# command:# Prefix for input files set to /projects/compbio/experiments/undertaker/atoms-inputs/ # command:# reading cullpdb_pc80_res1.2_R0.2_d070810_chains408.atoms.gz # #computed average backbone with maximum peptide_sq_deviance = 0.002 # computed average trans backbone unit from 1600 examples # computed average trans backbone unit before proline from 52 examples # trans (non-proline) backbone unit: # CA= -2.2097 1.0151 -0.0046 # O= -0.1488 2.2425 0.0020 # C= -0.6903 1.1357 0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4580 -0.0000 -0.0000 # cis backbone unit: # CA= -0.1462 2.4515 0.0018 # O= -2.0272 0.9713 0.0022 # C= -0.8006 1.0755 0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4659 0.0000 0.0000 # trans backbone unit before proline: # CA= -2.2063 1.0654 0.0002 # O= -0.1193 2.2442 0.0054 # C= -0.6842 1.1479 -0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4661 -0.0000 0.0000 # After reading cullpdb_pc80_res1.2_R0.2_d070810_chains408.atoms.gz have 408 chains in training database # Count of chains,residues,atoms: 408,82795,639989 # 81291 residues have no bad marker # 565 residues lack atoms needed to compute omega # 313 residues have cis peptide # number of each bad type: # NON_STANDARD_RESIDUE 1 # HAS_OXT 265 # TOO_MANY_ATOMS 0 # TOO_FEW_ATOMS 378 # HAS_UNKNOWN_ATOMS 0 # HAS_DUPLICATE_ATOMS 0 # CHAIN_BREAK_BEFORE 139 # NON_PLANAR_PEPTIDE 424 # BAD_PEPTIDE 803 # Note: may sum to more than number of residues, # because one residue may have multiple problems # command:# Reading rotamer library from dunbrack-40pc-3157.rot # command:# Prefix for input files set to /projects/compbio/experiments/undertaker/spots/ # command:# ReadAtomType exp-pdb.types Read AtomType exp-pdb with 49 types. # command:# ReadClashTable exp-pdb-2191-2symm.clash # Read ClashTable exp-pdb-2191-2symm checking bonds symmetric at MaxSep 2 # command:# command:# Prefix for input files set to # command:# Making conformation for sequence T0348 numbered 1 through 68 Created new target T0348 from T0348.a2m # command:CPU_time= 6.370 sec, elapsed time= 6.421 sec. # command:# reading script from file all-templates.under # Reading fragments from alignment file # Attempting to read fragment alignments from file 2ct7A/T0348-2ct7A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2ct7A expands to /projects/compbio/data/pdb/2ct7.pdb.gz 2ct7A:# T0348 read from 2ct7A/T0348-2ct7A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2ct7A read from 2ct7A/T0348-2ct7A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2ct7A to template set # found chain 2ct7A in template set T0348 10 :VCPLCKGPLVFDKSKDELICKGDRLAFPIKD 2ct7A 27 :WCAQCSFGFIYEREQLEATCPQCHQTFCVRC # choosing archetypes in rotamer library T0348 43 :PMMLESEARELAPEEEVKLEHHHHH 2ct7A 58 :KRQWEEQHRGRSCEDFQNWKRMNSG Number of specific fragments extracted= 2 number of extra gaps= 0 total=2 Will force an alignment to be made, even if fragment is small Number of alignments=1 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2ct7A/T0348-2ct7A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0348 read from 2ct7A/T0348-2ct7A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2ct7A read from 2ct7A/T0348-2ct7A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 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=4 Will force an alignment to be made, even if fragment is small Number of alignments=2 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2ct7A/T0348-2ct7A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0348 read from 2ct7A/T0348-2ct7A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2ct7A read from 2ct7A/T0348-2ct7A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.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=6 Will force an alignment to be made, even if fragment is small Number of alignments=3 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1pft/T0348-1pft-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 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/T0348-1pft-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1pft read from 1pft/T0348-1pft-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.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 :IKDGIPMM 1pft 34 :IEENIIDM Number of specific fragments extracted= 3 number of extra gaps= 0 total=9 Will force an alignment to be made, even if fragment is small Number of alignments=4 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1pft/T0348-1pft-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0348 read from 1pft/T0348-1pft-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1pft read from 1pft/T0348-1pft-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 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=12 Will force an alignment to be made, even if fragment is small Number of alignments=5 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1pft/T0348-1pft-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0348 read from 1pft/T0348-1pft-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1pft read from 1pft/T0348-1pft-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.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=16 Will force an alignment to be made, even if fragment is small Number of alignments=6 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1vk6A/T0348-1vk6A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 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 0.35 <= 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/T0348-1vk6A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1vk6A read from 1vk6A/T0348-1vk6A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1vk6A to template set # found chain 1vk6A in template set T0348 10 :VCPLCKGPLVFDKSKDELICKGDRLAF 1vk6A 97 :YCGYCGHEMYPSKTEWAMLCSHCRERY Number of specific fragments extracted= 1 number of extra gaps= 0 total=17 Will force an alignment to be made, even if fragment is small Number of alignments=7 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1vk6A/T0348-1vk6A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0348 read from 1vk6A/T0348-1vk6A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1vk6A read from 1vk6A/T0348-1vk6A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1vk6A in template set T0348 10 :VCPLCKGPLVFDKSKDELICKGDRLAFP 1vk6A 97 :YCGYCGHEMYPSKTEWAMLCSHCRERYY Number of specific fragments extracted= 1 number of extra gaps= 0 total=18 Will force an alignment to be made, even if fragment is small Number of alignments=8 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1vk6A/T0348-1vk6A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0348 read from 1vk6A/T0348-1vk6A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1vk6A read from 1vk6A/T0348-1vk6A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.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=19 Will force an alignment to be made, even if fragment is small Number of alignments=9 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1vqoZ/T0348-1vqoZ-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1vqoZ expands to /projects/compbio/data/pdb/1vqo.pdb.gz 1vqoZ:# T0348 read from 1vqoZ/T0348-1vqoZ-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1vqoZ read from 1vqoZ/T0348-1vqoZ-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.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 :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=23 Will force an alignment to be made, even if fragment is small Number of alignments=10 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1vqoZ/T0348-1vqoZ-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0348 read from 1vqoZ/T0348-1vqoZ-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1vqoZ read from 1vqoZ/T0348-1vqoZ-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.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 :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=27 Will force an alignment to be made, even if fragment is small Number of alignments=11 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1vqoZ/T0348-1vqoZ-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0348 read from 1vqoZ/T0348-1vqoZ-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1vqoZ read from 1vqoZ/T0348-1vqoZ-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.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=30 Will force an alignment to be made, even if fragment is small Number of alignments=12 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1rlyA/T0348-1rlyA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1rlyA expands to /projects/compbio/data/pdb/1rly.pdb.gz 1rlyA:# T0348 read from 1rlyA/T0348-1rlyA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1rlyA read from 1rlyA/T0348-1rlyA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1rlyA to template set # 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=32 Will force an alignment to be made, even if fragment is small Number of alignments=13 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1rlyA/T0348-1rlyA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0348 read from 1rlyA/T0348-1rlyA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1rlyA read from 1rlyA/T0348-1rlyA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 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=34 Will force an alignment to be made, even if fragment is small Number of alignments=14 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1rlyA/T0348-1rlyA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0348 read from 1rlyA/T0348-1rlyA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1rlyA read from 1rlyA/T0348-1rlyA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.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=36 Will force an alignment to be made, even if fragment is small Number of alignments=15 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1vckA/T0348-1vckA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1vckA expands to /projects/compbio/data/pdb/1vck.pdb.gz 1vckA:# T0348 read from 1vckA/T0348-1vckA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1vckA read from 1vckA/T0348-1vckA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1vckA to template set # found chain 1vckA in template set T0348 21 :DKSKDELICKGDRLAFPIKDGIPM 1vckA 57 :TLDGDVIECPFHGGAFNVCTGMPA Number of specific fragments extracted= 1 number of extra gaps= 0 total=37 Will force an alignment to be made, even if fragment is small Number of alignments=16 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1vckA/T0348-1vckA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0348 read from 1vckA/T0348-1vckA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1vckA read from 1vckA/T0348-1vckA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1vckA in template set T0348 23 :SKDELICKGDRLAFPIKDGIPM 1vckA 59 :DGDVIECPFHGGAFNVCTGMPA Number of specific fragments extracted= 1 number of extra gaps= 0 total=38 Will force an alignment to be made, even if fragment is small Number of alignments=17 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1vckA/T0348-1vckA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0348 read from 1vckA/T0348-1vckA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1vckA read from 1vckA/T0348-1vckA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.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=40 Will force an alignment to be made, even if fragment is small Number of alignments=18 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1dl6A/T0348-1dl6A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1dl6A expands to /projects/compbio/data/pdb/1dl6.pdb.gz 1dl6A:# T0348 read from 1dl6A/T0348-1dl6A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1dl6A read from 1dl6A/T0348-1dl6A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1dl6A to template set # 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=44 Will force an alignment to be made, even if fragment is small Number of alignments=19 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1dl6A/T0348-1dl6A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0348 read from 1dl6A/T0348-1dl6A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1dl6A read from 1dl6A/T0348-1dl6A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 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=46 Will force an alignment to be made, even if fragment is small Number of alignments=20 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1dl6A/T0348-1dl6A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0348 read from 1dl6A/T0348-1dl6A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1dl6A read from 1dl6A/T0348-1dl6A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.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=48 Will force an alignment to be made, even if fragment is small Number of alignments=21 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1odhA/T0348-1odhA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1odhA expands to /projects/compbio/data/pdb/1odh.pdb.gz 1odhA:# T0348 read from 1odhA/T0348-1odhA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1odhA read from 1odhA/T0348-1odhA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1odhA to template set # 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=50 Will force an alignment to be made, even if fragment is small Number of alignments=22 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1odhA/T0348-1odhA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0348 read from 1odhA/T0348-1odhA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1odhA read from 1odhA/T0348-1odhA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 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=53 Will force an alignment to be made, even if fragment is small Number of alignments=23 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1odhA/T0348-1odhA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0348 read from 1odhA/T0348-1odhA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1odhA read from 1odhA/T0348-1odhA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.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=55 Will force an alignment to be made, even if fragment is small Number of alignments=24 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1vd4A/T0348-1vd4A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1vd4A expands to /projects/compbio/data/pdb/1vd4.pdb.gz 1vd4A:# T0348 read from 1vd4A/T0348-1vd4A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1vd4A read from 1vd4A/T0348-1vd4A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1vd4A to template set # 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=58 Will force an alignment to be made, even if fragment is small Number of alignments=25 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1vd4A/T0348-1vd4A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0348 read from 1vd4A/T0348-1vd4A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1vd4A read from 1vd4A/T0348-1vd4A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 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=60 Will force an alignment to be made, even if fragment is small Number of alignments=26 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1vd4A/T0348-1vd4A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0348 read from 1vd4A/T0348-1vd4A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1vd4A read from 1vd4A/T0348-1vd4A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.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=62 Will force an alignment to be made, even if fragment is small Number of alignments=27 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1s72Z/T0348-1s72Z-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1s72Z expands to /projects/compbio/data/pdb/1s72.pdb.gz 1s72Z:# T0348 read from 1s72Z/T0348-1s72Z-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1s72Z read from 1s72Z/T0348-1s72Z-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1s72Z to template set # 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=66 Will force an alignment to be made, even if fragment is small Number of alignments=28 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1s72Z/T0348-1s72Z-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0348 read from 1s72Z/T0348-1s72Z-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1s72Z read from 1s72Z/T0348-1s72Z-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 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=70 Will force an alignment to be made, even if fragment is small Number of alignments=29 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1s72Z/T0348-1s72Z-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0348 read from 1s72Z/T0348-1s72Z-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1s72Z read from 1s72Z/T0348-1s72Z-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.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=73 Will force an alignment to be made, even if fragment is small Number of alignments=30 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ee8A/T0348-1ee8A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1ee8A expands to /projects/compbio/data/pdb/1ee8.pdb.gz 1ee8A:# T0348 read from 1ee8A/T0348-1ee8A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ee8A read from 1ee8A/T0348-1ee8A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1ee8A to template set # 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=75 Will force an alignment to be made, even if fragment is small Number of alignments=31 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ee8A/T0348-1ee8A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0348 read from 1ee8A/T0348-1ee8A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ee8A read from 1ee8A/T0348-1ee8A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 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=78 Will force an alignment to be made, even if fragment is small Number of alignments=32 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ee8A/T0348-1ee8A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0348 read from 1ee8A/T0348-1ee8A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ee8A read from 1ee8A/T0348-1ee8A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.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=80 Will force an alignment to be made, even if fragment is small Number of alignments=33 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ypvA/T0348-1ypvA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1ypvA expands to /projects/compbio/data/pdb/1ypv.pdb.gz 1ypvA:# T0348 read from 1ypvA/T0348-1ypvA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ypvA read from 1ypvA/T0348-1ypvA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1ypvA to template set # found chain 1ypvA in template set T0348 22 :KSKDELICKGDRLAFPIKDGIPMM 1ypvA 51 :TGTGTLSVFGMQARYSLRDEFPLL Number of specific fragments extracted= 1 number of extra gaps= 0 total=81 Will force an alignment to be made, even if fragment is small Number of alignments=34 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ypvA/T0348-1ypvA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0348 read from 1ypvA/T0348-1ypvA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ypvA read from 1ypvA/T0348-1ypvA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.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=82 Will force an alignment to be made, even if fragment is small Number of alignments=35 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ypvA/T0348-1ypvA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0348 read from 1ypvA/T0348-1ypvA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ypvA read from 1ypvA/T0348-1ypvA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.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=83 Will force an alignment to be made, even if fragment is small Number of alignments=36 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1d0qA/T0348-1d0qA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1d0qA expands to /projects/compbio/data/pdb/1d0q.pdb.gz 1d0qA:# T0348 read from 1d0qA/T0348-1d0qA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1d0qA read from 1d0qA/T0348-1d0qA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1d0qA to template set # found chain 1d0qA in template 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=85 Will force an alignment to be made, even if fragment is small Number of alignments=37 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1d0qA/T0348-1d0qA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0348 read from 1d0qA/T0348-1d0qA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1d0qA read from 1d0qA/T0348-1d0qA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1d0qA in template 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=87 Will force an alignment to be made, even if fragment is small Number of alignments=38 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1d0qA/T0348-1d0qA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0348 read from 1d0qA/T0348-1d0qA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1d0qA read from 1d0qA/T0348-1d0qA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1d0qA in template 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=89 Will force an alignment to be made, even if fragment is small Number of alignments=39 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1yk4A/T0348-1yk4A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0348 read from 1yk4A/T0348-1yk4A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1yk4A read from 1yk4A/T0348-1yk4A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1yk4A in training 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=92 Will force an alignment to be made, even if fragment is small Number of alignments=40 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1yk4A/T0348-1yk4A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0348 read from 1yk4A/T0348-1yk4A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1yk4A read from 1yk4A/T0348-1yk4A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1yk4A in training set T0348 26 :ELICKGDRLAFPIKDG 1yk4A 3 :KLSCKICGYIYDEDEG T0348 46 :LESE 1yk4A 19 :DPDN T0348 52 :ELAPEE 1yk4A 23 :GISPGT Number of specific fragments extracted= 3 number of extra gaps= 0 total=95 Will force an alignment to be made, even if fragment is small Number of alignments=41 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1yk4A/T0348-1yk4A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0348 read from 1yk4A/T0348-1yk4A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1yk4A read from 1yk4A/T0348-1yk4A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1yk4A in training 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=97 Will force an alignment to be made, even if fragment is small Number of alignments=42 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1rfs/T0348-1rfs-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 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/T0348-1rfs-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1rfs read from 1rfs/T0348-1rfs-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.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=98 Will force an alignment to be made, even if fragment is small Number of alignments=43 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1rfs/T0348-1rfs-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0348 read from 1rfs/T0348-1rfs-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1rfs read from 1rfs/T0348-1rfs-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.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=99 Will force an alignment to be made, even if fragment is small Number of alignments=44 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1rfs/T0348-1rfs-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0348 read from 1rfs/T0348-1rfs-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1rfs read from 1rfs/T0348-1rfs-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.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=101 Will force an alignment to be made, even if fragment is small Number of alignments=45 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1l1oC/T0348-1l1oC-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1l1oC expands to /projects/compbio/data/pdb/1l1o.pdb.gz 1l1oC:# T0348 read from 1l1oC/T0348-1l1oC-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1l1oC read from 1l1oC/T0348-1l1oC-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.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=104 Will force an alignment to be made, even if fragment is small Number of alignments=46 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1l1oC/T0348-1l1oC-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0348 read from 1l1oC/T0348-1l1oC-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1l1oC read from 1l1oC/T0348-1l1oC-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.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=107 Will force an alignment to be made, even if fragment is small Number of alignments=47 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1l1oC/T0348-1l1oC-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0348 read from 1l1oC/T0348-1l1oC-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1l1oC read from 1l1oC/T0348-1l1oC-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.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=110 Will force an alignment to be made, even if fragment is small Number of alignments=48 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2a1rA/T0348-2a1rA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2a1rA expands to /projects/compbio/data/pdb/2a1r.pdb.gz 2a1rA:# T0348 read from 2a1rA/T0348-2a1rA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2a1rA read from 2a1rA/T0348-2a1rA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.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 39 :KDGIPMMLESEAREL 2a1rA 128 :RNGIPYLNQEEERQL Number of specific fragments extracted= 1 number of extra gaps= 0 total=111 Will force an alignment to be made, even if fragment is small Number of alignments=49 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2a1rA/T0348-2a1rA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0348 read from 2a1rA/T0348-2a1rA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2a1rA read from 2a1rA/T0348-2a1rA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.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 :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=114 Will force an alignment to be made, even if fragment is small Number of alignments=50 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2a1rA/T0348-2a1rA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0348 read from 2a1rA/T0348-2a1rA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2a1rA read from 2a1rA/T0348-2a1rA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.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=117 Will force an alignment to be made, even if fragment is small Number of alignments=51 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ur6B/T0348-1ur6B-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1ur6B expands to /projects/compbio/data/pdb/1ur6.pdb.gz 1ur6B:# T0348 read from 1ur6B/T0348-1ur6B-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ur6B read from 1ur6B/T0348-1ur6B-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1ur6B to template set # 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=119 Will force an alignment to be made, even if fragment is small Number of alignments=52 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ur6B/T0348-1ur6B-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0348 read from 1ur6B/T0348-1ur6B-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ur6B read from 1ur6B/T0348-1ur6B-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 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=121 Will force an alignment to be made, even if fragment is small Number of alignments=53 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ur6B/T0348-1ur6B-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0348 read from 1ur6B/T0348-1ur6B-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ur6B read from 1ur6B/T0348-1ur6B-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.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=124 Will force an alignment to be made, even if fragment is small Number of alignments=54 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1rb9/T0348-1rb9-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0348 read from 1rb9/T0348-1rb9-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1rb9 read from 1rb9/T0348-1rb9-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.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=127 Will force an alignment to be made, even if fragment is small Number of alignments=55 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1rb9/T0348-1rb9-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0348 read from 1rb9/T0348-1rb9-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1rb9 read from 1rb9/T0348-1rb9-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.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=131 Will force an alignment to be made, even if fragment is small Number of alignments=56 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1rb9/T0348-1rb9-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0348 read from 1rb9/T0348-1rb9-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1rb9 read from 1rb9/T0348-1rb9-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.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=133 Will force an alignment to be made, even if fragment is small Number of alignments=57 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ptq/T0348-1ptq-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 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/T0348-1ptq-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ptq read from 1ptq/T0348-1ptq-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.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=135 Will force an alignment to be made, even if fragment is small Number of alignments=58 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ptq/T0348-1ptq-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0348 read from 1ptq/T0348-1ptq-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ptq read from 1ptq/T0348-1ptq-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.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=137 Will force an alignment to be made, even if fragment is small Number of alignments=59 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ptq/T0348-1ptq-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0348 read from 1ptq/T0348-1ptq-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ptq read from 1ptq/T0348-1ptq-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.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=139 Will force an alignment to be made, even if fragment is small Number of alignments=60 # command:CPU_time= 14.126 sec, elapsed time= 15.356 sec. # command:Using radius: 8.000 NUMB_ALIGNS: 60 Adding 2278 constraints to all_contacts Done adding distance constraints # command:CPU_time= 14.136 sec, elapsed time= 15.368 sec. # command:Reading probabilities from T0348.t06.CB8-sep9.rdb Reading constraints from ConstraintSet all_contacts maxweight: 18.605 Optimizing... Probability sum: -120.762, CN propb: -120.762 weights: 0.256 constraints: 80 # command:CPU_time= 14.529 sec, elapsed time= 15.778 sec. # command:Found ConstraintSet # PrintContacts log_align.constraints Number of constraints in align 80 # command:Found ConstraintSet # PrintContacts log_align_bonus.constraints Number of constraints in align.bonus 80 # command:Found ConstraintSet # PrintContacts log_rejected.constraints Number of constraints in rejected 175 # command:Found ConstraintSet # PrintContacts log_rejected_bonus.constraints Number of constraints in rejected.bonus 175 # command:Found ConstraintSet # PrintContacts log_noncontact.constraints Number of constraints in noncontact 1515 # command:Found ConstraintSet # PrintContacts log_noncontact_bonus.constraints Number of constraints in noncontact.bonus 1515 # command:CPU_time= 14.562 sec, elapsed time= 15.863 sec. # command: