments extracted= 9 number of extra gaps= 0 total=1038 Number of alignments=124 # 1z5yE read from 1z5yE/merged-good-all-a2m # found chain 1z5yE in template set Warning: unaligning (T0345)S10 because first residue in template chain is (1z5yE)R49 T0345 11 :AINL 1z5yE 50 :LESL T0345 15 :DGEKVDFNT 1z5yE 56 :PGQFYQADV T0345 24 :FRGRAVLIENVASLCGTTTRDFTQLNELQCR 1z5yE 66 :TQGKPVLLNVWATWCPTSRAEHQYLNQLSAQ T0345 56 :PRRLVVLGF 1z5yE 97 :GIRVVGMNY T0345 74 :NCQNEEILNSLKYV 1z5yE 106 :KDDRQKAISWLKEL T0345 92 :GYQPTFTLVQ 1z5yE 120 :GNPYALSLFD T0345 107 :GQN 1z5yE 130 :GDG T0345 112 :P 1z5yE 133 :M T0345 117 :LKDKLPYPYD 1z5yE 134 :LGLDLGVYGA T0345 152 :FEKFLIGPEGEPFRRYSRTFPTIN 1z5yE 144 :PETFLIDGNGIIRYRHAGDLNPRV T0345 176 :IEPDIKRL 1z5yE 172 :IKPLWEKY Number of specific fragments extracted= 11 number of extra gaps= 0 total=1049 Number of alignments=125 # 1z5yE read from 1z5yE/merged-good-all-a2m # found chain 1z5yE in template set Warning: unaligning (T0345)S10 because first residue in template chain is (1z5yE)R49 T0345 11 :AINL 1z5yE 50 :LESL T0345 15 :DGEKVDFNTF 1z5yE 56 :PGQFYQADVL T0345 25 :RGRAVLIENVASLC 1z5yE 67 :QGKPVLLNVWATWC T0345 42 :TRDFTQLNELQCRFPRRLVVLGFPC 1z5yE 81 :PTSRAEHQYLNQLSAQGIRVVGMNY T0345 74 :NCQNEEILNSLKYV 1z5yE 106 :KDDRQKAISWLKEL T0345 92 :GYQPTFTLV 1z5yE 120 :GNPYALSLF T0345 106 :NGQNE 1z5yE 129 :DGDGM T0345 117 :LKDKLPYPYD 1z5yE 134 :LGLDLGVYGA T0345 152 :FEKFLIGPEGEPFRRYSRTFPTINIEPDIKRLLK 1z5yE 144 :PETFLIDGNGIIRYRHAGDLNPRVWEEEIKPLWE Number of specific fragments extracted= 9 number of extra gaps= 0 total=1058 Number of alignments=126 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1xvwA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1xvwA expands to /projects/compbio/data/pdb/1xvw.pdb.gz 1xvwA:Bad short name: OD for alphabet: pdb_atoms # T0345 read from 1xvwA/merged-good-all-a2m # 1xvwA read from 1xvwA/merged-good-all-a2m # adding 1xvwA to template set # found chain 1xvwA in template set Warning: unaligning (T0345)T40 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1xvwA)Q46 Warning: unaligning (T0345)T42 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1xvwA)Q46 T0345 2 :IAKSFYDLSAINLDGEKVDFNTFRG 1xvwA 4 :VGATAPDFTLRDQNQQLVTLRGYRG T0345 27 :RAVLIENV 1xvwA 30 :KNVLLVFF T0345 35 :ASLCG 1xvwA 39 :LAFTG T0345 43 :RDFTQLNELQCRF 1xvwA 47 :GELDQLRDHLPEF T0345 56 :PRRLVVLGFPC 1xvwA 61 :NDDSAALAISV T0345 75 :CQNEEILNSLKY 1xvwA 72 :GPPPTHKIWATQ T0345 93 :YQPTFTLVQKC 1xvwA 84 :SGFTFPLLSDF T0345 108 :QNEHPVFAYLK 1xvwA 95 :WPHGAVSQAYG T0345 131 :LM 1xvwA 106 :VF T0345 144 :RRSDVAWNFEKFLIGPEGEPFRRYSRT 1xvwA 108 :NEQAGIANRGTFVVDRSGIIRFAEMKQ T0345 171 :FPTINIEPDIKR 1xvwA 139 :RDQRLWTDALAA Number of specific fragments extracted= 11 number of extra gaps= 0 total=1069 Number of alignments=127 # 1xvwA read from 1xvwA/merged-good-all-a2m # found chain 1xvwA in template set Warning: unaligning (T0345)R43 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1xvwA)Q46 Warning: unaligning (T0345)F45 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1xvwA)Q46 T0345 3 :AKSFYDLSAINLDGEKVDFNTFRG 1xvwA 5 :GATAPDFTLRDQNQQLVTLRGYRG T0345 27 :RAVLIENVASLCGT 1xvwA 30 :KNVLLVFFPLAFTG T0345 46 :TQLNELQCRF 1xvwA 47 :GELDQLRDHL T0345 56 :PRRLVVLGFPC 1xvwA 61 :NDDSAALAISV T0345 75 :CQNEEILNSLKY 1xvwA 72 :GPPPTHKIWATQ T0345 93 :YQPTFTLVQKC 1xvwA 84 :SGFTFPLLSDF T0345 108 :QNEHPVFAYLK 1xvwA 95 :WPHGAVSQAYG T0345 138 :IIWS 1xvwA 106 :VFNE T0345 146 :SDVAWNFEKFLIGPEGEPFRRYSRT 1xvwA 110 :QAGIANRGTFVVDRSGIIRFAEMKQ T0345 171 :FPTINIEPDIKRL 1xvwA 139 :RDQRLWTDALAAL Number of specific fragments extracted= 10 number of extra gaps= 0 total=1079 Number of alignments=128 # 1xvwA read from 1xvwA/merged-good-all-a2m # found chain 1xvwA in template set Warning: unaligning (T0345)R43 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1xvwA)Q46 Warning: unaligning (T0345)F45 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1xvwA)Q46 T0345 3 :AKSFYDLSAINLDGEKVDFNTFRG 1xvwA 5 :GATAPDFTLRDQNQQLVTLRGYRG T0345 27 :RAVLIENV 1xvwA 30 :KNVLLVFF T0345 37 :LCGTTT 1xvwA 38 :PLAFTG T0345 46 :TQLNELQCRFP 1xvwA 47 :GELDQLRDHLP T0345 57 :RRLVVLGFPC 1xvwA 62 :DDSAALAISV T0345 75 :CQNEEILNSLK 1xvwA 72 :GPPPTHKIWAT T0345 92 :GYQPTFTLVQK 1xvwA 83 :QSGFTFPLLSD T0345 107 :GQNEHPVFAYL 1xvwA 94 :FWPHGAVSQAY T0345 139 :IWSPVRRS 1xvwA 105 :GVFNEQAG T0345 149 :AWNFEKFLIGPEGEPFRRYSRT 1xvwA 113 :IANRGTFVVDRSGIIRFAEMKQ T0345 171 :FPTINIEPDIKRL 1xvwA 139 :RDQRLWTDALAAL Number of specific fragments extracted= 11 number of extra gaps= 0 total=1090 Number of alignments=129 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1kngA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0345 read from 1kngA/merged-good-all-a2m # 1kngA read from 1kngA/merged-good-all-a2m # found chain 1kngA in training set T0345 13 :NLDGEK 1kngA 64 :QADNVQ T0345 19 :VDFNTFRGRAVLIENVASLCGTTTRDFTQLNELQCR 1kngA 73 :LDPAAFKGKVSLVNVWASWCVPCHDEAPLLTELGKD T0345 57 :RRLVVLGFPC 1kngA 109 :KRFQLVGINY T0345 74 :NCQNEEILNSLKY 1kngA 119 :KDAADNARRFLGR T0345 93 :YQPTFTLVQKCE 1kngA 132 :YGNPFGRVGVDA T0345 106 :NG 1kngA 144 :NG T0345 112 :P 1kngA 146 :R T0345 117 :LKDKLPYPYD 1kngA 147 :ASIEWGVYGV T0345 152 :FEKFLIGPEGEPFRRYSRTFPTIN 1kngA 157 :PETFVVGREGTIVYKLVGPITPDN T0345 176 :IEPDIKRL 1kngA 185 :LLPQMEKA Number of specific fragments extracted= 10 number of extra gaps= 0 total=1100 Number of alignments=130 # 1kngA read from 1kngA/merged-good-all-a2m # found chain 1kngA in training set Warning: unaligning (T0345)L184 because last residue in template chain is (1kngA)L193 T0345 12 :INLDGEK 1kngA 63 :LQADNVQ T0345 19 :VDFNTFRGRAVLIENVASLCGTTTRDFTQLNELQC 1kngA 73 :LDPAAFKGKVSLVNVWASWCVPCHDEAPLLTELGK T0345 56 :PRRLVVLGF 1kngA 108 :DKRFQLVGI T0345 74 :NCQNEEILNSLKY 1kngA 119 :KDAADNARRFLGR T0345 93 :YQPTFTLVQ 1kngA 132 :YGNPFGRVG T0345 105 :VNGQNE 1kngA 141 :VDANGR T0345 117 :LKDKLPYPYD 1kngA 147 :ASIEWGVYGV T0345 152 :FEKFLIGPEGEPFRRYSRTFPTIN 1kngA 157 :PETFVVGREGTIVYKLVGPITPDN T0345 176 :IEPDIKRL 1kngA 185 :LLPQMEKA Number of specific fragments extracted= 9 number of extra gaps= 0 total=1109 Number of alignments=131 # 1kngA read from 1kngA/merged-good-all-a2m # found chain 1kngA in training set Warning: unaligning (T0345)K4 because first residue in template chain is (1kngA)R50 T0345 5 :SFYDLSAINLDG 1kngA 51 :PAPQTALPPLEG T0345 17 :EK 1kngA 68 :VQ T0345 19 :VDFNTFRGRAVLIENVASLC 1kngA 73 :LDPAAFKGKVSLVNVWASWC T0345 42 :TRDFTQLNELQCRFP 1kngA 93 :VPCHDEAPLLTELGK T0345 57 :RRLVVLGFPC 1kngA 109 :KRFQLVGINY T0345 74 :NCQNEEILNSLK 1kngA 119 :KDAADNARRFLG T0345 92 :GYQPTFT 1kngA 131 :RYGNPFG T0345 102 :KCEVNGQNE 1kngA 138 :RVGVDANGR T0345 117 :LKDKLPYPYD 1kngA 147 :ASIEWGVYGV T0345 152 :FEKFLIGPEGEPFRRYSRTFPTINIEPDIKRLLK 1kngA 157 :PETFVVGREGTIVYKLVGPITPDNLRSVLLPQME Number of specific fragments extracted= 10 number of extra gaps= 0 total=1119 Number of alignments=132 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1o6jA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1o6jA expands to /projects/compbio/data/pdb/1o6j.pdb.gz 1o6jA:Skipped atom 799, because occupancy 0.500 <= existing 0.500 in 1o6jA Skipped atom 801, because occupancy 0.500 <= existing 0.500 in 1o6jA Skipped atom 803, because occupancy 0.500 <= existing 0.500 in 1o6jA Skipped atom 805, because occupancy 0.500 <= existing 0.500 in 1o6jA Skipped atom 807, because occupancy 0.500 <= existing 0.500 in 1o6jA # T0345 read from 1o6jA/merged-good-all-a2m # 1o6jA read from 1o6jA/merged-good-all-a2m # adding 1o6jA to template set # found chain 1o6jA in template set T0345 17 :EKVDFNTFRGRAVLIENVASLCGTTTRDFTQLNELQCRF 1o6jA 35 :ADIALPSLAGKTVFFYFSASWCPPCRAFTPQLIDFYKAH T0345 56 :PRRLVVLGFPC 1o6jA 76 :KKNFEVMLISW T0345 74 :NCQNEEILNSLK 1o6jA 87 :DESAEDFKDYYA T0345 92 :GYQPTF 1o6jA 99 :KMPWLA T0345 100 :VQ 1o6jA 105 :LP T0345 108 :QNEHPVFAYLKDKLPYP 1o6jA 107 :FEDRKGMEFLTTGFDVK T0345 146 :SDVAWN 1o6jA 124 :SIPTLV T0345 155 :FLIGPEGEPFRR 1o6jA 130 :GVEADSGNIITT Number of specific fragments extracted= 8 number of extra gaps= 0 total=1127 Number of alignments=133 # 1o6jA read from 1o6jA/merged-good-all-a2m # found chain 1o6jA in template set T0345 18 :KVDFNTFRGRAVLIENVASLCGTTTRDFTQLNELQCRF 1o6jA 36 :DIALPSLAGKTVFFYFSASWCPPCRAFTPQLIDFYKAH T0345 56 :PRRLVVLGFPC 1o6jA 76 :KKNFEVMLISW T0345 74 :NCQNEEILNSLK 1o6jA 87 :DESAEDFKDYYA T0345 92 :GYQPTF 1o6jA 99 :KMPWLA T0345 99 :L 1o6jA 106 :P T0345 108 :QNEHPVFAYLKDKLPYP 1o6jA 107 :FEDRKGMEFLTTGFDVK T0345 146 :SDVAWN 1o6jA 124 :SIPTLV T0345 155 :FLIGPEGEPFR 1o6jA 130 :GVEADSGNIIT Number of specific fragments extracted= 8 number of extra gaps= 0 total=1135 Number of alignments=134 # 1o6jA read from 1o6jA/merged-good-all-a2m # found chain 1o6jA in template set T0345 18 :KVDFNTFRGRAVLIENVASLCGTTT 1o6jA 36 :DIALPSLAGKTVFFYFSASWCPPCR T0345 43 :RDFTQLNELQCRFP 1o6jA 62 :FTPQLIDFYKAHAE T0345 57 :RRLVVLGFP 1o6jA 77 :KNFEVMLIS T0345 73 :ENCQNEEILNSLK 1o6jA 86 :WDESAEDFKDYYA T0345 94 :QPTFTLVQ 1o6jA 99 :KMPWLALP T0345 108 :QNEHPVFAYLKDKLPYPYD 1o6jA 107 :FEDRKGMEFLTTGFDVKSI T0345 152 :FEKFLIG 1o6jA 126 :PTLVGVE T0345 159 :PEGEPFRR 1o6jA 134 :DSGNIITT Number of specific fragments extracted= 8 number of extra gaps= 0 total=1143 Number of alignments=135 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1psqA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1psqA expands to /projects/compbio/data/pdb/1psq.pdb.gz 1psqA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0345 read from 1psqA/merged-good-all-a2m # 1psqA read from 1psqA/merged-good-all-a2m # adding 1psqA to template set # found chain 1psqA in template set T0345 2 :IAKSFYDLSAINLDGEKVDFNTFRGRAVLIENVASLC 1psqA 18 :VGDKALDFSLTTTDLSKKSLADFDGKKKVLSVVPSID T0345 41 :TTRDFTQLNELQCRF 1psqA 55 :TGICSTQTRRFNEEL T0345 56 :P 1psqA 71 :G T0345 57 :RRLVVLGFPC 1psqA 73 :DNTVVLTVSM T0345 75 :CQNEEILNSLKYVRPGG 1psqA 83 :DLPFAQKRWCGAEGLDN T0345 93 :Y 1psqA 100 :A T0345 103 :CEVNGQNEHPVFAYLK 1psqA 101 :IMLSDYFDHSFGRDYA T0345 123 :YPYDDPFSL 1psqA 117 :LLINEWHLL T0345 151 :NFEKFLIGPEGEPFR 1psqA 126 :ARAVFVLDTDNTIRY T0345 166 :RYSRTFPTINIEPDIK 1psqA 146 :NINSEPNFEAAIAAAK Number of specific fragments extracted= 10 number of extra gaps= 0 total=1153 Number of alignments=136 # 1psqA read from 1psqA/merged-good-all-a2m # found chain 1psqA in template set T0345 2 :IAKSFYDLSAINLDGEKVDFNTFRGRAVLIENVASL 1psqA 18 :VGDKALDFSLTTTDLSKKSLADFDGKKKVLSVVPSI T0345 45 :FTQLNELQCRF 1psqA 59 :STQTRRFNEEL T0345 56 :P 1psqA 71 :G T0345 57 :RRLVVLGFPC 1psqA 73 :DNTVVLTVSM T0345 75 :CQNEEILNSLKYVRPGG 1psqA 83 :DLPFAQKRWCGAEGLDN T0345 93 :Y 1psqA 100 :A T0345 103 :CEVNGQNEHPVFAYLK 1psqA 101 :IMLSDYFDHSFGRDYA T0345 123 :YPYDD 1psqA 117 :LLINE T0345 145 :RSDV 1psqA 122 :WHLL T0345 151 :NFEKFLIGPEGEPFRR 1psqA 126 :ARAVFVLDTDNTIRYV T0345 167 :YSRTFPTINIEPDIKR 1psqA 147 :INSEPNFEAAIAAAKA Number of specific fragments extracted= 11 number of extra gaps= 0 total=1164 Number of alignments=137 # 1psqA read from 1psqA/merged-good-all-a2m # found chain 1psqA in template set T0345 3 :AKSFYDLSAINLDGEKVDFNTFRGRAVLIENVASL 1psqA 19 :GDKALDFSLTTTDLSKKSLADFDGKKKVLSVVPSI T0345 43 :RDFTQLNELQCRFP 1psqA 54 :DTGICSTQTRRFNE T0345 57 :RRLVVLGFPC 1psqA 73 :DNTVVLTVSM T0345 75 :CQNEEILNSLKYVRPGG 1psqA 83 :DLPFAQKRWCGAEGLDN T0345 93 :Y 1psqA 100 :A T0345 98 :TLVQ 1psqA 101 :IMLS T0345 107 :GQNEHPVFAY 1psqA 105 :DYFDHSFGRD T0345 121 :LPYPYD 1psqA 115 :YALLIN T0345 146 :SDVAWNFEKFLIGPEGEPFRRYS 1psqA 121 :EWHLLARAVFVLDTDNTIRYVEY T0345 169 :RTFPTINIEPDIK 1psqA 149 :SEPNFEAAIAAAK Number of specific fragments extracted= 10 number of extra gaps= 0 total=1174 Number of alignments=138 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1x0rA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1x0rA expands to /projects/compbio/data/pdb/1x0r.pdb.gz 1x0rA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0345 read from 1x0rA/merged-good-all-a2m # 1x0rA read from 1x0rA/merged-good-all-a2m # adding 1x0rA to template set # found chain 1x0rA in template set Warning: unaligning (T0345)R25 because of BadResidue code BAD_PEPTIDE at template residue (1x0rA)Q33 Warning: unaligning (T0345)F64 because of BadResidue code BAD_PEPTIDE in next template residue (1x0rA)S75 Warning: unaligning (T0345)P65 because of BadResidue code BAD_PEPTIDE at template residue (1x0rA)S75 Warning: unaligning (T0345)N77 because of BadResidue code BAD_PEPTIDE in next template residue (1x0rA)F80 Warning: unaligning (T0345)E78 because of BadResidue code BAD_PEPTIDE at template residue (1x0rA)F80 Warning: unaligning (T0345)P95 because of BadResidue code BAD_PEPTIDE in next template residue (1x0rA)P98 Warning: unaligning (T0345)T96 because of BadResidue code BAD_PEPTIDE at template residue (1x0rA)P98 Warning: unaligning (T0345)D126 because of BadResidue code BAD_PEPTIDE in next template residue (1x0rA)E119 Warning: unaligning (T0345)D127 because of BadResidue code BAD_PEPTIDE at template residue (1x0rA)E119 T0345 1 :MIAKSFYDLSAI 1x0rA 7 :LIGERFPEMEVT T0345 14 :LDGEKVDFNTF 1x0rA 19 :TDHGVIKLPDH T0345 26 :GRAVLIENVAS 1x0rA 34 :GKWFVLFSHPA T0345 39 :GTTTR 1x0rA 45 :DFTPV T0345 45 :FTQLNEL 1x0rA 61 :YEDFQRL T0345 58 :RLVVLG 1x0rA 68 :GVDLIG T0345 66 :C 1x0rA 76 :V T0345 75 :CQ 1x0rA 77 :DS T0345 79 :EILNSLKYVRPGGGYQ 1x0rA 81 :SHIKWKEWIERHIGVR T0345 97 :FTLVQ 1x0rA 99 :FPIIA T0345 108 :QNEHPVFAYL 1x0rA 104 :DPQGTVARRL T0345 122 :PYPY 1x0rA 114 :GLLH T0345 128 :P 1x0rA 120 :S T0345 145 :RSDVAWNF 1x0rA 121 :ATHTVRGV T0345 155 :FLIGPEGEPFR 1x0rA 129 :FIVDARGVIRT T0345 166 :RYSRT 1x0rA 141 :LYYPM T0345 171 :FPTINIE 1x0rA 149 :RLVDEIL Number of specific fragments extracted= 17 number of extra gaps= 5 total=1191 Number of alignments=139 # 1x0rA read from 1x0rA/merged-good-all-a2m # found chain 1x0rA in template set Warning: unaligning (T0345)R25 because of BadResidue code BAD_PEPTIDE at template residue (1x0rA)Q33 Warning: unaligning (T0345)F64 because of BadResidue code BAD_PEPTIDE in next template residue (1x0rA)S75 Warning: unaligning (T0345)P65 because of BadResidue code BAD_PEPTIDE at template residue (1x0rA)S75 Warning: unaligning (T0345)N77 because of BadResidue code BAD_PEPTIDE in next template residue (1x0rA)F80 Warning: unaligning (T0345)E78 because of BadResidue code BAD_PEPTIDE at template residue (1x0rA)F80 Warning: unaligning (T0345)P95 because of BadResidue code BAD_PEPTIDE in next template residue (1x0rA)P98 Warning: unaligning (T0345)T96 because of BadResidue code BAD_PEPTIDE at template residue (1x0rA)P98 Warning: unaligning (T0345)D126 because of BadResidue code BAD_PEPTIDE in next template residue (1x0rA)E119 Warning: unaligning (T0345)D127 because of BadResidue code BAD_PEPTIDE at template residue (1x0rA)E119 T0345 2 :IAKSFYDLSAI 1x0rA 8 :IGERFPEMEVT T0345 14 :LDGEKVDFNTF 1x0rA 19 :TDHGVIKLPDH T0345 26 :GRAVLIENVASL 1x0rA 34 :GKWFVLFSHPAD T0345 40 :TTT 1x0rA 46 :FTP T0345 45 :FTQLNEL 1x0rA 61 :YEDFQRL T0345 58 :RLVVLG 1x0rA 68 :GVDLIG T0345 66 :C 1x0rA 76 :V T0345 75 :CQ 1x0rA 77 :DS T0345 79 :EILNSLKYVRPGGGYQ 1x0rA 81 :SHIKWKEWIERHIGVR T0345 97 :FTLVQ 1x0rA 99 :FPIIA T0345 108 :QNEHPVFAYL 1x0rA 104 :DPQGTVARRL T0345 122 :PYPY 1x0rA 114 :GLLH T0345 144 :RRSDVAWNF 1x0rA 120 :SATHTVRGV T0345 155 :FLIGPEGEPFR 1x0rA 129 :FIVDARGVIRT T0345 166 :RYSRT 1x0rA 141 :LYYPM Number of specific fragments extracted= 15 number of extra gaps= 5 total=1206 Number of alignments=140 # 1x0rA read from 1x0rA/merged-good-all-a2m # found chain 1x0rA in template set Warning: unaligning (T0345)R25 because of BadResidue code BAD_PEPTIDE at template residue (1x0rA)Q33 Warning: unaligning (T0345)F64 because of BadResidue code BAD_PEPTIDE in next template residue (1x0rA)S75 Warning: unaligning (T0345)P65 because of BadResidue code BAD_PEPTIDE at template residue (1x0rA)S75 Warning: unaligning (T0345)N77 because of BadResidue code BAD_PEPTIDE in next template residue (1x0rA)F80 Warning: unaligning (T0345)E78 because of BadResidue code BAD_PEPTIDE at template residue (1x0rA)F80 Warning: unaligning (T0345)P95 because of BadResidue code BAD_PEPTIDE in next template residue (1x0rA)P98 Warning: unaligning (T0345)T96 because of BadResidue code BAD_PEPTIDE at template residue (1x0rA)P98 Warning: unaligning (T0345)D126 because of BadResidue code BAD_PEPTIDE in next template residue (1x0rA)E119 Warning: unaligning (T0345)D127 because of BadResidue code BAD_PEPTIDE at template residue (1x0rA)E119 T0345 2 :IAKSFYDLSAINLD 1x0rA 8 :IGERFPEMEVTTDH T0345 17 :EKVDFNTF 1x0rA 22 :GVIKLPDH T0345 26 :GRAVLIEN 1x0rA 34 :GKWFVLFS T0345 36 :SLCGTTT 1x0rA 42 :HPADFTP T0345 43 :RDFTQLNELQCRFPRRLVVLG 1x0rA 53 :EFVSFARRYEDFQRLGVDLIG T0345 66 :C 1x0rA 76 :V T0345 75 :CQ 1x0rA 77 :DS T0345 79 :EILNSLKYVRPGGGYQ 1x0rA 81 :SHIKWKEWIERHIGVR T0345 97 :FTLVQK 1x0rA 99 :FPIIAD T0345 109 :NEHPVFAY 1x0rA 105 :PQGTVARR T0345 121 :LPYPY 1x0rA 113 :LGLLH T0345 128 :PF 1x0rA 120 :SA T0345 146 :SDVAW 1x0rA 122 :THTVR T0345 153 :EKFLIGPEGEPFRR 1x0rA 127 :GVFIVDARGVIRTM Number of specific fragments extracted= 14 number of extra gaps= 5 total=1220 Number of alignments=141 # command:# PrintAlignmentsContacts allconstraints.under Using radius: 8.0000 NUMB_ALIGNS: 141 Done printing distance constraints # command: