# 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/T0383/ # command:# Making conformation for sequence T0383 numbered 1 through 127 Created new target T0383 from T0383.a2m # command:# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/T0383/ # command:Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0383//projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0383/manyalignments-good-all.under or /projects/compbio/experiments/protein-predict/casp7/T0383//projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0383/manyalignments-good-all.under.gz for input Trying /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0383/manyalignments-good-all.under # reading script from file /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0383/manyalignments-good-all.under # Reading fragments from alignment file # Attempting to read fragment alignments from file 1x5kA/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/T0383/1x5kA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0383/1x5kA/merged-good-all-a2m.gz for input Trying 1x5kA/merged-good-all-a2m Error: Couldn't open file 1x5kA/merged-good-all-a2m or 1x5kA/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1u6zA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 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/merged-good-all-a2m # 1u6zA read from 1u6zA/merged-good-all-a2m # adding 1u6zA to template set # found chain 1u6zA in template set T0383 55 :IVILSFMIVFDKFVISGTISQVNHIDG 1u6zA 23 :FHMVIARVVDGAMQIIGRLKQRVHLAD # choosing archetypes in rotamer library T0383 83 :IVNEPSELNQEEVETLARPCLNMLNRL 1u6zA 50 :GLGPDNMLSEEAMTRGLNCLSLFAERL Number of specific fragments extracted= 2 number of extra gaps= 0 total=2 Number of alignments=1 # 1u6zA read from 1u6zA/merged-good-all-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=4 Number of alignments=2 # 1u6zA read from 1u6zA/merged-good-all-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=6 Number of alignments=3 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1xx7A/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/T0383/1xx7A/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0383/1xx7A/merged-good-all-a2m.gz for input Trying 1xx7A/merged-good-all-a2m Error: Couldn't open file 1xx7A/merged-good-all-a2m or 1xx7A/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1o6iA/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/T0383/1o6iA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0383/1o6iA/merged-good-all-a2m.gz for input Trying 1o6iA/merged-good-all-a2m Error: Couldn't open file 1o6iA/merged-good-all-a2m or 1o6iA/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ijbA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0383 read from 1ijbA/merged-good-all-a2m # 1ijbA read from 1ijbA/merged-good-all-a2m # found chain 1ijbA in training set T0383 88 :SELNQEEVETLARPCLNMLNRL 1ijbA 523 :SRLSEAEFEVLKAFVVDMMERL Number of specific fragments extracted= 1 number of extra gaps= 0 total=7 Number of alignments=4 # 1ijbA read from 1ijbA/merged-good-all-a2m # found chain 1ijbA in training set T0383 88 :SELNQEEVETLARPCLNMLNRL 1ijbA 523 :SRLSEAEFEVLKAFVVDMMERL Number of specific fragments extracted= 1 number of extra gaps= 0 total=8 Number of alignments=5 # 1ijbA read from 1ijbA/merged-good-all-a2m # found chain 1ijbA in training set T0383 88 :SELNQEEVETLARPCLNMLNRL 1ijbA 523 :SRLSEAEFEVLKAFVVDMMERL Number of specific fragments extracted= 1 number of extra gaps= 0 total=9 Number of alignments=6 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1h0iA/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/T0383/1h0iA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0383/1h0iA/merged-good-all-a2m.gz for input Trying 1h0iA/merged-good-all-a2m Error: Couldn't open file 1h0iA/merged-good-all-a2m or 1h0iA/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1fcyA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0383 read from 1fcyA/merged-good-all-a2m # 1fcyA read from 1fcyA/merged-good-all-a2m # found chain 1fcyA in training set T0383 85 :NEPSEL 1fcyA 339 :GDRMDL T0383 91 :NQEEVETLARPCLNMLNRL 1fcyA 346 :EPEKVDKLQEPLLEALRLY Number of specific fragments extracted= 2 number of extra gaps= 0 total=11 Number of alignments=7 # 1fcyA read from 1fcyA/merged-good-all-a2m # found chain 1fcyA in training set T0383 84 :VNEPSEL 1fcyA 338 :CGDRMDL T0383 91 :NQEEVETLARPCLNMLNRL 1fcyA 346 :EPEKVDKLQEPLLEALRLY Number of specific fragments extracted= 2 number of extra gaps= 0 total=13 Number of alignments=8 # 1fcyA read from 1fcyA/merged-good-all-a2m # found chain 1fcyA in training set T0383 75 :QVNHIDGRIVNEPSEL 1fcyA 329 :GLLSAICLICGDRMDL T0383 91 :NQEEVETLARPCLNMLNRL 1fcyA 346 :EPEKVDKLQEPLLEALRLY Number of specific fragments extracted= 2 number of extra gaps= 0 total=15 Number of alignments=9 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1dkfB/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/T0383/1dkfB/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0383/1dkfB/merged-good-all-a2m.gz for input Trying 1dkfB/merged-good-all-a2m Error: Couldn't open file 1dkfB/merged-good-all-a2m or 1dkfB/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 2lbd/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2lbd expands to /projects/compbio/data/pdb/2lbd.pdb.gz 2lbd:Warning: there is no chain 2lbd will retry with 2lbdA Skipped atom 518, because occupancy 0.410 <= existing 0.590 in 2lbd Skipped atom 520, because occupancy 0.410 <= existing 0.590 in 2lbd Skipped atom 522, because occupancy 0.410 <= existing 0.590 in 2lbd Skipped atom 524, because occupancy 0.410 <= existing 0.590 in 2lbd Skipped atom 526, because occupancy 0.410 <= existing 0.590 in 2lbd Skipped atom 528, because occupancy 0.410 <= existing 0.590 in 2lbd Skipped atom 530, because occupancy 0.410 <= existing 0.590 in 2lbd Skipped atom 532, because occupancy 0.410 <= existing 0.590 in 2lbd Skipped atom 534, because occupancy 0.410 <= existing 0.590 in 2lbd # T0383 read from 2lbd/merged-good-all-a2m # 2lbd read from 2lbd/merged-good-all-a2m # adding 2lbd to template set # found chain 2lbd in template set T0383 85 :NEPSEL 2lbd 339 :GDRMDL T0383 91 :NQEEVETLARPCLNMLNRL 2lbd 346 :EPEKVDKLQEPLLEALRLY Number of specific fragments extracted= 2 number of extra gaps= 0 total=17 Number of alignments=10 # 2lbd read from 2lbd/merged-good-all-a2m # found chain 2lbd in template set T0383 84 :VNEPSEL 2lbd 338 :CGDRMDL T0383 91 :NQEEVETLARPCLNMLNRL 2lbd 346 :EPEKVDKLQEPLLEALRLY Number of specific fragments extracted= 2 number of extra gaps= 0 total=19 Number of alignments=11 # 2lbd read from 2lbd/merged-good-all-a2m # found chain 2lbd in template set T0383 71 :GTISQVNHIDGRIVNEPSEL 2lbd 325 :DTETGLLSAICLICGDRMDL T0383 91 :NQEEVETLARPCLNMLNRL 2lbd 346 :EPEKVDKLQEPLLEALRLY Number of specific fragments extracted= 2 number of extra gaps= 0 total=21 Number of alignments=12 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1bh9A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1bh9A expands to /projects/compbio/data/pdb/1bh9.pdb.gz 1bh9A:# T0383 read from 1bh9A/merged-good-all-a2m # 1bh9A read from 1bh9A/merged-good-all-a2m # adding 1bh9A to template set # found chain 1bh9A in template set T0383 85 :NEPSELNQEEVETLARPCLNMLNRLTYEV 1bh9A 44 :GDDQNPYTESVDILEDLVIEFITEMTHKA Number of specific fragments extracted= 1 number of extra gaps= 0 total=22 Number of alignments=13 # 1bh9A read from 1bh9A/merged-good-all-a2m # found chain 1bh9A in template set T0383 84 :VNEPSELNQEEVETLARPCLNMLNRLTYE 1bh9A 43 :FGDDQNPYTESVDILEDLVIEFITEMTHK Number of specific fragments extracted= 1 number of extra gaps= 0 total=23 Number of alignments=14 # 1bh9A read from 1bh9A/merged-good-all-a2m # found chain 1bh9A in template set T0383 81 :G 1bh9A 42 :G T0383 84 :VNEPSELNQEEVETLARPCLNMLNRLTYE 1bh9A 43 :FGDDQNPYTESVDILEDLVIEFITEMTHK Number of specific fragments extracted= 2 number of extra gaps= 0 total=25 Number of alignments=15 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ogbA/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/T0383/1ogbA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0383/1ogbA/merged-good-all-a2m.gz for input Trying 1ogbA/merged-good-all-a2m Error: Couldn't open file 1ogbA/merged-good-all-a2m or 1ogbA/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1xnzA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0383 read from 1xnzA/merged-good-all-a2m # 1xnzA read from 1xnzA/merged-good-all-a2m # found chain 1xnzA in training set T0383 55 :IVILSFMIVFDKF 1xnzA 93 :IVNIDVTVIKDGF T0383 70 :SGTISQVNHIDG 1xnzA 106 :HGDTSKMFIVGK T0383 91 :NQEEVETLARPCLNMLNRL 1xnzA 118 :PTIMGERLCRITQESLYLA T0383 116 :IALDLPGIN 1xnzA 137 :LRMVKPGIN Number of specific fragments extracted= 4 number of extra gaps= 0 total=29 Number of alignments=16 # 1xnzA read from 1xnzA/merged-good-all-a2m # found chain 1xnzA in training set T0383 55 :IVILSFMIVFDKF 1xnzA 93 :IVNIDVTVIKDGF T0383 70 :SGTISQVNHIDG 1xnzA 106 :HGDTSKMFIVGK T0383 91 :NQEEVETLARPCLNMLNRL 1xnzA 118 :PTIMGERLCRITQESLYLA T0383 116 :IALDLPGIN 1xnzA 137 :LRMVKPGIN Number of specific fragments extracted= 4 number of extra gaps= 0 total=33 Number of alignments=17 # 1xnzA read from 1xnzA/merged-good-all-a2m # found chain 1xnzA in training set T0383 53 :SLIVIL 1xnzA 93 :IVNIDV T0383 61 :MIVFDKF 1xnzA 99 :TVIKDGF T0383 70 :SGTISQVNHIDG 1xnzA 106 :HGDTSKMFIVGK T0383 91 :NQEEVETLARPCLNMLNRLTYE 1xnzA 118 :PTIMGERLCRITQESLYLALRM T0383 119 :DLPGINL 1xnzA 140 :VKPGINL Number of specific fragments extracted= 5 number of extra gaps= 0 total=38 Number of alignments=18 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1fx3B/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1fx3B expands to /projects/compbio/data/pdb/1fx3.pdb.gz 1fx3B:# T0383 read from 1fx3B/merged-good-all-a2m # 1fx3B read from 1fx3B/merged-good-all-a2m # adding 1fx3B to template set # 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=46 Number of alignments=19 # 1fx3B read from 1fx3B/merged-good-all-a2m # 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=53 Number of alignments=20 # 1fx3B read from 1fx3B/merged-good-all-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=60 Number of alignments=21 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ur9A/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/T0383/1ur9A/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0383/1ur9A/merged-good-all-a2m.gz for input Trying 1ur9A/merged-good-all-a2m Error: Couldn't open file 1ur9A/merged-good-all-a2m or 1ur9A/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1r8jA/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/T0383/1r8jA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0383/1r8jA/merged-good-all-a2m.gz for input Trying 1r8jA/merged-good-all-a2m Error: Couldn't open file 1r8jA/merged-good-all-a2m or 1r8jA/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 2ggcA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2ggcA expands to /projects/compbio/data/pdb/2ggc.pdb.gz 2ggcA:Skipped atom 96, because occupancy 0.400 <= existing 0.600 in 2ggcA Skipped atom 100, because occupancy 0.400 <= existing 0.600 in 2ggcA Skipped atom 102, because occupancy 0.400 <= existing 0.600 in 2ggcA Skipped atom 104, because occupancy 0.400 <= existing 0.600 in 2ggcA Skipped atom 106, because occupancy 0.400 <= existing 0.600 in 2ggcA Skipped atom 136, because occupancy 0.500 <= existing 0.500 in 2ggcA Skipped atom 140, because occupancy 0.500 <= existing 0.500 in 2ggcA Skipped atom 142, because occupancy 0.500 <= existing 0.500 in 2ggcA Skipped atom 144, because occupancy 0.500 <= existing 0.500 in 2ggcA Skipped atom 146, because occupancy 0.500 <= existing 0.500 in 2ggcA Skipped atom 148, because occupancy 0.500 <= existing 0.500 in 2ggcA Skipped atom 150, because occupancy 0.500 <= existing 0.500 in 2ggcA Skipped atom 152, because occupancy 0.500 <= existing 0.500 in 2ggcA Skipped atom 173, because occupancy 0.500 <= existing 0.500 in 2ggcA Skipped atom 177, because occupancy 0.500 <= existing 0.500 in 2ggcA Skipped atom 179, because occupancy 0.500 <= existing 0.500 in 2ggcA Skipped atom 181, because occupancy 0.500 <= existing 0.500 in 2ggcA Skipped atom 183, because occupancy 0.500 <= existing 0.500 in 2ggcA Skipped atom 185, because occupancy 0.500 <= existing 0.500 in 2ggcA Skipped atom 203, because occupancy 0.500 <= existing 0.500 in 2ggcA Skipped atom 207, because occupancy 0.500 <= existing 0.500 in 2ggcA Skipped atom 209, because occupancy 0.500 <= existing 0.500 in 2ggcA Skipped atom 211, because occupancy 0.500 <= existing 0.500 in 2ggcA Skipped atom 213, because occupancy 0.500 <= existing 0.500 in 2ggcA Skipped atom 215, because occupancy 0.500 <= existing 0.500 in 2ggcA Skipped atom 319, because occupancy 0.500 <= existing 0.500 in 2ggcA Skipped atom 323, because occupancy 0.500 <= existing 0.500 in 2ggcA Skipped atom 325, because occupancy 0.500 <= existing 0.500 in 2ggcA Skipped atom 327, because occupancy 0.500 <= existing 0.500 in 2ggcA Skipped atom 329, because occupancy 0.500 <= existing 0.500 in 2ggcA Skipped atom 331, because occupancy 0.500 <= existing 0.500 in 2ggcA Skipped atom 350, because occupancy 0.500 <= existing 0.500 in 2ggcA Skipped atom 354, because occupancy 0.500 <= existing 0.500 in 2ggcA Skipped atom 356, because occupancy 0.500 <= existing 0.500 in 2ggcA Skipped atom 358, because occupancy 0.500 <= existing 0.500 in 2ggcA Skipped atom 360, because occupancy 0.500 <= existing 0.500 in 2ggcA Skipped atom 362, because occupancy 0.500 <= existing 0.500 in 2ggcA Skipped atom 364, because occupancy 0.500 <= existing 0.500 in 2ggcA Skipped atom 366, because occupancy 0.500 <= existing 0.500 in 2ggcA Skipped atom 434, because occupancy 0.500 <= existing 0.500 in 2ggcA Skipped atom 438, because occupancy 0.500 <= existing 0.500 in 2ggcA Skipped atom 440, because occupancy 0.500 <= existing 0.500 in 2ggcA Skipped atom 442, because occupancy 0.500 <= existing 0.500 in 2ggcA Skipped atom 444, because occupancy 0.500 <= existing 0.500 in 2ggcA Skipped atom 446, because occupancy 0.500 <= existing 0.500 in 2ggcA Skipped atom 473, because occupancy 0.500 <= existing 0.500 in 2ggcA Skipped atom 477, because occupancy 0.500 <= existing 0.500 in 2ggcA Skipped atom 479, because occupancy 0.500 <= existing 0.500 in 2ggcA Skipped atom 481, because occupancy 0.500 <= existing 0.500 in 2ggcA Skipped atom 513, because occupancy 0.500 <= existing 0.500 in 2ggcA Skipped atom 517, because occupancy 0.500 <= existing 0.500 in 2ggcA Skipped atom 519, because occupancy 0.500 <= existing 0.500 in 2ggcA Skipped atom 521, because occupancy 0.500 <= existing 0.500 in 2ggcA Skipped atom 523, because occupancy 0.500 <= existing 0.500 in 2ggcA Skipped atom 525, because occupancy 0.500 <= existing 0.500 in 2ggcA Skipped atom 527, because occupancy 0.500 <= existing 0.500 in 2ggcA Skipped atom 529, because occupancy 0.500 <= existing 0.500 in 2ggcA Skipped atom 531, because occupancy 0.500 <= existing 0.500 in 2ggcA Skipped atom 534, because occupancy 0.300 <= existing 0.700 in 2ggcA Skipped atom 538, because occupancy 0.300 <= existing 0.700 in 2ggcA Skipped atom 540, because occupancy 0.300 <= existing 0.700 in 2ggcA Skipped atom 542, because occupancy 0.300 <= existing 0.700 in 2ggcA Skipped atom 544, because occupancy 0.300 <= existing 0.700 in 2ggcA Skipped atom 546, because occupancy 0.300 <= existing 0.700 in 2ggcA Skipped atom 548, because occupancy 0.300 <= existing 0.700 in 2ggcA Skipped atom 583, because occupancy 0.500 <= existing 0.500 in 2ggcA Skipped atom 587, because occupancy 0.500 <= existing 0.500 in 2ggcA Skipped atom 589, because occupancy 0.500 <= existing 0.500 in 2ggcA Skipped atom 748, because occupancy 0.300 <= existing 0.700 in 2ggcA Skipped atom 752, because occupancy 0.300 <= existing 0.700 in 2ggcA Skipped atom 754, because occupancy 0.300 <= existing 0.700 in 2ggcA Skipped atom 756, because occupancy 0.300 <= existing 0.700 in 2ggcA Skipped atom 758, because occupancy 0.300 <= existing 0.700 in 2ggcA Skipped atom 826, because occupancy 0.500 <= existing 0.500 in 2ggcA Skipped atom 830, because occupancy 0.500 <= existing 0.500 in 2ggcA Skipped atom 832, because occupancy 0.500 <= existing 0.500 in 2ggcA Skipped atom 834, because occupancy 0.500 <= existing 0.500 in 2ggcA Skipped atom 854, because occupancy 0.300 <= existing 0.700 in 2ggcA Skipped atom 858, because occupancy 0.300 <= existing 0.700 in 2ggcA Skipped atom 860, because occupancy 0.300 <= existing 0.700 in 2ggcA Skipped atom 862, because occupancy 0.300 <= existing 0.700 in 2ggcA Skipped atom 864, because occupancy 0.300 <= existing 0.700 in 2ggcA Skipped atom 964, because occupancy 0.500 <= existing 0.500 in 2ggcA Skipped atom 968, because occupancy 0.500 <= existing 0.500 in 2ggcA Skipped atom 970, because occupancy 0.500 <= existing 0.500 in 2ggcA Skipped atom 972, because occupancy 0.500 <= existing 0.500 in 2ggcA Skipped atom 974, because occupancy 0.500 <= existing 0.500 in 2ggcA Skipped atom 976, because occupancy 0.500 <= existing 0.500 in 2ggcA Skipped atom 993, because occupancy 0.200 <= existing 0.800 in 2ggcA Skipped atom 997, because occupancy 0.200 <= existing 0.800 in 2ggcA Skipped atom 999, because occupancy 0.200 <= existing 0.800 in 2ggcA Skipped atom 1001, because occupancy 0.200 <= existing 0.800 in 2ggcA Skipped atom 1003, because occupancy 0.200 <= existing 0.800 in 2ggcA Skipped atom 1006, because occupancy 0.500 <= existing 0.500 in 2ggcA Skipped atom 1010, because occupancy 0.500 <= existing 0.500 in 2ggcA Skipped atom 1012, because occupancy 0.500 <= existing 0.500 in 2ggcA Skipped atom 1014, because occupancy 0.500 <= existing 0.500 in 2ggcA Skipped atom 1016, because occupancy 0.500 <= existing 0.500 in 2ggcA Skipped atom 1023, because occupancy 0.500 <= existing 0.500 in 2ggcA Skipped atom 1027, because occupancy 0.500 <= existing 0.500 in 2ggcA Skipped atom 1029, because occupancy 0.500 <= existing 0.500 in 2ggcA Skipped atom 1031, because occupancy 0.500 <= existing 0.500 in 2ggcA Skipped atom 1033, because occupancy 0.500 <= existing 0.500 in 2ggcA Skipped atom 1035, because occupancy 0.500 <= existing 0.500 in 2ggcA Skipped atom 1038, because occupancy 0.500 <= existing 0.500 in 2ggcA Skipped atom 1042, because occupancy 0.500 <= existing 0.500 in 2ggcA Skipped atom 1044, because occupancy 0.500 <= existing 0.500 in 2ggcA Skipped atom 1046, because occupancy 0.500 <= existing 0.500 in 2ggcA Skipped atom 1048, because occupancy 0.500 <= existing 0.500 in 2ggcA Skipped atom 1050, because occupancy 0.500 <= existing 0.500 in 2ggcA Skipped atom 1052, because occupancy 0.500 <= existing 0.500 in 2ggcA Skipped atom 1054, because occupancy 0.500 <= existing 0.500 in 2ggcA Skipped atom 1106, because occupancy 0.500 <= existing 0.500 in 2ggcA Skipped atom 1110, because occupancy 0.500 <= existing 0.500 in 2ggcA Skipped atom 1112, because occupancy 0.500 <= existing 0.500 in 2ggcA Skipped atom 1114, because occupancy 0.500 <= existing 0.500 in 2ggcA Skipped atom 1116, because occupancy 0.500 <= existing 0.500 in 2ggcA Skipped atom 1118, because occupancy 0.500 <= existing 0.500 in 2ggcA Skipped atom 1147, because occupancy 0.500 <= existing 0.500 in 2ggcA Skipped atom 1151, because occupancy 0.500 <= existing 0.500 in 2ggcA Skipped atom 1153, because occupancy 0.500 <= existing 0.500 in 2ggcA Skipped atom 1155, because occupancy 0.500 <= existing 0.500 in 2ggcA Skipped atom 1157, because occupancy 0.500 <= existing 0.500 in 2ggcA Skipped atom 1243, because occupancy 0.500 <= existing 0.500 in 2ggcA Skipped atom 1247, because occupancy 0.500 <= existing 0.500 in 2ggcA Skipped atom 1249, because occupancy 0.500 <= existing 0.500 in 2ggcA Skipped atom 1251, because occupancy 0.500 <= existing 0.500 in 2ggcA Skipped atom 1253, because occupancy 0.500 <= existing 0.500 in 2ggcA Skipped atom 1255, because occupancy 0.500 <= existing 0.500 in 2ggcA Skipped atom 1257, because occupancy 0.500 <= existing 0.500 in 2ggcA Skipped atom 1259, because occupancy 0.500 <= existing 0.500 in 2ggcA Skipped atom 1262, because occupancy 0.300 <= existing 0.700 in 2ggcA Skipped atom 1266, because occupancy 0.300 <= existing 0.700 in 2ggcA Skipped atom 1268, because occupancy 0.300 <= existing 0.700 in 2ggcA Skipped atom 1270, because occupancy 0.300 <= existing 0.700 in 2ggcA Skipped atom 1272, because occupancy 0.300 <= existing 0.700 in 2ggcA Skipped atom 1274, because occupancy 0.300 <= existing 0.700 in 2ggcA Skipped atom 1381, because occupancy 0.300 <= existing 0.700 in 2ggcA Skipped atom 1385, because occupancy 0.300 <= existing 0.700 in 2ggcA Skipped atom 1387, because occupancy 0.300 <= existing 0.700 in 2ggcA Skipped atom 1390, because occupancy 0.500 <= existing 0.500 in 2ggcA Skipped atom 1394, because occupancy 0.500 <= existing 0.500 in 2ggcA Skipped atom 1396, because occupancy 0.500 <= existing 0.500 in 2ggcA Skipped atom 1398, because occupancy 0.500 <= existing 0.500 in 2ggcA Skipped atom 1428, because occupancy 0.200 <= existing 0.800 in 2ggcA Skipped atom 1432, because occupancy 0.200 <= existing 0.800 in 2ggcA Skipped atom 1434, because occupancy 0.200 <= existing 0.800 in 2ggcA Skipped atom 1436, because occupancy 0.200 <= existing 0.800 in 2ggcA Skipped atom 1438, because occupancy 0.200 <= existing 0.800 in 2ggcA Skipped atom 1440, because occupancy 0.200 <= existing 0.800 in 2ggcA Skipped atom 1442, because occupancy 0.200 <= existing 0.800 in 2ggcA Skipped atom 1444, because occupancy 0.200 <= existing 0.800 in 2ggcA Skipped atom 1446, because occupancy 0.200 <= existing 0.800 in 2ggcA Skipped atom 1449, because occupancy 0.300 <= existing 0.700 in 2ggcA Skipped atom 1453, because occupancy 0.300 <= existing 0.700 in 2ggcA Skipped atom 1455, because occupancy 0.300 <= existing 0.700 in 2ggcA Skipped atom 1595, because occupancy 0.200 <= existing 0.800 in 2ggcA Skipped atom 1599, because occupancy 0.200 <= existing 0.800 in 2ggcA Skipped atom 1601, because occupancy 0.200 <= existing 0.800 in 2ggcA Skipped atom 1603, because occupancy 0.200 <= existing 0.800 in 2ggcA Skipped atom 1605, because occupancy 0.200 <= existing 0.800 in 2ggcA Skipped atom 1607, because occupancy 0.400 <= existing 0.600 in 2ggcA Skipped atom 1609, because occupancy 0.400 <= existing 0.600 in 2ggcA Skipped atom 1611, because occupancy 0.400 <= existing 0.600 in 2ggcA Skipped atom 1613, because occupancy 0.400 <= existing 0.600 in 2ggcA Skipped atom 1615, because occupancy 0.400 <= existing 0.600 in 2ggcA Skipped atom 1617, because occupancy 0.400 <= existing 0.600 in 2ggcA Skipped atom 1630, because occupancy 0.500 <= existing 0.500 in 2ggcA Skipped atom 1632, because occupancy 0.500 <= existing 0.500 in 2ggcA Skipped atom 1634, because occupancy 0.500 <= existing 0.500 in 2ggcA Skipped atom 1636, because occupancy 0.500 <= existing 0.500 in 2ggcA Skipped atom 1638, because occupancy 0.500 <= existing 0.500 in 2ggcA Skipped atom 1640, because occupancy 0.500 <= existing 0.500 in 2ggcA Skipped atom 1642, because occupancy 0.500 <= existing 0.500 in 2ggcA Skipped atom 1644, because occupancy 0.500 <= existing 0.500 in 2ggcA Skipped atom 1646, because occupancy 0.500 <= existing 0.500 in 2ggcA Skipped atom 1648, because occupancy 0.500 <= existing 0.500 in 2ggcA Skipped atom 1650, because occupancy 0.500 <= existing 0.500 in 2ggcA Skipped atom 1652, because occupancy 0.500 <= existing 0.500 in 2ggcA Skipped atom 1654, because occupancy 0.500 <= existing 0.500 in 2ggcA Skipped atom 1656, because occupancy 0.500 <= existing 0.500 in 2ggcA Skipped atom 1658, because occupancy 0.500 <= existing 0.500 in 2ggcA Skipped atom 1660, because occupancy 0.500 <= existing 0.500 in 2ggcA Skipped atom 1662, because occupancy 0.500 <= existing 0.500 in 2ggcA Skipped atom 1664, because occupancy 0.500 <= existing 0.500 in 2ggcA Skipped atom 1666, because occupancy 0.500 <= existing 0.500 in 2ggcA Skipped atom 1668, because occupancy 0.500 <= existing 0.500 in 2ggcA Skipped atom 1670, because occupancy 0.500 <= existing 0.500 in 2ggcA Skipped atom 1672, because occupancy 0.500 <= existing 0.500 in 2ggcA Skipped atom 1674, because occupancy 0.500 <= existing 0.500 in 2ggcA Skipped atom 1676, because occupancy 0.500 <= existing 0.500 in 2ggcA Skipped atom 1701, because occupancy 0.500 <= existing 0.500 in 2ggcA Skipped atom 1705, because occupancy 0.500 <= existing 0.500 in 2ggcA Skipped atom 1707, because occupancy 0.500 <= existing 0.500 in 2ggcA Skipped atom 1709, because occupancy 0.500 <= existing 0.500 in 2ggcA Skipped atom 1711, because occupancy 0.500 <= existing 0.500 in 2ggcA Skipped atom 1713, because occupancy 0.500 <= existing 0.500 in 2ggcA Skipped atom 1816, because occupancy 0.400 <= existing 0.600 in 2ggcA Skipped atom 1820, because occupancy 0.400 <= existing 0.600 in 2ggcA Skipped atom 1822, because occupancy 0.400 <= existing 0.600 in 2ggcA Skipped atom 1824, because occupancy 0.400 <= existing 0.600 in 2ggcA Skipped atom 1826, because occupancy 0.400 <= existing 0.600 in 2ggcA Skipped atom 1828, because occupancy 0.400 <= existing 0.600 in 2ggcA Skipped atom 1857, because occupancy 0.500 <= existing 0.500 in 2ggcA Skipped atom 1861, because occupancy 0.500 <= existing 0.500 in 2ggcA Skipped atom 1863, because occupancy 0.500 <= existing 0.500 in 2ggcA Skipped atom 1865, because occupancy 0.500 <= existing 0.500 in 2ggcA Skipped atom 1867, because occupancy 0.500 <= existing 0.500 in 2ggcA Skipped atom 1869, because occupancy 0.500 <= existing 0.500 in 2ggcA Skipped atom 1871, because occupancy 0.500 <= existing 0.500 in 2ggcA Skipped atom 1873, because occupancy 0.500 <= existing 0.500 in 2ggcA Skipped atom 1912, because occupancy 0.500 <= existing 0.500 in 2ggcA Skipped atom 1916, because occupancy 0.500 <= existing 0.500 in 2ggcA Skipped atom 1918, because occupancy 0.500 <= existing 0.500 in 2ggcA Skipped atom 1920, because occupancy 0.500 <= existing 0.500 in 2ggcA Skipped atom 1922, because occupancy 0.500 <= existing 0.500 in 2ggcA Skipped atom 1924, because occupancy 0.500 <= existing 0.500 in 2ggcA Skipped atom 1926, because occupancy 0.500 <= existing 0.500 in 2ggcA Skipped atom 1928, because occupancy 0.500 <= existing 0.500 in 2ggcA Skipped atom 1930, because occupancy 0.500 <= existing 0.500 in 2ggcA Skipped atom 1932, because occupancy 0.500 <= existing 0.500 in 2ggcA Skipped atom 1934, because occupancy 0.500 <= existing 0.500 in 2ggcA Skipped atom 1984, because occupancy 0.500 <= existing 0.500 in 2ggcA Skipped atom 1988, because occupancy 0.500 <= existing 0.500 in 2ggcA Skipped atom 1990, because occupancy 0.500 <= existing 0.500 in 2ggcA Skipped atom 1992, because occupancy 0.500 <= existing 0.500 in 2ggcA Skipped atom 1994, because occupancy 0.500 <= existing 0.500 in 2ggcA Skipped atom 1996, because occupancy 0.500 <= existing 0.500 in 2ggcA Skipped atom 1998, because occupancy 0.500 <= existing 0.500 in 2ggcA Skipped atom 2000, because occupancy 0.500 <= existing 0.500 in 2ggcA Skipped atom 2075, because occupancy 0.500 <= existing 0.500 in 2ggcA Skipped atom 2079, because occupancy 0.500 <= existing 0.500 in 2ggcA Skipped atom 2081, because occupancy 0.500 <= existing 0.500 in 2ggcA Skipped atom 2083, because occupancy 0.500 <= existing 0.500 in 2ggcA Skipped atom 2085, because occupancy 0.500 <= existing 0.500 in 2ggcA Skipped atom 2143, because occupancy 0.500 <= existing 0.500 in 2ggcA Skipped atom 2145, because occupancy 0.500 <= existing 0.500 in 2ggcA Skipped atom 2147, because occupancy 0.500 <= existing 0.500 in 2ggcA Skipped atom 2149, because occupancy 0.500 <= existing 0.500 in 2ggcA Skipped atom 2151, because occupancy 0.500 <= existing 0.500 in 2ggcA Skipped atom 2153, because occupancy 0.500 <= existing 0.500 in 2ggcA Skipped atom 2155, because occupancy 0.500 <= existing 0.500 in 2ggcA Skipped atom 2157, because occupancy 0.500 <= existing 0.500 in 2ggcA Skipped atom 2218, because occupancy 0.500 <= existing 0.500 in 2ggcA Skipped atom 2220, because occupancy 0.500 <= existing 0.500 in 2ggcA Skipped atom 2222, because occupancy 0.500 <= existing 0.500 in 2ggcA Skipped atom 2224, because occupancy 0.500 <= existing 0.500 in 2ggcA Skipped atom 2226, because occupancy 0.500 <= existing 0.500 in 2ggcA Skipped atom 2228, because occupancy 0.500 <= existing 0.500 in 2ggcA Skipped atom 2230, because occupancy 0.500 <= existing 0.500 in 2ggcA Skipped atom 2269, because occupancy 0.500 <= existing 0.500 in 2ggcA Skipped atom 2273, because occupancy 0.500 <= existing 0.500 in 2ggcA Skipped atom 2275, because occupancy 0.500 <= existing 0.500 in 2ggcA Skipped atom 2287, because occupancy 0.500 <= existing 0.500 in 2ggcA Skipped atom 2289, because occupancy 0.500 <= existing 0.500 in 2ggcA Skipped atom 2291, because occupancy 0.500 <= existing 0.500 in 2ggcA Skipped atom 2293, because occupancy 0.500 <= existing 0.500 in 2ggcA Skipped atom 2295, because occupancy 0.500 <= existing 0.500 in 2ggcA Skipped atom 2297, because occupancy 0.500 <= existing 0.500 in 2ggcA Skipped atom 2299, because occupancy 0.500 <= existing 0.500 in 2ggcA Skipped atom 2301, because occupancy 0.500 <= existing 0.500 in 2ggcA # T0383 read from 2ggcA/merged-good-all-a2m # 2ggcA read from 2ggcA/merged-good-all-a2m # adding 2ggcA to template set # found chain 2ggcA in template set T0383 55 :IVILSFMIVFDKF 2ggcA 93 :IVNIDVTVIKDGF T0383 70 :SGTISQVN 2ggcA 106 :HGDTSKMF T0383 83 :IVNEPSELNQEEVETLARPCL 2ggcA 114 :IVGKPTIMGERLCRITQESLY T0383 112 :EV 2ggcA 135 :LA T0383 116 :IALDLPGIN 2ggcA 137 :LRMVKPGIN Number of specific fragments extracted= 5 number of extra gaps= 0 total=65 Number of alignments=22 # 2ggcA read from 2ggcA/merged-good-all-a2m # found chain 2ggcA in template set T0383 55 :IVILSFMIVFDKF 2ggcA 93 :IVNIDVTVIKDGF T0383 70 :SGTISQVN 2ggcA 106 :HGDTSKMF T0383 83 :IVNEPSELNQE 2ggcA 114 :IVGKPTIMGER T0383 98 :LARPCLNMLNRL 2ggcA 125 :LCRITQESLYLA T0383 116 :IALDLPGIN 2ggcA 137 :LRMVKPGIN Number of specific fragments extracted= 5 number of extra gaps= 0 total=70 Number of alignments=23 # 2ggcA read from 2ggcA/merged-good-all-a2m # found chain 2ggcA in template set T0383 49 :NQV 2ggcA 91 :GDI T0383 56 :VILSFMIVFDKF 2ggcA 94 :VNIDVTVIKDGF T0383 70 :SGTISQVN 2ggcA 106 :HGDTSKMF T0383 83 :IVNEPSELNQEEVETLARPCLNML 2ggcA 114 :IVGKPTIMGERLCRITQESLYLAL T0383 117 :ALDLPGINL 2ggcA 138 :RMVKPGINL Number of specific fragments extracted= 5 number of extra gaps= 0 total=75 Number of alignments=24 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1mugA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0383 read from 1mugA/merged-good-all-a2m # 1mugA read from 1mugA/merged-good-all-a2m # found chain 1mugA in training 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=77 Number of alignments=25 # 1mugA read from 1mugA/merged-good-all-a2m # found chain 1mugA in training 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=79 Number of alignments=26 # 1mugA read from 1mugA/merged-good-all-a2m # found chain 1mugA in training set T0383 81 :GRIVNEPSELNQEEVETLARPCLNMLNRL 1mugA 71 :DRPTVQANEVSKQELHAGGRKLIEKIEDY Number of specific fragments extracted= 1 number of extra gaps= 0 total=80 Number of alignments=27 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1e6zA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 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/merged-good-all-a2m # 1e6zA read from 1e6zA/merged-good-all-a2m # adding 1e6zA to template set # found chain 1e6zA in template set T0383 91 :NQEEVETLARPCLNMLNRL 1e6zA 116 :TPASRAKFAQSCVRIMKDY Number of specific fragments extracted= 1 number of extra gaps= 0 total=81 # 1e6zA read from 1e6zA/merged-good-all-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=82 Number of alignments=28 # 1e6zA read from 1e6zA/merged-good-all-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=83 Number of alignments=29 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2kfnA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2kfnA expands to /projects/compbio/data/pdb/2kfn.pdb.gz 2kfnA:# T0383 read from 2kfnA/merged-good-all-a2m # 2kfnA read from 2kfnA/merged-good-all-a2m # adding 2kfnA to template set # found chain 2kfnA in template set T0383 89 :ELNQEEVETLARPCLNMLNRLTYEVTEIA 2kfnA 546 :KIDPKVLHNHSEELTLRLAELEKKAHEIA T0383 120 :LPGINLE 2kfnA 575 :GEEFNLS Number of specific fragments extracted= 2 number of extra gaps= 0 total=85 Number of alignments=30 # 2kfnA read from 2kfnA/merged-good-all-a2m # found chain 2kfnA in template set T0383 90 :LNQEEVETLARPCLNMLNRLTYEVTEIALDL 2kfnA 547 :IDPKVLHNHSEELTLRLAELEKKAHEIAGEE T0383 123 :INLE 2kfnA 578 :FNLS Number of specific fragments extracted= 2 number of extra gaps= 0 total=87 Number of alignments=31 # 2kfnA read from 2kfnA/merged-good-all-a2m # found chain 2kfnA in template set T0383 89 :ELNQEEVETLARPCLNMLNRLTYEVTEIA 2kfnA 546 :KIDPKVLHNHSEELTLRLAELEKKAHEIA T0383 120 :LPGINLE 2kfnA 575 :GEEFNLS Number of specific fragments extracted= 2 number of extra gaps= 0 total=89 Number of alignments=32 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1oshA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0383 read from 1oshA/merged-good-all-a2m # 1oshA read from 1oshA/merged-good-all-a2m # found chain 1oshA in training set T0383 91 :NQEEVETLARPCLNMLNRLT 1oshA 404 :DREAVEKLQEPLLDVLQKLC Number of specific fragments extracted= 1 number of extra gaps= 0 total=90 Number of alignments=33 # 1oshA read from 1oshA/merged-good-all-a2m # found chain 1oshA in training 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=92 Number of alignments=34 # 1oshA read from 1oshA/merged-good-all-a2m # found chain 1oshA in training 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=95 Number of alignments=35 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1k3xA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0383 read from 1k3xA/merged-good-all-a2m # 1k3xA read from 1k3xA/merged-good-all-a2m # found chain 1k3xA in training set T0383 88 :SELNQEEVETLARPCLNMLNRLTY 1k3xA 187 :KDLNAAQLDALAHALLEIPRFSYA Number of specific fragments extracted= 1 number of extra gaps= 0 total=96 Number of alignments=36 # 1k3xA read from 1k3xA/merged-good-all-a2m # found chain 1k3xA in training set Warning: unaligning (T0383)T114 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1k3xA)A223 T0383 86 :EPSELNQEEVETLARPCLNMLNRLTYEV 1k3xA 185 :KAKDLNAAQLDALAHALLEIPRFSYATR Number of specific fragments extracted= 1 number of extra gaps= 0 total=97 Number of alignments=37 # 1k3xA read from 1k3xA/merged-good-all-a2m # found chain 1k3xA in training set Warning: unaligning (T0383)T114 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1k3xA)A223 T0383 76 :VNHIDGRIVN 1k3xA 174 :ILWQVGLTGN T0383 86 :EPSELNQEEVETLARPCLNMLNRLTYEV 1k3xA 185 :KAKDLNAAQLDALAHALLEIPRFSYATR Number of specific fragments extracted= 2 number of extra gaps= 0 total=99 Number of alignments=38 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2bl1A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2bl1A expands to /projects/compbio/data/pdb/2bl1.pdb.gz 2bl1A:Skipped atom 603, because occupancy 0.500 <= existing 0.500 in 2bl1A Skipped atom 604, because occupancy 0.500 <= existing 0.500 in 2bl1A Skipped atom 605, because occupancy 0.500 <= existing 0.500 in 2bl1A Skipped atom 606, because occupancy 0.500 <= existing 0.500 in 2bl1A Skipped atom 607, because occupancy 0.500 <= existing 0.500 in 2bl1A Skipped atom 608, because occupancy 0.500 <= existing 0.500 in 2bl1A Skipped atom 609, because occupancy 0.500 <= existing 0.500 in 2bl1A Skipped atom 610, because occupancy 0.500 <= existing 0.500 in 2bl1A Skipped atom 611, because occupancy 0.500 <= existing 0.500 in 2bl1A Skipped atom 612, because occupancy 0.500 <= existing 0.500 in 2bl1A Skipped atom 613, because occupancy 0.500 <= existing 0.500 in 2bl1A Skipped atom 800, because occupancy 0.500 <= existing 0.500 in 2bl1A Skipped atom 801, because occupancy 0.500 <= existing 0.500 in 2bl1A Skipped atom 802, because occupancy 0.500 <= existing 0.500 in 2bl1A Skipped atom 803, because occupancy 0.500 <= existing 0.500 in 2bl1A Skipped atom 804, because occupancy 0.500 <= existing 0.500 in 2bl1A Skipped atom 805, because occupancy 0.500 <= existing 0.500 in 2bl1A Skipped atom 806, because occupancy 0.500 <= existing 0.500 in 2bl1A Skipped atom 807, because occupancy 0.500 <= existing 0.500 in 2bl1A Skipped atom 808, because occupancy 0.500 <= existing 0.500 in 2bl1A 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 1037, because occupancy 0.500 <= existing 0.500 in 2bl1A Skipped atom 1038, because occupancy 0.500 <= existing 0.500 in 2bl1A Skipped atom 1039, because occupancy 0.500 <= existing 0.500 in 2bl1A Skipped atom 1040, because occupancy 0.500 <= existing 0.500 in 2bl1A Skipped atom 1041, because occupancy 0.500 <= existing 0.500 in 2bl1A Skipped atom 1042, because occupancy 0.500 <= existing 0.500 in 2bl1A Skipped atom 1043, because occupancy 0.500 <= existing 0.500 in 2bl1A Skipped atom 1044, because occupancy 0.500 <= existing 0.500 in 2bl1A Skipped atom 1045, because occupancy 0.500 <= existing 0.500 in 2bl1A Skipped atom 1046, because occupancy 0.500 <= existing 0.500 in 2bl1A Skipped atom 1047, because occupancy 0.500 <= existing 0.500 in 2bl1A 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 # T0383 read from 2bl1A/merged-good-all-a2m # 2bl1A read from 2bl1A/merged-good-all-a2m # adding 2bl1A to template set # found chain 2bl1A in template set T0383 47 :QENQVTSLIVILS 2bl1A 112 :RAQGLHVMVAAIE T0383 66 :KFVISGTISQVNHIDGRIV 2bl1A 138 :GFEISGQMPQVGQKFGRWL Number of specific fragments extracted= 2 number of extra gaps= 0 total=101 Number of alignments=39 # 2bl1A read from 2bl1A/merged-good-all-a2m # found chain 2bl1A in template set T0383 43 :LQHDQENQVTSLIVILS 2bl1A 108 :IERARAQGLHVMVAAIE T0383 66 :KFVISGTISQVNHIDGRIV 2bl1A 138 :GFEISGQMPQVGQKFGRWL Number of specific fragments extracted= 2 number of extra gaps= 0 total=103 Number of alignments=40 # 2bl1A read from 2bl1A/merged-good-all-a2m # found chain 2bl1A in template set T0383 41 :QLLQHDQENQV 2bl1A 73 :DWRPFEGFRGT T0383 56 :VILSFMIVFD 2bl1A 84 :VEHSVYVRDD T0383 83 :IVNEP 2bl1A 94 :QRGKG T0383 94 :EVETLARPCLNMLNRL 2bl1A 99 :LGVQLLQALIERARAQ Number of specific fragments extracted= 4 number of extra gaps= 0 total=107 Number of alignments=41 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1qynA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1qynA expands to /projects/compbio/data/pdb/1qyn.pdb.gz 1qynA:# T0383 read from 1qynA/merged-good-all-a2m # 1qynA read from 1qynA/merged-good-all-a2m # adding 1qynA to template set # 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=115 Number of alignments=42 # 1qynA read from 1qynA/merged-good-all-a2m # 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 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=124 Number of alignments=43 # 1qynA read from 1qynA/merged-good-all-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=132 Number of alignments=44 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1j93A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1j93A expands to /projects/compbio/data/pdb/1j93.pdb.gz 1j93A:# T0383 read from 1j93A/merged-good-all-a2m # 1j93A read from 1j93A/merged-good-all-a2m # adding 1j93A to template set # found chain 1j93A in template set T0383 89 :ELNQEEVETLARPCLNML 1j93A 218 :ELSPVDFEEFSLPYLKQI T0383 113 :VTEIALDLPGINL 1j93A 236 :VDSVKLTHPNLPL Number of specific fragments extracted= 2 number of extra gaps= 0 total=134 Number of alignments=45 # 1j93A read from 1j93A/merged-good-all-a2m # found chain 1j93A in template set T0383 89 :ELNQEEVETLARPCLNML 1j93A 218 :ELSPVDFEEFSLPYLKQI T0383 113 :VTEIALDLPGINL 1j93A 236 :VDSVKLTHPNLPL Number of specific fragments extracted= 2 number of extra gaps= 0 total=136 Number of alignments=46 # 1j93A read from 1j93A/merged-good-all-a2m # found chain 1j93A in template set T0383 89 :ELNQEEVETLARPCLNMLNR 1j93A 218 :ELSPVDFEEFSLPYLKQIVD Number of specific fragments extracted= 1 number of extra gaps= 0 total=137 Number of alignments=47 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1c24A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1c24A expands to /projects/compbio/data/pdb/1c24.pdb.gz 1c24A:# T0383 read from 1c24A/merged-good-all-a2m # 1c24A read from 1c24A/merged-good-all-a2m # adding 1c24A to template set # found chain 1c24A in template set T0383 47 :QENQ 1c24A 89 :KDGD T0383 55 :IVILSFMIVFDKF 1c24A 93 :IVNIDVTVIKDGF T0383 70 :SGTISQVNHIDG 1c24A 106 :HGDTSKMFIVGK T0383 91 :NQEEVETLARPCLNMLNRL 1c24A 118 :PTIMGERLCRITQESLYLA T0383 116 :IALDLPGIN 1c24A 137 :LRMVKPGIN Number of specific fragments extracted= 5 number of extra gaps= 0 total=142 Number of alignments=48 # 1c24A read from 1c24A/merged-good-all-a2m # found chain 1c24A in template set T0383 55 :IVILSFMIVFDKF 1c24A 93 :IVNIDVTVIKDGF T0383 70 :SGTISQVNHIDG 1c24A 106 :HGDTSKMFIVGK T0383 91 :NQEEVETLARPCLNMLNRL 1c24A 118 :PTIMGERLCRITQESLYLA T0383 116 :IALDLPGIN 1c24A 137 :LRMVKPGIN Number of specific fragments extracted= 4 number of extra gaps= 0 total=146 Number of alignments=49 # 1c24A read from 1c24A/merged-good-all-a2m # found chain 1c24A in template set T0383 48 :ENQV 1c24A 90 :DGDI T0383 54 :LIVILSF 1c24A 94 :VNIDVTV T0383 63 :VFDKF 1c24A 101 :IKDGF T0383 70 :SGTISQVNHIDG 1c24A 106 :HGDTSKMFIVGK T0383 91 :NQEEVETLARPCLNMLNRLTYEV 1c24A 118 :PTIMGERLCRITQESLYLALRMV T0383 120 :LPGINL 1c24A 141 :KPGINL Number of specific fragments extracted= 6 number of extra gaps= 0 total=152 Number of alignments=50 # command:Using radius: 8.0000 Alignment mode NUMB_ALIGNS: 50 Adding 561 constraints to all.constraints Done adding distance constraints # command:Reading probabilities from probabilities.dat Reading constraints from ConstraintSet all.constraints maxweight: 1.0000 Optimizing... Probability sum: -227.8319, CN propb: -227.8319 weights: 0.4038 constraints: 261 # command:Found ConstraintSet # PrintContacts align.constraints_v3 Number of constraints in align.constraints 261 # command:Found ConstraintSet # PrintContacts align_bonus.constraints_v3 Number of constraints in align.constraints.bonus 261 # command:Found ConstraintSet # PrintContacts rejected.constraints_v3 Number of constraints in rejected.constraints 300 # command:Found ConstraintSet # PrintContacts rejected_bonus.constraints_v3 Number of constraints in rejected.constraints.bonus 300 # command:Found ConstraintSet # PrintContacts non_contacts.constraints_v3 Number of constraints in noncontact.constraints 0 # command:Found ConstraintSet # PrintContacts non_contacts_bonus.constraints_v3 Number of constraints in noncontact.constraints.bonus 0 # command:Found ConstraintSet # PrintContacts all.constraints_v3 Number of constraints in all.constraints 561 # command: