parameters: 0.6 1.3 0.5 200 50 # command:# Prefix for input files set to /projects/compbio/experiments/undertaker/atoms-inputs/ # command:# reading dunbrack-2191.atoms # #computed average backbone with maximum peptide_sq_deviance = 0.002 # computed average trans backbone unit from 53157 examples # computed average trans backbone unit before proline from 2010 examples # computed average cis backbone unit from 97 examples # trans (non-proline) backbone unit: # CA= -2.2087 1.0126 -0.0030 # O= -0.1499 2.2440 0.0016 # C= -0.6889 1.1368 -0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4581 -0.0000 0.0000 # cis backbone unit: # CA= -0.1436 2.4534 -0.0002 # O= -2.0284 0.9742 0.0015 # C= -0.8018 1.0771 -0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4668 0.0000 0.0000 # trans backbone unit before proline: # CA= -2.2100 1.0631 -0.0014 # O= -0.1236 2.2458 0.0075 # C= -0.6872 1.1517 -0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4660 0.0000 0.0000 # After reading dunbrack-2191.atoms have 2191 chains in training database # Count of chains,residues,atoms: 2191,500310,3902258 # 493341 residues have no bad marker # 3226 residues lack atoms needed to compute omega # 1453 residues have cis peptide # number of each bad type: # NON_STANDARD_RESIDUE 4 # HAS_OXT 1167 # TOO_MANY_ATOMS 1 # TOO_FEW_ATOMS 3052 # HAS_UNKNOWN_ATOMS 9 # HAS_DUPLICATE_ATOMS 0 # CHAIN_BREAK_BEFORE 979 # NON_PLANAR_PEPTIDE 888 # BAD_PEPTIDE 2680 # Note: may sum to more than number of residues, # because one residue may have multiple problems # command:# Reading rotamer library from dunbrack-2191.rot # command:# Prefix for input files set to /projects/compbio/experiments/undertaker/spots/ # command:# ReadAtomType exp-pdb.types Read AtomType exp-pdb with 49 types. # command:# ReadClashTable exp-pdb-2191-2symm.clash # Read ClashTable exp-pdb-2191-2symm checking bonds symmetric at MaxSep 2 # command:# command:# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/T0335/ # command:# Making conformation for sequence T0335 numbered 1 through 85 Created new target T0335 from T0335.a2m # command:# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/T0335/ # command:Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0335//projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0335/manyalignments-good-all.under or /projects/compbio/experiments/protein-predict/casp7/T0335//projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0335/manyalignments-good-all.under.gz for input Trying /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0335/manyalignments-good-all.under # reading script from file /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0335/manyalignments-good-all.under # Reading fragments from alignment file # Attempting to read fragment alignments from file 1xhdA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1xhdA expands to /projects/compbio/data/pdb/1xhd.pdb.gz 1xhdA:Skipped atom 2, because occupancy 0.31 <= existing 0.690 in 1xhdA Skipped atom 4, because occupancy 0.310 <= existing 0.690 in 1xhdA Skipped atom 6, because occupancy 0.310 <= existing 0.690 in 1xhdA Skipped atom 8, because occupancy 0.310 <= existing 0.690 in 1xhdA Skipped atom 10, because occupancy 0.310 <= existing 0.690 in 1xhdA Skipped atom 12, because occupancy 0.310 <= existing 0.690 in 1xhdA Skipped atom 14, because occupancy 0.460 <= existing 0.540 in 1xhdA Skipped atom 16, because occupancy 0.460 <= existing 0.540 in 1xhdA Skipped atom 18, because occupancy 0.460 <= existing 0.540 in 1xhdA Skipped atom 20, because occupancy 0.460 <= existing 0.540 in 1xhdA Skipped atom 22, because occupancy 0.460 <= existing 0.540 in 1xhdA Skipped atom 24, because occupancy 0.460 <= existing 0.540 in 1xhdA Skipped atom 26, because occupancy 0.460 <= existing 0.540 in 1xhdA Skipped atom 28, because occupancy 0.460 <= existing 0.540 in 1xhdA Skipped atom 30, because occupancy 0.300 <= existing 0.700 in 1xhdA Skipped atom 32, because occupancy 0.300 <= existing 0.700 in 1xhdA Skipped atom 34, because occupancy 0.300 <= existing 0.700 in 1xhdA Skipped atom 36, because occupancy 0.300 <= existing 0.700 in 1xhdA Skipped atom 38, because occupancy 0.300 <= existing 0.700 in 1xhdA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 118, because occupancy 0.460 <= existing 0.540 in 1xhdA Skipped atom 120, because occupancy 0.460 <= existing 0.540 in 1xhdA Skipped atom 122, because occupancy 0.460 <= existing 0.540 in 1xhdA Skipped atom 124, because occupancy 0.460 <= existing 0.540 in 1xhdA Skipped atom 126, because occupancy 0.460 <= existing 0.540 in 1xhdA Skipped atom 161, because occupancy 0.500 <= existing 0.500 in 1xhdA Skipped atom 163, because occupancy 0.500 <= existing 0.500 in 1xhdA Skipped atom 295, because occupancy 0.440 <= existing 0.560 in 1xhdA Skipped atom 297, because occupancy 0.440 <= existing 0.560 in 1xhdA Skipped atom 299, because occupancy 0.440 <= existing 0.560 in 1xhdA Skipped atom 301, because occupancy 0.440 <= existing 0.560 in 1xhdA Skipped atom 303, because occupancy 0.440 <= existing 0.560 in 1xhdA Skipped atom 759, because occupancy 0.450 <= existing 0.550 in 1xhdA Skipped atom 761, because occupancy 0.450 <= existing 0.550 in 1xhdA Skipped atom 763, because occupancy 0.450 <= existing 0.550 in 1xhdA Skipped atom 765, because occupancy 0.450 <= existing 0.550 in 1xhdA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 973, because occupancy 0.490 <= existing 0.510 in 1xhdA Skipped atom 975, because occupancy 0.490 <= existing 0.510 in 1xhdA Skipped atom 1164, because occupancy 0.470 <= existing 0.530 in 1xhdA Skipped atom 1166, because occupancy 0.470 <= existing 0.530 in 1xhdA Skipped atom 1168, because occupancy 0.470 <= existing 0.530 in 1xhdA Skipped atom 1170, because occupancy 0.470 <= existing 0.530 in 1xhdA Skipped atom 1172, because occupancy 0.470 <= existing 0.530 in 1xhdA Skipped atom 1206, because occupancy 0.420 <= existing 0.580 in 1xhdA Skipped atom 1208, because occupancy 0.420 <= existing 0.580 in 1xhdA Skipped atom 1210, because occupancy 0.420 <= existing 0.580 in 1xhdA Skipped atom 1212, because occupancy 0.420 <= existing 0.580 in 1xhdA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0335 read from 1xhdA/merged-good-all-a2m # 1xhdA read from 1xhdA/merged-good-all-a2m # adding 1xhdA to template set # found chain 1xhdA in template set T0335 22 :ITEEEKAEQQKLRQEYLKGFRSSMKN 1xhdA 143 :LTAEDRKDMERIRTQYVEKGQYYKSL # choosing archetypes in rotamer library Number of specific fragments extracted= 1 number of extra gaps= 0 total=1 Number of alignments=1 # 1xhdA read from 1xhdA/merged-good-all-a2m # found chain 1xhdA in template set T0335 22 :ITEEEKAEQQKLRQEYLKGFRSSMKN 1xhdA 143 :LTAEDRKDMERIRTQYVEKGQYYKSL Number of specific fragments extracted= 1 number of extra gaps= 0 total=2 Number of alignments=2 # 1xhdA read from 1xhdA/merged-good-all-a2m # found chain 1xhdA in template set T0335 22 :ITEEEKAEQQKLRQEYLKGFRSSMKN 1xhdA 143 :LTAEDRKDMERIRTQYVEKGQYYKSL Number of specific fragments extracted= 1 number of extra gaps= 0 total=3 Number of alignments=3 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2au5A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2au5A expands to /projects/compbio/data/pdb/2au5.pdb.gz 2au5A:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 15, because occupancy 0.500 <= existing 0.500 in 2au5A Skipped atom 17, because occupancy 0.500 <= existing 0.500 in 2au5A Skipped atom 19, because occupancy 0.500 <= existing 0.500 in 2au5A Skipped atom 21, because occupancy 0.500 <= existing 0.500 in 2au5A Skipped atom 23, because occupancy 0.500 <= existing 0.500 in 2au5A Skipped atom 25, because occupancy 0.500 <= existing 0.500 in 2au5A Skipped atom 27, because occupancy 0.500 <= existing 0.500 in 2au5A Skipped atom 29, because occupancy 0.500 <= existing 0.500 in 2au5A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 379, because occupancy 0.500 <= existing 0.500 in 2au5A Skipped atom 381, because occupancy 0.500 <= existing 0.500 in 2au5A Skipped atom 383, because occupancy 0.500 <= existing 0.500 in 2au5A Skipped atom 385, because occupancy 0.500 <= existing 0.500 in 2au5A Skipped atom 387, because occupancy 0.500 <= existing 0.500 in 2au5A Skipped atom 389, because occupancy 0.500 <= existing 0.500 in 2au5A Skipped atom 391, because occupancy 0.500 <= existing 0.500 in 2au5A Skipped atom 393, because occupancy 0.500 <= existing 0.500 in 2au5A Skipped atom 395, because occupancy 0.500 <= existing 0.500 in 2au5A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 569, because occupancy 0.500 <= existing 0.500 in 2au5A Skipped atom 571, because occupancy 0.500 <= existing 0.500 in 2au5A Skipped atom 573, because occupancy 0.500 <= existing 0.500 in 2au5A Skipped atom 575, because occupancy 0.500 <= existing 0.500 in 2au5A Skipped atom 577, because occupancy 0.500 <= existing 0.500 in 2au5A Skipped atom 579, because occupancy 0.500 <= existing 0.500 in 2au5A Skipped atom 581, because occupancy 0.500 <= existing 0.500 in 2au5A Skipped atom 583, because occupancy 0.500 <= existing 0.500 in 2au5A Skipped atom 585, because occupancy 0.500 <= existing 0.500 in 2au5A Skipped atom 625, because occupancy 0.500 <= existing 0.500 in 2au5A Skipped atom 627, because occupancy 0.500 <= existing 0.500 in 2au5A Skipped atom 629, because occupancy 0.500 <= existing 0.500 in 2au5A Skipped atom 631, because occupancy 0.500 <= existing 0.500 in 2au5A Skipped atom 633, because occupancy 0.500 <= existing 0.500 in 2au5A Skipped atom 635, because occupancy 0.500 <= existing 0.500 in 2au5A Skipped atom 637, because occupancy 0.500 <= existing 0.500 in 2au5A Skipped atom 639, because occupancy 0.500 <= existing 0.500 in 2au5A Skipped atom 641, because occupancy 0.500 <= existing 0.500 in 2au5A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0335 read from 2au5A/merged-good-all-a2m # 2au5A read from 2au5A/merged-good-all-a2m # adding 2au5A to template set # found chain 2au5A in template set Warning: unaligning (T0335)K50 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2au5A)S132 T0335 3 :SNAKIARINELAAKAKAGVITEEEKAEQQKLRQEYLKGFR 2au5A 82 :LKGELARLIRLYFALAKDNLTENQESLYVDLFDKFTFLLL T0335 43 :SSMKNTL 2au5A 124 :DEFIMYL Number of specific fragments extracted= 2 number of extra gaps= 1 total=5 Number of alignments=4 # 2au5A read from 2au5A/merged-good-all-a2m # found chain 2au5A in template set Warning: unaligning (T0335)K50 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2au5A)S132 Warning: unaligning (T0335)S51 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2au5A)S132 T0335 3 :SNAKIARINELAAKAKAGVITEEEKAEQQKLRQEYLKGFR 2au5A 82 :LKGELARLIRLYFALAKDNLTENQESLYVDLFDKFTFLLL T0335 43 :SSMKNTL 2au5A 124 :DEFIMYL Number of specific fragments extracted= 2 number of extra gaps= 1 total=7 Number of alignments=5 # 2au5A read from 2au5A/merged-good-all-a2m # found chain 2au5A in template set Warning: unaligning (T0335)K50 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2au5A)S132 Warning: unaligning (T0335)S51 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2au5A)S132 T0335 4 :NAKIARINELAAKAKAGVITEEEKAEQQKLRQEYLKGFR 2au5A 83 :KGELARLIRLYFALAKDNLTENQESLYVDLFDKFTFLLL T0335 43 :SSMKNTL 2au5A 124 :DEFIMYL Number of specific fragments extracted= 2 number of extra gaps= 1 total=9 Number of alignments=6 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1t95A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1t95A expands to /projects/compbio/data/pdb/1t95.pdb.gz 1t95A:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0335 read from 1t95A/merged-good-all-a2m # 1t95A read from 1t95A/merged-good-all-a2m # adding 1t95A to template set # found chain 1t95A in template set Warning: unaligning (T0335)I55 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1t95A)D119 Warning: unaligning (T0335)D56 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1t95A)D119 Warning: unaligning (T0335)E58 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1t95A)T122 Warning: unaligning (T0335)G59 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1t95A)T122 Warning: unaligning (T0335)N60 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1t95A)N123 T0335 3 :SNAKIARI 1t95A 65 :SVDELRKI T0335 11 :NELAAKAKAG 1t95A 79 :FEIARKIILE T0335 21 :VITEEEKAEQ 1t95A 92 :QITAEQRREM T0335 31 :QKLRQEYLKGFRSS 1t95A 103 :EAKRKQIINFISRN T0335 54 :I 1t95A 117 :T T0335 57 :P 1t95A 120 :P T0335 61 :DV 1t95A 124 :AP T0335 63 :TPEKLKREQRNNKLHLEHH 1t95A 127 :PPSRIERALEEAKVHIDIF Number of specific fragments extracted= 8 number of extra gaps= 2 total=17 Number of alignments=7 # 1t95A read from 1t95A/merged-good-all-a2m # found chain 1t95A in template set Warning: unaligning (T0335)I55 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1t95A)D119 Warning: unaligning (T0335)D56 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1t95A)D119 Warning: unaligning (T0335)E58 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1t95A)T122 Warning: unaligning (T0335)G59 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1t95A)T122 Warning: unaligning (T0335)N60 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1t95A)N123 T0335 3 :SNAKIARI 1t95A 65 :SVDELRKI T0335 11 :NELAAKAKAG 1t95A 79 :FEIARKIILE T0335 21 :VITEEEKAE 1t95A 92 :QITAEQRRE T0335 30 :QQKLRQEYLKGFRSS 1t95A 102 :LEAKRKQIINFISRN T0335 54 :I 1t95A 117 :T T0335 57 :P 1t95A 120 :P T0335 61 :DV 1t95A 124 :AP T0335 63 :TPEKLKREQRNNKLHLEHH 1t95A 127 :PPSRIERALEEAKVHIDIF Number of specific fragments extracted= 8 number of extra gaps= 2 total=25 Number of alignments=8 # 1t95A read from 1t95A/merged-good-all-a2m # found chain 1t95A in template set Warning: unaligning (T0335)I55 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1t95A)D119 Warning: unaligning (T0335)D56 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1t95A)D119 Warning: unaligning (T0335)E58 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1t95A)T122 Warning: unaligning (T0335)G59 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1t95A)T122 Warning: unaligning (T0335)N60 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1t95A)N123 T0335 3 :SNAKIARI 1t95A 65 :SVDELRKI T0335 11 :NELAAKAKAG 1t95A 79 :FEIARKIILE T0335 21 :VITEEEKAEQ 1t95A 92 :QITAEQRREM T0335 31 :QKLRQEYLKGFRSS 1t95A 103 :EAKRKQIINFISRN T0335 54 :I 1t95A 117 :T T0335 57 :P 1t95A 120 :P T0335 61 :DV 1t95A 124 :AP T0335 63 :TPEKLKREQRNNKLHLEHHH 1t95A 127 :PPSRIERALEEAKVHIDIFK Number of specific fragments extracted= 8 number of extra gaps= 2 total=33 Number of alignments=9 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2amyA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2amyA expands to /projects/compbio/data/pdb/2amy.pdb.gz 2amyA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 359, because occupancy 0.350 <= existing 0.650 in 2amyA Skipped atom 361, because occupancy 0.350 <= existing 0.650 in 2amyA Skipped atom 363, because occupancy 0.350 <= existing 0.650 in 2amyA Skipped atom 365, because occupancy 0.350 <= existing 0.650 in 2amyA Skipped atom 367, because occupancy 0.350 <= existing 0.650 in 2amyA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0335 read from 2amyA/merged-good-all-a2m # 2amyA read from 2amyA/merged-good-all-a2m # adding 2amyA to template set # found chain 2amyA in template set T0335 3 :SNAKIARINELAAKAKA 2amyA 92 :GEALIQDLINYCLSYIA T0335 20 :GVITEEEKAEQQKLRQE 2amyA 134 :RSCSQEERIEFYELDKK T0335 37 :YLKGFRSSMKNTLKSVKI 2amyA 153 :IRQKFVADLRKEFAGKGL Number of specific fragments extracted= 3 number of extra gaps= 0 total=36 Number of alignments=10 # 2amyA read from 2amyA/merged-good-all-a2m # found chain 2amyA in template set T0335 3 :SNAKIARINELAAKAKA 2amyA 92 :GEALIQDLINYCLSYIA T0335 20 :GVITEEEKAEQQKLRQE 2amyA 134 :RSCSQEERIEFYELDKK T0335 37 :YLKGFRSSMKNTLKSVKII 2amyA 153 :IRQKFVADLRKEFAGKGLT Number of specific fragments extracted= 3 number of extra gaps= 0 total=39 Number of alignments=11 # 2amyA read from 2amyA/merged-good-all-a2m # found chain 2amyA in template set T0335 3 :SNAKIARINELAAKAKAG 2amyA 92 :GEALIQDLINYCLSYIAK T0335 21 :VITEEEKAEQQKLRQE 2amyA 135 :SCSQEERIEFYELDKK T0335 37 :YLKGFRSSMKNTLKSVKIID 2amyA 153 :IRQKFVADLRKEFAGKGLTF Number of specific fragments extracted= 3 number of extra gaps= 0 total=42 Number of alignments=12 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1il1A/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/T0335/1il1A/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0335/1il1A/merged-good-all-a2m.gz for input Trying 1il1A/merged-good-all-a2m Error: Couldn't open file 1il1A/merged-good-all-a2m or 1il1A/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1v3hA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0335 read from 1v3hA/merged-good-all-a2m # 1v3hA read from 1v3hA/merged-good-all-a2m # found chain 1v3hA in training set T0335 54 :IIDPEGNDVTPEKLKREQRN 1v3hA 22 :VVNVDNVFEDPDGLKEQLLQ Number of specific fragments extracted= 1 number of extra gaps= 0 total=43 Number of alignments=13 # 1v3hA read from 1v3hA/merged-good-all-a2m # found chain 1v3hA in training set T0335 55 :IDPEGNDVTPEKLKREQRN 1v3hA 23 :VNVDNVFEDPDGLKEQLLQ Number of specific fragments extracted= 1 number of extra gaps= 0 total=44 # 1v3hA read from 1v3hA/merged-good-all-a2m # found chain 1v3hA in training set T0335 54 :IIDPEGNDVTPEKLKREQR 1v3hA 22 :VVNVDNVFEDPDGLKEQLL Number of specific fragments extracted= 1 number of extra gaps= 0 total=45 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1aj4/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1aj4 expands to /projects/compbio/data/pdb/1aj4.pdb.gz 1aj4:Warning: there is no chain 1aj4 will retry with 1aj4A # T0335 read from 1aj4/merged-good-all-a2m # 1aj4 read from 1aj4/merged-good-all-a2m # adding 1aj4 to template set # found chain 1aj4 in template set T0335 16 :KAKAGVITEEEKA 1aj4 6 :KAAVEQLTEEQKN T0335 40 :GFRSSMKNTLKSVK 1aj4 19 :EFKAAFDIFVLGAE T0335 54 :IIDPE 1aj4 35 :SISTK T0335 59 :GNDVTPEKLKREQRNNK 1aj4 49 :GQNPTPEELQEMIDEVD Number of specific fragments extracted= 4 number of extra gaps= 0 total=49 Number of alignments=14 # 1aj4 read from 1aj4/merged-good-all-a2m # found chain 1aj4 in template set T0335 17 :AKAGVITEEEKA 1aj4 7 :AAVEQLTEEQKN T0335 40 :GFRSSMKNTLKSVK 1aj4 19 :EFKAAFDIFVLGAE T0335 54 :IIDPE 1aj4 35 :SISTK T0335 59 :GNDVTPEKLKREQRNNKL 1aj4 49 :GQNPTPEELQEMIDEVDE Number of specific fragments extracted= 4 number of extra gaps= 0 total=53 Number of alignments=15 # 1aj4 read from 1aj4/merged-good-all-a2m # found chain 1aj4 in template set T0335 17 :AKAGVITEEEKA 1aj4 7 :AAVEQLTEEQKN T0335 40 :GFRSSMKNTLKSVK 1aj4 19 :EFKAAFDIFVLGAE T0335 55 :IDPE 1aj4 36 :ISTK T0335 59 :GNDVTPEKLKREQRNN 1aj4 49 :GQNPTPEELQEMIDEV T0335 78 :LEHHH 1aj4 65 :DEDGS Number of specific fragments extracted= 5 number of extra gaps= 0 total=58 Number of alignments=16 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1f47B/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1f47B expands to /projects/compbio/data/pdb/1f47.pdb.gz 1f47B:# T0335 read from 1f47B/merged-good-all-a2m # 1f47B read from 1f47B/merged-good-all-a2m # adding 1f47B to template set # found chain 1f47B in template set T0335 26 :EKA 1f47B 94 :ELQ T0335 33 :LRQEYLKGFR 1f47B 97 :LFKLMLQSAQ T0335 44 :SMKNTL 1f47B 107 :HIADEV T0335 51 :SVKIIDPEGNDVTPEKLKREQRNNKLHLE 1f47B 113 :GGVVLDDQRRMMTPQKLREYQDIIREVKD Number of specific fragments extracted= 4 number of extra gaps= 0 total=62 Number of alignments=17 # 1f47B read from 1f47B/merged-good-all-a2m # found chain 1f47B in template set T0335 33 :LRQEYLKGF 1f47B 97 :LFKLMLQSA T0335 43 :SSMKNTL 1f47B 106 :QHIADEV T0335 51 :SVKIIDPEGNDVTPEKLKREQRNNKL 1f47B 113 :GGVVLDDQRRMMTPQKLREYQDIIRE Number of specific fragments extracted= 3 number of extra gaps= 0 total=65 Number of alignments=18 # 1f47B read from 1f47B/merged-good-all-a2m # found chain 1f47B in template set T0335 32 :KLRQEYLKGFR 1f47B 96 :QLFKLMLQSAQ T0335 44 :SMKNTL 1f47B 107 :HIADEV T0335 51 :SVKIIDPEGNDVTPEKLKREQR 1f47B 113 :GGVVLDDQRRMMTPQKLREYQD Number of specific fragments extracted= 3 number of extra gaps= 0 total=68 Number of alignments=19 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2fueA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2fueA expands to /projects/compbio/data/pdb/2fue.pdb.gz 2fueA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1384, because occupancy 0.500 <= existing 0.500 in 2fueA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1388, because occupancy 0.500 <= existing 0.500 in 2fueA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1390, because occupancy 0.500 <= existing 0.500 in 2fueA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1392, because occupancy 0.500 <= existing 0.500 in 2fueA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1394, because occupancy 0.500 <= existing 0.500 in 2fueA Skipped atom 1907, because occupancy 0.500 <= existing 0.500 in 2fueA Skipped atom 1909, because occupancy 0.500 <= existing 0.500 in 2fueA Skipped atom 1911, because occupancy 0.500 <= existing 0.500 in 2fueA Skipped atom 1913, because occupancy 0.500 <= existing 0.500 in 2fueA Skipped atom 1915, because occupancy 0.500 <= existing 0.500 in 2fueA Skipped atom 1917, because occupancy 0.500 <= existing 0.500 in 2fueA Skipped atom 1919, because occupancy 0.500 <= existing 0.500 in 2fueA Skipped atom 1921, because occupancy 0.500 <= existing 0.500 in 2fueA Skipped atom 1923, because occupancy 0.500 <= existing 0.500 in 2fueA Skipped atom 1925, because occupancy 0.500 <= existing 0.500 in 2fueA Skipped atom 1927, because occupancy 0.500 <= existing 0.500 in 2fueA # T0335 read from 2fueA/merged-good-all-a2m # 2fueA read from 2fueA/merged-good-all-a2m # adding 2fueA to template set # found chain 2fueA in template set T0335 2 :ISNAKIARINELAAKAKAG 2fueA 100 :LGEELLQDLINFCLSYMAL T0335 21 :VITEEEKAEQQKLRQE 2fueA 144 :SCTLEERIEFSELDKK T0335 37 :YLKGFRSSMKNTLKS 2fueA 162 :IREKFVEALKTEFAG Number of specific fragments extracted= 3 number of extra gaps= 0 total=71 Number of alignments=20 # 2fueA read from 2fueA/merged-good-all-a2m # found chain 2fueA in template set T0335 3 :SNAKIARINELAAKAKAG 2fueA 101 :GEELLQDLINFCLSYMAL T0335 21 :VITEEEKAEQQKLRQE 2fueA 144 :SCTLEERIEFSELDKK T0335 37 :YLKGFRSSMKNTLKS 2fueA 162 :IREKFVEALKTEFAG Number of specific fragments extracted= 3 number of extra gaps= 0 total=74 Number of alignments=21 # 2fueA read from 2fueA/merged-good-all-a2m # found chain 2fueA in template set T0335 3 :SNAKIARINELAAKAKAG 2fueA 101 :GEELLQDLINFCLSYMAL T0335 21 :VITEEEKAEQQKLRQE 2fueA 144 :SCTLEERIEFSELDKK T0335 37 :YLKGFRSSMKNTLKSVKII 2fueA 162 :IREKFVEALKTEFAGKGLR Number of specific fragments extracted= 3 number of extra gaps= 0 total=77 Number of alignments=22 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1lj9A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1lj9A expands to /projects/compbio/data/pdb/1lj9.pdb.gz 1lj9A:# T0335 read from 1lj9A/merged-good-all-a2m # 1lj9A read from 1lj9A/merged-good-all-a2m # adding 1lj9A to template set # found chain 1lj9A in template set T0335 5 :AKIARINELAAKAKAGVITEEEKAEQQKLRQEYLKGFRSSMKN 1lj9A 99 :PIIVRENQHSNQVALQGLSEVEISQLADYLVRMRKNVSEDWEF Number of specific fragments extracted= 1 number of extra gaps= 0 total=78 Number of alignments=23 # 1lj9A read from 1lj9A/merged-good-all-a2m # found chain 1lj9A in template set T0335 5 :AKIARINELAAKAKAGVITEEEKAEQQKLRQEYLKGFRSSMKNTLK 1lj9A 99 :PIIVRENQHSNQVALQGLSEVEISQLADYLVRMRKNVSEDWEFVKK Number of specific fragments extracted= 1 number of extra gaps= 0 total=79 Number of alignments=24 # 1lj9A read from 1lj9A/merged-good-all-a2m # found chain 1lj9A in template set T0335 5 :AKIARINELAAKAKAGVITEEEKAEQQKLRQEYLKGFRSSMKNTLK 1lj9A 99 :PIIVRENQHSNQVALQGLSEVEISQLADYLVRMRKNVSEDWEFVKK Number of specific fragments extracted= 1 number of extra gaps= 0 total=80 Number of alignments=25 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1gzqA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1gzqA expands to /projects/compbio/data/pdb/1gzq.pdb.gz 1gzqA:# T0335 read from 1gzqA/merged-good-all-a2m # 1gzqA read from 1gzqA/merged-good-all-a2m # adding 1gzqA to template set # found chain 1gzqA in template set T0335 21 :VITEEEKAEQQKLRQEYLKGFRSSMKNTLKS 1gzqA 57 :NFSDKEVAELEEIFRVYIFGFAREVQDFAGD Number of specific fragments extracted= 1 number of extra gaps= 0 total=81 Number of alignments=26 # 1gzqA read from 1gzqA/merged-good-all-a2m # found chain 1gzqA in template set T0335 21 :VITEEEKAEQQKLRQEYLKGFRSSMKNTLKS 1gzqA 57 :NFSDKEVAELEEIFRVYIFGFAREVQDFAGD Number of specific fragments extracted= 1 number of extra gaps= 0 total=82 Number of alignments=27 # 1gzqA read from 1gzqA/merged-good-all-a2m # found chain 1gzqA in template set T0335 21 :VITEEEKAEQQKLRQEYLKGFRSSMKNTLKSV 1gzqA 57 :NFSDKEVAELEEIFRVYIFGFAREVQDFAGDF Number of specific fragments extracted= 1 number of extra gaps= 0 total=83 Number of alignments=28 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ap4/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1ap4 expands to /projects/compbio/data/pdb/1ap4.pdb.gz 1ap4:Warning: there is no chain 1ap4 will retry with 1ap4A # T0335 read from 1ap4/merged-good-all-a2m # 1ap4 read from 1ap4/merged-good-all-a2m # adding 1ap4 to template set # found chain 1ap4 in template set T0335 6 :K 1ap4 5 :Y T0335 16 :KAKAGVITEEEKA 1ap4 6 :KAAVEQLTEEQKN T0335 40 :GFRSSMKNTLKSV 1ap4 19 :EFKAAFDIFVLGA T0335 58 :EGNDVTPEKLKREQRNNKLHLEH 1ap4 32 :EDGCISTKELGKVMRMLGQNPTP Number of specific fragments extracted= 4 number of extra gaps= 0 total=87 Number of alignments=29 # 1ap4 read from 1ap4/merged-good-all-a2m # found chain 1ap4 in template set T0335 3 :SNAKIARINE 1ap4 2 :DDIYKAAVEQ T0335 22 :ITEEEKA 1ap4 12 :LTEEQKN T0335 40 :GFRSSMKNTLKSV 1ap4 19 :EFKAAFDIFVLGA T0335 58 :EGNDVTPEKLKREQRNNKLHLE 1ap4 32 :EDGCISTKELGKVMRMLGQNPT Number of specific fragments extracted= 4 number of extra gaps= 0 total=91 Number of alignments=30 # 1ap4 read from 1ap4/merged-good-all-a2m # found chain 1ap4 in template set T0335 3 :SNAKIARI 1ap4 2 :DDIYKAAV T0335 20 :GVITEEEK 1ap4 10 :EQLTEEQK T0335 39 :KGFRSSMKNTLKSV 1ap4 18 :NEFKAAFDIFVLGA T0335 58 :EGNDVTPEKLKREQRNNKLHLEH 1ap4 32 :EDGCISTKELGKVMRMLGQNPTP Number of specific fragments extracted= 4 number of extra gaps= 0 total=95 Number of alignments=31 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1b5sA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1b5sA expands to /projects/compbio/data/pdb/1b5s.pdb.gz 1b5sA:# T0335 read from 1b5sA/merged-good-all-a2m # 1b5sA read from 1b5sA/merged-good-all-a2m # adding 1b5sA to template set # found chain 1b5sA in template set T0335 5 :AKIARINELAAKAKAGVITEEE 1b5sA 316 :ALAQEINELAEKARDGKLTPGE Number of specific fragments extracted= 1 number of extra gaps= 0 total=96 Number of alignments=32 # 1b5sA read from 1b5sA/merged-good-all-a2m # found chain 1b5sA in template set T0335 5 :AKIARINELAAKAKAGVITEEE 1b5sA 316 :ALAQEINELAEKARDGKLTPGE Number of specific fragments extracted= 1 number of extra gaps= 0 total=97 Number of alignments=33 # 1b5sA read from 1b5sA/merged-good-all-a2m # found chain 1b5sA in template set T0335 5 :AKIARINELAAKAKAGVITEEE 1b5sA 316 :ALAQEINELAEKARDGKLTPGE Number of specific fragments extracted= 1 number of extra gaps= 0 total=98 Number of alignments=34 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1qokA/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/T0335/1qokA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0335/1qokA/merged-good-all-a2m.gz for input Trying 1qokA/merged-good-all-a2m Error: Couldn't open file 1qokA/merged-good-all-a2m or 1qokA/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1wmhA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0335 read from 1wmhA/merged-good-all-a2m # 1wmhA read from 1wmhA/merged-good-all-a2m # found chain 1wmhA in training set T0335 40 :GFRSSMKNTLK 1wmhA 40 :GLCNEVRDMCS T0335 51 :SVKIIDPEGNDV 1wmhA 58 :TMKWIDEEGDPC T0335 63 :TPEKLKREQRNNKLH 1wmhA 73 :SQLELEEAFRLYELN Number of specific fragments extracted= 3 number of extra gaps= 0 total=101 Number of alignments=35 # 1wmhA read from 1wmhA/merged-good-all-a2m # found chain 1wmhA in training set T0335 40 :GFRSSMKNTLK 1wmhA 40 :GLCNEVRDMCS T0335 51 :SVKIIDPEGNDV 1wmhA 58 :TMKWIDEEGDPC T0335 63 :TPEKLKREQRNNKLH 1wmhA 73 :SQLELEEAFRLYELN Number of specific fragments extracted= 3 number of extra gaps= 0 total=104 Number of alignments=36 # 1wmhA read from 1wmhA/merged-good-all-a2m # found chain 1wmhA in training set T0335 40 :GFRSSMKNTLK 1wmhA 40 :GLCNEVRDMCS T0335 51 :SVKIIDPEGNDV 1wmhA 58 :TMKWIDEEGDPC T0335 63 :TPEKLKREQR 1wmhA 73 :SQLELEEAFR Number of specific fragments extracted= 3 number of extra gaps= 0 total=107 Number of alignments=37 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1y96B/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1y96B expands to /projects/compbio/data/pdb/1y96.pdb.gz 1y96B:# T0335 read from 1y96B/merged-good-all-a2m # 1y96B read from 1y96B/merged-good-all-a2m # adding 1y96B to template set # found chain 1y96B in template set T0335 23 :TEEEKAE 1y96B 50 :SLESQEQ T0335 30 :QQKLRQEYLKGFRS 1y96B 59 :RAALRERYLRSLLA Number of specific fragments extracted= 2 number of extra gaps= 0 total=109 Number of alignments=38 # 1y96B read from 1y96B/merged-good-all-a2m # found chain 1y96B in template set T0335 23 :TEEEKAE 1y96B 50 :SLESQEQ T0335 30 :QQKLRQEYLKGFRS 1y96B 59 :RAALRERYLRSLLA Number of specific fragments extracted= 2 number of extra gaps= 0 total=111 Number of alignments=39 # 1y96B read from 1y96B/merged-good-all-a2m # found chain 1y96B in template set T0335 23 :TEEEKAE 1y96B 50 :SLESQEQ T0335 30 :QQKLRQEYLKGFR 1y96B 59 :RAALRERYLRSLL T0335 47 :NTL 1y96B 72 :AMV T0335 50 :KSVKIIDPEGNDV 1y96B 76 :HQVSFTLHEGVRV Number of specific fragments extracted= 4 number of extra gaps= 0 total=115 Number of alignments=40 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2fzfA/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/T0335/2fzfA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0335/2fzfA/merged-good-all-a2m.gz for input Trying 2fzfA/merged-good-all-a2m Error: Couldn't open file 2fzfA/merged-good-all-a2m or 2fzfA/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1wdpA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1wdpA expands to /projects/compbio/data/pdb/1wdp.pdb.gz 1wdpA:Skipped atom 486, because occupancy 0.330 <= existing 0.670 in 1wdpA Skipped atom 488, because occupancy 0.330 <= existing 0.670 in 1wdpA Skipped atom 490, because occupancy 0.330 <= existing 0.670 in 1wdpA Skipped atom 492, because occupancy 0.330 <= existing 0.670 in 1wdpA Skipped atom 494, because occupancy 0.330 <= existing 0.670 in 1wdpA Skipped atom 582, because occupancy 0.500 <= existing 0.500 in 1wdpA Skipped atom 584, because occupancy 0.500 <= existing 0.500 in 1wdpA Skipped atom 1698, because occupancy 0.400 <= existing 0.610 in 1wdpA Skipped atom 1700, because occupancy 0.400 <= existing 0.610 in 1wdpA Skipped atom 1702, because occupancy 0.400 <= existing 0.610 in 1wdpA Skipped atom 1704, because occupancy 0.400 <= existing 0.610 in 1wdpA Skipped atom 1706, because occupancy 0.400 <= existing 0.610 in 1wdpA Skipped atom 1936, because occupancy 0.470 <= existing 0.530 in 1wdpA Skipped atom 1938, because occupancy 0.470 <= existing 0.530 in 1wdpA Skipped atom 1986, because occupancy 0.290 <= existing 0.700 in 1wdpA Skipped atom 1988, because occupancy 0.290 <= existing 0.700 in 1wdpA Skipped atom 2249, because occupancy 0.450 <= existing 0.550 in 1wdpA Skipped atom 2251, because occupancy 0.450 <= existing 0.550 in 1wdpA Skipped atom 2253, because occupancy 0.450 <= existing 0.550 in 1wdpA Skipped atom 2255, because occupancy 0.450 <= existing 0.550 in 1wdpA Skipped atom 2669, because occupancy 0.400 <= existing 0.600 in 1wdpA Skipped atom 2671, because occupancy 0.400 <= existing 0.600 in 1wdpA Skipped atom 2864, because occupancy 0.330 <= existing 0.670 in 1wdpA Skipped atom 2866, because occupancy 0.330 <= existing 0.670 in 1wdpA Skipped atom 3422, because occupancy 0.350 <= existing 0.640 in 1wdpA Skipped atom 3424, because occupancy 0.350 <= existing 0.640 in 1wdpA Skipped atom 3426, because occupancy 0.350 <= existing 0.640 in 1wdpA Skipped atom 3428, because occupancy 0.350 <= existing 0.640 in 1wdpA Skipped atom 3430, because occupancy 0.350 <= existing 0.640 in 1wdpA Skipped atom 3461, because occupancy 0.410 <= existing 0.590 in 1wdpA Skipped atom 3463, because occupancy 0.410 <= existing 0.590 in 1wdpA Skipped atom 3465, because occupancy 0.410 <= existing 0.590 in 1wdpA Skipped atom 3467, because occupancy 0.410 <= existing 0.590 in 1wdpA # T0335 read from 1wdpA/merged-good-all-a2m # 1wdpA read from 1wdpA/merged-good-all-a2m # adding 1wdpA to template set # found chain 1wdpA in template set Warning: unaligning (T0335)I55 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1wdpA)V23 Warning: unaligning (T0335)D61 because of BadResidue code BAD_PEPTIDE in next template residue (1wdpA)E30 Warning: unaligning (T0335)V62 because of BadResidue code BAD_PEPTIDE at template residue (1wdpA)E30 T0335 56 :DPEGN 1wdpA 24 :NVDNV T0335 63 :TPEKLKREQRN 1wdpA 31 :DPDGLKEQLLQ Number of specific fragments extracted= 2 number of extra gaps= 2 total=117 # 1wdpA read from 1wdpA/merged-good-all-a2m # found chain 1wdpA in template set Warning: unaligning (T0335)I55 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1wdpA)V23 Warning: unaligning (T0335)D61 because of BadResidue code BAD_PEPTIDE in next template residue (1wdpA)E30 Warning: unaligning (T0335)V62 because of BadResidue code BAD_PEPTIDE at template residue (1wdpA)E30 T0335 56 :DPEGN 1wdpA 24 :NVDNV T0335 63 :TPEKLKREQR 1wdpA 31 :DPDGLKEQLL Number of specific fragments extracted= 2 number of extra gaps= 2 total=119 # 1wdpA read from 1wdpA/merged-good-all-a2m # found chain 1wdpA in template set Warning: unaligning (T0335)I54 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1wdpA)V23 Warning: unaligning (T0335)I55 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1wdpA)V23 Warning: unaligning (T0335)D61 because of BadResidue code BAD_PEPTIDE in next template residue (1wdpA)E30 Warning: unaligning (T0335)V62 because of BadResidue code BAD_PEPTIDE at template residue (1wdpA)E30 T0335 56 :DPEGN 1wdpA 24 :NVDNV T0335 63 :TPEKLKREQR 1wdpA 31 :DPDGLKEQLL Number of specific fragments extracted= 2 number of extra gaps= 2 total=121 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1t3wA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1t3wA expands to /projects/compbio/data/pdb/1t3w.pdb.gz 1t3wA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0335 read from 1t3wA/merged-good-all-a2m # 1t3wA read from 1t3wA/merged-good-all-a2m # adding 1t3wA to template set # found chain 1t3wA in template set T0335 2 :ISNAKIARINELAAKAKAGVITEEEKAEQQKLRQE 1t3wA 543 :FDSLLELRQEELIARERTHGLSNEERLELWTLNQE Number of specific fragments extracted= 1 number of extra gaps= 0 total=122 Number of alignments=41 # 1t3wA read from 1t3wA/merged-good-all-a2m # found chain 1t3wA in template set T0335 2 :ISNAKIARINELAAKAKAGVITEEEKAEQQKLRQE 1t3wA 543 :FDSLLELRQEELIARERTHGLSNEERLELWTLNQE Number of specific fragments extracted= 1 number of extra gaps= 0 total=123 Number of alignments=42 # 1t3wA read from 1t3wA/merged-good-all-a2m # found chain 1t3wA in template set T0335 3 :SNAKIARINELAAKAKAGVITEEEKAEQQKLRQE 1t3wA 544 :DSLLELRQEELIARERTHGLSNEERLELWTLNQE Number of specific fragments extracted= 1 number of extra gaps= 0 total=124 Number of alignments=43 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1wdtA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1wdtA expands to /projects/compbio/data/pdb/1wdt.pdb.gz 1wdtA:# T0335 read from 1wdtA/merged-good-all-a2m # 1wdtA read from 1wdtA/merged-good-all-a2m # adding 1wdtA to template set # found chain 1wdtA in template set T0335 21 :VITEEEKAEQQKLRQEYLKGFR 1wdtA 192 :EVPPEERERVQRFRQEVLEAIV T0335 43 :SSMKNTLKS 1wdtA 217 :EGLLEKYLE T0335 59 :GNDVTPEKLKREQRN 1wdtA 226 :GEEVTGEALEKAFHE Number of specific fragments extracted= 3 number of extra gaps= 0 total=127 Number of alignments=44 # 1wdtA read from 1wdtA/merged-good-all-a2m # found chain 1wdtA in template set T0335 21 :VITEEEKAEQQKLRQEYLKGFRS 1wdtA 192 :EVPPEERERVQRFRQEVLEAIVE T0335 44 :SMKNTLKS 1wdtA 218 :GLLEKYLE T0335 59 :GNDVTPEKLKREQRN 1wdtA 226 :GEEVTGEALEKAFHE Number of specific fragments extracted= 3 number of extra gaps= 0 total=130 Number of alignments=45 # 1wdtA read from 1wdtA/merged-good-all-a2m # found chain 1wdtA in template set T0335 21 :VITEEEKAEQQKLRQEYLKGFRS 1wdtA 192 :EVPPEERERVQRFRQEVLEAIVE T0335 44 :SMKNTLKS 1wdtA 218 :GLLEKYLE T0335 59 :GNDVTPEKLKREQRN 1wdtA 226 :GEEVTGEALEKAFHE Number of specific fragments extracted= 3 number of extra gaps= 0 total=133 Number of alignments=46 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2aexA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2aexA expands to /projects/compbio/data/pdb/2aex.pdb.gz 2aexA:Skipped atom 178, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 180, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 182, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 184, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 186, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 188, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 190, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 192, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 194, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 196, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 198, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 402, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 404, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 406, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 408, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 410, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 412, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 414, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 416, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 418, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 681, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 683, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 685, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 687, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 689, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 691, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 969, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 971, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 973, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 975, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 977, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 979, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 1121, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 1123, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 1125, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 1127, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 1129, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 1131, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 1133, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 1135, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 1137, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 1139, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 1141, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 1205, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 1207, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 1209, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 1211, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 1213, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 1215, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 1217, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 1219, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 1373, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 1375, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 1377, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 1379, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 1381, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 1383, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 1385, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 1387, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 1389, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 1514, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 1516, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 1518, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 1520, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 1522, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 1524, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 1526, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 1528, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 1530, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 1823, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 1825, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 1827, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 1829, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 1831, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 1833, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 1835, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 1837, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 2093, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 2095, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 2097, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 2099, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 2101, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 2103, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 2105, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 2107, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 2175, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 2177, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 2179, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 2181, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 2183, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 2185, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 2187, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 2189, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 2323, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 2325, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 2327, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 2329, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 2331, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 2333, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 2335, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 2337, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 2476, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 2478, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 2480, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 2482, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 2484, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 2486, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 2653, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 2655, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 2657, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 2659, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 2661, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 2663, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 2722, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 2724, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 2726, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 2728, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 2730, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 2732, because occupancy 0.500 <= existing 0.500 in 2aexA Skipped atom 2734, because occupancy 0.500 <= existing 0.500 in 2aexA # T0335 read from 2aexA/merged-good-all-a2m # 2aexA read from 2aexA/merged-good-all-a2m # adding 2aexA to template set # found chain 2aexA in template set T0335 2 :ISNAKIARIN 2aexA 346 :SKEEVFRFVQ T0335 12 :ELAAKAKAGVITEEEKAEQQKLRQEYL 2aexA 367 :PLVKKHCDDSFTPQEKLWQQLRRGRYV Number of specific fragments extracted= 2 number of extra gaps= 0 total=135 Number of alignments=47 # 2aexA read from 2aexA/merged-good-all-a2m # found chain 2aexA in template set T0335 2 :ISNAKIARIN 2aexA 346 :SKEEVFRFVQ T0335 12 :ELAAKAKAGVITEEEKAEQQ 2aexA 367 :PLVKKHCDDSFTPQEKLWQQ Number of specific fragments extracted= 2 number of extra gaps= 0 total=137 Number of alignments=48 # 2aexA read from 2aexA/merged-good-all-a2m # found chain 2aexA in template set T0335 2 :ISNAKIARIN 2aexA 346 :SKEEVFRFVQ T0335 12 :ELAAKAKAGVITEEEKAEQQKLRQEYL 2aexA 367 :PLVKKHCDDSFTPQEKLWQQLRRGRYV Number of specific fragments extracted= 2 number of extra gaps= 0 total=139 Number of alignments=49 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1avsA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1avsA expands to /projects/compbio/data/pdb/1avs.pdb.gz 1avsA:# T0335 read from 1avsA/merged-good-all-a2m # 1avsA read from 1avsA/merged-good-all-a2m # adding 1avsA to template set # found chain 1avsA in template set Warning: unaligning (T0335)A28 because of BadResidue code BAD_PEPTIDE in next template residue (1avsA)E21 Warning: unaligning (T0335)E29 because of BadResidue code BAD_PEPTIDE at template residue (1avsA)E21 T0335 22 :ITEEEK 1avsA 14 :LSEEMI T0335 30 :QQKLRQEY 1avsA 22 :FKAAFDMF T0335 42 :RSSMKNTLKS 1avsA 39 :TKELGTVMRM T0335 58 :EGNDVTPEKLKREQRNN 1avsA 49 :LGQNPTKEELDAIIEEV Number of specific fragments extracted= 4 number of extra gaps= 1 total=143 Number of alignments=50 # 1avsA read from 1avsA/merged-good-all-a2m # found chain 1avsA in template set Warning: unaligning (T0335)A28 because of BadResidue code BAD_PEPTIDE in next template residue (1avsA)E21 Warning: unaligning (T0335)E29 because of BadResidue code BAD_PEPTIDE at template residue (1avsA)E21 T0335 21 :VITEEEK 1avsA 13 :FLSEEMI T0335 30 :QQKLRQEY 1avsA 22 :FKAAFDMF T0335 42 :RSSMKNTLKS 1avsA 39 :TKELGTVMRM T0335 58 :EGNDVTPEKLKREQRNNKL 1avsA 49 :LGQNPTKEELDAIIEEVDE Number of specific fragments extracted= 4 number of extra gaps= 1 total=147 Number of alignments=51 # 1avsA read from 1avsA/merged-good-all-a2m # found chain 1avsA in template set Warning: unaligning (T0335)A28 because of BadResidue code BAD_PEPTIDE in next template residue (1avsA)E21 Warning: unaligning (T0335)E29 because of BadResidue code BAD_PEPTIDE at template residue (1avsA)E21 T0335 19 :AGVITEEEK 1avsA 11 :RAFLSEEMI T0335 30 :QQKLRQEY 1avsA 22 :FKAAFDMF T0335 57 :PEGNDVTPEKLKREQRNNKLHLE 1avsA 32 :DGGGDISTKELGTVMRMLGQNPT Number of specific fragments extracted= 3 number of extra gaps= 1 total=150 Number of alignments=52 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1f46A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0335 read from 1f46A/merged-good-all-a2m # 1f46A read from 1f46A/merged-good-all-a2m # found chain 1f46A in training set T0335 28 :AEQQKLRQ 1f46A 96 :QLFKLMLQ T0335 37 :YLKGFRSSM 1f46A 104 :SAQHIADEV T0335 51 :SVKIIDPEGNDVTPEKLKREQRNNKLHLE 1f46A 113 :GGVVLDDQRRMMTPQKLREYQDIIREVKD Number of specific fragments extracted= 3 number of extra gaps= 0 total=153 Number of alignments=53 # 1f46A read from 1f46A/merged-good-all-a2m # found chain 1f46A in training set T0335 37 :YLKGFRSSMKNTLK 1f46A 97 :LFKLMLQSAQHIAD T0335 51 :SVKIIDPEGNDVTPEKLKREQRNNK 1f46A 113 :GGVVLDDQRRMMTPQKLREYQDIIR Number of specific fragments extracted= 2 number of extra gaps= 0 total=155 Number of alignments=54 # 1f46A read from 1f46A/merged-good-all-a2m # found chain 1f46A in training set T0335 33 :LRQEYLKGF 1f46A 97 :LFKLMLQSA T0335 43 :SSMKNTL 1f46A 106 :QHIADEV T0335 51 :SVKIIDPEGNDVTPEKLKREQR 1f46A 113 :GGVVLDDQRRMMTPQKLREYQD Number of specific fragments extracted= 3 number of extra gaps= 0 total=158 Number of alignments=55 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2c5kT/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2c5kT expands to /projects/compbio/data/pdb/2c5k.pdb.gz 2c5kT:Skipped atom 295, because occupancy 0.500 <= existing 0.500 in 2c5kT Skipped atom 299, because occupancy 0.500 <= existing 0.500 in 2c5kT Skipped atom 301, because occupancy 0.500 <= existing 0.500 in 2c5kT Skipped atom 303, because occupancy 0.500 <= existing 0.500 in 2c5kT Skipped atom 305, because occupancy 0.500 <= existing 0.500 in 2c5kT Skipped atom 307, because occupancy 0.500 <= existing 0.500 in 2c5kT Skipped atom 652, because occupancy 0.500 <= existing 0.500 in 2c5kT Skipped atom 656, because occupancy 0.500 <= existing 0.500 in 2c5kT Skipped atom 658, because occupancy 0.500 <= existing 0.500 in 2c5kT Skipped atom 660, because occupancy 0.500 <= existing 0.500 in 2c5kT # T0335 read from 2c5kT/merged-good-all-a2m # 2c5kT read from 2c5kT/merged-good-all-a2m # adding 2c5kT to template set # found chain 2c5kT in template set Warning: unaligning (T0335)T23 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2c5kT)D35 T0335 4 :NAKIARINELAAKAKAGVI 2c5kT 13 :KDTKEQLNRINNYITRHNT T0335 24 :EEEKAEQQKL 2c5kT 39 :EEIQDILKDV T0335 35 :QEYLKGFRSSMKNTLKS 2c5kT 49 :EETIVDLDRSIIVMKRD T0335 58 :EGNDV 2c5kT 66 :ENEDV T0335 65 :EKLKREQRNNKLHLE 2c5kT 71 :SGREAQVKNIKQQLD Number of specific fragments extracted= 5 number of extra gaps= 0 total=163 Number of alignments=56 # 2c5kT read from 2c5kT/merged-good-all-a2m # found chain 2c5kT in template set Warning: unaligning (T0335)T23 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2c5kT)D35 T0335 3 :SNAKIARINELAAKAKAGVI 2c5kT 12 :VKDTKEQLNRINNYITRHNT T0335 24 :EEEKAEQQKL 2c5kT 39 :EEIQDILKDV T0335 35 :QEYLKGFRSSMKNTLKS 2c5kT 49 :EETIVDLDRSIIVMKRD T0335 58 :EGNDV 2c5kT 66 :ENEDV T0335 65 :EKLKREQRNNK 2c5kT 71 :SGREAQVKNIK Number of specific fragments extracted= 5 number of extra gaps= 0 total=168 Number of alignments=57 # 2c5kT read from 2c5kT/merged-good-all-a2m # found chain 2c5kT in template set Warning: unaligning (T0335)T23 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2c5kT)D35 T0335 4 :NAKIARINELAAKAKAGVI 2c5kT 13 :KDTKEQLNRINNYITRHNT T0335 24 :EEEKAEQQKL 2c5kT 39 :EEIQDILKDV T0335 35 :QEYLKGFRSSMKNTLK 2c5kT 49 :EETIVDLDRSIIVMKR T0335 57 :PEGNDVT 2c5kT 65 :DENEDVS T0335 64 :PEKLKREQRN 2c5kT 77 :VKNIKQQLDA Number of specific fragments extracted= 5 number of extra gaps= 0 total=173 Number of alignments=58 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1xupO/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/T0335/1xupO/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0335/1xupO/merged-good-all-a2m.gz for input Trying 1xupO/merged-good-all-a2m Error: Couldn't open file 1xupO/merged-good-all-a2m or 1xupO/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1byb/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1byb expands to /projects/compbio/data/pdb/1byb.pdb.gz 1byb:Warning: there is no chain 1byb will retry with 1bybA # T0335 read from 1byb/merged-good-all-a2m # 1byb read from 1byb/merged-good-all-a2m # adding 1byb to template set # found chain 1byb in template set T0335 54 :IIDPEGNDVTPEKLKREQRN 1byb 22 :VVNVDNVFEDPDGLKEQLLQ Number of specific fragments extracted= 1 number of extra gaps= 0 total=174 Number of alignments=59 # 1byb read from 1byb/merged-good-all-a2m # found chain 1byb in template set T0335 55 :IDPEGNDVTPEKLKREQRN 1byb 23 :VNVDNVFEDPDGLKEQLLQ Number of specific fragments extracted= 1 number of extra gaps= 0 total=175 # 1byb read from 1byb/merged-good-all-a2m # found chain 1byb in template set T0335 54 :IIDPEGNDVTPEKLKREQR 1byb 22 :VVNVDNVFEDPDGLKEQLL Number of specific fragments extracted= 1 number of extra gaps= 0 total=176 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1r2uA/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/T0335/1r2uA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0335/1r2uA/merged-good-all-a2m.gz for input Trying 1r2uA/merged-good-all-a2m Error: Couldn't open file 1r2uA/merged-good-all-a2m or 1r2uA/merged-good-all-a2m.gz for input # command:# PrintAlignmentsContacts allconstraints.under Using radius: 8.0000 NUMB_ALIGNS: 59 Done printing distance constraints # command: