# 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: 408,82795,639989 # 81291 residues have no bad marker # 565 residues lack atoms needed to compute omega # 313 residues have cis peptide # number of each bad type: # NON_STANDARD_RESIDUE 1 # HAS_OXT 265 # TOO_MANY_ATOMS 0 # TOO_FEW_ATOMS 378 # HAS_UNKNOWN_ATOMS 0 # HAS_DUPLICATE_ATOMS 0 # CHAIN_BREAK_BEFORE 139 # NON_PLANAR_PEPTIDE 424 # BAD_PEPTIDE 803 # 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 T0383 numbered 1 through 127 Created new target T0383 from T0383.a2m # command:CPU_time= 6.399 sec, elapsed time= 6.683 sec. # command:# reading script from file all-templates.under # Reading fragments from alignment file # Attempting to read fragment alignments from file 1qynA/T0383-1qynA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1qynA expands to /projects/compbio/data/pdb/1qyn.pdb.gz 1qynA:# T0383 read from 1qynA/T0383-1qynA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1qynA read from 1qynA/T0383-1qynA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1qynA to template set # found chain 1qynA in template set Warning: unaligning (T0383)M4 because first residue in template chain is (1qynA)M9 T0383 5 :NLKREQEFVSQYHFDARNFEW 1qynA 10 :TFQIQRIYTKDISFEAPNAPH # choosing archetypes in rotamer library T0383 26 :ENENGAPETK 1qynA 33 :QKDWQPEVKL T0383 36 :VDVNFQLL 1qynA 44 :LDTASSQL T0383 48 :ENQVTSLIVILSFMIVFDK 1qynA 52 :ADDVYEVVLRVTVTASLGE T0383 67 :FVISGTISQVNHIDG 1qynA 74 :FLCEVQQGGIFSIAG T0383 90 :LNQEEVET 1qynA 89 :IEGTQMAH T0383 98 :LARPCLNMLNR 1qynA 102 :CPNILFPYARE T0383 109 :LTYEVTEIALDL 1qynA 114 :ITSMVSRGTFPQ T0383 123 :INLE 1qynA 126 :LNLA Number of specific fragments extracted= 9 number of extra gaps= 0 total=9 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 1qynA/T0383-1qynA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0383 read from 1qynA/T0383-1qynA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1qynA read from 1qynA/T0383-1qynA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1qynA in template set T0383 4 :MN 1qynA 21 :IS T0383 18 :FDARNFEWENENG 1qynA 23 :FEAPNAPHVFQKD T0383 32 :PETKVDVNFQLLQHDQENQVTSLIVILSFMIVFDK 1qynA 36 :WQPEVKLDLDTASSQLADDVYEVVLRVTVTASLGE T0383 67 :FVISGTISQVNHIDG 1qynA 74 :FLCEVQQGGIFSIAG T0383 90 :LNQEEVET 1qynA 89 :IEGTQMAH T0383 98 :LARPCLNMLNR 1qynA 102 :CPNILFPYARE T0383 109 :LTYEVTEIALDL 1qynA 114 :ITSMVSRGTFPQ T0383 123 :INLE 1qynA 126 :LNLA Number of specific fragments extracted= 8 number of extra gaps= 0 total=17 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 1qynA/T0383-1qynA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0383 read from 1qynA/T0383-1qynA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1qynA read from 1qynA/T0383-1qynA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1qynA in template set Warning: unaligning (T0383)M4 because first residue in template chain is (1qynA)M9 T0383 5 :NLKREQEFVSQYHFDARNFEWENENGAP 1qynA 10 :TFQIQRIYTKDISFEAPNAPHVFQKDWQ T0383 33 :ETKVDVNFQLLQ 1qynA 39 :EVKLDLDTASSQ T0383 47 :QENQVTSLIVILSFMIVFDK 1qynA 51 :LADDVYEVVLRVTVTASLGE T0383 67 :FVISGTISQVNHIDG 1qynA 74 :FLCEVQQGGIFSIAG T0383 90 :LNQEEVET 1qynA 89 :IEGTQMAH T0383 98 :LARPCLNMLNR 1qynA 102 :CPNILFPYARE T0383 109 :LTYEVTEIALDL 1qynA 114 :ITSMVSRGTFPQ T0383 123 :INLE 1qynA 126 :LNLA Number of specific fragments extracted= 8 number of extra gaps= 0 total=25 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 1mugA/T0383-1mugA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1mugA expands to /projects/compbio/data/pdb/1mug.pdb.gz 1mugA:# T0383 read from 1mugA/T0383-1mugA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1mugA read from 1mugA/T0383-1mugA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1mugA to template set # found chain 1mugA in template set T0383 79 :IDGRIVNEPSELNQEEVETLARPCLNMLNRLT 1mugA 69 :LVDRPTVQANEVSKQELHAGGRKLIEKIEDYQ T0383 111 :YEVTEIALDLPGIN 1mugA 109 :KQAYEQGFSQRGAQ Number of specific fragments extracted= 2 number of extra gaps= 0 total=27 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 1mugA/T0383-1mugA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0383 read from 1mugA/T0383-1mugA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1mugA read from 1mugA/T0383-1mugA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1mugA in template set T0383 76 :VNHIDGRIVNEPSELNQEEVETLARPCLNMLNRLT 1mugA 66 :VTKLVDRPTVQANEVSKQELHAGGRKLIEKIEDYQ T0383 111 :YEVTEIALDLPGIN 1mugA 109 :KQAYEQGFSQRGAQ Number of specific fragments extracted= 2 number of extra gaps= 0 total=29 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 1mugA/T0383-1mugA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0383 read from 1mugA/T0383-1mugA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1mugA read from 1mugA/T0383-1mugA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1mugA in template set T0383 81 :GRIVNEPSELNQEEVETLARPCLNMLNRL 1mugA 71 :DRPTVQANEVSKQELHAGGRKLIEKIEDY Number of specific fragments extracted= 1 number of extra gaps= 0 total=30 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 1u6zA/T0383-1u6zA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1u6zA expands to /projects/compbio/data/pdb/1u6z.pdb.gz 1u6zA:Skipped atom 15, because occupancy 0.5 <= existing 0.500 in 1u6zA Skipped atom 17, because occupancy 0.500 <= existing 0.500 in 1u6zA Skipped atom 19, because occupancy 0.500 <= existing 0.500 in 1u6zA Skipped atom 21, because occupancy 0.500 <= existing 0.500 in 1u6zA Skipped atom 23, because occupancy 0.500 <= existing 0.500 in 1u6zA Skipped atom 25, because occupancy 0.500 <= existing 0.500 in 1u6zA Skipped atom 27, because occupancy 0.500 <= existing 0.500 in 1u6zA Skipped atom 181, because occupancy 0.500 <= existing 0.500 in 1u6zA Skipped atom 183, because occupancy 0.500 <= existing 0.500 in 1u6zA Skipped atom 185, because occupancy 0.500 <= existing 0.500 in 1u6zA Skipped atom 187, because occupancy 0.500 <= existing 0.500 in 1u6zA Skipped atom 259, because occupancy 0.500 <= existing 0.500 in 1u6zA Skipped atom 261, because occupancy 0.500 <= existing 0.500 in 1u6zA Skipped atom 263, because occupancy 0.500 <= existing 0.500 in 1u6zA Skipped atom 265, because occupancy 0.500 <= existing 0.500 in 1u6zA Skipped atom 267, because occupancy 0.500 <= existing 0.500 in 1u6zA Skipped atom 269, because occupancy 0.500 <= existing 0.500 in 1u6zA Skipped atom 271, because occupancy 0.500 <= existing 0.500 in 1u6zA Skipped atom 459, because occupancy 0.500 <= existing 0.500 in 1u6zA Skipped atom 461, because occupancy 0.500 <= existing 0.500 in 1u6zA Skipped atom 561, because occupancy 0.500 <= existing 0.500 in 1u6zA Skipped atom 563, because occupancy 0.500 <= existing 0.500 in 1u6zA Skipped atom 814, because occupancy 0.500 <= existing 0.500 in 1u6zA Skipped atom 816, because occupancy 0.500 <= existing 0.500 in 1u6zA Skipped atom 818, because occupancy 0.500 <= existing 0.500 in 1u6zA Skipped atom 820, because occupancy 0.500 <= existing 0.500 in 1u6zA Skipped atom 844, because occupancy 0.500 <= existing 0.500 in 1u6zA Skipped atom 846, because occupancy 0.500 <= existing 0.500 in 1u6zA Skipped atom 848, because occupancy 0.500 <= existing 0.500 in 1u6zA Skipped atom 850, because occupancy 0.500 <= existing 0.500 in 1u6zA Skipped atom 1196, because occupancy 0.500 <= existing 0.500 in 1u6zA Skipped atom 1198, because occupancy 0.500 <= existing 0.500 in 1u6zA Skipped atom 1238, because occupancy 0.500 <= existing 0.500 in 1u6zA Skipped atom 1240, because occupancy 0.500 <= existing 0.500 in 1u6zA Skipped atom 1353, because occupancy 0.500 <= existing 0.500 in 1u6zA Skipped atom 1355, because occupancy 0.500 <= existing 0.500 in 1u6zA Skipped atom 1357, because occupancy 0.500 <= existing 0.500 in 1u6zA Skipped atom 1359, because occupancy 0.500 <= existing 0.500 in 1u6zA Skipped atom 1361, because occupancy 0.500 <= existing 0.500 in 1u6zA Skipped atom 1395, because occupancy 0.500 <= existing 0.500 in 1u6zA Skipped atom 1397, because occupancy 0.500 <= existing 0.500 in 1u6zA Skipped atom 1399, because occupancy 0.500 <= existing 0.500 in 1u6zA Skipped atom 1401, because occupancy 0.500 <= existing 0.500 in 1u6zA Skipped atom 1403, because occupancy 0.500 <= existing 0.500 in 1u6zA Skipped atom 1485, because occupancy 0.500 <= existing 0.500 in 1u6zA Skipped atom 1487, because occupancy 0.500 <= existing 0.500 in 1u6zA Skipped atom 1489, because occupancy 0.500 <= existing 0.500 in 1u6zA Skipped atom 1491, because occupancy 0.500 <= existing 0.500 in 1u6zA Skipped atom 1493, because occupancy 0.500 <= existing 0.500 in 1u6zA Skipped atom 1521, because occupancy 0.500 <= existing 0.500 in 1u6zA Skipped atom 1523, because occupancy 0.500 <= existing 0.500 in 1u6zA Skipped atom 1525, because occupancy 0.500 <= existing 0.500 in 1u6zA Skipped atom 1527, because occupancy 0.500 <= existing 0.500 in 1u6zA Skipped atom 1529, because occupancy 0.500 <= existing 0.500 in 1u6zA Skipped atom 1531, because occupancy 0.500 <= existing 0.500 in 1u6zA Skipped atom 1533, because occupancy 0.500 <= existing 0.500 in 1u6zA Skipped atom 1535, because occupancy 0.500 <= existing 0.500 in 1u6zA Skipped atom 1537, because occupancy 0.500 <= existing 0.500 in 1u6zA Skipped atom 1539, because occupancy 0.500 <= existing 0.500 in 1u6zA Skipped atom 1665, because occupancy 0.500 <= existing 0.500 in 1u6zA Skipped atom 1667, because occupancy 0.500 <= existing 0.500 in 1u6zA Skipped atom 1669, because occupancy 0.500 <= existing 0.500 in 1u6zA Skipped atom 1671, because occupancy 0.500 <= existing 0.500 in 1u6zA Skipped atom 1819, because occupancy 0.500 <= existing 0.500 in 1u6zA Skipped atom 1821, because occupancy 0.500 <= existing 0.500 in 1u6zA Skipped atom 1823, because occupancy 0.500 <= existing 0.500 in 1u6zA Skipped atom 1825, because occupancy 0.500 <= existing 0.500 in 1u6zA Skipped atom 1827, because occupancy 0.500 <= existing 0.500 in 1u6zA Skipped atom 1939, because occupancy 0.500 <= existing 0.500 in 1u6zA Skipped atom 1941, because occupancy 0.500 <= existing 0.500 in 1u6zA Skipped atom 1943, because occupancy 0.500 <= existing 0.500 in 1u6zA Skipped atom 1945, because occupancy 0.500 <= existing 0.500 in 1u6zA Skipped atom 1947, because occupancy 0.500 <= existing 0.500 in 1u6zA Skipped atom 1949, because occupancy 0.500 <= existing 0.500 in 1u6zA Skipped atom 1951, because occupancy 0.500 <= existing 0.500 in 1u6zA Skipped atom 2001, because occupancy 0.500 <= existing 0.500 in 1u6zA Skipped atom 2003, because occupancy 0.500 <= existing 0.500 in 1u6zA Skipped atom 2005, because occupancy 0.500 <= existing 0.500 in 1u6zA Skipped atom 2007, because occupancy 0.500 <= existing 0.500 in 1u6zA Skipped atom 2024, because occupancy 0.500 <= existing 0.500 in 1u6zA Skipped atom 2026, because occupancy 0.500 <= existing 0.500 in 1u6zA Skipped atom 2028, because occupancy 0.500 <= existing 0.500 in 1u6zA Skipped atom 2030, because occupancy 0.500 <= existing 0.500 in 1u6zA Skipped atom 2206, because occupancy 0.500 <= existing 0.500 in 1u6zA Skipped atom 2208, because occupancy 0.500 <= existing 0.500 in 1u6zA Skipped atom 2210, because occupancy 0.500 <= existing 0.500 in 1u6zA Skipped atom 2212, because occupancy 0.500 <= existing 0.500 in 1u6zA Skipped atom 2246, because occupancy 0.500 <= existing 0.500 in 1u6zA Skipped atom 2248, because occupancy 0.500 <= existing 0.500 in 1u6zA Skipped atom 2250, because occupancy 0.500 <= existing 0.500 in 1u6zA Skipped atom 2252, because occupancy 0.500 <= existing 0.500 in 1u6zA Skipped atom 2254, because occupancy 0.500 <= existing 0.500 in 1u6zA Skipped atom 2256, because occupancy 0.500 <= existing 0.500 in 1u6zA Skipped atom 2258, because occupancy 0.500 <= existing 0.500 in 1u6zA Skipped atom 2278, because occupancy 0.500 <= existing 0.500 in 1u6zA Skipped atom 2280, because occupancy 0.500 <= existing 0.500 in 1u6zA Skipped atom 2282, because occupancy 0.500 <= existing 0.500 in 1u6zA Skipped atom 2284, because occupancy 0.500 <= existing 0.500 in 1u6zA Skipped atom 2358, because occupancy 0.500 <= existing 0.500 in 1u6zA Skipped atom 2360, because occupancy 0.500 <= existing 0.500 in 1u6zA Skipped atom 2362, because occupancy 0.500 <= existing 0.500 in 1u6zA Skipped atom 2364, because occupancy 0.500 <= existing 0.500 in 1u6zA Skipped atom 2366, because occupancy 0.500 <= existing 0.500 in 1u6zA Skipped atom 2380, because occupancy 0.500 <= existing 0.500 in 1u6zA Skipped atom 2382, because occupancy 0.500 <= existing 0.500 in 1u6zA Skipped atom 2384, because occupancy 0.500 <= existing 0.500 in 1u6zA Skipped atom 2386, because occupancy 0.500 <= existing 0.500 in 1u6zA Skipped atom 2388, because occupancy 0.500 <= existing 0.500 in 1u6zA Skipped atom 2499, because occupancy 0.500 <= existing 0.500 in 1u6zA Skipped atom 2501, because occupancy 0.500 <= existing 0.500 in 1u6zA Skipped atom 2507, because occupancy 0.330 <= existing 0.330 in 1u6zA Skipped atom 2508, because occupancy 0.330 <= existing 0.330 in 1u6zA Skipped atom 2510, because occupancy 0.330 <= existing 0.330 in 1u6zA Skipped atom 2511, because occupancy 0.330 <= existing 0.330 in 1u6zA Skipped atom 2530, because occupancy 0.500 <= existing 0.500 in 1u6zA Skipped atom 2532, because occupancy 0.500 <= existing 0.500 in 1u6zA Skipped atom 2534, because occupancy 0.500 <= existing 0.500 in 1u6zA Skipped atom 2536, because occupancy 0.500 <= existing 0.500 in 1u6zA Skipped atom 2757, because occupancy 0.500 <= existing 0.500 in 1u6zA Skipped atom 2759, because occupancy 0.500 <= existing 0.500 in 1u6zA Skipped atom 2761, because occupancy 0.500 <= existing 0.500 in 1u6zA Skipped atom 2763, because occupancy 0.500 <= existing 0.500 in 1u6zA Skipped atom 2765, because occupancy 0.500 <= existing 0.500 in 1u6zA Skipped atom 2780, because occupancy 0.500 <= existing 0.500 in 1u6zA Skipped atom 2782, because occupancy 0.500 <= existing 0.500 in 1u6zA Skipped atom 2784, because occupancy 0.500 <= existing 0.500 in 1u6zA Skipped atom 2786, because occupancy 0.500 <= existing 0.500 in 1u6zA Skipped atom 2788, because occupancy 0.500 <= existing 0.500 in 1u6zA Skipped atom 2887, because occupancy 0.500 <= existing 0.500 in 1u6zA Skipped atom 2889, because occupancy 0.500 <= existing 0.500 in 1u6zA Skipped atom 2891, because occupancy 0.500 <= existing 0.500 in 1u6zA Skipped atom 2893, because occupancy 0.500 <= existing 0.500 in 1u6zA Skipped atom 2895, because occupancy 0.500 <= existing 0.500 in 1u6zA Skipped atom 2897, because occupancy 0.500 <= existing 0.500 in 1u6zA Skipped atom 2899, because occupancy 0.500 <= existing 0.500 in 1u6zA Skipped atom 2929, because occupancy 0.500 <= existing 0.500 in 1u6zA Skipped atom 2931, because occupancy 0.500 <= existing 0.500 in 1u6zA Skipped atom 2933, because occupancy 0.500 <= existing 0.500 in 1u6zA Skipped atom 2935, because occupancy 0.500 <= existing 0.500 in 1u6zA Skipped atom 3021, because occupancy 0.500 <= existing 0.500 in 1u6zA Skipped atom 3023, because occupancy 0.500 <= existing 0.500 in 1u6zA Skipped atom 3095, because occupancy 0.500 <= existing 0.500 in 1u6zA Skipped atom 3097, because occupancy 0.500 <= existing 0.500 in 1u6zA Skipped atom 3099, because occupancy 0.500 <= existing 0.500 in 1u6zA Skipped atom 3101, because occupancy 0.500 <= existing 0.500 in 1u6zA Skipped atom 3236, because occupancy 0.500 <= existing 0.500 in 1u6zA Skipped atom 3238, because occupancy 0.500 <= existing 0.500 in 1u6zA Skipped atom 3240, because occupancy 0.500 <= existing 0.500 in 1u6zA Skipped atom 3242, because occupancy 0.500 <= existing 0.500 in 1u6zA Skipped atom 3275, because occupancy 0.500 <= existing 0.500 in 1u6zA Skipped atom 3277, because occupancy 0.500 <= existing 0.500 in 1u6zA Skipped atom 3279, because occupancy 0.500 <= existing 0.500 in 1u6zA Skipped atom 3281, because occupancy 0.500 <= existing 0.500 in 1u6zA Skipped atom 3283, because occupancy 0.500 <= existing 0.500 in 1u6zA Skipped atom 3285, because occupancy 0.500 <= existing 0.500 in 1u6zA Skipped atom 3287, because occupancy 0.500 <= existing 0.500 in 1u6zA Skipped atom 3456, because occupancy 0.500 <= existing 0.500 in 1u6zA Skipped atom 3458, because occupancy 0.500 <= existing 0.500 in 1u6zA Skipped atom 3460, because occupancy 0.500 <= existing 0.500 in 1u6zA Skipped atom 3462, because occupancy 0.500 <= existing 0.500 in 1u6zA Skipped atom 3464, because occupancy 0.500 <= existing 0.500 in 1u6zA Skipped atom 3513, because occupancy 0.500 <= existing 0.500 in 1u6zA Skipped atom 3515, because occupancy 0.500 <= existing 0.500 in 1u6zA Skipped atom 3517, because occupancy 0.500 <= existing 0.500 in 1u6zA Skipped atom 3519, because occupancy 0.500 <= existing 0.500 in 1u6zA Skipped atom 3675, because occupancy 0.500 <= existing 0.500 in 1u6zA Skipped atom 3677, because occupancy 0.500 <= existing 0.500 in 1u6zA # T0383 read from 1u6zA/T0383-1u6zA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1u6zA read from 1u6zA/T0383-1u6zA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1u6zA to template set # found chain 1u6zA in template set T0383 55 :IVILSFMIVFDKFVISGTISQVNHIDG 1u6zA 23 :FHMVIARVVDGAMQIIGRLKQRVHLAD T0383 83 :IVNEPSELNQEEVETLARPCLNMLNRL 1u6zA 50 :GLGPDNMLSEEAMTRGLNCLSLFAERL Number of specific fragments extracted= 2 number of extra gaps= 0 total=32 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 1u6zA/T0383-1u6zA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0383 read from 1u6zA/T0383-1u6zA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1u6zA read from 1u6zA/T0383-1u6zA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1u6zA in template set T0383 55 :IVILSFMIVFDKFVISGTISQVNHIDG 1u6zA 23 :FHMVIARVVDGAMQIIGRLKQRVHLAD T0383 83 :IVNEPSELNQEEVETLARPCLNMLNRL 1u6zA 50 :GLGPDNMLSEEAMTRGLNCLSLFAERL Number of specific fragments extracted= 2 number of extra gaps= 0 total=34 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 1u6zA/T0383-1u6zA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0383 read from 1u6zA/T0383-1u6zA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1u6zA read from 1u6zA/T0383-1u6zA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1u6zA in template set T0383 55 :IVILSFMIVFDKFVISGTISQVNHIDG 1u6zA 23 :FHMVIARVVDGAMQIIGRLKQRVHLAD T0383 83 :IVNEPSELNQEEVETLARPCLNMLNRL 1u6zA 50 :GLGPDNMLSEEAMTRGLNCLSLFAERL Number of specific fragments extracted= 2 number of extra gaps= 0 total=36 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 1xx7A/T0383-1xx7A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # Reading fragments from alignment file # Attempting to read fragment alignments from file 1xx7A/T0383-1xx7A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # Reading fragments from alignment file # Attempting to read fragment alignments from file 1xx7A/T0383-1xx7A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # Reading fragments from alignment file # Attempting to read fragment alignments from file 1x5kA/T0383-1x5kA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # Reading fragments from alignment file # Attempting to read fragment alignments from file 1x5kA/T0383-1x5kA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # Reading fragments from alignment file # Attempting to read fragment alignments from file 1x5kA/T0383-1x5kA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # Reading fragments from alignment file # Attempting to read fragment alignments from file 1fx3B/T0383-1fx3B-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1fx3B expands to /projects/compbio/data/pdb/1fx3.pdb.gz 1fx3B:# T0383 read from 1fx3B/T0383-1fx3B-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1fx3B read from 1fx3B/T0383-1fx3B-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1fx3B to template set # found chain 1fx3B in template set T0383 5 :NLKREQEFVSQYHFDARNFEWENENGAPETK 1fx3B 17 :VLQIQRIYVKDVSFEAPNLPHIFQQEWKPKL T0383 36 :VDVNFQLLQHD 1fx3B 49 :FDLSTETTQVG T0383 49 :NQVTSLIVILSFMIVFDK 1fx3B 60 :DDLYEVVLNISVETTLED T0383 67 :FVISGTISQVNHIDG 1fx3B 83 :FICEVKQAGVFTISG T0383 90 :LNQEEVET 1fx3B 98 :LEDVQMAH T0383 98 :LARPCLNMLNRLTYEVTEIA 1fx3B 111 :CPNMLFPYARELVSNLVNRG T0383 119 :DLPGINLEF 1fx3B 131 :TFPALNLSP Number of specific fragments extracted= 7 number of extra gaps= 0 total=43 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 1fx3B/T0383-1fx3B-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0383 read from 1fx3B/T0383-1fx3B-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1fx3B read from 1fx3B/T0383-1fx3B-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1fx3B in template set T0383 3 :AMN 1fx3B 27 :DVS T0383 18 :FDARNFEWENENGAPETK 1fx3B 30 :FEAPNLPHIFQQEWKPKL T0383 36 :VDVNFQLLQHD 1fx3B 49 :FDLSTETTQVG T0383 49 :NQVTSLIVILSFMIVFDK 1fx3B 60 :DDLYEVVLNISVETTLED T0383 67 :FVISGTISQVNHIDG 1fx3B 83 :FICEVKQAGVFTISG T0383 90 :LNQEEVET 1fx3B 98 :LEDVQMAH T0383 98 :LARPCLNMLNRLTYEVTEIAL 1fx3B 111 :CPNMLFPYARELVSNLVNRGT T0383 120 :LPGINLE 1fx3B 132 :FPALNLS Number of specific fragments extracted= 8 number of extra gaps= 0 total=51 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 1fx3B/T0383-1fx3B-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0383 read from 1fx3B/T0383-1fx3B-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1fx3B read from 1fx3B/T0383-1fx3B-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1fx3B in template set Warning: unaligning (T0383)A3 because first residue in template chain is (1fx3B)Q15 T0383 4 :MNLKREQEFVSQYHFDARNFEWENENGAPETK 1fx3B 16 :PVLQIQRIYVKDVSFEAPNLPHIFQQEWKPKL T0383 36 :VDVNFQLLQHD 1fx3B 49 :FDLSTETTQVG T0383 49 :NQVTSLIVILSFMIVFDK 1fx3B 60 :DDLYEVVLNISVETTLED T0383 67 :FVISGTISQVNHIDG 1fx3B 83 :FICEVKQAGVFTISG T0383 90 :LNQEEVET 1fx3B 98 :LEDVQMAH T0383 98 :LARPCLNMLNRLTYEVTEIA 1fx3B 111 :CPNMLFPYARELVSNLVNRG T0383 119 :DLPGINLEF 1fx3B 131 :TFPALNLSP Number of specific fragments extracted= 7 number of extra gaps= 0 total=58 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 1r8jA/T0383-1r8jA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # Reading fragments from alignment file # Attempting to read fragment alignments from file 1r8jA/T0383-1r8jA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # Reading fragments from alignment file # Attempting to read fragment alignments from file 1r8jA/T0383-1r8jA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # Reading fragments from alignment file # Attempting to read fragment alignments from file 1e6zA/T0383-1e6zA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1e6zA expands to /projects/compbio/data/pdb/1e6z.pdb.gz 1e6zA:Skipped atom 615, because occupancy 0.500 <= existing 0.500 in 1e6zA Skipped atom 617, because occupancy 0.500 <= existing 0.500 in 1e6zA Skipped atom 619, because occupancy 0.500 <= existing 0.500 in 1e6zA Skipped atom 1003, because occupancy 0.500 <= existing 0.500 in 1e6zA Skipped atom 1005, because occupancy 0.500 <= existing 0.500 in 1e6zA Skipped atom 1007, because occupancy 0.500 <= existing 0.500 in 1e6zA Skipped atom 1009, because occupancy 0.500 <= existing 0.500 in 1e6zA Skipped atom 1011, because occupancy 0.500 <= existing 0.500 in 1e6zA Skipped atom 1112, because occupancy 0.500 <= existing 0.500 in 1e6zA Skipped atom 1114, because occupancy 0.500 <= existing 0.500 in 1e6zA Skipped atom 1116, because occupancy 0.500 <= existing 0.500 in 1e6zA Skipped atom 1118, because occupancy 0.500 <= existing 0.500 in 1e6zA Skipped atom 2343, because occupancy 0.500 <= existing 0.500 in 1e6zA Skipped atom 2345, because occupancy 0.500 <= existing 0.500 in 1e6zA Skipped atom 2347, because occupancy 0.500 <= existing 0.500 in 1e6zA # T0383 read from 1e6zA/T0383-1e6zA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1e6zA read from 1e6zA/T0383-1e6zA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1e6zA to template set # found chain 1e6zA in template set T0383 91 :NQEEVETLARPCLNMLNRLT 1e6zA 116 :TPASRAKFAQSCVRIMKDYG Number of specific fragments extracted= 1 number of extra gaps= 0 total=59 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 1e6zA/T0383-1e6zA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0383 read from 1e6zA/T0383-1e6zA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1e6zA read from 1e6zA/T0383-1e6zA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1e6zA in template set T0383 91 :NQEEVETLARPCLNMLNRL 1e6zA 116 :TPASRAKFAQSCVRIMKDY Number of specific fragments extracted= 1 number of extra gaps= 0 total=60 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 1e6zA/T0383-1e6zA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0383 read from 1e6zA/T0383-1e6zA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1e6zA read from 1e6zA/T0383-1e6zA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1e6zA in template set T0383 91 :NQEEVETLARPCLNMLNRLT 1e6zA 116 :TPASRAKFAQSCVRIMKDYG Number of specific fragments extracted= 1 number of extra gaps= 0 total=61 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 1oshA/T0383-1oshA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1oshA expands to /projects/compbio/data/pdb/1osh.pdb.gz 1oshA:# T0383 read from 1oshA/T0383-1oshA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1oshA read from 1oshA/T0383-1oshA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1oshA to template set # found chain 1oshA in template set T0383 88 :SEL 1oshA 400 :QYI T0383 91 :NQEEVETLARPCLNMLNRLT 1oshA 404 :DREAVEKLQEPLLDVLQKLC Number of specific fragments extracted= 2 number of extra gaps= 0 total=63 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 1oshA/T0383-1oshA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0383 read from 1oshA/T0383-1oshA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1oshA read from 1oshA/T0383-1oshA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1oshA in template set T0383 91 :NQEEVETLARPCLNMLNRLT 1oshA 404 :DREAVEKLQEPLLDVLQKLC Number of specific fragments extracted= 1 number of extra gaps= 0 total=64 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 1oshA/T0383-1oshA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0383 read from 1oshA/T0383-1oshA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1oshA read from 1oshA/T0383-1oshA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1oshA in template set T0383 81 :G 1oshA 398 :D T0383 87 :PSEL 1oshA 399 :RQYI T0383 91 :NQEEVETLARPCLNMLNRLT 1oshA 404 :DREAVEKLQEPLLDVLQKLC Number of specific fragments extracted= 3 number of extra gaps= 0 total=67 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 1o6iA/T0383-1o6iA-t06-local-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1o6iA expands to /projects/compbio/data/pdb/1o6i.pdb.gz 1o6iA:Skipped atom 198, because occupancy 0.500 <= existing 0.500 in 1o6iA Skipped atom 200, because occupancy 0.500 <= existing 0.500 in 1o6iA Skipped atom 202, because occupancy 0.500 <= existing 0.500 in 1o6iA Skipped atom 1653, because occupancy 0.500 <= existing 0.500 in 1o6iA Skipped atom 1655, because occupancy 0.500 <= existing 0.500 in 1o6iA Skipped atom 1657, because occupancy 0.500 <= existing 0.500 in 1o6iA Skipped atom 1659, because occupancy 0.500 <= existing 0.500 in 1o6iA Skipped atom 2173, because occupancy 0.500 <= existing 0.500 in 1o6iA Skipped atom 2175, because occupancy 0.500 <= existing 0.500 in 1o6iA Skipped atom 2177, because occupancy 0.500 <= existing 0.500 in 1o6iA Skipped atom 2179, because occupancy 0.500 <= existing 0.500 in 1o6iA Skipped atom 2181, because occupancy 0.500 <= existing 0.500 in 1o6iA Skipped atom 3010, because occupancy 0.500 <= existing 0.500 in 1o6iA Skipped atom 3012, because occupancy 0.500 <= existing 0.500 in 1o6iA Skipped atom 3014, because occupancy 0.500 <= existing 0.500 in 1o6iA Skipped atom 3016, because occupancy 0.500 <= existing 0.500 in 1o6iA Skipped atom 3018, because occupancy 0.500 <= existing 0.500 in 1o6iA Skipped atom 3062, because occupancy 0.500 <= existing 0.500 in 1o6iA Skipped atom 3064, because occupancy 0.500 <= existing 0.500 in 1o6iA Skipped atom 3066, because occupancy 0.500 <= existing 0.500 in 1o6iA Skipped atom 3068, because occupancy 0.500 <= existing 0.500 in 1o6iA Skipped atom 3070, because occupancy 0.500 <= existing 0.500 in 1o6iA # T0383 read from 1o6iA/T0383-1o6iA-t06-local-adpstyle5.a2m # 1o6iA read from 1o6iA/T0383-1o6iA-t06-local-adpstyle5.a2m # adding 1o6iA to template set # found chain 1o6iA in template set Warning: unaligning (T0383)E26 because of BadResidue code BAD_PEPTIDE in next template residue (1o6iA)Y145 Warning: unaligning (T0383)N27 because of BadResidue code BAD_PEPTIDE at template residue (1o6iA)Y145 T0383 12 :FVSQYHFDARNFEW 1o6iA 130 :IMKDYGFDGVDIDW T0383 28 :ENGAPETKVDVNFQ 1o6iA 146 :PQAAEVDGFIAALQ T0383 42 :LLQHDQENQVTSLIVILSFMIVFDKFVISGTISQVNHIDG 1o6iA 165 :LNQQTITDGRQALPYQLTIAGAGGAFFLSRYYSKLAQIVA T0383 102 :CLNMLNRLTYEV 1o6iA 205 :PLDYINLMTYDL Number of specific fragments extracted= 4 number of extra gaps= 1 total=71 Will force an alignment to be made, even if fragment is small Number of alignments=19 # command:CPU_time= 10.685 sec, elapsed time= 11.567 sec. # command:Using radius: 8.000 NUMB_ALIGNS: 19 Adding 8001 constraints to all_contacts Done adding distance constraints # command:CPU_time= 10.701 sec, elapsed time= 11.585 sec. # command:Reading probabilities from T0383.t06.CB8-sep9.rdb Reading constraints from ConstraintSet all_contacts maxweight: 5.467 Optimizing... Probability sum: -233.367, CN propb: -233.367 weights: 0.452 constraints: 251 # command:CPU_time= 11.999 sec, elapsed time= 12.912 sec. # command:Found ConstraintSet # PrintContacts log_align.constraints Number of constraints in align 251 # command:Found ConstraintSet # PrintContacts log_align_bonus.constraints Number of constraints in align.bonus 251 # command:Found ConstraintSet # PrintContacts log_rejected.constraints Number of constraints in rejected 236 # command:Found ConstraintSet # PrintContacts log_rejected_bonus.constraints Number of constraints in rejected.bonus 236 # command:Found ConstraintSet # PrintContacts log_noncontact.constraints Number of constraints in noncontact 6534 # command:Found ConstraintSet # PrintContacts log_noncontact_bonus.constraints Number of constraints in noncontact.bonus 6534 # command:CPU_time= 12.128 sec, elapsed time= 13.151 sec. # command: