# 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/T0348/ # command:# Making conformation for sequence T0348 numbered 1 through 68 Created new target T0348 from T0348.a2m # command:# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/T0348/ # command:Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0348//projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0348/manyalignments-good-all.under or /projects/compbio/experiments/protein-predict/casp7/T0348//projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0348/manyalignments-good-all.under.gz for input Trying /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0348/manyalignments-good-all.under # reading script from file /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0348/manyalignments-good-all.under # Reading fragments from alignment file # Attempting to read fragment alignments from file 1yk4A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1yk4A expands to /projects/compbio/data/pdb/1yk4.pdb.gz 1yk4A:Skipped atom 15, because occupancy 0.22 <= existing 0.780 in 1yk4A Skipped atom 19, because occupancy 0.220 <= existing 0.780 in 1yk4A Skipped atom 21, because occupancy 0.220 <= existing 0.780 in 1yk4A Skipped atom 23, because occupancy 0.220 <= existing 0.780 in 1yk4A Skipped atom 25, because occupancy 0.220 <= existing 0.780 in 1yk4A Skipped atom 27, because occupancy 0.220 <= existing 0.780 in 1yk4A Skipped atom 77, because occupancy 0.130 <= existing 0.610 in 1yk4A Skipped atom 78, because occupancy 0.260 <= existing 0.610 in 1yk4A Skipped atom 80, because occupancy 0.130 <= existing 0.610 in 1yk4A Skipped atom 81, because occupancy 0.260 <= existing 0.610 in 1yk4A Skipped atom 106, because occupancy 0.380 <= existing 0.620 in 1yk4A Skipped atom 108, because occupancy 0.380 <= existing 0.620 in 1yk4A Skipped atom 128, because occupancy 0.380 <= existing 0.620 in 1yk4A Skipped atom 130, because occupancy 0.380 <= existing 0.620 in 1yk4A Skipped atom 132, because occupancy 0.380 <= existing 0.620 in 1yk4A Skipped atom 134, because occupancy 0.380 <= existing 0.620 in 1yk4A Skipped atom 136, because occupancy 0.380 <= existing 0.620 in 1yk4A Skipped atom 138, because occupancy 0.380 <= existing 0.620 in 1yk4A Skipped atom 140, because occupancy 0.380 <= existing 0.620 in 1yk4A Skipped atom 142, because occupancy 0.380 <= existing 0.620 in 1yk4A Skipped atom 166, because occupancy 0.380 <= existing 0.620 in 1yk4A Skipped atom 323, because occupancy 0.220 <= existing 0.780 in 1yk4A Skipped atom 325, because occupancy 0.220 <= existing 0.780 in 1yk4A Skipped atom 327, because occupancy 0.220 <= existing 0.780 in 1yk4A Skipped atom 398, because occupancy 0.360 <= existing 0.590 in 1yk4A Skipped atom 399, because occupancy 0.060 <= existing 0.590 in 1yk4A Skipped atom 401, because occupancy 0.360 <= existing 0.590 in 1yk4A Skipped atom 402, because occupancy 0.060 <= existing 0.590 in 1yk4A Skipped atom 565, because occupancy 0.490 <= existing 0.510 in 1yk4A Skipped atom 567, because occupancy 0.490 <= existing 0.510 in 1yk4A Skipped atom 569, because occupancy 0.490 <= existing 0.510 in 1yk4A Skipped atom 571, because occupancy 0.490 <= existing 0.510 in 1yk4A Skipped atom 573, because occupancy 0.490 <= existing 0.510 in 1yk4A Skipped atom 575, because occupancy 0.490 <= existing 0.510 in 1yk4A Skipped atom 577, because occupancy 0.490 <= existing 0.510 in 1yk4A Skipped atom 579, because occupancy 0.490 <= existing 0.510 in 1yk4A Skipped atom 589, because occupancy 0.490 <= existing 0.510 in 1yk4A Skipped atom 591, because occupancy 0.490 <= existing 0.510 in 1yk4A Skipped atom 593, because occupancy 0.490 <= existing 0.510 in 1yk4A Skipped atom 595, because occupancy 0.490 <= existing 0.510 in 1yk4A Skipped atom 597, because occupancy 0.490 <= existing 0.510 in 1yk4A Skipped atom 599, because occupancy 0.490 <= existing 0.510 in 1yk4A Skipped atom 601, because occupancy 0.490 <= existing 0.510 in 1yk4A Skipped atom 603, because occupancy 0.490 <= existing 0.510 in 1yk4A Skipped atom 613, because occupancy 0.490 <= existing 0.510 in 1yk4A Skipped atom 666, because occupancy 0.340 <= existing 0.660 in 1yk4A Skipped atom 670, because occupancy 0.340 <= existing 0.660 in 1yk4A Skipped atom 672, because occupancy 0.340 <= existing 0.660 in 1yk4A Skipped atom 674, because occupancy 0.340 <= existing 0.660 in 1yk4A Skipped atom 822, because occupancy 0.390 <= existing 0.610 in 1yk4A Skipped atom 824, because occupancy 0.390 <= existing 0.610 in 1yk4A Skipped atom 826, because occupancy 0.390 <= existing 0.610 in 1yk4A Skipped atom 828, because occupancy 0.390 <= existing 0.610 in 1yk4A Skipped atom 830, because occupancy 0.390 <= existing 0.610 in 1yk4A Skipped atom 843, because occupancy 0.260 <= existing 0.740 in 1yk4A Skipped atom 847, because occupancy 0.260 <= existing 0.740 in 1yk4A Skipped atom 849, because occupancy 0.260 <= existing 0.740 in 1yk4A Skipped atom 851, because occupancy 0.260 <= existing 0.740 in 1yk4A Skipped atom 853, because occupancy 0.260 <= existing 0.740 in 1yk4A Skipped atom 855, because occupancy 0.260 <= existing 0.740 in 1yk4A Skipped atom 857, because occupancy 0.260 <= existing 0.740 in 1yk4A Skipped atom 859, because occupancy 0.260 <= existing 0.740 in 1yk4A # T0348 read from 1yk4A/merged-good-all-a2m # 1yk4A read from 1yk4A/merged-good-all-a2m # adding 1yk4A to template set # found chain 1yk4A in template set T0348 26 :ELICKGDRLAFPIKDG 1yk4A 3 :KLSCKICGYIYDEDEG # choosing archetypes in rotamer library T0348 46 :LESE 1yk4A 19 :DPDN T0348 52 :ELAPEE 1yk4A 23 :GISPGT Number of specific fragments extracted= 3 number of extra gaps= 0 total=3 Number of alignments=1 # 1yk4A read from 1yk4A/merged-good-all-a2m # found chain 1yk4A in template set T0348 26 :ELICKGDRLAFPIKDGIP 1yk4A 3 :KLSCKICGYIYDEDEGDP T0348 48 :S 1yk4A 21 :D T0348 51 :RELAPEEE 1yk4A 22 :NGISPGTK Number of specific fragments extracted= 3 number of extra gaps= 0 total=6 Number of alignments=2 # 1yk4A read from 1yk4A/merged-good-all-a2m # found chain 1yk4A in template set Warning: unaligning (T0348)D25 because first residue in template chain is (1yk4A)A2 T0348 26 :ELICKGDRLAFPIKDGIP 1yk4A 3 :KLSCKICGYIYDEDEGDP T0348 56 :EEEVKLEHHH 1yk4A 21 :DNGISPGTKF Number of specific fragments extracted= 2 number of extra gaps= 0 total=8 Number of alignments=3 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ptq/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1ptq expands to /projects/compbio/data/pdb/1ptq.pdb.gz 1ptq:Warning: there is no chain 1ptq will retry with 1ptqA # T0348 read from 1ptq/merged-good-all-a2m # 1ptq read from 1ptq/merged-good-all-a2m # adding 1ptq to template set # found chain 1ptq in template set T0348 10 :VCPLCKGPLV 1ptq 243 :FCDHCGSLLW T0348 21 :DKSKDELICKGDRLAF 1ptq 253 :GLVKQGLKCEDCGMNV Number of specific fragments extracted= 2 number of extra gaps= 0 total=10 Number of alignments=4 # 1ptq read from 1ptq/merged-good-all-a2m # found chain 1ptq in template set T0348 10 :VCPLCKGPLV 1ptq 243 :FCDHCGSLLW T0348 21 :DKSKDELICKGDRLAF 1ptq 253 :GLVKQGLKCEDCGMNV Number of specific fragments extracted= 2 number of extra gaps= 0 total=12 Number of alignments=5 # 1ptq read from 1ptq/merged-good-all-a2m # found chain 1ptq in template set T0348 11 :CPLCKGPLV 1ptq 244 :CDHCGSLLW T0348 21 :DKSKDELICKGDRLAF 1ptq 253 :GLVKQGLKCEDCGMNV Number of specific fragments extracted= 2 number of extra gaps= 0 total=14 Number of alignments=6 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1gnf/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1gnf expands to /projects/compbio/data/pdb/1gnf.pdb.gz 1gnf:Warning: there is no chain 1gnf will retry with 1gnfA # T0348 read from 1gnf/merged-good-all-a2m # 1gnf read from 1gnf/merged-good-all-a2m # adding 1gnf to template set # found chain 1gnf in template set T0348 53 :LAPEEEVKLEHHHHH 1gnf 224 :LCNACGLYHKMNGQN Number of specific fragments extracted= 1 number of extra gaps= 0 total=15 # 1gnf read from 1gnf/merged-good-all-a2m # found chain 1gnf in template set T0348 52 :ELAPEEEVKLEHHHHH 1gnf 223 :YLCNACGLYHKMNGQN Number of specific fragments extracted= 1 number of extra gaps= 0 total=16 # 1gnf read from 1gnf/merged-good-all-a2m # found chain 1gnf in template set T0348 44 :MMLESEARELAPEE 1gnf 223 :YLCNACGLYHKMNG Number of specific fragments extracted= 1 number of extra gaps= 0 total=17 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2ct7A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2ct7A expands to /projects/compbio/data/pdb/2ct7.pdb.gz 2ct7A:# T0348 read from 2ct7A/merged-good-all-a2m # 2ct7A read from 2ct7A/merged-good-all-a2m # adding 2ct7A to template set # found chain 2ct7A in template set T0348 10 :VCPLCKGPLVFDKSKDELICKGDRLAFPIKD 2ct7A 27 :WCAQCSFGFIYEREQLEATCPQCHQTFCVRC T0348 43 :PMMLESEARELAPEEEVKLEHHHHHH 2ct7A 58 :KRQWEEQHRGRSCEDFQNWKRMNSGP Number of specific fragments extracted= 2 number of extra gaps= 0 total=19 Number of alignments=7 # 2ct7A read from 2ct7A/merged-good-all-a2m # found chain 2ct7A in template set T0348 10 :VCPLCKGPLVFDKSKDELICKGDRLAFPIKD 2ct7A 27 :WCAQCSFGFIYEREQLEATCPQCHQTFCVRC T0348 43 :PMMLESEARELAPEEEVKLEHHHHH 2ct7A 58 :KRQWEEQHRGRSCEDFQNWKRMNSG Number of specific fragments extracted= 2 number of extra gaps= 0 total=21 Number of alignments=8 # 2ct7A read from 2ct7A/merged-good-all-a2m # found chain 2ct7A in template set T0348 11 :CPLCKGPLVFDKSKDELICKGDRLAFPIKD 2ct7A 28 :CAQCSFGFIYEREQLEATCPQCHQTFCVRC T0348 43 :PMMLESEARELA 2ct7A 58 :KRQWEEQHRGRS Number of specific fragments extracted= 2 number of extra gaps= 0 total=23 Number of alignments=9 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1bc8C/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1bc8C expands to /projects/compbio/data/pdb/1bc8.pdb.gz 1bc8C:# T0348 read from 1bc8C/merged-good-all-a2m # 1bc8C read from 1bc8C/merged-good-all-a2m # adding 1bc8C to template set # found chain 1bc8C in template set T0348 5 :FLEILVCPLCKGPLVFDKSKDELICKG 1bc8C 11 :LLQLLQKPQNKHMICWTSNDGQFKLLQ Number of specific fragments extracted= 1 number of extra gaps= 0 total=24 Number of alignments=10 # 1bc8C read from 1bc8C/merged-good-all-a2m # found chain 1bc8C in template set T0348 5 :FLEILVCPLCKGPLVFDKSKDELICKG 1bc8C 11 :LLQLLQKPQNKHMICWTSNDGQFKLLQ Number of specific fragments extracted= 1 number of extra gaps= 0 total=25 Number of alignments=11 # 1bc8C read from 1bc8C/merged-good-all-a2m # found chain 1bc8C in template set T0348 4 :KFLEILVCPLCKGPLVFDKSKDELICKG 1bc8C 10 :FLLQLLQKPQNKHMICWTSNDGQFKLLQ Number of specific fragments extracted= 1 number of extra gaps= 0 total=26 Number of alignments=12 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1pft/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1pft expands to /projects/compbio/data/pdb/1pft.pdb.gz 1pft:Warning: there is no chain 1pft will retry with 1pftA # T0348 read from 1pft/merged-good-all-a2m # 1pft read from 1pft/merged-good-all-a2m # adding 1pft to template set # found chain 1pft in template set T0348 10 :VCPLCKG 1pft 7 :VCPACES T0348 17 :PLVFDKSKDELICKGDRLA 1pft 15 :ELIYDPERGEIVCAKCGYV T0348 38 :IK 1pft 34 :IE Number of specific fragments extracted= 3 number of extra gaps= 0 total=29 Number of alignments=13 # 1pft read from 1pft/merged-good-all-a2m # found chain 1pft in template set T0348 10 :VCPLCKG 1pft 7 :VCPACES T0348 17 :PLVFDKSKDELICKGDRLA 1pft 15 :ELIYDPERGEIVCAKCGYV T0348 38 :IKDGIPMM 1pft 34 :IEENIIDM Number of specific fragments extracted= 3 number of extra gaps= 0 total=32 Number of alignments=14 # 1pft read from 1pft/merged-good-all-a2m # found chain 1pft in template set T0348 11 :CPLCKG 1pft 8 :CPACES T0348 17 :PLVFDKSKDELICKGDRLA 1pft 15 :ELIYDPERGEIVCAKCGYV T0348 38 :IKDGIP 1pft 34 :IEENII T0348 59 :VKLEHHHH 1pft 40 :DMGPEWRA Number of specific fragments extracted= 4 number of extra gaps= 0 total=36 Number of alignments=15 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1vd4A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1vd4A expands to /projects/compbio/data/pdb/1vd4.pdb.gz 1vd4A:# T0348 read from 1vd4A/merged-good-all-a2m # 1vd4A read from 1vd4A/merged-good-all-a2m # adding 1vd4A to template set # found chain 1vd4A in template set T0348 11 :CPLCKGPLV 1vd4A 129 :CPVCSSTFT T0348 20 :FDKSKDELICKGDRLA 1vd4A 145 :FDPMTGTFRCTFCHTE Number of specific fragments extracted= 2 number of extra gaps= 0 total=38 Number of alignments=16 # 1vd4A read from 1vd4A/merged-good-all-a2m # found chain 1vd4A in template set T0348 11 :CPLCKGPLV 1vd4A 129 :CPVCSSTFT T0348 20 :FDKSKDELICKGDRLA 1vd4A 145 :FDPMTGTFRCTFCHTE T0348 38 :IK 1vd4A 161 :VE Number of specific fragments extracted= 3 number of extra gaps= 0 total=41 Number of alignments=17 # 1vd4A read from 1vd4A/merged-good-all-a2m # found chain 1vd4A in template set T0348 11 :CPLCKGPLV 1vd4A 129 :CPVCSSTFT T0348 20 :FDKSKDELICKGDRLAF 1vd4A 145 :FDPMTGTFRCTFCHTEV Number of specific fragments extracted= 2 number of extra gaps= 0 total=43 Number of alignments=18 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1rfs/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1rfs expands to /projects/compbio/data/pdb/1rfs.pdb.gz 1rfs:Warning: there is no chain 1rfs will retry with 1rfsA # T0348 read from 1rfs/merged-good-all-a2m # 1rfs read from 1rfs/merged-good-all-a2m # adding 1rfs to template set # found chain 1rfs in template set T0348 10 :VCPLCKGPLVFDKSKDELICKGDRLAFP 1rfs 106 :VCTHLGCVVPFNAAENKFICPCHGSQYN Number of specific fragments extracted= 1 number of extra gaps= 0 total=44 Number of alignments=19 # 1rfs read from 1rfs/merged-good-all-a2m # found chain 1rfs in template set T0348 10 :VCPLCKGPLVFDKSKDELICKGDRLAFP 1rfs 106 :VCTHLGCVVPFNAAENKFICPCHGSQYN Number of specific fragments extracted= 1 number of extra gaps= 0 total=45 Number of alignments=20 # 1rfs read from 1rfs/merged-good-all-a2m # found chain 1rfs in template set T0348 10 :VCPLCKGPLVFDKSKDELICKGDRLAFP 1rfs 106 :VCTHLGCVVPFNAAENKFICPCHGSQYN T0348 38 :IKDGIPM 1rfs 139 :VRGPAPL Number of specific fragments extracted= 2 number of extra gaps= 0 total=47 Number of alignments=21 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1l1oC/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1l1oC expands to /projects/compbio/data/pdb/1l1o.pdb.gz 1l1oC:# T0348 read from 1l1oC/merged-good-all-a2m # 1l1oC read from 1l1oC/merged-good-all-a2m # adding 1l1oC to template set # found chain 1l1oC in template set T0348 10 :VCPL 1l1oC 480 :ACPT T0348 14 :CKGPLV 1l1oC 486 :CNKKVI T0348 21 :DKSKDELICKGDRLAFP 1l1oC 492 :DQQNGLYRCEKCDTEFP Number of specific fragments extracted= 3 number of extra gaps= 0 total=50 Number of alignments=22 # 1l1oC read from 1l1oC/merged-good-all-a2m # found chain 1l1oC in template set T0348 10 :VCPL 1l1oC 480 :ACPT T0348 14 :CKGPLV 1l1oC 486 :CNKKVI T0348 21 :DKSKDELICKGDRLAFP 1l1oC 492 :DQQNGLYRCEKCDTEFP Number of specific fragments extracted= 3 number of extra gaps= 0 total=53 Number of alignments=23 # 1l1oC read from 1l1oC/merged-good-all-a2m # found chain 1l1oC in template set T0348 10 :VCPL 1l1oC 480 :ACPT T0348 14 :CKGPLVFD 1l1oC 486 :CNKKVIDQ T0348 23 :SKDELICKGDRLAFP 1l1oC 494 :QNGLYRCEKCDTEFP Number of specific fragments extracted= 3 number of extra gaps= 0 total=56 Number of alignments=24 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1e4uA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1e4uA expands to /projects/compbio/data/pdb/1e4u.pdb.gz 1e4uA:# T0348 read from 1e4uA/merged-good-all-a2m # 1e4uA read from 1e4uA/merged-good-all-a2m # adding 1e4uA to template set # found chain 1e4uA in template set T0348 11 :CPLCKGPLV 1e4uA 14 :CPLCMEPLE T0348 23 :SKDE 1e4uA 23 :IDDI T0348 28 :ICKGDRLAF 1e4uA 52 :LCPACRKPY Number of specific fragments extracted= 3 number of extra gaps= 0 total=59 Number of alignments=25 # 1e4uA read from 1e4uA/merged-good-all-a2m # found chain 1e4uA in template set T0348 11 :CPLCKGPLVF 1e4uA 14 :CPLCMEPLEI T0348 24 :KDELICKGDRLAFP 1e4uA 48 :DENGLCPACRKPYP Number of specific fragments extracted= 2 number of extra gaps= 0 total=61 Number of alignments=26 # 1e4uA read from 1e4uA/merged-good-all-a2m # found chain 1e4uA in template set T0348 11 :CPLCKGPLV 1e4uA 14 :CPLCMEPLE T0348 30 :KGDRLAFPIKDGI 1e4uA 23 :IDDINFFPCTCGY T0348 44 :MMLESEARELAPEEEVKLEHHHHHH 1e4uA 36 :QICRFCWHRIRTDENGLCPACRKPY Number of specific fragments extracted= 3 number of extra gaps= 0 total=64 Number of alignments=27 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2a1rA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2a1rA expands to /projects/compbio/data/pdb/2a1r.pdb.gz 2a1rA:# T0348 read from 2a1rA/merged-good-all-a2m # 2a1rA read from 2a1rA/merged-good-all-a2m # adding 2a1rA to template set # found chain 2a1rA in template set Warning: unaligning (T0348)A54 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2a1rA)H257 T0348 18 :LVFDKSKDE 2a1rA 74 :FKYDYTDSK T0348 27 :LI 2a1rA 106 :FV T0348 39 :KDGIPMMLESEAREL 2a1rA 128 :RNGIPYLNQEEERQL Number of specific fragments extracted= 3 number of extra gaps= 0 total=67 Number of alignments=28 # 2a1rA read from 2a1rA/merged-good-all-a2m # found chain 2a1rA in template set Warning: unaligning (T0348)A54 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2a1rA)H257 T0348 39 :KDGIPMMLESEAREL 2a1rA 128 :RNGIPYLNQEEERQL Number of specific fragments extracted= 1 number of extra gaps= 0 total=68 # 2a1rA read from 2a1rA/merged-good-all-a2m # found chain 2a1rA in template set Warning: unaligning (T0348)A54 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2a1rA)H257 T0348 18 :LVFDKSKDELIC 2a1rA 74 :FKYDYTDSKYIT T0348 30 :KGDRLAFP 2a1rA 100 :SSPDVKFV T0348 39 :KDGIPMMLESEAREL 2a1rA 128 :RNGIPYLNQEEERQL Number of specific fragments extracted= 3 number of extra gaps= 0 total=71 Number of alignments=29 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1s72Z/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1s72Z expands to /projects/compbio/data/pdb/1s72.pdb.gz 1s72Z:# T0348 read from 1s72Z/merged-good-all-a2m # 1s72Z read from 1s72Z/merged-good-all-a2m # adding 1s72Z to template set # found chain 1s72Z in template set T0348 11 :CPLC 1s72Z 39 :CPNC T0348 15 :KGPLVFDKS 1s72Z 44 :EDRVDRQGT T0348 25 :DELICKGDRLAFPIKDGIP 1s72Z 53 :GIWQCSYCDYKFTGGSYKP T0348 53 :LAPEEEVKL 1s72Z 72 :ETPGGKTVR Number of specific fragments extracted= 4 number of extra gaps= 0 total=75 Number of alignments=30 # 1s72Z read from 1s72Z/merged-good-all-a2m # found chain 1s72Z in template set T0348 10 :VCPLC 1s72Z 38 :ACPNC T0348 15 :KGPLVFD 1s72Z 44 :EDRVDRQ T0348 23 :SKDELICKGDRLAFPIKDGIP 1s72Z 51 :GTGIWQCSYCDYKFTGGSYKP T0348 53 :LAPEEEVKL 1s72Z 72 :ETPGGKTVR Number of specific fragments extracted= 4 number of extra gaps= 0 total=79 Number of alignments=31 # 1s72Z read from 1s72Z/merged-good-all-a2m # found chain 1s72Z in template set T0348 11 :CPLCK 1s72Z 39 :CPNCG T0348 16 :GPLVFDKS 1s72Z 45 :DRVDRQGT T0348 25 :DELICKGDRLAFPIKD 1s72Z 53 :GIWQCSYCDYKFTGGS Number of specific fragments extracted= 3 number of extra gaps= 0 total=82 Number of alignments=32 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ee8A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1ee8A expands to /projects/compbio/data/pdb/1ee8.pdb.gz 1ee8A:# T0348 read from 1ee8A/merged-good-all-a2m # 1ee8A read from 1ee8A/merged-good-all-a2m # adding 1ee8A to template set # found chain 1ee8A in template set T0348 10 :VCPLCKGPLVFDK 1ee8A 237 :PCPACGRPVERRV T0348 23 :SKDE 1ee8A 251 :AGRG T0348 27 :LICKGD 1ee8A 256 :HFCPTC Number of specific fragments extracted= 3 number of extra gaps= 0 total=85 Number of alignments=33 # 1ee8A read from 1ee8A/merged-good-all-a2m # found chain 1ee8A in template set T0348 11 :CPLCKGPLVFDKSKD 1ee8A 238 :CPACGRPVERRVVAG T0348 26 :ELICKGD 1ee8A 255 :THFCPTC Number of specific fragments extracted= 2 number of extra gaps= 0 total=87 Number of alignments=34 # 1ee8A read from 1ee8A/merged-good-all-a2m # found chain 1ee8A in template set T0348 11 :CPLCKGPLVFDK 1ee8A 238 :CPACGRPVERRV T0348 23 :SKDELICKGD 1ee8A 252 :GRGTHFCPTC Number of specific fragments extracted= 2 number of extra gaps= 0 total=89 Number of alignments=35 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1vckA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1vckA expands to /projects/compbio/data/pdb/1vck.pdb.gz 1vckA:# T0348 read from 1vckA/merged-good-all-a2m # 1vckA read from 1vckA/merged-good-all-a2m # adding 1vckA to template set # found chain 1vckA in template set T0348 23 :SKDELICKGDRLAFPIKDGIPM 1vckA 59 :DGDVIECPFHGGAFNVCTGMPA Number of specific fragments extracted= 1 number of extra gaps= 0 total=90 Number of alignments=36 # 1vckA read from 1vckA/merged-good-all-a2m # found chain 1vckA in template set T0348 21 :DKSKDELICKGDRLAFPIKDGIPM 1vckA 57 :TLDGDVIECPFHGGAFNVCTGMPA Number of specific fragments extracted= 1 number of extra gaps= 0 total=91 Number of alignments=37 # 1vckA read from 1vckA/merged-good-all-a2m # found chain 1vckA in template set T0348 13 :LCKGPLV 1vckA 53 :LSEGTLD T0348 24 :KDELICKGDRLAFPIKDGIPM 1vckA 60 :GDVIECPFHGGAFNVCTGMPA Number of specific fragments extracted= 2 number of extra gaps= 0 total=93 Number of alignments=38 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ypvA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1ypvA expands to /projects/compbio/data/pdb/1ypv.pdb.gz 1ypvA:# T0348 read from 1ypvA/merged-good-all-a2m # 1ypvA read from 1ypvA/merged-good-all-a2m # adding 1ypvA to template set # found chain 1ypvA in template set T0348 21 :DKSKDELICKGDRLAFPIKDGIPMM 1ypvA 50 :RTGTGTLSVFGMQARYSLRDEFPLL Number of specific fragments extracted= 1 number of extra gaps= 0 total=94 Number of alignments=39 # 1ypvA read from 1ypvA/merged-good-all-a2m # found chain 1ypvA in template set T0348 22 :KSKDELICKGDRLAFPIKDGIPMM 1ypvA 51 :TGTGTLSVFGMQARYSLRDEFPLL Number of specific fragments extracted= 1 number of extra gaps= 0 total=95 Number of alignments=40 # 1ypvA read from 1ypvA/merged-good-all-a2m # found chain 1ypvA in template set T0348 21 :DKSKDELICKGDRLAFPIKDGIPMM 1ypvA 50 :RTGTGTLSVFGMQARYSLRDEFPLL Number of specific fragments extracted= 1 number of extra gaps= 0 total=96 Number of alignments=41 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ur6B/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1ur6B expands to /projects/compbio/data/pdb/1ur6.pdb.gz 1ur6B:# T0348 read from 1ur6B/merged-good-all-a2m # 1ur6B read from 1ur6B/merged-good-all-a2m # adding 1ur6B to template set # found chain 1ur6B in template set T0348 2 :DAKFLEIL 1ur6B 38 :CRFCWHRI T0348 10 :VCPLCKGPL 1ur6B 52 :LCPACRKPY Number of specific fragments extracted= 2 number of extra gaps= 0 total=98 Number of alignments=42 # 1ur6B read from 1ur6B/merged-good-all-a2m # found chain 1ur6B in template set T0348 2 :DAKFLEIL 1ur6B 38 :CRFCWHRI T0348 10 :VCPLCKGP 1ur6B 52 :LCPACRKP Number of specific fragments extracted= 2 number of extra gaps= 0 total=100 Number of alignments=43 # 1ur6B read from 1ur6B/merged-good-all-a2m # found chain 1ur6B in template set T0348 11 :CPLCKGPLVF 1ur6B 14 :CPLCMEPLEI T0348 31 :GDRLAFPIKDGI 1ur6B 24 :DDINFFPCTCGY T0348 44 :MMLESEARELAPEEEVKLEHHHHH 1ur6B 36 :QICRFCWHRIRTDENGLCPACRKP Number of specific fragments extracted= 3 number of extra gaps= 0 total=103 Number of alignments=44 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1rb9/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0348 read from 1rb9/merged-good-all-a2m # 1rb9 read from 1rb9/merged-good-all-a2m # found chain 1rb9 in training set T0348 25 :DELICKGDRLAFPIKDG 1rb9 2 :KKYVCTVCGYEYDPAEG T0348 46 :LESE 1rb9 19 :DPDN T0348 52 :ELAPE 1rb9 23 :GVKPG T0348 59 :VKL 1rb9 28 :TSF Number of specific fragments extracted= 4 number of extra gaps= 0 total=107 Number of alignments=45 # 1rb9 read from 1rb9/merged-good-all-a2m # found chain 1rb9 in training set T0348 25 :DELICKGDRLAFPIKDGIP 1rb9 2 :KKYVCTVCGYEYDPAEGDP T0348 48 :SE 1rb9 21 :DN T0348 52 :ELAPE 1rb9 23 :GVKPG Number of specific fragments extracted= 3 number of extra gaps= 0 total=110 Number of alignments=46 # 1rb9 read from 1rb9/merged-good-all-a2m # found chain 1rb9 in training set Warning: unaligning (T0348)K24 because first residue in template chain is (1rb9)M1 T0348 25 :DELICKGDRLAFPIKDGIP 1rb9 2 :KKYVCTVCGYEYDPAEGDP T0348 56 :EEEVKLEHH 1rb9 21 :DNGVKPGTS Number of specific fragments extracted= 2 number of extra gaps= 0 total=112 Number of alignments=47 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1jj2Y/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1jj2Y expands to /projects/compbio/data/pdb/1jj2.pdb.gz 1jj2Y:# T0348 read from 1jj2Y/merged-good-all-a2m # 1jj2Y read from 1jj2Y/merged-good-all-a2m # adding 1jj2Y to template set # found chain 1jj2Y in template set T0348 11 :CPLC 1jj2Y 39 :CPVC T0348 15 :KGPLVFDKS 1jj2Y 44 :FKKLKRAGT T0348 25 :DELICKGDRLAFP 1jj2Y 53 :GIWMCGHCGYKIA Number of specific fragments extracted= 3 number of extra gaps= 0 total=115 Number of alignments=48 # 1jj2Y read from 1jj2Y/merged-good-all-a2m # found chain 1jj2Y in template set T0348 11 :CPLC 1jj2Y 39 :CPVC T0348 15 :KGPLVFD 1jj2Y 44 :FKKLKRA T0348 23 :SKDELICKGDRLAFP 1jj2Y 51 :GTGIWMCGHCGYKIA Number of specific fragments extracted= 3 number of extra gaps= 0 total=118 Number of alignments=49 # 1jj2Y read from 1jj2Y/merged-good-all-a2m # found chain 1jj2Y in template set T0348 11 :CPLCK 1jj2Y 39 :CPVCG T0348 16 :GPLVFDKS 1jj2Y 45 :KKLKRAGT T0348 25 :DELICKGDRLA 1jj2Y 53 :GIWMCGHCGYK Number of specific fragments extracted= 3 number of extra gaps= 0 total=121 Number of alignments=50 # Reading fragments from alignment file # Attempting to read fragment alignments from file 5rxn/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 5rxn expands to /projects/compbio/data/pdb/5rxn.pdb.gz 5rxn:Warning: there is no chain 5rxn will retry with 5rxnA # T0348 read from 5rxn/merged-good-all-a2m # 5rxn read from 5rxn/merged-good-all-a2m # adding 5rxn to template set # found chain 5rxn in template set T0348 27 :LICKGDRLAFPIKDG 5rxn 4 :YTCTVCGYIYDPEDG T0348 46 :LESE 5rxn 19 :DPDD T0348 52 :ELAPE 5rxn 23 :GVNPG T0348 59 :VKLEHHHHH 5rxn 28 :TDFKDIPDD Number of specific fragments extracted= 4 number of extra gaps= 0 total=125 Number of alignments=51 # 5rxn read from 5rxn/merged-good-all-a2m # found chain 5rxn in template set T0348 26 :ELICKGDRLAFPIKDGIP 5rxn 3 :KYTCTVCGYIYDPEDGDP T0348 48 :SE 5rxn 21 :DD T0348 52 :ELAPE 5rxn 23 :GVNPG T0348 59 :VKLEH 5rxn 28 :TDFKD Number of specific fragments extracted= 4 number of extra gaps= 0 total=129 Number of alignments=52 # 5rxn read from 5rxn/merged-good-all-a2m # found chain 5rxn in template set T0348 26 :ELICKGDRLAFPIKDGIP 5rxn 3 :KYTCTVCGYIYDPEDGDP T0348 56 :EEEVKLEHH 5rxn 21 :DDGVNPGTD Number of specific fragments extracted= 2 number of extra gaps= 0 total=131 Number of alignments=53 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1d0qA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0348 read from 1d0qA/merged-good-all-a2m # 1d0qA read from 1d0qA/merged-good-all-a2m # found chain 1d0qA in training set T0348 11 :CPLC 1d0qA 40 :CPFH T0348 15 :KGPLVFDKSKDELICKGDRLA 1d0qA 47 :TPSFSVSPEKQIFHCFGCGAG Number of specific fragments extracted= 2 number of extra gaps= 0 total=133 Number of alignments=54 # 1d0qA read from 1d0qA/merged-good-all-a2m # found chain 1d0qA in training set T0348 11 :CPLC 1d0qA 40 :CPFH T0348 15 :KGPLVFDKSKDELICKGDRLA 1d0qA 47 :TPSFSVSPEKQIFHCFGCGAG Number of specific fragments extracted= 2 number of extra gaps= 0 total=135 Number of alignments=55 # 1d0qA read from 1d0qA/merged-good-all-a2m # found chain 1d0qA in training set T0348 11 :CPLC 1d0qA 40 :CPFH T0348 15 :KGPLVFDKSKDELICKGDRLA 1d0qA 47 :TPSFSVSPEKQIFHCFGCGAG Number of specific fragments extracted= 2 number of extra gaps= 0 total=137 Number of alignments=56 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1dl6A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1dl6A expands to /projects/compbio/data/pdb/1dl6.pdb.gz 1dl6A:# T0348 read from 1dl6A/merged-good-all-a2m # 1dl6A read from 1dl6A/merged-good-all-a2m # adding 1dl6A to template set # found chain 1dl6A in template set T0348 11 :CPLC 1dl6A 15 :CPNH T0348 15 :KGPLVFDKSKDELICKGDRLAFP 1dl6A 20 :DAILVEDYRAGDMICPECGLVVG Number of specific fragments extracted= 2 number of extra gaps= 0 total=139 Number of alignments=57 # 1dl6A read from 1dl6A/merged-good-all-a2m # found chain 1dl6A in template set T0348 11 :CPLC 1dl6A 15 :CPNH T0348 15 :KGPLVFDKSKDELICKGDRLAFP 1dl6A 20 :DAILVEDYRAGDMICPECGLVVG T0348 51 :RELAPEEEV 1dl6A 44 :RVIDVGSEW T0348 62 :EHHHHH 1dl6A 53 :RTFSND Number of specific fragments extracted= 4 number of extra gaps= 0 total=143 Number of alignments=58 # 1dl6A read from 1dl6A/merged-good-all-a2m # found chain 1dl6A in template set T0348 11 :CPLCK 1dl6A 15 :CPNHP T0348 16 :GPLVFDKSKDELICKGDRLAFP 1dl6A 21 :AILVEDYRAGDMICPECGLVVG Number of specific fragments extracted= 2 number of extra gaps= 0 total=145 Number of alignments=59 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1vqoZ/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1vqoZ expands to /projects/compbio/data/pdb/1vqo.pdb.gz 1vqoZ:# T0348 read from 1vqoZ/merged-good-all-a2m # 1vqoZ read from 1vqoZ/merged-good-all-a2m # adding 1vqoZ to template set # found chain 1vqoZ in template set Warning: unaligning (T0348)H63 because last residue in template chain is (1vqoZ)S82 T0348 10 :VCPLC 1vqoZ 38 :ACPNC T0348 15 :KGPLVFDKS 1vqoZ 44 :EDRVDRQGT T0348 25 :DELICKGDRLAFPIKDGIP 1vqoZ 53 :GIWQCSYCDYKFTGGSYKP T0348 53 :LAPEEEVKLE 1vqoZ 72 :ETPGGKTVRR Number of specific fragments extracted= 4 number of extra gaps= 0 total=149 Number of alignments=60 # 1vqoZ read from 1vqoZ/merged-good-all-a2m # found chain 1vqoZ in template set Warning: unaligning (T0348)H63 because last residue in template chain is (1vqoZ)S82 T0348 10 :VCPLC 1vqoZ 38 :ACPNC T0348 15 :KGPLVFD 1vqoZ 44 :EDRVDRQ T0348 23 :SKDELICKGDRLAFPIKDGIP 1vqoZ 51 :GTGIWQCSYCDYKFTGGSYKP T0348 53 :LAPEEEVKLE 1vqoZ 72 :ETPGGKTVRR Number of specific fragments extracted= 4 number of extra gaps= 0 total=153 Number of alignments=61 # 1vqoZ read from 1vqoZ/merged-good-all-a2m # found chain 1vqoZ in template set T0348 11 :CPLCKG 1vqoZ 39 :CPNCGE T0348 17 :PLVFDKS 1vqoZ 46 :RVDRQGT T0348 25 :DELICKGDRLAFPI 1vqoZ 53 :GIWQCSYCDYKFTG Number of specific fragments extracted= 3 number of extra gaps= 0 total=156 Number of alignments=62 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1odhA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1odhA expands to /projects/compbio/data/pdb/1odh.pdb.gz 1odhA:# T0348 read from 1odhA/merged-good-all-a2m # 1odhA read from 1odhA/merged-good-all-a2m # adding 1odhA to template set # found chain 1odhA in template set T0348 10 :VCPLCKGPLVFDK 1odhA 112 :SCPNCNGPLKLIP T0348 24 :KDE 1odhA 129 :GGF T0348 27 :LICKGDRLAFP 1odhA 137 :WRHDGRFIFFQ Number of specific fragments extracted= 3 number of extra gaps= 0 total=159 Number of alignments=63 # 1odhA read from 1odhA/merged-good-all-a2m # found chain 1odhA in template set T0348 10 :VCPLCKGPLVFDK 1odhA 112 :SCPNCNGPLKLIP T0348 29 :CKG 1odhA 125 :CRG Number of specific fragments extracted= 2 number of extra gaps= 0 total=161 Number of alignments=64 # 1odhA read from 1odhA/merged-good-all-a2m # found chain 1odhA in template set T0348 11 :CPLCKGPLVFDK 1odhA 113 :CPNCNGPLKLIP T0348 40 :DGIP 1odhA 129 :GGFP Number of specific fragments extracted= 2 number of extra gaps= 0 total=163 Number of alignments=65 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1faq/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1faq expands to /projects/compbio/data/pdb/1faq.pdb.gz 1faq:Warning: there is no chain 1faq will retry with 1faqA # T0348 read from 1faq/merged-good-all-a2m # 1faq read from 1faq/merged-good-all-a2m # adding 1faq to template set # found chain 1faq in template set T0348 11 :CPLCKGPLV 1faq 152 :CDICQKFLL T0348 25 :DELICKGDRLAFP 1faq 161 :NGFRCQTCGYKFH Number of specific fragments extracted= 2 number of extra gaps= 0 total=165 Number of alignments=66 # 1faq read from 1faq/merged-good-all-a2m # found chain 1faq in template set T0348 11 :CPLCKGPL 1faq 152 :CDICQKFL T0348 24 :KDELICKGDRLAFP 1faq 160 :LNGFRCQTCGYKFH Number of specific fragments extracted= 2 number of extra gaps= 0 total=167 Number of alignments=67 # 1faq read from 1faq/merged-good-all-a2m # found chain 1faq in template set T0348 11 :CPLCKGPL 1faq 152 :CDICQKFL T0348 24 :KDELICKGDRLAFP 1faq 160 :LNGFRCQTCGYKFH T0348 38 :IKDGIPM 1faq 176 :CSTKVPT Number of specific fragments extracted= 3 number of extra gaps= 0 total=170 Number of alignments=68 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1rlyA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1rlyA expands to /projects/compbio/data/pdb/1rly.pdb.gz 1rlyA:# T0348 read from 1rlyA/merged-good-all-a2m # 1rlyA read from 1rlyA/merged-good-all-a2m # adding 1rlyA to template set # found chain 1rlyA in template set T0348 11 :CPLC 1rlyA 15 :CPNH T0348 15 :KGPLVFDKSKDELICKGDRLA 1rlyA 20 :DAILVEDYRAGDMICPECGLV Number of specific fragments extracted= 2 number of extra gaps= 0 total=172 Number of alignments=69 # 1rlyA read from 1rlyA/merged-good-all-a2m # found chain 1rlyA in template set T0348 11 :CPLC 1rlyA 15 :CPNH T0348 15 :KGPLVFDKSKDELICKGDRLAF 1rlyA 20 :DAILVEDYRAGDMICPECGLVV Number of specific fragments extracted= 2 number of extra gaps= 0 total=174 Number of alignments=70 # 1rlyA read from 1rlyA/merged-good-all-a2m # found chain 1rlyA in template set T0348 11 :CPLCKGP 1rlyA 15 :CPNHPDA T0348 18 :LVFDKSKDELICKGDRLAF 1rlyA 23 :LVEDYRAGDMICPECGLVV Number of specific fragments extracted= 2 number of extra gaps= 0 total=176 Number of alignments=71 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1hvyA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1hvyA expands to /projects/compbio/data/pdb/1hvy.pdb.gz 1hvyA:# T0348 read from 1hvyA/merged-good-all-a2m # 1hvyA read from 1hvyA/merged-good-all-a2m # adding 1hvyA to template set # found chain 1hvyA in template set T0348 22 :KSKDELICKGDRLAFPIKDGIPMM 1hvyA 51 :TGTGTLSVFGMQARYSLRDEFPLL Number of specific fragments extracted= 1 number of extra gaps= 0 total=177 Number of alignments=72 # 1hvyA read from 1hvyA/merged-good-all-a2m # found chain 1hvyA in template set T0348 22 :KSKDELICKGDRLAFPIKDGIPMM 1hvyA 51 :TGTGTLSVFGMQARYSLRDEFPLL Number of specific fragments extracted= 1 number of extra gaps= 0 total=178 Number of alignments=73 # 1hvyA read from 1hvyA/merged-good-all-a2m # found chain 1hvyA in template set T0348 22 :KSKDELICKGDRLAFPIKDGIPMM 1hvyA 51 :TGTGTLSVFGMQARYSLRDEFPLL Number of specific fragments extracted= 1 number of extra gaps= 0 total=179 Number of alignments=74 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1vk6A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1vk6A expands to /projects/compbio/data/pdb/1vk6.pdb.gz 1vk6A:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 93, because occupancy 0.350 <= existing 0.650 in 1vk6A Skipped atom 95, because occupancy 0.350 <= existing 0.650 in 1vk6A Skipped atom 97, because occupancy 0.350 <= existing 0.650 in 1vk6A Skipped atom 99, because occupancy 0.350 <= existing 0.650 in 1vk6A Skipped atom 101, because occupancy 0.350 <= existing 0.650 in 1vk6A Skipped atom 103, because occupancy 0.350 <= existing 0.650 in 1vk6A Skipped atom 430, because occupancy 0.350 <= existing 0.650 in 1vk6A Skipped atom 432, because occupancy 0.350 <= existing 0.650 in 1vk6A Skipped atom 434, because occupancy 0.350 <= existing 0.650 in 1vk6A Skipped atom 436, because occupancy 0.350 <= existing 0.650 in 1vk6A Skipped atom 438, because occupancy 0.350 <= existing 0.650 in 1vk6A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 1634, because occupancy 0.350 <= existing 0.650 in 1vk6A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1636, because occupancy 0.350 <= existing 0.650 in 1vk6A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1638, because occupancy 0.350 <= existing 0.650 in 1vk6A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1640, because occupancy 0.350 <= existing 0.650 in 1vk6A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 1669, because occupancy 0.350 <= existing 0.650 in 1vk6A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1671, because occupancy 0.350 <= existing 0.650 in 1vk6A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1673, because occupancy 0.350 <= existing 0.650 in 1vk6A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1675, because occupancy 0.350 <= existing 0.650 in 1vk6A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0348 read from 1vk6A/merged-good-all-a2m # 1vk6A read from 1vk6A/merged-good-all-a2m # adding 1vk6A to template set # found chain 1vk6A in template set T0348 10 :VCPLCKGPLVFDKSKDELICKGDRLAFP 1vk6A 97 :YCGYCGHEMYPSKTEWAMLCSHCRERYY Number of specific fragments extracted= 1 number of extra gaps= 0 total=180 Number of alignments=75 # 1vk6A read from 1vk6A/merged-good-all-a2m # found chain 1vk6A in template set T0348 10 :VCPLCKGPLVFDKSKDELICKGDRLAF 1vk6A 97 :YCGYCGHEMYPSKTEWAMLCSHCRERY Number of specific fragments extracted= 1 number of extra gaps= 0 total=181 Number of alignments=76 # 1vk6A read from 1vk6A/merged-good-all-a2m # found chain 1vk6A in template set T0348 11 :CPLCKGPLVFDKSKDELICKGDRLAFP 1vk6A 98 :CGYCGHEMYPSKTEWAMLCSHCRERYY Number of specific fragments extracted= 1 number of extra gaps= 0 total=182 Number of alignments=77 # command:Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0348//projects/compbio/experiments/protein-predict/casp7/T0348/align.constraints_v3.costfcn or /projects/compbio/experiments/protein-predict/casp7/T0348//projects/compbio/experiments/protein-predict/casp7/T0348/align.constraints_v3.costfcn.gz for input Trying /projects/compbio/experiments/protein-predict/casp7/T0348/align.constraints_v3.costfcn # reading script from file /projects/compbio/experiments/protein-predict/casp7/T0348/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((T0348)L27.CB, (T0348)F36.CB) [> 3.0925 = 5.1542 < 6.7005] w=0.8458 to align # Constraint # added constraint: constraint((T0348)L18.CB, (T0348)L27.CB) [> 3.1831 = 5.3052 < 6.8968] w=0.8063 to align # Constraint # added constraint: constraint((T0348)L18.CB, (T0348)C29.CB) [> 3.1947 = 5.3245 < 6.9218] w=0.7873 to align # Constraint # added constraint: constraint((T0348)C14.CB, (T0348)G31.CA) [> 4.0200 = 6.7001 < 8.7101] w=0.7784 to align # Constraint # added constraint: constraint((T0348)C11.CB, (T0348)C29.CB) [> 2.6475 = 4.4125 < 5.7363] w=0.7784 to align # Constraint # added constraint: constraint((T0348)L18.CB, (T0348)I28.CB) [> 4.0365 = 6.7275 < 8.7457] w=0.7442 to align # Constraint # added constraint: constraint((T0348)V19.CB, (T0348)I28.CB) [> 3.4062 = 5.6771 < 7.3802] w=0.7442 to align # Constraint # added constraint: constraint((T0348)E26.CB, (T0348)F36.CB) [> 3.9985 = 6.6641 < 8.6633] w=0.7381 to align # Constraint # added constraint: constraint((T0348)V19.CB, (T0348)K30.CB) [> 3.7385 = 6.2309 < 8.1001] w=0.7244 to align # Constraint # added constraint: constraint((T0348)C14.CB, (T0348)C29.CB) [> 3.9582 = 6.5970 < 8.5761] w=0.7184 to align # Constraint # added constraint: constraint((T0348)G16.CA, (T0348)C29.CB) [> 4.1271 = 6.8785 < 8.9420] w=0.7181 to align # Constraint # added constraint: constraint((T0348)L13.CB, (T0348)C29.CB) [> 4.1017 = 6.8362 < 8.8871] w=0.6728 to align # Constraint # added constraint: constraint((T0348)C11.CB, (T0348)L34.CB) [> 3.7636 = 6.2727 < 8.1545] w=0.6579 to align # Constraint # added constraint: constraint((T0348)L13.CB, (T0348)L34.CB) [> 3.1901 = 5.3168 < 6.9119] w=0.6490 to align # Constraint # added constraint: constraint((T0348)E26.CB, (T0348)P37.CB) [> 3.5204 = 5.8674 < 7.6276] w=0.5961 to align # Constraint # added constraint: constraint((T0348)L27.CB, (T0348)P37.CB) [> 4.4160 = 7.3600 < 9.5680] w=0.5585 to align # Constraint # added constraint: constraint((T0348)P12.CB, (T0348)L34.CB) [> 4.0205 = 6.7009 < 8.7112] w=0.5045 to align # Constraint # added constraint: constraint((T0348)P12.CB, (T0348)F36.CB) [> 3.8414 = 6.4022 < 8.3229] w=0.4524 to align # Constraint # added constraint: constraint((T0348)P17.CB, (T0348)C29.CB) [> 3.7102 = 6.1837 < 8.0388] w=0.4174 to align # Constraint # added constraint: constraint((T0348)E26.CB, (T0348)I38.CB) [> 4.2955 = 7.1591 < 9.3069] w=0.4146 to align # Constraint # added constraint: constraint((T0348)C14.CB, (T0348)L34.CB) [> 4.2489 = 7.0815 < 9.2059] w=0.4083 to align # Constraint # added constraint: constraint((T0348)L18.CB, (T0348)F36.CB) [> 4.1590 = 6.9316 < 9.0111] w=0.3701 to align # Constraint # added constraint: constraint((T0348)L18.CB, (T0348)L34.CB) [> 4.3743 = 7.2905 < 9.4777] w=0.3092 to align # Constraint # added constraint: constraint((T0348)D21.CB, (T0348)A35.CB) [> 4.3010 = 7.1684 < 9.3189] w=0.2419 to align # Constraint # added constraint: constraint((T0348)C11.CB, (T0348)F36.CB) [> 3.4585 = 5.7642 < 7.4935] w=0.1820 to align # Constraint # added constraint: constraint((T0348)P12.CB, (T0348)P43.CB) [> 3.5293 = 5.8821 < 7.6468] w=0.1249 to align # Constraint # added constraint: constraint((T0348)P43.CB, (T0348)L53.CB) [> 3.3735 = 5.6226 < 7.3094] w=0.1246 to align # Constraint # added constraint: constraint((T0348)I42.CB, (T0348)L53.CB) [> 3.1845 = 5.3075 < 6.8998] w=0.1246 to align # Constraint # added constraint: constraint((T0348)L13.CB, (T0348)F36.CB) [> 3.2192 = 5.3654 < 6.9750] w=0.1182 to align # Constraint # added constraint: constraint((T0348)F36.CB, (T0348)L46.CB) [> 3.6710 = 6.1183 < 7.9538] w=0.1056 to align # Constraint # added constraint: constraint((T0348)K15.CB, (T0348)G31.CA) [> 3.5735 = 5.9559 < 7.7426] w=0.1055 to align # Constraint # added constraint: constraint((T0348)K15.CB, (T0348)C29.CB) [> 3.9391 = 6.5652 < 8.5347] w=0.1055 to align # Constraint # added constraint: constraint((T0348)I38.CB, (T0348)L61.CB) [> 3.4868 = 5.8113 < 7.5546] w=0.1055 to align # Constraint # added constraint: constraint((T0348)P12.CB, (T0348)M44.CB) [> 4.1044 = 6.8406 < 8.8928] w=0.1048 to align # Constraint # added constraint: constraint((T0348)P37.CB, (T0348)A50.CB) [> 3.6268 = 6.0447 < 7.8581] w=0.1043 to align # Constraint # added constraint: constraint((T0348)A35.CB, (T0348)L46.CB) [> 3.2701 = 5.4502 < 7.0852] w=0.1043 to align # Constraint # added constraint: constraint((T0348)A35.CB, (T0348)M45.CB) [> 4.4349 = 7.3916 < 9.6090] w=0.1043 to align # Constraint # added constraint: constraint((T0348)A35.CB, (T0348)M44.CB) [> 3.1712 = 5.2853 < 6.8709] w=0.1031 to align # Constraint # added constraint: constraint((T0348)C29.CB, (T0348)I38.CB) [> 4.2430 = 7.0717 < 9.1932] w=0.0846 to align # Constraint # added constraint: constraint((T0348)I28.CB, (T0348)I38.CB) [> 4.0407 = 6.7344 < 8.7548] w=0.0846 to align # Constraint # added constraint: constraint((T0348)L18.CB, (T0348)P43.CB) [> 3.4177 = 5.6961 < 7.4049] w=0.0831 to align # Constraint # added constraint: constraint((T0348)F20.CB, (T0348)G41.CA) [> 4.0736 = 6.7893 < 8.8261] w=0.0831 to align # Constraint # added constraint: constraint((T0348)L27.CB, (T0348)P43.CB) [> 2.8367 = 4.7278 < 6.1461] w=0.0831 to align # Constraint # added constraint: constraint((T0348)I42.CB, (T0348)A54.CB) [> 3.6380 = 6.0634 < 7.8824] w=0.0831 to align # Constraint # added constraint: constraint((T0348)D40.CB, (T0348)L61.CB) [> 3.3569 = 5.5948 < 7.2732] w=0.0818 to align # Constraint # added constraint: constraint((T0348)L9.CB, (T0348)L18.CB) [> 3.8206 = 6.3677 < 8.2780] w=0.0710 to align # Constraint # added constraint: constraint((T0348)C11.CB, (T0348)P43.CB) [> 4.6839 = 7.8064 < 10.1484] w=0.0641 to align # Constraint # added constraint: constraint((T0348)F20.CB, (T0348)I38.CB) [> 3.8869 = 6.4781 < 8.4215] w=0.0641 to align # Constraint # added constraint: constraint((T0348)D25.CB, (T0348)L46.CB) [> 4.3767 = 7.2944 < 9.4828] w=0.0641 to align # Constraint # added constraint: constraint((T0348)D25.CB, (T0348)A50.CB) [> 4.2545 = 7.0908 < 9.2180] w=0.0641 to align # Constraint # added constraint: constraint((T0348)L34.CB, (T0348)M45.CB) [> 4.2167 = 7.0279 < 9.1363] w=0.0641 to align # Constraint # added constraint: constraint((T0348)P37.CB, (T0348)L46.CB) [> 3.2927 = 5.4879 < 7.1343] w=0.0641 to align # Constraint # added constraint: constraint((T0348)E26.CB, (T0348)K39.CB) [> 4.0713 = 6.7854 < 8.8210] w=0.0639 to align # Constraint # added constraint: constraint((T0348)L34.CB, (T0348)P43.CB) [> 4.6395 = 7.7325 < 10.0522] w=0.0629 to align # Constraint # added constraint: constraint((T0348)I42.CB, (T0348)L61.CB) [> 4.1555 = 6.9258 < 9.0035] w=0.0603 to align # Constraint # added constraint: constraint((T0348)C11.CB, (T0348)L27.CB) [> 4.7345 = 7.8908 < 10.2581] w=0.0596 to align # Constraint # added constraint: constraint((T0348)F5.CB, (T0348)L18.CB) [> 3.9930 = 6.6550 < 8.6516] w=0.0515 to align # Constraint # added constraint: constraint((T0348)F5.CB, (T0348)L27.CB) [> 4.3353 = 7.2255 < 9.3931] w=0.0515 to align # Constraint # added constraint: constraint((T0348)I8.CB, (T0348)P17.CB) [> 4.2969 = 7.1615 < 9.3100] w=0.0515 to align # Constraint # added constraint: constraint((T0348)I8.CB, (T0348)L18.CB) [> 3.0447 = 5.0744 < 6.5967] w=0.0515 to align # Constraint # added constraint: constraint((T0348)L9.CB, (T0348)V19.CB) [> 4.6426 = 7.7377 < 10.0591] w=0.0515 to align # Constraint # added constraint: constraint((T0348)L9.CB, (T0348)F20.CB) [> 3.8485 = 6.4142 < 8.3384] w=0.0515 to align # Constraint # added constraint: constraint((T0348)L9.CB, (T0348)L27.CB) [> 3.6388 = 6.0647 < 7.8841] w=0.0515 to align # Constraint # added constraint: constraint((T0348)V10.CB, (T0348)C29.CB) [> 4.6185 = 7.6976 < 10.0069] w=0.0427 to align # Constraint # added constraint: constraint((T0348)E47.CB, (T0348)E58.CB) [> 4.1304 = 6.8840 < 8.9492] w=0.0427 to align # Constraint # added constraint: constraint((T0348)E49.CB, (T0348)E58.CB) [> 3.8181 = 6.3635 < 8.2726] w=0.0427 to align # Constraint # added constraint: constraint((T0348)D25.CB, (T0348)I42.CB) [> 2.5337 = 4.2228 < 5.4896] w=0.0426 to align # Constraint # added constraint: constraint((T0348)L18.CB, (T0348)L46.CB) [> 3.4894 = 5.8157 < 7.5604] w=0.0403 to align # Constraint # added constraint: constraint((T0348)G16.CA, (T0348)L46.CB) [> 4.2716 = 7.1193 < 9.2551] w=0.0403 to align # Constraint # added constraint: constraint((T0348)L13.CB, (T0348)M45.CB) [> 3.0315 = 5.0526 < 6.5683] w=0.0403 to align # Constraint # added constraint: constraint((T0348)P37.CB, (T0348)L53.CB) [> 4.2553 = 7.0922 < 9.2199] w=0.0403 to align # Constraint # added constraint: constraint((T0348)A35.CB, (T0348)A50.CB) [> 4.5300 = 7.5499 < 9.8149] w=0.0403 to align # Constraint # added constraint: constraint((T0348)A35.CB, (T0348)E47.CB) [> 4.1113 = 6.8521 < 8.9078] w=0.0403 to align # Constraint # added constraint: constraint((T0348)R33.CB, (T0348)M44.CB) [> 4.2418 = 7.0697 < 9.1906] w=0.0403 to align # Constraint # added constraint: constraint((T0348)D32.CB, (T0348)E47.CB) [> 3.8394 = 6.3991 < 8.3188] w=0.0403 to align # Constraint # added constraint: constraint((T0348)D32.CB, (T0348)L46.CB) [> 3.3984 = 5.6640 < 7.3632] w=0.0403 to align # Constraint # added constraint: constraint((T0348)C14.CB, (T0348)P37.CB) [> 3.4883 = 5.8139 < 7.5580] w=0.0392 to align # Constraint # added constraint: constraint((T0348)G16.CA, (T0348)I28.CB) [> 3.4298 = 5.7164 < 7.4313] w=0.0210 to align # Constraint # added constraint: constraint((T0348)P17.CB, (T0348)I28.CB) [> 2.5612 = 4.2687 < 5.5493] w=0.0210 to align # Constraint # added constraint: constraint((T0348)P37.CB, (T0348)R51.CB) [> 3.9392 = 6.5654 < 8.5351] w=0.0208 to align # Constraint # added constraint: constraint((T0348)C14.CB, (T0348)M45.CB) [> 4.7983 = 7.9972 < 10.3963] w=0.0207 to align # Constraint # added constraint: constraint((T0348)C14.CB, (T0348)L46.CB) [> 3.4263 = 5.7105 < 7.4237] w=0.0207 to align # Constraint # added constraint: constraint((T0348)L6.CB, (T0348)L18.CB) [> 4.3950 = 7.3249 < 9.5224] w=0.0195 to align # Constraint # added constraint: constraint((T0348)P12.CB, (T0348)M45.CB) [> 4.7103 = 7.8505 < 10.2057] w=0.0195 to align # Constraint # added constraint: constraint((T0348)L13.CB, (T0348)A50.CB) [> 4.7223 = 7.8705 < 10.2316] w=0.0195 to align # Constraint # added constraint: constraint((T0348)L18.CB, (T0348)M44.CB) [> 4.6389 = 7.7316 < 10.0510] w=0.0195 to align # Constraint # added constraint: constraint((T0348)D32.CB, (T0348)M44.CB) [> 4.6351 = 7.7252 < 10.0427] w=0.0195 to align # Constraint # added constraint: constraint((T0348)D32.CB, (T0348)M45.CB) [> 4.7753 = 7.9588 < 10.3465] w=0.0195 to align # SetCost created cost = # ( 1.0000 * align ) # command:# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0348/ # command:# reading script from file servers-clean.under # Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/T0348/decoys/ # ReadConformPDB reading from PDB file chimera-M1-K60-2-8.pdb.gz looking for model 1 # Found a chain break before 45 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS1.pdb.gz looking for model 1 # Found a chain break before 58 # 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 # Found a chain break before 42 # copying to AlignedFragments data structure # naming current conformation 3D-JIGSAW_POPULUS_TS2 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0348 can't currently be optimized by undertaker # 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 # Found a chain break before 58 # copying to AlignedFragments data structure # 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 58 # 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 T0348 can't currently be optimized by undertaker # copying to AlignedFragments data structure # 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 T0348 can't currently be optimized by undertaker # copying to AlignedFragments data structure # 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 T0348 can't currently be optimized by undertaker # copying to AlignedFragments data structure # 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 T0348 can't currently be optimized by undertaker # copying to AlignedFragments data structure # 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 T0348 can't currently be optimized by undertaker # copying to AlignedFragments data structure # 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 T0348 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation 3D-JIGSAW_TS1 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0348 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 T0348 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation 3D-JIGSAW_TS3 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0348 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 # Found a chain break before 58 # copying to AlignedFragments data structure # 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 # naming current conformation 3Dpro_TS2 # ReadConformPDB reading from PDB file servers/3Dpro_TS3.pdb.gz looking for model 1 # Found a chain break before 17 # 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 57 # 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 59 # 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 57 # 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 59 # 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 63 # 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 45 # 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 34 # 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 48 # 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 # Found a chain break before 67 # copying to AlignedFragments data structure # naming current conformation Bilab-ENABLE_TS2 # ReadConformPDB reading from PDB file servers/Bilab-ENABLE_TS3.pdb.gz looking for model 1 # Found a chain break before 67 # copying to AlignedFragments data structure # 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 67 # 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 67 # 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 64 # copying to AlignedFragments data structure # naming current conformation CIRCLE_TS1 # ReadConformPDB reading from PDB file servers/CIRCLE_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0348 can't currently be optimized by undertaker # naming current conformation CIRCLE_TS2 # ReadConformPDB reading from PDB file servers/CIRCLE_TS3.pdb.gz looking for model 1 # Found a chain break before 54 # 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 43 # 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 43 # 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 T0348 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 # Found a chain break before 54 # copying to AlignedFragments data structure # naming current conformation CaspIta-FOX_TS2 # ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0348 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 T0348 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: atoms too close: (T0348)S48.C and (T0348)E49.N only 0.000 apart, marking (T0348)E49.N as missing WARNING: atoms too close: (T0348)E49.N and (T0348)E49.CA only 0.000 apart, marking (T0348)E49.CA as missing WARNING: atoms too close: (T0348)S48.C and (T0348)E49.CA only 0.000 apart, marking (T0348)E49.CA as missing WARNING: atoms too close: (T0348)E49.CA and (T0348)E49.CB only 0.000 apart, marking (T0348)E49.CB as missing WARNING: atoms too close: (T0348)E49.N and (T0348)E49.CB only 0.000 apart, marking (T0348)E49.CB as missing WARNING: atoms too close: (T0348)S48.C and (T0348)E49.CB only 0.000 apart, marking (T0348)E49.CB as missing WARNING: atoms too close: (T0348)E49.CB and (T0348)E49.CG only 0.000 apart, marking (T0348)E49.CG as missing WARNING: atoms too close: (T0348)E49.CA and (T0348)E49.CG only 0.000 apart, marking (T0348)E49.CG as missing WARNING: atoms too close: (T0348)E49.N and (T0348)E49.CG only 0.000 apart, marking (T0348)E49.CG as missing WARNING: atoms too close: (T0348)S48.C and (T0348)E49.CG only 0.000 apart, marking (T0348)E49.CG as missing WARNING: atoms too close: (T0348)E49.CG and (T0348)E49.CD only 0.000 apart, marking (T0348)E49.CD as missing WARNING: atoms too close: (T0348)E49.CB and (T0348)E49.CD only 0.000 apart, marking (T0348)E49.CD as missing WARNING: atoms too close: (T0348)E49.CA and (T0348)E49.CD only 0.000 apart, marking (T0348)E49.CD as missing WARNING: atoms too close: (T0348)E49.N and (T0348)E49.CD only 0.000 apart, marking (T0348)E49.CD as missing WARNING: atoms too close: (T0348)S48.C and (T0348)E49.CD only 0.000 apart, marking (T0348)E49.CD as missing WARNING: atoms too close: (T0348)E49.CD and (T0348)E49.OE1 only 0.000 apart, marking (T0348)E49.OE1 as missing WARNING: atoms too close: (T0348)E49.CG and (T0348)E49.OE1 only 0.000 apart, marking (T0348)E49.OE1 as missing WARNING: atoms too close: (T0348)E49.CB and (T0348)E49.OE1 only 0.000 apart, marking (T0348)E49.OE1 as missing WARNING: atoms too close: (T0348)E49.CA and (T0348)E49.OE1 only 0.000 apart, marking (T0348)E49.OE1 as missing WARNING: atoms too close: (T0348)E49.N and (T0348)E49.OE1 only 0.000 apart, marking (T0348)E49.OE1 as missing WARNING: atoms too close: (T0348)S48.C and (T0348)E49.OE1 only 0.000 apart, marking (T0348)E49.OE1 as missing WARNING: atoms too close: (T0348)E49.OE1 and (T0348)E49.OE2 only 0.000 apart, marking (T0348)E49.OE2 as missing WARNING: atoms too close: (T0348)E49.CD and (T0348)E49.OE2 only 0.000 apart, marking (T0348)E49.OE2 as missing WARNING: atoms too close: (T0348)E49.CG and (T0348)E49.OE2 only 0.000 apart, marking (T0348)E49.OE2 as missing WARNING: atoms too close: (T0348)E49.CB and (T0348)E49.OE2 only 0.000 apart, marking (T0348)E49.OE2 as missing WARNING: atoms too close: (T0348)E49.CA and (T0348)E49.OE2 only 0.000 apart, marking (T0348)E49.OE2 as missing WARNING: atoms too close: (T0348)E49.N and (T0348)E49.OE2 only 0.000 apart, marking (T0348)E49.OE2 as missing WARNING: atoms too close: (T0348)S48.C and (T0348)E49.OE2 only 0.000 apart, marking (T0348)E49.OE2 as missing WARNING: atoms too close: (T0348)E49.OE2 and (T0348)E49.O only 0.000 apart, marking (T0348)E49.O as missing WARNING: atoms too close: (T0348)E49.OE1 and (T0348)E49.O only 0.000 apart, marking (T0348)E49.O as missing WARNING: atoms too close: (T0348)E49.CD and (T0348)E49.O only 0.000 apart, marking (T0348)E49.O as missing WARNING: atoms too close: (T0348)E49.CG and (T0348)E49.O only 0.000 apart, marking (T0348)E49.O as missing WARNING: atoms too close: (T0348)E49.CB and (T0348)E49.O only 0.000 apart, marking (T0348)E49.O as missing WARNING: atoms too close: (T0348)E49.CA and (T0348)E49.O only 0.000 apart, marking (T0348)E49.O as missing WARNING: atoms too close: (T0348)E49.N and (T0348)E49.O only 0.000 apart, marking (T0348)E49.O as missing WARNING: atoms too close: (T0348)S48.C and (T0348)E49.O only 0.000 apart, marking (T0348)E49.O as missing WARNING: atoms too close: (T0348)E49.O and (T0348)E49.C only 0.000 apart, marking (T0348)E49.C as missing WARNING: atoms too close: (T0348)E49.OE2 and (T0348)E49.C only 0.000 apart, marking (T0348)E49.C as missing WARNING: atoms too close: (T0348)E49.OE1 and (T0348)E49.C only 0.000 apart, marking (T0348)E49.C as missing WARNING: atoms too close: (T0348)E49.CD and (T0348)E49.C only 0.000 apart, marking (T0348)E49.C as missing WARNING: atoms too close: (T0348)E49.CG and (T0348)E49.C only 0.000 apart, marking (T0348)E49.C as missing WARNING: atoms too close: (T0348)E49.CB and (T0348)E49.C only 0.000 apart, marking (T0348)E49.C as missing WARNING: atoms too close: (T0348)E49.CA and (T0348)E49.C only 0.000 apart, marking (T0348)E49.C as missing WARNING: atoms too close: (T0348)E49.N and (T0348)E49.C only 0.000 apart, marking (T0348)E49.C as missing WARNING: atoms too close: (T0348)S48.C and (T0348)E49.C only 0.000 apart, marking (T0348)E49.C as missing # WARNING: incomplete conformation T0348 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 T0348 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 T0348 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 T0348 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 T0348 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 T0348 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 66 # 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 57 # 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 T0348 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation FAMSD_TS3 # ReadConformPDB reading from PDB file servers/FAMSD_TS4.pdb.gz looking for model 1 # Found a chain break before 56 # copying to AlignedFragments data structure # naming current conformation FAMSD_TS4 # ReadConformPDB reading from PDB file servers/FAMSD_TS5.pdb.gz looking for model 1 # Found a chain break before 46 # copying to AlignedFragments data structure # naming current conformation FAMSD_TS5 # ReadConformPDB reading from PDB file servers/FAMS_TS1.pdb.gz looking for model 1 # Found a chain break before 65 # 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 64 # copying to AlignedFragments data structure # naming current conformation FAMS_TS2 # ReadConformPDB reading from PDB file servers/FAMS_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0348 can't currently be optimized by undertaker # naming current conformation FAMS_TS3 # ReadConformPDB reading from PDB file servers/FAMS_TS4.pdb.gz looking for model 1 # Found a chain break before 54 # copying to AlignedFragments data structure # naming current conformation FAMS_TS4 # ReadConformPDB reading from PDB file servers/FAMS_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0348 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation FAMS_TS5 # ReadConformPDB reading from PDB file servers/FOLDpro_TS1.pdb.gz looking for model 1 # Found a chain break before 38 # copying to AlignedFragments data structure # naming current conformation FOLDpro_TS1 # ReadConformPDB reading from PDB file servers/FOLDpro_TS2.pdb.gz looking for model 1 # naming current conformation FOLDpro_TS2 # ReadConformPDB reading from PDB file servers/FOLDpro_TS3.pdb.gz looking for model 1 # naming current conformation FOLDpro_TS3 # ReadConformPDB reading from PDB file servers/FOLDpro_TS4.pdb.gz looking for model 1 # 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 T0348 can't currently be optimized by undertaker # naming current conformation FORTE1_AL1 # ReadConformPDB reading from PDB file servers/FORTE1_AL2.pdb.gz looking for model 1 Skipped atom 30, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL2.pdb.gz Skipped atom 32, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL2.pdb.gz Skipped atom 34, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL2.pdb.gz Skipped atom 36, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL2.pdb.gz # WARNING: incomplete conformation T0348 can't currently be optimized by undertaker # naming current conformation FORTE1_AL2 # ReadConformPDB reading from PDB file servers/FORTE1_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0348 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation FORTE1_AL3 # ReadConformPDB reading from PDB file servers/FORTE1_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0348 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation FORTE1_AL4 # ReadConformPDB reading from PDB file servers/FORTE1_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0348 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation FORTE1_AL5 # ReadConformPDB reading from PDB file servers/FORTE2_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0348 can't currently be optimized by undertaker # naming current conformation FORTE2_AL1 # ReadConformPDB reading from PDB file servers/FORTE2_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0348 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation FORTE2_AL2 # ReadConformPDB reading from PDB file servers/FORTE2_AL3.pdb.gz looking for model 1 Skipped atom 30, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL3.pdb.gz Skipped atom 32, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL3.pdb.gz Skipped atom 34, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL3.pdb.gz Skipped atom 36, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL3.pdb.gz # WARNING: incomplete conformation T0348 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 T0348 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation FORTE2_AL4 # ReadConformPDB reading from PDB file servers/FORTE2_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0348 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation FORTE2_AL5 # ReadConformPDB reading from PDB file servers/FPSOLVER-SERVER_TS1.pdb.gz looking for model 1 # 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 23 # 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 # Found a chain break before 16 # copying to AlignedFragments data structure # naming current conformation FPSOLVER-SERVER_TS3 # ReadConformPDB reading from PDB file servers/FPSOLVER-SERVER_TS4.pdb.gz looking for model 1 # naming current conformation FPSOLVER-SERVER_TS4 # ReadConformPDB reading from PDB file servers/FPSOLVER-SERVER_TS5.pdb.gz looking for model 1 # naming current conformation FPSOLVER-SERVER_TS5 # ReadConformPDB reading from PDB file servers/FUGMOD_TS1.pdb.gz looking for model 1 # Found a chain break before 21 # copying to AlignedFragments data structure # naming current conformation FUGMOD_TS1 # ReadConformPDB reading from PDB file servers/FUGMOD_TS2.pdb.gz looking for model 1 # naming current conformation FUGMOD_TS2 # ReadConformPDB reading from PDB file servers/FUGMOD_TS3.pdb.gz looking for model 1 # 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 # naming current conformation FUGMOD_TS5 # ReadConformPDB reading from PDB file servers/FUGUE_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0348 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 T0348 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation FUGUE_AL2 # ReadConformPDB reading from PDB file servers/FUGUE_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0348 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation FUGUE_AL3 # ReadConformPDB reading from PDB file servers/FUGUE_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0348 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation FUGUE_AL4 # ReadConformPDB reading from PDB file servers/FUGUE_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0348 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 # WARNING: incomplete conformation T0348 can't currently be optimized by undertaker # naming current conformation FUNCTION_TS1 # ReadConformPDB reading from PDB file servers/FUNCTION_TS2.pdb.gz looking for model 1 # Found a chain break before 67 # 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 63 # 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 55 # 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 58 # copying to AlignedFragments data structure # naming current conformation FUNCTION_TS5 # ReadConformPDB reading from PDB file servers/Frankenstein_TS1.pdb.gz looking for model 1 # naming current conformation Frankenstein_TS1 # ReadConformPDB reading from PDB file servers/Frankenstein_TS2.pdb.gz looking for model 1 # Found a chain break before 5 # copying to AlignedFragments data structure # naming current conformation Frankenstein_TS2 # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0348 can't currently be optimized by undertaker # naming current conformation GeneSilicoMetaServer_TS1 # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS2.pdb.gz looking for model 1 # naming current conformation GeneSilicoMetaServer_TS2 # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0348 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 T0348 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 # WARNING: incomplete conformation T0348 can't currently be optimized by undertaker # naming current conformation GeneSilicoMetaServer_TS5 # ReadConformPDB reading from PDB file servers/HHpred1_TS1.pdb.gz looking for model 1 # Found a chain break before 10 # 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 10 # copying to AlignedFragments data structure # naming current conformation HHpred2_TS1 # ReadConformPDB reading from PDB file servers/HHpred3_TS1.pdb.gz looking for model 1 # naming current conformation HHpred3_TS1 # ReadConformPDB reading from PDB file servers/Huber-Torda-Server_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0348 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 T0348 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 T0348 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 T0348 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 T0348 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 T0348 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 # WARNING: incomplete conformation T0348 can't currently be optimized by undertaker # naming current conformation LOOPP_TS2 # ReadConformPDB reading from PDB file servers/LOOPP_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0348 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 T0348 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 T0348 can't currently be optimized by undertaker # naming current conformation LOOPP_TS5 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server2_TS1.pdb.gz looking for model 1 # 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 # naming current conformation Ma-OPUS-server2_TS3 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server2_TS4.pdb.gz looking for model 1 # naming current conformation Ma-OPUS-server2_TS4 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server2_TS5.pdb.gz looking for model 1 # 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 # naming current conformation Ma-OPUS-server_TS2 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS3.pdb.gz looking for model 1 # Found a chain break before 37 # copying to AlignedFragments data structure # 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 52 # 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 # 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 49 # 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 66 # 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 64 # 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 54 # 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 67 # 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 # WARNING: incomplete conformation T0348 can't currently be optimized by undertaker # 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 28 # 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 33 # 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 67 # 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 65 # 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 39 # 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 # Found a chain break before 37 # copying to AlignedFragments data structure # naming current conformation PROTINFO_TS1 # ReadConformPDB reading from PDB file servers/PROTINFO_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0348 can't currently be optimized by undertaker # naming current conformation PROTINFO_TS2 # ReadConformPDB reading from PDB file servers/PROTINFO_TS3.pdb.gz looking for model 1 # Found a chain break before 46 # copying to AlignedFragments data structure # naming current conformation PROTINFO_TS3 # ReadConformPDB reading from PDB file servers/PROTINFO_TS4.pdb.gz looking for model 1 # Found a chain break before 37 # copying to AlignedFragments data structure # naming current conformation PROTINFO_TS4 # ReadConformPDB reading from PDB file servers/PROTINFO_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0348 can't currently be optimized by undertaker # naming current conformation PROTINFO_TS5 # ReadConformPDB reading from PDB file servers/Pcons6_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0348 can't currently be optimized by undertaker # naming current conformation Pcons6_TS1 # ReadConformPDB reading from PDB file servers/Pcons6_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0348 can't currently be optimized by undertaker # naming current conformation Pcons6_TS2 # ReadConformPDB reading from PDB file servers/Pcons6_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0348 can't currently be optimized by undertaker # naming current conformation Pcons6_TS3 # ReadConformPDB reading from PDB file servers/Pcons6_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0348 can't currently be optimized by undertaker # naming current conformation Pcons6_TS4 # ReadConformPDB reading from PDB file servers/Pcons6_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0348 can't currently be optimized by undertaker # naming current conformation Pcons6_TS5 # ReadConformPDB reading from PDB file servers/Phyre-1_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0348 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 # Found a chain break before 65 # copying to AlignedFragments data structure # naming current conformation Phyre-2_TS1 # ReadConformPDB reading from PDB file servers/Phyre-2_TS2.pdb.gz looking for model 1 # Found a chain break before 65 # 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 # Found a chain break before 65 # 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 # naming current conformation Phyre-2_TS4 # ReadConformPDB reading from PDB file servers/Phyre-2_TS5.pdb.gz looking for model 1 # Found a chain break before 20 # 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 # WARNING: incomplete conformation T0348 can't currently be optimized by undertaker # naming current conformation Pmodeller6_TS1 # ReadConformPDB reading from PDB file servers/Pmodeller6_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0348 can't currently be optimized by undertaker # naming current conformation Pmodeller6_TS2 # ReadConformPDB reading from PDB file servers/Pmodeller6_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0348 can't currently be optimized by undertaker # naming current conformation Pmodeller6_TS3 # ReadConformPDB reading from PDB file servers/Pmodeller6_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0348 can't currently be optimized by undertaker # naming current conformation Pmodeller6_TS4 # ReadConformPDB reading from PDB file servers/Pmodeller6_TS5.pdb.gz looking for model 1 # 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 # naming current conformation RAPTOR-ACE_TS3 # ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS4.pdb.gz looking for model 1 # Found a chain break before 10 # copying to AlignedFragments data structure # naming current conformation RAPTOR-ACE_TS4 # ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS5.pdb.gz looking for model 1 # Found a chain break before 17 # copying to AlignedFragments data structure # 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 36 # 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 36 # copying to AlignedFragments data structure # naming current conformation RAPTORESS_TS3 # ReadConformPDB reading from PDB file servers/RAPTORESS_TS4.pdb.gz looking for model 1 # Found a chain break before 36 # copying to AlignedFragments data structure # naming current conformation RAPTORESS_TS4 # ReadConformPDB reading from PDB file servers/RAPTORESS_TS5.pdb.gz looking for model 1 # Found a chain break before 42 # copying to AlignedFragments data structure # naming current conformation RAPTORESS_TS5 # ReadConformPDB reading from PDB file servers/RAPTOR_TS1.pdb.gz looking for model 1 # 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 40 # 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 21 # 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 T0348 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 T0348 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 T0348 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 T0348 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 T0348 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 T0348 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 T0348 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 T0348 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 T0348 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 T0348 can't currently be optimized by undertaker # naming current conformation SAM-T02_AL5 # ReadConformPDB reading from PDB file servers/SAM-T99_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0348 can't currently be optimized by undertaker # naming current conformation SAM-T99_AL1 # ReadConformPDB reading from PDB file servers/SAM_T06_server_TS1.pdb.gz looking for model 1 # Found a chain break before 62 # 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 T0348 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 T0348 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 T0348 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 T0348 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 # naming current conformation SP3_TS1 # ReadConformPDB reading from PDB file servers/SP3_TS2.pdb.gz looking for model 1 # Found a chain break before 41 # 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 8 # copying to AlignedFragments data structure # naming current conformation SP3_TS3 # ReadConformPDB reading from PDB file servers/SP3_TS4.pdb.gz looking for model 1 # 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 8 # copying to AlignedFragments data structure # naming current conformation SP4_TS2 # ReadConformPDB reading from PDB file servers/SP4_TS3.pdb.gz looking for model 1 # 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 # naming current conformation SP4_TS5 # ReadConformPDB reading from PDB file servers/SPARKS2_TS1.pdb.gz looking for model 1 # Found a chain break before 26 # 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 37 # copying to AlignedFragments data structure # naming current conformation SPARKS2_TS2 # ReadConformPDB reading from PDB file servers/SPARKS2_TS3.pdb.gz looking for model 1 # naming current conformation SPARKS2_TS3 # ReadConformPDB reading from PDB file servers/SPARKS2_TS4.pdb.gz looking for model 1 # naming current conformation SPARKS2_TS4 # ReadConformPDB reading from PDB file servers/SPARKS2_TS5.pdb.gz looking for model 1 # Found a chain break before 43 # 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 T0348 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 T0348 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 T0348 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 T0348 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 T0348 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 T0348 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 T0348 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 T0348 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 T0348 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 T0348 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 T0348 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 55 # 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 45 # 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 64 # 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 54 # 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 65 # 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 65 # 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 T0348 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 T0348 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation forecast-s_AL1 # ReadConformPDB reading from PDB file servers/forecast-s_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0348 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 T0348 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation forecast-s_AL3 # ReadConformPDB reading from PDB file servers/forecast-s_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0348 can't currently be optimized by undertaker # naming current conformation forecast-s_AL4 # ReadConformPDB reading from PDB file servers/forecast-s_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0348 can't currently be optimized by undertaker # copying to AlignedFragments data structure # 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 11 # 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 # naming current conformation karypis.srv.2_TS3 # ReadConformPDB reading from PDB file servers/karypis.srv.2_TS4.pdb.gz looking for model 1 # Found a chain break before 42 # copying to AlignedFragments data structure # 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 49 # 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 # Found a chain break before 65 # copying to AlignedFragments data structure # naming current conformation karypis.srv.4_TS1 # ReadConformPDB reading from PDB file servers/karypis.srv.4_TS3.pdb.gz looking for model 1 WARNING: atoms too close: (T0348)H65.O and (T0348)H66.N only 0.000 apart, marking (T0348)H66.N as missing # WARNING: incomplete conformation T0348 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_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0348 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 # WARNING: incomplete conformation T0348 can't currently be optimized by undertaker # naming current conformation karypis.srv_TS2 # ReadConformPDB reading from PDB file servers/karypis.srv_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0348 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 T0348 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 T0348 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 # naming current conformation keasar-server_TS1 # ReadConformPDB reading from PDB file servers/keasar-server_TS2.pdb.gz looking for model 1 # naming current conformation keasar-server_TS2 # ReadConformPDB reading from PDB file servers/keasar-server_TS3.pdb.gz looking for model 1 # naming current conformation keasar-server_TS3 # ReadConformPDB reading from PDB file servers/keasar-server_TS4.pdb.gz looking for model 1 # naming current conformation keasar-server_TS4 # ReadConformPDB reading from PDB file servers/keasar-server_TS5.pdb.gz looking for model 1 # naming current conformation keasar-server_TS5 # ReadConformPDB reading from PDB file servers/mGen-3D_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0348 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: incomplete conformation T0348 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 T0348 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: incomplete conformation T0348 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 T0348 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: incomplete conformation T0348 can't currently be optimized by undertaker # naming current conformation nFOLD_TS5 # ReadConformPDB reading from PDB file servers/shub_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0348 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 -0.2510 model score 1.5937 model score 2.4659 model score 1.7250 model score 2.1619 model score 2.4382 model score 1.3014 model score 1.1953 model score 1.1815 model score 1.1891 model score 1.1888 model score 1.4187 model score 0.8407 model score 1.5075 model score 1.4118 model score 2.2686 model score 0.1909 model score 1.1824 model score 0.3162 model score 0.0696 model score 0.4665 model score 0.0696 model score 0.4665 model score 0.2824 model score 0.5892 model score 0.2354 model score 0.1476 model score 1.6976 model score 2.0642 model score 2.0456 model score 2.0846 model score 2.1088 model score 0.6309 model score 0.6093 model score 1.3636 model score 1.1202 model score 1.2989 model score 1.2797 model score 2.6511 model score -0.0068 model score 1.2945 model score 1.1262 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 0.6607 model score 0.6464 model score 1.4543 model score 1.8042 model score 0.9972 model score 0.7596 model score 0.6309 model score 0.6093 model score 1.3636 model score 1.3713 model score 0.2684 model score 0.2489 model score 0.3115 model score 1.9559 model score 0.4214 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 1.9224 model score 1.8477 model score 1.2618 model score 1.8412 model score 1.5048 model score 1.5444 model score 2.0223 model score 1.5979 model score 1.6737 model score 2.6111 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 0.0318 model score 1.4301 model score 0.9449 model score 1.6566 model score 1.6668 model score 1.5400 model score 1.1926 model score 0.0098 model score -0.0062 model score 0.2372 model score 0.2093 model score 1.0979 model score -0.0222 model score -0.0222 model score -0.0357 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.3224 model score 0.7804 model score 1.4690 model score 0.4748 model score 1.4825 model score 1.5500 model score 1.7944 model score 0.1568 model score 1.2593 model score 1.5923 model score 1.5500 model score 1.2059 model score 1.7940 model score 1.1604 model score 1.7944 model score -0.2333 model score -0.1970 model score -0.1482 model score -0.2116 model score -0.1196 model score 1.2771 model score 1.0448 model score 0.9900 model score 1.8442 model score 2.4421 model score 1.6799 model score -0.2100 model score -0.1353 model score -0.2196 model score -0.2174 model score -0.1416 model score -0.2052 model score 0.0207 model score -0.2548 model score -0.1275 model score 0.1744 model score -0.2330 model score -0.0918 model score -0.1642 model score -0.2454 model score -0.2265 model score 0.2754 model score -0.1493 model score 0.3973 model score 0.3455 model score 0.2932 model score 0.3782 model score -0.2452 model score -0.2454 model score -0.0942 model score -0.2330 model score -0.0879 model score 1.8469 model score 1.8348 model score 0.8112 model score 1.6636 model score 0.9463 model score 1.2723 model score 1.1215 model score 1.1819 model score 1.5618 model score 0.9138 model score 1.1340 model score 1.1641 model score 1.2293 model score 1.4964 model score 0.5926 model score 0.0551 model score -0.0003 model score -0.0879 model score -0.1345 model score 0.1929 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 1.2771 model score -0.2799 model score 0.4441 model score 0.2375 model score -0.0584 model score -0.2935 model score 1.3281 model score 0.1393 model score 0.3222 model score 0.8030 model score 0.0791 model score 1.4335 model score 0.3222 model score 0.1172 model score 0.5462 model score 2.1344 model score 1.3623 model score 1.6632 model score 0.0845 model score 1.5905 model score 2.1300 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score -0.1906 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score -0.2166 model score -0.1657 model score -0.2351 model score 0.0763 model score -0.0356 model score 0.1706 model score 0.0215 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2510 model score 1.5109 model score 0.7339 model score 1.6413 model score 1.1834 model score 1.3458 model score 1.8082 model score 1.7858 model score 1.5415 model score 1.4839 model score 1.3539 model score 1.0947 model score 0.0959 model score -0.1843 model score 0.2642 model score -0.1568 model score 0.0324 model score 0.3077 model score 1.9368 model score 0.7942 model score 1.5181 model score 1.4584 model score 1.8380 model score 0.1318 USE_META, weight: 0.9870 cost: -0.2510 min: -0.2935 max: 2.6511 USE_META, weight: 0.4232 cost: 1.5937 min: -0.2935 max: 2.6511 USE_META, weight: 0.1566 cost: 2.4659 min: -0.2935 max: 2.6511 USE_META, weight: 0.3830 cost: 1.7250 min: -0.2935 max: 2.6511 USE_META, weight: 0.2495 cost: 2.1619 min: -0.2935 max: 2.6511 USE_META, weight: 0.1651 cost: 2.4382 min: -0.2935 max: 2.6511 USE_META, weight: 0.5125 cost: 1.3014 min: -0.2935 max: 2.6511 USE_META, weight: 0.5450 cost: 1.1953 min: -0.2935 max: 2.6511 USE_META, weight: 0.5492 cost: 1.1815 min: -0.2935 max: 2.6511 USE_META, weight: 0.5468 cost: 1.1891 min: -0.2935 max: 2.6511 USE_META, weight: 0.5470 cost: 1.1888 min: -0.2935 max: 2.6511 USE_META, weight: 0.4767 cost: 1.4187 min: -0.2935 max: 2.6511 USE_META, weight: 0.6533 cost: 0.8407 min: -0.2935 max: 2.6511 USE_META, weight: 0.4495 cost: 1.5075 min: -0.2935 max: 2.6511 USE_META, weight: 0.4788 cost: 1.4118 min: -0.2935 max: 2.6511 USE_META, weight: 0.2169 cost: 2.2686 min: -0.2935 max: 2.6511 USE_META, weight: 0.8519 cost: 0.1909 min: -0.2935 max: 2.6511 USE_META, weight: 0.5489 cost: 1.1824 min: -0.2935 max: 2.6511 USE_META, weight: 0.8137 cost: 0.3162 min: -0.2935 max: 2.6511 USE_META, weight: 0.8890 cost: 0.0696 min: -0.2935 max: 2.6511 USE_META, weight: 0.7677 cost: 0.4665 min: -0.2935 max: 2.6511 USE_META, weight: 0.8890 cost: 0.0696 min: -0.2935 max: 2.6511 USE_META, weight: 0.7677 cost: 0.4665 min: -0.2935 max: 2.6511 USE_META, weight: 0.8240 cost: 0.2824 min: -0.2935 max: 2.6511 USE_META, weight: 0.7302 cost: 0.5892 min: -0.2935 max: 2.6511 USE_META, weight: 0.8383 cost: 0.2354 min: -0.2935 max: 2.6511 USE_META, weight: 0.8652 cost: 0.1476 min: -0.2935 max: 2.6511 USE_META, weight: 0.3914 cost: 1.6976 min: -0.2935 max: 2.6511 USE_META, weight: 0.2794 cost: 2.0642 min: -0.2935 max: 2.6511 USE_META, weight: 0.2851 cost: 2.0456 min: -0.2935 max: 2.6511 USE_META, weight: 0.2732 cost: 2.0846 min: -0.2935 max: 2.6511 USE_META, weight: 0.2657 cost: 2.1088 min: -0.2935 max: 2.6511 USE_META, weight: 0.7175 cost: 0.6309 min: -0.2935 max: 2.6511 USE_META, weight: 0.7241 cost: 0.6093 min: -0.2935 max: 2.6511 USE_META, weight: 0.4935 cost: 1.3636 min: -0.2935 max: 2.6511 USE_META, weight: 0.5679 cost: 1.1202 min: -0.2935 max: 2.6511 USE_META, weight: 0.5133 cost: 1.2989 min: -0.2935 max: 2.6511 USE_META, weight: 0.5192 cost: 1.2797 min: -0.2935 max: 2.6511 USE_META, weight: 0.1000 cost: 2.6511 min: -0.2935 max: 2.6511 USE_META, weight: 0.9124 cost: -0.0068 min: -0.2935 max: 2.6511 USE_META, weight: 0.5146 cost: 1.2945 min: -0.2935 max: 2.6511 USE_META, weight: 0.5661 cost: 1.1262 min: -0.2935 max: 2.6511 USE_META, weight: 0.5200 cost: 1.2771 min: -0.2935 max: 2.6511 USE_META, weight: 0.5200 cost: 1.2771 min: -0.2935 max: 2.6511 USE_META, weight: 0.5200 cost: 1.2771 min: -0.2935 max: 2.6511 USE_META, weight: 0.5200 cost: 1.2771 min: -0.2935 max: 2.6511 USE_META, weight: 0.5200 cost: 1.2771 min: -0.2935 max: 2.6511 USE_META, weight: 0.7084 cost: 0.6607 min: -0.2935 max: 2.6511 USE_META, weight: 0.7127 cost: 0.6464 min: -0.2935 max: 2.6511 USE_META, weight: 0.4658 cost: 1.4543 min: -0.2935 max: 2.6511 USE_META, weight: 0.3589 cost: 1.8042 min: -0.2935 max: 2.6511 USE_META, weight: 0.6055 cost: 0.9972 min: -0.2935 max: 2.6511 USE_META, weight: 0.6781 cost: 0.7596 min: -0.2935 max: 2.6511 USE_META, weight: 0.7175 cost: 0.6309 min: -0.2935 max: 2.6511 USE_META, weight: 0.7241 cost: 0.6093 min: -0.2935 max: 2.6511 USE_META, weight: 0.4935 cost: 1.3636 min: -0.2935 max: 2.6511 USE_META, weight: 0.4912 cost: 1.3713 min: -0.2935 max: 2.6511 USE_META, weight: 0.8282 cost: 0.2684 min: -0.2935 max: 2.6511 USE_META, weight: 0.8342 cost: 0.2489 min: -0.2935 max: 2.6511 USE_META, weight: 0.8151 cost: 0.3115 min: -0.2935 max: 2.6511 USE_META, weight: 0.3125 cost: 1.9559 min: -0.2935 max: 2.6511 USE_META, weight: 0.7815 cost: 0.4214 min: -0.2935 max: 2.6511 USE_META, weight: 0.5200 cost: 1.2771 min: -0.2935 max: 2.6511 USE_META, weight: 0.5200 cost: 1.2771 min: -0.2935 max: 2.6511 USE_META, weight: 0.5200 cost: 1.2771 min: -0.2935 max: 2.6511 USE_META, weight: 0.5200 cost: 1.2771 min: -0.2935 max: 2.6511 USE_META, weight: 0.5200 cost: 1.2771 min: -0.2935 max: 2.6511 USE_META, weight: 0.5200 cost: 1.2771 min: -0.2935 max: 2.6511 USE_META, weight: 0.5200 cost: 1.2771 min: -0.2935 max: 2.6511 USE_META, weight: 0.5200 cost: 1.2771 min: -0.2935 max: 2.6511 USE_META, weight: 0.5200 cost: 1.2771 min: -0.2935 max: 2.6511 USE_META, weight: 0.5200 cost: 1.2771 min: -0.2935 max: 2.6511 USE_META, weight: 0.3227 cost: 1.9224 min: -0.2935 max: 2.6511 USE_META, weight: 0.3456 cost: 1.8477 min: -0.2935 max: 2.6511 USE_META, weight: 0.5246 cost: 1.2618 min: -0.2935 max: 2.6511 USE_META, weight: 0.3475 cost: 1.8412 min: -0.2935 max: 2.6511 USE_META, weight: 0.4504 cost: 1.5048 min: -0.2935 max: 2.6511 USE_META, weight: 0.4382 cost: 1.5444 min: -0.2935 max: 2.6511 USE_META, weight: 0.2922 cost: 2.0223 min: -0.2935 max: 2.6511 USE_META, weight: 0.4219 cost: 1.5979 min: -0.2935 max: 2.6511 USE_META, weight: 0.3987 cost: 1.6737 min: -0.2935 max: 2.6511 USE_META, weight: 0.1122 cost: 2.6111 min: -0.2935 max: 2.6511 USE_META, weight: 0.5200 cost: 1.2771 min: -0.2935 max: 2.6511 USE_META, weight: 0.5200 cost: 1.2771 min: -0.2935 max: 2.6511 USE_META, weight: 0.5200 cost: 1.2771 min: -0.2935 max: 2.6511 USE_META, weight: 0.5200 cost: 1.2771 min: -0.2935 max: 2.6511 USE_META, weight: 0.5200 cost: 1.2771 min: -0.2935 max: 2.6511 USE_META, weight: 0.9006 cost: 0.0318 min: -0.2935 max: 2.6511 USE_META, weight: 0.4732 cost: 1.4301 min: -0.2935 max: 2.6511 USE_META, weight: 0.6215 cost: 0.9449 min: -0.2935 max: 2.6511 USE_META, weight: 0.4040 cost: 1.6566 min: -0.2935 max: 2.6511 USE_META, weight: 0.4008 cost: 1.6668 min: -0.2935 max: 2.6511 USE_META, weight: 0.4396 cost: 1.5400 min: -0.2935 max: 2.6511 USE_META, weight: 0.5458 cost: 1.1926 min: -0.2935 max: 2.6511 USE_META, weight: 0.9073 cost: 0.0098 min: -0.2935 max: 2.6511 USE_META, weight: 0.9122 cost: -0.0062 min: -0.2935 max: 2.6511 USE_META, weight: 0.8378 cost: 0.2372 min: -0.2935 max: 2.6511 USE_META, weight: 0.8463 cost: 0.2093 min: -0.2935 max: 2.6511 USE_META, weight: 0.5747 cost: 1.0979 min: -0.2935 max: 2.6511 USE_META, weight: 0.9171 cost: -0.0222 min: -0.2935 max: 2.6511 USE_META, weight: 0.9171 cost: -0.0222 min: -0.2935 max: 2.6511 USE_META, weight: 0.9212 cost: -0.0357 min: -0.2935 max: 2.6511 USE_META, weight: 0.5200 cost: 1.2771 min: -0.2935 max: 2.6511 USE_META, weight: 0.5200 cost: 1.2771 min: -0.2935 max: 2.6511 USE_META, weight: 0.5200 cost: 1.2771 min: -0.2935 max: 2.6511 USE_META, weight: 0.5200 cost: 1.2771 min: -0.2935 max: 2.6511 USE_META, weight: 0.5200 cost: 1.2771 min: -0.2935 max: 2.6511 USE_META, weight: 0.5061 cost: 1.3224 min: -0.2935 max: 2.6511 USE_META, weight: 0.6718 cost: 0.7804 min: -0.2935 max: 2.6511 USE_META, weight: 0.4613 cost: 1.4690 min: -0.2935 max: 2.6511 USE_META, weight: 0.7652 cost: 0.4748 min: -0.2935 max: 2.6511 USE_META, weight: 0.4572 cost: 1.4825 min: -0.2935 max: 2.6511 USE_META, weight: 0.4366 cost: 1.5500 min: -0.2935 max: 2.6511 USE_META, weight: 0.3619 cost: 1.7944 min: -0.2935 max: 2.6511 USE_META, weight: 0.8624 cost: 0.1568 min: -0.2935 max: 2.6511 USE_META, weight: 0.5254 cost: 1.2593 min: -0.2935 max: 2.6511 USE_META, weight: 0.4236 cost: 1.5923 min: -0.2935 max: 2.6511 USE_META, weight: 0.4366 cost: 1.5500 min: -0.2935 max: 2.6511 USE_META, weight: 0.5417 cost: 1.2059 min: -0.2935 max: 2.6511 USE_META, weight: 0.3620 cost: 1.7940 min: -0.2935 max: 2.6511 USE_META, weight: 0.5556 cost: 1.1604 min: -0.2935 max: 2.6511 USE_META, weight: 0.3619 cost: 1.7944 min: -0.2935 max: 2.6511 USE_META, weight: 0.9816 cost: -0.2333 min: -0.2935 max: 2.6511 USE_META, weight: 0.9705 cost: -0.1970 min: -0.2935 max: 2.6511 USE_META, weight: 0.9556 cost: -0.1482 min: -0.2935 max: 2.6511 USE_META, weight: 0.9750 cost: -0.2116 min: -0.2935 max: 2.6511 USE_META, weight: 0.9469 cost: -0.1196 min: -0.2935 max: 2.6511 USE_META, weight: 0.5200 cost: 1.2771 min: -0.2935 max: 2.6511 USE_META, weight: 0.5910 cost: 1.0448 min: -0.2935 max: 2.6511 USE_META, weight: 0.6077 cost: 0.9900 min: -0.2935 max: 2.6511 USE_META, weight: 0.3466 cost: 1.8442 min: -0.2935 max: 2.6511 USE_META, weight: 0.1639 cost: 2.4421 min: -0.2935 max: 2.6511 USE_META, weight: 0.3968 cost: 1.6799 min: -0.2935 max: 2.6511 USE_META, weight: 0.9745 cost: -0.2100 min: -0.2935 max: 2.6511 USE_META, weight: 0.9516 cost: -0.1353 min: -0.2935 max: 2.6511 USE_META, weight: 0.9774 cost: -0.2196 min: -0.2935 max: 2.6511 USE_META, weight: 0.9767 cost: -0.2174 min: -0.2935 max: 2.6511 USE_META, weight: 0.9536 cost: -0.1416 min: -0.2935 max: 2.6511 USE_META, weight: 0.9730 cost: -0.2052 min: -0.2935 max: 2.6511 USE_META, weight: 0.9040 cost: 0.0207 min: -0.2935 max: 2.6511 USE_META, weight: 0.9882 cost: -0.2548 min: -0.2935 max: 2.6511 USE_META, weight: 0.9493 cost: -0.1275 min: -0.2935 max: 2.6511 USE_META, weight: 0.8570 cost: 0.1744 min: -0.2935 max: 2.6511 USE_META, weight: 0.9815 cost: -0.2330 min: -0.2935 max: 2.6511 USE_META, weight: 0.9384 cost: -0.0918 min: -0.2935 max: 2.6511 USE_META, weight: 0.9605 cost: -0.1642 min: -0.2935 max: 2.6511 USE_META, weight: 0.9853 cost: -0.2454 min: -0.2935 max: 2.6511 USE_META, weight: 0.9795 cost: -0.2265 min: -0.2935 max: 2.6511 USE_META, weight: 0.8261 cost: 0.2754 min: -0.2935 max: 2.6511 USE_META, weight: 0.9559 cost: -0.1493 min: -0.2935 max: 2.6511 USE_META, weight: 0.7889 cost: 0.3973 min: -0.2935 max: 2.6511 USE_META, weight: 0.8047 cost: 0.3455 min: -0.2935 max: 2.6511 USE_META, weight: 0.8207 cost: 0.2932 min: -0.2935 max: 2.6511 USE_META, weight: 0.7947 cost: 0.3782 min: -0.2935 max: 2.6511 USE_META, weight: 0.9852 cost: -0.2452 min: -0.2935 max: 2.6511 USE_META, weight: 0.9853 cost: -0.2454 min: -0.2935 max: 2.6511 USE_META, weight: 0.9391 cost: -0.0942 min: -0.2935 max: 2.6511 USE_META, weight: 0.9815 cost: -0.2330 min: -0.2935 max: 2.6511 USE_META, weight: 0.9372 cost: -0.0879 min: -0.2935 max: 2.6511 USE_META, weight: 0.3458 cost: 1.8469 min: -0.2935 max: 2.6511 USE_META, weight: 0.3495 cost: 1.8348 min: -0.2935 max: 2.6511 USE_META, weight: 0.6623 cost: 0.8112 min: -0.2935 max: 2.6511 USE_META, weight: 0.4018 cost: 1.6636 min: -0.2935 max: 2.6511 USE_META, weight: 0.6211 cost: 0.9463 min: -0.2935 max: 2.6511 USE_META, weight: 0.5214 cost: 1.2723 min: -0.2935 max: 2.6511 USE_META, weight: 0.5675 cost: 1.1215 min: -0.2935 max: 2.6511 USE_META, weight: 0.5491 cost: 1.1819 min: -0.2935 max: 2.6511 USE_META, weight: 0.4329 cost: 1.5618 min: -0.2935 max: 2.6511 USE_META, weight: 0.6310 cost: 0.9138 min: -0.2935 max: 2.6511 USE_META, weight: 0.5637 cost: 1.1340 min: -0.2935 max: 2.6511 USE_META, weight: 0.5545 cost: 1.1641 min: -0.2935 max: 2.6511 USE_META, weight: 0.5346 cost: 1.2293 min: -0.2935 max: 2.6511 USE_META, weight: 0.4529 cost: 1.4964 min: -0.2935 max: 2.6511 USE_META, weight: 0.7292 cost: 0.5926 min: -0.2935 max: 2.6511 USE_META, weight: 0.8935 cost: 0.0551 min: -0.2935 max: 2.6511 USE_META, weight: 0.9104 cost: -0.0003 min: -0.2935 max: 2.6511 USE_META, weight: 0.9372 cost: -0.0879 min: -0.2935 max: 2.6511 USE_META, weight: 0.9514 cost: -0.1345 min: -0.2935 max: 2.6511 USE_META, weight: 0.8513 cost: 0.1929 min: -0.2935 max: 2.6511 USE_META, weight: 0.5200 cost: 1.2771 min: -0.2935 max: 2.6511 USE_META, weight: 0.5200 cost: 1.2771 min: -0.2935 max: 2.6511 USE_META, weight: 0.5200 cost: 1.2771 min: -0.2935 max: 2.6511 USE_META, weight: 0.5200 cost: 1.2771 min: -0.2935 max: 2.6511 USE_META, weight: 0.5200 cost: 1.2771 min: -0.2935 max: 2.6511 USE_META, weight: 0.5200 cost: 1.2771 min: -0.2935 max: 2.6511 USE_META, weight: 0.5200 cost: 1.2771 min: -0.2935 max: 2.6511 USE_META, weight: 0.5200 cost: 1.2771 min: -0.2935 max: 2.6511 USE_META, weight: 0.5200 cost: 1.2771 min: -0.2935 max: 2.6511 USE_META, weight: 0.5200 cost: 1.2771 min: -0.2935 max: 2.6511 USE_META, weight: 0.5200 cost: 1.2771 min: -0.2935 max: 2.6511 USE_META, weight: 0.9958 cost: -0.2799 min: -0.2935 max: 2.6511 USE_META, weight: 0.7746 cost: 0.4441 min: -0.2935 max: 2.6511 USE_META, weight: 0.8377 cost: 0.2375 min: -0.2935 max: 2.6511 USE_META, weight: 0.9281 cost: -0.0584 min: -0.2935 max: 2.6511 USE_META, weight: 1.0000 cost: -0.2935 min: -0.2935 max: 2.6511 USE_META, weight: 0.5044 cost: 1.3281 min: -0.2935 max: 2.6511 USE_META, weight: 0.8677 cost: 0.1393 min: -0.2935 max: 2.6511 USE_META, weight: 0.8118 cost: 0.3222 min: -0.2935 max: 2.6511 USE_META, weight: 0.6649 cost: 0.8030 min: -0.2935 max: 2.6511 USE_META, weight: 0.8861 cost: 0.0791 min: -0.2935 max: 2.6511 USE_META, weight: 0.4722 cost: 1.4335 min: -0.2935 max: 2.6511 USE_META, weight: 0.8118 cost: 0.3222 min: -0.2935 max: 2.6511 USE_META, weight: 0.8745 cost: 0.1172 min: -0.2935 max: 2.6511 USE_META, weight: 0.7434 cost: 0.5462 min: -0.2935 max: 2.6511 USE_META, weight: 0.2579 cost: 2.1344 min: -0.2935 max: 2.6511 USE_META, weight: 0.4939 cost: 1.3623 min: -0.2935 max: 2.6511 USE_META, weight: 0.4020 cost: 1.6632 min: -0.2935 max: 2.6511 USE_META, weight: 0.8845 cost: 0.0845 min: -0.2935 max: 2.6511 USE_META, weight: 0.4242 cost: 1.5905 min: -0.2935 max: 2.6511 USE_META, weight: 0.2593 cost: 2.1300 min: -0.2935 max: 2.6511 USE_META, weight: 0.5200 cost: 1.2771 min: -0.2935 max: 2.6511 USE_META, weight: 0.5200 cost: 1.2771 min: -0.2935 max: 2.6511 USE_META, weight: 0.5200 cost: 1.2771 min: -0.2935 max: 2.6511 USE_META, weight: 0.5200 cost: 1.2771 min: -0.2935 max: 2.6511 USE_META, weight: 0.5200 cost: 1.2771 min: -0.2935 max: 2.6511 USE_META, weight: 0.9686 cost: -0.1906 min: -0.2935 max: 2.6511 USE_META, weight: 0.5200 cost: 1.2771 min: -0.2935 max: 2.6511 USE_META, weight: 0.5200 cost: 1.2771 min: -0.2935 max: 2.6511 USE_META, weight: 0.5200 cost: 1.2771 min: -0.2935 max: 2.6511 USE_META, weight: 0.5200 cost: 1.2771 min: -0.2935 max: 2.6511 USE_META, weight: 0.5200 cost: 1.2771 min: -0.2935 max: 2.6511 USE_META, weight: 0.9765 cost: -0.2166 min: -0.2935 max: 2.6511 USE_META, weight: 0.9609 cost: -0.1657 min: -0.2935 max: 2.6511 USE_META, weight: 0.9821 cost: -0.2351 min: -0.2935 max: 2.6511 USE_META, weight: 0.8870 cost: 0.0763 min: -0.2935 max: 2.6511 USE_META, weight: 0.9212 cost: -0.0356 min: -0.2935 max: 2.6511 USE_META, weight: 0.8581 cost: 0.1706 min: -0.2935 max: 2.6511 USE_META, weight: 0.9037 cost: 0.0215 min: -0.2935 max: 2.6511 USE_META, weight: 0.5200 cost: 1.2771 min: -0.2935 max: 2.6511 USE_META, weight: 0.5200 cost: 1.2771 min: -0.2935 max: 2.6511 USE_META, weight: 0.5200 cost: 1.2771 min: -0.2935 max: 2.6511 USE_META, weight: 0.5200 cost: 1.2771 min: -0.2935 max: 2.6511 USE_META, weight: 0.5200 cost: 1.2771 min: -0.2935 max: 2.6511 USE_META, weight: 0.5279 cost: 1.2510 min: -0.2935 max: 2.6511 USE_META, weight: 0.4485 cost: 1.5109 min: -0.2935 max: 2.6511 USE_META, weight: 0.6860 cost: 0.7339 min: -0.2935 max: 2.6511 USE_META, weight: 0.4087 cost: 1.6413 min: -0.2935 max: 2.6511 USE_META, weight: 0.5486 cost: 1.1834 min: -0.2935 max: 2.6511 USE_META, weight: 0.4990 cost: 1.3458 min: -0.2935 max: 2.6511 USE_META, weight: 0.3576 cost: 1.8082 min: -0.2935 max: 2.6511 USE_META, weight: 0.3645 cost: 1.7858 min: -0.2935 max: 2.6511 USE_META, weight: 0.4391 cost: 1.5415 min: -0.2935 max: 2.6511 USE_META, weight: 0.4568 cost: 1.4839 min: -0.2935 max: 2.6511 USE_META, weight: 0.4965 cost: 1.3539 min: -0.2935 max: 2.6511 USE_META, weight: 0.5757 cost: 1.0947 min: -0.2935 max: 2.6511 USE_META, weight: 0.8810 cost: 0.0959 min: -0.2935 max: 2.6511 USE_META, weight: 0.9666 cost: -0.1843 min: -0.2935 max: 2.6511 USE_META, weight: 0.8295 cost: 0.2642 min: -0.2935 max: 2.6511 USE_META, weight: 0.9582 cost: -0.1568 min: -0.2935 max: 2.6511 USE_META, weight: 0.9004 cost: 0.0324 min: -0.2935 max: 2.6511 USE_META, weight: 0.8162 cost: 0.3077 min: -0.2935 max: 2.6511 USE_META, weight: 0.3183 cost: 1.9368 min: -0.2935 max: 2.6511 USE_META, weight: 0.6676 cost: 0.7942 min: -0.2935 max: 2.6511 USE_META, weight: 0.4463 cost: 1.5181 min: -0.2935 max: 2.6511 USE_META, weight: 0.4645 cost: 1.4584 min: -0.2935 max: 2.6511 USE_META, weight: 0.3485 cost: 1.8380 min: -0.2935 max: 2.6511 USE_META, weight: 0.8700 cost: 0.1318 min: -0.2935 max: 2.6511 USE_EVALUE, weight: 0.9365 eval: 5.9077 min: 0.2294 max: 80.7000 USE_EVALUE, weight: 0.9365 eval: 5.9077 min: 0.2294 max: 80.7000 USE_EVALUE, weight: 0.9365 eval: 5.9077 min: 0.2294 max: 80.7000 USE_EVALUE, weight: 0.9064 eval: 8.5986 min: 0.2294 max: 80.7000 USE_EVALUE, weight: 0.9064 eval: 8.5986 min: 0.2294 max: 80.7000 USE_EVALUE, weight: 0.9064 eval: 8.5986 min: 0.2294 max: 80.7000 USE_EVALUE, weight: 1.0000 eval: 0.2294 min: 0.2294 max: 80.7000 USE_EVALUE, weight: 1.0000 eval: 0.2294 min: 0.2294 max: 80.7000 USE_EVALUE, weight: 1.0000 eval: 0.2294 min: 0.2294 max: 80.7000 USE_EVALUE, weight: 0.8035 eval: 17.8000 min: 0.2294 max: 80.7000 USE_EVALUE, weight: 0.8035 eval: 17.8000 min: 0.2294 max: 80.7000 USE_EVALUE, weight: 0.8035 eval: 17.8000 min: 0.2294 max: 80.7000 USE_EVALUE, weight: 0.9978 eval: 0.4266 min: 0.2294 max: 80.7000 USE_EVALUE, weight: 0.9978 eval: 0.4266 min: 0.2294 max: 80.7000 USE_EVALUE, weight: 0.9978 eval: 0.4266 min: 0.2294 max: 80.7000 USE_EVALUE, weight: 0.9704 eval: 2.8800 min: 0.2294 max: 80.7000 USE_EVALUE, weight: 0.9704 eval: 2.8800 min: 0.2294 max: 80.7000 USE_EVALUE, weight: 0.9704 eval: 2.8800 min: 0.2294 max: 80.7000 USE_EVALUE, weight: 0.9360 eval: 5.9538 min: 0.2294 max: 80.7000 USE_EVALUE, weight: 0.9360 eval: 5.9538 min: 0.2294 max: 80.7000 USE_EVALUE, weight: 0.9360 eval: 5.9538 min: 0.2294 max: 80.7000 USE_EVALUE, weight: 0.9303 eval: 6.4607 min: 0.2294 max: 80.7000 USE_EVALUE, weight: 0.9303 eval: 6.4607 min: 0.2294 max: 80.7000 USE_EVALUE, weight: 0.9303 eval: 6.4607 min: 0.2294 max: 80.7000 USE_EVALUE, weight: 0.9717 eval: 2.7600 min: 0.2294 max: 80.7000 USE_EVALUE, weight: 0.9717 eval: 2.7600 min: 0.2294 max: 80.7000 USE_EVALUE, weight: 0.9717 eval: 2.7600 min: 0.2294 max: 80.7000 USE_EVALUE, weight: 0.9178 eval: 7.5817 min: 0.2294 max: 80.7000 USE_EVALUE, weight: 0.9178 eval: 7.5817 min: 0.2294 max: 80.7000 USE_EVALUE, weight: 0.9568 eval: 4.0939 min: 0.2294 max: 80.7000 USE_EVALUE, weight: 0.9568 eval: 4.0939 min: 0.2294 max: 80.7000 USE_EVALUE, weight: 0.9568 eval: 4.0939 min: 0.2294 max: 80.7000 USE_EVALUE, weight: 0.9511 eval: 4.6005 min: 0.2294 max: 80.7000 USE_EVALUE, weight: 0.9511 eval: 4.6005 min: 0.2294 max: 80.7000 USE_EVALUE, weight: 0.9511 eval: 4.6005 min: 0.2294 max: 80.7000 USE_EVALUE, weight: 0.9814 eval: 1.8958 min: 0.2294 max: 80.7000 USE_EVALUE, weight: 0.9814 eval: 1.8958 min: 0.2294 max: 80.7000 USE_EVALUE, weight: 0.9814 eval: 1.8958 min: 0.2294 max: 80.7000 USE_EVALUE, weight: 0.9420 eval: 5.4135 min: 0.2294 max: 80.7000 USE_EVALUE, weight: 0.9420 eval: 5.4135 min: 0.2294 max: 80.7000 USE_EVALUE, weight: 0.9420 eval: 5.4135 min: 0.2294 max: 80.7000 USE_EVALUE, weight: 0.9150 eval: 7.8289 min: 0.2294 max: 80.7000 USE_EVALUE, weight: 0.9150 eval: 7.8289 min: 0.2294 max: 80.7000 USE_EVALUE, weight: 0.9150 eval: 7.8289 min: 0.2294 max: 80.7000 USE_EVALUE, weight: 0.9081 eval: 8.4430 min: 0.2294 max: 80.7000 USE_EVALUE, weight: 0.9081 eval: 8.4430 min: 0.2294 max: 80.7000 USE_EVALUE, weight: 0.9081 eval: 8.4430 min: 0.2294 max: 80.7000 USE_EVALUE, weight: 0.5250 eval: 42.7000 min: 0.2294 max: 80.7000 USE_EVALUE, weight: 0.5250 eval: 42.7000 min: 0.2294 max: 80.7000 USE_EVALUE, weight: 0.5250 eval: 42.7000 min: 0.2294 max: 80.7000 USE_EVALUE, weight: 0.1000 eval: 80.7000 min: 0.2294 max: 80.7000 USE_EVALUE, weight: 0.1000 eval: 80.7000 min: 0.2294 max: 80.7000 USE_EVALUE, weight: 0.1000 eval: 80.7000 min: 0.2294 max: 80.7000 USE_EVALUE, weight: 0.9405 eval: 5.5536 min: 0.2294 max: 80.7000 USE_EVALUE, weight: 0.9405 eval: 5.5536 min: 0.2294 max: 80.7000 USE_EVALUE, weight: 0.9405 eval: 5.5536 min: 0.2294 max: 80.7000 USE_EVALUE, weight: 0.9751 eval: 2.4528 min: 0.2294 max: 80.7000 USE_EVALUE, weight: 0.9751 eval: 2.4528 min: 0.2294 max: 80.7000 USE_EVALUE, weight: 0.9751 eval: 2.4528 min: 0.2294 max: 80.7000 USE_EVALUE, weight: 0.9900 eval: 1.1199 min: 0.2294 max: 80.7000 USE_EVALUE, weight: 0.9900 eval: 1.1199 min: 0.2294 max: 80.7000 USE_EVALUE, weight: 0.9900 eval: 1.1199 min: 0.2294 max: 80.7000 USE_EVALUE, weight: 0.9728 eval: 2.6588 min: 0.2294 max: 80.7000 USE_EVALUE, weight: 0.9728 eval: 2.6588 min: 0.2294 max: 80.7000 USE_EVALUE, weight: 0.9728 eval: 2.6588 min: 0.2294 max: 80.7000 USE_EVALUE, weight: 0.6122 eval: 34.9000 min: 0.2294 max: 80.7000 USE_EVALUE, weight: 0.6122 eval: 34.9000 min: 0.2294 max: 80.7000 USE_EVALUE, weight: 0.6122 eval: 34.9000 min: 0.2294 max: 80.7000 USE_EVALUE, weight: 0.9852 eval: 1.5490 min: 0.2294 max: 80.7000 USE_EVALUE, weight: 0.9852 eval: 1.5490 min: 0.2294 max: 80.7000 USE_EVALUE, weight: 0.9852 eval: 1.5490 min: 0.2294 max: 80.7000 USE_EVALUE, weight: 0.7576 eval: 21.9000 min: 0.2294 max: 80.7000 USE_EVALUE, weight: 0.7576 eval: 21.9000 min: 0.2294 max: 80.7000 USE_EVALUE, weight: 0.7576 eval: 21.9000 min: 0.2294 max: 80.7000 USE_EVALUE, weight: 0.9944 eval: 0.7314 min: 0.2294 max: 80.7000 USE_EVALUE, weight: 0.9944 eval: 0.7314 min: 0.2294 max: 80.7000 USE_EVALUE, weight: 0.9944 eval: 0.7314 min: 0.2294 max: 80.7000 Number of contacts in models: 257 Number of contacts in alignments: 77 NUMB_ALIGNS: 77 Adding 1685 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: -110.8508, CN propb: -110.8508 weights: 0.2681 constraints: 105 # command:Found ConstraintSet # PrintContacts align.constraints_meta03 Number of constraints in align3.constraints 105 # command:Found ConstraintSet # PrintContacts align_bonus.constraints_meta03 Number of constraints in align3.constraints.bonus 105 # command:Found ConstraintSet # PrintContacts rejected.constraints_meta03 Number of constraints in rejected3.constraints 1580 # command:Found ConstraintSet # PrintContacts rejected_bonus.constraints_meta03 Number of constraints in rejected3.constraints.bonus 1580 # 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 1685 # command: