parameters: 0.6 1.3 0.5 200 50 # 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:# PrintAlignmentsContacts allconstraints.under Using radius: 8.0000 NUMB_ALIGNS: 77 Done printing distance constraints # command: