# 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 T0321 numbered 1 through 251 Created new target T0321 from T0321.a2m # command:CPU_time= 6.148 sec, elapsed time= 6.208 sec. # command:# reading script from file all-templates.under # Reading fragments from alignment file # Attempting to read fragment alignments from file 1vpdA/T0321-1vpdA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1vpdA expands to /projects/compbio/data/pdb/1vpd.pdb.gz 1vpdA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 2, because occupancy 0.42 <= existing 0.580 in 1vpdA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 4, because occupancy 0.420 <= existing 0.580 in 1vpdA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 6, because occupancy 0.420 <= existing 0.580 in 1vpdA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 8, because occupancy 0.420 <= existing 0.580 in 1vpdA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 10, because occupancy 0.420 <= existing 0.580 in 1vpdA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 12, because occupancy 0.420 <= existing 0.580 in 1vpdA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 14, because occupancy 0.360 <= existing 0.510 in 1vpdA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 16, because occupancy 0.420 <= existing 0.580 in 1vpdA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 85, because occupancy 0.460 <= existing 0.540 in 1vpdA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 87, because occupancy 0.460 <= existing 0.540 in 1vpdA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 89, because occupancy 0.410 <= existing 0.480 in 1vpdA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 91, because occupancy 0.460 <= existing 0.540 in 1vpdA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 236, because occupancy 0.290 <= existing 0.710 in 1vpdA Skipped atom 238, because occupancy 0.290 <= existing 0.710 in 1vpdA Skipped atom 240, because occupancy 0.290 <= existing 0.710 in 1vpdA Skipped atom 242, because occupancy 0.290 <= existing 0.710 in 1vpdA Skipped atom 244, because occupancy 0.290 <= existing 0.710 in 1vpdA Skipped atom 246, because occupancy 0.290 <= existing 0.710 in 1vpdA Skipped atom 248, because occupancy 0.290 <= existing 0.710 in 1vpdA Skipped atom 296, because occupancy 0.480 <= existing 0.520 in 1vpdA Skipped atom 298, because occupancy 0.480 <= existing 0.520 in 1vpdA Skipped atom 300, because occupancy 0.480 <= existing 0.520 in 1vpdA Skipped atom 302, because occupancy 0.480 <= existing 0.520 in 1vpdA Skipped atom 315, because occupancy 0.330 <= existing 0.670 in 1vpdA Skipped atom 317, because occupancy 0.330 <= existing 0.670 in 1vpdA Skipped atom 319, because occupancy 0.330 <= existing 0.670 in 1vpdA Skipped atom 321, because occupancy 0.330 <= existing 0.670 in 1vpdA Skipped atom 436, because occupancy 0.400 <= existing 0.600 in 1vpdA Skipped atom 438, because occupancy 0.400 <= existing 0.600 in 1vpdA Skipped atom 440, because occupancy 0.400 <= existing 0.600 in 1vpdA Skipped atom 442, because occupancy 0.400 <= existing 0.600 in 1vpdA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 509, because occupancy 0.460 <= existing 0.540 in 1vpdA Skipped atom 511, because occupancy 0.460 <= existing 0.540 in 1vpdA Skipped atom 550, because occupancy 0.470 <= existing 0.530 in 1vpdA Skipped atom 552, because occupancy 0.470 <= existing 0.530 in 1vpdA Skipped atom 554, because occupancy 0.470 <= existing 0.530 in 1vpdA Skipped atom 556, because occupancy 0.470 <= existing 0.530 in 1vpdA Skipped atom 558, because occupancy 0.470 <= existing 0.530 in 1vpdA Skipped atom 588, because occupancy 0.480 <= existing 0.520 in 1vpdA Skipped atom 590, because occupancy 0.480 <= existing 0.520 in 1vpdA Skipped atom 592, because occupancy 0.480 <= existing 0.520 in 1vpdA Skipped atom 594, because occupancy 0.480 <= existing 0.520 in 1vpdA Skipped atom 596, because occupancy 0.480 <= existing 0.520 in 1vpdA Skipped atom 648, because occupancy 0.420 <= existing 0.580 in 1vpdA Skipped atom 650, because occupancy 0.420 <= existing 0.580 in 1vpdA Skipped atom 652, because occupancy 0.420 <= existing 0.580 in 1vpdA Skipped atom 654, because occupancy 0.420 <= existing 0.580 in 1vpdA Skipped atom 656, because occupancy 0.420 <= existing 0.580 in 1vpdA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 770, because occupancy 0.480 <= existing 0.520 in 1vpdA Skipped atom 772, because occupancy 0.480 <= existing 0.520 in 1vpdA Skipped atom 774, because occupancy 0.480 <= existing 0.520 in 1vpdA Skipped atom 776, because occupancy 0.480 <= existing 0.520 in 1vpdA Skipped atom 778, because occupancy 0.480 <= existing 0.520 in 1vpdA Skipped atom 780, because occupancy 0.480 <= existing 0.520 in 1vpdA Skipped atom 782, because occupancy 0.480 <= existing 0.520 in 1vpdA Skipped atom 832, because occupancy 0.490 <= existing 0.510 in 1vpdA Skipped atom 834, because occupancy 0.490 <= existing 0.510 in 1vpdA Skipped atom 836, because occupancy 0.490 <= existing 0.510 in 1vpdA Skipped atom 838, because occupancy 0.490 <= existing 0.510 in 1vpdA Skipped atom 840, because occupancy 0.490 <= existing 0.510 in 1vpdA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 953, because occupancy 0.500 <= existing 0.500 in 1vpdA Skipped atom 955, because occupancy 0.500 <= existing 0.500 in 1vpdA Skipped atom 957, because occupancy 0.500 <= existing 0.500 in 1vpdA Skipped atom 959, because occupancy 0.500 <= existing 0.500 in 1vpdA Skipped atom 961, because occupancy 0.500 <= existing 0.500 in 1vpdA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 1044, because occupancy 0.440 <= existing 0.560 in 1vpdA Skipped atom 1046, because occupancy 0.440 <= existing 0.560 in 1vpdA Skipped atom 1048, because occupancy 0.440 <= existing 0.560 in 1vpdA Skipped atom 1054, because occupancy 0.290 <= existing 0.710 in 1vpdA Skipped atom 1056, because occupancy 0.290 <= existing 0.710 in 1vpdA Skipped atom 1058, because occupancy 0.290 <= existing 0.710 in 1vpdA Skipped atom 1060, because occupancy 0.290 <= existing 0.710 in 1vpdA Skipped atom 1062, because occupancy 0.290 <= existing 0.710 in 1vpdA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 1346, because occupancy 0.360 <= existing 0.640 in 1vpdA Skipped atom 1348, because occupancy 0.360 <= existing 0.640 in 1vpdA Skipped atom 1350, because occupancy 0.360 <= existing 0.640 in 1vpdA Skipped atom 1352, because occupancy 0.360 <= existing 0.640 in 1vpdA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 1420, because occupancy 0.410 <= existing 0.590 in 1vpdA Skipped atom 1422, because occupancy 0.410 <= existing 0.590 in 1vpdA Skipped atom 1424, because occupancy 0.410 <= existing 0.590 in 1vpdA Skipped atom 1490, because occupancy 0.430 <= existing 0.570 in 1vpdA Skipped atom 1492, because occupancy 0.430 <= existing 0.570 in 1vpdA Skipped atom 1494, because occupancy 0.430 <= existing 0.570 in 1vpdA Skipped atom 1496, because occupancy 0.430 <= existing 0.570 in 1vpdA Skipped atom 1529, because occupancy 0.420 <= existing 0.580 in 1vpdA Skipped atom 1531, because occupancy 0.420 <= existing 0.580 in 1vpdA Skipped atom 1533, because occupancy 0.420 <= existing 0.580 in 1vpdA Skipped atom 1535, because occupancy 0.420 <= existing 0.580 in 1vpdA Skipped atom 1537, because occupancy 0.420 <= existing 0.580 in 1vpdA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 1757, because occupancy 0.340 <= existing 0.660 in 1vpdA Skipped atom 1759, because occupancy 0.340 <= existing 0.660 in 1vpdA Skipped atom 1761, because occupancy 0.340 <= existing 0.660 in 1vpdA Skipped atom 1763, because occupancy 0.340 <= existing 0.660 in 1vpdA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 2164, because occupancy 0.440 <= existing 0.560 in 1vpdA Skipped atom 2166, because occupancy 0.440 <= existing 0.560 in 1vpdA Skipped atom 2168, because occupancy 0.440 <= existing 0.560 in 1vpdA Skipped atom 2170, because occupancy 0.440 <= existing 0.560 in 1vpdA # T0321 read from 1vpdA/T0321-1vpdA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1vpdA read from 1vpdA/T0321-1vpdA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1vpdA to template set # found chain 1vpdA in template set Warning: unaligning (T0321)K123 because first residue in template chain is (1vpdA)M3 Warning: unaligning (T0321)K124 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1vpdA)K4 T0321 125 :VGVVGHF 1vpdA 5 :VGFIGLG # choosing archetypes in rotamer library T0321 132 :PHLESLLEPICDLSILEWSPE 1vpdA 16 :PMSKNLLKAGYSLVVSDRNPE T0321 158 :LPASEFILPECDYVYI 1vpdA 49 :ASTAKAIAEQCDVIIT T0321 181 :KTLPRL 1vpdA 67 :PNSPHV T0321 187 :LELSRNAR 1vpdA 83 :IEGAKPGT T0321 196 :ITLVGPGTP 1vpdA 91 :VLIDMSSIA T0321 205 :LAPVLFEHGLQELSGFMVK 1vpdA 106 :ISDALKAKGVEMLDAPVSG T0321 228 :AFRIVAGA 1vpdA 125 :GEPKAIDG Number of specific fragments extracted= 8 number of extra gaps= 0 total=8 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 1vpdA/T0321-1vpdA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0321 read from 1vpdA/T0321-1vpdA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1vpdA read from 1vpdA/T0321-1vpdA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1vpdA in template set Warning: unaligning (T0321)K123 because first residue in template chain is (1vpdA)M3 Warning: unaligning (T0321)K124 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1vpdA)K4 T0321 125 :VGVVGHF 1vpdA 5 :VGFIGLG T0321 132 :PHLESLLEPICDLSILEWSPE 1vpdA 16 :PMSKNLLKAGYSLVVSDRNPE T0321 158 :LPASEFILPECDYVYI 1vpdA 49 :ASTAKAIAEQCDVIIT T0321 181 :KTLPRL 1vpdA 67 :PNSPHV T0321 187 :LELSRNAR 1vpdA 83 :IEGAKPGT T0321 196 :ITLVGPGTP 1vpdA 91 :VLIDMSSIA T0321 205 :LAPVLFEHGLQELSGFMVK 1vpdA 106 :ISDALKAKGVEMLDAPVSG T0321 228 :AFRIVAGA 1vpdA 125 :GEPKAIDG Number of specific fragments extracted= 8 number of extra gaps= 0 total=16 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 1vpdA/T0321-1vpdA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0321 read from 1vpdA/T0321-1vpdA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1vpdA read from 1vpdA/T0321-1vpdA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1vpdA in template set Warning: unaligning (T0321)K123 because first residue in template chain is (1vpdA)M3 Warning: unaligning (T0321)K124 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1vpdA)K4 T0321 125 :VGVVGHFPH 1vpdA 5 :VGFIGLGIM T0321 134 :LESLLEPICDLSILEWSPE 1vpdA 18 :SKNLLKAGYSLVVSDRNPE T0321 158 :LPASEFILPECDYVYI 1vpdA 49 :ASTAKAIAEQCDVIIT T0321 175 :CA 1vpdA 65 :ML T0321 181 :KTLPR 1vpdA 67 :PNSPH T0321 186 :LLELSRNAR 1vpdA 82 :IIEGAKPGT T0321 196 :ITLVGPGTP 1vpdA 91 :VLIDMSSIA T0321 205 :LAPVLFEHGLQELSGFMVKD 1vpdA 106 :ISDALKAKGVEMLDAPVSGG T0321 229 :FRIVAG 1vpdA 126 :EPKAID Number of specific fragments extracted= 9 number of extra gaps= 0 total=25 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 1vmeA/T0321-1vmeA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1vmeA expands to /projects/compbio/data/pdb/1vme.pdb.gz 1vmeA:Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 38, because occupancy 0.500 <= existing 0.500 in 1vmeA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 42, because occupancy 0.500 <= existing 0.500 in 1vmeA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 44, because occupancy 0.500 <= existing 0.500 in 1vmeA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 46, because occupancy 0.500 <= existing 0.500 in 1vmeA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 48, because occupancy 0.500 <= existing 0.500 in 1vmeA Skipped atom 596, because occupancy 0.500 <= existing 0.500 in 1vmeA Skipped atom 600, because occupancy 0.500 <= existing 0.500 in 1vmeA Skipped atom 602, because occupancy 0.500 <= existing 0.500 in 1vmeA Skipped atom 604, because occupancy 0.500 <= existing 0.500 in 1vmeA Skipped atom 606, because occupancy 0.500 <= existing 0.500 in 1vmeA Skipped atom 625, because occupancy 0.500 <= existing 0.500 in 1vmeA Skipped atom 627, because occupancy 0.500 <= existing 0.500 in 1vmeA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 1349, because occupancy 0.500 <= existing 0.500 in 1vmeA Skipped atom 1351, because occupancy 0.500 <= existing 0.500 in 1vmeA Skipped atom 1353, because occupancy 0.500 <= existing 0.500 in 1vmeA Skipped atom 1355, because occupancy 0.500 <= existing 0.500 in 1vmeA Skipped atom 1357, because occupancy 0.500 <= existing 0.500 in 1vmeA Skipped atom 1359, because occupancy 0.500 <= existing 0.500 in 1vmeA Skipped atom 1361, because occupancy 0.500 <= existing 0.500 in 1vmeA Skipped atom 1697, because occupancy 0.500 <= existing 0.500 in 1vmeA Skipped atom 1699, because occupancy 0.500 <= existing 0.500 in 1vmeA Skipped atom 1701, because occupancy 0.500 <= existing 0.500 in 1vmeA Skipped atom 1703, because occupancy 0.500 <= existing 0.500 in 1vmeA Skipped atom 1705, because occupancy 0.500 <= existing 0.500 in 1vmeA Skipped atom 1707, because occupancy 0.500 <= existing 0.500 in 1vmeA Skipped atom 1709, because occupancy 0.500 <= existing 0.500 in 1vmeA Skipped atom 1787, because occupancy 0.500 <= existing 0.500 in 1vmeA Skipped atom 1791, because occupancy 0.500 <= existing 0.500 in 1vmeA Skipped atom 1793, because occupancy 0.500 <= existing 0.500 in 1vmeA Skipped atom 2013, because occupancy 0.500 <= existing 0.500 in 1vmeA Skipped atom 2015, because occupancy 0.500 <= existing 0.500 in 1vmeA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 2194, because occupancy 0.500 <= existing 0.500 in 1vmeA Skipped atom 2196, because occupancy 0.500 <= existing 0.500 in 1vmeA Skipped atom 2198, because occupancy 0.500 <= existing 0.500 in 1vmeA Skipped atom 2200, because occupancy 0.500 <= existing 0.500 in 1vmeA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 2553, because occupancy 0.500 <= existing 0.500 in 1vmeA Skipped atom 2555, because occupancy 0.500 <= existing 0.500 in 1vmeA Skipped atom 2557, because occupancy 0.500 <= existing 0.500 in 1vmeA Skipped atom 2559, because occupancy 0.500 <= existing 0.500 in 1vmeA Skipped atom 2561, because occupancy 0.500 <= existing 0.500 in 1vmeA Skipped atom 2563, because occupancy 0.500 <= existing 0.500 in 1vmeA Skipped atom 2565, because occupancy 0.500 <= existing 0.500 in 1vmeA Skipped atom 2567, because occupancy 0.500 <= existing 0.500 in 1vmeA Skipped atom 2569, because occupancy 0.500 <= existing 0.500 in 1vmeA Skipped atom 2571, because occupancy 0.500 <= existing 0.500 in 1vmeA Skipped atom 2573, because occupancy 0.500 <= existing 0.500 in 1vmeA Skipped atom 2575, because occupancy 0.500 <= existing 0.500 in 1vmeA Skipped atom 2577, because occupancy 0.500 <= existing 0.500 in 1vmeA Skipped atom 2579, because occupancy 0.500 <= existing 0.500 in 1vmeA Skipped atom 2581, because occupancy 0.500 <= existing 0.500 in 1vmeA Skipped atom 2583, because occupancy 0.500 <= existing 0.500 in 1vmeA Skipped atom 2585, because occupancy 0.500 <= existing 0.500 in 1vmeA Skipped atom 2587, because occupancy 0.500 <= existing 0.500 in 1vmeA Skipped atom 2589, because occupancy 0.500 <= existing 0.500 in 1vmeA Skipped atom 2591, because occupancy 0.500 <= existing 0.500 in 1vmeA Skipped atom 2593, because occupancy 0.500 <= existing 0.500 in 1vmeA Skipped atom 2595, because occupancy 0.500 <= existing 0.500 in 1vmeA Skipped atom 2597, because occupancy 0.500 <= existing 0.500 in 1vmeA Skipped atom 2599, because occupancy 0.500 <= existing 0.500 in 1vmeA Skipped atom 2601, because occupancy 0.500 <= existing 0.500 in 1vmeA Skipped atom 2603, because occupancy 0.500 <= existing 0.500 in 1vmeA Skipped atom 2605, because occupancy 0.500 <= existing 0.500 in 1vmeA Skipped atom 2607, because occupancy 0.500 <= existing 0.500 in 1vmeA Skipped atom 2609, because occupancy 0.500 <= existing 0.500 in 1vmeA Skipped atom 2611, because occupancy 0.500 <= existing 0.500 in 1vmeA Skipped atom 2613, because occupancy 0.500 <= existing 0.500 in 1vmeA Skipped atom 2615, because occupancy 0.500 <= existing 0.500 in 1vmeA Skipped atom 2617, because occupancy 0.500 <= existing 0.500 in 1vmeA Skipped atom 2619, because occupancy 0.500 <= existing 0.500 in 1vmeA Skipped atom 2621, because occupancy 0.500 <= existing 0.500 in 1vmeA Skipped atom 2623, because occupancy 0.500 <= existing 0.500 in 1vmeA Skipped atom 2625, because occupancy 0.500 <= existing 0.500 in 1vmeA Skipped atom 2627, because occupancy 0.500 <= existing 0.500 in 1vmeA Skipped atom 2629, because occupancy 0.500 <= existing 0.500 in 1vmeA Skipped atom 2631, because occupancy 0.500 <= existing 0.500 in 1vmeA Skipped atom 2633, because occupancy 0.500 <= existing 0.500 in 1vmeA Skipped atom 2635, because occupancy 0.500 <= existing 0.500 in 1vmeA Skipped atom 2637, because occupancy 0.500 <= existing 0.500 in 1vmeA Skipped atom 2639, because occupancy 0.500 <= existing 0.500 in 1vmeA Skipped atom 2641, because occupancy 0.500 <= existing 0.500 in 1vmeA Skipped atom 2643, because occupancy 0.500 <= existing 0.500 in 1vmeA Skipped atom 2645, because occupancy 0.500 <= existing 0.500 in 1vmeA Skipped atom 2647, because occupancy 0.500 <= existing 0.500 in 1vmeA Skipped atom 2649, because occupancy 0.500 <= existing 0.500 in 1vmeA Skipped atom 2651, because occupancy 0.500 <= existing 0.500 in 1vmeA Skipped atom 2653, because occupancy 0.500 <= existing 0.500 in 1vmeA Skipped atom 2655, because occupancy 0.500 <= existing 0.500 in 1vmeA Skipped atom 2657, because occupancy 0.500 <= existing 0.500 in 1vmeA Skipped atom 2659, because occupancy 0.500 <= existing 0.500 in 1vmeA Skipped atom 2661, because occupancy 0.500 <= existing 0.500 in 1vmeA Skipped atom 2663, because occupancy 0.500 <= existing 0.500 in 1vmeA Skipped atom 2665, because occupancy 0.500 <= existing 0.500 in 1vmeA Skipped atom 2667, because occupancy 0.500 <= existing 0.500 in 1vmeA Skipped atom 2669, because occupancy 0.500 <= existing 0.500 in 1vmeA Skipped atom 2671, because occupancy 0.500 <= existing 0.500 in 1vmeA Skipped atom 2673, because occupancy 0.500 <= existing 0.500 in 1vmeA Skipped atom 2675, because occupancy 0.500 <= existing 0.500 in 1vmeA Skipped atom 2677, because occupancy 0.500 <= existing 0.500 in 1vmeA Skipped atom 2679, because occupancy 0.500 <= existing 0.500 in 1vmeA Skipped atom 2681, because occupancy 0.500 <= existing 0.500 in 1vmeA Skipped atom 2683, because occupancy 0.500 <= existing 0.500 in 1vmeA Skipped atom 2685, because occupancy 0.500 <= existing 0.500 in 1vmeA Skipped atom 2687, because occupancy 0.500 <= existing 0.500 in 1vmeA Skipped atom 2691, because occupancy 0.500 <= existing 0.500 in 1vmeA Skipped atom 2693, because occupancy 0.500 <= existing 0.500 in 1vmeA Skipped atom 2695, because occupancy 0.500 <= existing 0.500 in 1vmeA Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 2706, because occupancy 0.500 <= existing 0.500 in 1vmeA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 2710, because occupancy 0.500 <= existing 0.500 in 1vmeA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 2712, because occupancy 0.500 <= existing 0.500 in 1vmeA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 2714, because occupancy 0.500 <= existing 0.500 in 1vmeA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 2716, because occupancy 0.500 <= existing 0.500 in 1vmeA Skipped atom 3086, because occupancy 0.500 <= existing 0.500 in 1vmeA Skipped atom 3088, because occupancy 0.500 <= existing 0.500 in 1vmeA Skipped atom 3090, because occupancy 0.500 <= existing 0.500 in 1vmeA Skipped atom 3092, because occupancy 0.500 <= existing 0.500 in 1vmeA Skipped atom 3094, because occupancy 0.500 <= existing 0.500 in 1vmeA Skipped atom 3096, because occupancy 0.500 <= existing 0.500 in 1vmeA Skipped atom 3098, because occupancy 0.500 <= existing 0.500 in 1vmeA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0321 read from 1vmeA/T0321-1vmeA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1vmeA read from 1vmeA/T0321-1vmeA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1vmeA to template set # found chain 1vmeA in template set T0321 5 :YDAMINGIP 1vmeA 114 :KRLLEGFYG T0321 14 :EDFLVD 1vmeA 124 :KDVTVV T0321 20 :ELVCGTT 1vmeA 141 :KFKFVMT T0321 27 :HSVI 1vmeA 156 :MVTY T0321 32 :SGNGVGLG 1vmeA 160 :LDGILFSC T0321 40 :PNRPFETRMPMLTQN 1vmeA 171 :GGYLLPEILDDSNES T0321 63 :AAGCVKS 1vmeA 186 :VVERYLP T0321 73 :VEASIGLAAI 1vmeA 193 :HVTKYIVTVI T0321 85 :YYNNPQVARE 1vmeA 209 :ILEGAEKLSS T0321 95 :HGVIF 1vmeA 229 :GLIWK T0321 103 :KRVEDRMNDPFIMSQNEVKGKKVGVVGHF 1vmeA 234 :KDPQRLLNHYVSVAKGDPKKGKVTVIYDS T0321 132 :PHL 1vmeA 265 :GFV T0321 135 :ESLLEPICDLSILEWSPEEGDYPLPASE 1vmeA 276 :DSLKEKGFTPVVYKFSDEERPAISEILK T0321 165 :LPECDYVYITCAS 1vmeA 305 :IPDSEALIFGVST T0321 178 :VVDKTLPRLLELSRNARRITLVGPGTP 1vmeA 325 :LMRFTLLEIIDKANYEKPVLVFGVHGW T0321 205 :LAPV 1vmeA 358 :TAGE T0321 209 :LFEHGLQELSGFMVK 1vmeA 363 :LKETKFRILSFTEIK T0321 224 :DNARAFRIVAG 1vmeA 382 :DERKIEEAISL Number of specific fragments extracted= 18 number of extra gaps= 0 total=43 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 1vmeA/T0321-1vmeA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0321 read from 1vmeA/T0321-1vmeA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1vmeA read from 1vmeA/T0321-1vmeA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1vmeA in template set T0321 4 :IYDAMINGIP 1vmeA 113 :GKRLLEGFYG T0321 14 :EDFLVD 1vmeA 124 :KDVTVV T0321 20 :ELVCGTT 1vmeA 141 :KFKFVMT T0321 27 :HSVIR 1vmeA 156 :MVTYL T0321 33 :GNGVGLG 1vmeA 161 :DGILFSC T0321 41 :NRPFETRMP 1vmeA 173 :YLLPEILDD T0321 68 :KSWNYVEAS 1vmeA 182 :SNESVVERY T0321 77 :IGLAAINAYYNNPQVARE 1vmeA 194 :VTKYIVTVIGHYKNYILE T0321 95 :HGVIF 1vmeA 228 :HGLIW T0321 102 :AKRVEDRMNDPFIMSQNEVKGKKVGVVGHF 1vmeA 233 :KKDPQRLLNHYVSVAKGDPKKGKVTVIYDS T0321 132 :PHL 1vmeA 265 :GFV T0321 135 :ESLLEPICDLSILEWSPEEGDYPLPASE 1vmeA 276 :DSLKEKGFTPVVYKFSDEERPAISEILK T0321 165 :LPECDYVYITCAS 1vmeA 305 :IPDSEALIFGVST T0321 178 :VVDKTLPRLLELSRNARRITLVGPGTPL 1vmeA 325 :LMRFTLLEIIDKANYEKPVLVFGVHGWA T0321 206 :APV 1vmeA 359 :AGE T0321 209 :LFEHGLQELSGFMVK 1vmeA 363 :LKETKFRILSFTEIK T0321 224 :DNARAFRIVAG 1vmeA 382 :DERKIEEAISL Number of specific fragments extracted= 17 number of extra gaps= 0 total=60 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 1vmeA/T0321-1vmeA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0321 read from 1vmeA/T0321-1vmeA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1vmeA read from 1vmeA/T0321-1vmeA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1vmeA in template set Warning: unaligning (T0321)P204 because of BadResidue code TOO_FEW_ATOMS+BAD_PEPTIDE at template residue (1vmeA)R357 T0321 4 :IYDAMINGI 1vmeA 211 :EGAEKLSSL T0321 17 :LVDELVCGTTH 1vmeA 220 :KIKALLPGHGL T0321 40 :P 1vmeA 231 :I T0321 56 :LGLPLRVAAGCVKSWNY 1vmeA 232 :WKKDPQRLLNHYVSVAK T0321 118 :NEVKGKKVGVVGHFPH 1vmeA 249 :GDPKKGKVTVIYDSMY T0321 134 :LESLLEPI 1vmeA 274 :AIDSLKEK T0321 142 :CDLSILEWS 1vmeA 283 :FTPVVYKFS T0321 152 :EEGDYPLPASEFILPECDYVYITCAS 1vmeA 292 :DEERPAISEILKDIPDSEALIFGVST T0321 178 :VVDKTLPRLLELSRNARRITLVGPGT 1vmeA 325 :LMRFTLLEIIDKANYEKPVLVFGVHG T0321 205 :LAPVLF 1vmeA 358 :TAGELL T0321 211 :EHGLQELSGFMVK 1vmeA 365 :ETKFRILSFTEIK T0321 224 :DNARAFRIVAG 1vmeA 382 :DERKIEEAISL Number of specific fragments extracted= 12 number of extra gaps= 1 total=72 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 1xdwA/T0321-1xdwA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1xdwA expands to /projects/compbio/data/pdb/1xdw.pdb.gz 1xdwA:# T0321 read from 1xdwA/T0321-1xdwA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1xdwA read from 1xdwA/T0321-1xdwA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1xdwA to template set # found chain 1xdwA in template set Warning: unaligning (T0321)K123 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1xdwA)T148 Warning: unaligning (T0321)K124 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1xdwA)T148 T0321 2 :WEIYDAMINGI 1xdwA 59 :KQNLDIYKKLG T0321 18 :VDELVCGTT 1xdwA 70 :VKYILTRTA T0321 36 :VGLGPNRP 1xdwA 93 :FPMAFVPR T0321 51 :L 1xdwA 101 :Y T0321 59 :PLRVAAGCVKS 1xdwA 102 :SPNAIAELAVT T0321 75 :ASIGL 1xdwA 113 :QAMML T0321 86 :YN 1xdwA 118 :LR T0321 88 :NPQVAREHGVIFSDA 1xdwA 123 :YTTSRTAKKNFKVDA T0321 108 :RMND 1xdwA 138 :FMFS T0321 118 :NEVKG 1xdwA 142 :KEVRN T0321 125 :VGVVGHFP 1xdwA 149 :VGVVGLGR T0321 133 :HLESLLEPICDLSILEWSP 1xdwA 161 :AAQIFHGMGATVIGEDVFE T0321 152 :EEG 1xdwA 185 :DYC T0321 155 :DYP 1xdwA 189 :QVS T0321 161 :SEFILPECDYVYI 1xdwA 192 :LDEVLEKSDIITI T0321 181 :KTLPRLLELSRNAR 1xdwA 215 :VVTRDFLKKMKDGA T0321 196 :ITLVGPGTPLA 1xdwA 229 :ILVNCARGQLV T0321 224 :DNARAFRIVAGAE 1xdwA 240 :DTEAVIEAVESGK Number of specific fragments extracted= 18 number of extra gaps= 1 total=90 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 1xdwA/T0321-1xdwA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0321 read from 1xdwA/T0321-1xdwA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1xdwA read from 1xdwA/T0321-1xdwA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1xdwA in template set Warning: unaligning (T0321)K123 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1xdwA)T148 Warning: unaligning (T0321)K124 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1xdwA)T148 T0321 2 :WEIYDAMINGI 1xdwA 59 :KQNLDIYKKLG T0321 18 :VDELVCGTT 1xdwA 70 :VKYILTRTA T0321 27 :HSV 1xdwA 93 :FPM T0321 39 :GPNR 1xdwA 96 :AFVP T0321 57 :GLPLRVAAGCVKS 1xdwA 100 :RYSPNAIAELAVT T0321 75 :ASIGLA 1xdwA 113 :QAMMLL T0321 84 :AYYN 1xdwA 122 :AYTT T0321 91 :VAREHG 1xdwA 126 :SRTAKK T0321 102 :AKRVEDRMND 1xdwA 132 :NFKVDAFMFS T0321 118 :NEVKG 1xdwA 142 :KEVRN T0321 125 :VGVVGHFP 1xdwA 149 :VGVVGLGR T0321 133 :HLESLLEPICDLSILEWSP 1xdwA 161 :AAQIFHGMGATVIGEDVFE T0321 152 :EEG 1xdwA 185 :DYC T0321 155 :DYP 1xdwA 189 :QVS T0321 161 :SEFILPECDYVYITC 1xdwA 192 :LDEVLEKSDIITIHA T0321 181 :KTLPRLLELSRNAR 1xdwA 215 :VVTRDFLKKMKDGA T0321 196 :ITLVGPGTPLA 1xdwA 229 :ILVNCARGQLV T0321 224 :DNARAFRIVAGAE 1xdwA 240 :DTEAVIEAVESGK Number of specific fragments extracted= 18 number of extra gaps= 1 total=108 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 1xdwA/T0321-1xdwA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0321 read from 1xdwA/T0321-1xdwA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1xdwA read from 1xdwA/T0321-1xdwA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1xdwA in template set Warning: unaligning (T0321)K123 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1xdwA)T148 Warning: unaligning (T0321)K124 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1xdwA)T148 T0321 2 :WEIYDAM 1xdwA 62 :LDIYKKL T0321 18 :VDELVCG 1xdwA 70 :VKYILTR T0321 39 :GPNRPF 1xdwA 77 :TAGTDH T0321 47 :R 1xdwA 97 :F T0321 55 :LLGLPLRVAAGCVKSWNYVE 1xdwA 98 :VPRYSPNAIAELAVTQAMML T0321 85 :YYN 1xdwA 118 :LRH T0321 88 :NPQVAREHGVIFSD 1xdwA 123 :YTTSRTAKKNFKVD T0321 113 :FIMSQNEVKG 1xdwA 137 :AFMFSKEVRN T0321 125 :VGVVGHFPH 1xdwA 149 :VGVVGLGRI T0321 134 :LESLLEPICDLSILEWSPE 1xdwA 161 :AAQIFHGMGATVIGEDVFE T0321 153 :EGDYPLPASEFILPECDYVYITC 1xdwA 184 :EDYCTQVSLDEVLEKSDIITIHA T0321 181 :KTLPRLLELSRNAR 1xdwA 215 :VVTRDFLKKMKDGA T0321 196 :ITLVGPGTPLA 1xdwA 229 :ILVNCARGQLV T0321 224 :DNARAFRIVAGA 1xdwA 240 :DTEAVIEAVESG Number of specific fragments extracted= 14 number of extra gaps= 1 total=122 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 1wwkA/T0321-1wwkA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1wwkA expands to /projects/compbio/data/pdb/1wwk.pdb.gz 1wwkA:# T0321 read from 1wwkA/T0321-1wwkA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1wwkA read from 1wwkA/T0321-1wwkA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1wwkA to template set # found chain 1wwkA in template set T0321 6 :DAMINGIPE 1wwkA 55 :RRVIESAPK T0321 16 :FL 1wwkA 64 :LK T0321 21 :LVCGTT 1wwkA 66 :VIARAG T0321 42 :RPF 1wwkA 73 :GLD T0321 49 :PMLTQ 1wwkA 90 :VNAPA T0321 67 :VKSWNYVEASIGLA 1wwkA 95 :ASSRSVAELAVGLM T0321 83 :NAYYNNP 1wwkA 109 :FSVARKI T0321 90 :QVAREHGVIFSDAKRVE 1wwkA 119 :DRKMREGVWAKKEAMGI T0321 119 :EVKGKKVGVVGHFP 1wwkA 136 :ELEGKTIGIIGFGR T0321 133 :HLESLLEPICDLSILEWSPE 1wwkA 154 :VAKIANALGMNILLYDPYPN T0321 153 :EG 1wwkA 181 :NG T0321 155 :DYPLP 1wwkA 184 :FVDLE T0321 163 :FILPECDYVYI 1wwkA 189 :TLLKESDVVTI T0321 178 :VVD 1wwkA 210 :LIN T0321 184 :PRLLELSRNAR 1wwkA 213 :EERLKLMKKTA T0321 197 :TLVGPGTPL 1wwkA 224 :ILINTSRGP T0321 222 :VKDNARAFRIVAGA 1wwkA 233 :VVDTNALVKALKEG Number of specific fragments extracted= 17 number of extra gaps= 0 total=139 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 1wwkA/T0321-1wwkA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0321 read from 1wwkA/T0321-1wwkA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1wwkA read from 1wwkA/T0321-1wwkA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1wwkA in template set T0321 6 :DAMINGIPE 1wwkA 55 :RRVIESAPK T0321 16 :FL 1wwkA 64 :LK T0321 21 :LVCGTT 1wwkA 66 :VIARAG T0321 45 :ETRMPMLTQ 1wwkA 86 :GIEVVNAPA T0321 67 :VKSWNYVEASIGLA 1wwkA 95 :ASSRSVAELAVGLM T0321 83 :NAYYNNP 1wwkA 109 :FSVARKI T0321 90 :QVAREHGVIFSDAKRVE 1wwkA 119 :DRKMREGVWAKKEAMGI T0321 119 :EVKGKKVGVVGHFP 1wwkA 136 :ELEGKTIGIIGFGR T0321 133 :HLESLLEPICDLSILEWSPE 1wwkA 154 :VAKIANALGMNILLYDPYPN T0321 153 :EG 1wwkA 181 :NG T0321 155 :DYPLP 1wwkA 184 :FVDLE T0321 163 :FILPECDYVYI 1wwkA 189 :TLLKESDVVTI T0321 178 :VVD 1wwkA 210 :LIN T0321 184 :PRLLELSRNAR 1wwkA 213 :EERLKLMKKTA T0321 197 :TLVGPGTPL 1wwkA 224 :ILINTSRGP T0321 222 :VKDNARAFRIVAGA 1wwkA 233 :VVDTNALVKALKEG Number of specific fragments extracted= 16 number of extra gaps= 0 total=155 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 1wwkA/T0321-1wwkA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0321 read from 1wwkA/T0321-1wwkA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1wwkA read from 1wwkA/T0321-1wwkA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1wwkA in template set T0321 3 :EIYDAMING 1wwkA 33 :DRLVELVKD T0321 18 :VDELVCG 1wwkA 42 :VEAIIVR T0321 40 :PNRPF 1wwkA 49 :SKPKV T0321 46 :TR 1wwkA 71 :GV T0321 54 :NLLGLPLRVAAGC 1wwkA 73 :GLDNIDVEAAKEK T0321 67 :VKSWNYVEASIGLAA 1wwkA 95 :ASSRSVAELAVGLMF T0321 84 :AYYN 1wwkA 110 :SVAR T0321 88 :NPQVAREHGVIFSDAKRVE 1wwkA 117 :FADRKMREGVWAKKEAMGI T0321 119 :EVKGKKVGVVGHFPH 1wwkA 136 :ELEGKTIGIIGFGRI T0321 134 :LESLLEP 1wwkA 154 :VAKIANA T0321 142 :CDLSILEWSPE 1wwkA 161 :LGMNILLYDPY T0321 154 :GDYPL 1wwkA 183 :KFVDL T0321 162 :EFILPECDYVYI 1wwkA 188 :ETLLKESDVVTI T0321 184 :PRLLELSRNAR 1wwkA 213 :EERLKLMKKTA T0321 196 :ITLVGPGTPL 1wwkA 224 :ILINTSRGPV T0321 223 :KDNARAFRIVAGA 1wwkA 234 :VDTNALVKALKEG Number of specific fragments extracted= 16 number of extra gaps= 0 total=171 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 1v8bA/T0321-1v8bA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1v8bA expands to /projects/compbio/data/pdb/1v8b.pdb.gz 1v8bA:# T0321 read from 1v8bA/T0321-1v8bA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1v8bA read from 1v8bA/T0321-1v8bA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1v8bA to template set # found chain 1v8bA in template set T0321 69 :SWN 1v8bA 232 :KYD T0321 73 :VEASIGLAAINAYYNNP 1v8bA 235 :NVYGCRHSLPDGLMRAT T0321 103 :K 1v8bA 252 :D T0321 118 :NEVKGKKVGVVGHF 1v8bA 253 :FLISGKIVVICGYG T0321 133 :HLESLLEPICDLSILEWSPE 1v8bA 272 :CASSMKGLGARVYITEIDPI T0321 153 :EGDYP 1v8bA 301 :FNVVT T0321 161 :SEFILPECDY 1v8bA 306 :LDEIVDKGDF T0321 172 :YITCA 1v8bA 316 :FITCT T0321 183 :LPRLL 1v8bA 328 :LEHLL T0321 189 :LSRNARRITLVGPG 1v8bA 333 :KMKNNAVVGNIGHF T0321 206 :APVLFEH 1v8bA 352 :VNELFNY T0321 213 :GLQE 1v8bA 360 :GIHI T0321 239 :KIYS 1v8bA 364 :ENVK T0321 243 :AGQKVTI 1v8bA 369 :QVDRITL Number of specific fragments extracted= 14 number of extra gaps= 0 total=185 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 1v8bA/T0321-1v8bA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0321 read from 1v8bA/T0321-1v8bA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1v8bA read from 1v8bA/T0321-1v8bA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1v8bA in template set T0321 27 :HSVIRSGNG 1v8bA 219 :FTAINVNDA T0321 65 :GCVKSWN 1v8bA 228 :VTKQKYD T0321 73 :VEASIGLAAINAYYNNPQ 1v8bA 235 :NVYGCRHSLPDGLMRATD T0321 118 :NEVKGKKVGVVGHF 1v8bA 253 :FLISGKIVVICGYG T0321 133 :HLESLLEPICDLSILEWSPE 1v8bA 272 :CASSMKGLGARVYITEIDPI T0321 153 :EGDYP 1v8bA 301 :FNVVT T0321 161 :SEFILPECDY 1v8bA 306 :LDEIVDKGDF T0321 172 :YITCA 1v8bA 316 :FITCT T0321 183 :LPRLLE 1v8bA 328 :LEHLLK T0321 190 :SRNARR 1v8bA 334 :MKNNAV T0321 199 :VGPGTPL 1v8bA 340 :VGNIGHF T0321 206 :APVLFEH 1v8bA 352 :VNELFNY T0321 213 :GLQE 1v8bA 360 :GIHI T0321 239 :KIYS 1v8bA 364 :ENVK T0321 243 :AGQKVTI 1v8bA 369 :QVDRITL Number of specific fragments extracted= 15 number of extra gaps= 0 total=200 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 1v8bA/T0321-1v8bA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0321 read from 1v8bA/T0321-1v8bA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1v8bA read from 1v8bA/T0321-1v8bA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1v8bA in template set T0321 2 :WEIYDAMINGIP 1v8bA 205 :VLRLKKMDKQNE T0321 25 :TTHSVIRSGNG 1v8bA 217 :LLFTAINVNDA T0321 62 :VAAGCVKSWNYVEASIGLAAINAY 1v8bA 228 :VTKQKYDNVYGCRHSLPDGLMRAT T0321 117 :QNEVKGKKVGVVGHFPH 1v8bA 252 :DFLISGKIVVICGYGDV T0321 134 :LESLLEPICDLSILEWSP 1v8bA 273 :ASSMKGLGARVYITEIDP T0321 154 :GDYPLPASEFILPECDY 1v8bA 299 :EGFNVVTLDEIVDKGDF T0321 172 :YITCAS 1v8bA 316 :FITCTG T0321 183 :LPRLLE 1v8bA 328 :LEHLLK T0321 190 :SRNARRITLVGPG 1v8bA 334 :MKNNAVVGNIGHF T0321 203 :TPLAPVLFEHG 1v8bA 349 :EIQVNELFNYK T0321 235 :AEKVKIYSAGQKV 1v8bA 360 :GIHIENVKPQVDR Number of specific fragments extracted= 11 number of extra gaps= 0 total=211 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 1o4sA/T0321-1o4sA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1o4sA expands to /projects/compbio/data/pdb/1o4s.pdb.gz 1o4sA:Skipped atom 146, because occupancy 0.330 <= existing 0.340 in 1o4sA Skipped atom 149, because occupancy 0.330 <= existing 0.340 in 1o4sA Skipped atom 152, because occupancy 0.330 <= existing 0.340 in 1o4sA Skipped atom 155, because occupancy 0.330 <= existing 0.340 in 1o4sA Skipped atom 507, because occupancy 0.500 <= existing 0.500 in 1o4sA Skipped atom 509, because occupancy 0.500 <= existing 0.500 in 1o4sA Skipped atom 511, because occupancy 0.500 <= existing 0.500 in 1o4sA Skipped atom 513, because occupancy 0.500 <= existing 0.500 in 1o4sA Skipped atom 515, because occupancy 0.500 <= existing 0.500 in 1o4sA Skipped atom 517, because occupancy 0.500 <= existing 0.500 in 1o4sA Skipped atom 709, because occupancy 0.350 <= existing 0.650 in 1o4sA Skipped atom 711, because occupancy 0.350 <= existing 0.650 in 1o4sA Skipped atom 713, because occupancy 0.350 <= existing 0.650 in 1o4sA Skipped atom 715, because occupancy 0.350 <= existing 0.650 in 1o4sA Skipped atom 1521, because occupancy 0.350 <= existing 0.650 in 1o4sA Skipped atom 1523, because occupancy 0.350 <= existing 0.650 in 1o4sA Skipped atom 1525, because occupancy 0.350 <= existing 0.650 in 1o4sA Skipped atom 1527, because occupancy 0.350 <= existing 0.650 in 1o4sA Skipped atom 2016, because occupancy 0.500 <= existing 0.500 in 1o4sA Skipped atom 2216, because occupancy 0.350 <= existing 0.650 in 1o4sA Skipped atom 2218, because occupancy 0.350 <= existing 0.650 in 1o4sA # T0321 read from 1o4sA/T0321-1o4sA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1o4sA read from 1o4sA/T0321-1o4sA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1o4sA to template set # found chain 1o4sA in template set Warning: unaligning (T0321)A176 because of BadResidue code BAD_PEPTIDE in next template residue (1o4sA)N172 T0321 2 :WEIYDAMINGIPEDFLVDELVCG 1o4sA 73 :EGIAKRIGERYKKDISPDQVVVT T0321 71 :NYVEASIGLAAI 1o4sA 96 :NGAKQALFNAFM T0321 84 :AYY 1o4sA 108 :ALL T0321 103 :K 1o4sA 111 :D T0321 121 :KGKKVGVVGHF 1o4sA 112 :PGDEVIVFSPV T0321 132 :PHLESLLEPICDLSILEWSPE 1o4sA 125 :SYIPQIILAGGTVNVVETFMS T0321 153 :EGDYPLPASE 1o4sA 147 :NFQPSLEEVE T0321 163 :FILPECDYVYITC 1o4sA 158 :LLVGKTKAVLINS T0321 183 :LPRLLELSRNARRITLVGPGTP 1o4sA 184 :LEGLVRLAKKRNFYIISDEVYD T0321 205 :LAPV 1o4sA 216 :ILDV T0321 212 :HGLQELSGFMV 1o4sA 221 :EGFDRIVYING Number of specific fragments extracted= 11 number of extra gaps= 1 total=222 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 1o4sA/T0321-1o4sA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0321 read from 1o4sA/T0321-1o4sA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1o4sA read from 1o4sA/T0321-1o4sA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1o4sA in template set Warning: unaligning (T0321)A176 because of BadResidue code BAD_PEPTIDE in next template residue (1o4sA)N172 T0321 2 :WEIYDAMINGIPEDFLVDELVCG 1o4sA 73 :EGIAKRIGERYKKDISPDQVVVT T0321 71 :NYVEASIGLAAI 1o4sA 96 :NGAKQALFNAFM T0321 84 :AYY 1o4sA 108 :ALL T0321 120 :VKGKKVGVVGHF 1o4sA 111 :DPGDEVIVFSPV T0321 132 :PHLESLLEPICDLSILEWSPE 1o4sA 125 :SYIPQIILAGGTVNVVETFMS T0321 153 :EGDYPLPASE 1o4sA 147 :NFQPSLEEVE T0321 163 :FILPECDYVYITC 1o4sA 158 :LLVGKTKAVLINS T0321 181 :KTLPRLLELSRNARRITLVGPGTPL 1o4sA 182 :EFLEGLVRLAKKRNFYIISDEVYDS T0321 206 :APV 1o4sA 217 :LDV T0321 212 :HGLQELSGFMV 1o4sA 221 :EGFDRIVYING Number of specific fragments extracted= 10 number of extra gaps= 1 total=232 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 1o4sA/T0321-1o4sA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0321 read from 1o4sA/T0321-1o4sA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1o4sA read from 1o4sA/T0321-1o4sA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1o4sA in template set Warning: unaligning (T0321)A176 because of BadResidue code BAD_PEPTIDE in next template residue (1o4sA)N172 Warning: unaligning (T0321)S177 because of BadResidue code BAD_PEPTIDE at template residue (1o4sA)N172 T0321 3 :EIYDAMING 1o4sA 19 :AKAKALIKK T0321 15 :DFLVDEL 1o4sA 28 :GEDVINL T0321 35 :GVGLGPNRPF 1o4sA 35 :TAGEPDFPTP T0321 46 :TRMPMLTQNLLGLPLRVAAGCVKSWN 1o4sA 58 :GEVKYTDPRGIYELREGIAKRIGERY T0321 72 :YVEASIGLA 1o4sA 97 :GAKQALFNA T0321 82 :INAYY 1o4sA 106 :FMALL T0321 120 :VKGKKVGVVGHFPH 1o4sA 111 :DPGDEVIVFSPVWV T0321 134 :LESLLEPICDLSILEWSPE 1o4sA 127 :IPQIILAGGTVNVVETFMS T0321 153 :EGDYPLPASE 1o4sA 147 :NFQPSLEEVE T0321 163 :FILPECDYVYITC 1o4sA 158 :LLVGKTKAVLINS T0321 178 :VV 1o4sA 173 :NP T0321 181 :KTLPRLLELSRNARRITLVGPGT 1o4sA 182 :EFLEGLVRLAKKRNFYIISDEVY Number of specific fragments extracted= 12 number of extra gaps= 1 total=244 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 1yqdA/T0321-1yqdA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1yqdA expands to /projects/compbio/data/pdb/1yqd.pdb.gz 1yqdA:# T0321 read from 1yqdA/T0321-1yqdA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1yqdA read from 1yqdA/T0321-1yqdA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1yqdA to template set # found chain 1yqdA in template set T0321 12 :IPEDFLV 1yqdA 128 :YHDGTIT T0321 49 :PMLTQ 1yqdA 153 :PDNMP T0321 55 :LLG 1yqdA 158 :LDG T0321 63 :AAGCVK 1yqdA 161 :GAPLLC T0321 78 :GLAAINAYYNNPQVAR 1yqdA 167 :AGITVYSPLKYFGLDE T0321 121 :KGKKVGVVGHF 1yqdA 183 :PGKHIGIVGLG T0321 135 :ESLLEPICDLSILEWSPE 1yqdA 201 :KFAKAFGSKVTVISTSPS T0321 154 :GDYPLPASEFILPECDYVYITCA 1yqdA 234 :VSRDQEQMQAAAGTLDGIIDTVS T0321 183 :LPRLLELSRNARRITLVGPGTP 1yqdA 261 :LLPLFGLLKSHGKLILVGAPEK T0321 205 :LAPVLFEHGL 1yqdA 287 :PAFSLIAGRK T0321 216 :ELSGFMVKDNARAFRIVAGA 1yqdA 297 :IVAGSGIGGMKETQEMIDFA Number of specific fragments extracted= 11 number of extra gaps= 0 total=255 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 1yqdA/T0321-1yqdA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0321 read from 1yqdA/T0321-1yqdA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1yqdA read from 1yqdA/T0321-1yqdA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1yqdA in template set T0321 13 :PEDFL 1yqdA 129 :HDGTI T0321 18 :VDELVCGTTHSVIRSGN 1yqdA 139 :SNHMVANERYIIRFPDN T0321 41 :NRPFETRM 1yqdA 156 :MPLDGGAP T0321 63 :AA 1yqdA 165 :LC T0321 77 :IGL 1yqdA 167 :AGI T0321 81 :AINAYYNNPQVAR 1yqdA 170 :TVYSPLKYFGLDE T0321 121 :KGKKVGVVGHF 1yqdA 183 :PGKHIGIVGLG T0321 134 :L 1yqdA 198 :V T0321 137 :LLEPICDLSILEWSPE 1yqdA 203 :AKAFGSKVTVISTSPS T0321 154 :GDYPLPASEFILPECDYVYITCA 1yqdA 234 :VSRDQEQMQAAAGTLDGIIDTVS T0321 183 :LPRLLELSRNARRITLVGPGTP 1yqdA 261 :LLPLFGLLKSHGKLILVGAPEK T0321 206 :APVLFEHGL 1yqdA 288 :AFSLIAGRK T0321 216 :ELSGFMVKDNARAFRIVAGA 1yqdA 297 :IVAGSGIGGMKETQEMIDFA Number of specific fragments extracted= 13 number of extra gaps= 0 total=268 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 1yqdA/T0321-1yqdA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0321 read from 1yqdA/T0321-1yqdA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1yqdA read from 1yqdA/T0321-1yqdA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1yqdA in template set T0321 76 :SIGLAAINAYYN 1yqdA 194 :GLGHVAVKFAKA T0321 121 :KGKKVGVVGHFPHLESLLEPICDLSILEWSP 1yqdA 206 :FGSKVTVISTSPSKKEEALKNFGADSFLVSR T0321 157 :PLPASEFILPECDYVYITCA 1yqdA 237 :DQEQMQAAAGTLDGIIDTVS T0321 182 :TLPRLLELSRNARRITLVGPGTPL 1yqdA 260 :PLLPLFGLLKSHGKLILVGAPEKP T0321 206 :APVLF 1yqdA 287 :PAFSL T0321 211 :EHGL 1yqdA 293 :AGRK T0321 216 :ELSGFMVKDNARAFRIVAGA 1yqdA 297 :IVAGSGIGGMKETQEMIDFA Number of specific fragments extracted= 7 number of extra gaps= 0 total=275 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 1qmgA/T0321-1qmgA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1qmgA expands to /projects/compbio/data/pdb/1qmg.pdb.gz 1qmgA:Skipped atom 906, because occupancy 0.500 <= existing 0.500 in 1qmgA Skipped atom 908, because occupancy 0.500 <= existing 0.500 in 1qmgA Skipped atom 2535, because occupancy 0.500 <= existing 0.500 in 1qmgA Skipped atom 2537, because occupancy 0.500 <= existing 0.500 in 1qmgA Skipped atom 3114, because occupancy 0.500 <= existing 0.500 in 1qmgA Skipped atom 3116, because occupancy 0.500 <= existing 0.500 in 1qmgA Skipped atom 3511, because occupancy 0.500 <= existing 0.500 in 1qmgA Skipped atom 3513, because occupancy 0.500 <= existing 0.500 in 1qmgA # T0321 read from 1qmgA/T0321-1qmgA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1qmgA read from 1qmgA/T0321-1qmgA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1qmgA to template set # found chain 1qmgA in template set T0321 102 :AKR 1qmgA 115 :FPL T0321 116 :SQNEVKG 1qmgA 118 :LPDAFKG T0321 123 :KKVGVVGHFPHL 1qmgA 126 :KQIGVIGWGSQA T0321 136 :SLLE 1qmgA 146 :DSLT T0321 140 :PICDLSIL 1qmgA 151 :AKSDVVVK T0321 148 :EWSPE 1qmgA 160 :GLRKG T0321 154 :GDYPLPA 1qmgA 174 :AGFSEEN T0321 161 :SEFILPECDYVYITCA 1qmgA 186 :MWETISGSDLVLLLIS T0321 177 :SVVDKTLPRLLELSRNAR 1qmgA 203 :SAQADNYEKVFSHMKPNS T0321 198 :LVGPGTPLAPV 1qmgA 221 :ILGLSHGFLLG T0321 209 :LFEHG 1qmgA 233 :LQSLG T0321 214 :LQELSGFMVKDNARAFRIVAGAEKVKIYSAGQKVTI 1qmgA 244 :ISVIAVCPKGMGPSVRRLYVQGKEVNGAGINSSFAV Number of specific fragments extracted= 12 number of extra gaps= 0 total=287 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 1qmgA/T0321-1qmgA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0321 read from 1qmgA/T0321-1qmgA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1qmgA read from 1qmgA/T0321-1qmgA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1qmgA in template set T0321 111 :DPFIMSQNEVKG 1qmgA 113 :NLFPLLPDAFKG T0321 123 :KKVGVVGHFPHL 1qmgA 126 :KQIGVIGWGSQA T0321 136 :SLLE 1qmgA 146 :DSLT T0321 140 :PICDLSILE 1qmgA 153 :SDVVVKIGL T0321 150 :SPE 1qmgA 162 :RKG T0321 154 :GDYPLPA 1qmgA 174 :AGFSEEN T0321 161 :SEFILPECDYVYITCA 1qmgA 186 :MWETISGSDLVLLLIS T0321 177 :SVVDKTLPRLLELSRNAR 1qmgA 203 :SAQADNYEKVFSHMKPNS T0321 198 :LVGPGTPLAPV 1qmgA 221 :ILGLSHGFLLG T0321 209 :LFEHG 1qmgA 233 :LQSLG T0321 214 :LQELSGFMVKDNARAFRIVAGAEKVKIYSAGQKVTI 1qmgA 244 :ISVIAVCPKGMGPSVRRLYVQGKEVNGAGINSSFAV Number of specific fragments extracted= 11 number of extra gaps= 0 total=298 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 1qmgA/T0321-1qmgA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0321 read from 1qmgA/T0321-1qmgA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1qmgA read from 1qmgA/T0321-1qmgA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1qmgA in template set T0321 111 :DPFIMSQNEVKG 1qmgA 113 :NLFPLLPDAFKG T0321 123 :KKVGVVGHFPH 1qmgA 126 :KQIGVIGWGSQ T0321 134 :LESLLEPICDLSILE 1qmgA 147 :SLTEAKSDVVVKIGL T0321 150 :SPE 1qmgA 162 :RKG T0321 155 :DYPLPA 1qmgA 175 :GFSEEN T0321 161 :SEFILPECDYVYIT 1qmgA 186 :MWETISGSDLVLLL T0321 175 :CASVVDKTLPRLLELSRNAR 1qmgA 201 :SDSAQADNYEKVFSHMKPNS T0321 198 :LVGPGTPLAPVLF 1qmgA 221 :ILGLSHGFLLGHL T0321 212 :HGLQELSGFMVKDNARAFRIVAGAEK 1qmgA 242 :KNISVIAVCPKGMGPSVRRLYVQGKE Number of specific fragments extracted= 9 number of extra gaps= 0 total=307 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 1y81A/T0321-1y81A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1y81A expands to /projects/compbio/data/pdb/1y81.pdb.gz 1y81A:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0321 read from 1y81A/T0321-1y81A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1y81A read from 1y81A/T0321-1y81A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1y81A to template set # found chain 1y81A in template set Warning: unaligning (T0321)G122 because first residue in template chain is (1y81A)F6 T0321 123 :KKVGVVGHF 1y81A 7 :RKIALVGAS T0321 132 :P 1y81A 18 :P T0321 133 :HLESLLEPICDLSILEWSPE 1y81A 25 :ILKDLLSKGFEVLPVNPNYD T0321 156 :Y 1y81A 50 :K T0321 158 :LPASEFILPECDYVYI 1y81A 52 :YRSVRELPKDVDVIVF T0321 182 :TLPRLLELSR 1y81A 70 :PPKVGLQVAK T0321 208 :VLFEHGLQELSGFMVKDNARAFRIVAGAEK 1y81A 80 :EAVEAGFKKLWFQPGAESEEIRRFLEKAGV Number of specific fragments extracted= 7 number of extra gaps= 0 total=314 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 1y81A/T0321-1y81A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0321 read from 1y81A/T0321-1y81A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1y81A read from 1y81A/T0321-1y81A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1y81A in template set Warning: unaligning (T0321)G122 because first residue in template chain is (1y81A)F6 T0321 123 :KKVGVVGHF 1y81A 7 :RKIALVGAS T0321 132 :P 1y81A 18 :P T0321 133 :HLESLLEPICDLSILEWSPE 1y81A 25 :ILKDLLSKGFEVLPVNPNYD T0321 156 :YPLPASEFILPECDYVYI 1y81A 50 :KCYRSVRELPKDVDVIVF T0321 182 :TLPRLLELS 1y81A 70 :PPKVGLQVA T0321 207 :PVLFEHGLQELSGFMVKDNARAFRIVAGAEK 1y81A 79 :KEAVEAGFKKLWFQPGAESEEIRRFLEKAGV Number of specific fragments extracted= 6 number of extra gaps= 0 total=320 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 1y81A/T0321-1y81A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0321 read from 1y81A/T0321-1y81A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1y81A read from 1y81A/T0321-1y81A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1y81A in template set Warning: unaligning (T0321)G122 because first residue in template chain is (1y81A)F6 T0321 123 :KKVGVVGHFPH 1y81A 7 :RKIALVGASKN T0321 134 :LESLLEPICDLSILEWSPE 1y81A 26 :LKDLLSKGFEVLPVNPNYD T0321 153 :EGDYPLPASEFILPECDYVYITC 1y81A 47 :EGLKCYRSVRELPKDVDVIVFVV T0321 182 :TLPRLLELSR 1y81A 70 :PPKVGLQVAK T0321 208 :VLFEHGLQELSGFMVKDNARAFRIVAGAEKVKIYSA 1y81A 80 :EAVEAGFKKLWFQPGAESEEIRRFLEKAGVEYSFGR Number of specific fragments extracted= 5 number of extra gaps= 0 total=325 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 2g76A/T0321-2g76A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2g76A expands to /projects/compbio/data/pdb/2g76.pdb.gz 2g76A:Skipped atom 746, because occupancy 0.500 <= existing 0.500 in 2g76A Skipped atom 750, because occupancy 0.500 <= existing 0.500 in 2g76A Skipped atom 752, because occupancy 0.500 <= existing 0.500 in 2g76A Skipped atom 754, because occupancy 0.500 <= existing 0.500 in 2g76A Skipped atom 756, because occupancy 0.500 <= existing 0.500 in 2g76A Skipped atom 767, because occupancy 0.300 <= existing 0.700 in 2g76A Skipped atom 771, because occupancy 0.300 <= existing 0.700 in 2g76A Skipped atom 773, because occupancy 0.300 <= existing 0.700 in 2g76A Skipped atom 775, because occupancy 0.300 <= existing 0.700 in 2g76A Skipped atom 777, because occupancy 0.300 <= existing 0.700 in 2g76A Skipped atom 1371, because occupancy 0.200 <= existing 0.800 in 2g76A Skipped atom 1375, because occupancy 0.200 <= existing 0.800 in 2g76A Skipped atom 1377, because occupancy 0.200 <= existing 0.800 in 2g76A Skipped atom 1379, because occupancy 0.200 <= existing 0.800 in 2g76A Skipped atom 1381, because occupancy 0.200 <= existing 0.800 in 2g76A Skipped atom 1383, because occupancy 0.200 <= existing 0.800 in 2g76A Skipped atom 2030, because occupancy 0.500 <= existing 0.500 in 2g76A Skipped atom 2034, because occupancy 0.500 <= existing 0.500 in 2g76A Skipped atom 2036, because occupancy 0.500 <= existing 0.500 in 2g76A # T0321 read from 2g76A/T0321-2g76A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2g76A read from 2g76A/T0321-2g76A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2g76A to template set # found chain 2g76A in template set T0321 69 :SWNYVEASIG 2g76A 102 :SLSAAELTCG T0321 81 :AINAYYNNPQVARE 2g76A 112 :MIMCLARQIPQATA T0321 95 :HGVIFSDAKRV 2g76A 130 :GKWERKKFMGT T0321 119 :EVKGKKVGVVGHFP 2g76A 141 :ELNGKTLGILGLGR T0321 133 :HLESLLEPICDLSILE 2g76A 159 :VATRMQSFGMKTIGYD T0321 154 :GDYPLPAS 2g76A 175 :PIISPEVS T0321 162 :EFILPECDYVYI 2g76A 193 :EEIWPLCDFITV T0321 178 :VVDKT 2g76A 215 :LLNDN T0321 186 :LLELSRNAR 2g76A 220 :TFAQCKKGV T0321 196 :ITLVGPGTPL 2g76A 229 :RVVNCARGGI T0321 223 :KDNARAFRIVAGAE 2g76A 239 :VDEGALLRALQSGQ Number of specific fragments extracted= 11 number of extra gaps= 0 total=336 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 2g76A/T0321-2g76A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0321 read from 2g76A/T0321-2g76A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2g76A read from 2g76A/T0321-2g76A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2g76A in template set T0321 60 :LRV 2g76A 105 :AAE T0321 63 :AAGCVKSWNYVEASIG 2g76A 112 :MIMCLARQIPQATASM T0321 93 :REHG 2g76A 128 :KDGK T0321 103 :KRVEDRMN 2g76A 132 :WERKKFMG T0321 118 :NEVKGKKVGVVGHFP 2g76A 140 :TELNGKTLGILGLGR T0321 133 :HLESLLEPICDLSILE 2g76A 159 :VATRMQSFGMKTIGYD T0321 154 :GDYPLPAS 2g76A 175 :PIISPEVS T0321 162 :EFILPECDYVYI 2g76A 193 :EEIWPLCDFITV T0321 178 :VVDKT 2g76A 215 :LLNDN T0321 186 :LLELSRNAR 2g76A 220 :TFAQCKKGV T0321 196 :ITLVGPGTPL 2g76A 229 :RVVNCARGGI T0321 223 :KDNARAFRIVAGAE 2g76A 239 :VDEGALLRALQSGQ Number of specific fragments extracted= 12 number of extra gaps= 0 total=348 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 2g76A/T0321-2g76A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0321 read from 2g76A/T0321-2g76A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2g76A read from 2g76A/T0321-2g76A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2g76A in template set T0321 67 :VKSWNYVEASIGLAAINAYY 2g76A 100 :GNSLSAAELTCGMIMCLARQ T0321 87 :NNPQVAREHG 2g76A 122 :QATASMKDGK T0321 110 :NDPFIMSQNEVKGKKVGVVGHFPH 2g76A 132 :WERKKFMGTELNGKTLGILGLGRI T0321 134 :LESLLEP 2g76A 159 :VATRMQS T0321 142 :CDLSILEWSP 2g76A 166 :FGMKTIGYDP T0321 155 :DYPLPA 2g76A 176 :IISPEV T0321 161 :SEFILPECDYVYITC 2g76A 192 :LEEIWPLCDFITVHT T0321 178 :VVD 2g76A 215 :LLN T0321 184 :PRLLELSRNAR 2g76A 218 :DNTFAQCKKGV T0321 196 :ITLVGPGTPL 2g76A 229 :RVVNCARGGI T0321 223 :KDNARAFRIVAGA 2g76A 239 :VDEGALLRALQSG Number of specific fragments extracted= 11 number of extra gaps= 0 total=359 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 1uufA/T0321-1uufA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1uufA expands to /projects/compbio/data/pdb/1uuf.pdb.gz 1uufA:# T0321 read from 1uufA/T0321-1uufA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1uufA read from 1uufA/T0321-1uufA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1uufA to template set # found chain 1uufA in template set Warning: unaligning (T0321)P201 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1uufA)P277 Warning: unaligning (T0321)G202 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1uufA)P277 T0321 49 :PMLTQNL 1uufA 143 :IRHPQEQ T0321 60 :LRVAAGCVK 1uufA 150 :LAAVAPLLC T0321 77 :IGLAAINAYYNN 1uufA 159 :AGITTYSPLRHW T0321 118 :NEVKGKKVGVVGHF 1uufA 171 :QAGPGKKVGVVGIG T0321 133 :HLESLLEPICDLSILEWSPE 1uufA 190 :GIKLAHAMGAHVVAFTTSEA T0321 156 :YPLPASEFILPECDYVYITCA 1uufA 226 :RNADEMAAHLKSFDFILNTVA T0321 181 :KTLPRLLELSRNARRITLVG 1uufA 249 :HNLDDFTTLLKRDGTMTLVG T0321 209 :LFEHGL 1uufA 282 :LIMKRR T0321 216 :ELSGFMVKDNARAFRIVAG 1uufA 288 :AIAGSMIGGIPETQEMLDF Number of specific fragments extracted= 9 number of extra gaps= 1 total=368 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 1uufA/T0321-1uufA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0321 read from 1uufA/T0321-1uufA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1uufA read from 1uufA/T0321-1uufA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1uufA in template set Warning: unaligning (T0321)P201 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1uufA)P277 Warning: unaligning (T0321)G202 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1uufA)P277 T0321 32 :SGNGVGLGP 1uufA 80 :PGDLVGVGC T0321 49 :PMLTQNL 1uufA 143 :IRHPQEQ T0321 60 :LRVAAGCVK 1uufA 150 :LAAVAPLLC T0321 77 :IGLAAINAYYNN 1uufA 159 :AGITTYSPLRHW T0321 118 :NEVKGKKVGVVGHF 1uufA 171 :QAGPGKKVGVVGIG T0321 133 :HLESLLEPICDLSILEWSPE 1uufA 190 :GIKLAHAMGAHVVAFTTSEA T0321 156 :YPLPASEFILPECDYVYITCA 1uufA 226 :RNADEMAAHLKSFDFILNTVA T0321 181 :KTLPRLLELSRNARRITLVG 1uufA 249 :HNLDDFTTLLKRDGTMTLVG T0321 209 :LFEHGL 1uufA 282 :LIMKRR T0321 216 :ELSGFMVKDNARAFRIVAG 1uufA 288 :AIAGSMIGGIPETQEMLDF Number of specific fragments extracted= 10 number of extra gaps= 1 total=378 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 1uufA/T0321-1uufA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0321 read from 1uufA/T0321-1uufA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1uufA read from 1uufA/T0321-1uufA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1uufA in template set Warning: unaligning (T0321)P201 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1uufA)P277 T0321 77 :IGLAAINAYYN 1uufA 159 :AGITTYSPLRH T0321 117 :QNEVKGKKVGVVGHFPH 1uufA 170 :WQAGPGKKVGVVGIGGL T0321 134 :LE 1uufA 193 :LA T0321 138 :LEPICDLSILEWSPE 1uufA 195 :HAMGAHVVAFTTSEA T0321 157 :PLPASEFILPECDYVYITCA 1uufA 227 :NADEMAAHLKSFDFILNTVA T0321 181 :KTLPRLLELSRNARRITLVG 1uufA 249 :HNLDDFTTLLKRDGTMTLVG T0321 207 :PVL 1uufA 280 :FNL T0321 211 :EHGLQ 1uufA 284 :MKRRA T0321 217 :LSGFMVKDNARAFRIVAG 1uufA 289 :IAGSMIGGIPETQEMLDF Number of specific fragments extracted= 9 number of extra gaps= 0 total=387 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 1np3A/T0321-1np3A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1np3A expands to /projects/compbio/data/pdb/1np3.pdb.gz 1np3A:# T0321 read from 1np3A/T0321-1np3A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1np3A read from 1np3A/T0321-1np3A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1np3A to template set # found chain 1np3A in template set T0321 117 :QNEVKGKKVGVVGHFP 1np3A 11 :LSIIQGKKVAIIGYGS T0321 133 :HLESLLEPICDLSIL 1np3A 31 :HACNLKDSGVDVTVG T0321 149 :WSPE 1np3A 46 :LRSG T0321 161 :SEFILPECDYVYI 1np3A 66 :VKTAVAAADVVMI T0321 181 :KTLPRLLELSRNA 1np3A 84 :FQGRLYKEEIEPN T0321 194 :R 1np3A 101 :A T0321 196 :ITLVGPGTPLA 1np3A 102 :TLAFAHGFSIH T0321 210 :FEH 1np3A 113 :YNQ T0321 213 :GLQELSGFMVKDNARAFRIVAGAEKVKI 1np3A 121 :DLDVIMIAPKAPGHTVRSEFVKGGGIPD Number of specific fragments extracted= 9 number of extra gaps= 0 total=396 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 1np3A/T0321-1np3A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0321 read from 1np3A/T0321-1np3A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1np3A read from 1np3A/T0321-1np3A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1np3A in template set T0321 100 :SDAKRVE 1np3A 4 :FYDKDCD T0321 117 :QNEVKGKKVGVVGHFP 1np3A 11 :LSIIQGKKVAIIGYGS T0321 133 :HLESLLEPICDLSIL 1np3A 31 :HACNLKDSGVDVTVG T0321 149 :WSPE 1np3A 46 :LRSG T0321 161 :SEFILPECDYVYI 1np3A 66 :VKTAVAAADVVMI T0321 181 :KTLPRLLELSRNA 1np3A 84 :FQGRLYKEEIEPN T0321 194 :R 1np3A 101 :A T0321 196 :ITLVGPGTPLA 1np3A 102 :TLAFAHGFSIH T0321 210 :FEH 1np3A 113 :YNQ T0321 213 :GLQELSGFMVKDNARAFRIVAGAEKVKI 1np3A 121 :DLDVIMIAPKAPGHTVRSEFVKGGGIPD Number of specific fragments extracted= 10 number of extra gaps= 0 total=406 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 1np3A/T0321-1np3A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0321 read from 1np3A/T0321-1np3A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1np3A read from 1np3A/T0321-1np3A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1np3A in template set T0321 112 :PFIMSQNEVKGKKVGVVGHFPH 1np3A 6 :DKDCDLSIIQGKKVAIIGYGSQ T0321 134 :LESLLEPICDLSILE 1np3A 32 :ACNLKDSGVDVTVGL T0321 150 :SPE 1np3A 47 :RSG T0321 160 :ASEFILPECDYVYITC 1np3A 65 :DVKTAVAAADVVMILT T0321 184 :PRLLELSRNARRITL 1np3A 91 :EEIEPNLKKGATLAF T0321 203 :TPLAPVLF 1np3A 106 :AHGFSIHY T0321 211 :EHGLQELSGFMVKDNARAFRIVAGAEKVK 1np3A 119 :RADLDVIMIAPKAPGHTVRSEFVKGGGIP Number of specific fragments extracted= 7 number of extra gaps= 0 total=413 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 1fl2A/T0321-1fl2A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1fl2A expands to /projects/compbio/data/pdb/1fl2.pdb.gz 1fl2A:# T0321 read from 1fl2A/T0321-1fl2A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1fl2A read from 1fl2A/T0321-1fl2A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1fl2A to template set # found chain 1fl2A in template set T0321 3 :EIYDAMINGIPE 1fl2A 268 :KLAGALKVHVDE T0321 15 :DFLVDELVCGTT 1fl2A 287 :SQSASKLIPAAV T0321 27 :HSVIRSGNGVGLG 1fl2A 303 :HQIETASGAVLKA T0321 40 :PNRPFETRMPMLTQNLLGL 1fl2A 322 :TGAKWRNMNVPGEDQYRTK T0321 104 :RVE 1fl2A 341 :GVT T0321 111 :DPFIMSQNEVKGKKVGVVGHF 1fl2A 344 :YCPHCDGPLFKGKRVAVIGGG T0321 132 :P 1fl2A 366 :S T0321 133 :HLESLLEPICDLSILEWSPE 1fl2A 370 :AAIDLAGIVEHVTLLEFAPE T0321 154 :GDYPLPASEFI 1fl2A 390 :MKADQVLQDKL T0321 165 :LPECDYV 1fl2A 403 :LKNVDII Number of specific fragments extracted= 10 number of extra gaps= 0 total=423 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 1fl2A/T0321-1fl2A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0321 read from 1fl2A/T0321-1fl2A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1fl2A read from 1fl2A/T0321-1fl2A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1fl2A in template set T0321 2 :WEIYDAMINGIP 1fl2A 267 :QKLAGALKVHVD T0321 14 :EDFLVDELVCGTT 1fl2A 286 :DSQSASKLIPAAV T0321 27 :HSVIRSGNGVGLG 1fl2A 303 :HQIETASGAVLKA T0321 40 :PNRPF 1fl2A 321 :ATGAK T0321 45 :ETRMPMLTQNLLG 1fl2A 327 :RNMNVPGEDQYRT T0321 95 :HGVIFS 1fl2A 340 :KGVTYC T0321 113 :FIMSQNEVKGKKVGVVGHF 1fl2A 346 :PHCDGPLFKGKRVAVIGGG T0321 132 :P 1fl2A 366 :S T0321 133 :HLESLLEPICDLSILEWSPE 1fl2A 370 :AAIDLAGIVEHVTLLEFAPE T0321 154 :GDYPLPASEFI 1fl2A 390 :MKADQVLQDKL T0321 165 :LPECDYV 1fl2A 403 :LKNVDII Number of specific fragments extracted= 11 number of extra gaps= 0 total=434 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 1fl2A/T0321-1fl2A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0321 read from 1fl2A/T0321-1fl2A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1fl2A read from 1fl2A/T0321-1fl2A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1fl2A in template set T0321 1 :MWEIYDAMINGIP 1fl2A 269 :LAGALKVHVDEYD T0321 14 :EDFLVDELV 1fl2A 286 :DSQSASKLI T0321 26 :THSVIRSGNGVGLGPN 1fl2A 301 :GLHQIETASGAVLKAR T0321 46 :TRMPMLTQNLLGL 1fl2A 328 :NMNVPGEDQYRTK T0321 96 :GVI 1fl2A 341 :GVT T0321 111 :DPFIMSQNEVKGKKVGVVGHFPHLESLLE 1fl2A 344 :YCPHCDGPLFKGKRVAVIGGGNSGVEAAI T0321 140 :PICDLSILEWSPEEGDYPLPASEFI 1fl2A 376 :GIVEHVTLLEFAPEMKADQVLQDKL T0321 165 :LPECDYV 1fl2A 403 :LKNVDII Number of specific fragments extracted= 8 number of extra gaps= 0 total=442 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 2d0iA/T0321-2d0iA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2d0iA expands to /projects/compbio/data/pdb/2d0i.pdb.gz 2d0iA:# T0321 read from 2d0iA/T0321-2d0iA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2d0iA read from 2d0iA/T0321-2d0iA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2d0iA to template set # found chain 2d0iA in template set T0321 2 :WEIYDAMINGI 2d0iA 13 :REALEELKKYA T0321 17 :LVD 2d0iA 24 :DVE T0321 20 :ELVCGTT 2d0iA 44 :DGIIVSP T0321 45 :ETRM 2d0iA 51 :TTKI T0321 50 :MLTQN 2d0iA 60 :ENAER T0321 55 :LLGLPLRVAAG 2d0iA 75 :YDNIDLEEATK T0321 66 :CVKSWNYVEASIGL 2d0iA 95 :GLLSEAVAEFTVGL T0321 81 :AINAY 2d0iA 109 :IINLM T0321 86 :YNNPQVAREHGVIFSD 2d0iA 116 :IHYADKFIRRGEWESH T0321 103 :KRVEDRMND 2d0iA 132 :AKIWTGFKR T0321 118 :NEVKGKKVGVVGHFP 2d0iA 142 :ESLYGKKVGILGMGA T0321 133 :HLESLLEPICDLSILEWSPE 2d0iA 161 :IARRLIPFGVKLYYWSRHRK T0321 153 :EGDYPL 2d0iA 189 :ARYMDI T0321 162 :EFILPECDYVYI 2d0iA 195 :DELLEKSDIVIL T0321 175 :CASVVDKT 2d0iA 207 :ALPLTRDT T0321 184 :PRLLELSRNA 2d0iA 220 :EERVKKLEGK T0321 197 :TLVGPGTPLA 2d0iA 230 :YLVNIGRGAL T0321 214 :L 2d0iA 240 :V T0321 224 :DNARAFRIVAGAE 2d0iA 241 :DEKAVTEAIKQGK Number of specific fragments extracted= 19 number of extra gaps= 0 total=461 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 2d0iA/T0321-2d0iA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0321 read from 2d0iA/T0321-2d0iA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2d0iA read from 2d0iA/T0321-2d0iA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2d0iA in template set T0321 3 :EIYDAMINGI 2d0iA 14 :EALEELKKYA T0321 17 :LVD 2d0iA 24 :DVE T0321 20 :ELVCG 2d0iA 44 :DGIIV T0321 32 :S 2d0iA 49 :S T0321 44 :FETRMP 2d0iA 50 :PTTKIT T0321 50 :MLTQN 2d0iA 60 :ENAER T0321 55 :LLGLPLRVAAG 2d0iA 75 :YDNIDLEEATK T0321 66 :CVKSWNYVEASIGL 2d0iA 95 :GLLSEAVAEFTVGL T0321 81 :AIN 2d0iA 109 :IIN T0321 85 :YYNNP 2d0iA 112 :LMRKI T0321 90 :QVARE 2d0iA 120 :DKFIR T0321 102 :AKRVED 2d0iA 125 :RGEWES T0321 112 :PFIMSQNE 2d0iA 131 :HAKIWTGF T0321 121 :KGKKVGVVGHFP 2d0iA 145 :YGKKVGILGMGA T0321 133 :HLESLLEPICDLSILEWSPE 2d0iA 161 :IARRLIPFGVKLYYWSRHRK T0321 153 :EGDYPL 2d0iA 189 :ARYMDI T0321 162 :EFILPECDYVYIT 2d0iA 195 :DELLEKSDIVILA T0321 176 :ASVVDKTL 2d0iA 208 :LPLTRDTY T0321 184 :PRLLELSRNA 2d0iA 220 :EERVKKLEGK T0321 197 :TLVGPGTPLA 2d0iA 230 :YLVNIGRGAL T0321 214 :L 2d0iA 240 :V T0321 224 :DNARAFRIVAGAE 2d0iA 241 :DEKAVTEAIKQGK Number of specific fragments extracted= 22 number of extra gaps= 0 total=483 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 2d0iA/T0321-2d0iA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0321 read from 2d0iA/T0321-2d0iA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2d0iA read from 2d0iA/T0321-2d0iA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2d0iA in template set T0321 55 :LLGLPLRVAAG 2d0iA 75 :YDNIDLEEATK T0321 67 :VKSWNYVEASIGL 2d0iA 96 :LLSEAVAEFTVGL T0321 81 :AINAYYNNPQV 2d0iA 109 :IINLMRKIHYA T0321 92 :AREHG 2d0iA 122 :FIRRG T0321 103 :KRVEDRMNDPFIMSQNEVKGKKVGVVGHFP 2d0iA 127 :EWESHAKIWTGFKRIESLYGKKVGILGMGA T0321 133 :HLESLLEPICDLSILEWSPE 2d0iA 160 :AIARRLIPFGVKLYYWSRHR T0321 160 :ASEFILPECDYVYITCA 2d0iA 193 :DIDELLEKSDIVILALP T0321 178 :VVD 2d0iA 217 :IIN T0321 184 :PRLLELSRNAR 2d0iA 220 :EERVKKLEGKY T0321 196 :ITLVGPGTP 2d0iA 231 :LVNIGRGAL T0321 223 :KDNARAFRIVAGAE 2d0iA 240 :VDEKAVTEAIKQGK Number of specific fragments extracted= 11 number of extra gaps= 0 total=494 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 2cdcA/T0321-2cdcA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2cdcA expands to /projects/compbio/data/pdb/2cdc.pdb.gz 2cdcA:Skipped atom 38, because occupancy 0.500 <= existing 0.500 in 2cdcA Skipped atom 40, because occupancy 0.500 <= existing 0.500 in 2cdcA Skipped atom 148, because occupancy 0.400 <= existing 0.600 in 2cdcA Skipped atom 150, because occupancy 0.400 <= existing 0.600 in 2cdcA Skipped atom 152, because occupancy 0.400 <= existing 0.600 in 2cdcA Skipped atom 154, because occupancy 0.400 <= existing 0.600 in 2cdcA Skipped atom 156, because occupancy 0.400 <= existing 0.600 in 2cdcA Skipped atom 246, because occupancy 0.500 <= existing 0.500 in 2cdcA Skipped atom 248, because occupancy 0.500 <= existing 0.500 in 2cdcA Skipped atom 256, because occupancy 0.500 <= existing 0.500 in 2cdcA Skipped atom 258, because occupancy 0.500 <= existing 0.500 in 2cdcA Skipped atom 260, because occupancy 0.500 <= existing 0.500 in 2cdcA Skipped atom 262, because occupancy 0.500 <= existing 0.500 in 2cdcA Skipped atom 264, because occupancy 0.500 <= existing 0.500 in 2cdcA Skipped atom 277, because occupancy 0.500 <= existing 0.500 in 2cdcA Skipped atom 279, because occupancy 0.500 <= existing 0.500 in 2cdcA Skipped atom 281, because occupancy 0.500 <= existing 0.500 in 2cdcA Skipped atom 283, because occupancy 0.500 <= existing 0.500 in 2cdcA Skipped atom 364, because occupancy 0.300 <= existing 0.700 in 2cdcA Skipped atom 366, because occupancy 0.300 <= existing 0.700 in 2cdcA Skipped atom 368, because occupancy 0.300 <= existing 0.700 in 2cdcA Skipped atom 370, because occupancy 0.300 <= existing 0.700 in 2cdcA Skipped atom 507, because occupancy 0.300 <= existing 0.700 in 2cdcA Skipped atom 509, because occupancy 0.300 <= existing 0.700 in 2cdcA Skipped atom 511, because occupancy 0.300 <= existing 0.700 in 2cdcA Skipped atom 548, because occupancy 0.500 <= existing 0.500 in 2cdcA Skipped atom 550, because occupancy 0.500 <= existing 0.500 in 2cdcA Skipped atom 552, because occupancy 0.500 <= existing 0.500 in 2cdcA Skipped atom 554, because occupancy 0.500 <= existing 0.500 in 2cdcA Skipped atom 556, because occupancy 0.500 <= existing 0.500 in 2cdcA Skipped atom 558, because occupancy 0.500 <= existing 0.500 in 2cdcA Skipped atom 560, because occupancy 0.500 <= existing 0.500 in 2cdcA Skipped atom 562, because occupancy 0.500 <= existing 0.500 in 2cdcA Skipped atom 600, because occupancy 0.400 <= existing 0.600 in 2cdcA Skipped atom 602, because occupancy 0.400 <= existing 0.600 in 2cdcA Skipped atom 604, because occupancy 0.400 <= existing 0.600 in 2cdcA Skipped atom 606, because occupancy 0.400 <= existing 0.600 in 2cdcA Skipped atom 706, because occupancy 0.700 <= existing 0.750 in 2cdcA Skipped atom 708, because occupancy 0.300 <= existing 0.700 in 2cdcA Skipped atom 710, because occupancy 0.300 <= existing 0.700 in 2cdcA Skipped atom 747, because occupancy 0.500 <= existing 0.500 in 2cdcA Skipped atom 749, because occupancy 0.500 <= existing 0.500 in 2cdcA Skipped atom 751, because occupancy 0.500 <= existing 0.500 in 2cdcA Skipped atom 753, because occupancy 0.500 <= existing 0.500 in 2cdcA Skipped atom 858, because occupancy 0.500 <= existing 0.500 in 2cdcA Skipped atom 860, because occupancy 0.500 <= existing 0.500 in 2cdcA Skipped atom 862, because occupancy 0.500 <= existing 0.500 in 2cdcA Skipped atom 864, because occupancy 0.500 <= existing 0.500 in 2cdcA Skipped atom 883, because occupancy 0.500 <= existing 0.500 in 2cdcA Skipped atom 885, because occupancy 0.500 <= existing 0.500 in 2cdcA Skipped atom 887, because occupancy 0.500 <= existing 0.500 in 2cdcA Skipped atom 889, because occupancy 0.500 <= existing 0.500 in 2cdcA Skipped atom 891, because occupancy 0.500 <= existing 0.500 in 2cdcA Skipped atom 893, because occupancy 0.500 <= existing 0.500 in 2cdcA Skipped atom 895, because occupancy 0.500 <= existing 0.500 in 2cdcA Skipped atom 897, because occupancy 0.500 <= existing 0.500 in 2cdcA Skipped atom 899, because occupancy 0.500 <= existing 0.500 in 2cdcA Skipped atom 901, because occupancy 0.500 <= existing 0.500 in 2cdcA Skipped atom 1282, because occupancy 0.300 <= existing 0.700 in 2cdcA Skipped atom 1284, because occupancy 0.300 <= existing 0.700 in 2cdcA Skipped atom 1286, because occupancy 0.300 <= existing 0.700 in 2cdcA Skipped atom 1288, because occupancy 0.300 <= existing 0.700 in 2cdcA Skipped atom 1290, because occupancy 0.300 <= existing 0.700 in 2cdcA Skipped atom 1474, because occupancy 0.500 <= existing 0.500 in 2cdcA Skipped atom 1476, because occupancy 0.500 <= existing 0.500 in 2cdcA Skipped atom 1478, because occupancy 0.500 <= existing 0.500 in 2cdcA Skipped atom 1480, because occupancy 0.500 <= existing 0.500 in 2cdcA Skipped atom 1482, because occupancy 0.500 <= existing 0.500 in 2cdcA Skipped atom 1484, because occupancy 0.500 <= existing 0.500 in 2cdcA Skipped atom 1486, because occupancy 0.500 <= existing 0.500 in 2cdcA Skipped atom 1488, because occupancy 0.500 <= existing 0.500 in 2cdcA Skipped atom 1490, because occupancy 0.500 <= existing 0.500 in 2cdcA Skipped atom 1492, because occupancy 0.500 <= existing 0.500 in 2cdcA Skipped atom 1494, because occupancy 0.500 <= existing 0.500 in 2cdcA Skipped atom 1496, because occupancy 0.500 <= existing 0.500 in 2cdcA Skipped atom 1498, because occupancy 0.500 <= existing 0.500 in 2cdcA Skipped atom 1500, because occupancy 0.500 <= existing 0.500 in 2cdcA Skipped atom 1502, because occupancy 0.500 <= existing 0.500 in 2cdcA Skipped atom 1504, because occupancy 0.500 <= existing 0.500 in 2cdcA Skipped atom 1506, because occupancy 0.500 <= existing 0.500 in 2cdcA Skipped atom 1508, because occupancy 0.500 <= existing 0.500 in 2cdcA Skipped atom 1510, because occupancy 0.500 <= existing 0.500 in 2cdcA Skipped atom 1512, because occupancy 0.500 <= existing 0.500 in 2cdcA Skipped atom 1514, because occupancy 0.500 <= existing 0.500 in 2cdcA Skipped atom 1516, because occupancy 0.500 <= existing 0.500 in 2cdcA Skipped atom 1668, because occupancy 0.500 <= existing 0.500 in 2cdcA Skipped atom 1670, because occupancy 0.500 <= existing 0.500 in 2cdcA Skipped atom 1950, because occupancy 0.400 <= existing 0.600 in 2cdcA Skipped atom 2022, because occupancy 0.500 <= existing 0.500 in 2cdcA Skipped atom 2024, because occupancy 0.500 <= existing 0.500 in 2cdcA Skipped atom 2026, because occupancy 0.500 <= existing 0.500 in 2cdcA Skipped atom 2028, because occupancy 0.500 <= existing 0.500 in 2cdcA Skipped atom 2030, because occupancy 0.500 <= existing 0.500 in 2cdcA Skipped atom 2032, because occupancy 0.500 <= existing 0.500 in 2cdcA Skipped atom 2034, because occupancy 0.500 <= existing 0.500 in 2cdcA Skipped atom 2036, because occupancy 0.500 <= existing 0.500 in 2cdcA Skipped atom 2038, because occupancy 0.500 <= existing 0.500 in 2cdcA Skipped atom 2040, because occupancy 0.500 <= existing 0.500 in 2cdcA Skipped atom 2042, because occupancy 0.500 <= existing 0.500 in 2cdcA Skipped atom 2044, because occupancy 0.500 <= existing 0.500 in 2cdcA Skipped atom 2046, because occupancy 0.500 <= existing 0.500 in 2cdcA Skipped atom 2048, because occupancy 0.500 <= existing 0.500 in 2cdcA Skipped atom 2050, because occupancy 0.500 <= existing 0.500 in 2cdcA Skipped atom 2052, because occupancy 0.500 <= existing 0.500 in 2cdcA Skipped atom 2054, because occupancy 0.500 <= existing 0.500 in 2cdcA Skipped atom 2056, because occupancy 0.500 <= existing 0.500 in 2cdcA Skipped atom 2058, because occupancy 0.500 <= existing 0.500 in 2cdcA Skipped atom 2060, because occupancy 0.500 <= existing 0.500 in 2cdcA Skipped atom 2062, because occupancy 0.500 <= existing 0.500 in 2cdcA Skipped atom 2164, because occupancy 0.500 <= existing 0.500 in 2cdcA Skipped atom 2166, because occupancy 0.500 <= existing 0.500 in 2cdcA Skipped atom 2168, because occupancy 0.500 <= existing 0.500 in 2cdcA Skipped atom 2170, because occupancy 0.500 <= existing 0.500 in 2cdcA Skipped atom 2292, because occupancy 0.500 <= existing 0.500 in 2cdcA Skipped atom 2294, because occupancy 0.500 <= existing 0.500 in 2cdcA Skipped atom 2296, because occupancy 0.500 <= existing 0.500 in 2cdcA Skipped atom 2298, because occupancy 0.500 <= existing 0.500 in 2cdcA Skipped atom 2340, because occupancy 0.300 <= existing 0.700 in 2cdcA Skipped atom 2342, because occupancy 0.300 <= existing 0.700 in 2cdcA Skipped atom 2344, because occupancy 0.300 <= existing 0.700 in 2cdcA Skipped atom 2346, because occupancy 0.300 <= existing 0.700 in 2cdcA Skipped atom 2348, because occupancy 0.300 <= existing 0.700 in 2cdcA Skipped atom 2354, because occupancy 0.500 <= existing 0.500 in 2cdcA Skipped atom 2356, because occupancy 0.500 <= existing 0.500 in 2cdcA Skipped atom 2358, because occupancy 0.500 <= existing 0.500 in 2cdcA Skipped atom 2360, because occupancy 0.500 <= existing 0.500 in 2cdcA Skipped atom 2362, because occupancy 0.500 <= existing 0.500 in 2cdcA Skipped atom 2412, because occupancy 0.400 <= existing 0.600 in 2cdcA Skipped atom 2418, because occupancy 0.500 <= existing 0.500 in 2cdcA Skipped atom 2420, because occupancy 0.500 <= existing 0.500 in 2cdcA Skipped atom 2422, because occupancy 0.500 <= existing 0.500 in 2cdcA Skipped atom 2436, because occupancy 0.500 <= existing 0.500 in 2cdcA Skipped atom 2438, because occupancy 0.500 <= existing 0.500 in 2cdcA Skipped atom 2440, because occupancy 0.500 <= existing 0.500 in 2cdcA Skipped atom 2442, because occupancy 0.500 <= existing 0.500 in 2cdcA Skipped atom 2534, because occupancy 0.400 <= existing 0.600 in 2cdcA Skipped atom 2536, because occupancy 0.400 <= existing 0.600 in 2cdcA Skipped atom 2538, because occupancy 0.400 <= existing 0.600 in 2cdcA Skipped atom 2540, because occupancy 0.400 <= existing 0.600 in 2cdcA Skipped atom 2542, because occupancy 0.400 <= existing 0.600 in 2cdcA Skipped atom 2627, because occupancy 0.300 <= existing 0.700 in 2cdcA Skipped atom 2629, because occupancy 0.300 <= existing 0.700 in 2cdcA Skipped atom 2631, because occupancy 0.300 <= existing 0.700 in 2cdcA Skipped atom 2760, because occupancy 0.500 <= existing 0.500 in 2cdcA Skipped atom 2762, because occupancy 0.500 <= existing 0.500 in 2cdcA Skipped atom 2764, because occupancy 0.500 <= existing 0.500 in 2cdcA Skipped atom 2766, because occupancy 0.500 <= existing 0.500 in 2cdcA # T0321 read from 2cdcA/T0321-2cdcA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2cdcA read from 2cdcA/T0321-2cdcA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2cdcA to template set # found chain 2cdcA in template set Warning: unaligning (T0321)F16 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2cdcA)G58 Warning: unaligning (T0321)F131 because of BadResidue code BAD_PEPTIDE in next template residue (2cdcA)P191 Warning: unaligning (T0321)P132 because of BadResidue code BAD_PEPTIDE at template residue (2cdcA)P191 T0321 8 :MINGIPED 2cdcA 42 :DREIVNGK T0321 20 :ELVCGTTHSVIR 2cdcA 61 :FLVLGHEAIGVV T0321 32 :SGNGVGLG 2cdcA 80 :SQGDLVMP T0321 40 :PNRPF 2cdcA 90 :RRGCG T0321 52 :TQNLLGL 2cdcA 139 :PKSIEDI T0321 60 :LRVAAGCV 2cdcA 149 :AQPLADIE T0321 83 :NAYYNNPQVAREHGVIFSDAKRV 2cdcA 157 :KSIEEILEVQKRVPVWTCDDGTL T0321 121 :KGKKVGVVGH 2cdcA 180 :NCRKVLVVGT T0321 133 :HL 2cdcA 192 :IG T0321 137 :LLEPICDLSILEWSPE 2cdcA 200 :FRTYGLEVWMANRREP T0321 155 :DYPLPASEFILPECDYVYI 2cdcA 234 :SNGYDKLKDSVGKFDVIID T0321 185 :RLLELSRNAR 2cdcA 259 :NILGNVIPLL T0321 195 :RITLVGPGTP 2cdcA 273 :VLGLFGFSTS T0321 205 :LAPVLFEHG 2cdcA 291 :TLQEIVHTN Number of specific fragments extracted= 14 number of extra gaps= 1 total=508 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 2cdcA/T0321-2cdcA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0321 read from 2cdcA/T0321-2cdcA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2cdcA read from 2cdcA/T0321-2cdcA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2cdcA in template set Warning: unaligning (T0321)P13 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2cdcA)G58 Warning: unaligning (T0321)F131 because of BadResidue code BAD_PEPTIDE in next template residue (2cdcA)P191 Warning: unaligning (T0321)P132 because of BadResidue code BAD_PEPTIDE at template residue (2cdcA)P191 T0321 6 :DAMINGI 2cdcA 43 :REIVNGK T0321 20 :ELVCGTTHSVIR 2cdcA 61 :FLVLGHEAIGVV T0321 32 :SGNGVGLG 2cdcA 80 :SQGDLVMP T0321 40 :PNRPF 2cdcA 90 :RRGCG T0321 49 :PML 2cdcA 132 :PKY T0321 52 :TQNLLGL 2cdcA 139 :PKSIEDI T0321 60 :LRVAAGCVKSWNY 2cdcA 149 :AQPLADIEKSIEE T0321 85 :YYNNPQVA 2cdcA 162 :ILEVQKRV T0321 96 :GVIFSDAKR 2cdcA 170 :PVWTCDDGT T0321 120 :VKGKKVGVVGH 2cdcA 179 :LNCRKVLVVGT T0321 133 :HL 2cdcA 192 :IG T0321 137 :LLEPICDLSILEWSPE 2cdcA 200 :FRTYGLEVWMANRREP T0321 155 :DYPLPASEFILPECDYVYI 2cdcA 234 :SNGYDKLKDSVGKFDVIID T0321 185 :RLLELSRNAR 2cdcA 259 :NILGNVIPLL T0321 195 :RITLVGPGTPL 2cdcA 273 :VLGLFGFSTSG T0321 206 :APVLFEHG 2cdcA 292 :LQEIVHTN T0321 225 :NARAFRIVA 2cdcA 310 :KPHFQQAVV Number of specific fragments extracted= 17 number of extra gaps= 1 total=525 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 2cdcA/T0321-2cdcA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0321 read from 2cdcA/T0321-2cdcA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2cdcA read from 2cdcA/T0321-2cdcA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2cdcA in template set Warning: unaligning (T0321)F131 because of BadResidue code BAD_PEPTIDE in next template residue (2cdcA)P191 Warning: unaligning (T0321)P132 because of BadResidue code BAD_PEPTIDE at template residue (2cdcA)P191 Warning: unaligning (T0321)M221 because of BadResidue code BAD_PEPTIDE in next template residue (2cdcA)N307 Warning: unaligning (T0321)V222 because of BadResidue code BAD_PEPTIDE at template residue (2cdcA)N307 T0321 52 :TQNLLGL 2cdcA 139 :PKSIEDI T0321 60 :LRVAAGCVKSWNYVEAS 2cdcA 149 :AQPLADIEKSIEEILEV T0321 92 :AREHGVIFSDA 2cdcA 166 :QKRVPVWTCDD T0321 118 :NEVKGKKVGVVGH 2cdcA 177 :GTLNCRKVLVVGT T0321 133 :H 2cdcA 192 :I T0321 134 :LE 2cdcA 199 :LF T0321 138 :LEPICDLSILEWSPE 2cdcA 201 :RTYGLEVWMANRREP T0321 153 :EGDY 2cdcA 234 :SNGY T0321 159 :PASEFILPECDYVYI 2cdcA 238 :DKLKDSVGKFDVIID T0321 175 :CA 2cdcA 253 :AT T0321 181 :KTLPRLLELSRNARRITLVGPGTPL 2cdcA 259 :NILGNVIPLLGRNGVLGLFGFSTSG T0321 206 :APVLFEHGLQELSG 2cdcA 292 :LQEIVHTNKTIIGL T0321 223 :KDNARAFRIVA 2cdcA 308 :GQKPHFQQAVV Number of specific fragments extracted= 13 number of extra gaps= 2 total=538 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 1sjdA/T0321-1sjdA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1sjdA expands to /projects/compbio/data/pdb/1sjd.pdb.gz 1sjdA:# T0321 read from 1sjdA/T0321-1sjdA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1sjdA read from 1sjdA/T0321-1sjdA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1sjdA to template set # found chain 1sjdA in template set T0321 23 :CGTTHSVIRSGNGVGLG 1sjdA 29 :RELLLLRAVTPAGEGWG T0321 40 :PNRPFETRM 1sjdA 47 :CVTMAGPLY T0321 54 :NLLGLPLRVAAGCVK 1sjdA 77 :AAEDITAAKVTPLLA T0321 69 :SWNYVEASIGLAAINAYYNNPQVA 1sjdA 95 :GHRMAKGALEMAVLDAELRAHERS T0321 93 :RE 1sjdA 127 :RD T0321 95 :HGVIFSDAKRVEDRMNDPFI 1sjdA 135 :SVGIMDTIPQLLDVVGGYLD T0321 115 :MSQNEVKGKKVGVVGHF 1sjdA 176 :VRERFGDDVLLQVDANT T0321 132 :PHLESLLEPICDLSILEWSPE 1sjdA 200 :PQLARLDPFGLLLIEQPLEEE T0321 157 :PLPASEFILPECDYVYITCASVV 1sjdA 221 :DVLGHAELARRIQTPICLDESIV T0321 182 :TLPRLLELSR 1sjdA 244 :SARAAADAIK T0321 192 :NARRITLVGPGTP 1sjdA 255 :GAVQIVNIKPGRV T0321 205 :LAPVLFEHGLQELSGFMV 1sjdA 276 :VHDVCAAHGIPVWCGGMI Number of specific fragments extracted= 12 number of extra gaps= 0 total=550 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 1sjdA/T0321-1sjdA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0321 read from 1sjdA/T0321-1sjdA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1sjdA read from 1sjdA/T0321-1sjdA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1sjdA in template set T0321 23 :CGTTHSVIRSGNGVGLG 1sjdA 29 :RELLLLRAVTPAGEGWG T0321 40 :PNRPFETRM 1sjdA 47 :CVTMAGPLY T0321 54 :NLLGLPLRVAAGCVKSWN 1sjdA 77 :AAEDITAAKVTPLLAKFK T0321 72 :YVEASIGLAAINAYYNNPQ 1sjdA 98 :MAKGALEMAVLDAELRAHE T0321 110 :NDPFIMSQNEVKG 1sjdA 117 :RSFAAELGSVRDS T0321 125 :VGVVGHF 1sjdA 133 :GVSVGIM T0321 132 :P 1sjdA 143 :P T0321 133 :HLESLLEPICDLSILEWSPEEG 1sjdA 148 :VVGGYLDEGYVRIKLKIEPGWD T0321 181 :KTLPRLLELSRNARRITLVGPGTP 1sjdA 171 :EPVRAVRERFGDDVLLQVDANTAY T0321 205 :LAPVLF 1sjdA 198 :DAPQLA T0321 211 :EHGLQELSGFM 1sjdA 207 :PFGLLLIEQPL T0321 222 :VKDNARAFRIVAG 1sjdA 219 :EEDVLGHAELARR Number of specific fragments extracted= 12 number of extra gaps= 0 total=562 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 1sjdA/T0321-1sjdA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0321 read from 1sjdA/T0321-1sjdA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1sjdA read from 1sjdA/T0321-1sjdA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1sjdA in template set T0321 24 :GTTHSVIRSGNGVGLGPNRPF 1sjdA 30 :ELLLLRAVTPAGEGWGECVTM T0321 45 :ETRMPMLTQ 1sjdA 52 :GPLYSSEYN T0321 55 :LLGLPLRVAAGCVK 1sjdA 78 :AEDITAAKVTPLLA T0321 69 :SWNYVEASIGLAAINAYYNNP 1sjdA 95 :GHRMAKGALEMAVLDAELRAH T0321 110 :NDPFIMSQNEVKGK 1sjdA 116 :ERSFAAELGSVRDS T0321 125 :VGVVGHFPH 1sjdA 133 :GVSVGIMDT T0321 134 :LESLLEPICDLSILEWSPE 1sjdA 149 :VGGYLDEGYVRIKLKIEPG T0321 181 :KTLPRLLELSRNARRITLVGPGTPL 1sjdA 171 :EPVRAVRERFGDDVLLQVDANTAYT T0321 206 :APVLF 1sjdA 199 :APQLA T0321 211 :EHGLQELSGFM 1sjdA 207 :PFGLLLIEQPL T0321 222 :VKDNARAFRIVAG 1sjdA 219 :EEDVLGHAELARR Number of specific fragments extracted= 11 number of extra gaps= 0 total=573 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 1sc6A/T0321-1sc6A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1sc6A expands to /projects/compbio/data/pdb/1sc6.pdb.gz 1sc6A:Skipped atom 1168, because occupancy 0.500 <= existing 0.500 in 1sc6A Skipped atom 1170, because occupancy 0.500 <= existing 0.500 in 1sc6A Skipped atom 1172, because occupancy 0.500 <= existing 0.500 in 1sc6A Skipped atom 1174, because occupancy 0.500 <= existing 0.500 in 1sc6A Skipped atom 1176, because occupancy 0.500 <= existing 0.500 in 1sc6A Skipped atom 1178, because occupancy 0.500 <= existing 0.500 in 1sc6A Skipped atom 1180, because occupancy 0.500 <= existing 0.500 in 1sc6A Skipped atom 1182, because occupancy 0.500 <= existing 0.500 in 1sc6A Skipped atom 1184, because occupancy 0.500 <= existing 0.500 in 1sc6A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0321 read from 1sc6A/T0321-1sc6A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1sc6A read from 1sc6A/T0321-1sc6A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1sc6A to template set # found chain 1sc6A in template set Warning: unaligning (T0321)D111 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1sc6A)S146 Warning: unaligning (T0321)Q117 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1sc6A)S146 Warning: unaligning (T0321)M221 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1sc6A)D275 T0321 62 :VAAGCVKS 1sc6A 111 :SVAELVIG T0321 81 :AINAYYNNP 1sc6A 119 :ELLLLLRGV T0321 92 :A 1sc6A 128 :P T0321 101 :DAKRVEDR 1sc6A 129 :EANAKAHR T0321 109 :MN 1sc6A 138 :VG T0321 118 :NEVKGKKVGVVGHFP 1sc6A 147 :FEARGKKLGIIGYGH T0321 133 :HLESLLEPICDLSILEWSPEEGDYP 1sc6A 166 :LGILAESLGMYVYFYDIENKLPLGN T0321 158 :LPASEFILPECDYVYI 1sc6A 194 :VQHLSDLLNMSDVVSL T0321 183 :LPR 1sc6A 223 :AKE T0321 187 :LELSRNA 1sc6A 226 :ISLMKPG T0321 196 :ITLVGPGTP 1sc6A 233 :SLLINASRG T0321 205 :LAPV 1sc6A 248 :ALAD T0321 209 :LFEHGLQELSGF 1sc6A 253 :LASKHLAGAAID Number of specific fragments extracted= 13 number of extra gaps= 0 total=586 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 1sc6A/T0321-1sc6A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0321 read from 1sc6A/T0321-1sc6A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1sc6A read from 1sc6A/T0321-1sc6A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1sc6A in template set Warning: unaligning (T0321)D111 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1sc6A)S146 Warning: unaligning (T0321)Q117 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1sc6A)S146 Warning: unaligning (T0321)M221 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1sc6A)D275 T0321 60 :LRVAAG 1sc6A 120 :LLLLLR T0321 70 :WNYVEAS 1sc6A 126 :GVPEANA T0321 105 :VEDRMN 1sc6A 134 :AHRGVG T0321 118 :NEVKGKKVGVVGHFP 1sc6A 147 :FEARGKKLGIIGYGH T0321 133 :HLESLLEPICDLSILEWSPE 1sc6A 166 :LGILAESLGMYVYFYDIENK T0321 153 :EGDYPLPASEFILPE 1sc6A 218 :KNMMGAKEISLMKPG T0321 170 :YVYITCA 1sc6A 233 :SLLINAS T0321 177 :SVVD 1sc6A 242 :TVVD T0321 183 :LPRLLELS 1sc6A 246 :IPALADAL T0321 210 :FEHGLQELSGF 1sc6A 254 :ASKHLAGAAID Number of specific fragments extracted= 10 number of extra gaps= 0 total=596 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 1sc6A/T0321-1sc6A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0321 read from 1sc6A/T0321-1sc6A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1sc6A read from 1sc6A/T0321-1sc6A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1sc6A in template set Warning: unaligning (T0321)D111 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1sc6A)S146 Warning: unaligning (T0321)Q117 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1sc6A)S146 T0321 61 :RVAAGCVKSWNYV 1sc6A 110 :RSVAELVIGELLL T0321 84 :AYYNNPQVAR 1sc6A 123 :LLRGVPEANA T0321 104 :RVEDRMN 1sc6A 133 :KAHRGVG T0321 118 :NEVKGKKVGVVGHFPHLESLLE 1sc6A 147 :FEARGKKLGIIGYGHIGTQLGI T0321 140 :PICDLSILEWSPEEGDYPLP 1sc6A 171 :ESLGMYVYFYDIENKLPLGN T0321 160 :ASEFILPECDYVYI 1sc6A 196 :HLSDLLNMSDVVSL T0321 184 :PRLLELSRNAR 1sc6A 223 :AKEISLMKPGS T0321 197 :TLVGPGTPL 1sc6A 234 :LLINASRGT T0321 222 :VKDNARAFRIVAG 1sc6A 243 :VVDIPALADALAS Number of specific fragments extracted= 9 number of extra gaps= 0 total=605 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 1xhcA/T0321-1xhcA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1xhcA expands to /projects/compbio/data/pdb/1xhc.pdb.gz 1xhcA:Skipped atom 303, because occupancy 0.350 <= existing 0.650 in 1xhcA Skipped atom 305, because occupancy 0.350 <= existing 0.650 in 1xhcA Skipped atom 307, because occupancy 0.350 <= existing 0.650 in 1xhcA Skipped atom 309, because occupancy 0.350 <= existing 0.650 in 1xhcA # T0321 read from 1xhcA/T0321-1xhcA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1xhcA read from 1xhcA/T0321-1xhcA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1xhcA to template set # found chain 1xhcA in template set Warning: unaligning (T0321)K123 because first residue in template chain is (1xhcA)S1 Warning: unaligning (T0321)P201 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1xhcA)G144 Warning: unaligning (T0321)G202 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1xhcA)G144 T0321 124 :KVGVVGHFP 1xhcA 2 :KVVIVGNGP T0321 133 :HLESLLEP 1xhcA 15 :LAKQLSQT T0321 142 :CDLSILEWSPE 1xhcA 23 :YEVTVIDKEPV T0321 153 :EGDYPLPAS 1xhcA 54 :LFPYSLDWY T0321 168 :CDYVYI 1xhcA 94 :YDTLVL T0321 174 :TCA 1xhcA 101 :TGA T0321 177 :SV 1xhcA 118 :TL T0321 181 :KT 1xhcA 120 :RT T0321 183 :LPRLLELSRNARRITLVG 1xhcA 125 :ADRIKESIENSGEAIIIG T0321 203 :TP 1xhcA 145 :FI T0321 205 :LAPVLFEHGLQELSGFMVK 1xhcA 150 :LAGNLAEAGYHVKLIHRGA T0321 225 :NARAFRIVAGAE 1xhcA 178 :SNMIKDMLEETG T0321 237 :KVKIYS 1xhcA 195 :NSELLE T0321 243 :AGQKVTI 1xhcA 202 :NEEGVLT Number of specific fragments extracted= 14 number of extra gaps= 1 total=619 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 1xhcA/T0321-1xhcA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0321 read from 1xhcA/T0321-1xhcA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1xhcA read from 1xhcA/T0321-1xhcA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1xhcA in template set Warning: unaligning (T0321)K123 because first residue in template chain is (1xhcA)S1 Warning: unaligning (T0321)P201 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1xhcA)G144 Warning: unaligning (T0321)G202 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1xhcA)G144 T0321 124 :KVGVVGHFP 1xhcA 2 :KVVIVGNGP T0321 133 :HLESLLEP 1xhcA 15 :LAKQLSQT T0321 142 :CDLSILEWSPE 1xhcA 23 :YEVTVIDKEPV T0321 153 :EGDYPLPAS 1xhcA 54 :LFPYSLDWY T0321 168 :CDYVYI 1xhcA 94 :YDTLVL T0321 174 :TCA 1xhcA 101 :TGA T0321 177 :SV 1xhcA 118 :TL T0321 182 :TLPRLLELSRNARRITLVG 1xhcA 124 :DADRIKESIENSGEAIIIG T0321 203 :TPLAPVLFEHGLQELSGFMVK 1xhcA 148 :LELAGNLAEAGYHVKLIHRGA T0321 225 :NARAFRIVAGAE 1xhcA 178 :SNMIKDMLEETG T0321 237 :KVKIYS 1xhcA 195 :NSELLE T0321 243 :AGQKVTI 1xhcA 202 :NEEGVLT Number of specific fragments extracted= 12 number of extra gaps= 1 total=631 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 1xhcA/T0321-1xhcA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0321 read from 1xhcA/T0321-1xhcA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1xhcA read from 1xhcA/T0321-1xhcA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1xhcA in template set Warning: unaligning (T0321)K123 because first residue in template chain is (1xhcA)S1 Warning: unaligning (T0321)P201 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1xhcA)G144 Warning: unaligning (T0321)G202 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1xhcA)G144 T0321 124 :KVGVVGHFPH 1xhcA 2 :KVVIVGNGPG T0321 134 :LESLLEPICDLSILEWSPE 1xhcA 15 :LAKQLSQTYEVTVIDKEPV T0321 153 :EGDYPLPAS 1xhcA 46 :AGFIPRNRL T0321 168 :CDYVYITCAS 1xhcA 94 :YDTLVLATGA T0321 182 :TLPRLLELSRNARRITLVG 1xhcA 124 :DADRIKESIENSGEAIIIG T0321 205 :LAPVLFEHGLQELSGFM 1xhcA 150 :LAGNLAEAGYHVKLIHR T0321 225 :NARAFRIVAGAE 1xhcA 178 :SNMIKDMLEETG T0321 238 :VKIYSAGQKVTIK 1xhcA 190 :VKFFLNSELLEAN Number of specific fragments extracted= 8 number of extra gaps= 1 total=639 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 2nacA/T0321-2nacA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2nacA expands to /projects/compbio/data/pdb/2nac.pdb.gz 2nacA:# T0321 read from 2nacA/T0321-2nacA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2nacA read from 2nacA/T0321-2nacA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2nacA to template set # found chain 2nacA in template set Warning: unaligning (T0321)V128 because of BadResidue code BAD_PEPTIDE in next template residue (2nacA)A198 Warning: unaligning (T0321)G129 because of BadResidue code BAD_PEPTIDE at template residue (2nacA)A198 T0321 70 :W 2nacA 148 :I T0321 72 :YVEASIGLAAINAYYNNPQVAREHGVIFSDAKRVEDRMND 2nacA 149 :SVAEHVVMMILSLVRNYLPSHEWARKGGWNIADCVSHAYD T0321 120 :VKGKKVGV 2nacA 189 :LEAMHVGT T0321 130 :HF 2nacA 199 :AG T0321 133 :HLESLLEPICDLSILEWS 2nacA 206 :VLRRLAPFDVHLHYTDRH T0321 155 :DYPLPAS 2nacA 224 :RLPESVE T0321 162 :EFILPECDYVYITC 2nacA 242 :EDMYPVCDVVTLNC T0321 179 :VDK 2nacA 265 :IND T0321 184 :PR 2nacA 268 :ET T0321 187 :LELSRNAR 2nacA 270 :LKLFKRGA T0321 197 :TLVGPGTP 2nacA 278 :YIVNTARG T0321 224 :DNARAFRIVAGAE 2nacA 289 :DRDAVARALESGR Number of specific fragments extracted= 12 number of extra gaps= 1 total=651 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 2nacA/T0321-2nacA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0321 read from 2nacA/T0321-2nacA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2nacA read from 2nacA/T0321-2nacA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2nacA in template set Warning: unaligning (T0321)V128 because of BadResidue code BAD_PEPTIDE in next template residue (2nacA)A198 Warning: unaligning (T0321)G129 because of BadResidue code BAD_PEPTIDE at template residue (2nacA)A198 T0321 71 :NYV 2nacA 149 :SVA T0321 75 :ASIGLAAINAYYNNPQVA 2nacA 152 :EHVVMMILSLVRNYLPSH T0321 103 :KRVEDRMNDPFIMSQNEV 2nacA 170 :EWARKGGWNIADCVSHAY T0321 121 :KGKKVGV 2nacA 190 :EAMHVGT T0321 130 :HF 2nacA 199 :AG T0321 133 :HLESLLEPICDLSILEWS 2nacA 206 :VLRRLAPFDVHLHYTDRH T0321 155 :DYPLPAS 2nacA 224 :RLPESVE T0321 162 :EFILPECDYVYITC 2nacA 242 :EDMYPVCDVVTLNC T0321 179 :VDK 2nacA 265 :IND T0321 185 :RLLELSRNAR 2nacA 268 :ETLKLFKRGA T0321 196 :ITLVGPGTPL 2nacA 278 :YIVNTARGKL T0321 224 :DNARAFRIVAGAE 2nacA 289 :DRDAVARALESGR Number of specific fragments extracted= 12 number of extra gaps= 1 total=663 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 2nacA/T0321-2nacA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0321 read from 2nacA/T0321-2nacA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2nacA read from 2nacA/T0321-2nacA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2nacA in template set Warning: unaligning (T0321)V128 because of BadResidue code BAD_PEPTIDE in next template residue (2nacA)A198 Warning: unaligning (T0321)G129 because of BadResidue code BAD_PEPTIDE at template residue (2nacA)A198 T0321 61 :RVAAGCVKS 2nacA 148 :ISVAEHVVM T0321 80 :AAINAYYNNPQV 2nacA 157 :MILSLVRNYLPS T0321 92 :AREH 2nacA 172 :ARKG T0321 107 :DRMNDPFIMSQNEVKGKKVGV 2nacA 176 :GWNIADCVSHAYDLEAMHVGT T0321 130 :HFP 2nacA 199 :AGR T0321 134 :LESLLEPI 2nacA 206 :VLRRLAPF T0321 143 :DLSILEWS 2nacA 214 :DVHLHYTD T0321 153 :EGDYPLPASEFI 2nacA 222 :RHRLPESVEKEL T0321 165 :LPECDYVYITC 2nacA 245 :YPVCDVVTLNC T0321 179 :VD 2nacA 265 :IN T0321 184 :PRLLELSRNAR 2nacA 267 :DETLKLFKRGA T0321 196 :ITLVGPGTPLA 2nacA 278 :YIVNTARGKLC T0321 224 :DNARAFRIVAGA 2nacA 289 :DRDAVARALESG Number of specific fragments extracted= 13 number of extra gaps= 1 total=676 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 1y0eA/T0321-1y0eA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1y0eA expands to /projects/compbio/data/pdb/1y0e.pdb.gz 1y0eA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0321 read from 1y0eA/T0321-1y0eA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1y0eA read from 1y0eA/T0321-1y0eA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1y0eA to template set # found chain 1y0eA in template set Warning: unaligning (T0321)C175 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1y0eA)T96 Warning: unaligning (T0321)A176 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1y0eA)T96 T0321 97 :VIFSDAKRV 1y0eA 11 :QALPDEPLH T0321 108 :RMNDPFIMSQNEV 1y0eA 20 :SSFIMSKMALAAY T0321 121 :KGKKVGVVGHFPHLESLLEPI 1y0eA 34 :GGAVGIRANTKEDILAIKETV T0321 143 :DLSIL 1y0eA 55 :DLPVI T0321 148 :EWSPEEGDYP 1y0eA 63 :KRDYDHSDVF T0321 158 :LPASEFILP 1y0eA 77 :SKEVDELIE T0321 167 :ECDYVYIT 1y0eA 87 :QCEVIALD T0321 180 :DKTLPRLLELSRN 1y0eA 102 :KETLDELVSYIRT T0321 193 :ARRITLVGPGTPLAPVLFEHGLQELS 1y0eA 118 :NVEIMADIATVEEAKNAARLGFDYIG Number of specific fragments extracted= 9 number of extra gaps= 1 total=685 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 1y0eA/T0321-1y0eA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0321 read from 1y0eA/T0321-1y0eA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1y0eA read from 1y0eA/T0321-1y0eA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1y0eA in template set Warning: unaligning (T0321)C175 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1y0eA)T96 Warning: unaligning (T0321)A176 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1y0eA)T96 T0321 112 :PFIMSQNEV 1y0eA 24 :MSKMALAAY T0321 121 :KGKKVGVVGHFPHLESLLEPIC 1y0eA 34 :GGAVGIRANTKEDILAIKETVD T0321 143 :DL 1y0eA 57 :PV T0321 145 :SILEWSPEEGDYP 1y0eA 60 :GIVKRDYDHSDVF T0321 158 :LPASEFILP 1y0eA 77 :SKEVDELIE T0321 167 :ECDYVYIT 1y0eA 87 :QCEVIALD T0321 180 :DKTLPRLLELSRN 1y0eA 102 :KETLDELVSYIRT T0321 193 :ARRITLVGPGTPLAPVLFEHGLQELS 1y0eA 118 :NVEIMADIATVEEAKNAARLGFDYIG Number of specific fragments extracted= 8 number of extra gaps= 1 total=693 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 1y0eA/T0321-1y0eA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0321 read from 1y0eA/T0321-1y0eA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1y0eA read from 1y0eA/T0321-1y0eA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1y0eA in template set Warning: unaligning (T0321)C175 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1y0eA)T96 Warning: unaligning (T0321)A176 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1y0eA)T96 T0321 126 :GVVGHFPHLESLLEPICDLSIL 1y0eA 38 :GIRANTKEDILAIKETVDLPVI T0321 148 :EWSPEEGDYP 1y0eA 63 :KRDYDHSDVF T0321 158 :LPASEFILP 1y0eA 77 :SKEVDELIE T0321 167 :ECDYVYIT 1y0eA 87 :QCEVIALD T0321 180 :DKTLPRLLELSR 1y0eA 102 :KETLDELVSYIR T0321 192 :NARRIT 1y0eA 118 :NVEIMA T0321 198 :LVGPGTP 1y0eA 141 :YIGTTLH T0321 205 :LAPVLF 1y0eA 165 :FLKDVL T0321 211 :EHGLQELSGFMVKDNARAFRIVAGA 1y0eA 172 :SVDAKVIAEGNVITPDMYKRVMDLG Number of specific fragments extracted= 9 number of extra gaps= 1 total=702 Will force an alignment to be made, even if fragment is small Number of alignments=60 # command:CPU_time= 19.571 sec, elapsed time= 21.200 sec. # command:Using radius: 8.000 NUMB_ALIGNS: 60 Adding 31375 constraints to all_contacts Done adding distance constraints # command:CPU_time= 19.663 sec, elapsed time= 21.304 sec. # command:Reading probabilities from T0321.t06.CB8-sep9.rdb Reading constraints from ConstraintSet all_contacts maxweight: 23.254 Optimizing... Probability sum: -456.323, CN propb: -456.323 weights: 0.155 constraints: 919 # command:CPU_time= 132.106 sec, elapsed time= 134.230 sec. # command:Found ConstraintSet # PrintContacts log_align.constraints Number of constraints in align 919 # command:Found ConstraintSet # PrintContacts log_align_bonus.constraints Number of constraints in align.bonus 919 # command:Found ConstraintSet # PrintContacts log_rejected.constraints Number of constraints in rejected 1896 # command:Found ConstraintSet # PrintContacts log_rejected_bonus.constraints Number of constraints in rejected.bonus 1896 # command:Found ConstraintSet # PrintContacts log_noncontact.constraints Number of constraints in noncontact 26588 # command:Found ConstraintSet # PrintContacts log_noncontact_bonus.constraints Number of constraints in noncontact.bonus 26588 # command:CPU_time= 132.621 sec, elapsed time= 135.120 sec. # command: