# 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: 408,82794,639987 # 79931 residues have no bad marker # 573 residues lack atoms needed to compute omega # 313 residues have cis peptide # number of each bad type: # NON_STANDARD_RESIDUE 0 # HAS_OXT 264 # TOO_MANY_ATOMS 0 # TOO_FEW_ATOMS 378 # HAS_UNKNOWN_ATOMS 0 # HAS_DUPLICATE_ATOMS 0 # CHAIN_BREAK_BEFORE 148 # NON_PLANAR_PEPTIDE 17 # BAD_PEPTIDE 812 # HIGH_B_FACTOR 1566 # 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 T0630 numbered 1 through 132 Created new target T0630 from T0630.a2m # command:CPU_time= 5.893 sec, elapsed time= 6.218 sec. # command:# reading script from file all-templates.under # Reading fragments from alignment file # Attempting to read fragment alignments from file 2evrA/T0630-2evrA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2evrA expands to /projects/compbio/data/pdb/2evr.pdb.gz 2evrA:Skipped atom 8, because occupancy 0.5 <= existing 0.500 in 2evrA Skipped atom 12, because occupancy 0.500 <= existing 0.500 in 2evrA Skipped atom 14, because occupancy 0.500 <= existing 0.500 in 2evrA Skipped atom 16, because occupancy 0.500 <= existing 0.500 in 2evrA Skipped atom 18, because occupancy 0.500 <= existing 0.500 in 2evrA Skipped atom 78, because occupancy 0.500 <= existing 0.500 in 2evrA Skipped atom 80, because occupancy 0.500 <= existing 0.500 in 2evrA Skipped atom 121, because occupancy 0.300 <= existing 0.700 in 2evrA Skipped atom 123, because occupancy 0.300 <= existing 0.700 in 2evrA Skipped atom 125, because occupancy 0.300 <= existing 0.700 in 2evrA Skipped atom 127, because occupancy 0.300 <= existing 0.700 in 2evrA Skipped atom 129, because occupancy 0.300 <= existing 0.700 in 2evrA Skipped atom 131, because occupancy 0.300 <= existing 0.700 in 2evrA Skipped atom 133, because occupancy 0.300 <= existing 0.700 in 2evrA Skipped atom 135, because occupancy 0.300 <= existing 0.700 in 2evrA Skipped atom 151, because occupancy 0.300 <= existing 0.700 in 2evrA Skipped atom 155, because occupancy 0.300 <= existing 0.700 in 2evrA Skipped atom 157, because occupancy 0.300 <= existing 0.700 in 2evrA Skipped atom 159, because occupancy 0.300 <= existing 0.700 in 2evrA Skipped atom 161, because occupancy 0.300 <= existing 0.700 in 2evrA Skipped atom 163, because occupancy 0.300 <= existing 0.700 in 2evrA Skipped atom 179, because occupancy 0.500 <= existing 0.500 in 2evrA Skipped atom 183, because occupancy 0.500 <= existing 0.500 in 2evrA Skipped atom 185, because occupancy 0.500 <= existing 0.500 in 2evrA Skipped atom 187, because occupancy 0.500 <= existing 0.500 in 2evrA Skipped atom 189, because occupancy 0.500 <= existing 0.500 in 2evrA Skipped atom 191, because occupancy 0.500 <= existing 0.500 in 2evrA Skipped atom 193, because occupancy 0.500 <= existing 0.500 in 2evrA Skipped atom 195, because occupancy 0.500 <= existing 0.500 in 2evrA Skipped atom 238, because occupancy 0.300 <= existing 0.700 in 2evrA Skipped atom 242, because occupancy 0.300 <= existing 0.700 in 2evrA Skipped atom 244, because occupancy 0.300 <= existing 0.700 in 2evrA Skipped atom 340, because occupancy 0.300 <= existing 0.700 in 2evrA Skipped atom 342, because occupancy 0.300 <= existing 0.700 in 2evrA Skipped atom 344, because occupancy 0.300 <= existing 0.700 in 2evrA Skipped atom 346, because occupancy 0.300 <= existing 0.700 in 2evrA Skipped atom 348, because occupancy 0.300 <= existing 0.700 in 2evrA Skipped atom 350, because occupancy 0.300 <= existing 0.700 in 2evrA Skipped atom 352, because occupancy 0.300 <= existing 0.700 in 2evrA Skipped atom 354, because occupancy 0.300 <= existing 0.700 in 2evrA Skipped atom 356, because occupancy 0.300 <= existing 0.700 in 2evrA Skipped atom 358, because occupancy 0.300 <= existing 0.700 in 2evrA Skipped atom 360, because occupancy 0.300 <= existing 0.700 in 2evrA Skipped atom 362, because occupancy 0.300 <= existing 0.700 in 2evrA Skipped atom 364, because occupancy 0.300 <= existing 0.700 in 2evrA Skipped atom 366, because occupancy 0.300 <= existing 0.700 in 2evrA Skipped atom 368, because occupancy 0.300 <= existing 0.700 in 2evrA Skipped atom 370, because occupancy 0.300 <= existing 0.700 in 2evrA Skipped atom 653, because occupancy 0.200 <= existing 0.800 in 2evrA Skipped atom 657, because occupancy 0.200 <= existing 0.800 in 2evrA Skipped atom 659, because occupancy 0.200 <= existing 0.800 in 2evrA Skipped atom 665, because occupancy 0.500 <= existing 0.500 in 2evrA Skipped atom 669, because occupancy 0.500 <= existing 0.500 in 2evrA Skipped atom 671, because occupancy 0.500 <= existing 0.500 in 2evrA Skipped atom 691, because occupancy 0.500 <= existing 0.500 in 2evrA Skipped atom 695, because occupancy 0.500 <= existing 0.500 in 2evrA Skipped atom 697, because occupancy 0.500 <= existing 0.500 in 2evrA Skipped atom 699, because occupancy 0.500 <= existing 0.500 in 2evrA Skipped atom 701, because occupancy 0.500 <= existing 0.500 in 2evrA Skipped atom 703, because occupancy 0.500 <= existing 0.500 in 2evrA Skipped atom 783, because occupancy 0.500 <= existing 0.500 in 2evrA Skipped atom 787, because occupancy 0.500 <= existing 0.500 in 2evrA Skipped atom 789, because occupancy 0.500 <= existing 0.500 in 2evrA Skipped atom 791, because occupancy 0.500 <= existing 0.500 in 2evrA Skipped atom 793, because occupancy 0.500 <= existing 0.500 in 2evrA Skipped atom 795, because occupancy 0.500 <= existing 0.500 in 2evrA 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 827, because occupancy 0.300 <= existing 0.700 in 2evrA Skipped atom 831, because occupancy 0.300 <= existing 0.700 in 2evrA Skipped atom 833, because occupancy 0.300 <= existing 0.700 in 2evrA Skipped atom 835, because occupancy 0.300 <= existing 0.700 in 2evrA Skipped atom 837, because occupancy 0.300 <= existing 0.700 in 2evrA Skipped atom 839, because occupancy 0.300 <= existing 0.700 in 2evrA Skipped atom 842, because occupancy 0.500 <= existing 0.500 in 2evrA Skipped atom 846, because occupancy 0.500 <= existing 0.500 in 2evrA Skipped atom 848, because occupancy 0.500 <= existing 0.500 in 2evrA Skipped atom 870, because occupancy 0.500 <= existing 0.500 in 2evrA Skipped atom 872, because occupancy 0.500 <= existing 0.500 in 2evrA Skipped atom 874, because occupancy 0.500 <= existing 0.500 in 2evrA Skipped atom 876, because occupancy 0.500 <= existing 0.500 in 2evrA Skipped atom 878, because occupancy 0.500 <= existing 0.500 in 2evrA Skipped atom 880, because occupancy 0.500 <= existing 0.500 in 2evrA Skipped atom 882, because occupancy 0.500 <= existing 0.500 in 2evrA Skipped atom 884, because occupancy 0.500 <= existing 0.500 in 2evrA Skipped atom 886, because occupancy 0.500 <= existing 0.500 in 2evrA Skipped atom 888, because occupancy 0.500 <= existing 0.500 in 2evrA Skipped atom 890, because occupancy 0.500 <= existing 0.500 in 2evrA Skipped atom 892, because occupancy 0.500 <= existing 0.500 in 2evrA 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 1245, because occupancy 0.400 <= existing 0.600 in 2evrA Skipped atom 1249, because occupancy 0.400 <= existing 0.600 in 2evrA Skipped atom 1251, because occupancy 0.400 <= existing 0.600 in 2evrA Skipped atom 1253, because occupancy 0.400 <= existing 0.600 in 2evrA Skipped atom 1321, because occupancy 0.300 <= existing 0.700 in 2evrA Skipped atom 1325, because occupancy 0.300 <= existing 0.700 in 2evrA Skipped atom 1327, because occupancy 0.300 <= existing 0.700 in 2evrA Skipped atom 1668, because occupancy 0.300 <= existing 0.700 in 2evrA Skipped atom 1672, because occupancy 0.300 <= existing 0.700 in 2evrA Skipped atom 1674, because occupancy 0.300 <= existing 0.700 in 2evrA Skipped atom 1676, because occupancy 0.300 <= existing 0.700 in 2evrA Skipped atom 1678, because occupancy 0.300 <= existing 0.700 in 2evrA Skipped atom 1680, because occupancy 0.300 <= existing 0.700 in 2evrA Skipped atom 1780, because occupancy 0.200 <= existing 0.800 in 2evrA Skipped atom 1784, because occupancy 0.200 <= existing 0.800 in 2evrA Skipped atom 1786, because occupancy 0.200 <= existing 0.800 in 2evrA Skipped atom 1788, because occupancy 0.200 <= existing 0.800 in 2evrA Skipped atom 1790, because occupancy 0.200 <= existing 0.800 in 2evrA Skipped atom 1792, because occupancy 0.200 <= existing 0.800 in 2evrA Skipped atom 1802, because occupancy 0.500 <= existing 0.500 in 2evrA Skipped atom 1806, because occupancy 0.500 <= existing 0.500 in 2evrA Skipped atom 1808, because occupancy 0.500 <= existing 0.500 in 2evrA # T0630 read from 2evrA/T0630-2evrA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2evrA read from 2evrA/T0630-2evrA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2evrA to template set # found chain 2evrA in template set T0630 2 :RAPIPEPKPGDLIEIFR 2evrA 154 :PITIAELVAGDLVFFGT # choosing archetypes in rotamer library T0630 19 :PFYRHWAIYVGDGYVVHLAPPSEVA 2evrA 172 :QKATHVGLYLADGYYIHSSGKDQGR T0630 58 :AIVKKELLY 2evrA 197 :DGIGIDILS Number of specific fragments extracted= 3 number of extra gaps= 0 total=3 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 2evrA/T0630-2evrA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0630 read from 2evrA/T0630-2evrA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2evrA read from 2evrA/T0630-2evrA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2evrA in template set T0630 3 :APIPEPKPGDLIEIFR 2evrA 155 :ITIAELVAGDLVFFGT T0630 19 :PFYRHWAIYVGDGYVVHLAPPSEV 2evrA 172 :QKATHVGLYLADGYYIHSSGKDQG T0630 57 :KAIVKKELL 2evrA 196 :RDGIGIDIL T0630 66 :YDVAG 2evrA 213 :LSYYQ T0630 72 :DKYQVNNKH 2evrA 218 :QLRGAGRVF T0630 82 :DKYSPL 2evrA 227 :KSYEPQ Number of specific fragments extracted= 6 number of extra gaps= 0 total=9 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 2evrA/T0630-2evrA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0630 read from 2evrA/T0630-2evrA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2evrA read from 2evrA/T0630-2evrA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2evrA in template set T0630 3 :APIPEPKPGDLIEIFR 2evrA 155 :ITIAELVAGDLVFFGT T0630 19 :PFYRHWAIYVGDGYVVHLAPPSEVAGAGAASVMSALT 2evrA 172 :QKATHVGLYLADGYYIHSSGKDQGRDGIGIDILSEQG T0630 90 :SKIIQRAEE 2evrA 209 :DAVSLSYYQ 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=3 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3h41A/T0630-3h41A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 3h41A expands to /projects/compbio/data/pdb/3h41.pdb.gz 3h41A:Skipped atom 121, because occupancy 0.500 <= existing 0.500 in 3h41A Skipped atom 125, because occupancy 0.500 <= existing 0.500 in 3h41A Skipped atom 127, because occupancy 0.500 <= existing 0.500 in 3h41A Skipped atom 129, because occupancy 0.500 <= existing 0.500 in 3h41A Skipped atom 131, because occupancy 0.500 <= existing 0.500 in 3h41A Skipped atom 305, because occupancy 0.400 <= existing 0.600 in 3h41A Skipped atom 309, because occupancy 0.400 <= existing 0.600 in 3h41A Skipped atom 311, because occupancy 0.400 <= existing 0.600 in 3h41A 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 687, because occupancy 0.300 <= existing 0.700 in 3h41A Skipped atom 691, because occupancy 0.300 <= existing 0.700 in 3h41A Skipped atom 693, because occupancy 0.300 <= existing 0.700 in 3h41A Skipped atom 695, because occupancy 0.300 <= existing 0.700 in 3h41A Skipped atom 697, because occupancy 0.300 <= existing 0.700 in 3h41A Skipped atom 699, because occupancy 0.300 <= existing 0.700 in 3h41A 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 880, because occupancy 0.400 <= existing 0.600 in 3h41A Skipped atom 884, because occupancy 0.400 <= existing 0.600 in 3h41A Skipped atom 886, because occupancy 0.400 <= existing 0.600 in 3h41A Skipped atom 888, because occupancy 0.400 <= existing 0.600 in 3h41A Skipped atom 1376, because occupancy 0.400 <= existing 0.600 in 3h41A Skipped atom 1380, because occupancy 0.400 <= existing 0.600 in 3h41A Skipped atom 1382, because occupancy 0.400 <= existing 0.600 in 3h41A Skipped atom 1384, because occupancy 0.400 <= existing 0.600 in 3h41A 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: OD3 for alphabet: pdb_atoms Skipped atom 1838, because occupancy 0.300 <= existing 0.700 in 3h41A Skipped atom 1842, because occupancy 0.300 <= existing 0.700 in 3h41A Skipped atom 1844, because occupancy 0.300 <= existing 0.700 in 3h41A Skipped atom 1923, because occupancy 0.400 <= existing 0.600 in 3h41A Skipped atom 1927, because occupancy 0.400 <= existing 0.600 in 3h41A Skipped atom 1929, because occupancy 0.400 <= existing 0.600 in 3h41A Skipped atom 1931, because occupancy 0.400 <= existing 0.600 in 3h41A Skipped atom 1933, because occupancy 0.400 <= existing 0.600 in 3h41A Skipped atom 1935, because occupancy 0.400 <= existing 0.600 in 3h41A Skipped atom 1999, because occupancy 0.400 <= existing 0.600 in 3h41A Skipped atom 2003, because occupancy 0.400 <= existing 0.600 in 3h41A Skipped atom 2005, because occupancy 0.400 <= existing 0.600 in 3h41A Skipped atom 2007, because occupancy 0.400 <= existing 0.600 in 3h41A Skipped atom 2009, because occupancy 0.400 <= existing 0.600 in 3h41A Skipped atom 2083, because occupancy 0.300 <= existing 0.700 in 3h41A Skipped atom 2087, because occupancy 0.300 <= existing 0.700 in 3h41A Skipped atom 2089, because occupancy 0.300 <= existing 0.700 in 3h41A Skipped atom 2109, because occupancy 0.300 <= existing 0.700 in 3h41A Skipped atom 2113, because occupancy 0.300 <= existing 0.700 in 3h41A Skipped atom 2115, because occupancy 0.300 <= existing 0.700 in 3h41A Skipped atom 2117, because occupancy 0.300 <= existing 0.700 in 3h41A Skipped atom 2119, because occupancy 0.300 <= existing 0.700 in 3h41A Skipped atom 2121, because occupancy 0.300 <= existing 0.700 in 3h41A Skipped atom 2123, because occupancy 0.300 <= existing 0.700 in 3h41A 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 2229, because occupancy 0.300 <= existing 0.700 in 3h41A Skipped atom 2233, because occupancy 0.300 <= existing 0.700 in 3h41A Skipped atom 2235, because occupancy 0.300 <= existing 0.700 in 3h41A Skipped atom 2237, because occupancy 0.300 <= existing 0.700 in 3h41A Skipped atom 2239, because occupancy 0.300 <= existing 0.700 in 3h41A Skipped atom 2241, because occupancy 0.300 <= existing 0.700 in 3h41A Skipped atom 2243, because occupancy 0.300 <= existing 0.700 in 3h41A Skipped atom 2245, because occupancy 0.300 <= existing 0.700 in 3h41A # T0630 read from 3h41A/T0630-3h41A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3h41A read from 3h41A/T0630-3h41A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3h41A to template set # found chain 3h41A in template set Warning: unaligning (T0630)L36 because of BadResidue code BAD_PEPTIDE in next template residue (3h41A)P305 Warning: unaligning (T0630)A37 because of BadResidue code BAD_PEPTIDE at template residue (3h41A)P305 T0630 2 :RAPIPEPKPGDLIEIFR 3h41A 266 :AVDKEHLQKGDLIFFAH T0630 19 :PFYRHWAIYVGDGYVVH 3h41A 287 :GSVHHVAMYIGDGNMIH T0630 38 :PP 3h41A 306 :RA T0630 71 :SDKYQVNNKHDD 3h41A 308 :ERSVEIIPLNTP Number of specific fragments extracted= 4 number of extra gaps= 1 total=16 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 3h41A/T0630-3h41A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0630 read from 3h41A/T0630-3h41A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3h41A read from 3h41A/T0630-3h41A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3h41A in template set Warning: unaligning (T0630)L36 because of BadResidue code BAD_PEPTIDE in next template residue (3h41A)P305 Warning: unaligning (T0630)A37 because of BadResidue code BAD_PEPTIDE at template residue (3h41A)P305 T0630 2 :RAPIPEPKPGDLIEIFR 3h41A 266 :AVDKEHLQKGDLIFFAH T0630 19 :PFYRHWAIYVGDGYVVH 3h41A 287 :GSVHHVAMYIGDGNMIH T0630 38 :PPSEV 3h41A 306 :RAERS T0630 43 :AGAGAASVMSALTD 3h41A 314 :IPLNTPGYIEEYAG Number of specific fragments extracted= 4 number of extra gaps= 1 total=20 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 3h41A/T0630-3h41A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0630 read from 3h41A/T0630-3h41A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3h41A read from 3h41A/T0630-3h41A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3h41A in template set Warning: unaligning (T0630)L36 because of BadResidue code BAD_PEPTIDE in next template residue (3h41A)P305 Warning: unaligning (T0630)A37 because of BadResidue code BAD_PEPTIDE at template residue (3h41A)P305 T0630 2 :RAPIPEPKPGDLIEIFR 3h41A 266 :AVDKEHLQKGDLIFFAH T0630 19 :PFYRHWAIYVGDGYVVH 3h41A 287 :GSVHHVAMYIGDGNMIH T0630 38 :PPSE 3h41A 306 :RAER T0630 44 :GAGAASVMSALTDKA 3h41A 310 :SVEIIPLNTPGYIEE Number of specific fragments extracted= 4 number of extra gaps= 1 total=24 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 2hbwA/T0630-2hbwA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0630 read from 2hbwA/T0630-2hbwA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2hbwA read from 2hbwA/T0630-2hbwA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2hbwA in training set Warning: unaligning (T0630)R18 because of BadResidue code BAD_PEPTIDE in next template residue (2hbwA)P171 T0630 3 :APIPEPKPGDLIEIF 2hbwA 155 :ITIDELAPGDLVFFG T0630 19 :PFYRHWAIYVGDGYVVHLAPPSEVA 2hbwA 172 :VKATHVGLYLGDGCYIHSSGKAQGR T0630 58 :AIVKKELL 2hbwA 197 :DGIGIDIL Number of specific fragments extracted= 3 number of extra gaps= 1 total=27 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 2hbwA/T0630-2hbwA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0630 read from 2hbwA/T0630-2hbwA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2hbwA read from 2hbwA/T0630-2hbwA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2hbwA in training set Warning: unaligning (T0630)R18 because of BadResidue code BAD_PEPTIDE in next template residue (2hbwA)P171 T0630 3 :APIPEPKPGDLIEIF 2hbwA 155 :ITIDELAPGDLVFFG T0630 19 :PFYRHWAIYVGDGYVVHLAPPSE 2hbwA 172 :VKATHVGLYLGDGCYIHSSGKAQ T0630 56 :DKAIVKKELL 2hbwA 195 :GRDGIGIDIL T0630 81 :DDKYS 2hbwA 205 :SEQGD T0630 91 :KIIQRAEE 2hbwA 210 :VVSRSYYQ Number of specific fragments extracted= 5 number of extra gaps= 1 total=32 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 2hbwA/T0630-2hbwA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0630 read from 2hbwA/T0630-2hbwA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2hbwA read from 2hbwA/T0630-2hbwA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2hbwA in training set Warning: unaligning (T0630)R18 because of BadResidue code BAD_PEPTIDE in next template residue (2hbwA)P171 T0630 3 :APIPEPKPGDLIEIF 2hbwA 155 :ITIDELAPGDLVFFG T0630 19 :PFYRHWAIYVGDGYVVHLAPPSEVAGAGAA 2hbwA 172 :VKATHVGLYLGDGCYIHSSGKAQGRDGIGI T0630 78 :NKH 2hbwA 202 :DIL T0630 86 :PLPCSKIIQRAEE 2hbwA 205 :SEQGDVVSRSYYQ Number of specific fragments extracted= 4 number of extra gaps= 1 total=36 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 3gt2A/T0630-3gt2A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 3gt2A expands to /projects/compbio/data/pdb/3gt2.pdb.gz 3gt2A: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 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 # T0630 read from 3gt2A/T0630-3gt2A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3gt2A read from 3gt2A/T0630-3gt2A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3gt2A to template set # found chain 3gt2A in template set T0630 3 :APIPEPKPGDLIEIFRPFYRHWAIYVGDGYVVHLAP 3gt2A 148 :ILPQQARKGDLIFYGPEGTQSVAMYLGNNQMLEVGD T0630 59 :IVKKELLYD 3gt2A 184 :VVQVSPVRT Number of specific fragments extracted= 2 number of extra gaps= 0 total=38 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 3gt2A/T0630-3gt2A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0630 read from 3gt2A/T0630-3gt2A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3gt2A read from 3gt2A/T0630-3gt2A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3gt2A in template set T0630 2 :RAPIPEPKPGDLIEIFRPFYRHWAIYVGDGYVVHLAP 3gt2A 147 :KILPQQARKGDLIFYGPEGTQSVAMYLGNNQMLEVGD T0630 59 :IVKKELL 3gt2A 184 :VVQVSPV 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=11 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3gt2A/T0630-3gt2A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0630 read from 3gt2A/T0630-3gt2A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3gt2A read from 3gt2A/T0630-3gt2A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3gt2A in template set T0630 2 :RAPIPEPKPGDLIEIFRPFYRHWAIYVGDGYVVHLAPPSEVAGAGAASV 3gt2A 147 :KILPQQARKGDLIFYGPEGTQSVAMYLGNNQMLEVGDVVQVSPVRTAGM Number of specific fragments extracted= 1 number of extra gaps= 0 total=41 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 2if6A/T0630-2if6A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2if6A expands to /projects/compbio/data/pdb/2if6.pdb.gz 2if6A:Skipped atom 305, because occupancy 0.500 <= existing 0.500 in 2if6A Skipped atom 309, because occupancy 0.500 <= existing 0.500 in 2if6A Skipped atom 311, because occupancy 0.500 <= existing 0.500 in 2if6A Skipped atom 313, because occupancy 0.500 <= existing 0.500 in 2if6A Skipped atom 315, because occupancy 0.500 <= existing 0.500 in 2if6A Skipped atom 500, because occupancy 0.500 <= existing 0.500 in 2if6A Skipped atom 504, because occupancy 0.500 <= existing 0.500 in 2if6A Skipped atom 506, because occupancy 0.500 <= existing 0.500 in 2if6A Skipped atom 508, because occupancy 0.500 <= existing 0.500 in 2if6A Skipped atom 510, because occupancy 0.500 <= existing 0.500 in 2if6A Skipped atom 512, because occupancy 0.500 <= existing 0.500 in 2if6A Skipped atom 514, because occupancy 0.500 <= existing 0.500 in 2if6A Skipped atom 703, because occupancy 0.500 <= existing 0.500 in 2if6A Skipped atom 707, because occupancy 0.500 <= existing 0.500 in 2if6A Skipped atom 709, because occupancy 0.500 <= existing 0.500 in 2if6A Skipped atom 711, because occupancy 0.500 <= existing 0.500 in 2if6A Skipped atom 713, because occupancy 0.500 <= existing 0.500 in 2if6A Skipped atom 715, because occupancy 0.500 <= existing 0.500 in 2if6A Skipped atom 1178, because occupancy 0.500 <= existing 0.500 in 2if6A Skipped atom 1182, because occupancy 0.500 <= existing 0.500 in 2if6A Skipped atom 1184, because occupancy 0.500 <= existing 0.500 in 2if6A Skipped atom 1186, because occupancy 0.500 <= existing 0.500 in 2if6A Skipped atom 1188, because occupancy 0.500 <= existing 0.500 in 2if6A Skipped atom 1190, because occupancy 0.500 <= existing 0.500 in 2if6A Skipped atom 1198, because occupancy 0.500 <= existing 0.500 in 2if6A Skipped atom 1202, because occupancy 0.500 <= existing 0.500 in 2if6A Skipped atom 1204, because occupancy 0.500 <= existing 0.500 in 2if6A Skipped atom 1206, because occupancy 0.500 <= existing 0.500 in 2if6A Skipped atom 1208, because occupancy 0.500 <= existing 0.500 in 2if6A Skipped atom 1210, because occupancy 0.500 <= existing 0.500 in 2if6A # T0630 read from 2if6A/T0630-2if6A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2if6A read from 2if6A/T0630-2if6A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2if6A to template set # found chain 2if6A in template set Warning: unaligning (T0630)P6 because first residue in template chain is (2if6A)W19 T0630 7 :EPKPGDLIEIFR 2if6A 20 :QPQTGDIIFQIS T0630 19 :PFYRHWAIYVGDG 2if6A 45 :SDYSHTGMLVMRN T0630 32 :YVVHLAP 2if6A 61 :YVFEAVG T0630 59 :IVKKELLYDVA 2if6A 68 :PVKYTPLKQWI T0630 70 :GSDKYQVNNKH 2if6A 82 :EKGKYVVRRVE T0630 82 :DKYS 2if6A 93 :GGLS T0630 90 :SKIIQRAEELVGQ 2if6A 97 :VEQQQKLAQTAKR T0630 121 :RYGVARSDQVR 2if6A 110 :YLGKPYDFSFS Number of specific fragments extracted= 8 number of extra gaps= 0 total=49 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 2if6A/T0630-2if6A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0630 read from 2if6A/T0630-2if6A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2if6A read from 2if6A/T0630-2if6A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2if6A in template set Warning: unaligning (T0630)P6 because first residue in template chain is (2if6A)W19 T0630 7 :EPKPGDLIEIFR 2if6A 20 :QPQTGDIIFQIS T0630 19 :PFYRHWAIYVGDG 2if6A 45 :SDYSHTGMLVMRN T0630 32 :YVVHLAPP 2if6A 61 :YVFEAVGP T0630 60 :VKKELLYDVAGSD 2if6A 69 :VKYTPLKQWIAHG T0630 73 :KYQVNNKH 2if6A 85 :KYVVRRVE T0630 82 :DKYSPLPCSKIIQRAEELVGQEV 2if6A 93 :GGLSVEQQQKLAQTAKRYLGKPY T0630 113 :CEHFVNELR 2if6A 128 :CSEVVWKVY Number of specific fragments extracted= 7 number of extra gaps= 0 total=56 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 2if6A/T0630-2if6A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0630 read from 2if6A/T0630-2if6A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2if6A read from 2if6A/T0630-2if6A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2if6A in template set T0630 7 :EPKPGDLIEIFR 2if6A 20 :QPQTGDIIFQIS T0630 19 :PFYRHWAIYVG 2if6A 45 :SDYSHTGMLVM T0630 30 :DGYVVHLAPPSEVAGAGAASVMSALTDK 2if6A 57 :NKKPYVFEAVGPVKYTPLKQWIAHGEKG T0630 73 :KYQVNN 2if6A 85 :KYVVRR T0630 84 :YSPLPCSKIIQRAEELVGQ 2if6A 91 :VEGGLSVEQQQKLAQTAKR Number of specific fragments extracted= 5 number of extra gaps= 0 total=61 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 3m1uA/T0630-3m1uA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 3m1uA expands to /projects/compbio/data/pdb/3m1u.pdb.gz 3m1uA: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 345, because occupancy 0.500 <= existing 0.500 in 3m1uA Skipped atom 349, because occupancy 0.500 <= existing 0.500 in 3m1uA Skipped atom 351, because occupancy 0.500 <= existing 0.500 in 3m1uA Skipped atom 353, because occupancy 0.500 <= existing 0.500 in 3m1uA Skipped atom 355, because occupancy 0.500 <= existing 0.500 in 3m1uA Skipped atom 357, because occupancy 0.500 <= existing 0.500 in 3m1uA Skipped atom 434, because occupancy 0.500 <= existing 0.500 in 3m1uA Skipped atom 438, because occupancy 0.500 <= existing 0.500 in 3m1uA Skipped atom 440, because occupancy 0.500 <= existing 0.500 in 3m1uA Skipped atom 442, because occupancy 0.500 <= existing 0.500 in 3m1uA Skipped atom 444, because occupancy 0.500 <= existing 0.500 in 3m1uA Skipped atom 446, because occupancy 0.500 <= existing 0.500 in 3m1uA Skipped atom 448, because occupancy 0.500 <= existing 0.500 in 3m1uA Skipped atom 450, because occupancy 0.500 <= existing 0.500 in 3m1uA 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 531, because occupancy 0.500 <= existing 0.500 in 3m1uA Skipped atom 535, because occupancy 0.500 <= existing 0.500 in 3m1uA Skipped atom 537, because occupancy 0.500 <= existing 0.500 in 3m1uA Skipped atom 539, because occupancy 0.500 <= existing 0.500 in 3m1uA Skipped atom 968, because occupancy 0.330 <= existing 0.330 in 3m1uA Skipped atom 973, because occupancy 0.330 <= existing 0.330 in 3m1uA Skipped atom 976, because occupancy 0.330 <= existing 0.330 in 3m1uA Skipped atom 1018, because occupancy 0.500 <= existing 0.500 in 3m1uA Skipped atom 1022, because occupancy 0.500 <= existing 0.500 in 3m1uA Skipped atom 1024, because occupancy 0.500 <= existing 0.500 in 3m1uA Skipped atom 1026, because occupancy 0.500 <= existing 0.500 in 3m1uA Skipped atom 1028, because occupancy 0.500 <= existing 0.500 in 3m1uA Skipped atom 1030, because occupancy 0.500 <= existing 0.500 in 3m1uA 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 1224, because occupancy 0.500 <= existing 0.500 in 3m1uA Skipped atom 1228, because occupancy 0.500 <= existing 0.500 in 3m1uA Skipped atom 1230, because occupancy 0.500 <= existing 0.500 in 3m1uA Skipped atom 1232, because occupancy 0.500 <= existing 0.500 in 3m1uA Skipped atom 1234, because occupancy 0.500 <= existing 0.500 in 3m1uA Skipped atom 1236, because occupancy 0.500 <= existing 0.500 in 3m1uA Skipped atom 1238, because occupancy 0.500 <= existing 0.500 in 3m1uA Skipped atom 1240, because occupancy 0.500 <= existing 0.500 in 3m1uA 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 1276, because occupancy 0.500 <= existing 0.500 in 3m1uA 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 1280, because occupancy 0.500 <= existing 0.500 in 3m1uA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1282, because occupancy 0.500 <= existing 0.500 in 3m1uA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1284, because occupancy 0.370 <= existing 0.380 in 3m1uA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1286, because occupancy 0.500 <= existing 0.500 in 3m1uA 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 1680, because occupancy 0.500 <= existing 0.500 in 3m1uA Skipped atom 1684, because occupancy 0.500 <= existing 0.500 in 3m1uA Skipped atom 1686, because occupancy 0.500 <= existing 0.500 in 3m1uA Skipped atom 1688, because occupancy 0.500 <= existing 0.500 in 3m1uA Skipped atom 1690, because occupancy 0.500 <= existing 0.500 in 3m1uA Skipped atom 1692, because occupancy 0.500 <= existing 0.500 in 3m1uA Skipped atom 1694, because occupancy 0.500 <= existing 0.500 in 3m1uA Skipped atom 1696, because occupancy 0.500 <= existing 0.500 in 3m1uA Skipped atom 1836, because occupancy 0.500 <= existing 0.500 in 3m1uA Skipped atom 1840, because occupancy 0.500 <= existing 0.500 in 3m1uA Skipped atom 1842, because occupancy 0.500 <= existing 0.500 in 3m1uA Skipped atom 1844, because occupancy 0.500 <= existing 0.500 in 3m1uA 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 2187, because occupancy 0.500 <= existing 0.500 in 3m1uA Skipped atom 2191, because occupancy 0.500 <= existing 0.500 in 3m1uA Skipped atom 2193, because occupancy 0.500 <= existing 0.500 in 3m1uA Skipped atom 2195, because occupancy 0.500 <= existing 0.500 in 3m1uA Skipped atom 2197, because occupancy 0.500 <= existing 0.500 in 3m1uA Skipped atom 2199, because occupancy 0.500 <= existing 0.500 in 3m1uA Skipped atom 2201, because occupancy 0.500 <= existing 0.500 in 3m1uA Skipped atom 2203, because occupancy 0.500 <= existing 0.500 in 3m1uA 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 2492, because occupancy 0.300 <= existing 0.700 in 3m1uA Skipped atom 2496, because occupancy 0.300 <= existing 0.700 in 3m1uA Skipped atom 2498, because occupancy 0.300 <= existing 0.700 in 3m1uA 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 2786, because occupancy 0.300 <= existing 0.700 in 3m1uA Skipped atom 2790, because occupancy 0.300 <= existing 0.700 in 3m1uA Skipped atom 2792, because occupancy 0.300 <= existing 0.700 in 3m1uA Skipped atom 2794, because occupancy 0.300 <= existing 0.700 in 3m1uA Skipped atom 2796, because occupancy 0.300 <= existing 0.700 in 3m1uA Skipped atom 2798, because occupancy 0.300 <= existing 0.700 in 3m1uA Skipped atom 2800, because occupancy 0.300 <= existing 0.700 in 3m1uA Skipped atom 2802, because occupancy 0.300 <= existing 0.700 in 3m1uA Skipped atom 2884, because occupancy 0.500 <= existing 0.500 in 3m1uA Skipped atom 2888, because occupancy 0.500 <= existing 0.500 in 3m1uA Skipped atom 2890, because occupancy 0.500 <= existing 0.500 in 3m1uA Skipped atom 2892, because occupancy 0.500 <= existing 0.500 in 3m1uA Skipped atom 2894, because occupancy 0.500 <= existing 0.500 in 3m1uA Skipped atom 2896, because occupancy 0.500 <= existing 0.500 in 3m1uA Skipped atom 2903, because occupancy 0.500 <= existing 0.500 in 3m1uA Skipped atom 2907, because occupancy 0.500 <= existing 0.500 in 3m1uA Skipped atom 2909, because occupancy 0.500 <= existing 0.500 in 3m1uA Skipped atom 2911, because occupancy 0.500 <= existing 0.500 in 3m1uA Skipped atom 2913, because occupancy 0.500 <= existing 0.500 in 3m1uA Skipped atom 2915, because occupancy 0.500 <= existing 0.500 in 3m1uA 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 3040, because occupancy 0.500 <= existing 0.500 in 3m1uA Skipped atom 3044, because occupancy 0.500 <= existing 0.500 in 3m1uA Skipped atom 3046, because occupancy 0.500 <= existing 0.500 in 3m1uA Skipped atom 3048, because occupancy 0.500 <= existing 0.500 in 3m1uA Skipped atom 3094, because occupancy 0.500 <= existing 0.500 in 3m1uA Skipped atom 3098, because occupancy 0.500 <= existing 0.500 in 3m1uA Skipped atom 3100, because occupancy 0.500 <= existing 0.500 in 3m1uA Skipped atom 3102, because occupancy 0.500 <= existing 0.500 in 3m1uA Skipped atom 3104, because occupancy 0.500 <= existing 0.500 in 3m1uA 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 # T0630 read from 3m1uA/T0630-3m1uA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3m1uA read from 3m1uA/T0630-3m1uA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3m1uA to template set # found chain 3m1uA in template set Warning: unaligning (T0630)L54 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (3m1uA)G272 Warning: unaligning (T0630)T55 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (3m1uA)G272 T0630 10 :PGDLIEIFRPF 3m1uA 188 :MGTPVFVGHAT T0630 23 :HWAIYVGDGY 3m1uA 202 :AWLYVETAFA T0630 33 :VVHLAP 3m1uA 236 :LAAILR T0630 40 :SEVA 3m1uA 250 :DGTH T0630 44 :GAGAASVMSA 3m1uA 256 :TAHIGTVLPL T0630 61 :KKELLYDVAGSDKYQVNNK 3m1uA 273 :RTVLVPVRAPEGHAVVVPV T0630 80 :HDDKYS 3m1uA 294 :TSGEAA T0630 86 :PLPCSKIIQRAEELVGQEVLYKLTSE 3m1uA 304 :PLTPGNMAELGNRMMGQPYGWGGLYE T0630 112 :NCEHFVNELR 3m1uA 332 :DCSSTLRDLF Number of specific fragments extracted= 9 number of extra gaps= 1 total=70 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 3m1uA/T0630-3m1uA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0630 read from 3m1uA/T0630-3m1uA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3m1uA read from 3m1uA/T0630-3m1uA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3m1uA in template set Warning: unaligning (T0630)L64 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (3m1uA)G272 Warning: unaligning (T0630)L65 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (3m1uA)G272 T0630 10 :PGDLIEIFR 3m1uA 188 :MGTPVFVGH T0630 19 :PFYR 3m1uA 199 :ADRA T0630 24 :WAIYVGDGY 3m1uA 203 :WLYVETAFA T0630 33 :VVHLAPPSEVAGAGAASVMSALTDKA 3m1uA 236 :LAAILRDDTSLNGADGTHLATAHIGT T0630 60 :VKKE 3m1uA 262 :VLPL T0630 71 :SDKYQVNNKHDDKYS 3m1uA 273 :RTVLVPVRAPEGHAV T0630 86 :PLPCSKIIQRAEELVGQEVLYKLTSE 3m1uA 304 :PLTPGNMAELGNRMMGQPYGWGGLYE T0630 112 :NCEHFVNELR 3m1uA 332 :DCSSTLRDLF Number of specific fragments extracted= 8 number of extra gaps= 1 total=78 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 3m1uA/T0630-3m1uA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0630 read from 3m1uA/T0630-3m1uA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3m1uA read from 3m1uA/T0630-3m1uA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3m1uA in template set Warning: unaligning (T0630)D56 because of BadResidue code BAD_PEPTIDE in next template residue (3m1uA)S235 Warning: unaligning (T0630)K57 because of BadResidue code BAD_PEPTIDE at template residue (3m1uA)S235 Warning: unaligning (T0630)P88 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (3m1uA)G272 Warning: unaligning (T0630)C89 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (3m1uA)G272 T0630 9 :KPGDLIEIFR 3m1uA 187 :WMGTPVFVGH T0630 24 :W 3m1uA 203 :W T0630 26 :IYVGDGYVVHLAPPSEVAGAGAASVMSALT 3m1uA 204 :LYVETAFAAGWMPAADVARVDDAFMTRYES T0630 58 :AIVKKELLYDVAGSDKYQVNNKHDDKYSPL 3m1uA 236 :LAAILRDDTSLNGADGTHLATAHIGTVLPL T0630 90 :SKIIQRAEELVGQEVLYKLTSE 3m1uA 308 :GNMAELGNRMMGQPYGWGGLYE T0630 112 :NCEHFVNEL 3m1uA 332 :DCSSTLRDL Number of specific fragments extracted= 6 number of extra gaps= 2 total=84 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 3ebqA/T0630-3ebqA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 3ebqA expands to /projects/compbio/data/pdb/3ebq.pdb.gz 3ebqA:Skipped atom 799, because occupancy 0.500 <= existing 0.500 in 3ebqA Skipped atom 801, because occupancy 0.500 <= existing 0.500 in 3ebqA Skipped atom 803, because occupancy 0.500 <= existing 0.500 in 3ebqA Skipped atom 805, because occupancy 0.500 <= existing 0.500 in 3ebqA Skipped atom 807, because occupancy 0.500 <= existing 0.500 in 3ebqA Skipped atom 809, because occupancy 0.500 <= existing 0.500 in 3ebqA Skipped atom 851, because occupancy 0.500 <= existing 0.500 in 3ebqA Skipped atom 853, because occupancy 0.500 <= existing 0.500 in 3ebqA Skipped atom 855, because occupancy 0.500 <= existing 0.500 in 3ebqA Skipped atom 857, because occupancy 0.500 <= existing 0.500 in 3ebqA Skipped atom 859, because occupancy 0.500 <= existing 0.500 in 3ebqA Skipped atom 861, because occupancy 0.500 <= existing 0.500 in 3ebqA Skipped atom 863, because occupancy 0.500 <= existing 0.500 in 3ebqA Skipped atom 865, because occupancy 0.500 <= existing 0.500 in 3ebqA Skipped atom 867, because occupancy 0.500 <= existing 0.500 in 3ebqA # T0630 read from 3ebqA/T0630-3ebqA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3ebqA read from 3ebqA/T0630-3ebqA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3ebqA to template set # found chain 3ebqA in template set T0630 19 :PFYRHWAIYVG 3ebqA 34 :EGIWHTSIVVH T0630 31 :GYVVHLAPP 3ebqA 45 :KDEFFFGSG T0630 41 :EVA 3ebqA 54 :GIS T0630 44 :GAGAASVMSALTDKAIVKKE 3ebqA 58 :CPPGGTLLGPPDSVVDVGST T0630 86 :PLPCSKIIQRAEELVGQEVL 3ebqA 78 :EVTEEIFLEYLSSLGESLFR T0630 106 :YKLTSENCEHFVNELR 3ebqA 101 :YNLFEHNCNTFSNEVA T0630 122 :YGVA 3ebqA 120 :TGRK Number of specific fragments extracted= 7 number of extra gaps= 0 total=91 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 3ebqA/T0630-3ebqA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0630 read from 3ebqA/T0630-3ebqA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3ebqA read from 3ebqA/T0630-3ebqA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3ebqA in template set T0630 19 :PFYRHWAIYV 3ebqA 34 :EGIWHTSIVV T0630 30 :DGYVVHLAPPSEVAGAGAASVMSALTDKAIVKKE 3ebqA 44 :HKDEFFFGSGGISSCPPGGTLLGPPDSVVDVGST T0630 86 :PLPCSKIIQRAEELVGQEV 3ebqA 78 :EVTEEIFLEYLSSLGESLF T0630 105 :LYKLTSENCEHFVNELR 3ebqA 100 :AYNLFEHNCNTFSNEVA T0630 122 :YGVAR 3ebqA 120 :TGRKI Number of specific fragments extracted= 5 number of extra gaps= 0 total=96 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 3ebqA/T0630-3ebqA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0630 read from 3ebqA/T0630-3ebqA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3ebqA read from 3ebqA/T0630-3ebqA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3ebqA in template set T0630 19 :PFYRHWAIYVGD 3ebqA 34 :EGIWHTSIVVHK T0630 32 :YVVH 3ebqA 46 :DEFF T0630 37 :APPSEVAGAGAASVM 3ebqA 50 :FGSGGISSCPPGGTL T0630 80 :HDDKYSP 3ebqA 65 :LGPPDSV T0630 90 :SKIIQRAEELVGQE 3ebqA 82 :EIFLEYLSSLGESL T0630 104 :VLYKLTSENCEHFVNEL 3ebqA 99 :EAYNLFEHNCNTFSNEV Number of specific fragments extracted= 6 number of extra gaps= 0 total=102 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 1yozA/T0630-1yozA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1yozA expands to /projects/compbio/data/pdb/1yoz.pdb.gz 1yozA:# T0630 read from 1yozA/T0630-1yozA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1yozA read from 1yozA/T0630-1yozA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1yozA to template set # found chain 1yozA in template set T0630 83 :KYSPL 1yozA 11 :MLYIN T0630 91 :KIIQRAEELVGQEV 1yozA 16 :SFLDRMGEIIRGEK T0630 106 :YKLTSENCEHFVNELRYGVARSDQV 1yozA 44 :FEMFRSDCEEILNLYKSGKAEKEEV Number of specific fragments extracted= 3 number of extra gaps= 0 total=105 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 1yozA/T0630-1yozA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0630 read from 1yozA/T0630-1yozA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1yozA read from 1yozA/T0630-1yozA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1yozA in template set T0630 91 :KIIQRAEELVGQEV 1yozA 16 :SFLDRMGEIIRGEK T0630 106 :YKLTSENCEHFVNELRYGVARSDQV 1yozA 44 :FEMFRSDCEEILNLYKSGKAEKEEV Number of specific fragments extracted= 2 number of extra gaps= 0 total=107 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 1yozA/T0630-1yozA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0630 read from 1yozA/T0630-1yozA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1yozA read from 1yozA/T0630-1yozA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1yozA in template set T0630 85 :SPLPCSKIIQRAEELVGQEVL 1yozA 10 :HMLYINSFLDRMGEIIRGEKS T0630 106 :YKLTSENCEHFVNELRYGVARSDQVR 1yozA 44 :FEMFRSDCEEILNLYKSGKAEKEEVQ Number of specific fragments extracted= 2 number of extra gaps= 0 total=109 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 1am2/T0630-1am2-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1am2 expands to /projects/compbio/data/pdb/1am2.pdb.gz 1am2:Warning: there is no chain 1am2 will retry with 1am2A # T0630 read from 1am2/T0630-1am2-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1am2 read from 1am2/T0630-1am2-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1am2 to template set # found chain 1am2 in template set T0630 15 :EIFRPFYRHWAIYVGDGYVVHLAPP 1am2 50 :LFHSGEHPVYAVRTVEGLRVTGTAN T0630 46 :GAASVMSALTDKAIVKKELLYDVAGSDKYQVN 1am2 75 :HPLLCLVDVAGVPTLLWKLIDEIKPGDYAVIQ T0630 78 :NKHDDK 1am2 143 :HHRDPD T0630 89 :CSKIIQRAE 1am2 149 :AKAIADELT Number of specific fragments extracted= 4 number of extra gaps= 0 total=113 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 1am2/T0630-1am2-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0630 read from 1am2/T0630-1am2-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1am2 read from 1am2/T0630-1am2-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1am2 in template set Warning: unaligning (T0630)D82 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (1am2)T130 T0630 14 :IEIFRPFYRHWAIYVGDGYVVHLAPPS 1am2 49 :RLFHSGEHPVYAVRTVEGLRVTGTANH T0630 47 :AASVMSALTDKAIVKKELLYDVAGSDKYQVNNKHD 1am2 76 :PLLCLVDVAGVPTLLWKLIDEIKPGDYAVIQRSAF Number of specific fragments extracted= 2 number of extra gaps= 0 total=115 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 1am2/T0630-1am2-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0630 read from 1am2/T0630-1am2-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1am2 read from 1am2/T0630-1am2-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1am2 in template set Warning: unaligning (T0630)R22 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (1am2)T130 Warning: unaligning (T0630)E41 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR at template residue (1am2)T130 T0630 7 :EPKPGDLIEIFRPFY 1am2 96 :EIKPGDYAVIQRSAF T0630 42 :VAGAGAASVMSALTDKAIV 1am2 131 :VGVPGLVRFLEAHHRDPDA T0630 62 :KELLYDVAGSDKYQVNNKH 1am2 150 :KAIADELTDGRFYYAKVAS Number of specific fragments extracted= 3 number of extra gaps= 0 total=118 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 2k3aA/T0630-2k3aA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2k3aA expands to /projects/compbio/data/pdb/2k3a.pdb.gz 2k3aA:# T0630 read from 2k3aA/T0630-2k3aA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2k3aA read from 2k3aA/T0630-2k3aA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2k3aA to template set # found chain 2k3aA in template set T0630 6 :PEPKPGDLIEIFRPFYRHWAIYV 2k3aA 92 :NSPEAGSILQSTAGGYGHVAYVE T0630 29 :GDGYVVHLAPPSEVA 2k3aA 118 :SDGSVEVSEMNYNGG T0630 57 :KAIVKKELLYD 2k3aA 133 :PFSVSERTISA T0630 90 :SKI 2k3aA 144 :GEA Number of specific fragments extracted= 4 number of extra gaps= 0 total=122 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 2k3aA/T0630-2k3aA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0630 read from 2k3aA/T0630-2k3aA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2k3aA read from 2k3aA/T0630-2k3aA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2k3aA in template set T0630 6 :PEPKPGDLIEIFRPFYRHWAIY 2k3aA 92 :NSPEAGSILQSTAGGYGHVAYV T0630 28 :VG 2k3aA 116 :VN T0630 30 :DG 2k3aA 119 :DG T0630 32 :YVVHLAPPSEVAG 2k3aA 123 :EVSEMNYNGGPFS T0630 58 :AIVKKELLYDVAG 2k3aA 136 :VSERTISAGEASS Number of specific fragments extracted= 5 number of extra gaps= 0 total=127 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 2k3aA/T0630-2k3aA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0630 read from 2k3aA/T0630-2k3aA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2k3aA read from 2k3aA/T0630-2k3aA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2k3aA in template set T0630 6 :PEPKPGDLIEIFRPFYRHWAI 2k3aA 92 :NSPEAGSILQSTAGGYGHVAY T0630 65 :LYDVAGSDKYQVNNKHDDKYSP 2k3aA 113 :VENVNSDGSVEVSEMNYNGGPF Number of specific fragments extracted= 2 number of extra gaps= 0 total=129 Will force an alignment to be made, even if fragment is small Number of alignments=30 # command:CPU_time= 10.146 sec, elapsed time= 12.435 sec. # command:DEBUG: alignment library has 30 conformations DEBUG: current conformations has 0 conformations # in ExtractAlignmentsContacts extracting from alignment library using radius 8.000 separation >= 9 style evalue NUMB_ALIGNS: 30 # Adding 970 constraints to all_contacts Done adding distance constraints # command:CPU_time= 10.167 sec, elapsed time= 12.457 sec. # command:Reading probabilities from T0630.t06.CB8-sep9.rdb Reading constraints from ConstraintSet all_contacts maxweight: 18.338 Optimizing... Probability sum: -263.812, CN propb: -263.812 weights: 0.197 constraints: 371 # command:CPU_time= 15.504 sec, elapsed time= 17.807 sec. # command:Found ConstraintSet # PrintContacts align.constraints Number of constraints in align 371 # command:Found ConstraintSet # PrintContacts align_bonus.constraints Number of constraints in align.bonus 371 # command:Found ConstraintSet # PrintContacts rejected.constraints Number of constraints in rejected 599 # command:Found ConstraintSet # PrintContacts rejected_bonus.constraints Number of constraints in rejected.bonus 599 # command:Found ConstraintSet # PrintContacts noncontact.constraints Number of constraints in noncontact 0 # command:Found ConstraintSet # PrintContacts noncontact_bonus.constraints Number of constraints in noncontact.bonus 0 # command:CPU_time= 15.520 sec, elapsed time= 18.530 sec. # command: