# 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:Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0345//projects/compbio/experiments/protein-predict/casp7/T0345/align.constraints_v3.costfcn or /projects/compbio/experiments/protein-predict/casp7/T0345//projects/compbio/experiments/protein-predict/casp7/T0345/align.constraints_v3.costfcn.gz for input Trying /projects/compbio/experiments/protein-predict/casp7/T0345/align.constraints_v3.costfcn # reading script from file /projects/compbio/experiments/protein-predict/casp7/T0345/align.constraints_v3.costfcn # future Constraint commands -> align # future HelixConstraint commands -> align # future StrandConstraint commands -> align # future SheetConstraint commands -> align # future Hbond commands -> align # future SSbond commands -> align # Constraint # added constraint: constraint((T0345)L30.CB, (T0345)V60.CB) [> 4.2832 = 7.1387 < 9.2803] w=1.0000 to align # Constraint # added constraint: constraint((T0345)L30.CB, (T0345)L59.CB) [> 3.6104 = 6.0174 < 7.8226] w=1.0000 to align # Constraint # added constraint: constraint((T0345)V29.CB, (T0345)V60.CB) [> 2.9785 = 4.9641 < 6.4534] w=1.0000 to align # Constraint # added constraint: constraint((T0345)N33.CB, (T0345)G63.CA) [> 4.3534 = 7.2556 < 9.4323] w=0.9769 to align # Constraint # added constraint: constraint((T0345)E32.CB, (T0345)L62.CB) [> 4.3118 = 7.1863 < 9.3422] w=0.9769 to align # Constraint # added constraint: constraint((T0345)I31.CB, (T0345)L62.CB) [> 3.0038 = 5.0063 < 6.5082] w=0.9769 to align # Constraint # added constraint: constraint((T0345)E32.CB, (T0345)V61.CB) [> 4.0240 = 6.7066 < 8.7186] w=0.9769 to align # Constraint # added constraint: constraint((T0345)V34.CB, (T0345)G63.CA) [> 3.8563 = 6.4271 < 8.3552] w=0.9617 to align # Constraint # added constraint: constraint((T0345)V29.CB, (T0345)L59.CB) [> 4.1994 = 6.9990 < 9.0987] w=0.9615 to align # Constraint # added constraint: constraint((T0345)L30.CB, (T0345)V61.CB) [> 2.9105 = 4.8508 < 6.3060] w=0.9483 to align # Constraint # added constraint: constraint((T0345)E32.CB, (T0345)G63.CA) [> 2.8969 = 4.8281 < 6.2765] w=0.9252 to align # Constraint # added constraint: constraint((T0345)I31.CB, (T0345)G63.CA) [> 3.8115 = 6.3525 < 8.2583] w=0.9252 to align # Constraint # added constraint: constraint((T0345)L30.CB, (T0345)L62.CB) [> 4.2406 = 7.0677 < 9.1880] w=0.9252 to align # Constraint # added constraint: constraint((T0345)V29.CB, (T0345)L62.CB) [> 3.7087 = 6.1811 < 8.0354] w=0.9252 to align # Constraint # added constraint: constraint((T0345)N33.CB, (T0345)F64.CB) [> 3.1515 = 5.2524 < 6.8282] w=0.9180 to align # Constraint # added constraint: constraint((T0345)L30.CB, (T0345)L156.CB) [> 3.5309 = 5.8849 < 7.6504] w=0.9053 to align # Constraint # added constraint: constraint((T0345)V29.CB, (T0345)I157.CB) [> 2.9432 = 4.9053 < 6.3769] w=0.9053 to align # Constraint # added constraint: constraint((T0345)V29.CB, (T0345)V61.CB) [> 4.5506 = 7.5843 < 9.8596] w=0.9024 to align # Constraint # added constraint: constraint((T0345)V34.CB, (T0345)F64.CB) [> 4.3213 = 7.2021 < 9.3628] w=0.9004 to align # Constraint # added constraint: constraint((T0345)I31.CB, (T0345)F155.CB) [> 2.9977 = 4.9961 < 6.4949] w=0.8977 to align # Constraint # added constraint: constraint((T0345)V29.CB, (T0345)G158.CA) [> 3.9014 = 6.5023 < 8.4529] w=0.8874 to align # Constraint # added constraint: constraint((T0345)E32.CB, (T0345)F64.CB) [> 4.1948 = 6.9914 < 9.0888] w=0.8795 to align # Constraint # added constraint: constraint((T0345)I31.CB, (T0345)F64.CB) [> 3.5930 = 5.9884 < 7.7849] w=0.8795 to align # Constraint # added constraint: constraint((T0345)A28.CB, (T0345)R58.CB) [> 3.9664 = 6.6107 < 8.5940] w=0.8617 to align # Constraint # added constraint: constraint((T0345)I31.CB, (T0345)I157.CB) [> 4.0957 = 6.8262 < 8.8741] w=0.8599 to align # Constraint # added constraint: constraint((T0345)V34.CB, (T0345)P65.CB) [> 3.4115 = 5.6858 < 7.3915] w=0.8588 to align # Constraint # added constraint: constraint((T0345)L30.CB, (T0345)F155.CB) [> 4.2216 = 7.0360 < 9.1469] w=0.8437 to align # Constraint # added constraint: constraint((T0345)A28.CB, (T0345)L59.CB) [> 2.7067 = 4.5111 < 5.8645] w=0.8408 to align # Constraint # added constraint: constraint((T0345)A28.CB, (T0345)V60.CB) [> 4.2827 = 7.1378 < 9.2792] w=0.8331 to align # Constraint # added constraint: constraint((T0345)A35.CB, (T0345)P65.CB) [> 3.8941 = 6.4902 < 8.4373] w=0.8303 to align # Constraint # added constraint: constraint((T0345)A28.CB, (T0345)I157.CB) [> 4.0923 = 6.8206 < 8.8667] w=0.8208 to align # Constraint # added constraint: constraint((T0345)L30.CB, (T0345)I157.CB) [> 4.4217 = 7.3695 < 9.5804] w=0.8056 to align # Constraint # added constraint: constraint((T0345)A28.CB, (T0345)G158.CA) [> 3.1269 = 5.2116 < 6.7750] w=0.8029 to align # Constraint # added constraint: constraint((T0345)R27.CB, (T0345)V60.CB) [> 3.2099 = 5.3498 < 6.9547] w=0.7999 to align # Constraint # added constraint: constraint((T0345)R27.CB, (T0345)L59.CB) [> 3.9357 = 6.5595 < 8.5273] w=0.7869 to align # Constraint # added constraint: constraint((T0345)V29.CB, (T0345)L156.CB) [> 4.3822 = 7.3036 < 9.4947] w=0.7797 to align # Constraint # added constraint: constraint((T0345)L30.CB, (T0345)I180.CB) [> 4.1740 = 6.9567 < 9.0437] w=0.7735 to align # Constraint # added constraint: constraint((T0345)R27.CB, (T0345)R58.CB) [> 3.6899 = 6.1498 < 7.9947] w=0.7684 to align # Constraint # added constraint: constraint((T0345)E32.CB, (T0345)K154.CB) [> 3.2334 = 5.3890 < 7.0058] w=0.7311 to align # Constraint # added constraint: constraint((T0345)F24.CB, (T0345)V60.CB) [> 3.5036 = 5.8393 < 7.5911] w=0.7168 to align # Constraint # added constraint: constraint((T0345)I31.CB, (T0345)K154.CB) [> 4.2511 = 7.0851 < 9.2106] w=0.7117 to align # Constraint # added constraint: constraint((T0345)L30.CB, (T0345)K154.CB) [> 3.7753 = 6.2922 < 8.1798] w=0.7117 to align # Constraint # added constraint: constraint((T0345)L51.CB, (T0345)V61.CB) [> 3.6825 = 6.1376 < 7.9788] w=0.6998 to align # Constraint # added constraint: constraint((T0345)A28.CB, (T0345)L156.CB) [> 4.0808 = 6.8013 < 8.8417] w=0.6959 to align # Constraint # added constraint: constraint((T0345)R165.CB, (T0345)D179.CB) [> 3.5461 = 5.9102 < 7.6833] w=0.6883 to align # Constraint # added constraint: constraint((T0345)K154.CB, (T0345)R166.CB) [> 4.1856 = 6.9761 < 9.0689] w=0.6793 to align # Constraint # added constraint: constraint((T0345)N33.CB, (T0345)E153.CB) [> 2.8993 = 4.8321 < 6.2818] w=0.6718 to align # Constraint # added constraint: constraint((T0345)A35.CB, (T0345)C66.CB) [> 3.4156 = 5.6926 < 7.4004] w=0.6661 to align # Constraint # added constraint: constraint((T0345)N33.CB, (T0345)K154.CB) [> 4.2649 = 7.1081 < 9.2406] w=0.6487 to align # Constraint # added constraint: constraint((T0345)A28.CB, (T0345)P159.CB) [> 3.4632 = 5.7720 < 7.5036] w=0.6432 to align # Constraint # added constraint: constraint((T0345)L48.CB, (T0345)V61.CB) [> 3.7967 = 6.3279 < 8.2262] w=0.6371 to align # Constraint # added constraint: constraint((T0345)S36.CB, (T0345)P65.CB) [> 4.1997 = 6.9995 < 9.0993] w=0.6333 to align # Constraint # added constraint: constraint((T0345)K154.CB, (T0345)Y167.CB) [> 2.9879 = 4.9798 < 6.4737] w=0.6327 to align # Constraint # added constraint: constraint((T0345)L59.CB, (T0345)I180.CB) [> 3.6697 = 6.1161 < 7.9509] w=0.6305 to align # Constraint # added constraint: constraint((T0345)E32.CB, (T0345)L48.CB) [> 3.7608 = 6.2680 < 8.1483] w=0.6202 to align # Constraint # added constraint: constraint((T0345)Q47.CB, (T0345)T173.CB) [> 3.4227 = 5.7045 < 7.4159] w=0.6182 to align # Constraint # added constraint: constraint((T0345)G26.CA, (T0345)E160.CB) [> 4.2010 = 7.0016 < 9.1021] w=0.5989 to align # Constraint # added constraint: constraint((T0345)E32.CB, (T0345)E153.CB) [> 4.5237 = 7.5395 < 9.8013] w=0.5980 to align # Constraint # added constraint: constraint((T0345)Q52.CB, (T0345)V61.CB) [> 2.9482 = 4.9136 < 6.3877] w=0.5929 to align # Constraint # added constraint: constraint((T0345)E153.CB, (T0345)R166.CB) [> 3.9655 = 6.6092 < 8.5919] w=0.5926 to align # Constraint # added constraint: constraint((T0345)F164.CB, (T0345)L183.CB) [> 3.6055 = 6.0092 < 7.8119] w=0.5848 to align # Constraint # added constraint: constraint((T0345)P65.CB, (T0345)I80.CB) [> 3.6279 = 6.0466 < 7.8605] w=0.5713 to align # Constraint # added constraint: constraint((T0345)N33.CB, (T0345)F152.CB) [> 3.8187 = 6.3646 < 8.2740] w=0.5694 to align # Constraint # added constraint: constraint((T0345)E153.CB, (T0345)Y167.CB) [> 4.0484 = 6.7473 < 8.7715] w=0.5450 to align # Constraint # added constraint: constraint((T0345)I31.CB, (T0345)V61.CB) [> 4.6695 = 7.7824 < 10.1172] w=0.5447 to align # Constraint # added constraint: constraint((T0345)I31.CB, (T0345)L156.CB) [> 4.2865 = 7.1442 < 9.2875] w=0.5441 to align # Constraint # added constraint: constraint((T0345)N33.CB, (T0345)F155.CB) [> 4.4333 = 7.3889 < 9.6055] w=0.5422 to align # Constraint # added constraint: constraint((T0345)N33.CB, (T0345)C66.CB) [> 3.3863 = 5.6439 < 7.3371] w=0.5379 to align # Constraint # added constraint: constraint((T0345)L156.CB, (T0345)I180.CB) [> 3.9839 = 6.6398 < 8.6317] w=0.5255 to align # Constraint # added constraint: constraint((T0345)V34.CB, (T0345)F45.CB) [> 4.2438 = 7.0730 < 9.1949] w=0.5253 to align # Constraint # added constraint: constraint((T0345)D8.CB, (T0345)F21.CB) [> 3.6165 = 6.0274 < 7.8357] w=0.5233 to align # Constraint # added constraint: constraint((T0345)Y167.CB, (T0345)D179.CB) [> 4.0524 = 6.7540 < 8.7802] w=0.5224 to align # Constraint # added constraint: constraint((T0345)V34.CB, (T0345)D44.CB) [> 4.1321 = 6.8869 < 8.9530] w=0.5156 to align # Constraint # added constraint: constraint((T0345)G63.CA, (T0345)V100.CB) [> 3.6825 = 6.1375 < 7.9788] w=0.5144 to align # Constraint # added constraint: constraint((T0345)L84.CB, (T0345)Y93.CB) [> 3.3331 = 5.5552 < 7.2217] w=0.5135 to align # Constraint # added constraint: constraint((T0345)V34.CB, (T0345)C66.CB) [> 4.0542 = 6.7571 < 8.7842] w=0.5105 to align # Constraint # added constraint: constraint((T0345)L62.CB, (T0345)V100.CB) [> 3.7555 = 6.2591 < 8.1369] w=0.5067 to align # Constraint # added constraint: constraint((T0345)L51.CB, (T0345)E177.CB) [> 3.9945 = 6.6575 < 8.6547] w=0.5022 to align # Constraint # added constraint: constraint((T0345)N33.CB, (T0345)N151.CB) [> 3.5526 = 5.9210 < 7.6973] w=0.5007 to align # Constraint # added constraint: constraint((T0345)L9.CB, (T0345)D20.CB) [> 4.3191 = 7.1985 < 9.3580] w=0.4935 to align # Constraint # added constraint: constraint((T0345)V34.CB, (T0345)F152.CB) [> 3.4635 = 5.7725 < 7.5043] w=0.4928 to align # Constraint # added constraint: constraint((T0345)N33.CB, (T0345)P65.CB) [> 4.4843 = 7.4739 < 9.7160] w=0.4877 to align # Constraint # added constraint: constraint((T0345)A28.CB, (T0345)I180.CB) [> 3.9471 = 6.5784 < 8.5520] w=0.4873 to align # Constraint # added constraint: constraint((T0345)E32.CB, (T0345)F152.CB) [> 3.6215 = 6.0359 < 7.8467] w=0.4869 to align # Constraint # added constraint: constraint((T0345)N33.CB, (T0345)Y123.CB) [> 3.1577 = 5.2628 < 6.8417] w=0.4864 to align # Constraint # added constraint: constraint((T0345)G63.CA, (T0345)F97.CB) [> 3.6691 = 6.1151 < 7.9496] w=0.4857 to align # Constraint # added constraint: constraint((T0345)A28.CB, (T0345)L183.CB) [> 3.4982 = 5.8303 < 7.5794] w=0.4796 to align # Constraint # added constraint: constraint((T0345)E153.CB, (T0345)S168.CB) [> 3.1482 = 5.2470 < 6.8211] w=0.4790 to align # Constraint # added constraint: constraint((T0345)L156.CB, (T0345)L183.CB) [> 3.8208 = 6.3679 < 8.2783] w=0.4774 to align # Constraint # added constraint: constraint((T0345)L84.CB, (T0345)P95.CB) [> 3.4121 = 5.6869 < 7.3929] w=0.4759 to align # Constraint # added constraint: constraint((T0345)R27.CB, (T0345)G158.CA) [> 4.5132 = 7.5221 < 9.7787] w=0.4723 to align # Constraint # added constraint: constraint((T0345)L30.CB, (T0345)I176.CB) [> 4.2170 = 7.0283 < 9.1369] w=0.4658 to align # Constraint # added constraint: constraint((T0345)F155.CB, (T0345)Y167.CB) [> 4.2363 = 7.0605 < 9.1787] w=0.4648 to align # Constraint # added constraint: constraint((T0345)L62.CB, (T0345)F97.CB) [> 3.9706 = 6.6176 < 8.6029] w=0.4626 to align # Constraint # added constraint: constraint((T0345)S10.CB, (T0345)F21.CB) [> 4.3924 = 7.3207 < 9.5169] w=0.4530 to align # Constraint # added constraint: constraint((T0345)S36.CB, (T0345)S83.CB) [> 2.6337 = 4.3895 < 5.7063] w=0.4527 to align # Constraint # added constraint: constraint((T0345)L51.CB, (T0345)I176.CB) [> 3.9845 = 6.6409 < 8.6331] w=0.4435 to align # Constraint # added constraint: constraint((T0345)K154.CB, (T0345)F171.CB) [> 3.7636 = 6.2727 < 8.1545] w=0.4419 to align # Constraint # added constraint: constraint((T0345)L156.CB, (T0345)D179.CB) [> 3.5696 = 5.9493 < 7.7340] w=0.4363 to align # Constraint # added constraint: constraint((T0345)P65.CB, (T0345)C75.CB) [> 2.9524 = 4.9206 < 6.3968] w=0.4344 to align # Constraint # added constraint: constraint((T0345)E32.CB, (T0345)F155.CB) [> 4.1753 = 6.9588 < 9.0464] w=0.4331 to align # Constraint # added constraint: constraint((T0345)L62.CB, (T0345)T98.CB) [> 3.2814 = 5.4690 < 7.1097] w=0.4330 to align # Constraint # added constraint: constraint((T0345)F6.CB, (T0345)P163.CB) [> 3.3778 = 5.6296 < 7.3185] w=0.4321 to align # Constraint # added constraint: constraint((T0345)N33.CB, (T0345)F114.CB) [> 4.0587 = 6.7645 < 8.7939] w=0.4248 to align # Constraint # added constraint: constraint((T0345)L14.CB, (T0345)L81.CB) [> 3.3580 = 5.5967 < 7.2757] w=0.4247 to align # Constraint # added constraint: constraint((T0345)K154.CB, (T0345)I176.CB) [> 4.0039 = 6.6731 < 8.6751] w=0.4246 to align # Constraint # added constraint: constraint((T0345)D8.CB, (T0345)N22.CB) [> 3.6108 = 6.0180 < 7.8233] w=0.4244 to align # Constraint # added constraint: constraint((T0345)R25.CB, (T0345)P159.CB) [> 4.1089 = 6.8482 < 8.9026] w=0.4226 to align # Constraint # added constraint: constraint((T0345)G63.CA, (T0345)T98.CB) [> 3.9608 = 6.6013 < 8.5817] w=0.4176 to align # Constraint # added constraint: constraint((T0345)F64.CB, (T0345)F114.CB) [> 3.9069 = 6.5114 < 8.4649] w=0.4172 to align # Constraint # added constraint: constraint((T0345)S36.CB, (T0345)C75.CB) [> 3.3412 = 5.5687 < 7.2393] w=0.4145 to align # Constraint # added constraint: constraint((T0345)P65.CB, (T0345)V100.CB) [> 4.2180 = 7.0300 < 9.1390] w=0.4102 to align # Constraint # added constraint: constraint((T0345)L9.CB, (T0345)V113.CB) [> 3.1963 = 5.3272 < 6.9254] w=0.4083 to align # Constraint # added constraint: constraint((T0345)C66.CB, (T0345)C75.CB) [> 3.7582 = 6.2637 < 8.1427] w=0.4030 to align # Constraint # added constraint: constraint((T0345)F6.CB, (T0345)I157.CB) [> 3.1694 = 5.2823 < 6.8670] w=0.4015 to align # Constraint # added constraint: constraint((T0345)A11.CB, (T0345)V100.CB) [> 2.7543 = 4.5904 < 5.9675] w=0.4004 to align # Constraint # added constraint: constraint((T0345)C38.CB, (T0345)F152.CB) [> 3.9600 = 6.6000 < 8.5800] w=0.3980 to align # Constraint # added constraint: constraint((T0345)L51.CB, (T0345)T173.CB) [> 3.9239 = 6.5398 < 8.5018] w=0.3963 to align # Constraint # added constraint: constraint((T0345)F64.CB, (T0345)V100.CB) [> 2.9364 = 4.8939 < 6.3621] w=0.3948 to align # Constraint # added constraint: constraint((T0345)F6.CB, (T0345)E162.CB) [> 4.2222 = 7.0370 < 9.1480] w=0.3937 to align # Constraint # added constraint: constraint((T0345)I80.CB, (T0345)L99.CB) [> 3.3075 = 5.5125 < 7.1663] w=0.3926 to align # Constraint # added constraint: constraint((T0345)C66.CB, (T0345)F114.CB) [> 3.8627 = 6.4378 < 8.3692] w=0.3863 to align # Constraint # added constraint: constraint((T0345)S36.CB, (T0345)E79.CB) [> 2.9830 = 4.9717 < 6.4632] w=0.3858 to align # Constraint # added constraint: constraint((T0345)F55.CB, (T0345)I180.CB) [> 3.9282 = 6.5470 < 8.5111] w=0.3856 to align # Constraint # added constraint: constraint((T0345)V19.CB, (T0345)T98.CB) [> 3.9322 = 6.5536 < 8.5197] w=0.3848 to align # Constraint # added constraint: constraint((T0345)V61.CB, (T0345)F97.CB) [> 2.6937 = 4.4894 < 5.8363] w=0.3842 to align # Constraint # added constraint: constraint((T0345)Q47.CB, (T0345)I176.CB) [> 4.0195 = 6.6992 < 8.7090] w=0.3839 to align # Constraint # added constraint: constraint((T0345)F45.CB, (T0345)Y93.CB) [> 3.6852 = 6.1420 < 7.9846] w=0.3835 to align # Constraint # added constraint: constraint((T0345)R54.CB, (T0345)E177.CB) [> 4.2080 = 7.0133 < 9.1173] w=0.3803 to align # Constraint # added constraint: constraint((T0345)T40.CB, (T0345)F152.CB) [> 3.5866 = 5.9777 < 7.7709] w=0.3749 to align # Constraint # added constraint: constraint((T0345)T41.CB, (T0345)F152.CB) [> 2.8140 = 4.6900 < 6.0970] w=0.3749 to align # Constraint # added constraint: constraint((T0345)I31.CB, (T0345)L117.CB) [> 4.2835 = 7.1392 < 9.2809] w=0.3747 to align # Constraint # added constraint: constraint((T0345)F64.CB, (T0345)V113.CB) [> 3.9538 = 6.5897 < 8.5666] w=0.3747 to align # Constraint # added constraint: constraint((T0345)K4.CB, (T0345)P163.CB) [> 3.1268 = 5.2113 < 6.7746] w=0.3707 to align # Constraint # added constraint: constraint((T0345)A28.CB, (T0345)L184.CB) [> 3.8907 = 6.4844 < 8.4298] w=0.3678 to align # Constraint # added constraint: constraint((T0345)Y167.CB, (T0345)I176.CB) [> 3.9757 = 6.6262 < 8.6140] w=0.3645 to align # Constraint # added constraint: constraint((T0345)L59.CB, (T0345)L184.CB) [> 3.7283 = 6.2138 < 8.0779] w=0.3598 to align # Constraint # added constraint: constraint((T0345)I31.CB, (T0345)L121.CB) [> 4.4391 = 7.3985 < 9.6181] w=0.3590 to align # Constraint # added constraint: constraint((T0345)A11.CB, (T0345)V113.CB) [> 3.8222 = 6.3703 < 8.2814] w=0.3554 to align # Constraint # added constraint: constraint((T0345)S5.CB, (T0345)P163.CB) [> 4.4432 = 7.4054 < 9.6270] w=0.3553 to align # Constraint # added constraint: constraint((T0345)A35.CB, (T0345)N67.CB) [> 3.3883 = 5.6472 < 7.3414] w=0.3545 to align # Constraint # added constraint: constraint((T0345)Q52.CB, (T0345)T96.CB) [> 3.5908 = 5.9847 < 7.7801] w=0.3544 to align # Constraint # added constraint: constraint((T0345)F24.CB, (T0345)I157.CB) [> 4.1365 = 6.8942 < 8.9624] w=0.3487 to align # Constraint # added constraint: constraint((T0345)F64.CB, (T0345)L99.CB) [> 4.4932 = 7.4887 < 9.7353] w=0.3481 to align # Constraint # added constraint: constraint((T0345)L14.CB, (T0345)L99.CB) [> 3.1383 = 5.2304 < 6.7995] w=0.3476 to align # Constraint # added constraint: constraint((T0345)I12.CB, (T0345)V100.CB) [> 4.0223 = 6.7038 < 8.7150] w=0.3476 to align # Constraint # added constraint: constraint((T0345)Y123.CB, (T0345)E153.CB) [> 3.1546 = 5.2576 < 6.8349] w=0.3473 to align # Constraint # added constraint: constraint((T0345)L84.CB, (T0345)L99.CB) [> 3.7407 = 6.2345 < 8.1049] w=0.3464 to align # Constraint # added constraint: constraint((T0345)N33.CB, (T0345)L121.CB) [> 4.2595 = 7.0991 < 9.2289] w=0.3407 to align # Constraint # added constraint: constraint((T0345)C66.CB, (T0345)V148.CB) [> 3.8758 = 6.4597 < 8.3975] w=0.3391 to align # Constraint # added constraint: constraint((T0345)A11.CB, (T0345)F64.CB) [> 4.1236 = 6.8726 < 8.9344] w=0.3390 to align # Constraint # added constraint: constraint((T0345)F152.CB, (T0345)T170.CB) [> 3.7171 = 6.1951 < 8.0536] w=0.3339 to align # Constraint # added constraint: constraint((T0345)N49.CB, (T0345)Y93.CB) [> 3.7346 = 6.2243 < 8.0917] w=0.3292 to align # Constraint # added constraint: constraint((T0345)N33.CB, (T0345)W150.CB) [> 3.7490 = 6.2483 < 8.1228] w=0.3277 to align # Constraint # added constraint: constraint((T0345)Q47.CB, (T0345)F171.CB) [> 3.9604 = 6.6007 < 8.5809] w=0.3256 to align # Constraint # added constraint: constraint((T0345)L9.CB, (T0345)Y116.CB) [> 3.9277 = 6.5462 < 8.5100] w=0.3249 to align # Constraint # added constraint: constraint((T0345)F64.CB, (T0345)L117.CB) [> 3.6460 = 6.0766 < 7.8996] w=0.3229 to align # Constraint # added constraint: constraint((T0345)F6.CB, (T0345)F155.CB) [> 4.1037 = 6.8396 < 8.8914] w=0.3170 to align # Constraint # added constraint: constraint((T0345)N33.CB, (T0345)K118.CB) [> 3.8275 = 6.3792 < 8.2930] w=0.3152 to align # Constraint # added constraint: constraint((T0345)L48.CB, (T0345)P95.CB) [> 4.0291 = 6.7152 < 8.7298] w=0.3123 to align # Constraint # added constraint: constraint((T0345)F64.CB, (T0345)K118.CB) [> 4.3224 = 7.2040 < 9.3652] w=0.3078 to align # Constraint # added constraint: constraint((T0345)C66.CB, (T0345)D147.CB) [> 3.5645 = 5.9408 < 7.7230] w=0.3072 to align # Constraint # added constraint: constraint((T0345)L117.CB, (T0345)F155.CB) [> 3.8943 = 6.4905 < 8.4377] w=0.3061 to align # Constraint # added constraint: constraint((T0345)N33.CB, (T0345)L117.CB) [> 4.3253 = 7.2087 < 9.3714] w=0.3014 to align # Constraint # added constraint: constraint((T0345)L30.CB, (T0345)L48.CB) [> 4.3867 = 7.3111 < 9.5044] w=0.3010 to align # Constraint # added constraint: constraint((T0345)V60.CB, (T0345)F97.CB) [> 4.3799 = 7.2998 < 9.4897] w=0.2996 to align # Constraint # added constraint: constraint((T0345)V29.CB, (T0345)F155.CB) [> 4.5260 = 7.5433 < 9.8063] w=0.2994 to align # Constraint # added constraint: constraint((T0345)A35.CB, (T0345)D147.CB) [> 3.1430 = 5.2382 < 6.8097] w=0.2977 to align # Constraint # added constraint: constraint((T0345)A3.CB, (T0345)P163.CB) [> 3.9693 = 6.6155 < 8.6001] w=0.2938 to align # Constraint # added constraint: constraint((T0345)E32.CB, (T0345)Q47.CB) [> 4.1028 = 6.8380 < 8.8894] w=0.2933 to align # Constraint # added constraint: constraint((T0345)I12.CB, (T0345)N77.CB) [> 3.2905 = 5.4842 < 7.1295] w=0.2929 to align # Constraint # added constraint: constraint((T0345)V34.CB, (T0345)V148.CB) [> 3.6942 = 6.1571 < 8.0042] w=0.2909 to align # Constraint # added constraint: constraint((T0345)V61.CB, (T0345)T98.CB) [> 4.1072 = 6.8453 < 8.8989] w=0.2906 to align # Constraint # added constraint: constraint((T0345)K154.CB, (T0345)S168.CB) [> 4.2773 = 7.1288 < 9.2674] w=0.2891 to align # Constraint # added constraint: constraint((T0345)Y7.CB, (T0345)Y116.CB) [> 3.3039 = 5.5065 < 7.1585] w=0.2857 to align # Constraint # added constraint: constraint((T0345)S36.CB, (T0345)N67.CB) [> 4.2412 = 7.0687 < 9.1893] w=0.2853 to align # Constraint # added constraint: constraint((T0345)A28.CB, (T0345)R57.CB) [> 4.1182 = 6.8636 < 8.9227] w=0.2839 to align # Constraint # added constraint: constraint((T0345)L156.CB, (T0345)Y167.CB) [> 4.5177 = 7.5295 < 9.7883] w=0.2838 to align # Constraint # added constraint: constraint((T0345)A28.CB, (T0345)F164.CB) [> 4.4746 = 7.4576 < 9.6949] w=0.2792 to align # Constraint # added constraint: constraint((T0345)F55.CB, (T0345)L184.CB) [> 3.7911 = 6.3185 < 8.2141] w=0.2748 to align # Constraint # added constraint: constraint((T0345)F114.CB, (T0345)V148.CB) [> 3.2781 = 5.4636 < 7.1026] w=0.2715 to align # Constraint # added constraint: constraint((T0345)A11.CB, (T0345)F21.CB) [> 4.0626 = 6.7709 < 8.8022] w=0.2697 to align # Constraint # added constraint: constraint((T0345)A35.CB, (T0345)N151.CB) [> 3.2658 = 5.4430 < 7.0760] w=0.2695 to align # Constraint # added constraint: constraint((T0345)Q52.CB, (T0345)Q94.CB) [> 3.7114 = 6.1857 < 8.0414] w=0.2685 to align # Constraint # added constraint: constraint((T0345)Q47.CB, (T0345)P172.CB) [> 4.1997 = 6.9994 < 9.0993] w=0.2658 to align # Constraint # added constraint: constraint((T0345)R58.CB, (T0345)L184.CB) [> 3.3817 = 5.6361 < 7.3270] w=0.2637 to align # Constraint # added constraint: constraint((T0345)V100.CB, (T0345)V113.CB) [> 3.9117 = 6.5195 < 8.4754] w=0.2619 to align # Constraint # added constraint: constraint((T0345)Y125.CB, (T0345)E153.CB) [> 3.9997 = 6.6662 < 8.6661] w=0.2602 to align # Constraint # added constraint: constraint((T0345)F24.CB, (T0345)L62.CB) [> 4.2779 = 7.1299 < 9.2689] w=0.2526 to align # Constraint # added constraint: constraint((T0345)V60.CB, (T0345)T98.CB) [> 4.0607 = 6.7679 < 8.7983] w=0.2521 to align # Constraint # added constraint: constraint((T0345)Q52.CB, (T0345)P95.CB) [> 3.7488 = 6.2481 < 8.1225] w=0.2489 to align # Constraint # added constraint: constraint((T0345)F6.CB, (T0345)V29.CB) [> 4.4951 = 7.4918 < 9.7393] w=0.2481 to align # Constraint # added constraint: constraint((T0345)G63.CA, (T0345)P95.CB) [> 3.9465 = 6.5775 < 8.5508] w=0.2447 to align # Constraint # added constraint: constraint((T0345)V34.CB, (T0345)N151.CB) [> 3.8112 = 6.3521 < 8.2577] w=0.2406 to align # Constraint # added constraint: constraint((T0345)L48.CB, (T0345)Y93.CB) [> 3.8066 = 6.3443 < 8.2476] w=0.2394 to align # Constraint # added constraint: constraint((T0345)R57.CB, (T0345)I180.CB) [> 3.7059 = 6.1765 < 8.0294] w=0.2390 to align # Constraint # added constraint: constraint((T0345)E32.CB, (T0345)F171.CB) [> 4.4442 = 7.4070 < 9.6292] w=0.2243 to align # Constraint # added constraint: constraint((T0345)T40.CB, (T0345)N151.CB) [> 4.2664 = 7.1106 < 9.2438] w=0.2240 to align # Constraint # added constraint: constraint((T0345)V34.CB, (T0345)W150.CB) [> 3.7322 = 6.2203 < 8.0864] w=0.2212 to align # Constraint # added constraint: constraint((T0345)E153.CB, (T0345)R169.CB) [> 4.4052 = 7.3420 < 9.5446] w=0.2210 to align # Constraint # added constraint: constraint((T0345)W150.CB, (T0345)R169.CB) [> 3.8541 = 6.4235 < 8.3506] w=0.2206 to align # Constraint # added constraint: constraint((T0345)N13.CB, (T0345)N77.CB) [> 4.1224 = 6.8707 < 8.9319] w=0.2171 to align # Constraint # added constraint: constraint((T0345)F6.CB, (T0345)I31.CB) [> 4.6435 = 7.7392 < 10.0610] w=0.2158 to align # Constraint # added constraint: constraint((T0345)L84.CB, (T0345)F97.CB) [> 3.6779 = 6.1298 < 7.9688] w=0.2065 to align # Constraint # added constraint: constraint((T0345)C38.CB, (T0345)N151.CB) [> 2.6885 = 4.4809 < 5.8251] w=0.2009 to align # Constraint # added constraint: constraint((T0345)V61.CB, (T0345)P95.CB) [> 3.0469 = 5.0782 < 6.6017] w=0.1992 to align # Constraint # added constraint: constraint((T0345)Y123.CB, (T0345)N151.CB) [> 3.4989 = 5.8316 < 7.5810] w=0.1978 to align # Constraint # added constraint: constraint((T0345)E32.CB, (T0345)F45.CB) [> 4.3749 = 7.2916 < 9.4791] w=0.1922 to align # Constraint # added constraint: constraint((T0345)W150.CB, (T0345)S168.CB) [> 3.7352 = 6.2254 < 8.0930] w=0.1910 to align # Constraint # added constraint: constraint((T0345)F21.CB, (T0345)L62.CB) [> 4.4064 = 7.3440 < 9.5472] w=0.1907 to align # Constraint # added constraint: constraint((T0345)Q47.CB, (T0345)V61.CB) [> 3.7833 = 6.3055 < 8.1971] w=0.1901 to align # Constraint # added constraint: constraint((T0345)Y7.CB, (T0345)L117.CB) [> 4.0780 = 6.7967 < 8.8357] w=0.1867 to align # Constraint # added constraint: constraint((T0345)L9.CB, (T0345)P112.CB) [> 4.1010 = 6.8350 < 8.8855] w=0.1866 to align # Constraint # added constraint: constraint((T0345)C38.CB, (T0345)C66.CB) [> 4.3094 = 7.1824 < 9.3371] w=0.1856 to align # Constraint # added constraint: constraint((T0345)V34.CB, (T0345)S83.CB) [> 4.5059 = 7.5099 < 9.7629] w=0.1839 to align # Constraint # added constraint: constraint((T0345)F21.CB, (T0345)I157.CB) [> 4.5563 = 7.5938 < 9.8719] w=0.1834 to align # Constraint # added constraint: constraint((T0345)F64.CB, (T0345)K102.CB) [> 3.5640 = 5.9401 < 7.7221] w=0.1810 to align # Constraint # added constraint: constraint((T0345)L14.CB, (T0345)V100.CB) [> 3.8891 = 6.4818 < 8.4263] w=0.1767 to align # Constraint # added constraint: constraint((T0345)A3.CB, (T0345)F164.CB) [> 4.2634 = 7.1057 < 9.2374] w=0.1763 to align # Constraint # added constraint: constraint((T0345)S83.CB, (T0345)P95.CB) [> 4.3966 = 7.3277 < 9.5260] w=0.1761 to align # Constraint # added constraint: constraint((T0345)C38.CB, (T0345)D147.CB) [> 3.1115 = 5.1858 < 6.7416] w=0.1743 to align # Constraint # added constraint: constraint((T0345)K102.CB, (T0345)H111.CB) [> 3.6343 = 6.0572 < 7.8744] w=0.1741 to align # Constraint # added constraint: constraint((T0345)L59.CB, (T0345)L156.CB) [> 4.4601 = 7.4335 < 9.6636] w=0.1732 to align # Constraint # added constraint: constraint((T0345)R57.CB, (T0345)K181.CB) [> 3.9799 = 6.6331 < 8.6231] w=0.1719 to align # Constraint # added constraint: constraint((T0345)L14.CB, (T0345)P95.CB) [> 4.1386 = 6.8977 < 8.9670] w=0.1687 to align # Constraint # added constraint: constraint((T0345)A11.CB, (T0345)K102.CB) [> 3.3977 = 5.6629 < 7.3617] w=0.1668 to align # Constraint # added constraint: constraint((T0345)A35.CB, (T0345)W150.CB) [> 3.9248 = 6.5413 < 8.5037] w=0.1655 to align # Constraint # added constraint: constraint((T0345)V61.CB, (T0345)T96.CB) [> 3.8727 = 6.4545 < 8.3908] w=0.1644 to align # Constraint # added constraint: constraint((T0345)A35.CB, (T0345)E73.CB) [> 2.8916 = 4.8193 < 6.2651] w=0.1611 to align # Constraint # added constraint: constraint((T0345)L9.CB, (T0345)L117.CB) [> 3.5501 = 5.9169 < 7.6919] w=0.1597 to align # Constraint # added constraint: constraint((T0345)F152.CB, (T0345)Y167.CB) [> 3.7271 = 6.2119 < 8.0755] w=0.1582 to align # Constraint # added constraint: constraint((T0345)P65.CB, (T0345)S83.CB) [> 4.4923 = 7.4872 < 9.7334] w=0.1565 to align # Constraint # added constraint: constraint((T0345)I157.CB, (T0345)L183.CB) [> 3.8271 = 6.3785 < 8.2921] w=0.1551 to align # Constraint # added constraint: constraint((T0345)N33.CB, (T0345)L84.CB) [> 4.1763 = 6.9605 < 9.0487] w=0.1546 to align # Constraint # added constraint: constraint((T0345)C66.CB, (T0345)N151.CB) [> 3.9605 = 6.6008 < 8.5811] w=0.1529 to align # Constraint # added constraint: constraint((T0345)Y7.CB, (T0345)K120.CB) [> 2.9002 = 4.8336 < 6.2836] w=0.1528 to align # Constraint # added constraint: constraint((T0345)E32.CB, (T0345)W150.CB) [> 3.8516 = 6.4193 < 8.3450] w=0.1518 to align # Constraint # added constraint: constraint((T0345)Q47.CB, (T0345)E177.CB) [> 3.3173 = 5.5288 < 7.1875] w=0.1497 to align # Constraint # added constraint: constraint((T0345)L30.CB, (T0345)L184.CB) [> 4.0995 = 6.8325 < 8.8822] w=0.1493 to align # Constraint # added constraint: constraint((T0345)Y7.CB, (T0345)V113.CB) [> 3.8131 = 6.3552 < 8.2617] w=0.1476 to align # Constraint # added constraint: constraint((T0345)K85.CB, (T0345)P95.CB) [> 4.5306 = 7.5510 < 9.8163] w=0.1455 to align # Constraint # added constraint: constraint((T0345)F64.CB, (T0345)I80.CB) [> 3.6092 = 6.0153 < 7.8199] w=0.1453 to align # Constraint # added constraint: constraint((T0345)I2.CB, (T0345)F164.CB) [> 3.7273 = 6.2122 < 8.0758] w=0.1430 to align # Constraint # added constraint: constraint((T0345)N33.CB, (T0345)D147.CB) [> 3.5106 = 5.8509 < 7.6062] w=0.1404 to align # Constraint # added constraint: constraint((T0345)L62.CB, (T0345)T96.CB) [> 3.0329 = 5.0549 < 6.5713] w=0.1378 to align # Constraint # added constraint: constraint((T0345)G63.CA, (T0345)L84.CB) [> 4.3960 = 7.3267 < 9.5247] w=0.1377 to align # Constraint # added constraint: constraint((T0345)K102.CB, (T0345)P112.CB) [> 3.7017 = 6.1695 < 8.0203] w=0.1360 to align # Constraint # added constraint: constraint((T0345)A35.CB, (T0345)Q72.CB) [> 3.0195 = 5.0325 < 6.5422] w=0.1307 to align # Constraint # added constraint: constraint((T0345)V60.CB, (T0345)P95.CB) [> 4.4609 = 7.4348 < 9.6653] w=0.1302 to align # Constraint # added constraint: constraint((T0345)P65.CB, (T0345)L84.CB) [> 4.3048 = 7.1746 < 9.3270] w=0.1301 to align # Constraint # added constraint: constraint((T0345)C66.CB, (T0345)L81.CB) [> 2.9964 = 4.9941 < 6.4923] w=0.1286 to align # Constraint # added constraint: constraint((T0345)A11.CB, (T0345)L62.CB) [> 4.5185 = 7.5309 < 9.7902] w=0.1281 to align # Constraint # added constraint: constraint((T0345)C38.CB, (T0345)V148.CB) [> 4.1223 = 6.8704 < 8.9316] w=0.1269 to align # Constraint # added constraint: constraint((T0345)G39.CA, (T0345)I80.CB) [> 4.5158 = 7.5264 < 9.7843] w=0.1238 to align # Constraint # added constraint: constraint((T0345)L9.CB, (T0345)K102.CB) [> 4.4420 = 7.4033 < 9.6243] w=0.1227 to align # Constraint # added constraint: constraint((T0345)V60.CB, (T0345)T96.CB) [> 3.7208 = 6.2014 < 8.0618] w=0.1226 to align # Constraint # added constraint: constraint((T0345)A11.CB, (T0345)C103.CB) [> 3.3858 = 5.6430 < 7.3359] w=0.1225 to align # Constraint # added constraint: constraint((T0345)A11.CB, (T0345)L99.CB) [> 3.6778 = 6.1297 < 7.9686] w=0.1218 to align # Constraint # added constraint: constraint((T0345)E32.CB, (T0345)N151.CB) [> 4.2443 = 7.0738 < 9.1960] w=0.1218 to align # Constraint # added constraint: constraint((T0345)Y125.CB, (T0345)V148.CB) [> 4.3131 = 7.1884 < 9.3450] w=0.1202 to align # Constraint # added constraint: constraint((T0345)V60.CB, (T0345)V100.CB) [> 4.2763 = 7.1272 < 9.2653] w=0.1194 to align # Constraint # added constraint: constraint((T0345)L37.CB, (T0345)N67.CB) [> 4.4725 = 7.4542 < 9.6904] w=0.1192 to align # Constraint # added constraint: constraint((T0345)F24.CB, (T0345)G158.CA) [> 3.9943 = 6.6571 < 8.6543] w=0.1189 to align # Constraint # added constraint: constraint((T0345)L9.CB, (T0345)V100.CB) [> 4.0236 = 6.7059 < 8.7177] w=0.1150 to align # Constraint # added constraint: constraint((T0345)V100.CB, (T0345)E110.CB) [> 3.6412 = 6.0686 < 7.8892] w=0.1147 to align # Constraint # added constraint: constraint((T0345)V34.CB, (T0345)Q47.CB) [> 4.1631 = 6.9384 < 9.0200] w=0.1131 to align # Constraint # added constraint: constraint((T0345)L156.CB, (T0345)L184.CB) [> 3.9960 = 6.6600 < 8.6580] w=0.1109 to align # Constraint # added constraint: constraint((T0345)E32.CB, (T0345)F97.CB) [> 4.0220 = 6.7034 < 8.7144] w=0.1108 to align # Constraint # added constraint: constraint((T0345)E32.CB, (T0345)V148.CB) [> 4.0294 = 6.7156 < 8.7303] w=0.1105 to align # Constraint # added constraint: constraint((T0345)L37.CB, (T0345)I80.CB) [> 3.7836 = 6.3060 < 8.1979] w=0.1077 to align # Constraint # added constraint: constraint((T0345)P65.CB, (T0345)C103.CB) [> 4.2983 = 7.1638 < 9.3130] w=0.1076 to align # Constraint # added constraint: constraint((T0345)F64.CB, (T0345)C103.CB) [> 3.4643 = 5.7738 < 7.5060] w=0.1072 to align # Constraint # added constraint: constraint((T0345)K154.CB, (T0345)T173.CB) [> 4.2163 = 7.0271 < 9.1353] w=0.1068 to align # Constraint # added constraint: constraint((T0345)G63.CA, (T0345)Y93.CB) [> 4.4194 = 7.3656 < 9.5753] w=0.1018 to align # Constraint # added constraint: constraint((T0345)N33.CB, (T0345)L156.CB) [> 4.4084 = 7.3474 < 9.5516] w=0.1018 to align # Constraint # added constraint: constraint((T0345)L30.CB, (T0345)G158.CA) [> 4.5061 = 7.5102 < 9.7632] w=0.1018 to align # Constraint # added constraint: constraint((T0345)P65.CB, (T0345)F97.CB) [> 4.1540 = 6.9233 < 9.0004] w=0.0995 to align # Constraint # added constraint: constraint((T0345)F64.CB, (T0345)F97.CB) [> 4.5491 = 7.5818 < 9.8564] w=0.0995 to align # Constraint # added constraint: constraint((T0345)Q47.CB, (T0345)F97.CB) [> 3.9077 = 6.5128 < 8.4666] w=0.0974 to align # Constraint # added constraint: constraint((T0345)Y7.CB, (T0345)L121.CB) [> 3.8980 = 6.4967 < 8.4457] w=0.0929 to align # Constraint # added constraint: constraint((T0345)Y7.CB, (T0345)F24.CB) [> 3.9241 = 6.5402 < 8.5022] w=0.0923 to align # Constraint # added constraint: constraint((T0345)I12.CB, (T0345)C103.CB) [> 4.2358 = 7.0597 < 9.1776] w=0.0918 to align # Constraint # added constraint: constraint((T0345)L30.CB, (T0345)Q47.CB) [> 4.4401 = 7.4002 < 9.6203] w=0.0862 to align # Constraint # added constraint: constraint((T0345)V19.CB, (T0345)C103.CB) [> 3.6941 = 6.1568 < 8.0039] w=0.0856 to align # Constraint # added constraint: constraint((T0345)L37.CB, (T0345)E73.CB) [> 4.5582 = 7.5969 < 9.8760] w=0.0844 to align # Constraint # added constraint: constraint((T0345)L9.CB, (T0345)F64.CB) [> 4.6156 = 7.6926 < 10.0004] w=0.0835 to align # Constraint # added constraint: constraint((T0345)V29.CB, (T0345)P159.CB) [> 4.3094 = 7.1823 < 9.3370] w=0.0829 to align # Constraint # added constraint: constraint((T0345)G39.CA, (T0345)P65.CB) [> 3.5894 = 5.9823 < 7.7769] w=0.0801 to align # Constraint # added constraint: constraint((T0345)F45.CB, (T0345)F97.CB) [> 3.7805 = 6.3008 < 8.1911] w=0.0760 to align # Constraint # added constraint: constraint((T0345)L37.CB, (T0345)C66.CB) [> 4.5844 = 7.6407 < 9.9329] w=0.0746 to align # Constraint # added constraint: constraint((T0345)N67.CB, (T0345)N77.CB) [> 4.0629 = 6.7716 < 8.8030] w=0.0719 to align # Constraint # added constraint: constraint((T0345)A115.CB, (T0345)P124.CB) [> 3.4599 = 5.7666 < 7.4966] w=0.0708 to align # Constraint # added constraint: constraint((T0345)L30.CB, (T0345)T173.CB) [> 4.6301 = 7.7168 < 10.0318] w=0.0692 to align # Constraint # added constraint: constraint((T0345)L37.CB, (T0345)Q72.CB) [> 3.4945 = 5.8241 < 7.5714] w=0.0692 to align # Constraint # added constraint: constraint((T0345)F6.CB, (T0345)Y116.CB) [> 4.3425 = 7.2375 < 9.4087] w=0.0692 to align # Constraint # added constraint: constraint((T0345)F155.CB, (T0345)F164.CB) [> 3.5874 = 5.9791 < 7.7728] w=0.0688 to align # Constraint # added constraint: constraint((T0345)V105.CB, (T0345)F114.CB) [> 2.8687 = 4.7811 < 6.2155] w=0.0687 to align # Constraint # added constraint: constraint((T0345)L30.CB, (T0345)N151.CB) [> 4.2636 = 7.1061 < 9.2379] w=0.0675 to align # Constraint # added constraint: constraint((T0345)V105.CB, (T0345)V148.CB) [> 3.0739 = 5.1231 < 6.6601] w=0.0615 to align # Constraint # added constraint: constraint((T0345)S10.CB, (T0345)V113.CB) [> 3.9986 = 6.6643 < 8.6636] w=0.0614 to align # Constraint # added constraint: constraint((T0345)T42.CB, (T0345)R88.CB) [> 3.7705 = 6.2841 < 8.1693] w=0.0609 to align # Constraint # added constraint: constraint((T0345)M132.CB, (T0345)W150.CB) [> 4.4866 = 7.4777 < 9.7210] w=0.0594 to align # Constraint # added constraint: constraint((T0345)L131.CB, (T0345)A149.CB) [> 3.2438 = 5.4063 < 7.0282] w=0.0594 to align # Constraint # added constraint: constraint((T0345)Q47.CB, (T0345)G63.CA) [> 4.4466 = 7.4110 < 9.6343] w=0.0584 to align # Constraint # added constraint: constraint((T0345)Y125.CB, (T0345)N151.CB) [> 3.4546 = 5.7576 < 7.4849] w=0.0555 to align # Constraint # added constraint: constraint((T0345)I80.CB, (T0345)E104.CB) [> 3.4123 = 5.6872 < 7.3933] w=0.0553 to align # Constraint # added constraint: constraint((T0345)P65.CB, (T0345)V105.CB) [> 3.9382 = 6.5637 < 8.5328] w=0.0548 to align # Constraint # added constraint: constraint((T0345)P65.CB, (T0345)E104.CB) [> 3.8312 = 6.3853 < 8.3009] w=0.0548 to align # Constraint # added constraint: constraint((T0345)N67.CB, (T0345)K102.CB) [> 3.8942 = 6.4902 < 8.4373] w=0.0538 to align # Constraint # added constraint: constraint((T0345)G63.CA, (T0345)V105.CB) [> 3.6880 = 6.1467 < 7.9907] w=0.0538 to align # Constraint # added constraint: constraint((T0345)F64.CB, (T0345)T98.CB) [> 3.4903 = 5.8172 < 7.5624] w=0.0537 to align # Constraint # added constraint: constraint((T0345)T41.CB, (T0345)R88.CB) [> 3.1375 = 5.2292 < 6.7980] w=0.0534 to align # Constraint # added constraint: constraint((T0345)I139.CB, (T0345)A149.CB) [> 3.7175 = 6.1958 < 8.0546] w=0.0532 to align # Constraint # added constraint: constraint((T0345)L9.CB, (T0345)Q101.CB) [> 3.7566 = 6.2610 < 8.1393] w=0.0528 to align # Constraint # added constraint: constraint((T0345)D8.CB, (T0345)V19.CB) [> 4.4026 = 7.3377 < 9.5390] w=0.0528 to align # Constraint # added constraint: constraint((T0345)I139.CB, (T0345)V148.CB) [> 4.0983 = 6.8304 < 8.8796] w=0.0527 to align # Constraint # added constraint: constraint((T0345)V29.CB, (T0345)R58.CB) [> 2.8026 = 4.6710 < 6.0724] w=0.0517 to align # Constraint # added constraint: constraint((T0345)E32.CB, (T0345)L59.CB) [> 4.1174 = 6.8624 < 8.9211] w=0.0517 to align # Constraint # added constraint: constraint((T0345)N33.CB, (T0345)L62.CB) [> 3.0867 = 5.1445 < 6.6879] w=0.0517 to align # Constraint # added constraint: constraint((T0345)V34.CB, (T0345)L62.CB) [> 4.2762 = 7.1270 < 9.2651] w=0.0517 to align # Constraint # added constraint: constraint((T0345)Q68.CB, (T0345)V105.CB) [> 3.9205 = 6.5342 < 8.4944] w=0.0461 to align # Constraint # added constraint: constraint((T0345)Q68.CB, (T0345)N106.CB) [> 3.4088 = 5.6813 < 7.3857] w=0.0461 to align # Constraint # added constraint: constraint((T0345)Q68.CB, (T0345)I139.CB) [> 3.9722 = 6.6203 < 8.6063] w=0.0461 to align # Constraint # added constraint: constraint((T0345)Q68.CB, (T0345)W140.CB) [> 3.4084 = 5.6807 < 7.3849] w=0.0461 to align # Constraint # added constraint: constraint((T0345)Q68.CB, (T0345)V148.CB) [> 4.6487 = 7.7479 < 10.0722] w=0.0461 to align # Constraint # added constraint: constraint((T0345)F69.CB, (T0345)L137.CB) [> 4.2220 = 7.0367 < 9.1477] w=0.0461 to align # Constraint # added constraint: constraint((T0345)F69.CB, (T0345)V148.CB) [> 4.6776 = 7.7959 < 10.1347] w=0.0461 to align # Constraint # added constraint: constraint((T0345)F69.CB, (T0345)W150.CB) [> 2.9267 = 4.8779 < 6.3412] w=0.0461 to align # Constraint # added constraint: constraint((T0345)F69.CB, (T0345)N151.CB) [> 2.9170 = 4.8618 < 6.3203] w=0.0461 to align # Constraint # added constraint: constraint((T0345)G70.CA, (T0345)L137.CB) [> 3.5188 = 5.8647 < 7.6241] w=0.0461 to align # Constraint # added constraint: constraint((T0345)G70.CA, (T0345)I139.CB) [> 4.6728 = 7.7880 < 10.1245] w=0.0461 to align # Constraint # added constraint: constraint((T0345)S36.CB, (T0345)V87.CB) [> 4.3038 = 7.1731 < 9.3250] w=0.0461 to align # Constraint # added constraint: constraint((T0345)A35.CB, (T0345)F69.CB) [> 3.9633 = 6.6056 < 8.5872] w=0.0461 to align # Constraint # added constraint: constraint((T0345)L131.CB, (T0345)R145.CB) [> 4.6929 = 7.8214 < 10.1679] w=0.0461 to align # Constraint # added constraint: constraint((T0345)N106.CB, (T0345)W140.CB) [> 2.6747 = 4.4578 < 5.7951] w=0.0461 to align # Constraint # added constraint: constraint((T0345)N106.CB, (T0345)V143.CB) [> 4.5681 = 7.6135 < 9.8975] w=0.0461 to align # Constraint # added constraint: constraint((T0345)A35.CB, (T0345)G63.CA) [> 3.7824 = 6.3041 < 8.1953] w=0.0461 to align # Constraint # added constraint: constraint((T0345)I138.CB, (T0345)A149.CB) [> 4.2772 = 7.1286 < 9.2672] w=0.0455 to align # Constraint # added constraint: constraint((T0345)L137.CB, (T0345)V148.CB) [> 2.9248 = 4.8746 < 6.3370] w=0.0451 to align # Constraint # added constraint: constraint((T0345)A35.CB, (T0345)I139.CB) [> 4.4324 = 7.3874 < 9.6036] w=0.0451 to align # Constraint # added constraint: constraint((T0345)F152.CB, (T0345)F164.CB) [> 3.0828 = 5.1379 < 6.6793] w=0.0447 to align # Constraint # added constraint: constraint((T0345)N67.CB, (T0345)E110.CB) [> 3.8100 = 6.3501 < 8.2551] w=0.0442 to align # Constraint # added constraint: constraint((T0345)C66.CB, (T0345)Y86.CB) [> 3.7123 = 6.1872 < 8.0433] w=0.0433 to align # Constraint # added constraint: constraint((T0345)N33.CB, (T0345)Y86.CB) [> 2.8533 = 4.7554 < 6.1821] w=0.0433 to align # Constraint # added constraint: constraint((T0345)V29.CB, (T0345)V100.CB) [> 2.3909 = 3.9848 < 5.1802] w=0.0425 to align # Constraint # added constraint: constraint((T0345)V29.CB, (T0345)L99.CB) [> 4.2057 = 7.0094 < 9.1123] w=0.0425 to align # Constraint # added constraint: constraint((T0345)A28.CB, (T0345)L99.CB) [> 3.8545 = 6.4241 < 8.3513] w=0.0425 to align # Constraint # added constraint: constraint((T0345)L37.CB, (T0345)N151.CB) [> 3.9031 = 6.5051 < 8.4567] w=0.0417 to align # Constraint # added constraint: constraint((T0345)T40.CB, (T0345)Y86.CB) [> 4.2746 = 7.1244 < 9.2617] w=0.0415 to align # Constraint # added constraint: constraint((T0345)R27.CB, (T0345)P56.CB) [> 4.3676 = 7.2793 < 9.4630] w=0.0412 to align # Constraint # added constraint: constraint((T0345)A35.CB, (T0345)F64.CB) [> 3.7081 = 6.1802 < 8.0343] w=0.0385 to align # Constraint # added constraint: constraint((T0345)A35.CB, (T0345)G70.CA) [> 3.7036 = 6.1726 < 8.0244] w=0.0385 to align # Constraint # added constraint: constraint((T0345)T42.CB, (T0345)V87.CB) [> 4.3447 = 7.2412 < 9.4136] w=0.0384 to align # Constraint # added constraint: constraint((T0345)C66.CB, (T0345)L99.CB) [> 4.3500 = 7.2500 < 9.4250] w=0.0383 to align # Constraint # added constraint: constraint((T0345)A28.CB, (T0345)F155.CB) [> 4.0216 = 6.7027 < 8.7135] w=0.0381 to align # Constraint # added constraint: constraint((T0345)H111.CB, (T0345)I138.CB) [> 4.3765 = 7.2942 < 9.4824] w=0.0374 to align # Constraint # added constraint: constraint((T0345)D8.CB, (T0345)K18.CB) [> 3.4822 = 5.8036 < 7.5447] w=0.0306 to align # Constraint # added constraint: constraint((T0345)I138.CB, (T0345)N151.CB) [> 3.3821 = 5.6368 < 7.3278] w=0.0302 to align # Constraint # added constraint: constraint((T0345)F114.CB, (T0345)I139.CB) [> 3.7367 = 6.2278 < 8.0962] w=0.0298 to align # Constraint # added constraint: constraint((T0345)A35.CB, (T0345)P142.CB) [> 3.0049 = 5.0081 < 6.5106] w=0.0231 to align # Constraint # added constraint: constraint((T0345)L30.CB, (T0345)G63.CA) [> 4.6940 = 7.8234 < 10.1704] w=0.0231 to align # Constraint # added constraint: constraint((T0345)P65.CB, (T0345)N151.CB) [> 4.7213 = 7.8687 < 10.2294] w=0.0231 to align # Constraint # added constraint: constraint((T0345)G39.CA, (T0345)N151.CB) [> 4.5448 = 7.5746 < 9.8470] w=0.0231 to align # Constraint # added constraint: constraint((T0345)R27.CB, (T0345)I157.CB) [> 4.6575 = 7.7626 < 10.0914] w=0.0231 to align # Constraint # added constraint: constraint((T0345)G39.CA, (T0345)R145.CB) [> 4.0282 = 6.7137 < 8.7277] w=0.0231 to align # Constraint # added constraint: constraint((T0345)W140.CB, (T0345)W150.CB) [> 3.6798 = 6.1329 < 7.9728] w=0.0230 to align # Constraint # added constraint: constraint((T0345)W140.CB, (T0345)N151.CB) [> 3.0360 = 5.0599 < 6.5779] w=0.0230 to align # Constraint # added constraint: constraint((T0345)M132.CB, (T0345)V148.CB) [> 3.4095 = 5.6824 < 7.3872] w=0.0230 to align # Constraint # added constraint: constraint((T0345)V34.CB, (T0345)T173.CB) [> 4.7318 = 7.8864 < 10.2523] w=0.0230 to align # Constraint # added constraint: constraint((T0345)C38.CB, (T0345)V143.CB) [> 4.0677 = 6.7796 < 8.8135] w=0.0229 to align # Constraint # added constraint: constraint((T0345)I139.CB, (T0345)N151.CB) [> 3.8320 = 6.3866 < 8.3026] w=0.0226 to align # Constraint # added constraint: constraint((T0345)Q47.CB, (T0345)F155.CB) [> 4.1951 = 6.9918 < 9.0894] w=0.0174 to align # Constraint # added constraint: constraint((T0345)F64.CB, (T0345)N151.CB) [> 4.3135 = 7.1892 < 9.3460] w=0.0166 to align # Constraint # added constraint: constraint((T0345)L131.CB, (T0345)N151.CB) [> 2.5959 = 4.3264 < 5.6244] w=0.0162 to align # Constraint # added constraint: constraint((T0345)Q47.CB, (T0345)N175.CB) [> 4.6628 = 7.7713 < 10.1027] w=0.0154 to align # Constraint # added constraint: constraint((T0345)H71.CB, (T0345)P142.CB) [> 3.3921 = 5.6535 < 7.3495] w=0.0154 to align # Constraint # added constraint: constraint((T0345)A3.CB, (T0345)R25.CB) [> 3.2230 = 5.3717 < 6.9832] w=0.0154 to align # Constraint # added constraint: constraint((T0345)A3.CB, (T0345)G161.CA) [> 4.7182 = 7.8637 < 10.2229] w=0.0154 to align # Constraint # added constraint: constraint((T0345)I2.CB, (T0345)L156.CB) [> 4.7791 = 7.9652 < 10.3548] w=0.0154 to align # Constraint # added constraint: constraint((T0345)N33.CB, (T0345)I138.CB) [> 3.1756 = 5.2926 < 6.8804] w=0.0153 to align # Constraint # added constraint: constraint((T0345)S141.CB, (T0345)N151.CB) [> 4.4929 = 7.4881 < 9.7345] w=0.0153 to align # Constraint # added constraint: constraint((T0345)C66.CB, (T0345)V143.CB) [> 4.4877 = 7.4796 < 9.7234] w=0.0153 to align # Constraint # added constraint: constraint((T0345)E32.CB, (T0345)L156.CB) [> 4.7940 = 7.9900 < 10.3870] w=0.0148 to align # Constraint # added constraint: constraint((T0345)A35.CB, (T0345)Q68.CB) [> 4.7645 = 7.9409 < 10.3231] w=0.0148 to align # Constraint # added constraint: constraint((T0345)G39.CA, (T0345)C66.CB) [> 4.7467 = 7.9113 < 10.2846] w=0.0111 to align # Constraint # added constraint: constraint((T0345)C66.CB, (T0345)S141.CB) [> 4.1844 = 6.9741 < 9.0663] w=0.0077 to align # Constraint # added constraint: constraint((T0345)A35.CB, (T0345)W140.CB) [> 4.6060 = 7.6766 < 9.9796] w=0.0077 to align # Constraint # added constraint: constraint((T0345)I2.CB, (T0345)F155.CB) [> 4.6776 = 7.7961 < 10.1349] w=0.0077 to align # Constraint # added constraint: constraint((T0345)S5.CB, (T0345)F155.CB) [> 3.9084 = 6.5141 < 8.4683] w=0.0077 to align # Constraint # added constraint: constraint((T0345)A35.CB, (T0345)K136.CB) [> 4.6961 = 7.8269 < 10.1749] w=0.0077 to align # Constraint # added constraint: constraint((T0345)T41.CB, (T0345)V87.CB) [> 3.8231 = 6.3717 < 8.2833] w=0.0077 to align # Constraint # added constraint: constraint((T0345)P124.CB, (T0345)I138.CB) [> 3.4672 = 5.7786 < 7.5122] w=0.0076 to align # Constraint # added constraint: constraint((T0345)S10.CB, (T0345)L131.CB) [> 4.4214 = 7.3690 < 9.5797] w=0.0076 to align # Constraint # added constraint: constraint((T0345)P124.CB, (T0345)R144.CB) [> 4.2778 = 7.1296 < 9.2685] w=0.0076 to align # Constraint # added constraint: constraint((T0345)L62.CB, (T0345)F155.CB) [> 4.0823 = 6.8038 < 8.8449] w=0.0072 to align # Constraint # added constraint: constraint((T0345)L62.CB, (T0345)L156.CB) [> 2.6732 = 4.4554 < 5.7920] w=0.0072 to align # Constraint # added constraint: constraint((T0345)L62.CB, (T0345)I157.CB) [> 4.6769 = 7.7949 < 10.1334] w=0.0072 to align # Constraint # added constraint: constraint((T0345)G63.CA, (T0345)F155.CB) [> 3.1041 = 5.1735 < 6.7256] w=0.0072 to align # Constraint # added constraint: constraint((T0345)G63.CA, (T0345)L156.CB) [> 4.3057 = 7.1761 < 9.3290] w=0.0072 to align # Constraint # added constraint: constraint((T0345)F64.CB, (T0345)F155.CB) [> 4.4125 = 7.3542 < 9.5605] w=0.0072 to align # Constraint # added constraint: constraint((T0345)F64.CB, (T0345)L156.CB) [> 4.5136 = 7.5226 < 9.7794] w=0.0072 to align # Constraint # added constraint: constraint((T0345)G39.CA, (T0345)G63.CA) [> 3.9365 = 6.5608 < 8.5291] w=0.0055 to align # Constraint # added constraint: constraint((T0345)G39.CA, (T0345)F64.CB) [> 4.6310 = 7.7184 < 10.0339] w=0.0055 to align # Constraint # added constraint: constraint((T0345)L62.CB, (T0345)N151.CB) [> 4.6539 = 7.7565 < 10.0835] w=0.0055 to align # Constraint # added constraint: constraint((T0345)G63.CA, (T0345)N151.CB) [> 4.3673 = 7.2789 < 9.4625] w=0.0055 to align # Constraint # added constraint: constraint((T0345)V87.CB, (T0345)L156.CB) [> 4.3649 = 7.2749 < 9.4573] w=0.0049 to align # Constraint # added constraint: constraint((T0345)Q47.CB, (T0345)P65.CB) [> 4.3411 = 7.2352 < 9.4057] w=0.0008 to align # Constraint # added constraint: constraint((T0345)A35.CB, (T0345)Q47.CB) [> 3.2336 = 5.3894 < 7.0062] w=0.0008 to align # SetCost created cost = # ( 1.0000 * align ) # command:# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0345/ # command:# reading script from file servers-clean.under # Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/T0345/decoys/ # ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0345 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_POPULUS_TS1 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0345 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_POPULUS_TS2 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0345 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_POPULUS_TS3 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0345 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_POPULUS_TS4 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0345 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_POPULUS_TS5 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_RECOM_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0345 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_RECOM_TS1 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0345 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_TS1 # ReadConformPDB reading from PDB file servers/3Dpro_TS1.pdb.gz looking for model 1 # Found a chain break before 72 # copying to AlignedFragments data structure # naming current conformation 3Dpro_TS1 # ReadConformPDB reading from PDB file servers/3Dpro_TS2.pdb.gz looking for model 1 # Found a chain break before 72 # copying to AlignedFragments data structure # naming current conformation 3Dpro_TS2 # ReadConformPDB reading from PDB file servers/3Dpro_TS3.pdb.gz looking for model 1 # Found a chain break before 72 # copying to AlignedFragments data structure # naming current conformation 3Dpro_TS3 # ReadConformPDB reading from PDB file servers/3Dpro_TS4.pdb.gz looking for model 1 # Found a chain break before 141 # copying to AlignedFragments data structure # naming current conformation 3Dpro_TS4 # ReadConformPDB reading from PDB file servers/3Dpro_TS5.pdb.gz looking for model 1 # Found a chain break before 72 # copying to AlignedFragments data structure # naming current conformation 3Dpro_TS5 # ReadConformPDB reading from PDB file servers/ABIpro_TS1.pdb.gz looking for model 1 # Found a chain break before 166 # copying to AlignedFragments data structure # naming current conformation ABIpro_TS1 # ReadConformPDB reading from PDB file servers/ABIpro_TS2.pdb.gz looking for model 1 # Found a chain break before 165 # copying to AlignedFragments data structure # naming current conformation ABIpro_TS2 # ReadConformPDB reading from PDB file servers/ABIpro_TS3.pdb.gz looking for model 1 # Found a chain break before 149 # copying to AlignedFragments data structure # naming current conformation ABIpro_TS3 # ReadConformPDB reading from PDB file servers/ABIpro_TS4.pdb.gz looking for model 1 # Found a chain break before 177 # copying to AlignedFragments data structure # naming current conformation ABIpro_TS4 # ReadConformPDB reading from PDB file servers/ABIpro_TS5.pdb.gz looking for model 1 # Found a chain break before 167 # copying to AlignedFragments data structure # naming current conformation ABIpro_TS5 # ReadConformPDB reading from PDB file servers/BayesHH_TS1.pdb.gz looking for model 1 # Found a chain break before 6 # copying to AlignedFragments data structure # naming current conformation BayesHH_TS1 # ReadConformPDB reading from PDB file servers/Bilab-ENABLE_TS1.pdb.gz looking for model 1 # Found a chain break before 72 # copying to AlignedFragments data structure # naming current conformation Bilab-ENABLE_TS1 # ReadConformPDB reading from PDB file servers/Bilab-ENABLE_TS2.pdb.gz looking for model 1 # Found a chain break before 72 # copying to AlignedFragments data structure # naming current conformation Bilab-ENABLE_TS2 # ReadConformPDB reading from PDB file servers/Bilab-ENABLE_TS3.pdb.gz looking for model 1 # Found a chain break before 129 # copying to AlignedFragments data structure # naming current conformation Bilab-ENABLE_TS3 # ReadConformPDB reading from PDB file servers/Bilab-ENABLE_TS4.pdb.gz looking for model 1 # Found a chain break before 147 # copying to AlignedFragments data structure # naming current conformation Bilab-ENABLE_TS4 # ReadConformPDB reading from PDB file servers/Bilab-ENABLE_TS5.pdb.gz looking for model 1 # Found a chain break before 138 # copying to AlignedFragments data structure # naming current conformation Bilab-ENABLE_TS5 # ReadConformPDB reading from PDB file servers/CIRCLE_TS1.pdb.gz looking for model 1 # Found a chain break before 183 # copying to AlignedFragments data structure # naming current conformation CIRCLE_TS1 # ReadConformPDB reading from PDB file servers/CIRCLE_TS2.pdb.gz looking for model 1 # Found a chain break before 177 # copying to AlignedFragments data structure # naming current conformation CIRCLE_TS2 # ReadConformPDB reading from PDB file servers/CIRCLE_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0345 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation CIRCLE_TS3 # ReadConformPDB reading from PDB file servers/CIRCLE_TS4.pdb.gz looking for model 1 # Found a chain break before 172 # copying to AlignedFragments data structure # naming current conformation CIRCLE_TS4 # ReadConformPDB reading from PDB file servers/CIRCLE_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0345 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation CIRCLE_TS5 # ReadConformPDB reading from PDB file servers/CPHmodels_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0345 can't currently be optimized by undertaker # naming current conformation CPHmodels_TS1 # ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0345 can't currently be optimized by undertaker # naming current conformation CaspIta-FOX_TS1 # ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0345 can't currently be optimized by undertaker # naming current conformation CaspIta-FOX_TS2 # ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0345 can't currently be optimized by undertaker # naming current conformation CaspIta-FOX_TS3 # ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0345 can't currently be optimized by undertaker # naming current conformation CaspIta-FOX_TS4 # ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0345 can't currently be optimized by undertaker # naming current conformation CaspIta-FOX_TS5 # ReadConformPDB reading from PDB file servers/Distill_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0345 can't currently be optimized by undertaker # naming current conformation Distill_TS1 # ReadConformPDB reading from PDB file servers/Distill_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0345 can't currently be optimized by undertaker # naming current conformation Distill_TS2 # ReadConformPDB reading from PDB file servers/Distill_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0345 can't currently be optimized by undertaker # naming current conformation Distill_TS3 # ReadConformPDB reading from PDB file servers/Distill_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0345 can't currently be optimized by undertaker # naming current conformation Distill_TS4 # ReadConformPDB reading from PDB file servers/Distill_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0345 can't currently be optimized by undertaker # naming current conformation Distill_TS5 # ReadConformPDB reading from PDB file servers/FAMSD_TS1.pdb.gz looking for model 1 # Found a chain break before 17 # copying to AlignedFragments data structure # naming current conformation FAMSD_TS1 # ReadConformPDB reading from PDB file servers/FAMSD_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0345 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation FAMSD_TS2 # ReadConformPDB reading from PDB file servers/FAMSD_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0345 can't currently be optimized by undertaker # naming current conformation FAMSD_TS3 # ReadConformPDB reading from PDB file servers/FAMSD_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0345 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation FAMSD_TS4 # ReadConformPDB reading from PDB file servers/FAMSD_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0345 can't currently be optimized by undertaker # naming current conformation FAMSD_TS5 # ReadConformPDB reading from PDB file servers/FAMS_TS1.pdb.gz looking for model 1 # Found a chain break before 177 # copying to AlignedFragments data structure # naming current conformation FAMS_TS1 # ReadConformPDB reading from PDB file servers/FAMS_TS2.pdb.gz looking for model 1 # Found a chain break before 184 # copying to AlignedFragments data structure # naming current conformation FAMS_TS2 # ReadConformPDB reading from PDB file servers/FAMS_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0345 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation FAMS_TS3 # ReadConformPDB reading from PDB file servers/FAMS_TS4.pdb.gz looking for model 1 # Found a chain break before 127 # copying to AlignedFragments data structure # naming current conformation FAMS_TS4 # ReadConformPDB reading from PDB file servers/FAMS_TS5.pdb.gz looking for model 1 # Found a chain break before 177 # copying to AlignedFragments data structure # naming current conformation FAMS_TS5 # ReadConformPDB reading from PDB file servers/FOLDpro_TS1.pdb.gz looking for model 1 # Found a chain break before 72 # copying to AlignedFragments data structure # naming current conformation FOLDpro_TS1 # ReadConformPDB reading from PDB file servers/FOLDpro_TS2.pdb.gz looking for model 1 # Found a chain break before 72 # copying to AlignedFragments data structure # naming current conformation FOLDpro_TS2 # ReadConformPDB reading from PDB file servers/FOLDpro_TS3.pdb.gz looking for model 1 # Found a chain break before 72 # copying to AlignedFragments data structure # naming current conformation FOLDpro_TS3 # ReadConformPDB reading from PDB file servers/FOLDpro_TS4.pdb.gz looking for model 1 # Found a chain break before 139 # copying to AlignedFragments data structure # naming current conformation FOLDpro_TS4 # ReadConformPDB reading from PDB file servers/FOLDpro_TS5.pdb.gz looking for model 1 # Found a chain break before 72 # copying to AlignedFragments data structure # naming current conformation FOLDpro_TS5 # ReadConformPDB reading from PDB file servers/FORTE1_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0345 can't currently be optimized by undertaker # naming current conformation FORTE1_AL1 # ReadConformPDB reading from PDB file servers/FORTE1_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0345 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation FORTE1_AL2 # ReadConformPDB reading from PDB file servers/FORTE1_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0345 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation FORTE1_AL3 # ReadConformPDB reading from PDB file servers/FORTE1_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0345 can't currently be optimized by undertaker # naming current conformation FORTE1_AL4 # ReadConformPDB reading from PDB file servers/FORTE1_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0345 can't currently be optimized by undertaker # naming current conformation FORTE1_AL5 # ReadConformPDB reading from PDB file servers/FORTE2_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0345 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation FORTE2_AL1 # ReadConformPDB reading from PDB file servers/FORTE2_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0345 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation FORTE2_AL2 # ReadConformPDB reading from PDB file servers/FORTE2_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0345 can't currently be optimized by undertaker # naming current conformation FORTE2_AL3 # ReadConformPDB reading from PDB file servers/FORTE2_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0345 can't currently be optimized by undertaker # naming current conformation FORTE2_AL4 # ReadConformPDB reading from PDB file servers/FORTE2_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0345 can't currently be optimized by undertaker # naming current conformation FORTE2_AL5 # ReadConformPDB reading from PDB file servers/FPSOLVER-SERVER_TS1.pdb.gz looking for model 1 # Found a chain break before 184 # copying to AlignedFragments data structure # naming current conformation FPSOLVER-SERVER_TS1 # ReadConformPDB reading from PDB file servers/FPSOLVER-SERVER_TS2.pdb.gz looking for model 1 # Found a chain break before 177 # copying to AlignedFragments data structure # naming current conformation FPSOLVER-SERVER_TS2 # ReadConformPDB reading from PDB file servers/FPSOLVER-SERVER_TS3.pdb.gz looking for model 1 # Found a chain break before 169 # copying to AlignedFragments data structure # naming current conformation FPSOLVER-SERVER_TS3 # ReadConformPDB reading from PDB file servers/FPSOLVER-SERVER_TS4.pdb.gz looking for model 1 # Found a chain break before 157 # copying to AlignedFragments data structure # naming current conformation FPSOLVER-SERVER_TS4 # ReadConformPDB reading from PDB file servers/FPSOLVER-SERVER_TS5.pdb.gz looking for model 1 # Found a chain break before 181 # copying to AlignedFragments data structure # naming current conformation FPSOLVER-SERVER_TS5 # ReadConformPDB reading from PDB file servers/FUGMOD_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0345 can't currently be optimized by undertaker # naming current conformation FUGMOD_TS1 # ReadConformPDB reading from PDB file servers/FUGMOD_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0345 can't currently be optimized by undertaker # naming current conformation FUGMOD_TS2 # ReadConformPDB reading from PDB file servers/FUGMOD_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0345 can't currently be optimized by undertaker # naming current conformation FUGMOD_TS3 # ReadConformPDB reading from PDB file servers/FUGMOD_TS4.pdb.gz looking for model 1 # Found a chain break before 171 # copying to AlignedFragments data structure # naming current conformation FUGMOD_TS4 # ReadConformPDB reading from PDB file servers/FUGMOD_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0345 can't currently be optimized by undertaker # naming current conformation FUGMOD_TS5 # ReadConformPDB reading from PDB file servers/FUGUE_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0345 can't currently be optimized by undertaker # naming current conformation FUGUE_AL1 # ReadConformPDB reading from PDB file servers/FUGUE_AL2.pdb.gz looking for model 1 Skipped atom 382, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL2.pdb.gz Skipped atom 384, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL2.pdb.gz Skipped atom 386, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL2.pdb.gz Skipped atom 388, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL2.pdb.gz Skipped atom 390, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL2.pdb.gz Skipped atom 392, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL2.pdb.gz Skipped atom 394, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL2.pdb.gz Skipped atom 396, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL2.pdb.gz Skipped atom 398, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL2.pdb.gz Skipped atom 400, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL2.pdb.gz Skipped atom 402, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL2.pdb.gz Skipped atom 404, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL2.pdb.gz Skipped atom 406, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL2.pdb.gz Skipped atom 408, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL2.pdb.gz Skipped atom 410, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL2.pdb.gz Skipped atom 412, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL2.pdb.gz # WARNING: incomplete conformation T0345 can't currently be optimized by undertaker # naming current conformation FUGUE_AL2 # ReadConformPDB reading from PDB file servers/FUGUE_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0345 can't currently be optimized by undertaker # naming current conformation FUGUE_AL3 # ReadConformPDB reading from PDB file servers/FUGUE_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0345 can't currently be optimized by undertaker # naming current conformation FUGUE_AL4 # ReadConformPDB reading from PDB file servers/FUGUE_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0345 can't currently be optimized by undertaker # naming current conformation FUGUE_AL5 # ReadConformPDB reading from PDB file servers/FUNCTION_TS1.pdb.gz looking for model 1 # Found a chain break before 163 # copying to AlignedFragments data structure # naming current conformation FUNCTION_TS1 # ReadConformPDB reading from PDB file servers/FUNCTION_TS2.pdb.gz looking for model 1 # Found a chain break before 127 # copying to AlignedFragments data structure # naming current conformation FUNCTION_TS2 # ReadConformPDB reading from PDB file servers/FUNCTION_TS3.pdb.gz looking for model 1 # Found a chain break before 172 # copying to AlignedFragments data structure # naming current conformation FUNCTION_TS3 # ReadConformPDB reading from PDB file servers/FUNCTION_TS4.pdb.gz looking for model 1 # Found a chain break before 184 # copying to AlignedFragments data structure # naming current conformation FUNCTION_TS4 # ReadConformPDB reading from PDB file servers/FUNCTION_TS5.pdb.gz looking for model 1 # Found a chain break before 172 # copying to AlignedFragments data structure # naming current conformation FUNCTION_TS5 # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS1.pdb.gz looking for model 1 # Found a chain break before 72 # copying to AlignedFragments data structure # naming current conformation GeneSilicoMetaServer_TS1 # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS2.pdb.gz looking for model 1 # Found a chain break before 72 # copying to AlignedFragments data structure # naming current conformation GeneSilicoMetaServer_TS2 # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0345 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation GeneSilicoMetaServer_TS3 # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS4.pdb.gz looking for model 1 # Found a chain break before 72 # copying to AlignedFragments data structure # naming current conformation GeneSilicoMetaServer_TS4 # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS5.pdb.gz looking for model 1 # Found a chain break before 177 # copying to AlignedFragments data structure # naming current conformation GeneSilicoMetaServer_TS5 # ReadConformPDB reading from PDB file servers/HHpred1_TS1.pdb.gz looking for model 1 # Found a chain break before 72 # copying to AlignedFragments data structure # naming current conformation HHpred1_TS1 # ReadConformPDB reading from PDB file servers/HHpred2_TS1.pdb.gz looking for model 1 # Found a chain break before 152 # copying to AlignedFragments data structure # naming current conformation HHpred2_TS1 # ReadConformPDB reading from PDB file servers/HHpred3_TS1.pdb.gz looking for model 1 # Found a chain break before 68 # copying to AlignedFragments data structure # naming current conformation HHpred3_TS1 # ReadConformPDB reading from PDB file servers/Huber-Torda-Server_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0345 can't currently be optimized by undertaker # naming current conformation Huber-Torda-Server_TS1 # ReadConformPDB reading from PDB file servers/Huber-Torda-Server_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0345 can't currently be optimized by undertaker # naming current conformation Huber-Torda-Server_TS2 # ReadConformPDB reading from PDB file servers/Huber-Torda-Server_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0345 can't currently be optimized by undertaker # naming current conformation Huber-Torda-Server_TS3 # ReadConformPDB reading from PDB file servers/Huber-Torda-Server_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0345 can't currently be optimized by undertaker # naming current conformation Huber-Torda-Server_TS4 # ReadConformPDB reading from PDB file servers/Huber-Torda-Server_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0345 can't currently be optimized by undertaker # naming current conformation Huber-Torda-Server_TS5 # ReadConformPDB reading from PDB file servers/LOOPP_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0345 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation LOOPP_TS1 # ReadConformPDB reading from PDB file servers/LOOPP_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0345 can't currently be optimized by undertaker # naming current conformation LOOPP_TS2 # ReadConformPDB reading from PDB file servers/LOOPP_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0345 can't currently be optimized by undertaker # naming current conformation LOOPP_TS3 # ReadConformPDB reading from PDB file servers/LOOPP_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0345 can't currently be optimized by undertaker # naming current conformation LOOPP_TS4 # ReadConformPDB reading from PDB file servers/LOOPP_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0345 can't currently be optimized by undertaker # naming current conformation LOOPP_TS5 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server2_TS1.pdb.gz looking for model 1 # Found a chain break before 72 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server2_TS1 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server2_TS2.pdb.gz looking for model 1 # Found a chain break before 72 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server2_TS2 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server2_TS3.pdb.gz looking for model 1 # Found a chain break before 169 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server2_TS3 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server2_TS4.pdb.gz looking for model 1 # Found a chain break before 123 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server2_TS4 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server2_TS5.pdb.gz looking for model 1 # Found a chain break before 151 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server2_TS5 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS1.pdb.gz looking for model 1 # Found a chain break before 72 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server_TS1 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS2.pdb.gz looking for model 1 # Found a chain break before 138 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server_TS2 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS3.pdb.gz looking for model 1 # Found a chain break before 123 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server_TS3 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS4.pdb.gz looking for model 1 # Found a chain break before 103 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server_TS4 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS5.pdb.gz looking for model 1 # Found a chain break before 84 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server_TS5 # ReadConformPDB reading from PDB file servers/MetaTasser_TS1.pdb.gz looking for model 1 # Found a chain break before 165 # copying to AlignedFragments data structure # naming current conformation MetaTasser_TS1 # ReadConformPDB reading from PDB file servers/MetaTasser_TS2.pdb.gz looking for model 1 # Found a chain break before 180 # copying to AlignedFragments data structure # naming current conformation MetaTasser_TS2 # ReadConformPDB reading from PDB file servers/MetaTasser_TS3.pdb.gz looking for model 1 # Found a chain break before 183 # copying to AlignedFragments data structure # naming current conformation MetaTasser_TS3 # ReadConformPDB reading from PDB file servers/MetaTasser_TS4.pdb.gz looking for model 1 # Found a chain break before 181 # copying to AlignedFragments data structure # naming current conformation MetaTasser_TS4 # ReadConformPDB reading from PDB file servers/MetaTasser_TS5.pdb.gz looking for model 1 # Found a chain break before 168 # copying to AlignedFragments data structure # naming current conformation MetaTasser_TS5 # ReadConformPDB reading from PDB file servers/NN_PUT_lab_TS1.pdb.gz looking for model 1 # Found a chain break before 72 # copying to AlignedFragments data structure # naming current conformation NN_PUT_lab_TS1 # ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS1.pdb.gz looking for model 1 # naming current conformation PROTINFO-AB_TS1 # ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS2.pdb.gz looking for model 1 # naming current conformation PROTINFO-AB_TS2 # ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS3.pdb.gz looking for model 1 # naming current conformation PROTINFO-AB_TS3 # ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS4.pdb.gz looking for model 1 # naming current conformation PROTINFO-AB_TS4 # ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS5.pdb.gz looking for model 1 # naming current conformation PROTINFO-AB_TS5 # ReadConformPDB reading from PDB file servers/PROTINFO_TS1.pdb.gz looking for model 1 # Found a chain break before 103 # copying to AlignedFragments data structure # naming current conformation PROTINFO_TS1 # ReadConformPDB reading from PDB file servers/PROTINFO_TS2.pdb.gz looking for model 1 # Found a chain break before 67 # copying to AlignedFragments data structure # naming current conformation PROTINFO_TS2 # ReadConformPDB reading from PDB file servers/PROTINFO_TS3.pdb.gz looking for model 1 # Found a chain break before 158 # copying to AlignedFragments data structure # naming current conformation PROTINFO_TS3 # ReadConformPDB reading from PDB file servers/PROTINFO_TS4.pdb.gz looking for model 1 # Found a chain break before 171 # copying to AlignedFragments data structure # naming current conformation PROTINFO_TS4 # ReadConformPDB reading from PDB file servers/PROTINFO_TS5.pdb.gz looking for model 1 # Found a chain break before 103 # copying to AlignedFragments data structure # naming current conformation PROTINFO_TS5 # ReadConformPDB reading from PDB file servers/Pcons6_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0345 can't currently be optimized by undertaker # naming current conformation Pcons6_TS1 # ReadConformPDB reading from PDB file servers/Pcons6_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0345 can't currently be optimized by undertaker # naming current conformation Pcons6_TS2 # ReadConformPDB reading from PDB file servers/Pcons6_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0345 can't currently be optimized by undertaker # naming current conformation Pcons6_TS3 # ReadConformPDB reading from PDB file servers/Pcons6_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0345 can't currently be optimized by undertaker # naming current conformation Pcons6_TS4 # ReadConformPDB reading from PDB file servers/Pcons6_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0345 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation Pcons6_TS5 # ReadConformPDB reading from PDB file servers/Phyre-1_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0345 can't currently be optimized by undertaker # naming current conformation Phyre-1_TS1 # ReadConformPDB reading from PDB file servers/Phyre-2_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0345 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation Phyre-2_TS1 # ReadConformPDB reading from PDB file servers/Phyre-2_TS2.pdb.gz looking for model 1 # Found a chain break before 152 # copying to AlignedFragments data structure # naming current conformation Phyre-2_TS2 # ReadConformPDB reading from PDB file servers/Phyre-2_TS3.pdb.gz looking for model 1 # Found a chain break before 152 # copying to AlignedFragments data structure # naming current conformation Phyre-2_TS3 # ReadConformPDB reading from PDB file servers/Phyre-2_TS4.pdb.gz looking for model 1 # Found a chain break before 152 # copying to AlignedFragments data structure # naming current conformation Phyre-2_TS4 # ReadConformPDB reading from PDB file servers/Phyre-2_TS5.pdb.gz looking for model 1 # Found a chain break before 152 # copying to AlignedFragments data structure # naming current conformation Phyre-2_TS5 # ReadConformPDB reading from PDB file servers/Pmodeller6_TS1.pdb.gz looking for model 1 # Found a chain break before 152 # copying to AlignedFragments data structure # naming current conformation Pmodeller6_TS1 # ReadConformPDB reading from PDB file servers/Pmodeller6_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0345 can't currently be optimized by undertaker # naming current conformation Pmodeller6_TS2 # ReadConformPDB reading from PDB file servers/Pmodeller6_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0345 can't currently be optimized by undertaker # naming current conformation Pmodeller6_TS3 # ReadConformPDB reading from PDB file servers/Pmodeller6_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0345 can't currently be optimized by undertaker # naming current conformation Pmodeller6_TS4 # ReadConformPDB reading from PDB file servers/Pmodeller6_TS5.pdb.gz looking for model 1 # Found a chain break before 152 # copying to AlignedFragments data structure # naming current conformation Pmodeller6_TS5 # ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS1.pdb.gz looking for model 1 # Found a chain break before 129 # copying to AlignedFragments data structure # naming current conformation RAPTOR-ACE_TS1 # ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS2.pdb.gz looking for model 1 # Found a chain break before 72 # copying to AlignedFragments data structure # naming current conformation RAPTOR-ACE_TS2 # ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS3.pdb.gz looking for model 1 # Found a chain break before 72 # copying to AlignedFragments data structure # naming current conformation RAPTOR-ACE_TS3 # ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS4.pdb.gz looking for model 1 # Found a chain break before 138 # copying to AlignedFragments data structure # naming current conformation RAPTOR-ACE_TS4 # ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS5.pdb.gz looking for model 1 # Found a chain break before 72 # copying to AlignedFragments data structure # naming current conformation RAPTOR-ACE_TS5 # ReadConformPDB reading from PDB file servers/RAPTORESS_TS1.pdb.gz looking for model 1 # Found a chain break before 152 # copying to AlignedFragments data structure # naming current conformation RAPTORESS_TS1 # ReadConformPDB reading from PDB file servers/RAPTORESS_TS2.pdb.gz looking for model 1 # Found a chain break before 158 # copying to AlignedFragments data structure # naming current conformation RAPTORESS_TS2 # ReadConformPDB reading from PDB file servers/RAPTORESS_TS3.pdb.gz looking for model 1 # Found a chain break before 142 # copying to AlignedFragments data structure # naming current conformation RAPTORESS_TS3 # ReadConformPDB reading from PDB file servers/RAPTORESS_TS4.pdb.gz looking for model 1 # Found a chain break before 151 # copying to AlignedFragments data structure # naming current conformation RAPTORESS_TS4 # ReadConformPDB reading from PDB file servers/RAPTORESS_TS5.pdb.gz looking for model 1 # Found a chain break before 151 # copying to AlignedFragments data structure # naming current conformation RAPTORESS_TS5 # ReadConformPDB reading from PDB file servers/RAPTOR_TS1.pdb.gz looking for model 1 # Found a chain break before 72 # copying to AlignedFragments data structure # naming current conformation RAPTOR_TS1 # ReadConformPDB reading from PDB file servers/RAPTOR_TS2.pdb.gz looking for model 1 # Found a chain break before 138 # copying to AlignedFragments data structure # naming current conformation RAPTOR_TS2 # ReadConformPDB reading from PDB file servers/RAPTOR_TS3.pdb.gz looking for model 1 # Found a chain break before 140 # copying to AlignedFragments data structure # naming current conformation RAPTOR_TS3 # ReadConformPDB reading from PDB file servers/RAPTOR_TS4.pdb.gz looking for model 1 # Found a chain break before 151 # copying to AlignedFragments data structure # naming current conformation RAPTOR_TS4 # ReadConformPDB reading from PDB file servers/RAPTOR_TS5.pdb.gz looking for model 1 # Found a chain break before 151 # copying to AlignedFragments data structure # naming current conformation RAPTOR_TS5 # ReadConformPDB reading from PDB file servers/ROBETTA_TS1.pdb.gz looking for model 1 # Found a chain break before 152 # copying to AlignedFragments data structure # naming current conformation ROBETTA_TS1 # ReadConformPDB reading from PDB file servers/ROBETTA_TS2.pdb.gz looking for model 1 # Found a chain break before 152 # copying to AlignedFragments data structure # naming current conformation ROBETTA_TS2 # ReadConformPDB reading from PDB file servers/ROBETTA_TS3.pdb.gz looking for model 1 # Found a chain break before 152 # copying to AlignedFragments data structure # naming current conformation ROBETTA_TS3 # ReadConformPDB reading from PDB file servers/ROBETTA_TS4.pdb.gz looking for model 1 # Found a chain break before 152 # copying to AlignedFragments data structure # naming current conformation ROBETTA_TS4 # ReadConformPDB reading from PDB file servers/ROBETTA_TS5.pdb.gz looking for model 1 # Found a chain break before 152 # copying to AlignedFragments data structure # naming current conformation ROBETTA_TS5 # ReadConformPDB reading from PDB file servers/ROKKY_TS1.pdb.gz looking for model 1 # Found a chain break before 72 # copying to AlignedFragments data structure # naming current conformation ROKKY_TS1 # ReadConformPDB reading from PDB file servers/ROKKY_TS2.pdb.gz looking for model 1 # Found a chain break before 72 # copying to AlignedFragments data structure # naming current conformation ROKKY_TS2 # ReadConformPDB reading from PDB file servers/ROKKY_TS3.pdb.gz looking for model 1 # Found a chain break before 175 # copying to AlignedFragments data structure # naming current conformation ROKKY_TS3 # ReadConformPDB reading from PDB file servers/SAM-T02_AL1.pdb.gz looking for model 1 Skipped atom 31, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL1.pdb.gz Skipped atom 76, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL1.pdb.gz Skipped atom 137, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL1.pdb.gz Skipped atom 190, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL1.pdb.gz Skipped atom 399, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL1.pdb.gz Skipped atom 508, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL1.pdb.gz Skipped atom 509, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL1.pdb.gz Skipped atom 558, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL1.pdb.gz Skipped atom 675, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL1.pdb.gz Skipped atom 704, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL1.pdb.gz # WARNING: incomplete conformation T0345 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation SAM-T02_AL1 # ReadConformPDB reading from PDB file servers/SAM-T02_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0345 can't currently be optimized by undertaker # naming current conformation SAM-T02_AL2 # ReadConformPDB reading from PDB file servers/SAM-T02_AL3.pdb.gz looking for model 1 Skipped atom 3, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL3.pdb.gz Skipped atom 580, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL3.pdb.gz # WARNING: incomplete conformation T0345 can't currently be optimized by undertaker # naming current conformation SAM-T02_AL3 # ReadConformPDB reading from PDB file servers/SAM-T02_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0345 can't currently be optimized by undertaker # naming current conformation SAM-T02_AL4 # ReadConformPDB reading from PDB file servers/SAM-T02_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0345 can't currently be optimized by undertaker # naming current conformation SAM-T02_AL5 # ReadConformPDB reading from PDB file servers/SAM-T99_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0345 can't currently be optimized by undertaker # naming current conformation SAM-T99_AL1 # ReadConformPDB reading from PDB file servers/SAM-T99_AL2.pdb.gz looking for model 1 Skipped atom 31, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL2.pdb.gz Skipped atom 76, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL2.pdb.gz Skipped atom 137, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL2.pdb.gz Skipped atom 194, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL2.pdb.gz Skipped atom 403, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL2.pdb.gz Skipped atom 512, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL2.pdb.gz Skipped atom 513, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL2.pdb.gz Skipped atom 562, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL2.pdb.gz Skipped atom 679, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL2.pdb.gz Skipped atom 708, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL2.pdb.gz # WARNING: incomplete conformation T0345 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation SAM-T99_AL2 # ReadConformPDB reading from PDB file servers/SAM-T99_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0345 can't currently be optimized by undertaker # naming current conformation SAM-T99_AL3 # ReadConformPDB reading from PDB file servers/SAM-T99_AL4.pdb.gz looking for model 1 Skipped atom 71, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL4.pdb.gz Skipped atom 80, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL4.pdb.gz Skipped atom 89, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL4.pdb.gz Skipped atom 170, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL4.pdb.gz Skipped atom 179, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL4.pdb.gz Skipped atom 300, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL4.pdb.gz Skipped atom 397, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL4.pdb.gz Skipped atom 506, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL4.pdb.gz Skipped atom 555, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL4.pdb.gz Skipped atom 648, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL4.pdb.gz Skipped atom 673, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL4.pdb.gz Skipped atom 718, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL4.pdb.gz # WARNING: incomplete conformation T0345 can't currently be optimized by undertaker # naming current conformation SAM-T99_AL4 # ReadConformPDB reading from PDB file servers/SAM-T99_AL5.pdb.gz looking for model 1 Skipped atom 7, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL5.pdb.gz Skipped atom 584, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL5.pdb.gz # WARNING: incomplete conformation T0345 can't currently be optimized by undertaker # naming current conformation SAM-T99_AL5 # ReadConformPDB reading from PDB file servers/SAM_T06_server_TS1.pdb.gz looking for model 1 # Found a chain break before 156 # copying to AlignedFragments data structure # naming current conformation SAM_T06_server_TS1 # ReadConformPDB reading from PDB file servers/SAM_T06_server_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0345 can't currently be optimized by undertaker # naming current conformation SAM_T06_server_TS2 # ReadConformPDB reading from PDB file servers/SAM_T06_server_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0345 can't currently be optimized by undertaker # naming current conformation SAM_T06_server_TS3 # ReadConformPDB reading from PDB file servers/SAM_T06_server_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0345 can't currently be optimized by undertaker # naming current conformation SAM_T06_server_TS4 # ReadConformPDB reading from PDB file servers/SAM_T06_server_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0345 can't currently be optimized by undertaker # naming current conformation SAM_T06_server_TS5 # ReadConformPDB reading from PDB file servers/SP3_TS1.pdb.gz looking for model 1 # Found a chain break before 138 # copying to AlignedFragments data structure # naming current conformation SP3_TS1 # ReadConformPDB reading from PDB file servers/SP3_TS2.pdb.gz looking for model 1 # naming current conformation SP3_TS2 # ReadConformPDB reading from PDB file servers/SP3_TS3.pdb.gz looking for model 1 # Found a chain break before 151 # copying to AlignedFragments data structure # naming current conformation SP3_TS3 # ReadConformPDB reading from PDB file servers/SP3_TS4.pdb.gz looking for model 1 # Found a chain break before 169 # copying to AlignedFragments data structure # naming current conformation SP3_TS4 # ReadConformPDB reading from PDB file servers/SP3_TS5.pdb.gz looking for model 1 # Found a chain break before 154 # copying to AlignedFragments data structure # naming current conformation SP3_TS5 # ReadConformPDB reading from PDB file servers/SP4_TS1.pdb.gz looking for model 1 # Found a chain break before 72 # copying to AlignedFragments data structure # naming current conformation SP4_TS1 # ReadConformPDB reading from PDB file servers/SP4_TS2.pdb.gz looking for model 1 # Found a chain break before 123 # copying to AlignedFragments data structure # naming current conformation SP4_TS2 # ReadConformPDB reading from PDB file servers/SP4_TS3.pdb.gz looking for model 1 # Found a chain break before 151 # copying to AlignedFragments data structure # naming current conformation SP4_TS3 # ReadConformPDB reading from PDB file servers/SP4_TS4.pdb.gz looking for model 1 # Found a chain break before 171 # copying to AlignedFragments data structure # naming current conformation SP4_TS4 # ReadConformPDB reading from PDB file servers/SP4_TS5.pdb.gz looking for model 1 # Found a chain break before 151 # copying to AlignedFragments data structure # naming current conformation SP4_TS5 # ReadConformPDB reading from PDB file servers/SPARKS2_TS1.pdb.gz looking for model 1 # Found a chain break before 72 # copying to AlignedFragments data structure # naming current conformation SPARKS2_TS1 # ReadConformPDB reading from PDB file servers/SPARKS2_TS2.pdb.gz looking for model 1 # Found a chain break before 5 # copying to AlignedFragments data structure # naming current conformation SPARKS2_TS2 # ReadConformPDB reading from PDB file servers/SPARKS2_TS3.pdb.gz looking for model 1 # Found a chain break before 172 # copying to AlignedFragments data structure # naming current conformation SPARKS2_TS3 # ReadConformPDB reading from PDB file servers/SPARKS2_TS4.pdb.gz looking for model 1 # Found a chain break before 151 # copying to AlignedFragments data structure # naming current conformation SPARKS2_TS4 # ReadConformPDB reading from PDB file servers/SPARKS2_TS5.pdb.gz looking for model 1 # Found a chain break before 151 # copying to AlignedFragments data structure # naming current conformation SPARKS2_TS5 # ReadConformPDB reading from PDB file servers/UNI-EID_bnmx_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0345 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation UNI-EID_bnmx_TS1 # ReadConformPDB reading from PDB file servers/UNI-EID_bnmx_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0345 can't currently be optimized by undertaker # naming current conformation UNI-EID_bnmx_TS2 # ReadConformPDB reading from PDB file servers/UNI-EID_bnmx_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0345 can't currently be optimized by undertaker # naming current conformation UNI-EID_bnmx_TS3 # ReadConformPDB reading from PDB file servers/UNI-EID_bnmx_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0345 can't currently be optimized by undertaker # naming current conformation UNI-EID_bnmx_TS4 # ReadConformPDB reading from PDB file servers/UNI-EID_bnmx_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0345 can't currently be optimized by undertaker # naming current conformation UNI-EID_bnmx_TS5 # ReadConformPDB reading from PDB file servers/UNI-EID_expm_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0345 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation UNI-EID_expm_TS1 # ReadConformPDB reading from PDB file servers/UNI-EID_sfst_AL1.pdb.gz looking for model 1 Skipped atom 31, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL1.pdb.gz Skipped atom 76, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL1.pdb.gz Skipped atom 137, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL1.pdb.gz Skipped atom 194, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL1.pdb.gz Skipped atom 403, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL1.pdb.gz Skipped atom 512, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL1.pdb.gz Skipped atom 513, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL1.pdb.gz Skipped atom 562, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL1.pdb.gz Skipped atom 679, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL1.pdb.gz Skipped atom 708, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL1.pdb.gz # WARNING: incomplete conformation T0345 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation UNI-EID_sfst_AL1 # ReadConformPDB reading from PDB file servers/UNI-EID_sfst_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0345 can't currently be optimized by undertaker # naming current conformation UNI-EID_sfst_AL2 # ReadConformPDB reading from PDB file servers/UNI-EID_sfst_AL3.pdb.gz looking for model 1 Skipped atom 3, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL3.pdb.gz Skipped atom 584, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL3.pdb.gz # WARNING: incomplete conformation T0345 can't currently be optimized by undertaker # naming current conformation UNI-EID_sfst_AL3 # ReadConformPDB reading from PDB file servers/UNI-EID_sfst_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0345 can't currently be optimized by undertaker # naming current conformation UNI-EID_sfst_AL4 # ReadConformPDB reading from PDB file servers/UNI-EID_sfst_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0345 can't currently be optimized by undertaker # naming current conformation UNI-EID_sfst_AL5 # ReadConformPDB reading from PDB file servers/Zhang-Server_TS1.pdb.gz looking for model 1 # Found a chain break before 128 # copying to AlignedFragments data structure # naming current conformation Zhang-Server_TS1 # ReadConformPDB reading from PDB file servers/Zhang-Server_TS2.pdb.gz looking for model 1 # Found a chain break before 141 # copying to AlignedFragments data structure # naming current conformation Zhang-Server_TS2 # ReadConformPDB reading from PDB file servers/Zhang-Server_TS3.pdb.gz looking for model 1 # Found a chain break before 152 # copying to AlignedFragments data structure # naming current conformation Zhang-Server_TS3 # ReadConformPDB reading from PDB file servers/Zhang-Server_TS4.pdb.gz looking for model 1 # Found a chain break before 141 # copying to AlignedFragments data structure # naming current conformation Zhang-Server_TS4 # ReadConformPDB reading from PDB file servers/Zhang-Server_TS5.pdb.gz looking for model 1 # Found a chain break before 151 # copying to AlignedFragments data structure # naming current conformation Zhang-Server_TS5 # ReadConformPDB reading from PDB file servers/beautshot_TS1.pdb.gz looking for model 1 # Found a chain break before 175 # copying to AlignedFragments data structure # naming current conformation beautshot_TS1 # ReadConformPDB reading from PDB file servers/beautshotbase_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0345 can't currently be optimized by undertaker # naming current conformation beautshotbase_TS1 # ReadConformPDB reading from PDB file servers/forecast-s_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0345 can't currently be optimized by undertaker # naming current conformation forecast-s_AL1 # ReadConformPDB reading from PDB file servers/forecast-s_AL2.pdb.gz looking for model 1 Skipped atom 382, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL2.pdb.gz Skipped atom 384, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL2.pdb.gz Skipped atom 386, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL2.pdb.gz Skipped atom 388, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL2.pdb.gz Skipped atom 390, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL2.pdb.gz Skipped atom 392, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL2.pdb.gz Skipped atom 394, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL2.pdb.gz Skipped atom 396, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL2.pdb.gz Skipped atom 398, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL2.pdb.gz Skipped atom 400, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL2.pdb.gz Skipped atom 402, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL2.pdb.gz Skipped atom 404, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL2.pdb.gz Skipped atom 406, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL2.pdb.gz Skipped atom 408, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL2.pdb.gz Skipped atom 410, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL2.pdb.gz Skipped atom 412, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL2.pdb.gz # WARNING: incomplete conformation T0345 can't currently be optimized by undertaker # naming current conformation forecast-s_AL2 # ReadConformPDB reading from PDB file servers/forecast-s_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0345 can't currently be optimized by undertaker # naming current conformation forecast-s_AL3 # ReadConformPDB reading from PDB file servers/forecast-s_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0345 can't currently be optimized by undertaker # naming current conformation forecast-s_AL4 # ReadConformPDB reading from PDB file servers/forecast-s_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0345 can't currently be optimized by undertaker # naming current conformation forecast-s_AL5 # ReadConformPDB reading from PDB file servers/gtg_AL1.pdb.gz looking for model 1 Skipped atom 158, because occupancy 1.000 <= existing 1.000 in servers/gtg_AL1.pdb.gz Skipped atom 160, because occupancy 1.000 <= existing 1.000 in servers/gtg_AL1.pdb.gz Skipped atom 162, because occupancy 1.000 <= existing 1.000 in servers/gtg_AL1.pdb.gz Skipped atom 164, because occupancy 1.000 <= existing 1.000 in servers/gtg_AL1.pdb.gz Skipped atom 258, because occupancy 1.000 <= existing 1.000 in servers/gtg_AL1.pdb.gz Skipped atom 260, because occupancy 1.000 <= existing 1.000 in servers/gtg_AL1.pdb.gz Skipped atom 262, because occupancy 1.000 <= existing 1.000 in servers/gtg_AL1.pdb.gz Skipped atom 264, because occupancy 1.000 <= existing 1.000 in servers/gtg_AL1.pdb.gz # WARNING: incomplete conformation T0345 can't currently be optimized by undertaker # naming current conformation gtg_AL1 # ReadConformPDB reading from PDB file servers/gtg_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0345 can't currently be optimized by undertaker # naming current conformation gtg_AL2 # ReadConformPDB reading from PDB file servers/gtg_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0345 can't currently be optimized by undertaker # naming current conformation gtg_AL3 # ReadConformPDB reading from PDB file servers/gtg_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0345 can't currently be optimized by undertaker # naming current conformation gtg_AL4 # ReadConformPDB reading from PDB file servers/gtg_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0345 can't currently be optimized by undertaker # naming current conformation gtg_AL5 # ReadConformPDB reading from PDB file servers/karypis.srv.2_TS1.pdb.gz looking for model 1 # Found a chain break before 122 # copying to AlignedFragments data structure # naming current conformation karypis.srv.2_TS1 # ReadConformPDB reading from PDB file servers/karypis.srv.2_TS2.pdb.gz looking for model 1 # Found a chain break before 159 # copying to AlignedFragments data structure # naming current conformation karypis.srv.2_TS2 # ReadConformPDB reading from PDB file servers/karypis.srv.2_TS3.pdb.gz looking for model 1 # Found a chain break before 149 # copying to AlignedFragments data structure # naming current conformation karypis.srv.2_TS3 # ReadConformPDB reading from PDB file servers/karypis.srv.2_TS4.pdb.gz looking for model 1 # Found a chain break before 167 # copying to AlignedFragments data structure # naming current conformation karypis.srv.2_TS4 # ReadConformPDB reading from PDB file servers/karypis.srv.2_TS5.pdb.gz looking for model 1 # Found a chain break before 144 # copying to AlignedFragments data structure # naming current conformation karypis.srv.2_TS5 # ReadConformPDB reading from PDB file servers/karypis.srv.4_TS1.pdb.gz looking for model 1 # Found a chain break before 182 # copying to AlignedFragments data structure # naming current conformation karypis.srv.4_TS1 # ReadConformPDB reading from PDB file servers/karypis.srv.4_TS2.pdb.gz looking for model 1 # Found a chain break before 183 # copying to AlignedFragments data structure # naming current conformation karypis.srv.4_TS2 # ReadConformPDB reading from PDB file servers/karypis.srv.4_TS4.pdb.gz looking for model 1 # Found a chain break before 182 # copying to AlignedFragments data structure # naming current conformation karypis.srv.4_TS4 # ReadConformPDB reading from PDB file servers/karypis.srv.4_TS5.pdb.gz looking for model 1 # Found a chain break before 183 # copying to AlignedFragments data structure # naming current conformation karypis.srv.4_TS5 # ReadConformPDB reading from PDB file servers/karypis.srv_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0345 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation karypis.srv_TS1 # ReadConformPDB reading from PDB file servers/karypis.srv_TS2.pdb.gz looking for model 1 # Found a chain break before 151 # copying to AlignedFragments data structure # naming current conformation karypis.srv_TS2 # ReadConformPDB reading from PDB file servers/karypis.srv_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0345 can't currently be optimized by undertaker # naming current conformation karypis.srv_TS3 # ReadConformPDB reading from PDB file servers/karypis.srv_TS4.pdb.gz looking for model 1 # Found a chain break before 151 # copying to AlignedFragments data structure # naming current conformation karypis.srv_TS4 # ReadConformPDB reading from PDB file servers/karypis.srv_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0345 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation karypis.srv_TS5 # ReadConformPDB reading from PDB file servers/keasar-server_TS1.pdb.gz looking for model 1 # naming current conformation keasar-server_TS1 # ReadConformPDB reading from PDB file servers/keasar-server_TS2.pdb.gz looking for model 1 # Found a chain break before 28 # copying to AlignedFragments data structure # naming current conformation keasar-server_TS2 # ReadConformPDB reading from PDB file servers/keasar-server_TS3.pdb.gz looking for model 1 # naming current conformation keasar-server_TS3 # ReadConformPDB reading from PDB file servers/keasar-server_TS4.pdb.gz looking for model 1 # naming current conformation keasar-server_TS4 # ReadConformPDB reading from PDB file servers/keasar-server_TS5.pdb.gz looking for model 1 # naming current conformation keasar-server_TS5 # ReadConformPDB reading from PDB file servers/mGen-3D_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0345 can't currently be optimized by undertaker # naming current conformation mGen-3D_TS1 # ReadConformPDB reading from PDB file servers/nFOLD_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0345 can't currently be optimized by undertaker # naming current conformation nFOLD_TS1 # ReadConformPDB reading from PDB file servers/nFOLD_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0345 can't currently be optimized by undertaker # naming current conformation nFOLD_TS2 # ReadConformPDB reading from PDB file servers/nFOLD_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0345 can't currently be optimized by undertaker # naming current conformation nFOLD_TS3 # ReadConformPDB reading from PDB file servers/nFOLD_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0345 can't currently be optimized by undertaker # naming current conformation nFOLD_TS4 # ReadConformPDB reading from PDB file servers/nFOLD_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0345 can't currently be optimized by undertaker # naming current conformation nFOLD_TS5 # ReadConformPDB reading from PDB file servers/shub_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0345 can't currently be optimized by undertaker # naming current conformation shub_TS1 # command:Using radius: 8.0000 Using models AND alignments for constraints model score -0.2365 model score -0.2365 model score -0.2365 model score -0.2365 model score -0.2365 model score -0.2365 model score 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score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 2.4975 model score 2.1310 model score 2.3265 model score 2.1237 model score 2.2105 model score -0.3540 model score 0.6589 model score 0.1560 model score 0.1814 model score 0.8822 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score -0.3623 model score -0.3539 model score -0.3391 model score -0.3620 model score -0.3514 model score -0.3626 model score -0.3668 model score -0.3422 model score -0.3626 model score -0.3797 model score -0.0577 model score -0.0487 model score -0.0439 model score -0.3683 model score -0.3816 model score -0.2698 model score 1.6092 model score 1.4814 model score -0.2998 model score -0.2864 model score -0.2868 model score 0.7625 model score 0.2111 model score -0.3666 model score -0.3726 model score -0.0810 model score -0.0465 model score 0.0809 model score -0.3666 model score -0.3701 model score -0.0465 model score -0.1452 model score 0.2611 model score -0.4441 model score -0.3464 model score -0.3954 model score -0.3796 model score -0.3014 model score -0.3700 model score -0.3345 model score -0.3561 model score -0.3435 model score -0.3498 model score -0.3345 model score -0.3702 model score -0.0671 model score -0.2390 model score -0.2748 model score -0.3686 model score -0.3843 model score -0.3733 model score -0.3796 model score -0.3638 model score -0.3440 model score -0.3690 model score -0.3409 model score -0.3625 model score -0.3604 model score -0.3615 model score -0.3620 model score -0.3806 model score -0.3716 model score -0.3733 model score -0.3733 model score -0.3793 model score -0.3674 model score -0.3683 model score -0.3781 model score -0.3652 model score -0.3881 model score -0.3806 model score -0.3872 model score -0.2991 model score -0.2668 model score -0.0221 model score -0.3869 model score -0.3847 model score -0.3326 model score -0.2938 model score -0.0799 model score -0.3865 model score -0.3794 model score -0.3848 model score -0.3806 model score -0.3793 model score -0.3871 model score -0.3697 model score -0.1434 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score -0.3670 model score 0.1433 model score 0.5583 model score -0.1621 model score 0.5438 model score -0.3652 model score -0.3332 model score -0.0115 model score -0.0964 model score -0.0971 model score -0.3660 model score -0.3379 model score 0.0025 model score -0.0409 model score -0.1666 model score -0.3700 model score -0.3238 model score -0.1188 model score -0.0451 model score -0.3818 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score -0.3753 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score -0.3778 model score -0.3702 model score -0.3805 model score -0.3831 model score -0.3721 model score -0.3851 model score -0.3517 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score -0.3860 model score -0.0648 model score -0.2757 model score -0.1215 model score 0.1800 model score 1.4681 model score 1.9005 model score 2.0249 model score 1.6266 model score -0.1027 model score 0.1912 model score -0.0448 model score 0.0319 model score 0.2256 model score -0.0300 model score -0.3345 model score -0.3564 model score -0.3276 model score 0.4108 model score -0.1317 model score -0.3478 model score 0.1932 model score -0.0010 model score -0.1459 model score 0.3106 model score -0.3617 USE_META, weight: 0.9365 cost: -0.2365 min: -0.4441 max: 2.4975 USE_META, weight: 0.9365 cost: -0.2365 min: -0.4441 max: 2.4975 USE_META, weight: 0.9365 cost: -0.2365 min: -0.4441 max: 2.4975 USE_META, weight: 0.9365 cost: -0.2365 min: -0.4441 max: 2.4975 USE_META, weight: 0.9365 cost: -0.2365 min: -0.4441 max: 2.4975 USE_META, weight: 0.9365 cost: -0.2365 min: -0.4441 max: 2.4975 USE_META, weight: 0.9365 cost: -0.2365 min: -0.4441 max: 2.4975 USE_META, weight: 0.9820 cost: -0.3853 min: -0.4441 max: 2.4975 USE_META, weight: 0.9821 cost: -0.3856 min: -0.4441 max: 2.4975 USE_META, weight: 0.9793 cost: -0.3766 min: -0.4441 max: 2.4975 USE_META, weight: 0.9468 cost: -0.2702 min: -0.4441 max: 2.4975 USE_META, weight: 0.9813 cost: -0.3832 min: -0.4441 max: 2.4975 USE_META, weight: 0.3174 cost: 1.7871 min: -0.4441 max: 2.4975 USE_META, weight: 0.4395 cost: 1.3880 min: -0.4441 max: 2.4975 USE_META, weight: 0.4032 cost: 1.5066 min: -0.4441 max: 2.4975 USE_META, weight: 0.4496 cost: 1.3549 min: -0.4441 max: 2.4975 USE_META, weight: 0.4172 cost: 1.4608 min: -0.4441 max: 2.4975 USE_META, weight: 0.9832 cost: -0.3892 min: -0.4441 max: 2.4975 USE_META, weight: 0.9811 cost: -0.3823 min: 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weight: 0.7951 cost: 0.2256 min: -0.4441 max: 2.4975 USE_META, weight: 0.8733 cost: -0.0300 min: -0.4441 max: 2.4975 USE_META, weight: 0.9665 cost: -0.3345 min: -0.4441 max: 2.4975 USE_META, weight: 0.9731 cost: -0.3564 min: -0.4441 max: 2.4975 USE_META, weight: 0.9643 cost: -0.3276 min: -0.4441 max: 2.4975 USE_META, weight: 0.7384 cost: 0.4108 min: -0.4441 max: 2.4975 USE_META, weight: 0.9044 cost: -0.1317 min: -0.4441 max: 2.4975 USE_META, weight: 0.9705 cost: -0.3478 min: -0.4441 max: 2.4975 USE_META, weight: 0.8050 cost: 0.1932 min: -0.4441 max: 2.4975 USE_META, weight: 0.8644 cost: -0.0010 min: -0.4441 max: 2.4975 USE_META, weight: 0.9088 cost: -0.1459 min: -0.4441 max: 2.4975 USE_META, weight: 0.7691 cost: 0.3106 min: -0.4441 max: 2.4975 USE_META, weight: 0.9748 cost: -0.3617 min: -0.4441 max: 2.4975 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.1987 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.1987 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.1987 USE_EVALUE, weight: 0.9422 eval: 0.0128 min: 0.0000 max: 0.1987 USE_EVALUE, weight: 0.9422 eval: 0.0128 min: 0.0000 max: 0.1987 USE_EVALUE, weight: 0.9422 eval: 0.0128 min: 0.0000 max: 0.1987 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.1987 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.1987 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.1987 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.1987 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.1987 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.1987 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.1987 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.1987 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.1987 USE_EVALUE, weight: 0.9313 eval: 0.0152 min: 0.0000 max: 0.1987 USE_EVALUE, weight: 0.9313 eval: 0.0152 min: 0.0000 max: 0.1987 USE_EVALUE, weight: 0.9313 eval: 0.0152 min: 0.0000 max: 0.1987 USE_EVALUE, weight: 0.6410 eval: 0.0792 min: 0.0000 max: 0.1987 USE_EVALUE, weight: 0.6410 eval: 0.0792 min: 0.0000 max: 0.1987 USE_EVALUE, weight: 0.6410 eval: 0.0792 min: 0.0000 max: 0.1987 USE_EVALUE, weight: 0.9918 eval: 0.0018 min: 0.0000 max: 0.1987 USE_EVALUE, weight: 0.9918 eval: 0.0018 min: 0.0000 max: 0.1987 USE_EVALUE, weight: 0.9918 eval: 0.0018 min: 0.0000 max: 0.1987 USE_EVALUE, weight: 0.8884 eval: 0.0246 min: 0.0000 max: 0.1987 USE_EVALUE, weight: 0.8884 eval: 0.0246 min: 0.0000 max: 0.1987 USE_EVALUE, weight: 0.8884 eval: 0.0246 min: 0.0000 max: 0.1987 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.1987 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.1987 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.1987 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.1987 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.1987 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.1987 USE_EVALUE, weight: 0.9579 eval: 0.0093 min: 0.0000 max: 0.1987 USE_EVALUE, weight: 0.9579 eval: 0.0093 min: 0.0000 max: 0.1987 USE_EVALUE, weight: 0.9579 eval: 0.0093 min: 0.0000 max: 0.1987 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.1987 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.1987 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.1987 USE_EVALUE, weight: 0.9586 eval: 0.0091 min: 0.0000 max: 0.1987 USE_EVALUE, weight: 0.9586 eval: 0.0091 min: 0.0000 max: 0.1987 USE_EVALUE, weight: 0.9586 eval: 0.0091 min: 0.0000 max: 0.1987 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.1987 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.1987 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.1987 USE_EVALUE, weight: 0.9983 eval: 0.0004 min: 0.0000 max: 0.1987 USE_EVALUE, weight: 0.9983 eval: 0.0004 min: 0.0000 max: 0.1987 USE_EVALUE, weight: 0.9983 eval: 0.0004 min: 0.0000 max: 0.1987 USE_EVALUE, weight: 0.7206 eval: 0.0617 min: 0.0000 max: 0.1987 USE_EVALUE, weight: 0.7206 eval: 0.0617 min: 0.0000 max: 0.1987 USE_EVALUE, weight: 0.7206 eval: 0.0617 min: 0.0000 max: 0.1987 USE_EVALUE, weight: 0.9998 eval: 0.0001 min: 0.0000 max: 0.1987 USE_EVALUE, weight: 0.9998 eval: 0.0001 min: 0.0000 max: 0.1987 USE_EVALUE, weight: 0.9998 eval: 0.0001 min: 0.0000 max: 0.1987 USE_EVALUE, weight: 0.9150 eval: 0.0188 min: 0.0000 max: 0.1987 USE_EVALUE, weight: 0.9150 eval: 0.0188 min: 0.0000 max: 0.1987 USE_EVALUE, weight: 0.9150 eval: 0.0188 min: 0.0000 max: 0.1987 USE_EVALUE, weight: 0.9947 eval: 0.0012 min: 0.0000 max: 0.1987 USE_EVALUE, weight: 0.9947 eval: 0.0012 min: 0.0000 max: 0.1987 USE_EVALUE, weight: 0.9947 eval: 0.0012 min: 0.0000 max: 0.1987 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.1987 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.1987 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.1987 USE_EVALUE, weight: 0.9934 eval: 0.0015 min: 0.0000 max: 0.1987 USE_EVALUE, weight: 0.9934 eval: 0.0015 min: 0.0000 max: 0.1987 USE_EVALUE, 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max: 0.1987 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.1987 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.1987 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.1987 USE_EVALUE, weight: 0.8903 eval: 0.0242 min: 0.0000 max: 0.1987 USE_EVALUE, weight: 0.8903 eval: 0.0242 min: 0.0000 max: 0.1987 USE_EVALUE, weight: 0.8903 eval: 0.0242 min: 0.0000 max: 0.1987 USE_EVALUE, weight: 0.9622 eval: 0.0083 min: 0.0000 max: 0.1987 USE_EVALUE, weight: 0.9622 eval: 0.0083 min: 0.0000 max: 0.1987 USE_EVALUE, weight: 0.9622 eval: 0.0083 min: 0.0000 max: 0.1987 USE_EVALUE, weight: 0.9888 eval: 0.0025 min: 0.0000 max: 0.1987 USE_EVALUE, weight: 0.9888 eval: 0.0025 min: 0.0000 max: 0.1987 USE_EVALUE, weight: 0.9888 eval: 0.0025 min: 0.0000 max: 0.1987 USE_EVALUE, weight: 0.9997 eval: 0.0001 min: 0.0000 max: 0.1987 USE_EVALUE, weight: 0.9997 eval: 0.0001 min: 0.0000 max: 0.1987 USE_EVALUE, weight: 0.9997 eval: 0.0001 min: 0.0000 max: 0.1987 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.1987 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.1987 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.1987 USE_EVALUE, weight: 0.9942 eval: 0.0013 min: 0.0000 max: 0.1987 USE_EVALUE, weight: 0.9942 eval: 0.0013 min: 0.0000 max: 0.1987 USE_EVALUE, weight: 0.9942 eval: 0.0013 min: 0.0000 max: 0.1987 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.1987 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.1987 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.1987 USE_EVALUE, weight: 0.9297 eval: 0.0155 min: 0.0000 max: 0.1987 USE_EVALUE, weight: 0.9297 eval: 0.0155 min: 0.0000 max: 0.1987 USE_EVALUE, weight: 0.9297 eval: 0.0155 min: 0.0000 max: 0.1987 USE_EVALUE, weight: 0.6402 eval: 0.0794 min: 0.0000 max: 0.1987 USE_EVALUE, weight: 0.6402 eval: 0.0794 min: 0.0000 max: 0.1987 USE_EVALUE, weight: 0.6402 eval: 0.0794 min: 0.0000 max: 0.1987 USE_EVALUE, weight: 0.9952 eval: 0.0011 min: 0.0000 max: 0.1987 USE_EVALUE, weight: 0.9952 eval: 0.0011 min: 0.0000 max: 0.1987 USE_EVALUE, weight: 0.9952 eval: 0.0011 min: 0.0000 max: 0.1987 USE_EVALUE, weight: 0.6598 eval: 0.0751 min: 0.0000 max: 0.1987 USE_EVALUE, weight: 0.6598 eval: 0.0751 min: 0.0000 max: 0.1987 USE_EVALUE, weight: 0.6598 eval: 0.0751 min: 0.0000 max: 0.1987 USE_EVALUE, weight: 0.6946 eval: 0.0674 min: 0.0000 max: 0.1987 USE_EVALUE, weight: 0.6946 eval: 0.0674 min: 0.0000 max: 0.1987 USE_EVALUE, weight: 0.6946 eval: 0.0674 min: 0.0000 max: 0.1987 USE_EVALUE, weight: 0.9983 eval: 0.0004 min: 0.0000 max: 0.1987 USE_EVALUE, weight: 0.9983 eval: 0.0004 min: 0.0000 max: 0.1987 USE_EVALUE, weight: 0.9983 eval: 0.0004 min: 0.0000 max: 0.1987 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.1987 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.1987 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.1987 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.1987 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.1987 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.1987 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.1987 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.1987 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.1987 USE_EVALUE, weight: 0.9812 eval: 0.0042 min: 0.0000 max: 0.1987 USE_EVALUE, weight: 0.9812 eval: 0.0042 min: 0.0000 max: 0.1987 USE_EVALUE, weight: 0.9812 eval: 0.0042 min: 0.0000 max: 0.1987 USE_EVALUE, weight: 0.1000 eval: 0.1987 min: 0.0000 max: 0.1987 USE_EVALUE, weight: 0.1000 eval: 0.1987 min: 0.0000 max: 0.1987 USE_EVALUE, weight: 0.1000 eval: 0.1987 min: 0.0000 max: 0.1987 USE_EVALUE, weight: 0.9884 eval: 0.0026 min: 0.0000 max: 0.1987 USE_EVALUE, weight: 0.9884 eval: 0.0026 min: 0.0000 max: 0.1987 USE_EVALUE, weight: 0.9884 eval: 0.0026 min: 0.0000 max: 0.1987 Number of contacts in models: 251 Number of contacts in alignments: 141 NUMB_ALIGNS: 141 Adding 7000 constraints to all3.constraints Done adding distance constraints # command:Reading probabilities from probabilities.dat Reading constraints from ConstraintSet all3.constraints maxweight: 1.0000 Optimizing... Probability sum: -317.8330, CN propb: -317.8330 weights: 0.4181 constraints: 401 # command:Found ConstraintSet # PrintContacts align.constraints_meta03 Number of constraints in align3.constraints 401 # command:Found ConstraintSet # PrintContacts align_bonus.constraints_meta03 Number of constraints in align3.constraints.bonus 401 # command:Found ConstraintSet # PrintContacts rejected.constraints_meta03 Number of constraints in rejected3.constraints 6599 # command:Found ConstraintSet # PrintContacts rejected_bonus.constraints_meta03 Number of constraints in rejected3.constraints.bonus 6599 # command:Found ConstraintSet # PrintContacts non_contacts.constraints_meta03 Number of constraints in noncontact3.constraints 0 # command:Found ConstraintSet # PrintContacts non_contacts_bonus.constraints_meta03 Number of constraints in noncontact3.constraints.bonus 0 # command:Found ConstraintSet # PrintContacts all.constraints_meta03 Number of constraints in all3.constraints 7000 # command: