# 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:Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0383//projects/compbio/experiments/protein-predict/casp7/T0383/align.constraints_v3.costfcn or /projects/compbio/experiments/protein-predict/casp7/T0383//projects/compbio/experiments/protein-predict/casp7/T0383/align.constraints_v3.costfcn.gz for input Trying /projects/compbio/experiments/protein-predict/casp7/T0383/align.constraints_v3.costfcn # reading script from file /projects/compbio/experiments/protein-predict/casp7/T0383/align.constraints_v3.costfcn # future Constraint commands -> align # future HelixConstraint commands -> align # future StrandConstraint commands -> align # future SheetConstraint commands -> align # future Hbond commands -> align # future SSbond commands -> align # Constraint # added constraint: constraint((T0383)L58.CB, (T0383)I73.CB) [> 4.2645 = 7.1075 < 9.2398] w=0.9795 to align # Constraint # added constraint: constraint((T0383)I57.CB, (T0383)T72.CB) [> 3.6845 = 6.1408 < 7.9830] w=0.9795 to align # Constraint # added constraint: constraint((T0383)V56.CB, (T0383)S74.CB) [> 4.0307 = 6.7179 < 8.7332] w=0.9795 to align # Constraint # added constraint: constraint((T0383)I55.CB, (T0383)Q75.CB) [> 4.1104 = 6.8507 < 8.9059] w=0.9795 to align # Constraint # added constraint: constraint((T0383)I55.CB, (T0383)S74.CB) [> 3.1645 = 5.2742 < 6.8564] w=0.9795 to align # Constraint # added constraint: constraint((T0383)I79.CB, (T0383)L90.CB) [> 4.1731 = 6.9551 < 9.0417] w=0.9453 to align # Constraint # added constraint: constraint((T0383)L58.CB, (T0383)G71.CA) [> 3.5743 = 5.9572 < 7.7444] w=0.9185 to align # Constraint # added constraint: constraint((T0383)F60.CB, (T0383)S70.CB) [> 4.2198 = 7.0331 < 9.1430] w=0.9082 to align # Constraint # added constraint: constraint((T0383)S59.CB, (T0383)G71.CA) [> 3.7817 = 6.3029 < 8.1938] w=0.9082 to align # Constraint # added constraint: constraint((T0383)I57.CB, (T0383)S74.CB) [> 3.5041 = 5.8402 < 7.5923] w=0.8903 to align # Constraint # added constraint: constraint((T0383)I55.CB, (T0383)C102.CB) [> 4.6815 = 7.8026 < 10.1433] w=0.8472 to align # Constraint # added constraint: constraint((T0383)V56.CB, (T0383)T72.CB) [> 4.5427 = 7.5712 < 9.8425] w=0.8472 to align # Constraint # added constraint: constraint((T0383)V56.CB, (T0383)I73.CB) [> 3.3826 = 5.6376 < 7.3289] w=0.8472 to align # Constraint # added constraint: constraint((T0383)S59.CB, (T0383)I69.CB) [> 4.3861 = 7.3101 < 9.5031] w=0.8472 to align # Constraint # added constraint: constraint((T0383)F60.CB, (T0383)I69.CB) [> 2.9573 = 4.9288 < 6.4074] w=0.8472 to align # Constraint # added constraint: constraint((T0383)I73.CB, (T0383)M105.CB) [> 3.4394 = 5.7323 < 7.4520] w=0.8472 to align # Constraint # added constraint: constraint((T0383)Q75.CB, (T0383)P101.CB) [> 3.5367 = 5.8945 < 7.6628] w=0.8472 to align # Constraint # added constraint: constraint((T0383)N77.CB, (T0383)L98.CB) [> 3.3340 = 5.5567 < 7.2237] w=0.8472 to align # Constraint # added constraint: constraint((T0383)M61.CB, (T0383)S70.CB) [> 3.5543 = 5.9239 < 7.7011] w=0.8294 to align # Constraint # added constraint: constraint((T0383)I55.CB, (T0383)N77.CB) [> 3.9434 = 6.5723 < 8.5440] w=0.8227 to align # Constraint # added constraint: constraint((T0383)S59.CB, (T0383)T72.CB) [> 4.4063 = 7.3439 < 9.5471] w=0.8191 to align # Constraint # added constraint: constraint((T0383)D80.CB, (T0383)L90.CB) [> 4.0811 = 6.8018 < 8.8423] w=0.7526 to align # Constraint # added constraint: constraint((T0383)I79.CB, (T0383)V95.CB) [> 3.9155 = 6.5259 < 8.4837] w=0.7526 to align # Constraint # added constraint: constraint((T0383)I57.CB, (T0383)I73.CB) [> 3.7227 = 6.2045 < 8.0659] w=0.7355 to align # Constraint # added constraint: constraint((T0383)L58.CB, (T0383)T72.CB) [> 4.1170 = 6.8617 < 8.9202] w=0.7355 to align # Constraint # added constraint: constraint((T0383)L54.CB, (T0383)V76.CB) [> 4.6626 = 7.7710 < 10.1023] w=0.6887 to align # Constraint # added constraint: constraint((T0383)V51.CB, (T0383)N77.CB) [> 4.3636 = 7.2727 < 9.4545] w=0.6850 to align # Constraint # added constraint: constraint((T0383)V51.CB, (T0383)V76.CB) [> 3.8060 = 6.3433 < 8.2463] w=0.6850 to align # Constraint # added constraint: constraint((T0383)Q50.CB, (T0383)I79.CB) [> 3.4491 = 5.7485 < 7.4731] w=0.6783 to align # Constraint # added constraint: constraint((T0383)T114.CB, (T0383)I123.CB) [> 3.5888 = 5.9813 < 7.7758] w=0.6313 to align # Constraint # added constraint: constraint((T0383)G81.CA, (T0383)L90.CB) [> 2.9004 = 4.8341 < 6.2843] w=0.6290 to align # Constraint # added constraint: constraint((T0383)S53.CB, (T0383)N77.CB) [> 4.4977 = 7.4961 < 9.7450] w=0.6277 to align # Constraint # added constraint: constraint((T0383)S53.CB, (T0383)V76.CB) [> 3.0254 = 5.0422 < 6.5549] w=0.6277 to align # Constraint # added constraint: constraint((T0383)I55.CB, (T0383)L98.CB) [> 4.2482 = 7.0803 < 9.2044] w=0.6229 to align # Constraint # added constraint: constraint((T0383)V76.CB, (T0383)C102.CB) [> 4.0187 = 6.6979 < 8.7072] w=0.6223 to align # Constraint # added constraint: constraint((T0383)V51.CB, (T0383)H78.CB) [> 3.3788 = 5.6314 < 7.3208] w=0.6174 to align # Constraint # added constraint: constraint((T0383)L58.CB, (T0383)I69.CB) [> 4.2696 = 7.1160 < 9.2508] w=0.6033 to align # Constraint # added constraint: constraint((T0383)L58.CB, (T0383)S74.CB) [> 3.7636 = 6.2726 < 8.1544] w=0.5995 to align # Constraint # added constraint: constraint((T0383)V56.CB, (T0383)N77.CB) [> 3.1235 = 5.2058 < 6.7675] w=0.5995 to align # Constraint # added constraint: constraint((T0383)V56.CB, (T0383)L106.CB) [> 3.4656 = 5.7760 < 7.5088] w=0.5668 to align # Constraint # added constraint: constraint((T0383)V113.CB, (T0383)I123.CB) [> 3.6216 = 6.0359 < 7.8467] w=0.5646 to align # Constraint # added constraint: constraint((T0383)T34.CB, (T0383)I62.CB) [> 3.6463 = 6.0771 < 7.9003] w=0.5564 to align # Constraint # added constraint: constraint((T0383)T34.CB, (T0383)V63.CB) [> 3.5078 = 5.8464 < 7.6003] w=0.5564 to align # Constraint # added constraint: constraint((T0383)D37.CB, (T0383)S59.CB) [> 3.3905 = 5.6508 < 7.3460] w=0.5564 to align # Constraint # added constraint: constraint((T0383)N39.CB, (T0383)I57.CB) [> 3.2945 = 5.4909 < 7.1382] w=0.5564 to align # Constraint # added constraint: constraint((T0383)V51.CB, (T0383)I79.CB) [> 4.7786 = 7.9643 < 10.3536] w=0.5564 to align # Constraint # added constraint: constraint((T0383)T52.CB, (T0383)V76.CB) [> 4.4106 = 7.3509 < 9.5562] w=0.5564 to align # Constraint # added constraint: constraint((T0383)T52.CB, (T0383)N77.CB) [> 3.2461 = 5.4102 < 7.0332] w=0.5564 to align # Constraint # added constraint: constraint((T0383)T52.CB, (T0383)I79.CB) [> 3.4585 = 5.7642 < 7.4934] w=0.5564 to align # Constraint # added constraint: constraint((T0383)T52.CB, (T0383)L98.CB) [> 4.6689 = 7.7814 < 10.1159] w=0.5564 to align # Constraint # added constraint: constraint((T0383)S53.CB, (T0383)Q75.CB) [> 4.1564 = 6.9273 < 9.0054] w=0.5564 to align # Constraint # added constraint: constraint((T0383)L54.CB, (T0383)S74.CB) [> 4.0624 = 6.7707 < 8.8019] w=0.5564 to align # Constraint # added constraint: constraint((T0383)L54.CB, (T0383)Q75.CB) [> 3.1476 = 5.2460 < 6.8198] w=0.5564 to align # Constraint # added constraint: constraint((T0383)N29.CB, (T0383)F64.CB) [> 3.3811 = 5.6352 < 7.3257] w=0.5564 to align # Constraint # added constraint: constraint((T0383)D19.CB, (T0383)I69.CB) [> 4.5540 = 7.5901 < 9.8671] w=0.5564 to align # Constraint # added constraint: constraint((T0383)F18.CB, (T0383)I116.CB) [> 4.1288 = 6.8813 < 8.9457] w=0.5564 to align # Constraint # added constraint: constraint((T0383)F18.CB, (T0383)V113.CB) [> 3.7503 = 6.2505 < 8.1256] w=0.5564 to align # Constraint # added constraint: constraint((T0383)F18.CB, (T0383)S70.CB) [> 4.7058 = 7.8430 < 10.1959] w=0.5564 to align # Constraint # added constraint: constraint((T0383)F18.CB, (T0383)I69.CB) [> 2.9750 = 4.9584 < 6.4459] w=0.5564 to align # Constraint # added constraint: constraint((T0383)F18.CB, (T0383)V68.CB) [> 4.3099 = 7.1831 < 9.3381] w=0.5564 to align # Constraint # added constraint: constraint((T0383)F18.CB, (T0383)F67.CB) [> 4.0531 = 6.7552 < 8.7818] w=0.5564 to align # Constraint # added constraint: constraint((T0383)T110.CB, (T0383)I123.CB) [> 3.8436 = 6.4061 < 8.3279] w=0.5564 to align # Constraint # added constraint: constraint((T0383)N107.CB, (T0383)L125.CB) [> 2.8128 = 4.6881 < 6.0945] w=0.5564 to align # Constraint # added constraint: constraint((T0383)L103.CB, (T0383)L125.CB) [> 4.6396 = 7.7326 < 10.0524] w=0.5564 to align # Constraint # added constraint: constraint((T0383)Q75.CB, (T0383)C102.CB) [> 3.1418 = 5.2363 < 6.8072] w=0.5564 to align # Constraint # added constraint: constraint((T0383)Q75.CB, (T0383)L98.CB) [> 3.8528 = 6.4214 < 8.3478] w=0.5564 to align # Constraint # added constraint: constraint((T0383)I73.CB, (T0383)L103.CB) [> 4.6889 = 7.8148 < 10.1593] w=0.5564 to align # Constraint # added constraint: constraint((T0383)I73.CB, (T0383)C102.CB) [> 2.9299 = 4.8832 < 6.3482] w=0.5564 to align # Constraint # added constraint: constraint((T0383)I69.CB, (T0383)V113.CB) [> 3.5725 = 5.9541 < 7.7404] w=0.5564 to align # Constraint # added constraint: constraint((T0383)I62.CB, (T0383)I123.CB) [> 4.5052 = 7.5087 < 9.7614] w=0.5564 to align # Constraint # added constraint: constraint((T0383)F60.CB, (T0383)L125.CB) [> 4.5881 = 7.6469 < 9.9410] w=0.5564 to align # Constraint # added constraint: constraint((T0383)L54.CB, (T0383)L98.CB) [> 2.5050 = 4.1751 < 5.4276] w=0.5564 to align # Constraint # added constraint: constraint((T0383)L54.CB, (T0383)A99.CB) [> 3.7206 = 6.2010 < 8.0613] w=0.5564 to align # Constraint # added constraint: constraint((T0383)L54.CB, (T0383)C102.CB) [> 3.8173 = 6.3622 < 8.2708] w=0.5564 to align # Constraint # added constraint: constraint((T0383)I55.CB, (T0383)T72.CB) [> 3.3769 = 5.6282 < 7.3167] w=0.5564 to align # Constraint # added constraint: constraint((T0383)V56.CB, (T0383)A99.CB) [> 2.9676 = 4.9460 < 6.4298] w=0.5564 to align # Constraint # added constraint: constraint((T0383)V56.CB, (T0383)L103.CB) [> 3.9324 = 6.5540 < 8.5202] w=0.5564 to align # Constraint # added constraint: constraint((T0383)I57.CB, (T0383)S70.CB) [> 4.4876 = 7.4793 < 9.7231] w=0.5564 to align # Constraint # added constraint: constraint((T0383)I57.CB, (T0383)G71.CA) [> 3.8723 = 6.4539 < 8.3901] w=0.5564 to align # Constraint # added constraint: constraint((T0383)L58.CB, (T0383)S70.CB) [> 4.3270 = 7.2116 < 9.3751] w=0.5564 to align # Constraint # added constraint: constraint((T0383)L58.CB, (T0383)L106.CB) [> 2.9809 = 4.9681 < 6.4585] w=0.5564 to align # Constraint # added constraint: constraint((T0383)L58.CB, (T0383)L125.CB) [> 4.3889 = 7.3148 < 9.5092] w=0.5564 to align # Constraint # added constraint: constraint((T0383)F60.CB, (T0383)I123.CB) [> 4.3425 = 7.2375 < 9.4087] w=0.5564 to align # Constraint # added constraint: constraint((T0383)M61.CB, (T0383)G71.CA) [> 3.5393 = 5.8988 < 7.6684] w=0.5386 to align # Constraint # added constraint: constraint((T0383)M61.CB, (T0383)T72.CB) [> 2.5826 = 4.3043 < 5.5956] w=0.5386 to align # Constraint # added constraint: constraint((T0383)M61.CB, (T0383)I73.CB) [> 4.6168 = 7.6946 < 10.0030] w=0.5386 to align # Constraint # added constraint: constraint((T0383)I62.CB, (T0383)G71.CA) [> 3.2702 = 5.4504 < 7.0855] w=0.5386 to align # Constraint # added constraint: constraint((T0383)Q75.CB, (T0383)M105.CB) [> 4.7078 = 7.8463 < 10.2002] w=0.5347 to align # Constraint # added constraint: constraint((T0383)I55.CB, (T0383)V76.CB) [> 3.4672 = 5.7786 < 7.5122] w=0.5319 to align # Constraint # added constraint: constraint((T0383)I83.CB, (T0383)V95.CB) [> 3.9887 = 6.6478 < 8.6422] w=0.5168 to align # Constraint # added constraint: constraint((T0383)I57.CB, (T0383)Q75.CB) [> 4.2866 = 7.1444 < 9.2877] w=0.4673 to align # Constraint # added constraint: constraint((T0383)I57.CB, (T0383)V76.CB) [> 3.5205 = 5.8674 < 7.6277] w=0.4673 to align # Constraint # added constraint: constraint((T0383)I57.CB, (T0383)N77.CB) [> 4.6673 = 7.7789 < 10.1126] w=0.4673 to align # Constraint # added constraint: constraint((T0383)L58.CB, (T0383)Q75.CB) [> 3.8741 = 6.4568 < 8.3938] w=0.4673 to align # Constraint # added constraint: constraint((T0383)L58.CB, (T0383)N77.CB) [> 4.0365 = 6.7275 < 8.7457] w=0.4673 to align # Constraint # added constraint: constraint((T0383)S59.CB, (T0383)S74.CB) [> 2.1525 = 3.5875 < 4.6638] w=0.4673 to align # Constraint # added constraint: constraint((T0383)F60.CB, (T0383)T72.CB) [> 4.4056 = 7.3427 < 9.5455] w=0.4673 to align # Constraint # added constraint: constraint((T0383)F60.CB, (T0383)I73.CB) [> 3.3860 = 5.6434 < 7.3364] w=0.4673 to align # Constraint # added constraint: constraint((T0383)F60.CB, (T0383)S74.CB) [> 4.0189 = 6.6982 < 8.7077] w=0.4673 to align # Constraint # added constraint: constraint((T0383)V76.CB, (T0383)L103.CB) [> 4.2773 = 7.1289 < 9.2676] w=0.4643 to align # Constraint # added constraint: constraint((T0383)V38.CB, (T0383)V56.CB) [> 4.2885 = 7.1475 < 9.2917] w=0.4523 to align # Constraint # added constraint: constraint((T0383)V36.CB, (T0383)M61.CB) [> 4.5541 = 7.5902 < 9.8673] w=0.4523 to align # Constraint # added constraint: constraint((T0383)V36.CB, (T0383)F60.CB) [> 3.2974 = 5.4957 < 7.1444] w=0.4523 to align # Constraint # added constraint: constraint((T0383)V36.CB, (T0383)S59.CB) [> 4.2995 = 7.1659 < 9.3156] w=0.4523 to align # Constraint # added constraint: constraint((T0383)V36.CB, (T0383)L58.CB) [> 4.2728 = 7.1213 < 9.2577] w=0.4523 to align # Constraint # added constraint: constraint((T0383)K35.CB, (T0383)M61.CB) [> 4.1480 = 6.9134 < 8.9874] w=0.4523 to align # Constraint # added constraint: constraint((T0383)K35.CB, (T0383)F60.CB) [> 3.9964 = 6.6607 < 8.6589] w=0.4523 to align # Constraint # added constraint: constraint((T0383)P32.CB, (T0383)D65.CB) [> 3.3109 = 5.5182 < 7.1737] w=0.4523 to align # Constraint # added constraint: constraint((T0383)A31.CB, (T0383)F64.CB) [> 4.2738 = 7.1231 < 9.2600] w=0.4523 to align # Constraint # added constraint: constraint((T0383)L43.CB, (T0383)S53.CB) [> 3.1758 = 5.2929 < 6.8808] w=0.4523 to align # Constraint # added constraint: constraint((T0383)L43.CB, (T0383)T52.CB) [> 3.9777 = 6.6295 < 8.6183] w=0.4523 to align # Constraint # added constraint: constraint((T0383)L42.CB, (T0383)L54.CB) [> 3.5078 = 5.8464 < 7.6003] w=0.4523 to align # Constraint # added constraint: constraint((T0383)L42.CB, (T0383)S53.CB) [> 4.4959 = 7.4932 < 9.7411] w=0.4523 to align # Constraint # added constraint: constraint((T0383)L42.CB, (T0383)T52.CB) [> 3.4763 = 5.7939 < 7.5321] w=0.4523 to align # Constraint # added constraint: constraint((T0383)F40.CB, (T0383)I57.CB) [> 4.2726 = 7.1210 < 9.2573] w=0.4523 to align # Constraint # added constraint: constraint((T0383)F40.CB, (T0383)V56.CB) [> 3.6164 = 6.0273 < 7.8355] w=0.4523 to align # Constraint # added constraint: constraint((T0383)F40.CB, (T0383)L54.CB) [> 4.0922 = 6.8204 < 8.8665] w=0.4523 to align # Constraint # added constraint: constraint((T0383)V38.CB, (T0383)S59.CB) [> 4.5654 = 7.6090 < 9.8918] w=0.4523 to align # Constraint # added constraint: constraint((T0383)V38.CB, (T0383)L58.CB) [> 3.7030 = 6.1717 < 8.0232] w=0.4523 to align # Constraint # added constraint: constraint((T0383)V38.CB, (T0383)I57.CB) [> 4.1887 = 6.9813 < 9.0756] w=0.4523 to align # Constraint # added constraint: constraint((T0383)L106.CB, (T0383)I116.CB) [> 3.6973 = 6.1622 < 8.0108] w=0.4485 to align # Constraint # added constraint: constraint((T0383)Y111.CB, (T0383)I123.CB) [> 3.6547 = 6.0911 < 7.9184] w=0.4401 to align # Constraint # added constraint: constraint((T0383)T110.CB, (T0383)L125.CB) [> 4.0580 = 6.7633 < 8.7923] w=0.4351 to align # Constraint # added constraint: constraint((T0383)L109.CB, (T0383)D119.CB) [> 4.2199 = 7.0331 < 9.1431] w=0.4034 to align # Constraint # added constraint: constraint((T0383)H78.CB, (T0383)V95.CB) [> 3.5527 = 5.9212 < 7.6975] w=0.3967 to align # Constraint # added constraint: constraint((T0383)H78.CB, (T0383)A99.CB) [> 3.9363 = 6.5605 < 8.5286] w=0.3967 to align # Constraint # added constraint: constraint((T0383)E11.CB, (T0383)Q75.CB) [> 2.8133 = 4.6888 < 6.0954] w=0.3709 to align # Constraint # added constraint: constraint((T0383)Q10.CB, (T0383)V76.CB) [> 2.8445 = 4.7408 < 6.1631] w=0.3709 to align # Constraint # added constraint: constraint((T0383)R8.CB, (T0383)P101.CB) [> 4.1778 = 6.9630 < 9.0519] w=0.3709 to align # Constraint # added constraint: constraint((T0383)R8.CB, (T0383)Q75.CB) [> 3.8778 = 6.4630 < 8.4019] w=0.3709 to align # Constraint # added constraint: constraint((T0383)K7.CB, (T0383)H78.CB) [> 2.7145 = 4.5242 < 5.8814] w=0.3709 to align # Constraint # added constraint: constraint((T0383)L6.CB, (T0383)I79.CB) [> 3.6036 = 6.0061 < 7.8079] w=0.3709 to align # Constraint # added constraint: constraint((T0383)L6.CB, (T0383)H78.CB) [> 4.4066 = 7.3443 < 9.5476] w=0.3709 to align # Constraint # added constraint: constraint((T0383)L6.CB, (T0383)N77.CB) [> 4.0916 = 6.8193 < 8.8651] w=0.3709 to align # Constraint # added constraint: constraint((T0383)N5.CB, (T0383)D80.CB) [> 2.6156 = 4.3594 < 5.6673] w=0.3709 to align # Constraint # added constraint: constraint((T0383)H17.CB, (T0383)G71.CA) [> 3.8970 = 6.4950 < 8.4436] w=0.3709 to align # Constraint # added constraint: constraint((T0383)H17.CB, (T0383)I69.CB) [> 4.0589 = 6.7648 < 8.7943] w=0.3709 to align # Constraint # added constraint: constraint((T0383)H17.CB, (T0383)V68.CB) [> 4.3522 = 7.2537 < 9.4298] w=0.3709 to align # Constraint # added constraint: constraint((T0383)Y16.CB, (T0383)T72.CB) [> 4.2871 = 7.1451 < 9.2886] w=0.3709 to align # Constraint # added constraint: constraint((T0383)Y16.CB, (T0383)G71.CA) [> 3.0051 = 5.0084 < 6.5110] w=0.3709 to align # Constraint # added constraint: constraint((T0383)Y16.CB, (T0383)S70.CB) [> 4.3468 = 7.2446 < 9.4180] w=0.3709 to align # Constraint # added constraint: constraint((T0383)Q15.CB, (T0383)T72.CB) [> 2.4125 = 4.0208 < 5.2271] w=0.3709 to align # Constraint # added constraint: constraint((T0383)F12.CB, (T0383)S74.CB) [> 3.3852 = 5.6420 < 7.3346] w=0.3709 to align # Constraint # added constraint: constraint((T0383)F12.CB, (T0383)Q75.CB) [> 4.2790 = 7.1317 < 9.2711] w=0.3709 to align # Constraint # added constraint: constraint((T0383)V13.CB, (T0383)G71.CA) [> 4.1381 = 6.8968 < 8.9658] w=0.3709 to align # Constraint # added constraint: constraint((T0383)V13.CB, (T0383)T72.CB) [> 3.9160 = 6.5266 < 8.4846] w=0.3709 to align # Constraint # added constraint: constraint((T0383)V13.CB, (T0383)I73.CB) [> 3.4231 = 5.7051 < 7.4167] w=0.3709 to align # Constraint # added constraint: constraint((T0383)V13.CB, (T0383)M105.CB) [> 4.7095 = 7.8491 < 10.2038] w=0.3709 to align # Constraint # added constraint: constraint((T0383)R82.CB, (T0383)E94.CB) [> 4.1908 = 6.9847 < 9.0802] w=0.3614 to align # Constraint # added constraint: constraint((T0383)L43.CB, (T0383)L54.CB) [> 4.7006 = 7.8343 < 10.1846] w=0.3585 to align # Constraint # added constraint: constraint((T0383)I79.CB, (T0383)T97.CB) [> 4.6087 = 7.6811 < 9.9854] w=0.3580 to align # Constraint # added constraint: constraint((T0383)E33.CB, (T0383)V63.CB) [> 3.7663 = 6.2772 < 8.1604] w=0.3481 to align # Constraint # added constraint: constraint((T0383)T34.CB, (T0383)F64.CB) [> 4.0465 = 6.7441 < 8.7674] w=0.3481 to align # Constraint # added constraint: constraint((T0383)V36.CB, (T0383)L125.CB) [> 4.3099 = 7.1832 < 9.3381] w=0.3481 to align # Constraint # added constraint: constraint((T0383)L42.CB, (T0383)I55.CB) [> 4.4977 = 7.4962 < 9.7450] w=0.3481 to align # Constraint # added constraint: constraint((T0383)N107.CB, (T0383)I116.CB) [> 3.2028 = 5.3380 < 6.9394] w=0.3321 to align # Constraint # added constraint: constraint((T0383)R108.CB, (T0383)A117.CB) [> 3.5090 = 5.8484 < 7.6029] w=0.3321 to align # Constraint # added constraint: constraint((T0383)R108.CB, (T0383)L118.CB) [> 4.0803 = 6.8005 < 8.8406] w=0.3321 to align # Constraint # added constraint: constraint((T0383)L109.CB, (T0383)L118.CB) [> 3.3527 = 5.5879 < 7.2642] w=0.3321 to align # Constraint # added constraint: constraint((T0383)F18.CB, (T0383)E112.CB) [> 2.5781 = 4.2968 < 5.5858] w=0.3125 to align # Constraint # added constraint: constraint((T0383)F18.CB, (T0383)E115.CB) [> 4.3693 = 7.2821 < 9.4668] w=0.3125 to align # Constraint # added constraint: constraint((T0383)A20.CB, (T0383)I116.CB) [> 2.8713 = 4.7855 < 6.2212] w=0.3125 to align # Constraint # added constraint: constraint((T0383)A20.CB, (T0383)L118.CB) [> 4.7196 = 7.8660 < 10.2257] w=0.3125 to align # Constraint # added constraint: constraint((T0383)F23.CB, (T0383)F67.CB) [> 4.7296 = 7.8826 < 10.2474] w=0.3125 to align # Constraint # added constraint: constraint((T0383)F23.CB, (T0383)I116.CB) [> 4.0883 = 6.8137 < 8.8579] w=0.3125 to align # Constraint # added constraint: constraint((T0383)F60.CB, (T0383)V113.CB) [> 4.7644 = 7.9406 < 10.3228] w=0.3125 to align # Constraint # added constraint: constraint((T0383)I62.CB, (T0383)L118.CB) [> 4.4172 = 7.3621 < 9.5707] w=0.3125 to align # Constraint # added constraint: constraint((T0383)F67.CB, (T0383)V113.CB) [> 4.1605 = 6.9342 < 9.0145] w=0.3125 to align # Constraint # added constraint: constraint((T0383)F67.CB, (T0383)I116.CB) [> 3.2716 = 5.4526 < 7.0884] w=0.3125 to align # Constraint # added constraint: constraint((T0383)F67.CB, (T0383)L118.CB) [> 3.7106 = 6.1843 < 8.0396] w=0.3125 to align # Constraint # added constraint: constraint((T0383)L109.CB, (T0383)I123.CB) [> 4.0858 = 6.8096 < 8.8525] w=0.3125 to align # Constraint # added constraint: constraint((T0383)T110.CB, (T0383)L120.CB) [> 4.0464 = 6.7439 < 8.7671] w=0.3125 to align # Constraint # added constraint: constraint((T0383)T110.CB, (T0383)N124.CB) [> 3.5620 = 5.9367 < 7.7177] w=0.3125 to align # Constraint # added constraint: constraint((T0383)V113.CB, (T0383)L125.CB) [> 3.7978 = 6.3297 < 8.2286] w=0.3076 to align # Constraint # added constraint: constraint((T0383)I55.CB, (T0383)I79.CB) [> 4.7415 = 7.9025 < 10.2733] w=0.2908 to align # Constraint # added constraint: constraint((T0383)I55.CB, (T0383)M105.CB) [> 4.2616 = 7.1027 < 9.2335] w=0.2908 to align # Constraint # added constraint: constraint((T0383)I57.CB, (T0383)M105.CB) [> 3.3908 = 5.6514 < 7.3468] w=0.2908 to align # Constraint # added constraint: constraint((T0383)I55.CB, (T0383)H78.CB) [> 3.3839 = 5.6398 < 7.3317] w=0.2645 to align # Constraint # added constraint: constraint((T0383)K35.CB, (T0383)I123.CB) [> 4.5194 = 7.5323 < 9.7920] w=0.2439 to align # Constraint # added constraint: constraint((T0383)E33.CB, (T0383)P121.CB) [> 4.3628 = 7.2713 < 9.4527] w=0.2439 to align # Constraint # added constraint: constraint((T0383)A31.CB, (T0383)P121.CB) [> 3.6028 = 6.0046 < 7.8060] w=0.2439 to align # Constraint # added constraint: constraint((T0383)N29.CB, (T0383)K66.CB) [> 4.2906 = 7.1510 < 9.2963] w=0.2439 to align # Constraint # added constraint: constraint((T0383)F23.CB, (T0383)A117.CB) [> 4.6189 = 7.6981 < 10.0076] w=0.2439 to align # Constraint # added constraint: constraint((T0383)R21.CB, (T0383)V68.CB) [> 4.6807 = 7.8011 < 10.1414] w=0.2439 to align # Constraint # added constraint: constraint((T0383)A20.CB, (T0383)L120.CB) [> 4.5159 = 7.5265 < 9.7845] w=0.2439 to align # Constraint # added constraint: constraint((T0383)A20.CB, (T0383)A117.CB) [> 2.7726 = 4.6209 < 6.0072] w=0.2439 to align # Constraint # added constraint: constraint((T0383)F18.CB, (T0383)T114.CB) [> 4.5517 = 7.5862 < 9.8620] w=0.2439 to align # Constraint # added constraint: constraint((T0383)Y111.CB, (T0383)N124.CB) [> 3.1420 = 5.2366 < 6.8076] w=0.2439 to align # Constraint # added constraint: constraint((T0383)Y111.CB, (T0383)G122.CA) [> 3.8294 = 6.3823 < 8.2970] w=0.2439 to align # Constraint # added constraint: constraint((T0383)I69.CB, (T0383)T114.CB) [> 3.8155 = 6.3592 < 8.2669] w=0.2439 to align # Constraint # added constraint: constraint((T0383)F67.CB, (T0383)L120.CB) [> 3.6901 = 6.1502 < 7.9953] w=0.2439 to align # Constraint # added constraint: constraint((T0383)F67.CB, (T0383)A117.CB) [> 3.2023 = 5.3372 < 6.9383] w=0.2439 to align # Constraint # added constraint: constraint((T0383)I62.CB, (T0383)L120.CB) [> 4.4161 = 7.3601 < 9.5682] w=0.2439 to align # Constraint # added constraint: constraint((T0383)I62.CB, (T0383)T114.CB) [> 4.7605 = 7.9341 < 10.3143] w=0.2439 to align # Constraint # added constraint: constraint((T0383)K7.CB, (T0383)I79.CB) [> 4.7087 = 7.8478 < 10.2022] w=0.2083 to align # Constraint # added constraint: constraint((T0383)R8.CB, (T0383)V76.CB) [> 4.5269 = 7.5448 < 9.8082] w=0.2083 to align # Constraint # added constraint: constraint((T0383)F12.CB, (T0383)I73.CB) [> 4.6768 = 7.7946 < 10.1330] w=0.2083 to align # Constraint # added constraint: constraint((T0383)Y16.CB, (T0383)E112.CB) [> 4.3349 = 7.2249 < 9.3924] w=0.2083 to align # Constraint # added constraint: constraint((T0383)T34.CB, (T0383)F60.CB) [> 3.9997 = 6.6662 < 8.6660] w=0.2083 to align # Constraint # added constraint: constraint((T0383)T34.CB, (T0383)M61.CB) [> 3.1792 = 5.2987 < 6.8883] w=0.2083 to align # Constraint # added constraint: constraint((T0383)D37.CB, (T0383)M61.CB) [> 3.3777 = 5.6295 < 7.3184] w=0.2083 to align # Constraint # added constraint: constraint((T0383)N39.CB, (T0383)S59.CB) [> 3.5352 = 5.8920 < 7.6596] w=0.2083 to align # Constraint # added constraint: constraint((T0383)V56.CB, (T0383)V84.CB) [> 3.9028 = 6.5047 < 8.4561] w=0.2028 to align # Constraint # added constraint: constraint((T0383)V76.CB, (T0383)L98.CB) [> 4.2549 = 7.0915 < 9.2189] w=0.2024 to align # Constraint # added constraint: constraint((T0383)I79.CB, (T0383)V113.CB) [> 3.2629 = 5.4382 < 7.0697] w=0.1962 to align # Constraint # added constraint: constraint((T0383)I79.CB, (T0383)A117.CB) [> 3.0764 = 5.1273 < 6.6656] w=0.1962 to align # Constraint # added constraint: constraint((T0383)V95.CB, (T0383)A117.CB) [> 2.9604 = 4.9340 < 6.4142] w=0.1962 to align # Constraint # added constraint: constraint((T0383)E96.CB, (T0383)I116.CB) [> 3.3916 = 5.6527 < 7.3485] w=0.1962 to align # Constraint # added constraint: constraint((T0383)A99.CB, (T0383)I116.CB) [> 4.4734 = 7.4557 < 9.6924] w=0.1962 to align # Constraint # added constraint: constraint((T0383)A99.CB, (T0383)L118.CB) [> 3.2563 = 5.4271 < 7.0552] w=0.1962 to align # Constraint # added constraint: constraint((T0383)A99.CB, (T0383)D119.CB) [> 4.2031 = 7.0052 < 9.1067] w=0.1962 to align # Constraint # added constraint: constraint((T0383)C102.CB, (T0383)A117.CB) [> 3.8180 = 6.3633 < 8.2723] w=0.1962 to align # Constraint # added constraint: constraint((T0383)M4.CB, (T0383)S70.CB) [> 4.4368 = 7.3947 < 9.6131] w=0.1855 to align # Constraint # added constraint: constraint((T0383)M4.CB, (T0383)G71.CA) [> 3.1553 = 5.2588 < 6.8365] w=0.1855 to align # Constraint # added constraint: constraint((T0383)M4.CB, (T0383)T72.CB) [> 4.3836 = 7.3060 < 9.4978] w=0.1855 to align # Constraint # added constraint: constraint((T0383)F12.CB, (T0383)V76.CB) [> 4.6417 = 7.7361 < 10.0570] w=0.1626 to align # Constraint # added constraint: constraint((T0383)Y16.CB, (T0383)I69.CB) [> 4.6954 = 7.8257 < 10.1734] w=0.1626 to align # Constraint # added constraint: constraint((T0383)Y16.CB, (T0383)L109.CB) [> 3.7014 = 6.1689 < 8.0196] w=0.1626 to align # Constraint # added constraint: constraint((T0383)Y16.CB, (T0383)V113.CB) [> 4.4356 = 7.3927 < 9.6105] w=0.1626 to align # Constraint # added constraint: constraint((T0383)L103.CB, (T0383)A117.CB) [> 3.8586 = 6.4311 < 8.3604] w=0.1352 to align # Constraint # added constraint: constraint((T0383)I55.CB, (T0383)V84.CB) [> 4.4848 = 7.4747 < 9.7171] w=0.1352 to align # Constraint # added constraint: constraint((T0383)P87.CB, (T0383)L98.CB) [> 4.5844 = 7.6407 < 9.9330] w=0.1343 to align # Constraint # added constraint: constraint((T0383)L54.CB, (T0383)H78.CB) [> 4.7709 = 7.9515 < 10.3369] w=0.1322 to align # Constraint # added constraint: constraint((T0383)I116.CB, (T0383)L125.CB) [> 4.0717 = 6.7862 < 8.8220] w=0.1165 to align # Constraint # added constraint: constraint((T0383)L106.CB, (T0383)E115.CB) [> 3.3820 = 5.6367 < 7.3277] w=0.1165 to align # Constraint # added constraint: constraint((T0383)M105.CB, (T0383)T114.CB) [> 3.5279 = 5.8798 < 7.6437] w=0.1165 to align # Constraint # added constraint: constraint((T0383)N104.CB, (T0383)T114.CB) [> 3.5552 = 5.9254 < 7.7030] w=0.1165 to align # Constraint # added constraint: constraint((T0383)V36.CB, (T0383)E126.CB) [> 4.7702 = 7.9504 < 10.3355] w=0.1042 to align # Constraint # added constraint: constraint((T0383)V36.CB, (T0383)I123.CB) [> 4.1615 = 6.9359 < 9.0166] w=0.1042 to align # Constraint # added constraint: constraint((T0383)V36.CB, (T0383)I62.CB) [> 3.0635 = 5.1058 < 6.6375] w=0.1042 to align # Constraint # added constraint: constraint((T0383)V36.CB, (T0383)I57.CB) [> 4.3308 = 7.2181 < 9.3835] w=0.1042 to align # Constraint # added constraint: constraint((T0383)K35.CB, (T0383)E126.CB) [> 4.7810 = 7.9684 < 10.3589] w=0.1042 to align # Constraint # added constraint: constraint((T0383)P32.CB, (T0383)D119.CB) [> 3.6677 = 6.1129 < 7.9468] w=0.1042 to align # Constraint # added constraint: constraint((T0383)P32.CB, (T0383)L118.CB) [> 4.7235 = 7.8726 < 10.2343] w=0.1042 to align # Constraint # added constraint: constraint((T0383)P32.CB, (T0383)V63.CB) [> 2.7293 = 4.5489 < 5.9136] w=0.1042 to align # Constraint # added constraint: constraint((T0383)A31.CB, (T0383)D119.CB) [> 3.6084 = 6.0140 < 7.8182] w=0.1042 to align # Constraint # added constraint: constraint((T0383)A31.CB, (T0383)V63.CB) [> 3.8693 = 6.4488 < 8.3834] w=0.1042 to align # Constraint # added constraint: constraint((T0383)N29.CB, (T0383)D119.CB) [> 3.6568 = 6.0947 < 7.9231] w=0.1042 to align # Constraint # added constraint: constraint((T0383)M4.CB, (T0383)E112.CB) [> 4.3328 = 7.2214 < 9.3878] w=0.1042 to align # Constraint # added constraint: constraint((T0383)D37.CB, (T0383)V63.CB) [> 4.4445 = 7.4075 < 9.6298] w=0.1042 to align # Constraint # added constraint: constraint((T0383)V38.CB, (T0383)L54.CB) [> 4.3973 = 7.3288 < 9.5275] w=0.1042 to align # Constraint # added constraint: constraint((T0383)V38.CB, (T0383)I55.CB) [> 4.5020 = 7.5033 < 9.7543] w=0.1042 to align # Constraint # added constraint: constraint((T0383)V38.CB, (T0383)F60.CB) [> 3.6356 = 6.0593 < 7.8770] w=0.1042 to align # Constraint # added constraint: constraint((T0383)V38.CB, (T0383)L125.CB) [> 4.1359 = 6.8932 < 8.9611] w=0.1042 to align # Constraint # added constraint: constraint((T0383)V38.CB, (T0383)E126.CB) [> 4.7644 = 7.9407 < 10.3229] w=0.1042 to align # Constraint # added constraint: constraint((T0383)N39.CB, (T0383)L54.CB) [> 4.5586 = 7.5977 < 9.8770] w=0.1042 to align # Constraint # added constraint: constraint((T0383)N39.CB, (T0383)F60.CB) [> 4.7674 = 7.9457 < 10.3295] w=0.1042 to align # Constraint # added constraint: constraint((T0383)A3.CB, (T0383)S70.CB) [> 4.4976 = 7.4960 < 9.7448] w=0.0813 to align # Constraint # added constraint: constraint((T0383)A3.CB, (T0383)T72.CB) [> 2.3090 = 3.8484 < 5.0029] w=0.0813 to align # Constraint # added constraint: constraint((T0383)M4.CB, (T0383)D80.CB) [> 3.9499 = 6.5831 < 8.5580] w=0.0813 to align # Constraint # added constraint: constraint((T0383)S53.CB, (T0383)H78.CB) [> 3.4934 = 5.8224 < 7.5691] w=0.0713 to align # Constraint # added constraint: constraint((T0383)R100.CB, (T0383)E112.CB) [> 3.7875 = 6.3125 < 8.2063] w=0.0676 to align # Constraint # added constraint: constraint((T0383)L106.CB, (T0383)L118.CB) [> 4.2363 = 7.0605 < 9.1786] w=0.0676 to align # Constraint # added constraint: constraint((T0383)L106.CB, (T0383)A117.CB) [> 3.2187 = 5.3645 < 6.9739] w=0.0676 to align # Constraint # added constraint: constraint((T0383)I79.CB, (T0383)P101.CB) [> 2.9275 = 4.8792 < 6.3430] w=0.0672 to align # Constraint # added constraint: constraint((T0383)T72.CB, (T0383)L109.CB) [> 3.7552 = 6.2586 < 8.1362] w=0.0432 to align # Constraint # added constraint: constraint((T0383)Q75.CB, (T0383)V84.CB) [> 4.3252 = 7.2087 < 9.3713] w=0.0208 to align # Constraint # added constraint: constraint((T0383)I62.CB, (T0383)V84.CB) [> 3.6663 = 6.1104 < 7.9436] w=0.0104 to align # Constraint # added constraint: constraint((T0383)V63.CB, (T0383)I83.CB) [> 2.2358 = 3.7263 < 4.8442] w=0.0104 to align # Constraint # added constraint: constraint((T0383)F64.CB, (T0383)I83.CB) [> 4.0281 = 6.7135 < 8.7276] w=0.0104 to align # Constraint # added constraint: constraint((T0383)D65.CB, (T0383)I83.CB) [> 3.0436 = 5.0726 < 6.5944] w=0.0104 to align # SetCost created cost = # ( 1.0000 * align ) # command:# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0383/ # command:# reading script from file servers-clean.under # Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/T0383/decoys/ # ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS1.pdb.gz looking for model 1 # Found a chain break before 119 # copying to AlignedFragments data structure # naming current conformation 3D-JIGSAW_POPULUS_TS1 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0383 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_POPULUS_TS2 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS3.pdb.gz looking for model 1 # Found a chain break before 120 # copying to AlignedFragments data structure # naming current conformation 3D-JIGSAW_POPULUS_TS3 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0383 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_POPULUS_TS4 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS5.pdb.gz looking for model 1 # Found a chain break before 119 # copying to AlignedFragments data structure # naming current conformation 3D-JIGSAW_POPULUS_TS5 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_RECOM_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0383 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_RECOM_TS1 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_RECOM_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0383 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_RECOM_TS2 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_RECOM_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0383 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_RECOM_TS3 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_RECOM_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0383 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_RECOM_TS4 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_RECOM_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0383 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_RECOM_TS5 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0383 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_TS1 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0383 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_TS2 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0383 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_TS3 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0383 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_TS4 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0383 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_TS5 # ReadConformPDB reading from PDB file servers/3Dpro_TS1.pdb.gz looking for model 1 # naming current conformation 3Dpro_TS1 # ReadConformPDB reading from PDB file servers/3Dpro_TS2.pdb.gz looking for model 1 # Found a chain break before 116 # copying to AlignedFragments data structure # naming current conformation 3Dpro_TS2 # ReadConformPDB reading from PDB file servers/3Dpro_TS3.pdb.gz looking for model 1 # Found a chain break before 88 # copying to AlignedFragments data structure # naming current conformation 3Dpro_TS3 # ReadConformPDB reading from PDB file servers/3Dpro_TS4.pdb.gz looking for model 1 # Found a chain break before 59 # copying to AlignedFragments data structure # naming current conformation 3Dpro_TS4 # ReadConformPDB reading from PDB file servers/3Dpro_TS5.pdb.gz looking for model 1 # Found a chain break before 100 # copying to AlignedFragments data structure # naming current conformation 3Dpro_TS5 # ReadConformPDB reading from PDB file servers/ABIpro_TS1.pdb.gz looking for model 1 # Found a chain break before 100 # copying to AlignedFragments data structure # naming current conformation ABIpro_TS1 # ReadConformPDB reading from PDB file servers/ABIpro_TS2.pdb.gz looking for model 1 # Found a chain break before 118 # copying to AlignedFragments data structure # naming current conformation ABIpro_TS2 # ReadConformPDB reading from PDB file servers/ABIpro_TS3.pdb.gz looking for model 1 # Found a chain break before 123 # copying to AlignedFragments data structure # naming current conformation ABIpro_TS3 # ReadConformPDB reading from PDB file servers/ABIpro_TS4.pdb.gz looking for model 1 # Found a chain break before 123 # copying to AlignedFragments data structure # naming current conformation ABIpro_TS4 # ReadConformPDB reading from PDB file servers/ABIpro_TS5.pdb.gz looking for model 1 # Found a chain break before 117 # copying to AlignedFragments data structure # naming current conformation ABIpro_TS5 # ReadConformPDB reading from PDB file servers/BayesHH_TS1.pdb.gz looking for model 1 # Found a chain break before 111 # copying to AlignedFragments data structure # naming current conformation BayesHH_TS1 # ReadConformPDB reading from PDB file servers/Bilab-ENABLE_TS1.pdb.gz looking for model 1 # naming current conformation Bilab-ENABLE_TS1 # ReadConformPDB reading from PDB file servers/Bilab-ENABLE_TS2.pdb.gz looking for model 1 # naming current conformation Bilab-ENABLE_TS2 # ReadConformPDB reading from PDB file servers/Bilab-ENABLE_TS3.pdb.gz looking for model 1 # naming current conformation Bilab-ENABLE_TS3 # ReadConformPDB reading from PDB file servers/Bilab-ENABLE_TS4.pdb.gz looking for model 1 # Found a chain break before 126 # copying to AlignedFragments data structure # naming current conformation Bilab-ENABLE_TS4 # ReadConformPDB reading from PDB file servers/Bilab-ENABLE_TS5.pdb.gz looking for model 1 # Found a chain break before 126 # copying to AlignedFragments data structure # naming current conformation Bilab-ENABLE_TS5 # ReadConformPDB reading from PDB file servers/CIRCLE_TS1.pdb.gz looking for model 1 # Found a chain break before 117 # copying to AlignedFragments data structure # naming current conformation CIRCLE_TS1 # ReadConformPDB reading from PDB file servers/CIRCLE_TS2.pdb.gz looking for model 1 # Found a chain break before 120 # copying to AlignedFragments data structure # naming current conformation CIRCLE_TS2 # ReadConformPDB reading from PDB file servers/CIRCLE_TS3.pdb.gz looking for model 1 # Found a chain break before 117 # copying to AlignedFragments data structure # naming current conformation CIRCLE_TS3 # ReadConformPDB reading from PDB file servers/CIRCLE_TS4.pdb.gz looking for model 1 # Found a chain break before 115 # copying to AlignedFragments data structure # naming current conformation CIRCLE_TS4 # ReadConformPDB reading from PDB file servers/CIRCLE_TS5.pdb.gz looking for model 1 # Found a chain break before 126 # copying to AlignedFragments data structure # naming current conformation CIRCLE_TS5 # ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0383 can't currently be optimized by undertaker # naming current conformation CaspIta-FOX_TS1 # ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0383 can't currently be optimized by undertaker # naming current conformation CaspIta-FOX_TS2 # ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0383 can't currently be optimized by undertaker # naming current conformation CaspIta-FOX_TS3 # ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0383 can't currently be optimized by undertaker # naming current conformation CaspIta-FOX_TS4 # ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0383 can't currently be optimized by undertaker # naming current conformation CaspIta-FOX_TS5 # ReadConformPDB reading from PDB file servers/Distill_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0383 can't currently be optimized by undertaker # naming current conformation Distill_TS1 # ReadConformPDB reading from PDB file servers/Distill_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0383 can't currently be optimized by undertaker # naming current conformation Distill_TS2 # ReadConformPDB reading from PDB file servers/Distill_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0383 can't currently be optimized by undertaker # naming current conformation Distill_TS3 # ReadConformPDB reading from PDB file servers/Distill_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0383 can't currently be optimized by undertaker # naming current conformation Distill_TS4 # ReadConformPDB reading from PDB file servers/Distill_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0383 can't currently be optimized by undertaker # naming current conformation Distill_TS5 # ReadConformPDB reading from PDB file servers/FAMSD_TS1.pdb.gz looking for model 1 # Found a chain break before 117 # copying to AlignedFragments data structure # naming current conformation FAMSD_TS1 # ReadConformPDB reading from PDB file servers/FAMSD_TS2.pdb.gz looking for model 1 # Found a chain break before 120 # copying to AlignedFragments data structure # naming current conformation FAMSD_TS2 # ReadConformPDB reading from PDB file servers/FAMSD_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0383 can't currently be optimized by undertaker # naming current conformation FAMSD_TS3 # ReadConformPDB reading from PDB file servers/FAMSD_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0383 can't currently be optimized by undertaker # naming current conformation FAMSD_TS4 # ReadConformPDB reading from PDB file servers/FAMSD_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0383 can't currently be optimized by undertaker # naming current conformation FAMSD_TS5 # ReadConformPDB reading from PDB file servers/FAMS_TS1.pdb.gz looking for model 1 # Found a chain break before 121 # copying to AlignedFragments data structure # naming current conformation FAMS_TS1 # ReadConformPDB reading from PDB file servers/FAMS_TS2.pdb.gz looking for model 1 # Found a chain break before 117 # copying to AlignedFragments data structure # naming current conformation FAMS_TS2 # ReadConformPDB reading from PDB file servers/FAMS_TS3.pdb.gz looking for model 1 # Found a chain break before 120 # copying to AlignedFragments data structure # naming current conformation FAMS_TS3 # ReadConformPDB reading from PDB file servers/FAMS_TS4.pdb.gz looking for model 1 # Found a chain break before 120 # copying to AlignedFragments data structure # naming current conformation FAMS_TS4 # ReadConformPDB reading from PDB file servers/FAMS_TS5.pdb.gz looking for model 1 # Found a chain break before 117 # copying to AlignedFragments data structure # naming current conformation FAMS_TS5 # ReadConformPDB reading from PDB file servers/FOLDpro_TS1.pdb.gz looking for model 1 # naming current conformation FOLDpro_TS1 # ReadConformPDB reading from PDB file servers/FOLDpro_TS2.pdb.gz looking for model 1 # Found a chain break before 116 # copying to AlignedFragments data structure # naming current conformation FOLDpro_TS2 # ReadConformPDB reading from PDB file servers/FOLDpro_TS3.pdb.gz looking for model 1 # Found a chain break before 88 # copying to AlignedFragments data structure # naming current conformation FOLDpro_TS3 # ReadConformPDB reading from PDB file servers/FOLDpro_TS4.pdb.gz looking for model 1 # Found a chain break before 59 # copying to AlignedFragments data structure # naming current conformation FOLDpro_TS4 # ReadConformPDB reading from PDB file servers/FOLDpro_TS5.pdb.gz looking for model 1 # naming current conformation FOLDpro_TS5 # ReadConformPDB reading from PDB file servers/FORTE1_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0383 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation FORTE1_AL1 # ReadConformPDB reading from PDB file servers/FORTE1_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0383 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation FORTE1_AL2 # ReadConformPDB reading from PDB file servers/FORTE1_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0383 can't currently be optimized by undertaker # naming current conformation FORTE1_AL3 # ReadConformPDB reading from PDB file servers/FORTE1_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0383 can't currently be optimized by undertaker # naming current conformation FORTE1_AL4 # ReadConformPDB reading from PDB file servers/FORTE1_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0383 can't currently be optimized by undertaker # naming current conformation FORTE1_AL5 # ReadConformPDB reading from PDB file servers/FORTE2_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0383 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation FORTE2_AL1 # ReadConformPDB reading from PDB file servers/FORTE2_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0383 can't currently be optimized by undertaker # naming current conformation FORTE2_AL2 # ReadConformPDB reading from PDB file servers/FORTE2_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0383 can't currently be optimized by undertaker # naming current conformation FORTE2_AL3 # ReadConformPDB reading from PDB file servers/FORTE2_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0383 can't currently be optimized by undertaker # naming current conformation FORTE2_AL4 # ReadConformPDB reading from PDB file servers/FORTE2_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0383 can't currently be optimized by undertaker # naming current conformation FORTE2_AL5 # ReadConformPDB reading from PDB file servers/FPSOLVER-SERVER_TS1.pdb.gz looking for model 1 # Found a chain break before 107 # copying to AlignedFragments data structure # naming current conformation FPSOLVER-SERVER_TS1 # ReadConformPDB reading from PDB file servers/FPSOLVER-SERVER_TS2.pdb.gz looking for model 1 # Found a chain break before 109 # copying to AlignedFragments data structure # naming current conformation FPSOLVER-SERVER_TS2 # ReadConformPDB reading from PDB file servers/FPSOLVER-SERVER_TS3.pdb.gz looking for model 1 # naming current conformation FPSOLVER-SERVER_TS3 # ReadConformPDB reading from PDB file servers/FPSOLVER-SERVER_TS4.pdb.gz looking for model 1 # Found a chain break before 113 # copying to AlignedFragments data structure # naming current conformation FPSOLVER-SERVER_TS4 # ReadConformPDB reading from PDB file servers/FPSOLVER-SERVER_TS5.pdb.gz looking for model 1 # Found a chain break before 48 # copying to AlignedFragments data structure # naming current conformation FPSOLVER-SERVER_TS5 # ReadConformPDB reading from PDB file servers/FUGMOD_TS1.pdb.gz looking for model 1 # naming current conformation FUGMOD_TS1 # ReadConformPDB reading from PDB file servers/FUGMOD_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0383 can't currently be optimized by undertaker # naming current conformation FUGMOD_TS2 # ReadConformPDB reading from PDB file servers/FUGMOD_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0383 can't currently be optimized by undertaker # naming current conformation FUGMOD_TS3 # ReadConformPDB reading from PDB file servers/FUGMOD_TS4.pdb.gz looking for model 1 # naming current conformation FUGMOD_TS4 # ReadConformPDB reading from PDB file servers/FUGMOD_TS5.pdb.gz looking for model 1 # Found a chain break before 30 # copying to AlignedFragments data structure # naming current conformation FUGMOD_TS5 # ReadConformPDB reading from PDB file servers/FUGUE_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0383 can't currently be optimized by undertaker # naming current conformation FUGUE_AL1 # ReadConformPDB reading from PDB file servers/FUGUE_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0383 can't currently be optimized by undertaker # naming current conformation FUGUE_AL2 # ReadConformPDB reading from PDB file servers/FUGUE_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0383 can't currently be optimized by undertaker # naming current conformation FUGUE_AL3 # ReadConformPDB reading from PDB file servers/FUGUE_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0383 can't currently be optimized by undertaker # naming current conformation FUGUE_AL4 # ReadConformPDB reading from PDB file servers/FUGUE_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0383 can't currently be optimized by undertaker # naming current conformation FUGUE_AL5 # ReadConformPDB reading from PDB file servers/FUNCTION_TS1.pdb.gz looking for model 1 # Found a chain break before 120 # copying to AlignedFragments data structure # naming current conformation FUNCTION_TS1 # ReadConformPDB reading from PDB file servers/FUNCTION_TS2.pdb.gz looking for model 1 # Found a chain break before 122 # copying to AlignedFragments data structure # naming current conformation FUNCTION_TS2 # ReadConformPDB reading from PDB file servers/FUNCTION_TS3.pdb.gz looking for model 1 # Found a chain break before 124 # copying to AlignedFragments data structure # naming current conformation FUNCTION_TS3 # ReadConformPDB reading from PDB file servers/FUNCTION_TS4.pdb.gz looking for model 1 # Found a chain break before 122 # copying to AlignedFragments data structure # naming current conformation FUNCTION_TS4 # ReadConformPDB reading from PDB file servers/FUNCTION_TS5.pdb.gz looking for model 1 # Found a chain break before 120 # copying to AlignedFragments data structure # naming current conformation FUNCTION_TS5 # ReadConformPDB reading from PDB file servers/Frankenstein_TS1.pdb.gz looking for model 1 # Found a chain break before 86 # copying to AlignedFragments data structure # naming current conformation Frankenstein_TS1 # ReadConformPDB reading from PDB file servers/Frankenstein_TS2.pdb.gz looking for model 1 # Found a chain break before 101 # copying to AlignedFragments data structure # naming current conformation Frankenstein_TS2 # ReadConformPDB reading from PDB file servers/Frankenstein_TS3.pdb.gz looking for model 1 # Found a chain break before 86 # copying to AlignedFragments data structure # naming current conformation Frankenstein_TS3 # ReadConformPDB reading from PDB file servers/Frankenstein_TS4.pdb.gz looking for model 1 # Found a chain break before 19 # copying to AlignedFragments data structure # naming current conformation Frankenstein_TS4 # ReadConformPDB reading from PDB file servers/Frankenstein_TS5.pdb.gz looking for model 1 # Found a chain break before 38 # copying to AlignedFragments data structure # naming current conformation Frankenstein_TS5 # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS1.pdb.gz looking for model 1 # Found a chain break before 74 # copying to AlignedFragments data structure # naming current conformation GeneSilicoMetaServer_TS1 # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0383 can't currently be optimized by undertaker # naming current conformation GeneSilicoMetaServer_TS2 # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0383 can't currently be optimized by undertaker # naming current conformation GeneSilicoMetaServer_TS3 # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0383 can't currently be optimized by undertaker # naming current conformation GeneSilicoMetaServer_TS4 # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS5.pdb.gz looking for model 1 # Found a chain break before 86 # copying to AlignedFragments data structure # naming current conformation GeneSilicoMetaServer_TS5 # ReadConformPDB reading from PDB file servers/HHpred1_TS1.pdb.gz looking for model 1 # Found a chain break before 66 # copying to AlignedFragments data structure # naming current conformation HHpred1_TS1 # ReadConformPDB reading from PDB file servers/HHpred2_TS1.pdb.gz looking for model 1 # Found a chain break before 66 # copying to AlignedFragments data structure # naming current conformation HHpred2_TS1 # ReadConformPDB reading from PDB file servers/HHpred3_TS1.pdb.gz looking for model 1 # Found a chain break before 62 # copying to AlignedFragments data structure # naming current conformation HHpred3_TS1 # ReadConformPDB reading from PDB file servers/Huber-Torda-Server_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0383 can't currently be optimized by undertaker # naming current conformation Huber-Torda-Server_TS1 # ReadConformPDB reading from PDB file servers/Huber-Torda-Server_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0383 can't currently be optimized by undertaker # naming current conformation Huber-Torda-Server_TS2 # ReadConformPDB reading from PDB file servers/Huber-Torda-Server_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0383 can't currently be optimized by undertaker # naming current conformation Huber-Torda-Server_TS3 # ReadConformPDB reading from PDB file servers/Huber-Torda-Server_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0383 can't currently be optimized by undertaker # naming current conformation Huber-Torda-Server_TS4 # ReadConformPDB reading from PDB file servers/Huber-Torda-Server_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0383 can't currently be optimized by undertaker # naming current conformation Huber-Torda-Server_TS5 # ReadConformPDB reading from PDB file servers/LOOPP_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0383 can't currently be optimized by undertaker # naming current conformation LOOPP_TS1 # ReadConformPDB reading from PDB file servers/LOOPP_TS2.pdb.gz looking for model 1 # naming current conformation LOOPP_TS2 # ReadConformPDB reading from PDB file servers/LOOPP_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0383 can't currently be optimized by undertaker # naming current conformation LOOPP_TS3 # ReadConformPDB reading from PDB file servers/LOOPP_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0383 can't currently be optimized by undertaker # naming current conformation LOOPP_TS4 # ReadConformPDB reading from PDB file servers/LOOPP_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0383 can't currently be optimized by undertaker # naming current conformation LOOPP_TS5 # ReadConformPDB reading from PDB file servers/MIG_FROST_AL1.pdb.gz looking for model 1 Error: Reading chain '' from PDB file servers/MIG_FROST_AL1.pdb.gz failed---no such chain. # naming current conformation MIG_FROST_AL1 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server2_TS1.pdb.gz looking for model 1 # Found a chain break before 54 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server2_TS1 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server2_TS2.pdb.gz looking for model 1 # naming current conformation Ma-OPUS-server2_TS2 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server2_TS3.pdb.gz looking for model 1 # Found a chain break before 7 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server2_TS3 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server2_TS4.pdb.gz looking for model 1 # Found a chain break before 81 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server2_TS4 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server2_TS5.pdb.gz looking for model 1 # Found a chain break before 120 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server2_TS5 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS1.pdb.gz looking for model 1 # naming current conformation Ma-OPUS-server_TS1 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS2.pdb.gz looking for model 1 # Found a chain break before 38 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server_TS2 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS3.pdb.gz looking for model 1 # naming current conformation Ma-OPUS-server_TS3 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS4.pdb.gz looking for model 1 # Found a chain break before 7 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server_TS4 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS5.pdb.gz looking for model 1 # Found a chain break before 81 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server_TS5 # ReadConformPDB reading from PDB file servers/MetaTasser_TS1.pdb.gz looking for model 1 # Found a chain break before 125 # copying to AlignedFragments data structure # naming current conformation MetaTasser_TS1 # ReadConformPDB reading from PDB file servers/MetaTasser_TS2.pdb.gz looking for model 1 # Found a chain break before 126 # copying to AlignedFragments data structure # naming current conformation MetaTasser_TS2 # ReadConformPDB reading from PDB file servers/MetaTasser_TS3.pdb.gz looking for model 1 # Found a chain break before 126 # copying to AlignedFragments data structure # naming current conformation MetaTasser_TS3 # ReadConformPDB reading from PDB file servers/MetaTasser_TS4.pdb.gz looking for model 1 # Found a chain break before 126 # copying to AlignedFragments data structure # naming current conformation MetaTasser_TS4 # ReadConformPDB reading from PDB file servers/MetaTasser_TS5.pdb.gz looking for model 1 # Found a chain break before 126 # copying to AlignedFragments data structure # naming current conformation MetaTasser_TS5 # ReadConformPDB reading from PDB file servers/NN_PUT_lab_TS1.pdb.gz looking for model 1 # Found a chain break before 80 # copying to AlignedFragments data structure # naming current conformation NN_PUT_lab_TS1 # ReadConformPDB reading from PDB file servers/POMYSL_TS1.pdb.gz looking for model 1 # Found a chain break before 108 # copying to AlignedFragments data structure # naming current conformation POMYSL_TS1 # ReadConformPDB reading from PDB file servers/POMYSL_TS2.pdb.gz looking for model 1 # Found a chain break before 112 # copying to AlignedFragments data structure # naming current conformation POMYSL_TS2 # ReadConformPDB reading from PDB file servers/POMYSL_TS3.pdb.gz looking for model 1 # Found a chain break before 101 # copying to AlignedFragments data structure # naming current conformation POMYSL_TS3 # ReadConformPDB reading from PDB file servers/POMYSL_TS4.pdb.gz looking for model 1 # Found a chain break before 111 # copying to AlignedFragments data structure # naming current conformation POMYSL_TS4 # ReadConformPDB reading from PDB file servers/POMYSL_TS5.pdb.gz looking for model 1 # Found a chain break before 100 # copying to AlignedFragments data structure # naming current conformation POMYSL_TS5 # ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS1.pdb.gz looking for model 1 # naming current conformation PROTINFO-AB_TS1 # ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS2.pdb.gz looking for model 1 # naming current conformation PROTINFO-AB_TS2 # ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS3.pdb.gz looking for model 1 # naming current conformation PROTINFO-AB_TS3 # ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS4.pdb.gz looking for model 1 # naming current conformation PROTINFO-AB_TS4 # ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS5.pdb.gz looking for model 1 # naming current conformation PROTINFO-AB_TS5 # ReadConformPDB reading from PDB file servers/PROTINFO_TS1.pdb.gz looking for model 1 # naming current conformation PROTINFO_TS1 # ReadConformPDB reading from PDB file servers/PROTINFO_TS2.pdb.gz looking for model 1 # Found a chain break before 53 # copying to AlignedFragments data structure # naming current conformation PROTINFO_TS2 # ReadConformPDB reading from PDB file servers/PROTINFO_TS3.pdb.gz looking for model 1 # naming current conformation PROTINFO_TS3 # ReadConformPDB reading from PDB file servers/PROTINFO_TS4.pdb.gz looking for model 1 # naming current conformation PROTINFO_TS4 # ReadConformPDB reading from PDB file servers/PROTINFO_TS5.pdb.gz looking for model 1 # Found a chain break before 100 # copying to AlignedFragments data structure # naming current conformation PROTINFO_TS5 # ReadConformPDB reading from PDB file servers/Pcons6_TS1.pdb.gz looking for model 1 # Found a chain break before 3 # copying to AlignedFragments data structure # naming current conformation Pcons6_TS1 # ReadConformPDB reading from PDB file servers/Pcons6_TS2.pdb.gz looking for model 1 # naming current conformation Pcons6_TS2 # ReadConformPDB reading from PDB file servers/Pcons6_TS3.pdb.gz looking for model 1 # Found a chain break before 118 # copying to AlignedFragments data structure # naming current conformation Pcons6_TS3 # ReadConformPDB reading from PDB file servers/Pcons6_TS4.pdb.gz looking for model 1 # Found a chain break before 118 # copying to AlignedFragments data structure # naming current conformation Pcons6_TS4 # ReadConformPDB reading from PDB file servers/Pcons6_TS5.pdb.gz looking for model 1 # Found a chain break before 118 # copying to AlignedFragments data structure # naming current conformation Pcons6_TS5 # ReadConformPDB reading from PDB file servers/Phyre-1_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0383 can't currently be optimized by undertaker # naming current conformation Phyre-1_TS1 # ReadConformPDB reading from PDB file servers/Phyre-2_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0383 can't currently be optimized by undertaker # naming current conformation Phyre-2_TS1 # ReadConformPDB reading from PDB file servers/Phyre-2_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0383 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation Phyre-2_TS2 # ReadConformPDB reading from PDB file servers/Phyre-2_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0383 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation Phyre-2_TS3 # ReadConformPDB reading from PDB file servers/Phyre-2_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0383 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation Phyre-2_TS4 # ReadConformPDB reading from PDB file servers/Phyre-2_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0383 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation Phyre-2_TS5 # ReadConformPDB reading from PDB file servers/Pmodeller6_TS1.pdb.gz looking for model 1 # naming current conformation Pmodeller6_TS1 # ReadConformPDB reading from PDB file servers/Pmodeller6_TS2.pdb.gz looking for model 1 # naming current conformation Pmodeller6_TS2 # ReadConformPDB reading from PDB file servers/Pmodeller6_TS3.pdb.gz looking for model 1 # naming current conformation Pmodeller6_TS3 # ReadConformPDB reading from PDB file servers/Pmodeller6_TS4.pdb.gz looking for model 1 # Found a chain break before 121 # copying to AlignedFragments data structure # naming current conformation Pmodeller6_TS4 # ReadConformPDB reading from PDB file servers/Pmodeller6_TS5.pdb.gz looking for model 1 # Found a chain break before 125 # copying to AlignedFragments data structure # naming current conformation Pmodeller6_TS5 # ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS1.pdb.gz looking for model 1 # naming current conformation RAPTOR-ACE_TS1 # ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS2.pdb.gz looking for model 1 # naming current conformation RAPTOR-ACE_TS2 # ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS3.pdb.gz looking for model 1 # Found a chain break before 19 # copying to AlignedFragments data structure # naming current conformation RAPTOR-ACE_TS3 # ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS4.pdb.gz looking for model 1 # naming current conformation RAPTOR-ACE_TS4 # ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS5.pdb.gz looking for model 1 # naming current conformation RAPTOR-ACE_TS5 # ReadConformPDB reading from PDB file servers/RAPTORESS_TS1.pdb.gz looking for model 1 # naming current conformation RAPTORESS_TS1 # ReadConformPDB reading from PDB file servers/RAPTORESS_TS2.pdb.gz looking for model 1 # Found a chain break before 63 # copying to AlignedFragments data structure # naming current conformation RAPTORESS_TS2 # ReadConformPDB reading from PDB file servers/RAPTORESS_TS3.pdb.gz looking for model 1 # Found a chain break before 126 # copying to AlignedFragments data structure # naming current conformation RAPTORESS_TS3 # ReadConformPDB reading from PDB file servers/RAPTORESS_TS4.pdb.gz looking for model 1 # naming current conformation RAPTORESS_TS4 # ReadConformPDB reading from PDB file servers/RAPTORESS_TS5.pdb.gz looking for model 1 # Found a chain break before 91 # copying to AlignedFragments data structure # naming current conformation RAPTORESS_TS5 # ReadConformPDB reading from PDB file servers/RAPTOR_TS1.pdb.gz looking for model 1 # Found a chain break before 117 # copying to AlignedFragments data structure # naming current conformation RAPTOR_TS1 # ReadConformPDB reading from PDB file servers/RAPTOR_TS2.pdb.gz looking for model 1 # naming current conformation RAPTOR_TS2 # ReadConformPDB reading from PDB file servers/RAPTOR_TS3.pdb.gz looking for model 1 # Found a chain break before 115 # copying to AlignedFragments data structure # naming current conformation RAPTOR_TS3 # ReadConformPDB reading from PDB file servers/RAPTOR_TS4.pdb.gz looking for model 1 # naming current conformation RAPTOR_TS4 # ReadConformPDB reading from PDB file servers/RAPTOR_TS5.pdb.gz looking for model 1 # Found a chain break before 109 # copying to AlignedFragments data structure # naming current conformation RAPTOR_TS5 # ReadConformPDB reading from PDB file servers/ROBETTA_TS1.pdb.gz looking for model 1 # naming current conformation ROBETTA_TS1 # ReadConformPDB reading from PDB file servers/ROBETTA_TS2.pdb.gz looking for model 1 # naming current conformation ROBETTA_TS2 # ReadConformPDB reading from PDB file servers/ROBETTA_TS3.pdb.gz looking for model 1 # naming current conformation ROBETTA_TS3 # ReadConformPDB reading from PDB file servers/ROBETTA_TS4.pdb.gz looking for model 1 # naming current conformation ROBETTA_TS4 # ReadConformPDB reading from PDB file servers/ROBETTA_TS5.pdb.gz looking for model 1 # naming current conformation ROBETTA_TS5 # ReadConformPDB reading from PDB file servers/ROKKY_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0383 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation ROKKY_TS1 # ReadConformPDB reading from PDB file servers/ROKKY_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0383 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation ROKKY_TS2 # ReadConformPDB reading from PDB file servers/ROKKY_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0383 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation ROKKY_TS3 # ReadConformPDB reading from PDB file servers/ROKKY_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0383 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation ROKKY_TS4 # ReadConformPDB reading from PDB file servers/ROKKY_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0383 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation ROKKY_TS5 # ReadConformPDB reading from PDB file servers/SAM-T02_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0383 can't currently be optimized by undertaker # naming current conformation SAM-T02_AL1 # ReadConformPDB reading from PDB file servers/SAM-T02_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0383 can't currently be optimized by undertaker # naming current conformation SAM-T02_AL2 # ReadConformPDB reading from PDB file servers/SAM-T02_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0383 can't currently be optimized by undertaker # naming current conformation SAM-T02_AL3 # ReadConformPDB reading from PDB file servers/SAM-T02_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0383 can't currently be optimized by undertaker # naming current conformation SAM-T02_AL4 # ReadConformPDB reading from PDB file servers/SAM-T02_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0383 can't currently be optimized by undertaker # naming current conformation SAM-T02_AL5 # ReadConformPDB reading from PDB file servers/SAM_T06_server_TS1.pdb.gz looking for model 1 # Found a chain break before 120 # copying to AlignedFragments data structure # naming current conformation SAM_T06_server_TS1 # ReadConformPDB reading from PDB file servers/SAM_T06_server_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0383 can't currently be optimized by undertaker # naming current conformation SAM_T06_server_TS2 # ReadConformPDB reading from PDB file servers/SAM_T06_server_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0383 can't currently be optimized by undertaker # naming current conformation SAM_T06_server_TS3 # ReadConformPDB reading from PDB file servers/SAM_T06_server_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0383 can't currently be optimized by undertaker # naming current conformation SAM_T06_server_TS4 # ReadConformPDB reading from PDB file servers/SAM_T06_server_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0383 can't currently be optimized by undertaker # naming current conformation SAM_T06_server_TS5 # ReadConformPDB reading from PDB file servers/SP3_TS1.pdb.gz looking for model 1 # Found a chain break before 69 # copying to AlignedFragments data structure # naming current conformation SP3_TS1 # ReadConformPDB reading from PDB file servers/SP3_TS2.pdb.gz looking for model 1 # Found a chain break before 66 # copying to AlignedFragments data structure # naming current conformation SP3_TS2 # ReadConformPDB reading from PDB file servers/SP3_TS3.pdb.gz looking for model 1 # Found a chain break before 50 # copying to AlignedFragments data structure # naming current conformation SP3_TS3 # ReadConformPDB reading from PDB file servers/SP3_TS4.pdb.gz looking for model 1 # Found a chain break before 98 # copying to AlignedFragments data structure # naming current conformation SP3_TS4 # ReadConformPDB reading from PDB file servers/SP3_TS5.pdb.gz looking for model 1 # naming current conformation SP3_TS5 # ReadConformPDB reading from PDB file servers/SP4_TS1.pdb.gz looking for model 1 # naming current conformation SP4_TS1 # ReadConformPDB reading from PDB file servers/SP4_TS2.pdb.gz looking for model 1 # Found a chain break before 122 # copying to AlignedFragments data structure # naming current conformation SP4_TS2 # ReadConformPDB reading from PDB file servers/SP4_TS3.pdb.gz looking for model 1 # Found a chain break before 105 # copying to AlignedFragments data structure # naming current conformation SP4_TS3 # ReadConformPDB reading from PDB file servers/SP4_TS4.pdb.gz looking for model 1 # naming current conformation SP4_TS4 # ReadConformPDB reading from PDB file servers/SP4_TS5.pdb.gz looking for model 1 # Found a chain break before 121 # copying to AlignedFragments data structure # naming current conformation SP4_TS5 # ReadConformPDB reading from PDB file servers/SPARKS2_TS1.pdb.gz looking for model 1 # Found a chain break before 80 # copying to AlignedFragments data structure # naming current conformation SPARKS2_TS1 # ReadConformPDB reading from PDB file servers/SPARKS2_TS2.pdb.gz looking for model 1 # Found a chain break before 119 # copying to AlignedFragments data structure # naming current conformation SPARKS2_TS2 # ReadConformPDB reading from PDB file servers/SPARKS2_TS3.pdb.gz looking for model 1 # Found a chain break before 66 # copying to AlignedFragments data structure # naming current conformation SPARKS2_TS3 # ReadConformPDB reading from PDB file servers/SPARKS2_TS4.pdb.gz looking for model 1 # Found a chain break before 59 # copying to AlignedFragments data structure # naming current conformation SPARKS2_TS4 # ReadConformPDB reading from PDB file servers/SPARKS2_TS5.pdb.gz looking for model 1 # Found a chain break before 86 # copying to AlignedFragments data structure # naming current conformation SPARKS2_TS5 # ReadConformPDB reading from PDB file servers/UNI-EID_bnmx_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0383 can't currently be optimized by undertaker # naming current conformation UNI-EID_bnmx_TS1 # ReadConformPDB reading from PDB file servers/UNI-EID_bnmx_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0383 can't currently be optimized by undertaker # naming current conformation UNI-EID_bnmx_TS2 # ReadConformPDB reading from PDB file servers/UNI-EID_bnmx_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0383 can't currently be optimized by undertaker # naming current conformation UNI-EID_bnmx_TS3 # ReadConformPDB reading from PDB file servers/UNI-EID_bnmx_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0383 can't currently be optimized by undertaker # naming current conformation UNI-EID_bnmx_TS4 # ReadConformPDB reading from PDB file servers/UNI-EID_bnmx_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0383 can't currently be optimized by undertaker # naming current conformation UNI-EID_bnmx_TS5 # ReadConformPDB reading from PDB file servers/UNI-EID_expm_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0383 can't currently be optimized by undertaker # naming current conformation UNI-EID_expm_TS1 # ReadConformPDB reading from PDB file servers/UNI-EID_sfst_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0383 can't currently be optimized by undertaker # naming current conformation UNI-EID_sfst_AL1 # ReadConformPDB reading from PDB file servers/UNI-EID_sfst_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0383 can't currently be optimized by undertaker # naming current conformation UNI-EID_sfst_AL2 # ReadConformPDB reading from PDB file servers/UNI-EID_sfst_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0383 can't currently be optimized by undertaker # naming current conformation UNI-EID_sfst_AL3 # ReadConformPDB reading from PDB file servers/UNI-EID_sfst_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0383 can't currently be optimized by undertaker # naming current conformation UNI-EID_sfst_AL4 # ReadConformPDB reading from PDB file servers/UNI-EID_sfst_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0383 can't currently be optimized by undertaker # naming current conformation UNI-EID_sfst_AL5 # ReadConformPDB reading from PDB file servers/Zhang-Server_TS1.pdb.gz looking for model 1 # Found a chain break before 121 # copying to AlignedFragments data structure # naming current conformation Zhang-Server_TS1 # ReadConformPDB reading from PDB file servers/Zhang-Server_TS2.pdb.gz looking for model 1 # Found a chain break before 117 # copying to AlignedFragments data structure # naming current conformation Zhang-Server_TS2 # ReadConformPDB reading from PDB file servers/Zhang-Server_TS3.pdb.gz looking for model 1 # Found a chain break before 101 # copying to AlignedFragments data structure # naming current conformation Zhang-Server_TS3 # ReadConformPDB reading from PDB file servers/Zhang-Server_TS4.pdb.gz looking for model 1 # Found a chain break before 125 # copying to AlignedFragments data structure # naming current conformation Zhang-Server_TS4 # ReadConformPDB reading from PDB file servers/Zhang-Server_TS5.pdb.gz looking for model 1 # Found a chain break before 118 # copying to AlignedFragments data structure # naming current conformation Zhang-Server_TS5 # ReadConformPDB reading from PDB file servers/beautshot_TS1.pdb.gz looking for model 1 # Found a chain break before 124 # copying to AlignedFragments data structure # naming current conformation beautshot_TS1 # ReadConformPDB reading from PDB file servers/beautshotbase_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0383 can't currently be optimized by undertaker # naming current conformation beautshotbase_TS1 # ReadConformPDB reading from PDB file servers/forecast-s_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0383 can't currently be optimized by undertaker # naming current conformation forecast-s_AL1 # ReadConformPDB reading from PDB file servers/forecast-s_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0383 can't currently be optimized by undertaker # naming current conformation forecast-s_AL2 # ReadConformPDB reading from PDB file servers/forecast-s_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0383 can't currently be optimized by undertaker # naming current conformation forecast-s_AL3 # ReadConformPDB reading from PDB file servers/forecast-s_AL4.pdb.gz looking for model 1 Skipped atom 462, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL4.pdb.gz Skipped atom 464, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL4.pdb.gz Skipped atom 466, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL4.pdb.gz Skipped atom 468, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL4.pdb.gz # WARNING: incomplete conformation T0383 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation forecast-s_AL4 # ReadConformPDB reading from PDB file servers/forecast-s_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0383 can't currently be optimized by undertaker # naming current conformation forecast-s_AL5 # ReadConformPDB reading from PDB file servers/karypis.srv.2_TS1.pdb.gz looking for model 1 # naming current conformation karypis.srv.2_TS1 # ReadConformPDB reading from PDB file servers/karypis.srv.2_TS2.pdb.gz looking for model 1 # Found a chain break before 124 # copying to AlignedFragments data structure # naming current conformation karypis.srv.2_TS2 # ReadConformPDB reading from PDB file servers/karypis.srv.2_TS3.pdb.gz looking for model 1 # Found a chain break before 101 # copying to AlignedFragments data structure # naming current conformation karypis.srv.2_TS3 # ReadConformPDB reading from PDB file servers/karypis.srv.2_TS4.pdb.gz looking for model 1 # naming current conformation karypis.srv.2_TS4 # ReadConformPDB reading from PDB file servers/karypis.srv.2_TS5.pdb.gz looking for model 1 # Found a chain break before 118 # copying to AlignedFragments data structure # naming current conformation karypis.srv.2_TS5 # ReadConformPDB reading from PDB file servers/karypis.srv.4_TS1.pdb.gz looking for model 1 WARNING: atoms too close: (T0383)D80.O and (T0383)G81.N only 0.000 apart, marking (T0383)G81.N as missing WARNING: atoms too close: (T0383)L103.O and (T0383)N104.N only 0.000 apart, marking (T0383)N104.N as missing WARNING: atoms too close: (T0383)N124.O and (T0383)L125.N only 0.000 apart, marking (T0383)L125.N as missing # WARNING: incomplete conformation T0383 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation karypis.srv.4_TS1 # ReadConformPDB reading from PDB file servers/karypis.srv.4_TS2.pdb.gz looking for model 1 WARNING: atoms too close: (T0383)L120.O and (T0383)P121.N only 0.000 apart, marking (T0383)P121.N as missing # WARNING: incomplete conformation T0383 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation karypis.srv.4_TS2 # ReadConformPDB reading from PDB file servers/karypis.srv.4_TS3.pdb.gz looking for model 1 WARNING: atoms too close: (T0383)R8.O and (T0383)E9.N only 0.000 apart, marking (T0383)E9.N as missing # WARNING: incomplete conformation T0383 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation karypis.srv.4_TS3 # ReadConformPDB reading from PDB file servers/karypis.srv.4_TS4.pdb.gz looking for model 1 # Found a chain break before 124 # copying to AlignedFragments data structure # naming current conformation karypis.srv.4_TS4 # ReadConformPDB reading from PDB file servers/karypis.srv.4_TS5.pdb.gz looking for model 1 # Found a chain break before 124 # copying to AlignedFragments data structure # naming current conformation karypis.srv.4_TS5 # ReadConformPDB reading from PDB file servers/karypis.srv_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0383 can't currently be optimized by undertaker # naming current conformation karypis.srv_TS1 # ReadConformPDB reading from PDB file servers/karypis.srv_TS2.pdb.gz looking for model 1 # Found a chain break before 54 # copying to AlignedFragments data structure # naming current conformation karypis.srv_TS2 # ReadConformPDB reading from PDB file servers/karypis.srv_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0383 can't currently be optimized by undertaker # naming current conformation karypis.srv_TS3 # ReadConformPDB reading from PDB file servers/karypis.srv_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0383 can't currently be optimized by undertaker # naming current conformation karypis.srv_TS4 # ReadConformPDB reading from PDB file servers/karypis.srv_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0383 can't currently be optimized by undertaker # naming current conformation karypis.srv_TS5 # ReadConformPDB reading from PDB file servers/keasar-server_TS1.pdb.gz looking for model 1 # Found a chain break before 79 # copying to AlignedFragments data structure # naming current conformation keasar-server_TS1 # ReadConformPDB reading from PDB file servers/keasar-server_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0383 can't currently be optimized by undertaker # naming current conformation keasar-server_TS2 # ReadConformPDB reading from PDB file servers/keasar-server_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0383 can't currently be optimized by undertaker # naming current conformation keasar-server_TS3 # ReadConformPDB reading from PDB file servers/keasar-server_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0383 can't currently be optimized by undertaker # naming current conformation keasar-server_TS4 # ReadConformPDB reading from PDB file servers/keasar-server_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0383 can't currently be optimized by undertaker # naming current conformation keasar-server_TS5 # ReadConformPDB reading from PDB file servers/mGen-3D_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0383 can't currently be optimized by undertaker # naming current conformation mGen-3D_TS1 # ReadConformPDB reading from PDB file servers/nFOLD_TS1.pdb.gz looking for model 1 WARNING: atom 1 has residue number 1 < previous residue 127 in servers/nFOLD_TS1.pdb.gz # WARNING: incomplete conformation T0383 can't currently be optimized by undertaker # naming current conformation nFOLD_TS1 # ReadConformPDB reading from PDB file servers/nFOLD_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0383 can't currently be optimized by undertaker # naming current conformation nFOLD_TS2 # ReadConformPDB reading from PDB file servers/nFOLD_TS3.pdb.gz looking for model 1 WARNING: atom 1 has residue number 1 < previous residue 127 in servers/nFOLD_TS3.pdb.gz # WARNING: incomplete conformation T0383 can't currently be optimized by undertaker # naming current conformation nFOLD_TS3 # ReadConformPDB reading from PDB file servers/nFOLD_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0383 can't currently be optimized by undertaker # naming current conformation nFOLD_TS4 # ReadConformPDB reading from PDB file servers/nFOLD_TS5.pdb.gz looking for model 1 WARNING: atom 1 has residue number 1 < previous residue 127 in servers/nFOLD_TS5.pdb.gz # WARNING: incomplete conformation T0383 can't currently be optimized by undertaker # naming current conformation nFOLD_TS5 # ReadConformPDB reading from PDB file servers/panther2_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0383 can't currently be optimized by undertaker # naming current conformation panther2_TS1 # ReadConformPDB reading from PDB file servers/shub_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0383 can't currently be optimized by undertaker # naming current conformation shub_TS1 # command:Using radius: 8.0000 Using models AND alignments for constraints model score 1.0188 model score 1.0287 model score 1.1719 model score 1.0331 model score 1.0116 model score 1.0077 model score 1.0078 model score 1.0068 model score 1.0078 model score 1.0077 model score 2.0222 model score 1.6626 model score 1.0077 model score 1.3989 model score 1.7523 model score 0.7309 model score 0.7288 model score 1.8137 model score 1.9344 model score 1.0106 model score 1.0106 model score 0.9797 model score 1.0001 model score 1.2380 model score 1.1088 model score 1.6096 model score 1.2410 model score 0.8585 model score 1.2385 model score 1.4558 model score 1.5443 model score -0.0402 model score -0.0480 model score -0.0227 model score -0.0336 model score -0.0053 model score 1.1063 model score 1.2727 model score 1.5983 model score 0.8108 model score 1.6133 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score -0.0402 model score -0.0480 model score -0.0734 model score -0.0742 model score 1.0643 model score -0.0612 model score -0.0402 model score -0.0480 model score -0.0480 model score -0.0227 model score 0.7309 model score 0.7288 model score 1.8137 model score 1.9344 model score 0.6976 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.8672 model score 2.0474 model score 1.8483 model score 1.9310 model score 1.8285 model score 2.0739 model score 1.2771 model score 1.5300 model score 1.7126 model score 2.1718 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score -0.0732 model score -0.0334 model score 1.9554 model score 1.6837 model score 1.3401 model score 1.4813 model score 1.2964 model score 1.4813 model score 1.9602 model score 1.8535 model score 2.4631 model score 1.2909 model score 1.2857 model score 1.3636 model score 1.4386 model score 0.0139 model score 0.0139 model score 1.6239 model score 1.6205 model score 1.8920 model score 1.4469 model score 1.9810 model score 1.9440 model score 0.6542 model score 0.6312 model score 0.3470 model score 1.1664 model score 1.0113 model score 2.1146 model score 1.3300 model score 0.4465 model score 1.3894 model score 2.0205 model score 1.6093 model score 0.9642 model score 1.9085 model score 0.4465 model score 1.3894 model score 0.4874 model score 0.7572 model score 0.8355 model score 1.0871 model score 0.8827 model score 1.5804 model score 1.6539 model score 1.9140 model score 2.1022 model score 1.9569 model score 2.0332 model score 1.5065 model score 1.5117 model score 1.4774 model score 1.5110 model score 1.5308 model score 1.5720 model score 1.4569 model score 1.5111 model score 1.4928 model score 1.8354 model score 2.0721 model score 0.7839 model score 1.0194 model score 2.3435 model score 1.0194 model score 1.3952 model score 1.3037 model score 2.0164 model score 1.9937 model score 1.6286 model score 1.8598 model score 0.7839 model score 0.7804 model score 0.7268 model score 1.8038 model score 2.0122 model score -0.0765 model score -0.0463 model score 2.0879 model score 2.3619 model score 0.2454 model score -0.0428 model score -0.0243 model score 1.2904 model score 0.2684 model score 1.2651 model score -0.0784 model score -0.0417 model score 1.4323 model score 0.2626 model score 1.2756 model score 0.7804 model score 0.7268 model score 1.3738 model score 0.7839 model score 1.0160 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 0.6896 model score -0.1762 model score 1.1912 model score 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max: 2.4631 USE_META, weight: 0.5044 cost: 1.2771 min: -0.1762 max: 2.4631 USE_META, weight: 0.3225 cost: 1.8105 min: -0.1762 max: 2.4631 USE_META, weight: 0.3472 cost: 1.7382 min: -0.1762 max: 2.4631 USE_META, weight: 0.2269 cost: 2.0910 min: -0.1762 max: 2.4631 USE_META, weight: 0.4130 cost: 1.5451 min: -0.1762 max: 2.4631 USE_META, weight: 0.4250 cost: 1.5099 min: -0.1762 max: 2.4631 USE_META, weight: 0.2243 cost: 2.0986 min: -0.1762 max: 2.4631 USE_META, weight: 0.2462 cost: 2.0345 min: -0.1762 max: 2.4631 USE_META, weight: 0.1430 cost: 2.3371 min: -0.1762 max: 2.4631 USE_META, weight: 0.3453 cost: 1.7438 min: -0.1762 max: 2.4631 USE_META, weight: 0.3276 cost: 1.7958 min: -0.1762 max: 2.4631 USE_META, weight: 0.3739 cost: 1.6597 min: -0.1762 max: 2.4631 USE_META, weight: 0.8605 cost: 0.2328 min: -0.1762 max: 2.4631 USE_META, weight: 0.8979 cost: 0.1233 min: -0.1762 max: 2.4631 USE_META, weight: 0.4147 cost: 1.5401 min: -0.1762 max: 2.4631 USE_META, weight: 0.3929 cost: 1.6042 min: -0.1762 max: 2.4631 USE_META, weight: 0.4488 cost: 1.4402 min: -0.1762 max: 2.4631 USE_META, weight: 0.2973 cost: 1.8844 min: -0.1762 max: 2.4631 USE_META, weight: 0.2895 cost: 1.9074 min: -0.1762 max: 2.4631 USE_META, weight: 0.3885 cost: 1.6170 min: -0.1762 max: 2.4631 USE_META, weight: 0.3885 cost: 1.6170 min: -0.1762 max: 2.4631 USE_META, weight: 0.6085 cost: 0.9719 min: -0.1762 max: 2.4631 USE_META, weight: 0.4095 cost: 1.5555 min: -0.1762 max: 2.4631 USE_META, weight: 0.3971 cost: 1.5918 min: -0.1762 max: 2.4631 USE_META, weight: 0.4095 cost: 1.5555 min: -0.1762 max: 2.4631 USE_META, weight: 0.6085 cost: 0.9719 min: -0.1762 max: 2.4631 USE_META, weight: 0.4102 cost: 1.5535 min: -0.1762 max: 2.4631 USE_META, weight: 0.4181 cost: 1.5301 min: -0.1762 max: 2.4631 USE_META, weight: 0.5356 cost: 1.1858 min: -0.1762 max: 2.4631 USE_EVALUE, weight: 0.9306 eval: 5.6849 min: 2.3577 max: 45.5000 USE_EVALUE, weight: 0.9306 eval: 5.6849 min: 2.3577 max: 45.5000 USE_EVALUE, weight: 0.9306 eval: 5.6849 min: 2.3577 max: 45.5000 USE_EVALUE, weight: 0.6573 eval: 18.7870 min: 2.3577 max: 45.5000 USE_EVALUE, weight: 0.6573 eval: 18.7870 min: 2.3577 max: 45.5000 USE_EVALUE, weight: 0.6573 eval: 18.7870 min: 2.3577 max: 45.5000 USE_EVALUE, weight: 0.4567 eval: 28.4000 min: 2.3577 max: 45.5000 USE_EVALUE, weight: 0.4567 eval: 28.4000 min: 2.3577 max: 45.5000 USE_EVALUE, weight: 0.4567 eval: 28.4000 min: 2.3577 max: 45.5000 USE_EVALUE, weight: 0.4150 eval: 30.4000 min: 2.3577 max: 45.5000 USE_EVALUE, weight: 0.4150 eval: 30.4000 min: 2.3577 max: 45.5000 USE_EVALUE, weight: 0.4150 eval: 30.4000 min: 2.3577 max: 45.5000 USE_EVALUE, weight: 0.6294 eval: 20.1210 min: 2.3577 max: 45.5000 USE_EVALUE, weight: 0.6294 eval: 20.1210 min: 2.3577 max: 45.5000 USE_EVALUE, weight: 0.6294 eval: 20.1210 min: 2.3577 max: 45.5000 USE_EVALUE, weight: 0.6843 eval: 17.4910 min: 2.3577 max: 45.5000 USE_EVALUE, weight: 0.6843 eval: 17.4910 min: 2.3577 max: 45.5000 USE_EVALUE, weight: 0.6843 eval: 17.4910 min: 2.3577 max: 45.5000 USE_EVALUE, weight: 0.7806 eval: 12.8740 min: 2.3577 max: 45.5000 USE_EVALUE, weight: 0.7806 eval: 12.8740 min: 2.3577 max: 45.5000 USE_EVALUE, weight: 0.7806 eval: 12.8740 min: 2.3577 max: 45.5000 USE_EVALUE, weight: 0.6491 eval: 19.1790 min: 2.3577 max: 45.5000 USE_EVALUE, weight: 0.6491 eval: 19.1790 min: 2.3577 max: 45.5000 USE_EVALUE, weight: 0.6491 eval: 19.1790 min: 2.3577 max: 45.5000 USE_EVALUE, weight: 0.9417 eval: 5.1510 min: 2.3577 max: 45.5000 USE_EVALUE, weight: 0.9417 eval: 5.1510 min: 2.3577 max: 45.5000 USE_EVALUE, weight: 0.9417 eval: 5.1510 min: 2.3577 max: 45.5000 USE_EVALUE, weight: 0.6967 eval: 16.8980 min: 2.3577 max: 45.5000 USE_EVALUE, weight: 0.6967 eval: 16.8980 min: 2.3577 max: 45.5000 USE_EVALUE, weight: 0.6117 eval: 20.9700 min: 2.3577 max: 45.5000 USE_EVALUE, weight: 0.6117 eval: 20.9700 min: 2.3577 max: 45.5000 USE_EVALUE, weight: 0.6117 eval: 20.9700 min: 2.3577 max: 45.5000 USE_EVALUE, weight: 0.6966 eval: 16.9000 min: 2.3577 max: 45.5000 USE_EVALUE, weight: 0.6966 eval: 16.9000 min: 2.3577 max: 45.5000 USE_EVALUE, weight: 0.6966 eval: 16.9000 min: 2.3577 max: 45.5000 USE_EVALUE, weight: 0.6448 eval: 19.3860 min: 2.3577 max: 45.5000 USE_EVALUE, weight: 0.6448 eval: 19.3860 min: 2.3577 max: 45.5000 USE_EVALUE, weight: 0.6448 eval: 19.3860 min: 2.3577 max: 45.5000 USE_EVALUE, weight: 0.1000 eval: 45.5000 min: 2.3577 max: 45.5000 USE_EVALUE, weight: 0.1000 eval: 45.5000 min: 2.3577 max: 45.5000 USE_EVALUE, weight: 0.1000 eval: 45.5000 min: 2.3577 max: 45.5000 USE_EVALUE, weight: 1.0000 eval: 2.3577 min: 2.3577 max: 45.5000 USE_EVALUE, weight: 1.0000 eval: 2.3577 min: 2.3577 max: 45.5000 USE_EVALUE, weight: 1.0000 eval: 2.3577 min: 2.3577 max: 45.5000 USE_EVALUE, weight: 0.5590 eval: 23.4960 min: 2.3577 max: 45.5000 USE_EVALUE, weight: 0.5590 eval: 23.4960 min: 2.3577 max: 45.5000 USE_EVALUE, weight: 0.5590 eval: 23.4960 min: 2.3577 max: 45.5000 USE_EVALUE, weight: 0.5852 eval: 22.2400 min: 2.3577 max: 45.5000 USE_EVALUE, weight: 0.5852 eval: 22.2400 min: 2.3577 max: 45.5000 USE_EVALUE, weight: 0.5852 eval: 22.2400 min: 2.3577 max: 45.5000 Number of contacts in models: 262 Number of contacts in alignments: 50 NUMB_ALIGNS: 50 Adding 5835 constraints to all3.constraints Done adding distance constraints # command:Reading probabilities from probabilities.dat Reading constraints from ConstraintSet all3.constraints maxweight: 1.0000 Optimizing... Probability sum: -220.4828, CN propb: -220.4828 weights: 0.3981 constraints: 300 # command:Found ConstraintSet # PrintContacts align.constraints_meta03 Number of constraints in align3.constraints 300 # command:Found ConstraintSet # PrintContacts align_bonus.constraints_meta03 Number of constraints in align3.constraints.bonus 300 # command:Found ConstraintSet # PrintContacts rejected.constraints_meta03 Number of constraints in rejected3.constraints 5535 # command:Found ConstraintSet # PrintContacts rejected_bonus.constraints_meta03 Number of constraints in rejected3.constraints.bonus 5535 # command:Found ConstraintSet # PrintContacts non_contacts.constraints_meta03 Number of constraints in noncontact3.constraints 0 # command:Found ConstraintSet # PrintContacts non_contacts_bonus.constraints_meta03 Number of constraints in noncontact3.constraints.bonus 0 # command:Found ConstraintSet # PrintContacts all.constraints_meta03 Number of constraints in all3.constraints 5835 # command: