# 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/T0351/ # command:# Making conformation for sequence T0351 numbered 1 through 117 Created new target T0351 from T0351.a2m # command:# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/T0351/ # command:Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0351//projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0351/manyalignments-good-all.under or /projects/compbio/experiments/protein-predict/casp7/T0351//projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0351/manyalignments-good-all.under.gz for input Trying /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0351/manyalignments-good-all.under # reading script from file /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0351/manyalignments-good-all.under # Reading fragments from alignment file # Attempting to read fragment alignments from file 1g0uG/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1g0uG expands to /projects/compbio/data/pdb/1g0u.pdb.gz 1g0uG:# T0351 read from 1g0uG/merged-good-all-a2m # 1g0uG read from 1g0uG/merged-good-all-a2m # adding 1g0uG to template set # found chain 1g0uG in template set T0351 4 :YDAIMYK 1g0uG 191 :EFAITHM # choosing archetypes in rotamer library T0351 11 :YPNAVSRKDFELR 1g0uG 201 :LGTEFSKNDLEVG T0351 24 :NDGNGSYI 1g0uG 216 :TKDKFFTL T0351 42 :TQAELETWWEELQKN 1g0uG 225 :SAENIEERLVAIAEQ Number of specific fragments extracted= 4 number of extra gaps= 0 total=4 Number of alignments=1 # 1g0uG read from 1g0uG/merged-good-all-a2m # found chain 1g0uG in template set Warning: unaligning (T0351)P57 because last residue in template chain is (1g0uG)D240 T0351 5 :DAIMYK 1g0uG 192 :FAITHM T0351 11 :YPNAVSRKDFELR 1g0uG 201 :LGTEFSKNDLEVG T0351 24 :NDGNGSYI 1g0uG 216 :TKDKFFTL T0351 42 :TQAELETWWEELQKN 1g0uG 225 :SAENIEERLVAIAEQ Number of specific fragments extracted= 4 number of extra gaps= 0 total=8 Number of alignments=2 # 1g0uG read from 1g0uG/merged-good-all-a2m # found chain 1g0uG in template set T0351 3 :LYDA 1g0uG 197 :MIDA T0351 11 :YPNAVSRKDFELR 1g0uG 201 :LGTEFSKNDLEVG T0351 30 :YIEKWNLRA 1g0uG 214 :VATKDKFFT T0351 41 :PTQAELETWWEELQK 1g0uG 224 :LSAENIEERLVAIAE Number of specific fragments extracted= 4 number of extra gaps= 0 total=12 Number of alignments=3 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1nkwL/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/T0351/1nkwL/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0351/1nkwL/merged-good-all-a2m.gz for input Trying 1nkwL/merged-good-all-a2m Error: Couldn't open file 1nkwL/merged-good-all-a2m or 1nkwL/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1f1sA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1f1sA expands to /projects/compbio/data/pdb/1f1s.pdb.gz 1f1sA:# T0351 read from 1f1sA/merged-good-all-a2m # 1f1sA read from 1f1sA/merged-good-all-a2m # adding 1f1sA to template set # found chain 1f1sA in template set T0351 11 :YPNAVSRKDFELR 1f1sA 218 :YPNATGSTTVKIS T0351 25 :DGNGSYIEKWNLRAPLPTQAELETWWEELQKN 1f1sA 231 :DKSGKIIKEVPLSVTASTEDNFTKLLDKWNDV T0351 57 :PPYEPPDQVELL 1f1sA 269 :YDTNDSNMQKLN T0351 70 :Q 1f1sA 281 :Q T0351 77 :LARKQLEELNKTL 1f1sA 282 :KLDETNAKNIEAI Number of specific fragments extracted= 5 number of extra gaps= 0 total=17 Number of alignments=4 # 1f1sA read from 1f1sA/merged-good-all-a2m # found chain 1f1sA in template set T0351 13 :NAVSRKDFELR 1f1sA 220 :NATGSTTVKIS T0351 25 :DGNGSYIEKWNLRAPLPTQAELETWWEELQK 1f1sA 231 :DKSGKIIKEVPLSVTASTEDNFTKLLDKWND T0351 57 :PPYEP 1f1sA 269 :YDTND T0351 63 :DQVELLAQEL 1f1sA 274 :SNMQKLNQKL T0351 75 :EKLARKQLEE 1f1sA 284 :DETNAKNIEA Number of specific fragments extracted= 5 number of extra gaps= 0 total=22 Number of alignments=5 # 1f1sA read from 1f1sA/merged-good-all-a2m # found chain 1f1sA in template set T0351 12 :PNAVSRKDFELR 1f1sA 219 :PNATGSTTVKIS T0351 25 :DGNGSYIEKWNLRAPLPTQAELETWWEELQK 1f1sA 231 :DKSGKIIKEVPLSVTASTEDNFTKLLDKWND T0351 57 :PPYE 1f1sA 269 :YDTN T0351 62 :PDQVELL 1f1sA 273 :DSNMQKL T0351 82 :LEELNKTLGNELSDIKL 1f1sA 280 :NQKLDETNAKNIEAIKL Number of specific fragments extracted= 5 number of extra gaps= 0 total=27 Number of alignments=6 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2fi9A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2fi9A expands to /projects/compbio/data/pdb/2fi9.pdb.gz 2fi9A:# T0351 read from 2fi9A/merged-good-all-a2m # 2fi9A read from 2fi9A/merged-good-all-a2m # adding 2fi9A to template set # found chain 2fi9A in template set Warning: unaligning (T0351)Y11 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2fi9A)F12 T0351 12 :PNAVSRKDF 2fi9A 13 :PGRAPIDAY T0351 21 :ELRNDG 2fi9A 25 :GFRFAD T0351 27 :N 2fi9A 35 :G T0351 29 :SYIEKWNLRAPLPTQAELETWWE 2fi9A 42 :SGIYGIDMTGPVPTQEDISRVLE T0351 54 :QKNPPYEPPDQVELLAQE 2fi9A 77 :GVELLRLPEELRVLLWEK T0351 75 :EKLARKQLEELN 2fi9A 103 :TGAAVRTFNVLL Number of specific fragments extracted= 6 number of extra gaps= 1 total=33 Number of alignments=7 # 2fi9A read from 2fi9A/merged-good-all-a2m # found chain 2fi9A in template set Warning: unaligning (T0351)Y11 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2fi9A)F12 T0351 12 :PNAVSRKDF 2fi9A 13 :PGRAPIDAY T0351 21 :ELRNDG 2fi9A 25 :GFRFAD T0351 27 :NG 2fi9A 35 :GS T0351 31 :IEKWNLRAPLPTQAELETWWE 2fi9A 44 :IYGIDMTGPVPTQEDISRVLE T0351 57 :PPYEPPDQVELLAQELS 2fi9A 79 :ELLRLPEELRVLLWEKR T0351 74 :QEKLARKQLEELNKT 2fi9A 102 :STGAAVRTFNVLLAE Number of specific fragments extracted= 6 number of extra gaps= 1 total=39 Number of alignments=8 # 2fi9A read from 2fi9A/merged-good-all-a2m # found chain 2fi9A in template set Warning: unaligning (T0351)Y11 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2fi9A)F12 T0351 12 :PNAVS 2fi9A 13 :PGRAP T0351 22 :LRNDGNG 2fi9A 18 :IDAYGNG T0351 29 :SYIEKWNLRAPLPTQAELETWWE 2fi9A 42 :SGIYGIDMTGPVPTQEDISRVLE T0351 54 :QKNPPYEPPDQVELLAQE 2fi9A 77 :GVELLRLPEELRVLLWEK Number of specific fragments extracted= 4 number of extra gaps= 1 total=43 Number of alignments=9 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1rqlA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1rqlA expands to /projects/compbio/data/pdb/1rql.pdb.gz 1rqlA:# T0351 read from 1rqlA/merged-good-all-a2m # 1rqlA read from 1rqlA/merged-good-all-a2m # adding 1rqlA to template set # found chain 1rqlA in template set T0351 38 :APLPTQAELETWWEELQKN 1rqlA 75 :RQLPTEADIQEMYEEFEEI T0351 64 :QVELLAQELS 1rqlA 94 :LFAILPRYAS T0351 74 :QEKLARKQLEEL 1rqlA 107 :AVKEVIASLRER T0351 89 :LGNELSDIKLSLLSLKG 1rqlA 128 :YTREMMDIVAKEAALQG Number of specific fragments extracted= 4 number of extra gaps= 0 total=47 Number of alignments=10 # 1rqlA read from 1rqlA/merged-good-all-a2m # found chain 1rqlA in template set T0351 38 :APLPTQAELETWWEELQKN 1rqlA 75 :RQLPTEADIQEMYEEFEEI T0351 57 :PPYEPP 1rqlA 99 :PRYASP T0351 72 :LSQEKLARKQLEELN 1rqlA 105 :INAVKEVIASLRERG T0351 90 :GNELSDIKLSLLSLKG 1rqlA 129 :TREMMDIVAKEAALQG Number of specific fragments extracted= 4 number of extra gaps= 0 total=51 Number of alignments=11 # 1rqlA read from 1rqlA/merged-good-all-a2m # found chain 1rqlA in template set T0351 39 :PLPTQAELETWWEELQK 1rqlA 76 :QLPTEADIQEMYEEFEE Number of specific fragments extracted= 1 number of extra gaps= 0 total=52 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1yrvA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1yrvA expands to /projects/compbio/data/pdb/1yrv.pdb.gz 1yrvA:# T0351 read from 1yrvA/merged-good-all-a2m # 1yrvA read from 1yrvA/merged-good-all-a2m # adding 1yrvA to template set # found chain 1yrvA in template set Warning: unaligning (T0351)N86 because last residue in template chain is (1yrvA)N148 T0351 46 :LETWWEELQK 1yrvA 105 :LSSILLALQV T0351 56 :NPPYEPPDQVELLAQELSQEKLARKQLEEL 1yrvA 118 :NPVLENPVNLEAARILVKDESLYRTILRLF Number of specific fragments extracted= 2 number of extra gaps= 0 total=54 Number of alignments=12 # 1yrvA read from 1yrvA/merged-good-all-a2m # found chain 1yrvA in template set Warning: unaligning (T0351)N86 because last residue in template chain is (1yrvA)N148 T0351 32 :EKWNLRAP 1yrvA 97 :EKWNTNYT T0351 46 :LETWWEELQK 1yrvA 105 :LSSILLALQV T0351 56 :NPPYEPPDQVELLAQELSQEKLARKQLEEL 1yrvA 118 :NPVLENPVNLEAARILVKDESLYRTILRLF Number of specific fragments extracted= 3 number of extra gaps= 0 total=57 Number of alignments=13 # 1yrvA read from 1yrvA/merged-good-all-a2m # found chain 1yrvA in template set Warning: unaligning (T0351)N86 because last residue in template chain is (1yrvA)N148 T0351 47 :ETWWEELQK 1yrvA 106 :SSILLALQV T0351 56 :NPPYEPPDQVELLAQELSQEKLARKQLEEL 1yrvA 118 :NPVLENPVNLEAARILVKDESLYRTILRLF Number of specific fragments extracted= 2 number of extra gaps= 0 total=59 Number of alignments=14 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1nknA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1nknA expands to /projects/compbio/data/pdb/1nkn.pdb.gz 1nknA:# T0351 read from 1nknA/merged-good-all-a2m # 1nknA read from 1nknA/merged-good-all-a2m # adding 1nknA to template set # found chain 1nknA in template set T0351 43 :QAELETWWEELQKN 1nknA 850 :LKQMDKMKEDLAKT T0351 63 :DQVELLAQELSQEKLARK 1nknA 866 :IKKELEEQNVTLLEQKND T0351 82 :LEELNKTLGNELSDIKLSLLSLKGDYAELEHHHHHH 1nknA 884 :LFGSMKQLEDKVEELLSKNYHLENEVARLKKLVGER Number of specific fragments extracted= 3 number of extra gaps= 0 total=62 Number of alignments=15 # 1nknA read from 1nknA/merged-good-all-a2m # found chain 1nknA in template set T0351 43 :QAELETWWEELQKN 1nknA 850 :LKQMDKMKEDLAKT T0351 63 :DQVELLAQELSQE 1nknA 866 :IKKELEEQNVTLL T0351 77 :LARKQLEELNKTLGNELSDIKLSLLSLKGDYAELEHHHHHH 1nknA 879 :EQKNDLFGSMKQLEDKVEELLSKNYHLENEVARLKKLVGER Number of specific fragments extracted= 3 number of extra gaps= 0 total=65 Number of alignments=16 # 1nknA read from 1nknA/merged-good-all-a2m # found chain 1nknA in template set T0351 43 :QA 1nknA 867 :KK T0351 63 :DQVELLAQELSQEKLARKQLEELNKTLGNELSD 1nknA 869 :ELEEQNVTLLEQKNDLFGSMKQLEDKVEELLSK T0351 100 :LLSLKGDYAELEHHHHHH 1nknA 902 :NYHLENEVARLKKLVGER Number of specific fragments extracted= 3 number of extra gaps= 0 total=68 Number of alignments=17 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2ahqA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2ahqA expands to /projects/compbio/data/pdb/2ahq.pdb.gz 2ahqA:# T0351 read from 2ahqA/merged-good-all-a2m # 2ahqA read from 2ahqA/merged-good-all-a2m # adding 2ahqA to template set # found chain 2ahqA in template set Warning: unaligning (T0351)G90 because last residue in template chain is (2ahqA)G67 T0351 37 :RAPLPTQAELETWWEELQKN 2ahqA 12 :SAEGLTQGELMKLIKEIVEN T0351 57 :PPYEPP 2ahqA 33 :DKRKPY T0351 64 :QVELLAQELSQ 2ahqA 39 :SDQEIANILKE T0351 79 :RKQLEELNKTL 2ahqA 56 :RRTVAKYREML Number of specific fragments extracted= 4 number of extra gaps= 0 total=72 Number of alignments=18 # 2ahqA read from 2ahqA/merged-good-all-a2m # found chain 2ahqA in template set Warning: unaligning (T0351)G90 because last residue in template chain is (2ahqA)G67 T0351 36 :LRAPLPTQAELETWWEELQKNPPYEPPDQVELLAQELS 2ahqA 11 :ESAEGLTQGELMKLIKEIVENEDKRKPYSDQEIANILK T0351 79 :RKQLEELNKTL 2ahqA 56 :RRTVAKYREML Number of specific fragments extracted= 2 number of extra gaps= 0 total=74 Number of alignments=19 # 2ahqA read from 2ahqA/merged-good-all-a2m # found chain 2ahqA in template set Warning: unaligning (T0351)G90 because last residue in template chain is (2ahqA)G67 T0351 37 :RAPLPTQAELETWWEELQKNPPYEPPDQVELLAQELSQ 2ahqA 12 :SAEGLTQGELMKLIKEIVENEDKRKPYSDQEIANILKE T0351 79 :RKQLEELNKTL 2ahqA 56 :RRTVAKYREML Number of specific fragments extracted= 2 number of extra gaps= 0 total=76 Number of alignments=20 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2ap1A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2ap1A expands to /projects/compbio/data/pdb/2ap1.pdb.gz 2ap1A:Skipped atom 67, because occupancy 0.5 <= existing 0.500 in 2ap1A Skipped atom 69, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 71, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 319, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 655, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 728, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 730, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 732, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 734, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 736, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 738, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 740, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 742, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 744, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 746, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 748, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 759, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 763, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 765, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 767, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 769, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 833, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 837, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 839, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 841, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 843, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 1053, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 1055, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 1376, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 1380, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 1382, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 1384, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 1386, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 1388, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 1390, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 1392, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 1718, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 1722, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 1724, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 1726, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 1728, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 1730, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 1869, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 1873, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 1875, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 1877, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 1983, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 1987, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 1989, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 1991, because occupancy 0.500 <= existing 0.500 in 2ap1A # T0351 read from 2ap1A/merged-good-all-a2m # 2ap1A read from 2ap1A/merged-good-all-a2m # adding 2ap1A to template set # found chain 2ap1A in template set T0351 27 :NGSYIEKWNLRAPLPTQAELETW 2ap1A 20 :TRRLQWEKRVPTPHTSYSAFLDA T0351 78 :ARKQLEELNKTLG 2ap1A 43 :VCELVEEADQRFG Number of specific fragments extracted= 2 number of extra gaps= 0 total=78 Number of alignments=21 # 2ap1A read from 2ap1A/merged-good-all-a2m # found chain 2ap1A in template set T0351 16 :SRKDFELRN 2ap1A 8 :GGTKIALGV T0351 25 :DGNGSYIEKWNLRAPLPTQAELETWW 2ap1A 18 :DSTRRLQWEKRVPTPHTSYSAFLDAV T0351 79 :RKQLEELNKTLGN 2ap1A 44 :CELVEEADQRFGV Number of specific fragments extracted= 3 number of extra gaps= 0 total=81 Number of alignments=22 # 2ap1A read from 2ap1A/merged-good-all-a2m # found chain 2ap1A in template set T0351 17 :RKDFELR 2ap1A 9 :GTKIALG T0351 25 :DGNGSYIEKWNLRAPLPTQAELETWWEEL 2ap1A 18 :DSTRRLQWEKRVPTPHTSYSAFLDAVCEL T0351 82 :LEELNKTLG 2ap1A 47 :VEEADQRFG Number of specific fragments extracted= 3 number of extra gaps= 0 total=84 Number of alignments=23 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1fjcA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1fjcA expands to /projects/compbio/data/pdb/1fjc.pdb.gz 1fjcA:# T0351 read from 1fjcA/merged-good-all-a2m # 1fjcA read from 1fjcA/merged-good-all-a2m # adding 1fjcA to template set # found chain 1fjcA in template set T0351 22 :LRNDGNGSYIEKWNLR 1fjcA 46 :VSQDGKSKGIAYIEFK T0351 42 :TQAELETWWEE 1fjcA 62 :SEADAEKNLEE Number of specific fragments extracted= 2 number of extra gaps= 0 total=86 Number of alignments=24 # 1fjcA read from 1fjcA/merged-good-all-a2m # found chain 1fjcA in template set T0351 22 :LRNDGNGSYIEKWNLR 1fjcA 46 :VSQDGKSKGIAYIEFK T0351 42 :TQAELETWWEE 1fjcA 62 :SEADAEKNLEE Number of specific fragments extracted= 2 number of extra gaps= 0 total=88 Number of alignments=25 # 1fjcA read from 1fjcA/merged-good-all-a2m # found chain 1fjcA in template set T0351 22 :LRNDGNGSYIEKWNLR 1fjcA 46 :VSQDGKSKGIAYIEFK T0351 42 :TQAELETWWEELQ 1fjcA 62 :SEADAEKNLEEKQ Number of specific fragments extracted= 2 number of extra gaps= 0 total=90 Number of alignments=26 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1khhA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1khhA expands to /projects/compbio/data/pdb/1khh.pdb.gz 1khhA:# T0351 read from 1khhA/merged-good-all-a2m # 1khhA read from 1khhA/merged-good-all-a2m # adding 1khhA to template set # found chain 1khhA in template set T0351 50 :WEELQK 1khhA 173 :WGELMK T0351 57 :PPYEP 1khhA 179 :SKYTD T0351 64 :QVELLAQEL 1khhA 184 :ITAMFEETQ T0351 79 :RKQLEE 1khhA 193 :VPALLE Number of specific fragments extracted= 4 number of extra gaps= 0 total=94 Number of alignments=27 # 1khhA read from 1khhA/merged-good-all-a2m # found chain 1khhA in template set Number of specific fragments extracted= 0 number of extra gaps= 0 total=94 # 1khhA read from 1khhA/merged-good-all-a2m # found chain 1khhA in template set T0351 42 :TQAELETWWEELQK 1khhA 91 :NDGVFQRLQNWALK Number of specific fragments extracted= 1 number of extra gaps= 0 total=95 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1xm2A/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/T0351/1xm2A/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0351/1xm2A/merged-good-all-a2m.gz for input Trying 1xm2A/merged-good-all-a2m Error: Couldn't open file 1xm2A/merged-good-all-a2m or 1xm2A/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1vorO/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/T0351/1vorO/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0351/1vorO/merged-good-all-a2m.gz for input Trying 1vorO/merged-good-all-a2m Error: Couldn't open file 1vorO/merged-good-all-a2m or 1vorO/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1gl6A/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/T0351/1gl6A/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0351/1gl6A/merged-good-all-a2m.gz for input Trying 1gl6A/merged-good-all-a2m Error: Couldn't open file 1gl6A/merged-good-all-a2m or 1gl6A/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1fseA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1fseA expands to /projects/compbio/data/pdb/1fse.pdb.gz 1fseA:Skipped atom 52, because occupancy 0.500 <= existing 0.500 in 1fseA Skipped atom 54, because occupancy 0.500 <= existing 0.500 in 1fseA Skipped atom 56, because occupancy 0.500 <= existing 0.500 in 1fseA Skipped atom 58, because occupancy 0.500 <= existing 0.500 in 1fseA Skipped atom 164, because occupancy 0.500 <= existing 0.500 in 1fseA Skipped atom 166, because occupancy 0.500 <= existing 0.500 in 1fseA Skipped atom 168, because occupancy 0.500 <= existing 0.500 in 1fseA Skipped atom 286, because occupancy 1.000 <= existing 1.000 in 1fseA Skipped atom 288, because occupancy 0.500 <= existing 0.500 in 1fseA Skipped atom 290, because occupancy 0.500 <= existing 0.500 in 1fseA Skipped atom 292, because occupancy 0.500 <= existing 0.500 in 1fseA # T0351 read from 1fseA/merged-good-all-a2m # 1fseA read from 1fseA/merged-good-all-a2m # adding 1fseA to template set # found chain 1fseA in template set Warning: unaligning (T0351)R37 because first residue in template chain is (1fseA)S8 T0351 38 :APLPT 1fseA 9 :KPLLT T0351 44 :AELETWWEELQK 1fseA 14 :KREREVFELLVQ T0351 59 :YEPPD 1fseA 26 :DKTTK T0351 66 :E 1fseA 31 :E T0351 68 :LAQEL 1fseA 32 :IASEL T0351 73 :SQEKLARKQLEELNKTLG 1fseA 38 :ISEKTVRNHISNAMQKLG T0351 93 :LSDIKLSLL 1fseA 59 :RSQAVVELL Number of specific fragments extracted= 7 number of extra gaps= 0 total=102 Number of alignments=28 # 1fseA read from 1fseA/merged-good-all-a2m # found chain 1fseA in template set Warning: unaligning (T0351)R37 because first residue in template chain is (1fseA)S8 T0351 38 :APLPTQ 1fseA 9 :KPLLTK T0351 45 :ELETWWEELQKNP 1fseA 15 :REREVFELLVQDK T0351 64 :QVELLAQELS 1fseA 28 :TTKEIASELF T0351 74 :QEKLARKQLEELNKTLGN 1fseA 39 :SEKTVRNHISNAMQKLGV T0351 92 :ELSDIKLSLLSL 1fseA 58 :GRSQAVVELLRM Number of specific fragments extracted= 5 number of extra gaps= 0 total=107 Number of alignments=29 # 1fseA read from 1fseA/merged-good-all-a2m # found chain 1fseA in template set Warning: unaligning (T0351)R37 because first residue in template chain is (1fseA)S8 T0351 38 :APLPT 1fseA 9 :KPLLT T0351 44 :AELETWWEELQKNPP 1fseA 14 :KREREVFELLVQDKT T0351 64 :QVELLAQELSQEKLARKQLEELNKTLG 1fseA 29 :TKEIASELFISEKTVRNHISNAMQKLG Number of specific fragments extracted= 3 number of extra gaps= 0 total=110 Number of alignments=30 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1xqaA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0351 read from 1xqaA/merged-good-all-a2m # 1xqaA read from 1xqaA/merged-good-all-a2m # found chain 1xqaA in training set T0351 15 :VSRKDFELRNDGNGSY 1xqaA 32 :RGNAFAVMRDNDGFIL T0351 31 :IEK 1xqaA 49 :LMK T0351 36 :LRAP 1xqaA 55 :VQYP T0351 40 :LPTQAELETWWEELQKNPPYEPP 1xqaA 67 :QESEEQVDKINQRLKEDGFLVEP Number of specific fragments extracted= 4 number of extra gaps= 0 total=114 Number of alignments=31 # 1xqaA read from 1xqaA/merged-good-all-a2m # found chain 1xqaA in training set T0351 15 :VSRKDFELRNDGNGSY 1xqaA 32 :RGNAFAVMRDNDGFIL T0351 31 :IEK 1xqaA 49 :LMK T0351 35 :NLRAP 1xqaA 54 :EVQYP T0351 40 :LPTQAELETWWEELQKN 1xqaA 67 :QESEEQVDKINQRLKED T0351 57 :PPYEP 1xqaA 85 :FLVEP Number of specific fragments extracted= 5 number of extra gaps= 0 total=119 Number of alignments=32 # 1xqaA read from 1xqaA/merged-good-all-a2m # found chain 1xqaA in training set T0351 17 :RKDFELRNDGNGSYIEKWNLRAPLPTQAELETWWEELQKNP 1xqaA 44 :GFILTLMKGKEVQYPKTFHVGFPQESEEQVDKINQRLKEDG T0351 58 :PYEPP 1xqaA 86 :LVEPP Number of specific fragments extracted= 2 number of extra gaps= 0 total=121 Number of alignments=33 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1cll/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1cll expands to /projects/compbio/data/pdb/1cll.pdb.gz 1cll:Warning: there is no chain 1cll will retry with 1cllA Skipped atom 897, because occupancy 0.500 <= existing 0.500 in 1cll Skipped atom 899, because occupancy 0.500 <= existing 0.500 in 1cll Skipped atom 901, because occupancy 0.500 <= existing 0.500 in 1cll # T0351 read from 1cll/merged-good-all-a2m # 1cll read from 1cll/merged-good-all-a2m # adding 1cll to template set # found chain 1cll in template set T0351 3 :LYDAIMYKYPNAVSRKD 1cll 12 :FKEAFSLFDKDGDGTIT T0351 24 :ND 1cll 38 :SL T0351 38 :APLPTQAELETWWEELQKNPPYE 1cll 40 :GQNPTEAELQDMINEVDADGNGT T0351 62 :PDQVELLAQELSQEKLARKQLEE 1cll 66 :PEFLTMMARKMKDTDSEEEIREA T0351 86 :NKTL 1cll 89 :FRVF T0351 90 :GNELSDI 1cll 102 :AAELRHV T0351 98 :LSLLSLKGDYAELEH 1cll 109 :MTNLGEKLTDEEVDE Number of specific fragments extracted= 7 number of extra gaps= 0 total=128 Number of alignments=34 # 1cll read from 1cll/merged-good-all-a2m # found chain 1cll in template set T0351 3 :LYDAIMYKYPNAVSRKD 1cll 12 :FKEAFSLFDKDGDGTIT T0351 34 :WNLRAPLPTQAELETWWEELQKNPPYE 1cll 36 :MRSLGQNPTEAELQDMINEVDADGNGT T0351 63 :DQVELLAQELSQEKLARKQLEELNKTLGN 1cll 70 :TMMARKMKDTDSEEEIREAFRVFDKDGNG T0351 92 :ELSDIKLSLLSLKGDYAELE 1cll 101 :SAAELRHVMTNLGEKLTDEE Number of specific fragments extracted= 4 number of extra gaps= 0 total=132 Number of alignments=35 # 1cll read from 1cll/merged-good-all-a2m # found chain 1cll in template set T0351 24 :NDGNGSY 1cll 21 :KDGDGTI T0351 39 :PLPTQAELETWWEELQKNPPYE 1cll 41 :QNPTEAELQDMINEVDADGNGT T0351 61 :PPDQVELLAQELSQEKLARKQLEELNK 1cll 65 :FPEFLTMMARKMKDTDSEEEIREAFRV T0351 89 :L 1cll 92 :F T0351 90 :GNELSD 1cll 102 :AAELRH Number of specific fragments extracted= 5 number of extra gaps= 0 total=137 Number of alignments=36 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1jl5A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1jl5A expands to /projects/compbio/data/pdb/1jl5.pdb.gz 1jl5A:# T0351 read from 1jl5A/merged-good-all-a2m # 1jl5A read from 1jl5A/merged-good-all-a2m # adding 1jl5A to template set # found chain 1jl5A in template set Warning: unaligning (T0351)P41 because first residue in template chain is (1jl5A)K1034 T0351 42 :TQAELETWWEELQKN 1jl5A 1035 :SKTEYYNAWSEWERN T0351 57 :PPYEPP 1jl5A 1051 :PPGNGE T0351 74 :QEKLARKQLEELNKT 1jl5A 1057 :QREMAVSRLRDCLDR Number of specific fragments extracted= 3 number of extra gaps= 0 total=140 Number of alignments=37 # 1jl5A read from 1jl5A/merged-good-all-a2m # found chain 1jl5A in template set Warning: unaligning (T0351)P41 because first residue in template chain is (1jl5A)K1034 T0351 42 :TQAELETWWEELQKN 1jl5A 1035 :SKTEYYNAWSEWERN T0351 57 :PPYEPP 1jl5A 1051 :PPGNGE T0351 74 :QEKLARKQLEELNKTL 1jl5A 1057 :QREMAVSRLRDCLDRQ Number of specific fragments extracted= 3 number of extra gaps= 0 total=143 Number of alignments=38 # 1jl5A read from 1jl5A/merged-good-all-a2m # found chain 1jl5A in template set Warning: unaligning (T0351)P41 because first residue in template chain is (1jl5A)K1034 T0351 42 :TQAELETWWEELQKNPPYEPPDQVELLAQEL 1jl5A 1035 :SKTEYYNAWSEWERNAPPGNGEQREMAVSRL T0351 79 :RKQL 1jl5A 1066 :RDCL Number of specific fragments extracted= 2 number of extra gaps= 0 total=145 Number of alignments=39 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1vhfA/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/T0351/1vhfA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0351/1vhfA/merged-good-all-a2m.gz for input Trying 1vhfA/merged-good-all-a2m Error: Couldn't open file 1vhfA/merged-good-all-a2m or 1vhfA/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1swvA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1swvA expands to /projects/compbio/data/pdb/1swv.pdb.gz 1swvA:# T0351 read from 1swvA/merged-good-all-a2m # 1swvA read from 1swvA/merged-good-all-a2m # adding 1swvA to template set # found chain 1swvA in template set T0351 38 :APLPTQAELETWWEELQK 1swvA 75 :RQLPTEADIQEMYEEFEE T0351 63 :DQVELLAQE 1swvA 93 :ILFAILPRY T0351 72 :LSQEKLARKQLEEL 1swvA 105 :INGVKEVIASLRER T0351 89 :LGNELSDIKLSLLSLKG 1swvA 128 :YTREMMDIVAKEAALQG Number of specific fragments extracted= 4 number of extra gaps= 0 total=149 Number of alignments=40 # 1swvA read from 1swvA/merged-good-all-a2m # found chain 1swvA in template set T0351 38 :APLPTQAELETWWEELQKN 1swvA 75 :RQLPTEADIQEMYEEFEEI T0351 57 :PPYEPP 1swvA 99 :PRYASP T0351 72 :LSQEKLARKQLEELN 1swvA 105 :INGVKEVIASLRERG T0351 90 :GNELSDIKLSLLSLKG 1swvA 129 :TREMMDIVAKEAALQG Number of specific fragments extracted= 4 number of extra gaps= 0 total=153 Number of alignments=41 # 1swvA read from 1swvA/merged-good-all-a2m # found chain 1swvA in template set T0351 39 :PLPTQAELETWWEELQK 1swvA 76 :QLPTEADIQEMYEEFEE Number of specific fragments extracted= 1 number of extra gaps= 0 total=154 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ggzA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1ggzA expands to /projects/compbio/data/pdb/1ggz.pdb.gz 1ggzA:# T0351 read from 1ggzA/merged-good-all-a2m # 1ggzA read from 1ggzA/merged-good-all-a2m # adding 1ggzA to template set # found chain 1ggzA in template set T0351 38 :APLPTQAELETWWEELQKNPPYE 1ggzA 40 :GQNPTEAELRDMMSEIDRDGNGT T0351 62 :PDQVELLAQELSQEKLARKQ 1ggzA 66 :PEFLGMMARKMKDTDNEEEI T0351 83 :EELNKTL 1ggzA 86 :REAFRVF T0351 90 :GNELSDIK 1ggzA 102 :AAELRHVM T0351 99 :SLLSLKGDYAELEH 1ggzA 110 :TRLGEKLSDEEVDE Number of specific fragments extracted= 5 number of extra gaps= 0 total=159 Number of alignments=42 # 1ggzA read from 1ggzA/merged-good-all-a2m # found chain 1ggzA in template set T0351 3 :LYDAIMYKYPNAVSRKD 1ggzA 12 :FKEAFSLFDKDGDGCIT T0351 37 :RAPLPTQAELETWWEELQKNPPYE 1ggzA 39 :LGQNPTEAELRDMMSEIDRDGNGT T0351 62 :P 1ggzA 66 :P T0351 63 :DQVELLAQELSQEKLARKQLEELNKTLGN 1ggzA 70 :GMMARKMKDTDNEEEIREAFRVFDKDGNG T0351 92 :ELSDIKLSLLSLKGDYAELE 1ggzA 101 :SAAELRHVMTRLGEKLSDEE Number of specific fragments extracted= 5 number of extra gaps= 0 total=164 Number of alignments=43 # 1ggzA read from 1ggzA/merged-good-all-a2m # found chain 1ggzA in template set T0351 24 :NDGNGSY 1ggzA 21 :KDGDGCI T0351 39 :PLPTQAELETWWEELQKNPPYE 1ggzA 41 :QNPTEAELRDMMSEIDRDGNGT T0351 61 :PPDQVELLAQELSQEKLARKQLEEL 1ggzA 65 :FPEFLGMMARKMKDTDNEEEIREAF T0351 87 :KTL 1ggzA 90 :RVF T0351 90 :GNELSDI 1ggzA 102 :AAELRHV Number of specific fragments extracted= 5 number of extra gaps= 0 total=169 Number of alignments=44 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1z5bA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1z5bA expands to /projects/compbio/data/pdb/1z5b.pdb.gz 1z5bA:# T0351 read from 1z5bA/merged-good-all-a2m # 1z5bA read from 1z5bA/merged-good-all-a2m # adding 1z5bA to template set # found chain 1z5bA in template set T0351 1 :MILYDAIMYKY 1z5bA 185 :SRIYEYIKRTY T0351 15 :VSRKDFELRN 1z5bA 198 :TPYAEFIFKD T0351 25 :DGNGSYIEKWNLRAPLP 1z5bA 209 :EGNVTYYPRLTNKIPKP T0351 42 :TQAELET 1z5bA 237 :DREEIKI T0351 53 :LQKNPPYEP 1z5bA 244 :LINNLKRDY T0351 63 :DQVELLAQELS 1z5bA 253 :TIKEFLVNEFQ T0351 76 :KLARKQL 1z5bA 267 :DTTADKI T0351 98 :LSLLSLKGDY 1z5bA 274 :LELAGLKPNK Number of specific fragments extracted= 8 number of extra gaps= 0 total=177 Number of alignments=45 # 1z5bA read from 1z5bA/merged-good-all-a2m # found chain 1z5bA in template set T0351 2 :ILYDAIMYKY 1z5bA 186 :RIYEYIKRTY T0351 15 :VSRKDFELRNDG 1z5bA 198 :TPYAEFIFKDPE T0351 27 :NGSYIEKWNLRAPLP 1z5bA 211 :NVTYYPRLTNKIPKP T0351 42 :TQAELETWWEE 1z5bA 237 :DREEIKILINN T0351 57 :PPYEP 1z5bA 248 :LKRDY T0351 63 :D 1z5bA 253 :T T0351 78 :ARKQLEELNKTLGNELSDIKLSLLSLKGD 1z5bA 254 :IKEFLVNEFQSIGDTTADKILELAGLKPN Number of specific fragments extracted= 7 number of extra gaps= 0 total=184 Number of alignments=46 # 1z5bA read from 1z5bA/merged-good-all-a2m # found chain 1z5bA in template set T0351 43 :QAELETWWEELQK 1z5bA 437 :EKEIKNALMEVAR T0351 67 :LLAQELSQEKLARKQLEEL 1z5bA 450 :KLKQYLSEKRKEQEAKKKL Number of specific fragments extracted= 2 number of extra gaps= 0 total=186 Number of alignments=47 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1fezA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1fezA expands to /projects/compbio/data/pdb/1fez.pdb.gz 1fezA:# T0351 read from 1fezA/merged-good-all-a2m # 1fezA read from 1fezA/merged-good-all-a2m # adding 1fezA to template set # found chain 1fezA in template set T0351 39 :PLPTQAELETWWEELQKN 1fezA 76 :QLPTEADIQEMYEEFEEI T0351 64 :QVELLAQELS 1fezA 94 :LFAILPRYAS T0351 74 :QEKLARKQLEEL 1fezA 107 :AVKEVIASLRER T0351 89 :LGNELSDIKLSLLSLKG 1fezA 128 :YTREMMDIVAKEAALQG Number of specific fragments extracted= 4 number of extra gaps= 0 total=190 Number of alignments=48 # 1fezA read from 1fezA/merged-good-all-a2m # found chain 1fezA in template set T0351 39 :PLPTQAELETWWEELQKN 1fezA 76 :QLPTEADIQEMYEEFEEI T0351 57 :PPYEPP 1fezA 99 :PRYASP T0351 76 :KLARKQLEELNKTL 1fezA 106 :NAVKEVIASLRERG T0351 90 :GNELSDIKLSLLSLKG 1fezA 129 :TREMMDIVAKEAALQG Number of specific fragments extracted= 4 number of extra gaps= 0 total=194 Number of alignments=49 # 1fezA read from 1fezA/merged-good-all-a2m # found chain 1fezA in template set T0351 40 :LPTQAELETWWEELQK 1fezA 77 :LPTEADIQEMYEEFEE Number of specific fragments extracted= 1 number of extra gaps= 0 total=195 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1z8uA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1z8uA expands to /projects/compbio/data/pdb/1z8u.pdb.gz 1z8uA:# T0351 read from 1z8uA/merged-good-all-a2m # 1z8uA read from 1z8uA/merged-good-all-a2m # adding 1z8uA to template set # found chain 1z8uA in template set T0351 40 :LPTQAELETWWEELQK 1z8uA 31 :LVSEEDMVTVVEDWMN T0351 63 :DQVELLAQELS 1z8uA 47 :FYINYYRQQVT T0351 74 :QEKLARKQLEELNKTLGNEL 1z8uA 62 :ERDKALQELRQELNTLANPF T0351 94 :SDIK 1z8uA 83 :AKYR Number of specific fragments extracted= 4 number of extra gaps= 0 total=199 Number of alignments=50 # 1z8uA read from 1z8uA/merged-good-all-a2m # found chain 1z8uA in template set T0351 38 :APLPTQAELETWWEELQKN 1z8uA 29 :DALVSEEDMVTVVEDWMNF T0351 57 :PPYEPPDQVELLAQEL 1z8uA 55 :QVTGEPQERDKALQEL T0351 79 :RKQLEELNKTL 1z8uA 71 :RQELNTLANPF T0351 107 :YAELEHH 1z8uA 82 :LAKYRDF Number of specific fragments extracted= 4 number of extra gaps= 0 total=203 Number of alignments=51 # 1z8uA read from 1z8uA/merged-good-all-a2m # found chain 1z8uA in template set T0351 40 :LPTQAELETWWEELQK 1z8uA 31 :LVSEEDMVTVVEDWMN T0351 56 :NPPYEPPDQVELLAQEL 1z8uA 54 :QQVTGEPQERDKALQEL T0351 79 :RKQLEELNKTLGNELSDI 1z8uA 71 :RQELNTLANPFLAKYRDF Number of specific fragments extracted= 3 number of extra gaps= 0 total=206 Number of alignments=52 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1mx0A/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/T0351/1mx0A/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0351/1mx0A/merged-good-all-a2m.gz for input Trying 1mx0A/merged-good-all-a2m Error: Couldn't open file 1mx0A/merged-good-all-a2m or 1mx0A/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ahr/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1ahr expands to /projects/compbio/data/pdb/1ahr.pdb.gz 1ahr:Warning: there is no chain 1ahr will retry with 1ahrA # T0351 read from 1ahr/merged-good-all-a2m # 1ahr read from 1ahr/merged-good-all-a2m # adding 1ahr to template set # found chain 1ahr in template set T0351 3 :LYDAIMYKYPNAVSRKD 1ahr 12 :FKEAFSLFDKDGDGTIT T0351 37 :RAPLPTQAELETWWEELQKNPPYE 1ahr 39 :LGQNPTEAELQDMINEVDADGNGT T0351 62 :PDQVELLAQEL 1ahr 66 :PEFLTMMARKM T0351 73 :SQEKLARKQLEEL 1ahr 78 :DSEEEIREAFRVF T0351 90 :GNELSDI 1ahr 102 :AAELRHV T0351 98 :LSLLSLKGDYAELEHHHH 1ahr 109 :MTNLGEKLTDEEVDEMIR Number of specific fragments extracted= 6 number of extra gaps= 0 total=212 Number of alignments=53 # 1ahr read from 1ahr/merged-good-all-a2m # found chain 1ahr in template set T0351 3 :LYDAIMYKYPNAVSRKD 1ahr 12 :FKEAFSLFDKDGDGTIT T0351 34 :WNLRAPLPTQAELETWWEELQKNPPYE 1ahr 36 :MRSLGQNPTEAELQDMINEVDADGNGT T0351 62 :PDQVELLAQELS 1ahr 66 :PEFLTMMARKMK T0351 74 :QEKLARKQLEELNKTLGN 1ahr 81 :SEEEIREAFRVFDKDGNG T0351 92 :ELSDIKLSLLSLKGDYAELE 1ahr 101 :SAAELRHVMTNLGEKLTDEE Number of specific fragments extracted= 5 number of extra gaps= 0 total=217 Number of alignments=54 # 1ahr read from 1ahr/merged-good-all-a2m # found chain 1ahr in template set T0351 38 :APLPTQAELETWWEELQKNPPYE 1ahr 40 :GQNPTEAELQDMINEVDADGNGT T0351 61 :PPDQVELLAQEL 1ahr 65 :FPEFLTMMARKM T0351 73 :SQEKLARKQLEELNKT 1ahr 78 :DSEEEIREAFRVFDKD T0351 90 :GNELSDI 1ahr 102 :AAELRHV Number of specific fragments extracted= 4 number of extra gaps= 0 total=221 Number of alignments=55 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2a3qA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2a3qA expands to /projects/compbio/data/pdb/2a3q.pdb.gz 2a3qA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0351 read from 2a3qA/merged-good-all-a2m # 2a3qA read from 2a3qA/merged-good-all-a2m # adding 2a3qA to template set # found chain 2a3qA in template set Warning: unaligning (T0351)P41 because of BadResidue code BAD_PEPTIDE in next template residue (2a3qA)T30 Warning: unaligning (T0351)T42 because of BadResidue code BAD_PEPTIDE at template residue (2a3qA)T30 Warning: unaligning (T0351)P61 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2a3qA)W47 Warning: unaligning (T0351)P62 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2a3qA)W47 Warning: unaligning (T0351)D63 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2a3qA)Q49 Warning: unaligning (T0351)Q64 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2a3qA)Q49 T0351 37 :RAPL 2a3qA 25 :FSPE T0351 43 :QAELETWWEELQKN 2a3qA 31 :LEDIRRLHAEFAAE T0351 60 :E 2a3qA 45 :R T0351 65 :VE 2a3qA 50 :FH T0351 67 :LLAQELSQEKLARKQLE 2a3qA 55 :NLLLALVGEVGELAELF T0351 84 :ELNKTLGNELSDIKLSLLSLKG 2a3qA 87 :KERAALQEELSDVLIYLVALAA T0351 106 :DYAELEHHHHHH 2a3qA 121 :KMDTNRQRYPVH Number of specific fragments extracted= 7 number of extra gaps= 2 total=228 Number of alignments=56 # 2a3qA read from 2a3qA/merged-good-all-a2m # found chain 2a3qA in template set Warning: unaligning (T0351)P41 because of BadResidue code BAD_PEPTIDE in next template residue (2a3qA)T30 Warning: unaligning (T0351)T42 because of BadResidue code BAD_PEPTIDE at template residue (2a3qA)T30 Warning: unaligning (T0351)P57 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2a3qA)W47 T0351 38 :APL 2a3qA 26 :SPE T0351 43 :QAEL 2a3qA 31 :LEDI T0351 47 :ETWWEELQKN 2a3qA 36 :RLHAEFAAER T0351 61 :PPDQVELLAQELS 2a3qA 52 :QPRNLLLALVGEV T0351 74 :QEKLA 2a3qA 66 :ELAEL T0351 79 :RKQLEELNKTLGN 2a3qA 89 :RAALQEELSDVLI T0351 96 :IK 2a3qA 102 :YL T0351 98 :LSLLSLKGDYAELEHHHHHH 2a3qA 114 :LPQAVISKMDTNRQRYPVHL Number of specific fragments extracted= 8 number of extra gaps= 2 total=236 Number of alignments=57 # 2a3qA read from 2a3qA/merged-good-all-a2m # found chain 2a3qA in template set Warning: unaligning (T0351)P41 because of BadResidue code BAD_PEPTIDE in next template residue (2a3qA)T30 Warning: unaligning (T0351)T42 because of BadResidue code BAD_PEPTIDE at template residue (2a3qA)T30 Warning: unaligning (T0351)P57 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2a3qA)W47 Warning: unaligning (T0351)Y59 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2a3qA)W47 Warning: unaligning (T0351)E60 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2a3qA)Q49 Warning: unaligning (T0351)P61 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2a3qA)Q49 T0351 38 :APL 2a3qA 26 :SPE T0351 43 :QAEL 2a3qA 31 :LEDI T0351 47 :ETWWEELQKN 2a3qA 36 :RLHAEFAAER T0351 62 :PDQVELLAQEL 2a3qA 50 :FHQPRNLLLAL T0351 76 :KLARKQLEEL 2a3qA 61 :VGEVGELAEL T0351 86 :NKTLGNELSDIKL 2a3qA 89 :RAALQEELSDVLI Number of specific fragments extracted= 6 number of extra gaps= 2 total=242 Number of alignments=58 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1exrA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0351 read from 1exrA/merged-good-all-a2m # 1exrA read from 1exrA/merged-good-all-a2m # found chain 1exrA in training set T0351 38 :APLPTQAELETWWEELQKNPPYE 1exrA 40 :GQNPTEAELQDMINEVDADGNGT T0351 62 :PDQVELLAQELSQEKLARK 1exrA 66 :PEFLSLMARKMKEQDSEEE T0351 82 :LEELNKTL 1exrA 85 :LIEAFKVF T0351 90 :GNELSDI 1exrA 102 :AAELRHV T0351 98 :LSLLSLKGDYAELEH 1exrA 109 :MTNLGEKLTDDEVDE Number of specific fragments extracted= 5 number of extra gaps= 0 total=247 Number of alignments=59 # 1exrA read from 1exrA/merged-good-all-a2m # found chain 1exrA in training set T0351 24 :NDGNGSY 1exrA 21 :KDGDGTI T0351 38 :APLPTQAELETWWEELQKNPPYE 1exrA 40 :GQNPTEAELQDMINEVDADGNGT T0351 62 :PDQVELLAQELS 1exrA 66 :PEFLSLMARKMK T0351 74 :QEKLARKQLEELNKTLGNEL 1exrA 81 :SEEELIEAFKVFDRDGNGLI T0351 94 :SDIKLSLLSLKGDYAELE 1exrA 103 :AELRHVMTNLGEKLTDDE Number of specific fragments extracted= 5 number of extra gaps= 0 total=252 Number of alignments=60 # 1exrA read from 1exrA/merged-good-all-a2m # found chain 1exrA in training set T0351 24 :NDGNGSY 1exrA 21 :KDGDGTI T0351 39 :PLPTQAELETWWEELQKNPPYE 1exrA 41 :QNPTEAELQDMINEVDADGNGT T0351 61 :PPDQVELLAQELSQEKLARKQLEELNK 1exrA 65 :FPEFLSLMARKMKEQDSEEELIEAFKV T0351 89 :L 1exrA 92 :F T0351 90 :GNELSDI 1exrA 102 :AAELRHV Number of specific fragments extracted= 5 number of extra gaps= 0 total=257 Number of alignments=61 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1yirA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1yirA expands to /projects/compbio/data/pdb/1yir.pdb.gz 1yirA:# T0351 read from 1yirA/merged-good-all-a2m # 1yirA read from 1yirA/merged-good-all-a2m # adding 1yirA to template set # found chain 1yirA in template set T0351 3 :LYDAIMYKYPNAVSRKDFELRNDGNG 1yirA 26 :MMQAVLHNYPNAEVEWEFRCRNQEDL T0351 43 :QAELETWWEELQKNP 1yirA 55 :LPAIREQLEYLAGLA T0351 60 :EPPDQVELLAQ 1yirA 70 :ISDEQLAFLER T0351 76 :KLARKQLE 1yirA 86 :PDFIRFLG Number of specific fragments extracted= 4 number of extra gaps= 0 total=261 Number of alignments=62 # 1yirA read from 1yirA/merged-good-all-a2m # found chain 1yirA in template set T0351 3 :LYDAIMYKYPNA 1yirA 26 :MMQAVLHNYPNA T0351 17 :RKDFELRNDGNGSY 1yirA 38 :EVEWEFRCRNQEDL T0351 43 :QAELETWWEELQKNP 1yirA 55 :LPAIREQLEYLAGLA T0351 60 :EPPDQVELLAQ 1yirA 70 :ISDEQLAFLER T0351 75 :EKLARKQL 1yirA 85 :APDFIRFL Number of specific fragments extracted= 5 number of extra gaps= 0 total=266 Number of alignments=63 # 1yirA read from 1yirA/merged-good-all-a2m # found chain 1yirA in template set T0351 3 :LYDAIMYKYPNAV 1yirA 26 :MMQAVLHNYPNAE T0351 22 :L 1yirA 39 :V T0351 33 :KWNLRAPLPT 1yirA 40 :EWEFRCRNQE T0351 44 :AELETWWEELQKNPP 1yirA 56 :PAIREQLEYLAGLAI T0351 61 :PPDQVELLAQ 1yirA 71 :SDEQLAFLER T0351 88 :TLGNELSDIKLS 1yirA 87 :DFIRFLGLFRFN Number of specific fragments extracted= 6 number of extra gaps= 0 total=272 Number of alignments=64 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1rypA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1rypA expands to /projects/compbio/data/pdb/1ryp.pdb.gz 1rypA:# T0351 read from 1rypA/merged-good-all-a2m # 1rypA read from 1rypA/merged-good-all-a2m # adding 1rypA to template set # found chain 1rypA in template set T0351 4 :YDAIMYK 1rypA 204 :EFAITHM T0351 11 :YPNAVSRKDFELR 1rypA 214 :LGTEFSKNDLEVG T0351 24 :NDGNGSYI 1rypA 229 :TKDKFFTL T0351 42 :TQAELETWWEELQKN 1rypA 237 :SAENIEERLVAIAEQ Number of specific fragments extracted= 4 number of extra gaps= 0 total=276 Number of alignments=65 # 1rypA read from 1rypA/merged-good-all-a2m # found chain 1rypA in template set Warning: unaligning (T0351)P57 because last residue in template chain is (1rypA)D252 T0351 5 :DAIMYK 1rypA 205 :FAITHM T0351 11 :YPNAVSRKDFELR 1rypA 214 :LGTEFSKNDLEVG T0351 24 :NDGNGSYI 1rypA 229 :TKDKFFTL T0351 42 :TQAELETWWEELQKN 1rypA 237 :SAENIEERLVAIAEQ Number of specific fragments extracted= 4 number of extra gaps= 0 total=280 Number of alignments=66 # 1rypA read from 1rypA/merged-good-all-a2m # found chain 1rypA in template set T0351 3 :LYDA 1rypA 210 :MIDA T0351 11 :YPNAVSRKDFELR 1rypA 214 :LGTEFSKNDLEVG T0351 30 :YIEKWNLRA 1rypA 227 :VATKDKFFT T0351 41 :PTQAELETWWEELQK 1rypA 236 :LSAENIEERLVAIAE Number of specific fragments extracted= 4 number of extra gaps= 0 total=284 Number of alignments=67 # command:Using radius: 8.0000 Alignment mode NUMB_ALIGNS: 67 Adding 678 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: -200.0119, CN propb: -200.0119 weights: 0.2372 constraints: 163 # command:Found ConstraintSet # PrintContacts align.constraints_v3 Number of constraints in align.constraints 163 # command:Found ConstraintSet # PrintContacts align_bonus.constraints_v3 Number of constraints in align.constraints.bonus 163 # command:Found ConstraintSet # PrintContacts rejected.constraints_v3 Number of constraints in rejected.constraints 515 # command:Found ConstraintSet # PrintContacts rejected_bonus.constraints_v3 Number of constraints in rejected.constraints.bonus 515 # 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 678 # command: