# command:# Prefix for input files set to /projects/compbio/experiments/undertaker/atoms-inputs/ # command:# reading cullpdb_pc80_res1.2_R0.2_d070810_chains408.atoms.gz # #computed average backbone with maximum peptide_sq_deviance = 0.002 # computed average trans backbone unit from 1600 examples # computed average trans backbone unit before proline from 52 examples # trans (non-proline) backbone unit: # CA= -2.2097 1.0151 -0.0046 # O= -0.1488 2.2425 0.0020 # C= -0.6903 1.1357 0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4580 -0.0000 -0.0000 # cis backbone unit: # CA= -0.1462 2.4515 0.0018 # O= -2.0272 0.9713 0.0022 # C= -0.8006 1.0755 0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4659 0.0000 0.0000 # trans backbone unit before proline: # CA= -2.2063 1.0654 0.0002 # O= -0.1193 2.2442 0.0054 # C= -0.6842 1.1479 -0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4661 -0.0000 0.0000 # After reading cullpdb_pc80_res1.2_R0.2_d070810_chains408.atoms.gz have 408 chains in training database # Count of chains,residues,atoms: 408,82794,639987 # 79931 residues have no bad marker # 573 residues lack atoms needed to compute omega # 313 residues have cis peptide # number of each bad type: # NON_STANDARD_RESIDUE 0 # HAS_OXT 264 # TOO_MANY_ATOMS 0 # TOO_FEW_ATOMS 378 # HAS_UNKNOWN_ATOMS 0 # HAS_DUPLICATE_ATOMS 0 # CHAIN_BREAK_BEFORE 148 # NON_PLANAR_PEPTIDE 17 # BAD_PEPTIDE 812 # HIGH_B_FACTOR 1566 # Note: may sum to more than number of residues, # because one residue may have multiple problems # command:# Reading rotamer library from dunbrack-40pc-3157.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 # command:# Making conformation for sequence T0643 numbered 1 through 83 Created new target T0643 from T0643.a2m # command:CPU_time= 5.511 sec, elapsed time= 10.163 sec. # command:# reading script from file all-templates.under # Reading fragments from alignment file # Attempting to read fragment alignments from file 2ictA/T0643-2ictA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2ictA expands to /projects/compbio/data/pdb/2ict.pdb.gz 2ictA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0643 read from 2ictA/T0643-2ictA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2ictA read from 2ictA/T0643-2ictA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2ictA to template set # found chain 2ictA in template set T0643 22 :VRNALKDLLKDM 2ictA 9 :PGDIIQESLDEL # choosing archetypes in rotamer library T0643 34 :NQSSLAKECPLSQSMISSIVNSTYYAN 2ictA 23 :SLREFARAMEIAPSTASRLLTGKAALT T0643 62 :SAAKCQEFGRWYKHFKKTKDMM 2ictA 63 :SPQMWLNLQNAWSLAEAEKTVD Number of specific fragments extracted= 3 number of extra gaps= 0 total=3 Will force an alignment to be made, even if fragment is small Number of alignments=1 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2ictA/T0643-2ictA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0643 read from 2ictA/T0643-2ictA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2ictA read from 2ictA/T0643-2ictA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2ictA in template set T0643 22 :VRNALKDLLKDM 2ictA 9 :PGDIIQESLDEL T0643 34 :NQSSLAKECPLSQSMISSIVNSTYYA 2ictA 23 :SLREFARAMEIAPSTASRLLTGKAAL T0643 60 :NVSAAKCQEFGRWYKHFKKTKDMM 2ictA 61 :GSSPQMWLNLQNAWSLAEAEKTVD Number of specific fragments extracted= 3 number of extra gaps= 0 total=6 Will force an alignment to be made, even if fragment is small Number of alignments=2 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2ictA/T0643-2ictA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0643 read from 2ictA/T0643-2ictA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2ictA read from 2ictA/T0643-2ictA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2ictA in template set T0643 22 :VRNALKDLLKDM 2ictA 9 :PGDIIQESLDEL T0643 34 :NQSSLAKECPLSQSMISSIVNSTYYA 2ictA 23 :SLREFARAMEIAPSTASRLLTGKAAL T0643 60 :NVSAAKCQEFGRWYKHFKKTKDMM 2ictA 61 :GSSPQMWLNLQNAWSLAEAEKTVD Number of specific fragments extracted= 3 number of extra gaps= 0 total=9 Will force an alignment to be made, even if fragment is small Number of alignments=3 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3cecA/T0643-3cecA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 3cecA expands to /projects/compbio/data/pdb/3cec.pdb.gz 3cecA:Skipped atom 28, because occupancy 0.5 <= existing 0.500 in 3cecA Skipped atom 30, because occupancy 0.500 <= existing 0.500 in 3cecA Skipped atom 32, because occupancy 0.500 <= existing 0.500 in 3cecA Skipped atom 34, because occupancy 0.500 <= existing 0.500 in 3cecA Skipped atom 36, because occupancy 0.500 <= existing 0.500 in 3cecA Skipped atom 38, because occupancy 0.500 <= existing 0.500 in 3cecA Skipped atom 40, because occupancy 0.500 <= existing 0.500 in 3cecA Skipped atom 42, because occupancy 0.500 <= existing 0.500 in 3cecA Skipped atom 44, because occupancy 0.500 <= existing 0.500 in 3cecA Skipped atom 46, because occupancy 0.500 <= existing 0.500 in 3cecA Skipped atom 112, because occupancy 0.500 <= existing 0.500 in 3cecA Skipped atom 114, because occupancy 0.500 <= existing 0.500 in 3cecA Skipped atom 116, because occupancy 0.500 <= existing 0.500 in 3cecA Skipped atom 118, because occupancy 0.500 <= existing 0.500 in 3cecA Skipped atom 120, because occupancy 0.500 <= existing 0.500 in 3cecA Skipped atom 122, because occupancy 0.500 <= existing 0.500 in 3cecA Skipped atom 124, because occupancy 0.500 <= existing 0.500 in 3cecA Skipped atom 126, because occupancy 0.500 <= existing 0.500 in 3cecA Skipped atom 144, because occupancy 0.500 <= existing 0.500 in 3cecA Skipped atom 146, because occupancy 0.500 <= existing 0.500 in 3cecA Skipped atom 148, because occupancy 0.500 <= existing 0.500 in 3cecA Skipped atom 150, because occupancy 0.500 <= existing 0.500 in 3cecA Skipped atom 152, because occupancy 0.500 <= existing 0.500 in 3cecA Skipped atom 154, because occupancy 0.500 <= existing 0.500 in 3cecA Skipped atom 156, because occupancy 0.500 <= existing 0.500 in 3cecA Skipped atom 158, because occupancy 0.500 <= existing 0.500 in 3cecA Skipped atom 262, because occupancy 0.500 <= existing 0.500 in 3cecA Skipped atom 264, because occupancy 0.500 <= existing 0.500 in 3cecA Skipped atom 266, because occupancy 0.500 <= existing 0.500 in 3cecA Skipped atom 268, because occupancy 0.500 <= existing 0.500 in 3cecA Skipped atom 270, because occupancy 0.500 <= existing 0.500 in 3cecA Skipped atom 272, because occupancy 0.500 <= existing 0.500 in 3cecA Skipped atom 274, because occupancy 0.500 <= existing 0.500 in 3cecA Skipped atom 276, because occupancy 0.500 <= existing 0.500 in 3cecA Skipped atom 278, because occupancy 0.500 <= existing 0.500 in 3cecA Skipped atom 295, because occupancy 0.500 <= existing 0.500 in 3cecA Skipped atom 297, because occupancy 0.500 <= existing 0.500 in 3cecA Skipped atom 299, because occupancy 0.500 <= existing 0.500 in 3cecA Skipped atom 301, because occupancy 0.500 <= existing 0.500 in 3cecA Skipped atom 303, because occupancy 0.500 <= existing 0.500 in 3cecA Skipped atom 305, because occupancy 0.500 <= existing 0.500 in 3cecA Skipped atom 307, because occupancy 0.500 <= existing 0.500 in 3cecA Skipped atom 309, because occupancy 0.500 <= existing 0.500 in 3cecA Skipped atom 311, because occupancy 0.500 <= existing 0.500 in 3cecA Skipped atom 494, because occupancy 0.500 <= existing 0.500 in 3cecA Skipped atom 496, because occupancy 0.500 <= existing 0.500 in 3cecA Skipped atom 498, because occupancy 0.500 <= existing 0.500 in 3cecA Skipped atom 500, because occupancy 0.500 <= existing 0.500 in 3cecA Skipped atom 502, because occupancy 0.500 <= existing 0.500 in 3cecA Skipped atom 504, because occupancy 0.500 <= existing 0.500 in 3cecA Skipped atom 506, because occupancy 0.500 <= existing 0.500 in 3cecA Skipped atom 508, because occupancy 0.500 <= existing 0.500 in 3cecA Skipped atom 510, because occupancy 0.500 <= existing 0.500 in 3cecA Skipped atom 512, because occupancy 0.500 <= existing 0.500 in 3cecA Skipped atom 514, because occupancy 0.500 <= existing 0.500 in 3cecA Skipped atom 705, because occupancy 0.500 <= existing 0.500 in 3cecA Skipped atom 707, because occupancy 0.500 <= existing 0.500 in 3cecA Skipped atom 709, because occupancy 0.500 <= existing 0.500 in 3cecA Skipped atom 711, because occupancy 0.500 <= existing 0.500 in 3cecA Skipped atom 713, because occupancy 0.500 <= existing 0.500 in 3cecA Skipped atom 715, because occupancy 0.500 <= existing 0.500 in 3cecA Skipped atom 717, because occupancy 0.500 <= existing 0.500 in 3cecA Skipped atom 719, because occupancy 0.500 <= existing 0.500 in 3cecA Skipped atom 721, because occupancy 0.500 <= existing 0.500 in 3cecA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 735, because occupancy 0.300 <= existing 0.500 in 3cecA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 736, because occupancy 0.200 <= existing 0.500 in 3cecA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 738, because occupancy 0.300 <= existing 0.500 in 3cecA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 739, because occupancy 0.200 <= existing 0.500 in 3cecA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 741, because occupancy 0.300 <= existing 0.500 in 3cecA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 742, because occupancy 0.200 <= existing 0.500 in 3cecA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 744, because occupancy 0.300 <= existing 0.500 in 3cecA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 745, because occupancy 0.200 <= existing 0.500 in 3cecA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 747, because occupancy 0.300 <= existing 0.500 in 3cecA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 748, because occupancy 0.200 <= existing 0.500 in 3cecA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 750, because occupancy 0.300 <= existing 0.500 in 3cecA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 751, because occupancy 0.200 <= existing 0.500 in 3cecA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 753, because occupancy 0.220 <= existing 0.380 in 3cecA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 754, because occupancy 0.150 <= existing 0.380 in 3cecA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 756, because occupancy 0.300 <= existing 0.300 in 3cecA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 757, because occupancy 0.200 <= existing 0.300 in 3cecA # T0643 read from 3cecA/T0643-3cecA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3cecA read from 3cecA/T0643-3cecA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3cecA to template set # found chain 3cecA in template set T0643 22 :VRNALKDLLKDM 3cecA 18 :PGEVIADILDDL T0643 34 :NQSSLAKECPLSQSMISSIVNSTYY 3cecA 32 :NTANFAEILGVSNQTIQEVINGQRS T0643 61 :VSAAKCQEFGRWY 3cecA 57 :ITVDIAIRLGKAL Number of specific fragments extracted= 3 number of extra gaps= 0 total=12 Will force an alignment to be made, even if fragment is small Number of alignments=4 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3cecA/T0643-3cecA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0643 read from 3cecA/T0643-3cecA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3cecA read from 3cecA/T0643-3cecA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3cecA in template set T0643 22 :VRNALKDLLKDM 3cecA 18 :PGEVIADILDDL T0643 34 :NQSSLAKECPLSQSMISSIVNSTY 3cecA 32 :NTANFAEILGVSNQTIQEVINGQR T0643 60 :NVSAAKCQEFGRWY 3cecA 56 :SITVDIAIRLGKAL Number of specific fragments extracted= 3 number of extra gaps= 0 total=15 Will force an alignment to be made, even if fragment is small Number of alignments=5 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3cecA/T0643-3cecA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0643 read from 3cecA/T0643-3cecA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3cecA read from 3cecA/T0643-3cecA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3cecA in template set T0643 22 :VRNALKDLLKDM 3cecA 18 :PGEVIADILDDL T0643 34 :NQSSLAKECPLSQSMISSIVNSTYY 3cecA 32 :NTANFAEILGVSNQTIQEVINGQRS T0643 61 :VSAAKCQEFGRWY 3cecA 57 :ITVDIAIRLGKAL Number of specific fragments extracted= 3 number of extra gaps= 0 total=18 Will force an alignment to be made, even if fragment is small Number of alignments=6 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1y9qA/T0643-1y9qA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1y9qA expands to /projects/compbio/data/pdb/1y9q.pdb.gz 1y9qA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0643 read from 1y9qA/T0643-1y9qA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1y9qA read from 1y9qA/T0643-1y9qA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1y9qA to template set # found chain 1y9qA in template set T0643 19 :HTTVRNALKDLLKDM 1y9qA 9 :KSQIANQLKNLRKSR T0643 34 :NQSSLAKECPLSQSMISSIVNSTYYA 1y9qA 26 :SLDATAQLTGVSKAMLGQIERGESSP Number of specific fragments extracted= 2 number of extra gaps= 0 total=20 Will force an alignment to be made, even if fragment is small Number of alignments=7 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1y9qA/T0643-1y9qA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0643 read from 1y9qA/T0643-1y9qA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1y9qA read from 1y9qA/T0643-1y9qA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1y9qA in template set T0643 19 :HTTVRNALKDLLKDM 1y9qA 9 :KSQIANQLKNLRKSR T0643 34 :NQSSLAKECPLSQSMISSIVNSTYYA 1y9qA 26 :SLDATAQLTGVSKAMLGQIERGESSP Number of specific fragments extracted= 2 number of extra gaps= 0 total=22 Will force an alignment to be made, even if fragment is small Number of alignments=8 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1y9qA/T0643-1y9qA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0643 read from 1y9qA/T0643-1y9qA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1y9qA read from 1y9qA/T0643-1y9qA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1y9qA in template set T0643 19 :HTTVRNALKDLLKDM 1y9qA 9 :KSQIANQLKNLRKSR T0643 34 :NQSSLAKECPLSQSMISSIVNSTYYA 1y9qA 26 :SLDATAQLTGVSKAMLGQIERGESSP Number of specific fragments extracted= 2 number of extra gaps= 0 total=24 Will force an alignment to be made, even if fragment is small Number of alignments=9 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2jvlA/T0643-2jvlA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2jvlA expands to /projects/compbio/data/pdb/2jvl.pdb.gz 2jvlA:# T0643 read from 2jvlA/T0643-2jvlA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2jvlA read from 2jvlA/T0643-2jvlA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2jvlA to template set # found chain 2jvlA in template set T0643 2 :GHHHHHHSHMLPPEQW 2jvlA 64 :LTKVDRSDDIIKPKTV T0643 19 :HTTVRNALKDLLKDM 2jvlA 80 :GKEVGKAIEQGRQKF T0643 34 :NQSSLAKECPLSQSMISSIVNSTY 2jvlA 99 :TQAELGKEIGETAATVASYERGTA T0643 60 :NVSAAKCQE 2jvlA 123 :TPDQNILSK Number of specific fragments extracted= 4 number of extra gaps= 0 total=28 Will force an alignment to be made, even if fragment is small Number of alignments=10 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2jvlA/T0643-2jvlA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0643 read from 2jvlA/T0643-2jvlA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2jvlA read from 2jvlA/T0643-2jvlA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2jvlA in template set T0643 1 :MGHHHHHHSHMLPPEQWSHTTVRNALKDLLKD 2jvlA 62 :QRLTKVDRSDDIIKPKTVGKEVGKAIEQGRQK T0643 33 :MNQSSLAKECPLSQSMISSIVNSTY 2jvlA 98 :MTQAELGKEIGETAATVASYERGTA T0643 60 :NVSAAKCQE 2jvlA 123 :TPDQNILSK Number of specific fragments extracted= 3 number of extra gaps= 0 total=31 Will force an alignment to be made, even if fragment is small Number of alignments=11 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2jvlA/T0643-2jvlA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0643 read from 2jvlA/T0643-2jvlA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2jvlA read from 2jvlA/T0643-2jvlA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2jvlA in template set T0643 3 :HHHHHHSHMLPPEQWSHTTVRNALKDLLKD 2jvlA 64 :LTKVDRSDDIIKPKTVGKEVGKAIEQGRQK T0643 33 :MNQSSLAKECPLSQSMISSIVNSTY 2jvlA 98 :MTQAELGKEIGETAATVASYERGTA Number of specific fragments extracted= 2 number of extra gaps= 0 total=33 Will force an alignment to be made, even if fragment is small Number of alignments=12 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3b7hA/T0643-3b7hA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 3b7hA expands to /projects/compbio/data/pdb/3b7h.pdb.gz 3b7hA:# T0643 read from 3b7hA/T0643-3b7hA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3b7hA read from 3b7hA/T0643-3b7hA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3b7hA to template set # found chain 3b7hA in template set T0643 19 :HTTVRNALKDLLKDM 3b7hA 5 :GEFVSEHLMELITQQ T0643 34 :NQSSLAKECPLSQSMISSIVNSTYY 3b7hA 22 :TINRVATLAGLNQSTVNAMFEGRSK T0643 60 :NVSAAKCQEFGRW 3b7hA 47 :RPTITTIRKVCGT Number of specific fragments extracted= 3 number of extra gaps= 0 total=36 Will force an alignment to be made, even if fragment is small Number of alignments=13 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3b7hA/T0643-3b7hA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0643 read from 3b7hA/T0643-3b7hA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3b7hA read from 3b7hA/T0643-3b7hA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3b7hA in template set T0643 20 :TTVRNALKDLLKDM 3b7hA 6 :EFVSEHLMELITQQ T0643 34 :NQSSLAKECPLSQSMISSIVNSTY 3b7hA 22 :TINRVATLAGLNQSTVNAMFEGRS T0643 59 :ANVSAAKCQEFGRWY 3b7hA 46 :KRPTITTIRKVCGTL Number of specific fragments extracted= 3 number of extra gaps= 0 total=39 Will force an alignment to be made, even if fragment is small Number of alignments=14 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3b7hA/T0643-3b7hA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0643 read from 3b7hA/T0643-3b7hA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3b7hA read from 3b7hA/T0643-3b7hA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3b7hA in template set T0643 19 :HTTVRNALKDLLKDM 3b7hA 5 :GEFVSEHLMELITQQ T0643 34 :NQSSLAKECPLSQSMISSIVNSTY 3b7hA 22 :TINRVATLAGLNQSTVNAMFEGRS T0643 59 :ANVSAAKCQEFGRWY 3b7hA 46 :KRPTITTIRKVCGTL Number of specific fragments extracted= 3 number of extra gaps= 0 total=42 Will force an alignment to be made, even if fragment is small Number of alignments=15 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3ivpA/T0643-3ivpA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 3ivpA expands to /projects/compbio/data/pdb/3ivp.pdb.gz 3ivpA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0643 read from 3ivpA/T0643-3ivpA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3ivpA read from 3ivpA/T0643-3ivpA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3ivpA to template set # found chain 3ivpA in template set Warning: unaligning (T0643)L12 because first residue in template chain is (3ivpA)K3 T0643 13 :PPEQWSHTTVRNALKDLLKDM 3ivpA 4 :KEDKYDFRALGLAIKEARKKQ T0643 34 :NQSSLAKECPLSQSMISSIVNST 3ivpA 27 :TREQVGAMIEIDPRYLTNIENKG T0643 59 :ANVSAAKCQEFGRWY 3ivpA 50 :QHPSLQVLYDLVSLL Number of specific fragments extracted= 3 number of extra gaps= 0 total=45 Will force an alignment to be made, even if fragment is small Number of alignments=16 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3ivpA/T0643-3ivpA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0643 read from 3ivpA/T0643-3ivpA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3ivpA read from 3ivpA/T0643-3ivpA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3ivpA in template set T0643 13 :PPEQWSHTTVRNALKDLLKDM 3ivpA 4 :KEDKYDFRALGLAIKEARKKQ T0643 34 :NQSSLAKECPLSQSMISSIVNST 3ivpA 27 :TREQVGAMIEIDPRYLTNIENKG T0643 59 :ANVSAAKCQEFGRWY 3ivpA 50 :QHPSLQVLYDLVSLL Number of specific fragments extracted= 3 number of extra gaps= 0 total=48 Will force an alignment to be made, even if fragment is small Number of alignments=17 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3ivpA/T0643-3ivpA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0643 read from 3ivpA/T0643-3ivpA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3ivpA read from 3ivpA/T0643-3ivpA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3ivpA in template set Warning: unaligning (T0643)L12 because first residue in template chain is (3ivpA)K3 T0643 13 :PPEQWSHTTVRNALKDLLKDM 3ivpA 4 :KEDKYDFRALGLAIKEARKKQ T0643 34 :NQSSLAKECPLSQSMISSIVNST 3ivpA 27 :TREQVGAMIEIDPRYLTNIENKG T0643 59 :ANVSAAKCQEFGRWY 3ivpA 50 :QHPSLQVLYDLVSLL Number of specific fragments extracted= 3 number of extra gaps= 0 total=51 Will force an alignment to be made, even if fragment is small Number of alignments=18 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1lliA/T0643-1lliA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1lliA expands to /projects/compbio/data/pdb/1lli.pdb.gz 1lliA:# T0643 read from 1lliA/T0643-1lliA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1lliA read from 1lliA/T0643-1lliA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1lliA to template set # found chain 1lliA in template set Warning: unaligning (T0643)S9 because first residue in template chain is (1lliA)K4 T0643 10 :HMLPPEQWS 1lliA 5 :KPLTQEQLE T0643 19 :HTTVRNALKDLLKDM 1lliA 15 :ARRLKAIYEKKKNEL T0643 34 :NQSSLAKECPLSQSMISSIVNSTY 1lliA 32 :SQESLADKLGMGQSGIGALFNGIN T0643 60 :NVSAAKCQEFGRWY 1lliA 56 :ALNAYNAALLAKIL Number of specific fragments extracted= 4 number of extra gaps= 0 total=55 Will force an alignment to be made, even if fragment is small Number of alignments=19 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1lliA/T0643-1lliA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0643 read from 1lliA/T0643-1lliA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1lliA read from 1lliA/T0643-1lliA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1lliA in template set Warning: unaligning (T0643)S9 because first residue in template chain is (1lliA)K4 T0643 10 :HMLPPEQWS 1lliA 5 :KPLTQEQLE T0643 19 :HTTVRNALKDLLKDM 1lliA 15 :ARRLKAIYEKKKNEL T0643 34 :NQSSLAKECPLSQSMISSIVNSTY 1lliA 32 :SQESLADKLGMGQSGIGALFNGIN T0643 60 :NVSAAKCQEFGRWY 1lliA 56 :ALNAYNAALLAKIL Number of specific fragments extracted= 4 number of extra gaps= 0 total=59 Will force an alignment to be made, even if fragment is small Number of alignments=20 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1lliA/T0643-1lliA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0643 read from 1lliA/T0643-1lliA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1lliA read from 1lliA/T0643-1lliA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1lliA in template set T0643 10 :HMLPPEQWSH 1lliA 5 :KPLTQEQLED T0643 20 :TTVRNALKDLLKDM 1lliA 16 :RRLKAIYEKKKNEL T0643 34 :NQSSLAKECPLSQSMISSIVNSTY 1lliA 32 :SQESLADKLGMGQSGIGALFNGIN T0643 60 :NVSAAKCQEFGRWY 1lliA 56 :ALNAYNAALLAKIL Number of specific fragments extracted= 4 number of extra gaps= 0 total=63 Will force an alignment to be made, even if fragment is small Number of alignments=21 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2bnmA/T0643-2bnmA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2bnmA expands to /projects/compbio/data/pdb/2bnm.pdb.gz 2bnmA:Skipped atom 64, because occupancy 0.500 <= existing 0.500 in 2bnmA Skipped atom 65, because occupancy 0.500 <= existing 0.500 in 2bnmA Skipped atom 66, because occupancy 0.500 <= existing 0.500 in 2bnmA Skipped atom 67, because occupancy 0.500 <= existing 0.500 in 2bnmA Skipped atom 68, because occupancy 0.500 <= existing 0.500 in 2bnmA Skipped atom 142, because occupancy 0.250 <= existing 0.750 in 2bnmA Skipped atom 143, because occupancy 0.250 <= existing 0.750 in 2bnmA Skipped atom 144, because occupancy 0.250 <= existing 0.750 in 2bnmA Skipped atom 145, because occupancy 0.250 <= existing 0.750 in 2bnmA Skipped atom 146, because occupancy 0.250 <= existing 0.750 in 2bnmA Skipped atom 218, because occupancy 0.500 <= existing 0.500 in 2bnmA Skipped atom 219, because occupancy 0.500 <= existing 0.500 in 2bnmA Skipped atom 272, because occupancy 0.250 <= existing 0.750 in 2bnmA Skipped atom 273, because occupancy 0.250 <= existing 0.750 in 2bnmA Skipped atom 274, because occupancy 0.250 <= existing 0.750 in 2bnmA Skipped atom 275, because occupancy 0.250 <= existing 0.750 in 2bnmA Skipped atom 276, because occupancy 0.250 <= existing 0.750 in 2bnmA Skipped atom 332, because occupancy 0.250 <= existing 0.750 in 2bnmA Skipped atom 333, because occupancy 0.250 <= existing 0.750 in 2bnmA Skipped atom 334, because occupancy 0.250 <= existing 0.750 in 2bnmA Skipped atom 335, because occupancy 0.250 <= existing 0.750 in 2bnmA Skipped atom 428, because occupancy 0.250 <= existing 0.250 in 2bnmA Skipped atom 429, because occupancy 0.250 <= existing 0.250 in 2bnmA Skipped atom 430, because occupancy 0.250 <= existing 0.250 in 2bnmA Skipped atom 431, because occupancy 0.250 <= existing 0.250 in 2bnmA Skipped atom 432, because occupancy 0.250 <= existing 0.250 in 2bnmA Skipped atom 433, because occupancy 0.250 <= existing 0.250 in 2bnmA Skipped atom 434, because occupancy 0.250 <= existing 0.250 in 2bnmA Skipped atom 472, because occupancy 0.500 <= existing 0.500 in 2bnmA Skipped atom 473, because occupancy 0.500 <= existing 0.500 in 2bnmA Skipped atom 474, because occupancy 0.500 <= existing 0.500 in 2bnmA Skipped atom 622, because occupancy 0.250 <= existing 0.750 in 2bnmA Skipped atom 623, because occupancy 0.250 <= existing 0.750 in 2bnmA Skipped atom 624, because occupancy 0.250 <= existing 0.750 in 2bnmA Skipped atom 625, because occupancy 0.250 <= existing 0.750 in 2bnmA Skipped atom 658, because occupancy 0.500 <= existing 0.500 in 2bnmA Skipped atom 659, because occupancy 0.500 <= existing 0.500 in 2bnmA Skipped atom 660, because occupancy 0.500 <= existing 0.500 in 2bnmA Skipped atom 661, because occupancy 0.500 <= existing 0.500 in 2bnmA Skipped atom 671, because occupancy 0.500 <= existing 0.500 in 2bnmA Skipped atom 672, because occupancy 0.500 <= existing 0.500 in 2bnmA Skipped atom 673, because occupancy 0.500 <= existing 0.500 in 2bnmA Skipped atom 674, because occupancy 0.500 <= existing 0.500 in 2bnmA Skipped atom 675, because occupancy 0.500 <= existing 0.500 in 2bnmA Skipped atom 772, because occupancy 0.250 <= existing 0.500 in 2bnmA Skipped atom 773, because occupancy 0.250 <= existing 0.500 in 2bnmA Skipped atom 774, because occupancy 0.250 <= existing 0.500 in 2bnmA Skipped atom 775, because occupancy 0.250 <= existing 0.500 in 2bnmA Skipped atom 776, because occupancy 0.250 <= existing 0.500 in 2bnmA Skipped atom 777, because occupancy 0.250 <= existing 0.500 in 2bnmA Skipped atom 778, because occupancy 0.250 <= existing 0.500 in 2bnmA Skipped atom 779, because occupancy 0.250 <= existing 0.500 in 2bnmA Skipped atom 908, because occupancy 0.250 <= existing 0.750 in 2bnmA Skipped atom 909, because occupancy 0.250 <= existing 0.750 in 2bnmA Skipped atom 1062, because occupancy 0.250 <= existing 0.750 in 2bnmA Skipped atom 1063, because occupancy 0.250 <= existing 0.750 in 2bnmA Skipped atom 1149, because occupancy 0.250 <= existing 0.750 in 2bnmA Skipped atom 1150, because occupancy 0.250 <= existing 0.750 in 2bnmA Skipped atom 1151, because occupancy 0.250 <= existing 0.750 in 2bnmA Skipped atom 1152, because occupancy 0.250 <= existing 0.750 in 2bnmA Skipped atom 1162, because occupancy 0.250 <= existing 0.750 in 2bnmA Skipped atom 1163, because occupancy 0.250 <= existing 0.750 in 2bnmA Skipped atom 1164, because occupancy 0.250 <= existing 0.750 in 2bnmA Skipped atom 1165, because occupancy 0.250 <= existing 0.750 in 2bnmA Skipped atom 1166, because occupancy 0.250 <= existing 0.750 in 2bnmA Skipped atom 1206, because occupancy 0.500 <= existing 0.500 in 2bnmA Skipped atom 1207, because occupancy 0.500 <= existing 0.500 in 2bnmA Skipped atom 1208, because occupancy 0.500 <= existing 0.500 in 2bnmA Skipped atom 1209, because occupancy 0.500 <= existing 0.500 in 2bnmA Skipped atom 1309, because occupancy 0.250 <= existing 0.750 in 2bnmA Skipped atom 1310, because occupancy 0.250 <= existing 0.750 in 2bnmA Skipped atom 1311, because occupancy 0.250 <= existing 0.750 in 2bnmA Skipped atom 1312, because occupancy 0.250 <= existing 0.750 in 2bnmA Skipped atom 1358, because occupancy 0.500 <= existing 0.500 in 2bnmA Skipped atom 1359, because occupancy 0.500 <= existing 0.500 in 2bnmA Skipped atom 1360, because occupancy 0.500 <= existing 0.500 in 2bnmA Skipped atom 1361, because occupancy 0.500 <= existing 0.500 in 2bnmA Skipped atom 1448, because occupancy 0.500 <= existing 0.500 in 2bnmA Skipped atom 1449, because occupancy 0.500 <= existing 0.500 in 2bnmA Skipped atom 1450, because occupancy 0.500 <= existing 0.500 in 2bnmA Skipped atom 1451, because occupancy 0.500 <= existing 0.500 in 2bnmA Skipped atom 1452, because occupancy 0.500 <= existing 0.500 in 2bnmA Skipped atom 1453, because occupancy 0.500 <= existing 0.500 in 2bnmA Skipped atom 1454, because occupancy 0.500 <= existing 0.500 in 2bnmA Skipped atom 1462, because occupancy 0.500 <= existing 0.500 in 2bnmA Skipped atom 1463, because occupancy 0.500 <= existing 0.500 in 2bnmA Skipped atom 1464, because occupancy 0.500 <= existing 0.500 in 2bnmA Skipped atom 1527, because occupancy 0.250 <= existing 0.750 in 2bnmA Skipped atom 1528, because occupancy 0.250 <= existing 0.750 in 2bnmA Skipped atom 1529, because occupancy 0.250 <= existing 0.750 in 2bnmA Skipped atom 1530, because occupancy 0.250 <= existing 0.750 in 2bnmA Skipped atom 1539, because occupancy 0.500 <= existing 0.500 in 2bnmA Skipped atom 1540, because occupancy 0.500 <= existing 0.500 in 2bnmA Skipped atom 1541, because occupancy 0.500 <= existing 0.500 in 2bnmA Skipped atom 1542, because occupancy 0.500 <= existing 0.500 in 2bnmA # T0643 read from 2bnmA/T0643-2bnmA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2bnmA read from 2bnmA/T0643-2bnmA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2bnmA to template set # found chain 2bnmA in template set Warning: unaligning (T0643)Q16 because first residue in template chain is (2bnmA)K5 T0643 17 :WSHTTVRNALKDLLKDM 2bnmA 6 :TASTGFAELLKDRREQV T0643 34 :NQSSLAKECPLSQSMISSIVNSTYY 2bnmA 25 :DHAALASLLGETPETVAAWENGEGG T0643 60 :NVSAAKCQEFGR 2bnmA 50 :ELTLTQLGRIAH Number of specific fragments extracted= 3 number of extra gaps= 0 total=66 Will force an alignment to be made, even if fragment is small Number of alignments=22 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2bnmA/T0643-2bnmA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0643 read from 2bnmA/T0643-2bnmA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2bnmA read from 2bnmA/T0643-2bnmA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2bnmA in template set T0643 18 :SHTTVRNALKDLLKDM 2bnmA 7 :ASTGFAELLKDRREQV T0643 34 :NQSSLAKECPLSQSMISSIVNSTYY 2bnmA 25 :DHAALASLLGETPETVAAWENGEGG T0643 60 :NVSAAKCQEFGR 2bnmA 50 :ELTLTQLGRIAH Number of specific fragments extracted= 3 number of extra gaps= 0 total=69 Will force an alignment to be made, even if fragment is small Number of alignments=23 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2bnmA/T0643-2bnmA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0643 read from 2bnmA/T0643-2bnmA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2bnmA read from 2bnmA/T0643-2bnmA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2bnmA in template set T0643 17 :WSHTTVRNALKDLLKDM 2bnmA 6 :TASTGFAELLKDRREQV T0643 34 :NQSSLAKECPLSQSMISSIVNSTYY 2bnmA 25 :DHAALASLLGETPETVAAWENGEGG T0643 60 :NVSAAKCQEFGR 2bnmA 50 :ELTLTQLGRIAH Number of specific fragments extracted= 3 number of extra gaps= 0 total=72 Will force an alignment to be made, even if fragment is small Number of alignments=24 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2croA/T0643-2croA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2croA expands to /projects/compbio/data/pdb/2cro.pdb.gz 2croA:# T0643 read from 2croA/T0643-2croA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2croA read from 2croA/T0643-2croA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2croA to template set # found chain 2croA in template set T0643 21 :TVRNALKDLLKDM 2croA 1 :TLSERLKKRRIAL T0643 34 :NQSSLAKECPLSQSMISSIVNST 2croA 16 :TQTELATKAGVKQQSIQLIEAGV Number of specific fragments extracted= 2 number of extra gaps= 0 total=74 Will force an alignment to be made, even if fragment is small Number of alignments=25 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2croA/T0643-2croA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0643 read from 2croA/T0643-2croA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2croA read from 2croA/T0643-2croA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2croA in template set T0643 20 :TTVRNALKDLLKDM 2croA 0 :QTLSERLKKRRIAL T0643 34 :NQSSLAKECPLSQSMISSIVNST 2croA 16 :TQTELATKAGVKQQSIQLIEAGV Number of specific fragments extracted= 2 number of extra gaps= 0 total=76 Will force an alignment to be made, even if fragment is small Number of alignments=26 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2croA/T0643-2croA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0643 read from 2croA/T0643-2croA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2croA read from 2croA/T0643-2croA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2croA in template set T0643 20 :TTVRNALKDLLKDM 2croA 0 :QTLSERLKKRRIAL T0643 34 :NQSSLAKECPLSQSMISSIVNST 2croA 16 :TQTELATKAGVKQQSIQLIEAGV Number of specific fragments extracted= 2 number of extra gaps= 0 total=78 Will force an alignment to be made, even if fragment is small Number of alignments=27 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2cro/T0643-2cro-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2cro expands to /projects/compbio/data/pdb/2cro.pdb.gz 2cro:Warning: there is no chain 2cro will retry with 2croA # T0643 read from 2cro/T0643-2cro-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2cro read from 2cro/T0643-2cro-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2cro to template set # found chain 2cro in template set T0643 21 :TVRNALKDLLKDM 2cro 1 :TLSERLKKRRIAL T0643 34 :NQSSLAKECPLSQSMISSIVNST 2cro 16 :TQTELATKAGVKQQSIQLIEAGV Number of specific fragments extracted= 2 number of extra gaps= 0 total=80 Will force an alignment to be made, even if fragment is small Number of alignments=28 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2cro/T0643-2cro-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0643 read from 2cro/T0643-2cro-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2cro read from 2cro/T0643-2cro-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2cro in template set T0643 20 :TTVRNALKDLLKDM 2cro 0 :QTLSERLKKRRIAL T0643 34 :NQSSLAKECPLSQSMISSIVNSTYY 2cro 16 :TQTELATKAGVKQQSIQLIEAGVTK Number of specific fragments extracted= 2 number of extra gaps= 0 total=82 Will force an alignment to be made, even if fragment is small Number of alignments=29 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2cro/T0643-2cro-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0643 read from 2cro/T0643-2cro-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2cro read from 2cro/T0643-2cro-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2cro in template set T0643 21 :TVRNALKDLLKDM 2cro 1 :TLSERLKKRRIAL T0643 34 :NQSSLAKECPLSQSMISSIVNST 2cro 16 :TQTELATKAGVKQQSIQLIEAGV Number of specific fragments extracted= 2 number of extra gaps= 0 total=84 Will force an alignment to be made, even if fragment is small Number of alignments=30 # command:CPU_time= 9.299 sec, elapsed time= 20.970 sec. # command:DEBUG: alignment library has 30 conformations DEBUG: current conformations has 0 conformations # in ExtractAlignmentsContacts extracting from alignment library using radius 8.000 separation >= 9 style evalue NUMB_ALIGNS: 30 # Adding 125 constraints to all_contacts Done adding distance constraints # command:CPU_time= 9.309 sec, elapsed time= 20.980 sec. # command:Reading probabilities from T0643.t06.CB8-sep9.rdb Reading constraints from ConstraintSet all_contacts maxweight: 12.361 Optimizing... Probability sum: -152.175, CN propb: -152.175 weights: 0.372 constraints: 70 # command:CPU_time= 9.360 sec, elapsed time= 21.110 sec. # command:Found ConstraintSet # PrintContacts align.constraints Number of constraints in align 70 # command:Found ConstraintSet # PrintContacts align_bonus.constraints Number of constraints in align.bonus 70 # command:Found ConstraintSet # PrintContacts rejected.constraints Number of constraints in rejected 55 # command:Found ConstraintSet # PrintContacts rejected_bonus.constraints Number of constraints in rejected.bonus 55 # command:Found ConstraintSet # PrintContacts noncontact.constraints Number of constraints in noncontact 0 # command:Found ConstraintSet # PrintContacts noncontact_bonus.constraints Number of constraints in noncontact.bonus 0 # command:CPU_time= 9.363 sec, elapsed time= 22.416 sec. # command: