# 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/T0319/ # command:# Making conformation for sequence T0319 numbered 1 through 135 Created new target T0319 from T0319.a2m # command:# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/T0319/ # command:Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0319//projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0319/manyalignments-good-all.under or /projects/compbio/experiments/protein-predict/casp7/T0319//projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0319/manyalignments-good-all.under.gz for input Trying /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0319/manyalignments-good-all.under # reading script from file /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0319/manyalignments-good-all.under # Reading fragments from alignment file # Attempting to read fragment alignments from file 2aa1B/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2aa1B expands to /projects/compbio/data/pdb/2aa1.pdb.gz 2aa1B:Skipped atom 1243, because occupancy 0.42 <= existing 0.580 in 2aa1B Skipped atom 1245, because occupancy 0.420 <= existing 0.580 in 2aa1B Skipped atom 1247, because occupancy 0.420 <= existing 0.580 in 2aa1B Skipped atom 1249, because occupancy 0.420 <= existing 0.580 in 2aa1B Skipped atom 1251, because occupancy 0.420 <= existing 0.580 in 2aa1B Skipped atom 1253, because occupancy 0.420 <= existing 0.580 in 2aa1B Skipped atom 2204, because occupancy 0.260 <= existing 0.740 in 2aa1B Skipped atom 2206, because occupancy 0.260 <= existing 0.740 in 2aa1B Skipped atom 2208, because occupancy 0.260 <= existing 0.740 in 2aa1B Skipped atom 2210, because occupancy 0.260 <= existing 0.740 in 2aa1B Skipped atom 2212, because occupancy 0.260 <= existing 0.740 in 2aa1B Skipped atom 2214, because occupancy 0.260 <= existing 0.740 in 2aa1B # T0319 read from 2aa1B/merged-good-all-a2m # 2aa1B read from 2aa1B/merged-good-all-a2m # adding 2aa1B to template set # found chain 2aa1B in template set T0319 38 :ESIEFNPEFLLNIV 2aa1B 94 :EKLHVDPDNFKLLA # choosing archetypes in rotamer library T0319 57 :PAVLTVAAELGN 2aa1B 108 :DCLTIVVAARFG T0319 83 :QELTDDDMAILNDLHTLLLQ 2aa1B 120 :SAFTGEVQAAFQKFMAVVVS Number of specific fragments extracted= 3 number of extra gaps= 0 total=3 Number of alignments=1 # 2aa1B read from 2aa1B/merged-good-all-a2m # found chain 2aa1B in template set T0319 38 :ESIEFNPEFLLNIV 2aa1B 94 :EKLHVDPDNFKLLA T0319 57 :PAVLTVAAELGN 2aa1B 108 :DCLTIVVAARFG T0319 83 :QELTDDDMAILNDLHTLLLQ 2aa1B 120 :SAFTGEVQAAFQKFMAVVVS Number of specific fragments extracted= 3 number of extra gaps= 0 total=6 Number of alignments=2 # 2aa1B read from 2aa1B/merged-good-all-a2m # found chain 2aa1B in template set T0319 38 :ESIEFNPEFLLNIV 2aa1B 94 :EKLHVDPDNFKLLA T0319 57 :PAVLTVAAELGN 2aa1B 108 :DCLTIVVAARFG T0319 83 :QELTDDDMAILNDLHTLLLQ 2aa1B 120 :SAFTGEVQAAFQKFMAVVVS Number of specific fragments extracted= 3 number of extra gaps= 0 total=9 Number of alignments=3 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1fp1D/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1fp1D expands to /projects/compbio/data/pdb/1fp1.pdb.gz 1fp1D:# T0319 read from 1fp1D/merged-good-all-a2m # 1fp1D read from 1fp1D/merged-good-all-a2m # adding 1fp1D to template set # found chain 1fp1D in template set T0319 37 :DESIEFNPEFLLNIVDR 1fp1D 58 :PPGAFMSPSEIASKLPA T0319 83 :QELTDDDMAILNDLHTLLLQTS 1fp1D 75 :STQHSDLPNRLDRMLRLLASYS T0319 105 :IAEGEMKCRNCG 1fp1D 98 :LTSTTRTIEDGG T0319 117 :HIYYIKNGIPNLLL 1fp1D 112 :RVYGLSMVGKYLVP Number of specific fragments extracted= 4 number of extra gaps= 0 total=13 Number of alignments=4 # 1fp1D read from 1fp1D/merged-good-all-a2m # found chain 1fp1D in template set T0319 37 :DESIEFNPEFLLNIV 1fp1D 58 :PPGAFMSPSEIASKL T0319 72 :P 1fp1D 73 :P T0319 80 :S 1fp1D 74 :A T0319 83 :QELTDDDMAILNDLHTLLLQTS 1fp1D 75 :STQHSDLPNRLDRMLRLLASYS T0319 105 :IAEGEMKCRNCG 1fp1D 98 :LTSTTRTIEDGG T0319 117 :HIYYIKNGIPNLLLP 1fp1D 112 :RVYGLSMVGKYLVPD Number of specific fragments extracted= 6 number of extra gaps= 0 total=19 Number of alignments=5 # 1fp1D read from 1fp1D/merged-good-all-a2m # found chain 1fp1D in template set T0319 37 :DESIEFNPEFLLN 1fp1D 58 :PPGAFMSPSEIAS T0319 77 :SFPS 1fp1D 71 :KLPA T0319 83 :QELTDDDMAILNDLHTLLLQTS 1fp1D 75 :STQHSDLPNRLDRMLRLLASYS T0319 105 :IAEGEMKCRNCG 1fp1D 98 :LTSTTRTIEDGG T0319 117 :HIYY 1fp1D 112 :RVYG Number of specific fragments extracted= 5 number of extra gaps= 0 total=24 Number of alignments=6 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1rb9/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0319 read from 1rb9/merged-good-all-a2m # 1rb9 read from 1rb9/merged-good-all-a2m # found chain 1rb9 in training set T0319 110 :MKCRNCGHIYYIKNGIPNLLLPPHLV 1rb9 4 :YVCTVCGYEYDPAEGDPDNGVKPGTS Number of specific fragments extracted= 1 number of extra gaps= 0 total=25 Number of alignments=7 # 1rb9 read from 1rb9/merged-good-all-a2m # found chain 1rb9 in training set T0319 110 :MKCRNCGHIYYIKNGIPNLLLPPHLV 1rb9 4 :YVCTVCGYEYDPAEGDPDNGVKPGTS Number of specific fragments extracted= 1 number of extra gaps= 0 total=26 Number of alignments=8 # 1rb9 read from 1rb9/merged-good-all-a2m # found chain 1rb9 in training set T0319 111 :KCRNCGHIYYIKNG 1rb9 5 :VCTVCGYEYDPAEG Number of specific fragments extracted= 1 number of extra gaps= 0 total=27 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1dx8A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1dx8A expands to /projects/compbio/data/pdb/1dx8.pdb.gz 1dx8A:# T0319 read from 1dx8A/merged-good-all-a2m # 1dx8A read from 1dx8A/merged-good-all-a2m # adding 1dx8A to template set # found chain 1dx8A in template set T0319 104 :SIAEGEMKCRNCGHIYY 1dx8A 2 :EIDEGKYECEACGYIYE T0319 121 :IKNGIPNLLLPPH 1dx8A 28 :IPPGTPFVDLSDS Number of specific fragments extracted= 2 number of extra gaps= 0 total=29 Number of alignments=9 # 1dx8A read from 1dx8A/merged-good-all-a2m # found chain 1dx8A in template set T0319 104 :SIAEGEMKCRNCGHIYY 1dx8A 2 :EIDEGKYECEACGYIYE T0319 121 :IKNGIPNLLLPPH 1dx8A 28 :IPPGTPFVDLSDS Number of specific fragments extracted= 2 number of extra gaps= 0 total=31 Number of alignments=10 # 1dx8A read from 1dx8A/merged-good-all-a2m # found chain 1dx8A in template set T0319 104 :SIAEGEMKCRNCGHIYY 1dx8A 2 :EIDEGKYECEACGYIYE Number of specific fragments extracted= 1 number of extra gaps= 0 total=32 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2f4mA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2f4mA expands to /projects/compbio/data/pdb/2f4m.pdb.gz 2f4mA:# T0319 read from 2f4mA/merged-good-all-a2m # 2f4mA read from 2f4mA/merged-good-all-a2m # adding 2f4mA to template set # found chain 2f4mA in template set T0319 43 :NPEFLLNIVDRVDWPAVLTVAAE 2f4mA 184 :NPVLQEKALTCIPVSELKRKAQE T0319 73 :PTKPSF 2f4mA 212 :RKLDKG T0319 83 :QELTDD 2f4mA 218 :TNVSDE T0319 90 :MAILNDLHTLLLQTSIAE 2f4mA 224 :DFLLLELLHWFKEEFFRW T0319 108 :GEMKCRNCGHI 2f4mA 243 :NNIVCSKCGGE T0319 121 :IKNGIPNLLLPPHL 2f4mA 254 :TRSRDEALLPNDDE Number of specific fragments extracted= 6 number of extra gaps= 0 total=38 Number of alignments=11 # 2f4mA read from 2f4mA/merged-good-all-a2m # found chain 2f4mA in template set T0319 43 :NPEFLLNIVDRVDWPAVLTVAAE 2f4mA 184 :NPVLQEKALTCIPVSELKRKAQE T0319 67 :GN 2f4mA 212 :RK T0319 72 :PPTKPSFPS 2f4mA 214 :LDKGTNVSD T0319 89 :DMAILNDLHTLLLQTSIAE 2f4mA 223 :EDFLLLELLHWFKEEFFRW T0319 108 :GEMKCRNCGHI 2f4mA 243 :NNIVCSKCGGE T0319 121 :IKNGIPNLLLPPHL 2f4mA 254 :TRSRDEALLPNDDE Number of specific fragments extracted= 6 number of extra gaps= 0 total=44 Number of alignments=12 # 2f4mA read from 2f4mA/merged-good-all-a2m # found chain 2f4mA in template set T0319 43 :NPEFLLNIVDRVDWPAVLTVAAE 2f4mA 184 :NPVLQEKALTCIPVSELKRKAQE T0319 66 :LGN 2f4mA 211 :ARK T0319 72 :PPTKP 2f4mA 214 :LDKGT T0319 85 :LTDDDMAILNDLHTLLLQTSIAE 2f4mA 219 :NVSDEDFLLLELLHWFKEEFFRW T0319 108 :GEMKCRNCGH 2f4mA 243 :NNIVCSKCGG Number of specific fragments extracted= 5 number of extra gaps= 0 total=49 Number of alignments=13 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1rlyA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1rlyA expands to /projects/compbio/data/pdb/1rly.pdb.gz 1rlyA:# T0319 read from 1rlyA/merged-good-all-a2m # 1rlyA read from 1rlyA/merged-good-all-a2m # adding 1rlyA to template set # found chain 1rlyA in template set T0319 69 :NALP 1rlyA 8 :DALP T0319 73 :PTKPSFPSS 1rlyA 13 :VTCPNHPDA T0319 82 :IQELTDDD 1rlyA 24 :VEDYRAGD T0319 110 :MKCRNCGHI 1rlyA 32 :MICPECGLV Number of specific fragments extracted= 4 number of extra gaps= 0 total=53 Number of alignments=14 # 1rlyA read from 1rlyA/merged-good-all-a2m # found chain 1rlyA in template set T0319 68 :NNALP 1rlyA 7 :LDALP T0319 73 :PTKPSFPS 1rlyA 13 :VTCPNHPD T0319 83 :QELTDDD 1rlyA 21 :AILVEDY T0319 106 :AEGEMKCRNCGHI 1rlyA 28 :RAGDMICPECGLV Number of specific fragments extracted= 4 number of extra gaps= 0 total=57 Number of alignments=15 # 1rlyA read from 1rlyA/merged-good-all-a2m # found chain 1rlyA in template set T0319 69 :NALPPTKPSFPSSIQELTDD 1rlyA 10 :LPRVTCPNHPDAILVEDYRA T0319 108 :GEMKCRNCGHI 1rlyA 30 :GDMICPECGLV Number of specific fragments extracted= 2 number of extra gaps= 0 total=59 Number of alignments=16 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1v87A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1v87A expands to /projects/compbio/data/pdb/1v87.pdb.gz 1v87A:# T0319 read from 1v87A/merged-good-all-a2m # 1v87A read from 1v87A/merged-good-all-a2m # adding 1v87A to template set # found chain 1v87A in template set T0319 58 :AVLTVAAELGNNA 1v87A 69 :CLLAMYCNGNKDG Number of specific fragments extracted= 1 number of extra gaps= 0 total=60 # 1v87A read from 1v87A/merged-good-all-a2m # found chain 1v87A in template set Number of specific fragments extracted= 0 number of extra gaps= 0 total=60 # 1v87A read from 1v87A/merged-good-all-a2m # found chain 1v87A in template set T0319 87 :DDDMAILNDL 1v87A 7 :GEPEQVIRKY Number of specific fragments extracted= 1 number of extra gaps= 0 total=61 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1vq0A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1vq0A expands to /projects/compbio/data/pdb/1vq0.pdb.gz 1vq0A:# T0319 read from 1vq0A/merged-good-all-a2m # 1vq0A read from 1vq0A/merged-good-all-a2m # adding 1vq0A to template set # found chain 1vq0A in template set T0319 4 :LTTNFLKCSVKACDTS 1vq0A 140 :LAYYFAVSEQIPSAFS T0319 23 :FPLQYDGSKCQL 1vq0A 156 :IGVLVDSDGVKI T0319 35 :VQDESIEFNPEF 1vq0A 173 :VQIIDRTLEQEK T0319 47 :LLNIVDRVDWPAVLTVAA 1vq0A 198 :ISKLFQEAEPLDVLERIF T0319 68 :NNALPPT 1vq0A 216 :GEKVGFV T0319 77 :SFPSSIQE 1vq0A 230 :KCDCNREK T0319 85 :LTDDDMAILNDLH 1vq0A 242 :LLVLDKKELEDMR T0319 106 :AEGEMKCRNCGHIYYIK 1vq0A 257 :GKGEVVCKWCNTRYVFS Number of specific fragments extracted= 8 number of extra gaps= 0 total=69 Number of alignments=17 # 1vq0A read from 1vq0A/merged-good-all-a2m # found chain 1vq0A in template set T0319 6 :TNFLKCSVKACDTS 1vq0A 142 :YYFAVSEQIPSAFS T0319 23 :FPLQYDGSKCQL 1vq0A 156 :IGVLVDSDGVKI T0319 35 :VQDESIEFNPEF 1vq0A 173 :VQIIDRTLEQEK T0319 47 :LLNIVDRVDWPAVLTVAA 1vq0A 198 :ISKLFQEAEPLDVLERIF T0319 68 :NNALPP 1vq0A 216 :GEKVGF T0319 74 :TKPSFPSSIQELT 1vq0A 230 :KCDCNREKAKNAL T0319 87 :DDDMAILNDLHTL 1vq0A 244 :VLDKKELEDMRKE T0319 106 :AEGEMKCRNCGHIYYIK 1vq0A 257 :GKGEVVCKWCNTRYVFS Number of specific fragments extracted= 8 number of extra gaps= 0 total=77 Number of alignments=18 # 1vq0A read from 1vq0A/merged-good-all-a2m # found chain 1vq0A in template set T0319 27 :YDGSKCQLVQD 1vq0A 219 :VGFVETAEIKY T0319 39 :SIEFNPEFLLNIVDRVDWPAVLTVAAE 1vq0A 230 :KCDCNREKAKNALLVLDKKELEDMRKE T0319 67 :G 1vq0A 257 :G T0319 107 :EGEMKCRNCGHIYYIK 1vq0A 258 :KGEVVCKWCNTRYVFS Number of specific fragments extracted= 4 number of extra gaps= 0 total=81 Number of alignments=19 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1woyA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1woyA expands to /projects/compbio/data/pdb/1woy.pdb.gz 1woyA:# T0319 read from 1woyA/merged-good-all-a2m # 1woyA read from 1woyA/merged-good-all-a2m # adding 1woyA to template set # found chain 1woyA in template set T0319 44 :PEFLLNIVDR 1woyA 68 :KAFVDRVSGR T0319 59 :VLTVAAELGNNA 1woyA 78 :FKRAWDLLGIAY T0319 83 :QE 1woyA 90 :DD T0319 85 :LTDDDMAILNDLHTLLLQT 1woyA 96 :TEERHKKVVQLVLKKVYEA T0319 104 :SIAEGE 1woyA 116 :DIYYGE T0319 110 :MKCRNCGHIY 1woyA 125 :LYCVSCERFY T0319 131 :PPHL 1woyA 135 :TEKE Number of specific fragments extracted= 7 number of extra gaps= 0 total=88 Number of alignments=20 # 1woyA read from 1woyA/merged-good-all-a2m # found chain 1woyA in template set T0319 44 :PEFLLNIVDR 1woyA 68 :KAFVDRVSGR T0319 59 :VLTVAAELGNN 1woyA 78 :FKRAWDLLGIA T0319 82 :IQE 1woyA 89 :YDD T0319 85 :LTDDDMAILNDLHTLLLQT 1woyA 96 :TEERHKKVVQLVLKKVYEA T0319 104 :SIAEGE 1woyA 116 :DIYYGE T0319 110 :MKCRNCGHIY 1woyA 125 :LYCVSCERFY T0319 131 :PPHL 1woyA 135 :TEKE Number of specific fragments extracted= 7 number of extra gaps= 0 total=95 Number of alignments=21 # 1woyA read from 1woyA/merged-good-all-a2m # found chain 1woyA in template set T0319 4 :LTTNFLKC 1woyA 44 :FFLTGTDE T0319 27 :YDGSKCQLVQDESIE 1woyA 52 :HGETVYRAAQAAGED T0319 43 :NPEFLLNIVDR 1woyA 67 :PKAFVDRVSGR T0319 59 :VLTVAAELGN 1woyA 78 :FKRAWDLLGI T0319 77 :SFPSSIQELTDDDMAILNDLHTLLLQT 1woyA 88 :AYDDFIRTTEERHKKVVQLVLKKVYEA T0319 104 :SIAEGE 1woyA 116 :DIYYGE T0319 110 :MKCRNCGHIY 1woyA 125 :LYCVSCERFY T0319 131 :PPHLV 1woyA 135 :TEKEL Number of specific fragments extracted= 8 number of extra gaps= 0 total=103 Number of alignments=22 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1w2lA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1w2lA expands to /projects/compbio/data/pdb/1w2l.pdb.gz 1w2lA:# T0319 read from 1w2lA/merged-good-all-a2m # 1w2lA read from 1w2lA/merged-good-all-a2m # adding 1w2lA to template set # found chain 1w2lA in template set T0319 21 :DNFPLQYDGSKCQLV 1w2lA 38 :YGSTRTFEDGTTAVA T0319 55 :DWPAVLTVAAELGNNALPPTKPSFPSSIQELTDDDMAILNDLH 1w2lA 53 :DENYLRESILQPGAKVVQGYPNVMPASYASLSEREVAALIEFI Number of specific fragments extracted= 2 number of extra gaps= 0 total=105 Number of alignments=23 # 1w2lA read from 1w2lA/merged-good-all-a2m # found chain 1w2lA in template set T0319 21 :DNFPLQYDGSKCQLV 1w2lA 38 :YGSTRTFEDGTTAVA T0319 55 :DWPAVLTVAAELGNNALPPTKPSFPSSIQELTDDDMAILNDLH 1w2lA 53 :DENYLRESILQPGAKVVQGYPNVMPASYASLSEREVAALIEFI Number of specific fragments extracted= 2 number of extra gaps= 0 total=107 Number of alignments=24 # 1w2lA read from 1w2lA/merged-good-all-a2m # found chain 1w2lA in template set T0319 18 :TSNDNFPLQYDGSKCQL 1w2lA 35 :KGLYGSTRTFEDGTTAV T0319 54 :VDWPAVLTVAAELGNNALPPTKPSFPSSIQELTDDDMAILNDLH 1w2lA 52 :ADENYLRESILQPGAKVVQGYPNVMPASYASLSEREVAALIEFI Number of specific fragments extracted= 2 number of extra gaps= 0 total=109 Number of alignments=25 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1b7yB/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1b7yB expands to /projects/compbio/data/pdb/1b7y.pdb.gz 1b7yB:# T0319 read from 1b7yB/merged-good-all-a2m # 1b7yB read from 1b7yB/merged-good-all-a2m # adding 1b7yB to template set # found chain 1b7yB in template set T0319 15 :ACDTSNDNFPLQYDGSKC 1b7yB 432 :GCRVEGEGPTYRVTPPSH T0319 39 :SIEFN 1b7yB 450 :RLDLR T0319 55 :DWPAVLTVAAEL 1b7yB 455 :LEEDLVEEVARI T0319 67 :GNNALPPTKPSFPSSIQELT 1b7yB 468 :GYETIPLALPAFFPAPDNRG T0319 87 :DDDMAILNDLHTLLLQTSIAE 1b7yB 489 :EAPYRKEQRLREVLSGLGFQE Number of specific fragments extracted= 5 number of extra gaps= 0 total=114 Number of alignments=26 # 1b7yB read from 1b7yB/merged-good-all-a2m # found chain 1b7yB in template set T0319 15 :ACDTSNDNFPLQYDGSKC 1b7yB 432 :GCRVEGEGPTYRVTPPSH T0319 39 :SIEFN 1b7yB 450 :RLDLR T0319 55 :DWPAVLTVAAEL 1b7yB 455 :LEEDLVEEVARI T0319 67 :GNNALPPTKPSFPSSIQELT 1b7yB 468 :GYETIPLALPAFFPAPDNRG T0319 87 :DDDMAILNDLHTLLLQTSIAE 1b7yB 489 :EAPYRKEQRLREVLSGLGFQE Number of specific fragments extracted= 5 number of extra gaps= 0 total=119 Number of alignments=27 # 1b7yB read from 1b7yB/merged-good-all-a2m # found chain 1b7yB in template set T0319 14 :KACDTSNDNFPLQYDGSK 1b7yB 433 :CRVEGEGPTYRVTPPSHR T0319 40 :IEFN 1b7yB 451 :LDLR T0319 55 :DWPAVLTVAAEL 1b7yB 455 :LEEDLVEEVARI T0319 67 :GNNALPPTKPS 1b7yB 468 :GYETIPLALPA T0319 78 :FPSSIQELTDDDMAILNDLHTLLLQTSIAE 1b7yB 480 :FPAPDNRGVEAPYRKEQRLREVLSGLGFQE Number of specific fragments extracted= 5 number of extra gaps= 0 total=124 Number of alignments=28 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1rdg/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1rdg expands to /projects/compbio/data/pdb/1rdg.pdb.gz 1rdg:Warning: there is no chain 1rdg will retry with 1rdgA # T0319 read from 1rdg/merged-good-all-a2m # 1rdg read from 1rdg/merged-good-all-a2m # adding 1rdg to template set # found chain 1rdg in template set T0319 110 :MKCRNCGHIYYIKNGIPNLLLPPHLV 1rdg 4 :YVCTVCGYEYDPAKGDPDSGIKPGTK Number of specific fragments extracted= 1 number of extra gaps= 0 total=125 Number of alignments=29 # 1rdg read from 1rdg/merged-good-all-a2m # found chain 1rdg in template set T0319 110 :MKCRNCGHIYYIKNGIPNLLLPPHLV 1rdg 4 :YVCTVCGYEYDPAKGDPDSGIKPGTK Number of specific fragments extracted= 1 number of extra gaps= 0 total=126 Number of alignments=30 # 1rdg read from 1rdg/merged-good-all-a2m # found chain 1rdg in template set T0319 111 :KCRNCGHIYYIKNG 1rdg 5 :VCTVCGYEYDPAKG Number of specific fragments extracted= 1 number of extra gaps= 0 total=127 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1weoA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1weoA expands to /projects/compbio/data/pdb/1weo.pdb.gz 1weoA:# T0319 read from 1weoA/merged-good-all-a2m # 1weoA read from 1weoA/merged-good-all-a2m # adding 1weoA to template set # found chain 1weoA in template set T0319 12 :SVKACDTSNDNFPL 1weoA 22 :CGDQIGLTVEGDLF T0319 33 :QLVQDESIEFNPEFLLNIVDRV 1weoA 36 :VACNECGFPACRPCYEYERREG T0319 66 :LG 1weoA 63 :QC T0319 68 :NNALPPTKPSFPSSIQELTDD 1weoA 67 :RYKRLRGSPRVEGDEDEEDID Number of specific fragments extracted= 4 number of extra gaps= 0 total=131 Number of alignments=31 # 1weoA read from 1weoA/merged-good-all-a2m # found chain 1weoA in template set T0319 12 :SVKACDTSNDNFPLQ 1weoA 22 :CGDQIGLTVEGDLFV T0319 34 :LVQDESIEFNPEFLLNIVDRVD 1weoA 37 :ACNECGFPACRPCYEYERREGT T0319 67 :GNNAL 1weoA 64 :CKTRY T0319 72 :PPTKPSF 1weoA 71 :LRGSPRV T0319 80 :SSIQELTDDD 1weoA 78 :EGDEDEEDID Number of specific fragments extracted= 5 number of extra gaps= 0 total=136 Number of alignments=32 # 1weoA read from 1weoA/merged-good-all-a2m # found chain 1weoA in template set T0319 13 :VKACDTSNDNFPL 1weoA 25 :QIGLTVEGDLFVA T0319 35 :VQDESIEFNPEFLLNIVDRVD 1weoA 38 :CNECGFPACRPCYEYERREGT T0319 69 :NALPPTKPSFP 1weoA 59 :QNCPQCKTRYK T0319 81 :SIQ 1weoA 70 :RLR Number of specific fragments extracted= 4 number of extra gaps= 0 total=140 Number of alignments=33 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1wdjA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1wdjA expands to /projects/compbio/data/pdb/1wdj.pdb.gz 1wdjA:# T0319 read from 1wdjA/merged-good-all-a2m # 1wdjA read from 1wdjA/merged-good-all-a2m # adding 1wdjA to template set # found chain 1wdjA in template set T0319 37 :DESIEFNPEF 1wdjA 6 :DLARPVSEEE T0319 59 :VLTVAAELGN 1wdjA 16 :LRRLSELNPG T0319 72 :PPTKP 1wdjA 31 :SPEGR T0319 82 :IQELTDDDMAILNDLHTLLLQT 1wdjA 38 :VSPTGGESGRRSLQLAYQLARW T0319 104 :SIA 1wdjA 67 :VVF T0319 114 :NCGHIYYIKNG 1wdjA 70 :DSSTGFKFPDG Number of specific fragments extracted= 6 number of extra gaps= 0 total=146 Number of alignments=34 # 1wdjA read from 1wdjA/merged-good-all-a2m # found chain 1wdjA in template set T0319 37 :DESIEFNPEFLLN 1wdjA 6 :DLARPVSEEELRR T0319 62 :VAAELG 1wdjA 19 :LSELNP T0319 70 :A 1wdjA 25 :G T0319 72 :PPTK 1wdjA 31 :SPEG T0319 82 :IQELTDDDMAILNDLHTLLLQT 1wdjA 38 :VSPTGGESGRRSLQLAYQLARW T0319 108 :GEMK 1wdjA 66 :GVVF T0319 114 :NCGHIYYIKNGI 1wdjA 70 :DSSTGFKFPDGS Number of specific fragments extracted= 7 number of extra gaps= 0 total=153 Number of alignments=35 # 1wdjA read from 1wdjA/merged-good-all-a2m # found chain 1wdjA in template set T0319 36 :QDESIEFNPEFLL 1wdjA 5 :LDLARPVSEEELR T0319 61 :TVAAE 1wdjA 18 :RLSEL T0319 75 :KPS 1wdjA 23 :NPG T0319 78 :FPSS 1wdjA 31 :SPEG T0319 85 :LTDDDMAILNDLHTLLLQTSIAEGEMKCRNCGHIYYIKNGI 1wdjA 41 :TGGESGRRSLQLAYQLARWNEERGLGVVFDSSTGFKFPDGS Number of specific fragments extracted= 5 number of extra gaps= 0 total=158 Number of alignments=36 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2cc0A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2cc0A expands to /projects/compbio/data/pdb/2cc0.pdb.gz 2cc0A:Skipped atom 13, because occupancy 0.200 <= existing 0.800 in 2cc0A Skipped atom 17, because occupancy 0.200 <= existing 0.800 in 2cc0A Skipped atom 19, because occupancy 0.200 <= existing 0.800 in 2cc0A Skipped atom 120, because occupancy 0.500 <= existing 0.500 in 2cc0A Skipped atom 124, because occupancy 0.500 <= existing 0.500 in 2cc0A Skipped atom 126, because occupancy 0.500 <= existing 0.500 in 2cc0A Skipped atom 346, because occupancy 0.500 <= existing 0.500 in 2cc0A Skipped atom 350, because occupancy 0.500 <= existing 0.500 in 2cc0A Skipped atom 352, because occupancy 0.500 <= existing 0.500 in 2cc0A Skipped atom 523, because occupancy 0.500 <= existing 0.500 in 2cc0A Skipped atom 527, because occupancy 0.500 <= existing 0.500 in 2cc0A Skipped atom 529, because occupancy 0.500 <= existing 0.500 in 2cc0A Skipped atom 531, because occupancy 0.500 <= existing 0.500 in 2cc0A Skipped atom 533, because occupancy 0.500 <= existing 0.500 in 2cc0A Skipped atom 626, because occupancy 0.500 <= existing 0.500 in 2cc0A Skipped atom 630, because occupancy 0.500 <= existing 0.500 in 2cc0A Skipped atom 632, because occupancy 0.500 <= existing 0.500 in 2cc0A Skipped atom 635, because occupancy 0.500 <= existing 0.500 in 2cc0A Skipped atom 639, because occupancy 0.500 <= existing 0.500 in 2cc0A Skipped atom 641, because occupancy 0.500 <= existing 0.500 in 2cc0A Skipped atom 643, because occupancy 0.500 <= existing 0.500 in 2cc0A Skipped atom 645, because occupancy 0.500 <= existing 0.500 in 2cc0A Skipped atom 647, because occupancy 0.500 <= existing 0.500 in 2cc0A Skipped atom 649, because occupancy 0.500 <= existing 0.500 in 2cc0A Skipped atom 651, because occupancy 0.500 <= existing 0.500 in 2cc0A Skipped atom 732, because occupancy 0.500 <= existing 0.500 in 2cc0A Skipped atom 736, because occupancy 0.500 <= existing 0.500 in 2cc0A Skipped atom 738, because occupancy 0.500 <= existing 0.500 in 2cc0A Skipped atom 740, because occupancy 0.500 <= existing 0.500 in 2cc0A Skipped atom 742, because occupancy 0.500 <= existing 0.500 in 2cc0A Skipped atom 744, because occupancy 0.500 <= existing 0.500 in 2cc0A Skipped atom 862, because occupancy 0.330 <= existing 0.330 in 2cc0A Skipped atom 863, because occupancy 0.330 <= existing 0.330 in 2cc0A Skipped atom 867, because occupancy 0.330 <= existing 0.330 in 2cc0A Skipped atom 868, because occupancy 0.330 <= existing 0.330 in 2cc0A Skipped atom 870, because occupancy 0.330 <= existing 0.330 in 2cc0A Skipped atom 871, because occupancy 0.330 <= existing 0.330 in 2cc0A Skipped atom 951, because occupancy 0.500 <= existing 0.500 in 2cc0A Skipped atom 955, because occupancy 0.500 <= existing 0.500 in 2cc0A Skipped atom 957, because occupancy 0.500 <= existing 0.500 in 2cc0A Skipped atom 959, because occupancy 0.500 <= existing 0.500 in 2cc0A Skipped atom 961, because occupancy 0.500 <= existing 0.500 in 2cc0A Skipped atom 1100, because occupancy 0.500 <= existing 0.500 in 2cc0A Skipped atom 1104, because occupancy 0.500 <= existing 0.500 in 2cc0A Skipped atom 1106, because occupancy 0.500 <= existing 0.500 in 2cc0A Skipped atom 1108, because occupancy 0.500 <= existing 0.500 in 2cc0A Skipped atom 1110, because occupancy 0.500 <= existing 0.500 in 2cc0A Skipped atom 1112, because occupancy 0.500 <= existing 0.500 in 2cc0A Skipped atom 1378, because occupancy 0.200 <= existing 0.800 in 2cc0A Skipped atom 1382, because occupancy 0.200 <= existing 0.800 in 2cc0A Skipped atom 1384, because occupancy 0.200 <= existing 0.800 in 2cc0A Skipped atom 1397, because occupancy 0.500 <= existing 0.500 in 2cc0A Skipped atom 1401, because occupancy 0.500 <= existing 0.500 in 2cc0A Skipped atom 1403, because occupancy 0.500 <= existing 0.500 in 2cc0A Skipped atom 1405, because occupancy 0.500 <= existing 0.500 in 2cc0A Skipped atom 1407, because occupancy 0.500 <= existing 0.500 in 2cc0A Skipped atom 1431, because occupancy 0.500 <= existing 0.500 in 2cc0A Skipped atom 1435, because occupancy 0.500 <= existing 0.500 in 2cc0A Skipped atom 1437, because occupancy 0.500 <= existing 0.500 in 2cc0A Skipped atom 1439, because occupancy 0.500 <= existing 0.500 in 2cc0A Skipped atom 1441, because occupancy 0.500 <= existing 0.500 in 2cc0A Skipped atom 1443, because occupancy 0.500 <= existing 0.500 in 2cc0A Skipped atom 1457, because occupancy 0.330 <= existing 0.330 in 2cc0A Skipped atom 1458, because occupancy 0.330 <= existing 0.330 in 2cc0A Skipped atom 1462, because occupancy 0.330 <= existing 0.330 in 2cc0A Skipped atom 1463, because occupancy 0.330 <= existing 0.330 in 2cc0A Skipped atom 1465, because occupancy 0.330 <= existing 0.330 in 2cc0A Skipped atom 1466, because occupancy 0.330 <= existing 0.330 in 2cc0A Skipped atom 1468, because occupancy 0.330 <= existing 0.330 in 2cc0A Skipped atom 1469, because occupancy 0.330 <= existing 0.330 in 2cc0A Skipped atom 1471, because occupancy 0.330 <= existing 0.330 in 2cc0A Skipped atom 1472, because occupancy 0.330 <= existing 0.330 in 2cc0A Skipped atom 1474, because occupancy 0.330 <= existing 0.330 in 2cc0A Skipped atom 1475, because occupancy 0.330 <= existing 0.330 in 2cc0A Skipped atom 1477, because occupancy 0.330 <= existing 0.330 in 2cc0A Skipped atom 1478, because occupancy 0.330 <= existing 0.330 in 2cc0A Skipped atom 1480, because occupancy 0.330 <= existing 0.330 in 2cc0A Skipped atom 1481, because occupancy 0.330 <= existing 0.330 in 2cc0A # T0319 read from 2cc0A/merged-good-all-a2m # 2cc0A read from 2cc0A/merged-good-all-a2m # adding 2cc0A to template set # found chain 2cc0A in template set T0319 51 :VDRVDWPAVLTVAAELGNNA 2cc0A 131 :WNNASTDAIVQAVSRLGNGQ T0319 73 :PTKP 2cc0A 155 :HDWP T0319 87 :DDDMAILNDLHTLLLQTSIAEGEMK 2cc0A 159 :ANTLAAIPRIAQTLAGKGLCSGMIS T0319 113 :RNCGHIY 2cc0A 184 :PQTGRAV Number of specific fragments extracted= 4 number of extra gaps= 0 total=162 Number of alignments=37 # 2cc0A read from 2cc0A/merged-good-all-a2m # found chain 2cc0A in template set T0319 50 :IVDRVDWPAVLTVAAELGNNAL 2cc0A 130 :DWNNASTDAIVQAVSRLGNGQV T0319 75 :K 2cc0A 157 :W T0319 86 :TDDDMAILNDLHTLLLQTSIAEGEMK 2cc0A 158 :PANTLAAIPRIAQTLAGKGLCSGMIS T0319 113 :RNCGHIY 2cc0A 184 :PQTGRAV Number of specific fragments extracted= 4 number of extra gaps= 0 total=166 Number of alignments=38 # 2cc0A read from 2cc0A/merged-good-all-a2m # found chain 2cc0A in template set T0319 51 :VDRVDWPAVLTVAAELGNNAL 2cc0A 131 :WNNASTDAIVQAVSRLGNGQV T0319 85 :LTDDDMAILNDLHTLLLQTSIAEGEMK 2cc0A 157 :WPANTLAAIPRIAQTLAGKGLCSGMIS T0319 113 :RNCGHI 2cc0A 184 :PQTGRA Number of specific fragments extracted= 3 number of extra gaps= 0 total=169 Number of alignments=39 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1dv1A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1dv1A expands to /projects/compbio/data/pdb/1dv1.pdb.gz 1dv1A:Skipped atom 1338, because occupancy 0.500 <= existing 0.500 in 1dv1A Skipped atom 1340, because occupancy 0.500 <= existing 0.500 in 1dv1A Skipped atom 1342, because occupancy 0.500 <= existing 0.500 in 1dv1A Skipped atom 1344, because occupancy 0.500 <= existing 0.500 in 1dv1A Skipped atom 1346, because occupancy 0.500 <= existing 0.500 in 1dv1A Skipped atom 3132, because occupancy 0.500 <= existing 0.500 in 1dv1A Skipped atom 3134, because occupancy 0.500 <= existing 0.500 in 1dv1A Skipped atom 3136, because occupancy 0.500 <= existing 0.500 in 1dv1A Skipped atom 3138, because occupancy 0.500 <= existing 0.500 in 1dv1A # T0319 read from 1dv1A/merged-good-all-a2m # 1dv1A read from 1dv1A/merged-good-all-a2m # adding 1dv1A to template set # found chain 1dv1A in template set T0319 42 :FNPEFLLNIVDR 1dv1A 105 :PKAETIRLMGDK T0319 57 :PAVLTVAAELGNNALPPTKPSFPSS 1dv1A 117 :VSAIAAMKKAGVPCVPGSDGPLGDD T0319 86 :TDDDMAILNDL 1dv1A 142 :MDKNRAIAKRI T0319 102 :QTSIAEG 1dv1A 153 :GYPVIIK Number of specific fragments extracted= 4 number of extra gaps= 0 total=173 Number of alignments=40 # 1dv1A read from 1dv1A/merged-good-all-a2m # found chain 1dv1A in template set T0319 42 :FNPEFLLNIVDR 1dv1A 105 :PKAETIRLMGDK T0319 57 :PAVLTVAAELGNNALPPTKPSFPSSIQ 1dv1A 117 :VSAIAAMKKAGVPCVPGSDGPLGDDMD T0319 88 :DDMAILNDL 1dv1A 144 :KNRAIAKRI T0319 102 :QTSIAEG 1dv1A 153 :GYPVIIK Number of specific fragments extracted= 4 number of extra gaps= 0 total=177 Number of alignments=41 # 1dv1A read from 1dv1A/merged-good-all-a2m # found chain 1dv1A in template set T0319 42 :FNPEFLLNIVDR 1dv1A 105 :PKAETIRLMGDK T0319 57 :PAVLTVAAELGNNALP 1dv1A 117 :VSAIAAMKKAGVPCVP T0319 77 :SFPSSIQELTDDDMAILNDL 1dv1A 133 :GSDGPLGDDMDKNRAIAKRI Number of specific fragments extracted= 3 number of extra gaps= 0 total=180 Number of alignments=42 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1iro/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1iro expands to /projects/compbio/data/pdb/1iro.pdb.gz 1iro:Warning: there is no chain 1iro will retry with 1iroA Skipped atom 81, because occupancy 0.310 <= existing 0.690 in 1iro Skipped atom 83, because occupancy 0.310 <= existing 0.690 in 1iro Skipped atom 85, because occupancy 0.310 <= existing 0.690 in 1iro Skipped atom 172, because occupancy 0.450 <= existing 0.550 in 1iro Skipped atom 175, because occupancy 0.450 <= existing 0.550 in 1iro Skipped atom 220, because occupancy 0.490 <= existing 0.510 in 1iro Skipped atom 222, because occupancy 0.490 <= existing 0.510 in 1iro Skipped atom 568, because occupancy 0.260 <= existing 0.740 in 1iro Skipped atom 570, because occupancy 0.260 <= existing 0.740 in 1iro Skipped atom 572, because occupancy 0.260 <= existing 0.740 in 1iro Skipped atom 574, because occupancy 0.260 <= existing 0.740 in 1iro Skipped atom 691, because occupancy 0.450 <= existing 0.550 in 1iro Skipped atom 693, because occupancy 0.450 <= existing 0.550 in 1iro Skipped atom 695, because occupancy 0.450 <= existing 0.550 in 1iro Skipped atom 697, because occupancy 0.450 <= existing 0.550 in 1iro Skipped atom 699, because occupancy 0.450 <= existing 0.550 in 1iro # T0319 read from 1iro/merged-good-all-a2m # 1iro read from 1iro/merged-good-all-a2m # adding 1iro to template set # found chain 1iro in template set T0319 110 :MKCRNCGHIYYIKNGIPNLLLPPHLV 1iro 4 :YTCTVCGYIYNPEDGDPDNGVNPGTD Number of specific fragments extracted= 1 number of extra gaps= 0 total=181 Number of alignments=43 # 1iro read from 1iro/merged-good-all-a2m # found chain 1iro in template set T0319 110 :MKCRNCGHIYYIKNGIPNLLLPPHLV 1iro 4 :YTCTVCGYIYNPEDGDPDNGVNPGTD Number of specific fragments extracted= 1 number of extra gaps= 0 total=182 Number of alignments=44 # 1iro read from 1iro/merged-good-all-a2m # found chain 1iro in template set T0319 110 :MKCRNCGHIYYIKNGIP 1iro 4 :YTCTVCGYIYNPEDGDP Number of specific fragments extracted= 1 number of extra gaps= 0 total=183 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1brfA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1brfA expands to /projects/compbio/data/pdb/1brf.pdb.gz 1brfA:# T0319 read from 1brfA/merged-good-all-a2m # 1brfA read from 1brfA/merged-good-all-a2m # adding 1brfA to template set # found chain 1brfA in template set T0319 109 :EMKCRNCGHIYYIKNGIPNLLLPPHLV 1brfA 2 :KWVCKICGYIYDEDAGDPDNGISPGTK Number of specific fragments extracted= 1 number of extra gaps= 0 total=184 Number of alignments=45 # 1brfA read from 1brfA/merged-good-all-a2m # found chain 1brfA in template set T0319 109 :EMKCRNCGHIYYIKNGIPNLLLPPHLV 1brfA 2 :KWVCKICGYIYDEDAGDPDNGISPGTK Number of specific fragments extracted= 1 number of extra gaps= 0 total=185 Number of alignments=46 # 1brfA read from 1brfA/merged-good-all-a2m # found chain 1brfA in template set T0319 109 :EMKCRNCGHIYYIKNGI 1brfA 2 :KWVCKICGYIYDEDAGD Number of specific fragments extracted= 1 number of extra gaps= 0 total=186 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1dl6A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1dl6A expands to /projects/compbio/data/pdb/1dl6.pdb.gz 1dl6A:# T0319 read from 1dl6A/merged-good-all-a2m # 1dl6A read from 1dl6A/merged-good-all-a2m # adding 1dl6A to template set # found chain 1dl6A in template set T0319 70 :ALPPTKPSFPSSIQELTDDD 1dl6A 10 :LPRVTCPNHPDAILVEDYRA T0319 108 :GEMKCRNCGHIY 1dl6A 30 :GDMICPECGLVV Number of specific fragments extracted= 2 number of extra gaps= 0 total=188 Number of alignments=47 # 1dl6A read from 1dl6A/merged-good-all-a2m # found chain 1dl6A in template set T0319 77 :SFPSSIQELTDD 1dl6A 10 :LPRVTCPNHPDA T0319 104 :SIAE 1dl6A 22 :ILVE T0319 108 :GEMKCRNCGHIY 1dl6A 30 :GDMICPECGLVV Number of specific fragments extracted= 3 number of extra gaps= 0 total=191 Number of alignments=48 # 1dl6A read from 1dl6A/merged-good-all-a2m # found chain 1dl6A in template set T0319 77 :SFPSSIQELTDD 1dl6A 10 :LPRVTCPNHPDA T0319 104 :SIAE 1dl6A 22 :ILVE T0319 108 :GEMKCRNCGHIY 1dl6A 30 :GDMICPECGLVV Number of specific fragments extracted= 3 number of extra gaps= 0 total=194 Number of alignments=49 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1yk4A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1yk4A expands to /projects/compbio/data/pdb/1yk4.pdb.gz 1yk4A:Skipped atom 15, because occupancy 0.220 <= existing 0.780 in 1yk4A Skipped atom 19, because occupancy 0.220 <= existing 0.780 in 1yk4A Skipped atom 21, because occupancy 0.220 <= existing 0.780 in 1yk4A Skipped atom 23, because occupancy 0.220 <= existing 0.780 in 1yk4A Skipped atom 25, because occupancy 0.220 <= existing 0.780 in 1yk4A Skipped atom 27, because occupancy 0.220 <= existing 0.780 in 1yk4A Skipped atom 77, because occupancy 0.130 <= existing 0.610 in 1yk4A Skipped atom 78, because occupancy 0.260 <= existing 0.610 in 1yk4A Skipped atom 80, because occupancy 0.130 <= existing 0.610 in 1yk4A Skipped atom 81, because occupancy 0.260 <= existing 0.610 in 1yk4A Skipped atom 106, because occupancy 0.380 <= existing 0.620 in 1yk4A Skipped atom 108, because occupancy 0.380 <= existing 0.620 in 1yk4A Skipped atom 128, because occupancy 0.380 <= existing 0.620 in 1yk4A Skipped atom 130, because occupancy 0.380 <= existing 0.620 in 1yk4A Skipped atom 132, because occupancy 0.380 <= existing 0.620 in 1yk4A Skipped atom 134, because occupancy 0.380 <= existing 0.620 in 1yk4A Skipped atom 136, because occupancy 0.380 <= existing 0.620 in 1yk4A Skipped atom 138, because occupancy 0.380 <= existing 0.620 in 1yk4A Skipped atom 140, because occupancy 0.380 <= existing 0.620 in 1yk4A Skipped atom 142, because occupancy 0.380 <= existing 0.620 in 1yk4A Skipped atom 166, because occupancy 0.380 <= existing 0.620 in 1yk4A Skipped atom 323, because occupancy 0.220 <= existing 0.780 in 1yk4A Skipped atom 325, because occupancy 0.220 <= existing 0.780 in 1yk4A Skipped atom 327, because occupancy 0.220 <= existing 0.780 in 1yk4A Skipped atom 398, because occupancy 0.360 <= existing 0.590 in 1yk4A Skipped atom 399, because occupancy 0.060 <= existing 0.590 in 1yk4A Skipped atom 401, because occupancy 0.360 <= existing 0.590 in 1yk4A Skipped atom 402, because occupancy 0.060 <= existing 0.590 in 1yk4A Skipped atom 565, because occupancy 0.490 <= existing 0.510 in 1yk4A Skipped atom 567, because occupancy 0.490 <= existing 0.510 in 1yk4A Skipped atom 569, because occupancy 0.490 <= existing 0.510 in 1yk4A Skipped atom 571, because occupancy 0.490 <= existing 0.510 in 1yk4A Skipped atom 573, because occupancy 0.490 <= existing 0.510 in 1yk4A Skipped atom 575, because occupancy 0.490 <= existing 0.510 in 1yk4A Skipped atom 577, because occupancy 0.490 <= existing 0.510 in 1yk4A Skipped atom 579, because occupancy 0.490 <= existing 0.510 in 1yk4A Skipped atom 589, because occupancy 0.490 <= existing 0.510 in 1yk4A Skipped atom 591, because occupancy 0.490 <= existing 0.510 in 1yk4A Skipped atom 593, because occupancy 0.490 <= existing 0.510 in 1yk4A Skipped atom 595, because occupancy 0.490 <= existing 0.510 in 1yk4A Skipped atom 597, because occupancy 0.490 <= existing 0.510 in 1yk4A Skipped atom 599, because occupancy 0.490 <= existing 0.510 in 1yk4A Skipped atom 601, because occupancy 0.490 <= existing 0.510 in 1yk4A Skipped atom 603, because occupancy 0.490 <= existing 0.510 in 1yk4A Skipped atom 613, because occupancy 0.490 <= existing 0.510 in 1yk4A Skipped atom 666, because occupancy 0.340 <= existing 0.660 in 1yk4A Skipped atom 670, because occupancy 0.340 <= existing 0.660 in 1yk4A Skipped atom 672, because occupancy 0.340 <= existing 0.660 in 1yk4A Skipped atom 674, because occupancy 0.340 <= existing 0.660 in 1yk4A Skipped atom 822, because occupancy 0.390 <= existing 0.610 in 1yk4A Skipped atom 824, because occupancy 0.390 <= existing 0.610 in 1yk4A Skipped atom 826, because occupancy 0.390 <= existing 0.610 in 1yk4A Skipped atom 828, because occupancy 0.390 <= existing 0.610 in 1yk4A Skipped atom 830, because occupancy 0.390 <= existing 0.610 in 1yk4A Skipped atom 843, because occupancy 0.260 <= existing 0.740 in 1yk4A Skipped atom 847, because occupancy 0.260 <= existing 0.740 in 1yk4A Skipped atom 849, because occupancy 0.260 <= existing 0.740 in 1yk4A Skipped atom 851, because occupancy 0.260 <= existing 0.740 in 1yk4A Skipped atom 853, because occupancy 0.260 <= existing 0.740 in 1yk4A Skipped atom 855, because occupancy 0.260 <= existing 0.740 in 1yk4A Skipped atom 857, because occupancy 0.260 <= existing 0.740 in 1yk4A Skipped atom 859, because occupancy 0.260 <= existing 0.740 in 1yk4A # T0319 read from 1yk4A/merged-good-all-a2m # 1yk4A read from 1yk4A/merged-good-all-a2m # adding 1yk4A to template set # found chain 1yk4A in template set T0319 109 :EMKCRNCGHIYYIKNGIPNLLLPPHLV 1yk4A 3 :KLSCKICGYIYDEDEGDPDNGISPGTK Number of specific fragments extracted= 1 number of extra gaps= 0 total=195 Number of alignments=50 # 1yk4A read from 1yk4A/merged-good-all-a2m # found chain 1yk4A in template set T0319 109 :EMKCRNCGHIYYIKNGIPNLLLPPHLV 1yk4A 3 :KLSCKICGYIYDEDEGDPDNGISPGTK Number of specific fragments extracted= 1 number of extra gaps= 0 total=196 Number of alignments=51 # 1yk4A read from 1yk4A/merged-good-all-a2m # found chain 1yk4A in template set T0319 109 :EMKCRNCGHIYYIKNGIP 1yk4A 3 :KLSCKICGYIYDEDEGDP Number of specific fragments extracted= 1 number of extra gaps= 0 total=197 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1zin/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0319 read from 1zin/merged-good-all-a2m # 1zin read from 1zin/merged-good-all-a2m # found chain 1zin in training set T0319 45 :EFLLNIVDR 1zin 66 :GIVRERLSK T0319 56 :WPAVLTVAAELGNN 1zin 93 :AEALETMLADIGRK T0319 71 :LP 1zin 107 :LD T0319 89 :DMAILNDLHT 1zin 116 :RQDVLMERLT T0319 108 :GEMKCRNCGHIYY 1zin 126 :GRRICRNCGATYH Number of specific fragments extracted= 5 number of extra gaps= 0 total=202 Number of alignments=52 # 1zin read from 1zin/merged-good-all-a2m # found chain 1zin in training set T0319 45 :EFLLNIVDR 1zin 66 :GIVRERLSK T0319 56 :WPAVLTVAAELGNN 1zin 93 :AEALETMLADIGRK T0319 71 :LP 1zin 107 :LD T0319 84 :EL 1zin 114 :DV T0319 89 :DMAILNDLHT 1zin 116 :RQDVLMERLT T0319 108 :GEMKCRNCGHIYY 1zin 126 :GRRICRNCGATYH Number of specific fragments extracted= 6 number of extra gaps= 0 total=208 Number of alignments=53 # 1zin read from 1zin/merged-good-all-a2m # found chain 1zin in training set T0319 56 :WPAVLTVAAELGN 1zin 93 :AEALETMLADIGR T0319 77 :SFP 1zin 106 :KLD T0319 89 :DMAIL 1zin 116 :RQDVL T0319 97 :HTLLL 1zin 121 :MERLT T0319 108 :GEMKCRNCGHIY 1zin 126 :GRRICRNCGATY Number of specific fragments extracted= 5 number of extra gaps= 0 total=213 Number of alignments=54 # command:Using radius: 8.0000 Alignment mode NUMB_ALIGNS: 54 Adding 824 constraints to all.constraints Done adding distance constraints # command:Reading probabilities from probabilities.dat Reading constraints from ConstraintSet all.constraints maxweight: 1.0000 Optimizing... Probability sum: -264.4720, CN propb: -264.4720 weights: 0.0990 constraints: 233 # command:Found ConstraintSet # PrintContacts align.constraints_v3 Number of constraints in align.constraints 233 # command:Found ConstraintSet # PrintContacts align_bonus.constraints_v3 Number of constraints in align.constraints.bonus 233 # command:Found ConstraintSet # PrintContacts rejected.constraints_v3 Number of constraints in rejected.constraints 591 # command:Found ConstraintSet # PrintContacts rejected_bonus.constraints_v3 Number of constraints in rejected.constraints.bonus 591 # command:Found ConstraintSet # PrintContacts non_contacts.constraints_v3 Number of constraints in noncontact.constraints 0 # command:Found ConstraintSet # PrintContacts non_contacts_bonus.constraints_v3 Number of constraints in noncontact.constraints.bonus 0 # command:Found ConstraintSet # PrintContacts all.constraints_v3 Number of constraints in all.constraints 824 # command: