Starting phenix.real_space_refine on Tue Nov 19 03:42:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5yw8_6848/11_2024/5yw8_6848.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5yw8_6848/11_2024/5yw8_6848.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5yw8_6848/11_2024/5yw8_6848.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5yw8_6848/11_2024/5yw8_6848.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5yw8_6848/11_2024/5yw8_6848.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5yw8_6848/11_2024/5yw8_6848.cif" } resolution = 4.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 24 5.49 5 S 272 5.16 5 C 32848 2.51 5 N 8540 2.21 5 O 8840 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 145 residue(s): 0.17s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 50524 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 2457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2457 Classifications: {'peptide': 325} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 25} Link IDs: {'PTRANS': 13, 'TRANS': 311} Unresolved non-hydrogen bonds: 96 Unresolved non-hydrogen angles: 121 Unresolved non-hydrogen dihedrals: 75 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLU:plan': 7, 'HIS:plan': 2, 'ARG:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 66 Chain: "B" Number of atoms: 10112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1305, 10112 Classifications: {'peptide': 1305} Incomplete info: {'truncation_to_alanine': 48} Link IDs: {'PTRANS': 45, 'TRANS': 1259} Chain breaks: 12 Unresolved non-hydrogen bonds: 213 Unresolved non-hydrogen angles: 266 Unresolved non-hydrogen dihedrals: 182 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 9, 'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 5, 'GLU:plan': 6, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 159 Chain: "C" Number of atoms: 2457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2457 Classifications: {'peptide': 325} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 25} Link IDs: {'PTRANS': 13, 'TRANS': 311} Unresolved non-hydrogen bonds: 96 Unresolved non-hydrogen angles: 121 Unresolved non-hydrogen dihedrals: 75 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLU:plan': 7, 'HIS:plan': 2, 'ARG:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 66 Chain: "D" Number of atoms: 10112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1305, 10112 Classifications: {'peptide': 1305} Incomplete info: {'truncation_to_alanine': 48} Link IDs: {'PTRANS': 45, 'TRANS': 1259} Chain breaks: 12 Unresolved non-hydrogen bonds: 213 Unresolved non-hydrogen angles: 266 Unresolved non-hydrogen dihedrals: 182 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 9, 'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 5, 'GLU:plan': 6, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 159 Chain: "E" Number of atoms: 2457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2457 Classifications: {'peptide': 325} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 25} Link IDs: {'PTRANS': 13, 'TRANS': 311} Unresolved non-hydrogen bonds: 96 Unresolved non-hydrogen angles: 121 Unresolved non-hydrogen dihedrals: 75 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLU:plan': 7, 'HIS:plan': 2, 'ARG:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 66 Chain: "F" Number of atoms: 10112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1305, 10112 Classifications: {'peptide': 1305} Incomplete info: {'truncation_to_alanine': 48} Link IDs: {'PTRANS': 45, 'TRANS': 1259} Chain breaks: 12 Unresolved non-hydrogen bonds: 213 Unresolved non-hydrogen angles: 266 Unresolved non-hydrogen dihedrals: 182 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 9, 'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 5, 'GLU:plan': 6, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 159 Chain: "G" Number of atoms: 2457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2457 Classifications: {'peptide': 325} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 25} Link IDs: {'PTRANS': 13, 'TRANS': 311} Unresolved non-hydrogen bonds: 96 Unresolved non-hydrogen angles: 121 Unresolved non-hydrogen dihedrals: 75 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLU:plan': 7, 'HIS:plan': 2, 'ARG:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 66 Chain: "H" Number of atoms: 10112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1305, 10112 Classifications: {'peptide': 1305} Incomplete info: {'truncation_to_alanine': 48} Link IDs: {'PTRANS': 45, 'TRANS': 1259} Chain breaks: 12 Unresolved non-hydrogen bonds: 213 Unresolved non-hydrogen angles: 266 Unresolved non-hydrogen dihedrals: 182 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 9, 'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 5, 'GLU:plan': 6, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 159 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Time building chain proxies: 26.49, per 1000 atoms: 0.52 Number of scatterers: 50524 At special positions: 0 Unit cell: (210.38, 210.38, 143.38, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 272 16.00 P 24 15.00 O 8840 8.00 N 8540 7.00 C 32848 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 110 " - pdb=" SG CYS A 142 " distance=2.03 Simple disulfide: pdb=" SG CYS C 110 " - pdb=" SG CYS C 142 " distance=2.03 Simple disulfide: pdb=" SG CYS E 110 " - pdb=" SG CYS E 142 " distance=2.03 Simple disulfide: pdb=" SG CYS G 110 " - pdb=" SG CYS G 142 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 12.81 Conformation dependent library (CDL) restraints added in 6.7 seconds 12816 Ramachandran restraints generated. 6408 Oldfield, 0 Emsley, 6408 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 12312 Finding SS restraints... Secondary structure from input PDB file: 212 helices and 40 sheets defined 64.3% alpha, 7.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.62 Creating SS restraints... Processing helix chain 'A' and resid 53 through 58 Processing helix chain 'A' and resid 58 through 64 removed outlier: 3.631A pdb=" N LEU A 63 " --> pdb=" O VAL A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 98 removed outlier: 3.614A pdb=" N GLY A 98 " --> pdb=" O ALA A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 129 removed outlier: 3.618A pdb=" N VAL A 129 " --> pdb=" O ILE A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 172 removed outlier: 3.622A pdb=" N ILE A 146 " --> pdb=" O CYS A 142 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ILE A 154 " --> pdb=" O ILE A 150 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ILE A 167 " --> pdb=" O MET A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 181 removed outlier: 3.902A pdb=" N LEU A 181 " --> pdb=" O ARG A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 270 removed outlier: 4.360A pdb=" N ASP A 269 " --> pdb=" O PRO A 266 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU A 270 " --> pdb=" O LEU A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 356 Processing helix chain 'B' and resid 25 through 52 Proline residue: B 35 - end of helix removed outlier: 3.941A pdb=" N PHE B 44 " --> pdb=" O LEU B 40 " (cutoff:3.500A) Proline residue: B 45 - end of helix Processing helix chain 'B' and resid 70 through 96 Processing helix chain 'B' and resid 104 through 130 Proline residue: B 109 - end of helix removed outlier: 3.757A pdb=" N MET B 115 " --> pdb=" O GLY B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 133 through 160 removed outlier: 3.823A pdb=" N ILE B 137 " --> pdb=" O PRO B 133 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N TYR B 142 " --> pdb=" O ALA B 138 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N HIS B 160 " --> pdb=" O LYS B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 193 removed outlier: 3.518A pdb=" N ARG B 193 " --> pdb=" O VAL B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 212 Processing helix chain 'B' and resid 225 through 230 Processing helix chain 'B' and resid 232 through 243 removed outlier: 4.250A pdb=" N PHE B 236 " --> pdb=" O TRP B 232 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LYS B 242 " --> pdb=" O LYS B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 275 removed outlier: 3.616A pdb=" N ASN B 262 " --> pdb=" O ARG B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 329 removed outlier: 6.309A pdb=" N ARG B 297 " --> pdb=" O HIS B 293 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N ARG B 298 " --> pdb=" O ALA B 294 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N LEU B 299 " --> pdb=" O PHE B 295 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ILE B 300 " --> pdb=" O GLY B 296 " (cutoff:3.500A) Proline residue: B 317 - end of helix Processing helix chain 'B' and resid 355 through 402 removed outlier: 3.630A pdb=" N MET B 400 " --> pdb=" O TYR B 396 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N HIS B 401 " --> pdb=" O ASN B 397 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU B 402 " --> pdb=" O LYS B 398 " (cutoff:3.500A) Processing helix chain 'B' and resid 412 through 423 Processing helix chain 'B' and resid 423 through 457 Proline residue: B 436 - end of helix removed outlier: 3.536A pdb=" N TRP B 439 " --> pdb=" O CYS B 435 " (cutoff:3.500A) Proline residue: B 442 - end of helix Processing helix chain 'B' and resid 457 through 503 removed outlier: 3.732A pdb=" N LEU B 461 " --> pdb=" O GLY B 457 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE B 462 " --> pdb=" O VAL B 458 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ILE B 468 " --> pdb=" O ALA B 464 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ALA B 471 " --> pdb=" O ILE B 467 " (cutoff:3.500A) Proline residue: B 472 - end of helix removed outlier: 3.595A pdb=" N GLU B 501 " --> pdb=" O LYS B 497 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N MET B 502 " --> pdb=" O GLN B 498 " (cutoff:3.500A) Processing helix chain 'B' and resid 505 through 512 removed outlier: 4.017A pdb=" N TYR B 512 " --> pdb=" O LEU B 508 " (cutoff:3.500A) Processing helix chain 'B' and resid 514 through 560 removed outlier: 3.654A pdb=" N ARG B 521 " --> pdb=" O ILE B 517 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LYS B 528 " --> pdb=" O VAL B 524 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ALA B 535 " --> pdb=" O THR B 531 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N THR B 548 " --> pdb=" O ILE B 544 " (cutoff:3.500A) Proline residue: B 551 - end of helix removed outlier: 3.554A pdb=" N VAL B 555 " --> pdb=" O PRO B 551 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 615 removed outlier: 3.531A pdb=" N ALA B 576 " --> pdb=" O SER B 572 " (cutoff:3.500A) Proline residue: B 589 - end of helix removed outlier: 4.446A pdb=" N LEU B 592 " --> pdb=" O THR B 588 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU B 593 " --> pdb=" O PRO B 589 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N SER B 594 " --> pdb=" O LEU B 590 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N SER B 595 " --> pdb=" O PHE B 591 " (cutoff:3.500A) Processing helix chain 'B' and resid 718 through 727 Processing helix chain 'B' and resid 783 through 790 Processing helix chain 'B' and resid 796 through 806 Processing helix chain 'B' and resid 808 through 815 removed outlier: 3.578A pdb=" N LEU B 815 " --> pdb=" O ASP B 811 " (cutoff:3.500A) Processing helix chain 'B' and resid 831 through 846 removed outlier: 3.541A pdb=" N GLN B 846 " --> pdb=" O ARG B 842 " (cutoff:3.500A) Processing helix chain 'B' and resid 861 through 872 Processing helix chain 'B' and resid 893 through 897 removed outlier: 3.651A pdb=" N ALA B 897 " --> pdb=" O LEU B 894 " (cutoff:3.500A) Processing helix chain 'B' and resid 914 through 919 Processing helix chain 'B' and resid 997 through 1007 removed outlier: 4.440A pdb=" N CYS B1001 " --> pdb=" O PRO B 997 " (cutoff:3.500A) Processing helix chain 'B' and resid 1009 through 1039 removed outlier: 3.532A pdb=" N LEU B1013 " --> pdb=" O GLY B1009 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N SER B1014 " --> pdb=" O ILE B1010 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N LEU B1015 " --> pdb=" O LEU B1011 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N SER B1019 " --> pdb=" O LEU B1015 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ASP B1031 " --> pdb=" O LEU B1027 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LYS B1036 " --> pdb=" O TYR B1032 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N ASP B1039 " --> pdb=" O ALA B1035 " (cutoff:3.500A) Processing helix chain 'B' and resid 1061 through 1107 removed outlier: 3.540A pdb=" N LEU B1107 " --> pdb=" O ASN B1103 " (cutoff:3.500A) Processing helix chain 'B' and resid 1109 through 1116 Processing helix chain 'B' and resid 1117 through 1127 removed outlier: 3.829A pdb=" N ILE B1121 " --> pdb=" O PRO B1117 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N PHE B1125 " --> pdb=" O ILE B1121 " (cutoff:3.500A) Processing helix chain 'B' and resid 1127 through 1161 Proline residue: B1137 - end of helix Processing helix chain 'B' and resid 1161 through 1210 removed outlier: 4.302A pdb=" N VAL B1166 " --> pdb=" O PRO B1162 " (cutoff:3.500A) Proline residue: B1170 - end of helix removed outlier: 3.539A pdb=" N PHE B1177 " --> pdb=" O VAL B1173 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N TYR B1181 " --> pdb=" O PHE B1177 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N PHE B1182 " --> pdb=" O ILE B1178 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ALA B1185 " --> pdb=" O TYR B1181 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N ASP B1188 " --> pdb=" O VAL B1184 " (cutoff:3.500A) Proline residue: B1199 - end of helix removed outlier: 3.525A pdb=" N GLY B1210 " --> pdb=" O GLU B1206 " (cutoff:3.500A) Processing helix chain 'B' and resid 1210 through 1218 Processing helix chain 'B' and resid 1219 through 1271 removed outlier: 3.723A pdb=" N ALA B1237 " --> pdb=" O SER B1233 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N THR B1242 " --> pdb=" O SER B1238 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N VAL B1260 " --> pdb=" O GLY B1256 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N SER B1269 " --> pdb=" O ALA B1265 " (cutoff:3.500A) Processing helix chain 'B' and resid 1278 through 1289 removed outlier: 4.012A pdb=" N GLY B1282 " --> pdb=" O ALA B1278 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N LEU B1283 " --> pdb=" O GLY B1279 " (cutoff:3.500A) Processing helix chain 'B' and resid 1290 through 1320 removed outlier: 3.638A pdb=" N TYR B1294 " --> pdb=" O MET B1290 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N ARG B1314 " --> pdb=" O GLY B1310 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N ILE B1315 " --> pdb=" O ALA B1311 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N HIS B1316 " --> pdb=" O VAL B1312 " (cutoff:3.500A) Processing helix chain 'B' and resid 1384 through 1393 Processing helix chain 'B' and resid 1414 through 1420 Processing helix chain 'B' and resid 1435 through 1441 Processing helix chain 'B' and resid 1447 through 1458 Processing helix chain 'B' and resid 1460 through 1466 Processing helix chain 'B' and resid 1483 through 1499 removed outlier: 3.856A pdb=" N LYS B1499 " --> pdb=" O ALA B1495 " (cutoff:3.500A) Processing helix chain 'B' and resid 1513 through 1528 removed outlier: 4.096A pdb=" N ILE B1519 " --> pdb=" O ALA B1515 " (cutoff:3.500A) Processing helix chain 'B' and resid 1539 through 1546 removed outlier: 3.675A pdb=" N ILE B1543 " --> pdb=" O ARG B1539 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA B1546 " --> pdb=" O THR B1542 " (cutoff:3.500A) Processing helix chain 'B' and resid 1562 through 1570 removed outlier: 4.307A pdb=" N SER B1568 " --> pdb=" O GLU B1564 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N LYS B1570 " --> pdb=" O LEU B1566 " (cutoff:3.500A) Processing helix chain 'C' and resid 53 through 58 Processing helix chain 'C' and resid 58 through 64 removed outlier: 3.632A pdb=" N LEU C 63 " --> pdb=" O VAL C 59 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 98 removed outlier: 3.613A pdb=" N GLY C 98 " --> pdb=" O ALA C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 116 through 129 removed outlier: 3.618A pdb=" N VAL C 129 " --> pdb=" O ILE C 125 " (cutoff:3.500A) Processing helix chain 'C' and resid 142 through 172 removed outlier: 3.622A pdb=" N ILE C 146 " --> pdb=" O CYS C 142 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N ILE C 154 " --> pdb=" O ILE C 150 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N ILE C 167 " --> pdb=" O MET C 163 " (cutoff:3.500A) Processing helix chain 'C' and resid 174 through 181 removed outlier: 3.902A pdb=" N LEU C 181 " --> pdb=" O ARG C 177 " (cutoff:3.500A) Processing helix chain 'C' and resid 265 through 270 removed outlier: 4.360A pdb=" N ASP C 269 " --> pdb=" O PRO C 266 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU C 270 " --> pdb=" O LEU C 267 " (cutoff:3.500A) Processing helix chain 'C' and resid 345 through 356 Processing helix chain 'D' and resid 25 through 52 Proline residue: D 35 - end of helix removed outlier: 3.941A pdb=" N PHE D 44 " --> pdb=" O LEU D 40 " (cutoff:3.500A) Proline residue: D 45 - end of helix Processing helix chain 'D' and resid 70 through 96 Processing helix chain 'D' and resid 104 through 130 Proline residue: D 109 - end of helix removed outlier: 3.757A pdb=" N MET D 115 " --> pdb=" O GLY D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 133 through 160 removed outlier: 3.823A pdb=" N ILE D 137 " --> pdb=" O PRO D 133 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N TYR D 142 " --> pdb=" O ALA D 138 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N HIS D 160 " --> pdb=" O LYS D 156 " (cutoff:3.500A) Processing helix chain 'D' and resid 168 through 193 removed outlier: 3.518A pdb=" N ARG D 193 " --> pdb=" O VAL D 189 " (cutoff:3.500A) Processing helix chain 'D' and resid 207 through 212 Processing helix chain 'D' and resid 225 through 230 Processing helix chain 'D' and resid 232 through 243 removed outlier: 4.250A pdb=" N PHE D 236 " --> pdb=" O TRP D 232 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LYS D 242 " --> pdb=" O LYS D 238 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 275 removed outlier: 3.616A pdb=" N ASN D 262 " --> pdb=" O ARG D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 284 through 329 removed outlier: 6.309A pdb=" N ARG D 297 " --> pdb=" O HIS D 293 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N ARG D 298 " --> pdb=" O ALA D 294 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N LEU D 299 " --> pdb=" O PHE D 295 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ILE D 300 " --> pdb=" O GLY D 296 " (cutoff:3.500A) Proline residue: D 317 - end of helix Processing helix chain 'D' and resid 355 through 402 removed outlier: 3.631A pdb=" N MET D 400 " --> pdb=" O TYR D 396 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N HIS D 401 " --> pdb=" O ASN D 397 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU D 402 " --> pdb=" O LYS D 398 " (cutoff:3.500A) Processing helix chain 'D' and resid 412 through 423 Processing helix chain 'D' and resid 423 through 457 Proline residue: D 436 - end of helix removed outlier: 3.535A pdb=" N TRP D 439 " --> pdb=" O CYS D 435 " (cutoff:3.500A) Proline residue: D 442 - end of helix Processing helix chain 'D' and resid 457 through 503 removed outlier: 3.732A pdb=" N LEU D 461 " --> pdb=" O GLY D 457 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE D 462 " --> pdb=" O VAL D 458 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE D 468 " --> pdb=" O ALA D 464 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ALA D 471 " --> pdb=" O ILE D 467 " (cutoff:3.500A) Proline residue: D 472 - end of helix removed outlier: 3.595A pdb=" N GLU D 501 " --> pdb=" O LYS D 497 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N MET D 502 " --> pdb=" O GLN D 498 " (cutoff:3.500A) Processing helix chain 'D' and resid 505 through 512 removed outlier: 4.017A pdb=" N TYR D 512 " --> pdb=" O LEU D 508 " (cutoff:3.500A) Processing helix chain 'D' and resid 514 through 560 removed outlier: 3.655A pdb=" N ARG D 521 " --> pdb=" O ILE D 517 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LYS D 528 " --> pdb=" O VAL D 524 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ALA D 535 " --> pdb=" O THR D 531 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N THR D 548 " --> pdb=" O ILE D 544 " (cutoff:3.500A) Proline residue: D 551 - end of helix removed outlier: 3.554A pdb=" N VAL D 555 " --> pdb=" O PRO D 551 " (cutoff:3.500A) Processing helix chain 'D' and resid 572 through 615 removed outlier: 3.531A pdb=" N ALA D 576 " --> pdb=" O SER D 572 " (cutoff:3.500A) Proline residue: D 589 - end of helix removed outlier: 4.446A pdb=" N LEU D 592 " --> pdb=" O THR D 588 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU D 593 " --> pdb=" O PRO D 589 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N SER D 594 " --> pdb=" O LEU D 590 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N SER D 595 " --> pdb=" O PHE D 591 " (cutoff:3.500A) Processing helix chain 'D' and resid 718 through 727 Processing helix chain 'D' and resid 783 through 790 Processing helix chain 'D' and resid 796 through 806 Processing helix chain 'D' and resid 808 through 815 removed outlier: 3.579A pdb=" N LEU D 815 " --> pdb=" O ASP D 811 " (cutoff:3.500A) Processing helix chain 'D' and resid 831 through 846 removed outlier: 3.542A pdb=" N GLN D 846 " --> pdb=" O ARG D 842 " (cutoff:3.500A) Processing helix chain 'D' and resid 861 through 872 Processing helix chain 'D' and resid 893 through 897 removed outlier: 3.651A pdb=" N ALA D 897 " --> pdb=" O LEU D 894 " (cutoff:3.500A) Processing helix chain 'D' and resid 914 through 919 Processing helix chain 'D' and resid 997 through 1007 removed outlier: 4.440A pdb=" N CYS D1001 " --> pdb=" O PRO D 997 " (cutoff:3.500A) Processing helix chain 'D' and resid 1009 through 1039 removed outlier: 3.531A pdb=" N LEU D1013 " --> pdb=" O GLY D1009 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N SER D1014 " --> pdb=" O ILE D1010 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N LEU D1015 " --> pdb=" O LEU D1011 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N SER D1019 " --> pdb=" O LEU D1015 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ASP D1031 " --> pdb=" O LEU D1027 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LYS D1036 " --> pdb=" O TYR D1032 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N ASP D1039 " --> pdb=" O ALA D1035 " (cutoff:3.500A) Processing helix chain 'D' and resid 1061 through 1107 removed outlier: 3.540A pdb=" N LEU D1107 " --> pdb=" O ASN D1103 " (cutoff:3.500A) Processing helix chain 'D' and resid 1109 through 1116 Processing helix chain 'D' and resid 1117 through 1127 removed outlier: 3.828A pdb=" N ILE D1121 " --> pdb=" O PRO D1117 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N PHE D1125 " --> pdb=" O ILE D1121 " (cutoff:3.500A) Processing helix chain 'D' and resid 1127 through 1161 Proline residue: D1137 - end of helix Processing helix chain 'D' and resid 1161 through 1210 removed outlier: 4.301A pdb=" N VAL D1166 " --> pdb=" O PRO D1162 " (cutoff:3.500A) Proline residue: D1170 - end of helix removed outlier: 3.539A pdb=" N PHE D1177 " --> pdb=" O VAL D1173 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N TYR D1181 " --> pdb=" O PHE D1177 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N PHE D1182 " --> pdb=" O ILE D1178 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ALA D1185 " --> pdb=" O TYR D1181 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N ASP D1188 " --> pdb=" O VAL D1184 " (cutoff:3.500A) Proline residue: D1199 - end of helix removed outlier: 3.525A pdb=" N GLY D1210 " --> pdb=" O GLU D1206 " (cutoff:3.500A) Processing helix chain 'D' and resid 1210 through 1218 Processing helix chain 'D' and resid 1219 through 1271 removed outlier: 3.723A pdb=" N ALA D1237 " --> pdb=" O SER D1233 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N THR D1242 " --> pdb=" O SER D1238 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N VAL D1260 " --> pdb=" O GLY D1256 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N SER D1269 " --> pdb=" O ALA D1265 " (cutoff:3.500A) Processing helix chain 'D' and resid 1278 through 1289 removed outlier: 4.012A pdb=" N GLY D1282 " --> pdb=" O ALA D1278 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N LEU D1283 " --> pdb=" O GLY D1279 " (cutoff:3.500A) Processing helix chain 'D' and resid 1290 through 1320 removed outlier: 3.638A pdb=" N TYR D1294 " --> pdb=" O MET D1290 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ARG D1314 " --> pdb=" O GLY D1310 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N ILE D1315 " --> pdb=" O ALA D1311 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N HIS D1316 " --> pdb=" O VAL D1312 " (cutoff:3.500A) Processing helix chain 'D' and resid 1384 through 1393 Processing helix chain 'D' and resid 1414 through 1420 Processing helix chain 'D' and resid 1435 through 1441 Processing helix chain 'D' and resid 1447 through 1458 Processing helix chain 'D' and resid 1460 through 1466 Processing helix chain 'D' and resid 1483 through 1499 removed outlier: 3.856A pdb=" N LYS D1499 " --> pdb=" O ALA D1495 " (cutoff:3.500A) Processing helix chain 'D' and resid 1513 through 1528 removed outlier: 4.095A pdb=" N ILE D1519 " --> pdb=" O ALA D1515 " (cutoff:3.500A) Processing helix chain 'D' and resid 1539 through 1546 removed outlier: 3.676A pdb=" N ILE D1543 " --> pdb=" O ARG D1539 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ALA D1546 " --> pdb=" O THR D1542 " (cutoff:3.500A) Processing helix chain 'D' and resid 1562 through 1570 removed outlier: 3.500A pdb=" N LEU D1567 " --> pdb=" O PRO D1563 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N SER D1568 " --> pdb=" O GLU D1564 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N LYS D1570 " --> pdb=" O LEU D1566 " (cutoff:3.500A) Processing helix chain 'E' and resid 53 through 58 Processing helix chain 'E' and resid 58 through 64 removed outlier: 3.631A pdb=" N LEU E 63 " --> pdb=" O VAL E 59 " (cutoff:3.500A) Processing helix chain 'E' and resid 67 through 98 removed outlier: 3.615A pdb=" N GLY E 98 " --> pdb=" O ALA E 94 " (cutoff:3.500A) Processing helix chain 'E' and resid 116 through 129 removed outlier: 3.618A pdb=" N VAL E 129 " --> pdb=" O ILE E 125 " (cutoff:3.500A) Processing helix chain 'E' and resid 142 through 172 removed outlier: 3.622A pdb=" N ILE E 146 " --> pdb=" O CYS E 142 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ILE E 154 " --> pdb=" O ILE E 150 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ILE E 167 " --> pdb=" O MET E 163 " (cutoff:3.500A) Processing helix chain 'E' and resid 174 through 181 removed outlier: 3.901A pdb=" N LEU E 181 " --> pdb=" O ARG E 177 " (cutoff:3.500A) Processing helix chain 'E' and resid 265 through 270 removed outlier: 4.360A pdb=" N ASP E 269 " --> pdb=" O PRO E 266 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU E 270 " --> pdb=" O LEU E 267 " (cutoff:3.500A) Processing helix chain 'E' and resid 345 through 356 Processing helix chain 'F' and resid 25 through 52 Proline residue: F 35 - end of helix removed outlier: 3.941A pdb=" N PHE F 44 " --> pdb=" O LEU F 40 " (cutoff:3.500A) Proline residue: F 45 - end of helix Processing helix chain 'F' and resid 70 through 96 Processing helix chain 'F' and resid 104 through 130 Proline residue: F 109 - end of helix removed outlier: 3.758A pdb=" N MET F 115 " --> pdb=" O GLY F 111 " (cutoff:3.500A) Processing helix chain 'F' and resid 133 through 160 removed outlier: 3.823A pdb=" N ILE F 137 " --> pdb=" O PRO F 133 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N TYR F 142 " --> pdb=" O ALA F 138 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N HIS F 160 " --> pdb=" O LYS F 156 " (cutoff:3.500A) Processing helix chain 'F' and resid 168 through 193 removed outlier: 3.518A pdb=" N ARG F 193 " --> pdb=" O VAL F 189 " (cutoff:3.500A) Processing helix chain 'F' and resid 207 through 212 Processing helix chain 'F' and resid 225 through 230 Processing helix chain 'F' and resid 232 through 243 removed outlier: 4.251A pdb=" N PHE F 236 " --> pdb=" O TRP F 232 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LYS F 242 " --> pdb=" O LYS F 238 " (cutoff:3.500A) Processing helix chain 'F' and resid 258 through 275 removed outlier: 3.616A pdb=" N ASN F 262 " --> pdb=" O ARG F 258 " (cutoff:3.500A) Processing helix chain 'F' and resid 284 through 329 removed outlier: 6.309A pdb=" N ARG F 297 " --> pdb=" O HIS F 293 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N ARG F 298 " --> pdb=" O ALA F 294 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N LEU F 299 " --> pdb=" O PHE F 295 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ILE F 300 " --> pdb=" O GLY F 296 " (cutoff:3.500A) Proline residue: F 317 - end of helix Processing helix chain 'F' and resid 355 through 402 removed outlier: 3.630A pdb=" N MET F 400 " --> pdb=" O TYR F 396 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N HIS F 401 " --> pdb=" O ASN F 397 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU F 402 " --> pdb=" O LYS F 398 " (cutoff:3.500A) Processing helix chain 'F' and resid 412 through 423 Processing helix chain 'F' and resid 423 through 457 Proline residue: F 436 - end of helix removed outlier: 3.536A pdb=" N TRP F 439 " --> pdb=" O CYS F 435 " (cutoff:3.500A) Proline residue: F 442 - end of helix Processing helix chain 'F' and resid 457 through 503 removed outlier: 3.732A pdb=" N LEU F 461 " --> pdb=" O GLY F 457 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE F 462 " --> pdb=" O VAL F 458 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE F 468 " --> pdb=" O ALA F 464 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ALA F 471 " --> pdb=" O ILE F 467 " (cutoff:3.500A) Proline residue: F 472 - end of helix removed outlier: 3.595A pdb=" N GLU F 501 " --> pdb=" O LYS F 497 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N MET F 502 " --> pdb=" O GLN F 498 " (cutoff:3.500A) Processing helix chain 'F' and resid 505 through 512 removed outlier: 4.017A pdb=" N TYR F 512 " --> pdb=" O LEU F 508 " (cutoff:3.500A) Processing helix chain 'F' and resid 514 through 560 removed outlier: 3.655A pdb=" N ARG F 521 " --> pdb=" O ILE F 517 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LYS F 528 " --> pdb=" O VAL F 524 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ALA F 535 " --> pdb=" O THR F 531 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N THR F 548 " --> pdb=" O ILE F 544 " (cutoff:3.500A) Proline residue: F 551 - end of helix removed outlier: 3.554A pdb=" N VAL F 555 " --> pdb=" O PRO F 551 " (cutoff:3.500A) Processing helix chain 'F' and resid 572 through 615 removed outlier: 3.531A pdb=" N ALA F 576 " --> pdb=" O SER F 572 " (cutoff:3.500A) Proline residue: F 589 - end of helix removed outlier: 4.446A pdb=" N LEU F 592 " --> pdb=" O THR F 588 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU F 593 " --> pdb=" O PRO F 589 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N SER F 594 " --> pdb=" O LEU F 590 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N SER F 595 " --> pdb=" O PHE F 591 " (cutoff:3.500A) Processing helix chain 'F' and resid 718 through 727 Processing helix chain 'F' and resid 783 through 790 Processing helix chain 'F' and resid 796 through 806 Processing helix chain 'F' and resid 808 through 815 removed outlier: 3.578A pdb=" N LEU F 815 " --> pdb=" O ASP F 811 " (cutoff:3.500A) Processing helix chain 'F' and resid 831 through 846 removed outlier: 3.542A pdb=" N GLN F 846 " --> pdb=" O ARG F 842 " (cutoff:3.500A) Processing helix chain 'F' and resid 861 through 872 Processing helix chain 'F' and resid 893 through 897 removed outlier: 3.652A pdb=" N ALA F 897 " --> pdb=" O LEU F 894 " (cutoff:3.500A) Processing helix chain 'F' and resid 914 through 919 Processing helix chain 'F' and resid 997 through 1007 removed outlier: 4.440A pdb=" N CYS F1001 " --> pdb=" O PRO F 997 " (cutoff:3.500A) Processing helix chain 'F' and resid 1009 through 1039 removed outlier: 3.531A pdb=" N LEU F1013 " --> pdb=" O GLY F1009 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N SER F1014 " --> pdb=" O ILE F1010 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N LEU F1015 " --> pdb=" O LEU F1011 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N SER F1019 " --> pdb=" O LEU F1015 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ASP F1031 " --> pdb=" O LEU F1027 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LYS F1036 " --> pdb=" O TYR F1032 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N ASP F1039 " --> pdb=" O ALA F1035 " (cutoff:3.500A) Processing helix chain 'F' and resid 1061 through 1107 removed outlier: 3.540A pdb=" N LEU F1107 " --> pdb=" O ASN F1103 " (cutoff:3.500A) Processing helix chain 'F' and resid 1109 through 1116 Processing helix chain 'F' and resid 1117 through 1127 removed outlier: 3.828A pdb=" N ILE F1121 " --> pdb=" O PRO F1117 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N PHE F1125 " --> pdb=" O ILE F1121 " (cutoff:3.500A) Processing helix chain 'F' and resid 1127 through 1161 Proline residue: F1137 - end of helix Processing helix chain 'F' and resid 1161 through 1210 removed outlier: 4.301A pdb=" N VAL F1166 " --> pdb=" O PRO F1162 " (cutoff:3.500A) Proline residue: F1170 - end of helix removed outlier: 3.539A pdb=" N PHE F1177 " --> pdb=" O VAL F1173 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N TYR F1181 " --> pdb=" O PHE F1177 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N PHE F1182 " --> pdb=" O ILE F1178 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ALA F1185 " --> pdb=" O TYR F1181 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N ASP F1188 " --> pdb=" O VAL F1184 " (cutoff:3.500A) Proline residue: F1199 - end of helix removed outlier: 3.526A pdb=" N GLY F1210 " --> pdb=" O GLU F1206 " (cutoff:3.500A) Processing helix chain 'F' and resid 1210 through 1218 Processing helix chain 'F' and resid 1219 through 1271 removed outlier: 3.724A pdb=" N ALA F1237 " --> pdb=" O SER F1233 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N THR F1242 " --> pdb=" O SER F1238 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N VAL F1260 " --> pdb=" O GLY F1256 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N SER F1269 " --> pdb=" O ALA F1265 " (cutoff:3.500A) Processing helix chain 'F' and resid 1278 through 1289 removed outlier: 4.011A pdb=" N GLY F1282 " --> pdb=" O ALA F1278 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N LEU F1283 " --> pdb=" O GLY F1279 " (cutoff:3.500A) Processing helix chain 'F' and resid 1290 through 1320 removed outlier: 3.638A pdb=" N TYR F1294 " --> pdb=" O MET F1290 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N ARG F1314 " --> pdb=" O GLY F1310 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N ILE F1315 " --> pdb=" O ALA F1311 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N HIS F1316 " --> pdb=" O VAL F1312 " (cutoff:3.500A) Processing helix chain 'F' and resid 1384 through 1393 Processing helix chain 'F' and resid 1414 through 1420 Processing helix chain 'F' and resid 1435 through 1441 Processing helix chain 'F' and resid 1447 through 1458 Processing helix chain 'F' and resid 1460 through 1466 Processing helix chain 'F' and resid 1483 through 1499 removed outlier: 3.857A pdb=" N LYS F1499 " --> pdb=" O ALA F1495 " (cutoff:3.500A) Processing helix chain 'F' and resid 1513 through 1528 removed outlier: 4.096A pdb=" N ILE F1519 " --> pdb=" O ALA F1515 " (cutoff:3.500A) Processing helix chain 'F' and resid 1539 through 1546 removed outlier: 3.675A pdb=" N ILE F1543 " --> pdb=" O ARG F1539 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA F1546 " --> pdb=" O THR F1542 " (cutoff:3.500A) Processing helix chain 'F' and resid 1562 through 1570 removed outlier: 3.500A pdb=" N LEU F1567 " --> pdb=" O PRO F1563 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N SER F1568 " --> pdb=" O GLU F1564 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N LYS F1570 " --> pdb=" O LEU F1566 " (cutoff:3.500A) Processing helix chain 'G' and resid 53 through 58 Processing helix chain 'G' and resid 58 through 64 removed outlier: 3.632A pdb=" N LEU G 63 " --> pdb=" O VAL G 59 " (cutoff:3.500A) Processing helix chain 'G' and resid 67 through 98 removed outlier: 3.614A pdb=" N GLY G 98 " --> pdb=" O ALA G 94 " (cutoff:3.500A) Processing helix chain 'G' and resid 116 through 129 removed outlier: 3.618A pdb=" N VAL G 129 " --> pdb=" O ILE G 125 " (cutoff:3.500A) Processing helix chain 'G' and resid 142 through 172 removed outlier: 3.622A pdb=" N ILE G 146 " --> pdb=" O CYS G 142 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N ILE G 154 " --> pdb=" O ILE G 150 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ILE G 167 " --> pdb=" O MET G 163 " (cutoff:3.500A) Processing helix chain 'G' and resid 174 through 181 removed outlier: 3.901A pdb=" N LEU G 181 " --> pdb=" O ARG G 177 " (cutoff:3.500A) Processing helix chain 'G' and resid 265 through 270 removed outlier: 4.360A pdb=" N ASP G 269 " --> pdb=" O PRO G 266 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU G 270 " --> pdb=" O LEU G 267 " (cutoff:3.500A) Processing helix chain 'G' and resid 345 through 356 Processing helix chain 'H' and resid 25 through 52 Proline residue: H 35 - end of helix removed outlier: 3.941A pdb=" N PHE H 44 " --> pdb=" O LEU H 40 " (cutoff:3.500A) Proline residue: H 45 - end of helix Processing helix chain 'H' and resid 70 through 96 Processing helix chain 'H' and resid 104 through 130 Proline residue: H 109 - end of helix removed outlier: 3.757A pdb=" N MET H 115 " --> pdb=" O GLY H 111 " (cutoff:3.500A) Processing helix chain 'H' and resid 133 through 160 removed outlier: 3.823A pdb=" N ILE H 137 " --> pdb=" O PRO H 133 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N TYR H 142 " --> pdb=" O ALA H 138 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N HIS H 160 " --> pdb=" O LYS H 156 " (cutoff:3.500A) Processing helix chain 'H' and resid 168 through 193 removed outlier: 3.518A pdb=" N ARG H 193 " --> pdb=" O VAL H 189 " (cutoff:3.500A) Processing helix chain 'H' and resid 207 through 212 Processing helix chain 'H' and resid 225 through 230 Processing helix chain 'H' and resid 232 through 243 removed outlier: 4.250A pdb=" N PHE H 236 " --> pdb=" O TRP H 232 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LYS H 242 " --> pdb=" O LYS H 238 " (cutoff:3.500A) Processing helix chain 'H' and resid 258 through 275 removed outlier: 3.616A pdb=" N ASN H 262 " --> pdb=" O ARG H 258 " (cutoff:3.500A) Processing helix chain 'H' and resid 284 through 329 removed outlier: 6.308A pdb=" N ARG H 297 " --> pdb=" O HIS H 293 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N ARG H 298 " --> pdb=" O ALA H 294 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N LEU H 299 " --> pdb=" O PHE H 295 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ILE H 300 " --> pdb=" O GLY H 296 " (cutoff:3.500A) Proline residue: H 317 - end of helix Processing helix chain 'H' and resid 355 through 402 removed outlier: 3.630A pdb=" N MET H 400 " --> pdb=" O TYR H 396 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N HIS H 401 " --> pdb=" O ASN H 397 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU H 402 " --> pdb=" O LYS H 398 " (cutoff:3.500A) Processing helix chain 'H' and resid 412 through 423 Processing helix chain 'H' and resid 423 through 457 Proline residue: H 436 - end of helix removed outlier: 3.536A pdb=" N TRP H 439 " --> pdb=" O CYS H 435 " (cutoff:3.500A) Proline residue: H 442 - end of helix Processing helix chain 'H' and resid 457 through 503 removed outlier: 3.732A pdb=" N LEU H 461 " --> pdb=" O GLY H 457 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE H 462 " --> pdb=" O VAL H 458 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE H 468 " --> pdb=" O ALA H 464 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ALA H 471 " --> pdb=" O ILE H 467 " (cutoff:3.500A) Proline residue: H 472 - end of helix removed outlier: 3.595A pdb=" N GLU H 501 " --> pdb=" O LYS H 497 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N MET H 502 " --> pdb=" O GLN H 498 " (cutoff:3.500A) Processing helix chain 'H' and resid 505 through 512 removed outlier: 4.018A pdb=" N TYR H 512 " --> pdb=" O LEU H 508 " (cutoff:3.500A) Processing helix chain 'H' and resid 514 through 560 removed outlier: 3.654A pdb=" N ARG H 521 " --> pdb=" O ILE H 517 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LYS H 528 " --> pdb=" O VAL H 524 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ALA H 535 " --> pdb=" O THR H 531 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N THR H 548 " --> pdb=" O ILE H 544 " (cutoff:3.500A) Proline residue: H 551 - end of helix removed outlier: 3.553A pdb=" N VAL H 555 " --> pdb=" O PRO H 551 " (cutoff:3.500A) Processing helix chain 'H' and resid 572 through 615 removed outlier: 3.531A pdb=" N ALA H 576 " --> pdb=" O SER H 572 " (cutoff:3.500A) Proline residue: H 589 - end of helix removed outlier: 4.446A pdb=" N LEU H 592 " --> pdb=" O THR H 588 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU H 593 " --> pdb=" O PRO H 589 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N SER H 594 " --> pdb=" O LEU H 590 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N SER H 595 " --> pdb=" O PHE H 591 " (cutoff:3.500A) Processing helix chain 'H' and resid 718 through 727 Processing helix chain 'H' and resid 783 through 790 Processing helix chain 'H' and resid 796 through 806 Processing helix chain 'H' and resid 808 through 815 removed outlier: 3.579A pdb=" N LEU H 815 " --> pdb=" O ASP H 811 " (cutoff:3.500A) Processing helix chain 'H' and resid 831 through 846 removed outlier: 3.542A pdb=" N GLN H 846 " --> pdb=" O ARG H 842 " (cutoff:3.500A) Processing helix chain 'H' and resid 861 through 872 Processing helix chain 'H' and resid 893 through 897 removed outlier: 3.651A pdb=" N ALA H 897 " --> pdb=" O LEU H 894 " (cutoff:3.500A) Processing helix chain 'H' and resid 914 through 919 Processing helix chain 'H' and resid 997 through 1007 removed outlier: 4.440A pdb=" N CYS H1001 " --> pdb=" O PRO H 997 " (cutoff:3.500A) Processing helix chain 'H' and resid 1009 through 1039 removed outlier: 3.532A pdb=" N LEU H1013 " --> pdb=" O GLY H1009 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N SER H1014 " --> pdb=" O ILE H1010 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N LEU H1015 " --> pdb=" O LEU H1011 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N SER H1019 " --> pdb=" O LEU H1015 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ASP H1031 " --> pdb=" O LEU H1027 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LYS H1036 " --> pdb=" O TYR H1032 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N ASP H1039 " --> pdb=" O ALA H1035 " (cutoff:3.500A) Processing helix chain 'H' and resid 1061 through 1107 removed outlier: 3.540A pdb=" N LEU H1107 " --> pdb=" O ASN H1103 " (cutoff:3.500A) Processing helix chain 'H' and resid 1109 through 1116 Processing helix chain 'H' and resid 1117 through 1127 removed outlier: 3.828A pdb=" N ILE H1121 " --> pdb=" O PRO H1117 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N PHE H1125 " --> pdb=" O ILE H1121 " (cutoff:3.500A) Processing helix chain 'H' and resid 1127 through 1161 Proline residue: H1137 - end of helix Processing helix chain 'H' and resid 1161 through 1210 removed outlier: 4.301A pdb=" N VAL H1166 " --> pdb=" O PRO H1162 " (cutoff:3.500A) Proline residue: H1170 - end of helix removed outlier: 3.539A pdb=" N PHE H1177 " --> pdb=" O VAL H1173 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N TYR H1181 " --> pdb=" O PHE H1177 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N PHE H1182 " --> pdb=" O ILE H1178 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ALA H1185 " --> pdb=" O TYR H1181 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N ASP H1188 " --> pdb=" O VAL H1184 " (cutoff:3.500A) Proline residue: H1199 - end of helix removed outlier: 3.525A pdb=" N GLY H1210 " --> pdb=" O GLU H1206 " (cutoff:3.500A) Processing helix chain 'H' and resid 1210 through 1218 Processing helix chain 'H' and resid 1219 through 1271 removed outlier: 3.723A pdb=" N ALA H1237 " --> pdb=" O SER H1233 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N THR H1242 " --> pdb=" O SER H1238 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N VAL H1260 " --> pdb=" O GLY H1256 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N SER H1269 " --> pdb=" O ALA H1265 " (cutoff:3.500A) Processing helix chain 'H' and resid 1278 through 1289 removed outlier: 4.012A pdb=" N GLY H1282 " --> pdb=" O ALA H1278 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N LEU H1283 " --> pdb=" O GLY H1279 " (cutoff:3.500A) Processing helix chain 'H' and resid 1290 through 1320 removed outlier: 3.638A pdb=" N TYR H1294 " --> pdb=" O MET H1290 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N ARG H1314 " --> pdb=" O GLY H1310 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N ILE H1315 " --> pdb=" O ALA H1311 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N HIS H1316 " --> pdb=" O VAL H1312 " (cutoff:3.500A) Processing helix chain 'H' and resid 1384 through 1393 Processing helix chain 'H' and resid 1414 through 1420 Processing helix chain 'H' and resid 1435 through 1441 Processing helix chain 'H' and resid 1447 through 1458 Processing helix chain 'H' and resid 1460 through 1466 Processing helix chain 'H' and resid 1483 through 1499 removed outlier: 3.856A pdb=" N LYS H1499 " --> pdb=" O ALA H1495 " (cutoff:3.500A) Processing helix chain 'H' and resid 1513 through 1528 removed outlier: 4.096A pdb=" N ILE H1519 " --> pdb=" O ALA H1515 " (cutoff:3.500A) Processing helix chain 'H' and resid 1539 through 1546 removed outlier: 3.675A pdb=" N ILE H1543 " --> pdb=" O ARG H1539 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ALA H1546 " --> pdb=" O THR H1542 " (cutoff:3.500A) Processing helix chain 'H' and resid 1562 through 1570 removed outlier: 4.307A pdb=" N SER H1568 " --> pdb=" O GLU H1564 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N LYS H1570 " --> pdb=" O LEU H1566 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 45 through 47 removed outlier: 3.727A pdb=" N VAL C 328 " --> pdb=" O ALA A 45 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 188 through 192 removed outlier: 3.781A pdb=" N HIS A 259 " --> pdb=" O PHE A 198 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU A 200 " --> pdb=" O ILE A 257 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 236 through 238 removed outlier: 4.391A pdb=" N MET A 217 " --> pdb=" O ILE A 238 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ALA A 213 " --> pdb=" O GLU A 288 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N GLU A 288 " --> pdb=" O ALA A 213 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N ILE A 215 " --> pdb=" O ILE A 286 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ILE A 286 " --> pdb=" O ILE A 215 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N MET A 217 " --> pdb=" O ILE A 284 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ILE A 284 " --> pdb=" O MET A 217 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N VAL A 219 " --> pdb=" O GLU A 282 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N GLU A 282 " --> pdb=" O VAL A 219 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 223 through 224 Processing sheet with id=AA5, first strand: chain 'A' and resid 313 through 315 Processing sheet with id=AA6, first strand: chain 'A' and resid 320 through 321 removed outlier: 6.012A pdb=" N TYR A 326 " --> pdb=" O ALA G 45 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N LYS G 47 " --> pdb=" O TYR A 326 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N VAL A 328 " --> pdb=" O LYS G 47 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 701 through 703 Processing sheet with id=AA8, first strand: chain 'B' and resid 685 through 686 Processing sheet with id=AA9, first strand: chain 'B' and resid 771 through 773 removed outlier: 6.710A pdb=" N ALA B 771 " --> pdb=" O PHE B 852 " (cutoff:3.500A) removed outlier: 8.227A pdb=" N ASP B 854 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N ALA B 773 " --> pdb=" O ASP B 854 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N VAL B 851 " --> pdb=" O VAL B 885 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N VAL B 887 " --> pdb=" O VAL B 851 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N LEU B 853 " --> pdb=" O VAL B 887 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N ILE B 900 " --> pdb=" O GLU B 911 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N GLU B 911 " --> pdb=" O ILE B 900 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N ALA B 902 " --> pdb=" O GLN B 909 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 1365 through 1369 removed outlier: 7.090A pdb=" N ALA B1367 " --> pdb=" O GLN B1348 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N GLN B1348 " --> pdb=" O ALA B1367 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N ILE B1369 " --> pdb=" O GLN B1346 " (cutoff:3.500A) removed outlier: 5.529A pdb=" N GLN B1346 " --> pdb=" O ILE B1369 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N ILE B1347 " --> pdb=" O ILE B1404 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N ILE B1404 " --> pdb=" O ILE B1347 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N ASN B1349 " --> pdb=" O ARG B1402 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N ARG B1402 " --> pdb=" O ASN B1349 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N MET B1398 " --> pdb=" O ARG B1353 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 1423 through 1425 removed outlier: 6.594A pdb=" N SER B1423 " --> pdb=" O ILE B1504 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N ASP B1506 " --> pdb=" O SER B1423 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N ILE B1425 " --> pdb=" O ASP B1506 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N PHE B1503 " --> pdb=" O VAL B1534 " (cutoff:3.500A) removed outlier: 8.255A pdb=" N ILE B1536 " --> pdb=" O PHE B1503 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N MET B1505 " --> pdb=" O ILE B1536 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N MET B1550 " --> pdb=" O GLY B1376 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 45 through 47 removed outlier: 3.727A pdb=" N VAL E 328 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 188 through 192 removed outlier: 3.782A pdb=" N HIS C 259 " --> pdb=" O PHE C 198 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU C 200 " --> pdb=" O ILE C 257 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 236 through 238 removed outlier: 4.391A pdb=" N MET C 217 " --> pdb=" O ILE C 238 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ALA C 213 " --> pdb=" O GLU C 288 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N GLU C 288 " --> pdb=" O ALA C 213 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N ILE C 215 " --> pdb=" O ILE C 286 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ILE C 286 " --> pdb=" O ILE C 215 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N MET C 217 " --> pdb=" O ILE C 284 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ILE C 284 " --> pdb=" O MET C 217 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N VAL C 219 " --> pdb=" O GLU C 282 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N GLU C 282 " --> pdb=" O VAL C 219 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 223 through 224 Processing sheet with id=AB7, first strand: chain 'C' and resid 313 through 315 Processing sheet with id=AB8, first strand: chain 'D' and resid 701 through 703 Processing sheet with id=AB9, first strand: chain 'D' and resid 685 through 686 Processing sheet with id=AC1, first strand: chain 'D' and resid 771 through 773 removed outlier: 6.710A pdb=" N ALA D 771 " --> pdb=" O PHE D 852 " (cutoff:3.500A) removed outlier: 8.227A pdb=" N ASP D 854 " --> pdb=" O ALA D 771 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N ALA D 773 " --> pdb=" O ASP D 854 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N VAL D 851 " --> pdb=" O VAL D 885 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N VAL D 887 " --> pdb=" O VAL D 851 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N LEU D 853 " --> pdb=" O VAL D 887 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N ILE D 900 " --> pdb=" O GLU D 911 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N GLU D 911 " --> pdb=" O ILE D 900 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N ALA D 902 " --> pdb=" O GLN D 909 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 1365 through 1369 removed outlier: 7.090A pdb=" N ALA D1367 " --> pdb=" O GLN D1348 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N GLN D1348 " --> pdb=" O ALA D1367 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N ILE D1369 " --> pdb=" O GLN D1346 " (cutoff:3.500A) removed outlier: 5.529A pdb=" N GLN D1346 " --> pdb=" O ILE D1369 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N ILE D1347 " --> pdb=" O ILE D1404 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N ILE D1404 " --> pdb=" O ILE D1347 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N ASN D1349 " --> pdb=" O ARG D1402 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N ARG D1402 " --> pdb=" O ASN D1349 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N MET D1398 " --> pdb=" O ARG D1353 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 1423 through 1425 removed outlier: 6.594A pdb=" N SER D1423 " --> pdb=" O ILE D1504 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N ASP D1506 " --> pdb=" O SER D1423 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N ILE D1425 " --> pdb=" O ASP D1506 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N PHE D1503 " --> pdb=" O VAL D1534 " (cutoff:3.500A) removed outlier: 8.254A pdb=" N ILE D1536 " --> pdb=" O PHE D1503 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N MET D1505 " --> pdb=" O ILE D1536 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N MET D1550 " --> pdb=" O GLY D1376 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 45 through 47 removed outlier: 3.727A pdb=" N VAL G 328 " --> pdb=" O ALA E 45 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 188 through 192 removed outlier: 3.781A pdb=" N HIS E 259 " --> pdb=" O PHE E 198 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU E 200 " --> pdb=" O ILE E 257 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 236 through 238 removed outlier: 4.391A pdb=" N MET E 217 " --> pdb=" O ILE E 238 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ALA E 213 " --> pdb=" O GLU E 288 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N GLU E 288 " --> pdb=" O ALA E 213 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N ILE E 215 " --> pdb=" O ILE E 286 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ILE E 286 " --> pdb=" O ILE E 215 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N MET E 217 " --> pdb=" O ILE E 284 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ILE E 284 " --> pdb=" O MET E 217 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N VAL E 219 " --> pdb=" O GLU E 282 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N GLU E 282 " --> pdb=" O VAL E 219 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 223 through 224 Processing sheet with id=AC8, first strand: chain 'E' and resid 313 through 315 Processing sheet with id=AC9, first strand: chain 'F' and resid 701 through 703 Processing sheet with id=AD1, first strand: chain 'F' and resid 685 through 686 Processing sheet with id=AD2, first strand: chain 'F' and resid 771 through 773 removed outlier: 6.710A pdb=" N ALA F 771 " --> pdb=" O PHE F 852 " (cutoff:3.500A) removed outlier: 8.228A pdb=" N ASP F 854 " --> pdb=" O ALA F 771 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N ALA F 773 " --> pdb=" O ASP F 854 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N VAL F 851 " --> pdb=" O VAL F 885 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N VAL F 887 " --> pdb=" O VAL F 851 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N LEU F 853 " --> pdb=" O VAL F 887 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N ILE F 900 " --> pdb=" O GLU F 911 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N GLU F 911 " --> pdb=" O ILE F 900 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N ALA F 902 " --> pdb=" O GLN F 909 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 1365 through 1369 removed outlier: 7.090A pdb=" N ALA F1367 " --> pdb=" O GLN F1348 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N GLN F1348 " --> pdb=" O ALA F1367 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N ILE F1369 " --> pdb=" O GLN F1346 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N GLN F1346 " --> pdb=" O ILE F1369 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N ILE F1347 " --> pdb=" O ILE F1404 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N ILE F1404 " --> pdb=" O ILE F1347 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N ASN F1349 " --> pdb=" O ARG F1402 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N ARG F1402 " --> pdb=" O ASN F1349 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N MET F1398 " --> pdb=" O ARG F1353 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 1423 through 1425 removed outlier: 6.594A pdb=" N SER F1423 " --> pdb=" O ILE F1504 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N ASP F1506 " --> pdb=" O SER F1423 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N ILE F1425 " --> pdb=" O ASP F1506 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N PHE F1503 " --> pdb=" O VAL F1534 " (cutoff:3.500A) removed outlier: 8.255A pdb=" N ILE F1536 " --> pdb=" O PHE F1503 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N MET F1505 " --> pdb=" O ILE F1536 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N MET F1550 " --> pdb=" O GLY F1376 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'G' and resid 188 through 192 removed outlier: 3.781A pdb=" N HIS G 259 " --> pdb=" O PHE G 198 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU G 200 " --> pdb=" O ILE G 257 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'G' and resid 236 through 238 removed outlier: 4.391A pdb=" N MET G 217 " --> pdb=" O ILE G 238 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ALA G 213 " --> pdb=" O GLU G 288 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N GLU G 288 " --> pdb=" O ALA G 213 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N ILE G 215 " --> pdb=" O ILE G 286 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N ILE G 286 " --> pdb=" O ILE G 215 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N MET G 217 " --> pdb=" O ILE G 284 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ILE G 284 " --> pdb=" O MET G 217 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N VAL G 219 " --> pdb=" O GLU G 282 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N GLU G 282 " --> pdb=" O VAL G 219 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'G' and resid 223 through 224 Processing sheet with id=AD8, first strand: chain 'G' and resid 313 through 315 Processing sheet with id=AD9, first strand: chain 'H' and resid 701 through 703 Processing sheet with id=AE1, first strand: chain 'H' and resid 685 through 686 Processing sheet with id=AE2, first strand: chain 'H' and resid 771 through 773 removed outlier: 6.710A pdb=" N ALA H 771 " --> pdb=" O PHE H 852 " (cutoff:3.500A) removed outlier: 8.226A pdb=" N ASP H 854 " --> pdb=" O ALA H 771 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N ALA H 773 " --> pdb=" O ASP H 854 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N VAL H 851 " --> pdb=" O VAL H 885 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N VAL H 887 " --> pdb=" O VAL H 851 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N LEU H 853 " --> pdb=" O VAL H 887 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N ILE H 900 " --> pdb=" O GLU H 911 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N GLU H 911 " --> pdb=" O ILE H 900 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N ALA H 902 " --> pdb=" O GLN H 909 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'H' and resid 1365 through 1369 removed outlier: 7.091A pdb=" N ALA H1367 " --> pdb=" O GLN H1348 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N GLN H1348 " --> pdb=" O ALA H1367 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N ILE H1369 " --> pdb=" O GLN H1346 " (cutoff:3.500A) removed outlier: 5.529A pdb=" N GLN H1346 " --> pdb=" O ILE H1369 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N ILE H1347 " --> pdb=" O ILE H1404 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N ILE H1404 " --> pdb=" O ILE H1347 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N ASN H1349 " --> pdb=" O ARG H1402 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N ARG H1402 " --> pdb=" O ASN H1349 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N MET H1398 " --> pdb=" O ARG H1353 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'H' and resid 1423 through 1425 removed outlier: 6.594A pdb=" N SER H1423 " --> pdb=" O ILE H1504 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N ASP H1506 " --> pdb=" O SER H1423 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N ILE H1425 " --> pdb=" O ASP H1506 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N PHE H1503 " --> pdb=" O VAL H1534 " (cutoff:3.500A) removed outlier: 8.254A pdb=" N ILE H1536 " --> pdb=" O PHE H1503 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N MET H1505 " --> pdb=" O ILE H1536 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N MET H1550 " --> pdb=" O GLY H1376 " (cutoff:3.500A) 3132 hydrogen bonds defined for protein. 9195 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 23.49 Time building geometry restraints manager: 14.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.39: 20094 1.39 - 1.58: 31022 1.58 - 1.76: 32 1.76 - 1.94: 420 1.94 - 2.12: 8 Bond restraints: 51576 Sorted by residual: bond pdb=" PG AGS A 401 " pdb=" S1G AGS A 401 " ideal model delta sigma weight residual 1.949 2.122 -0.173 2.00e-02 2.50e+03 7.49e+01 bond pdb=" PG AGS G 401 " pdb=" S1G AGS G 401 " ideal model delta sigma weight residual 1.949 2.122 -0.173 2.00e-02 2.50e+03 7.49e+01 bond pdb=" PG AGS E 401 " pdb=" S1G AGS E 401 " ideal model delta sigma weight residual 1.949 2.122 -0.173 2.00e-02 2.50e+03 7.49e+01 bond pdb=" PG AGS C 401 " pdb=" S1G AGS C 401 " ideal model delta sigma weight residual 1.949 2.122 -0.173 2.00e-02 2.50e+03 7.49e+01 bond pdb=" C4 AGS F2501 " pdb=" C5 AGS F2501 " ideal model delta sigma weight residual 1.386 1.471 -0.085 1.00e-02 1.00e+04 7.26e+01 ... (remaining 51571 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.31: 68512 2.31 - 4.62: 1365 4.62 - 6.92: 215 6.92 - 9.23: 52 9.23 - 11.54: 28 Bond angle restraints: 70172 Sorted by residual: angle pdb=" C5 AGS F2501 " pdb=" C4 AGS F2501 " pdb=" N3 AGS F2501 " ideal model delta sigma weight residual 126.80 118.60 8.20 7.41e-01 1.82e+00 1.23e+02 angle pdb=" C5 AGS D2501 " pdb=" C4 AGS D2501 " pdb=" N3 AGS D2501 " ideal model delta sigma weight residual 126.80 118.60 8.20 7.41e-01 1.82e+00 1.22e+02 angle pdb=" C5 AGS B2501 " pdb=" C4 AGS B2501 " pdb=" N3 AGS B2501 " ideal model delta sigma weight residual 126.80 118.60 8.20 7.41e-01 1.82e+00 1.22e+02 angle pdb=" C5 AGS H2501 " pdb=" C4 AGS H2501 " pdb=" N3 AGS H2501 " ideal model delta sigma weight residual 126.80 118.61 8.19 7.41e-01 1.82e+00 1.22e+02 angle pdb=" C5 AGS G 401 " pdb=" C4 AGS G 401 " pdb=" N3 AGS G 401 " ideal model delta sigma weight residual 126.80 119.10 7.70 7.41e-01 1.82e+00 1.08e+02 ... (remaining 70167 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.24: 29654 31.24 - 62.49: 918 62.49 - 93.73: 12 93.73 - 124.97: 8 124.97 - 156.22: 4 Dihedral angle restraints: 30596 sinusoidal: 11668 harmonic: 18928 Sorted by residual: dihedral pdb=" CA ASP B 212 " pdb=" C ASP B 212 " pdb=" N LEU B 213 " pdb=" CA LEU B 213 " ideal model delta harmonic sigma weight residual -180.00 -153.56 -26.44 0 5.00e+00 4.00e-02 2.80e+01 dihedral pdb=" CA ASP H 212 " pdb=" C ASP H 212 " pdb=" N LEU H 213 " pdb=" CA LEU H 213 " ideal model delta harmonic sigma weight residual -180.00 -153.60 -26.40 0 5.00e+00 4.00e-02 2.79e+01 dihedral pdb=" CA ASP D 212 " pdb=" C ASP D 212 " pdb=" N LEU D 213 " pdb=" CA LEU D 213 " ideal model delta harmonic sigma weight residual -180.00 -153.61 -26.39 0 5.00e+00 4.00e-02 2.79e+01 ... (remaining 30593 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.158: 8424 0.158 - 0.316: 72 0.316 - 0.474: 16 0.474 - 0.632: 0 0.632 - 0.790: 4 Chirality restraints: 8516 Sorted by residual: chirality pdb=" PB AGS A 401 " pdb=" O2B AGS A 401 " pdb=" O3A AGS A 401 " pdb=" O3B AGS A 401 " both_signs ideal model delta sigma weight residual True 3.18 -2.39 0.79 2.00e-01 2.50e+01 1.56e+01 chirality pdb=" PB AGS C 401 " pdb=" O2B AGS C 401 " pdb=" O3A AGS C 401 " pdb=" O3B AGS C 401 " both_signs ideal model delta sigma weight residual True 3.18 -2.39 0.79 2.00e-01 2.50e+01 1.56e+01 chirality pdb=" PB AGS G 401 " pdb=" O2B AGS G 401 " pdb=" O3A AGS G 401 " pdb=" O3B AGS G 401 " both_signs ideal model delta sigma weight residual True 3.18 -2.39 0.79 2.00e-01 2.50e+01 1.55e+01 ... (remaining 8513 not shown) Planarity restraints: 8588 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA HIS F1273 " 0.020 2.00e-02 2.50e+03 4.08e-02 1.67e+01 pdb=" C HIS F1273 " -0.071 2.00e-02 2.50e+03 pdb=" O HIS F1273 " 0.027 2.00e-02 2.50e+03 pdb=" N ARG F1274 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS D1273 " 0.020 2.00e-02 2.50e+03 4.06e-02 1.65e+01 pdb=" C HIS D1273 " -0.070 2.00e-02 2.50e+03 pdb=" O HIS D1273 " 0.026 2.00e-02 2.50e+03 pdb=" N ARG D1274 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS H1273 " -0.020 2.00e-02 2.50e+03 4.05e-02 1.64e+01 pdb=" C HIS H1273 " 0.070 2.00e-02 2.50e+03 pdb=" O HIS H1273 " -0.026 2.00e-02 2.50e+03 pdb=" N ARG H1274 " -0.023 2.00e-02 2.50e+03 ... (remaining 8585 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 468 2.60 - 3.18: 45550 3.18 - 3.75: 79780 3.75 - 4.33: 102235 4.33 - 4.90: 167732 Nonbonded interactions: 395765 Sorted by model distance: nonbonded pdb=" O ILE B 196 " pdb=" O PHE B 197 " model vdw 2.030 3.040 nonbonded pdb=" O ILE D 196 " pdb=" O PHE D 197 " model vdw 2.030 3.040 nonbonded pdb=" O ILE F 196 " pdb=" O PHE F 197 " model vdw 2.030 3.040 nonbonded pdb=" O ILE H 196 " pdb=" O PHE H 197 " model vdw 2.030 3.040 nonbonded pdb=" CD1 LEU C 200 " pdb=" N ARG C 201 " model vdw 2.049 3.540 ... (remaining 395760 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'G' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.070 Extract box with map and model: 2.010 Check model and map are aligned: 0.390 Set scattering table: 0.450 Process input model: 107.930 Find NCS groups from input model: 2.060 Set up NCS constraints: 0.240 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 116.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7136 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.173 51576 Z= 0.350 Angle : 0.804 11.538 70172 Z= 0.504 Chirality : 0.052 0.790 8516 Planarity : 0.005 0.074 8588 Dihedral : 13.785 156.217 18272 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 19.10 Ramachandran Plot: Outliers : 0.44 % Allowed : 4.43 % Favored : 95.13 % Rotamer: Outliers : 8.11 % Allowed : 9.38 % Favored : 82.51 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.46 (0.09), residues: 6408 helix: -1.03 (0.07), residues: 3948 sheet: -1.58 (0.20), residues: 536 loop : -2.64 (0.12), residues: 1924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D1339 HIS 0.012 0.001 HIS C 175 PHE 0.035 0.002 PHE G 168 TYR 0.015 0.002 TYR B 378 ARG 0.003 0.000 ARG D 193 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12816 Ramachandran restraints generated. 6408 Oldfield, 0 Emsley, 6408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12816 Ramachandran restraints generated. 6408 Oldfield, 0 Emsley, 6408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1576 residues out of total 5672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 436 poor density : 1140 time to evaluate : 5.825 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 MET cc_start: 0.8703 (mmt) cc_final: 0.8378 (tpt) REVERT: A 78 SER cc_start: 0.9341 (OUTLIER) cc_final: 0.8778 (p) REVERT: A 81 CYS cc_start: 0.7980 (OUTLIER) cc_final: 0.7697 (p) REVERT: A 88 MET cc_start: 0.9003 (OUTLIER) cc_final: 0.8642 (tmm) REVERT: A 92 LEU cc_start: 0.9626 (OUTLIER) cc_final: 0.9405 (tt) REVERT: A 95 PHE cc_start: 0.8860 (t80) cc_final: 0.8646 (t80) REVERT: A 163 MET cc_start: 0.7818 (ttp) cc_final: 0.7241 (ttt) REVERT: A 182 ILE cc_start: 0.7892 (OUTLIER) cc_final: 0.7684 (pt) REVERT: A 204 ASP cc_start: 0.7999 (OUTLIER) cc_final: 0.7771 (t0) REVERT: A 238 ILE cc_start: 0.7860 (OUTLIER) cc_final: 0.6990 (tt) REVERT: A 286 ILE cc_start: 0.4594 (OUTLIER) cc_final: 0.3925 (tt) REVERT: A 293 THR cc_start: 0.5405 (OUTLIER) cc_final: 0.5182 (t) REVERT: A 332 LYS cc_start: 0.8171 (mtmt) cc_final: 0.7529 (mtmm) REVERT: B 89 ILE cc_start: 0.9164 (mt) cc_final: 0.8844 (mm) REVERT: B 91 GLU cc_start: 0.8449 (mt-10) cc_final: 0.8175 (tm-30) REVERT: B 135 LEU cc_start: 0.8255 (mt) cc_final: 0.7834 (mt) REVERT: B 175 LEU cc_start: 0.9072 (mt) cc_final: 0.8698 (tt) REVERT: B 233 MET cc_start: 0.9398 (mmm) cc_final: 0.8902 (mmm) REVERT: B 253 LEU cc_start: 0.9129 (OUTLIER) cc_final: 0.8872 (mt) REVERT: B 319 CYS cc_start: 0.9056 (m) cc_final: 0.8748 (p) REVERT: B 327 LEU cc_start: 0.8649 (OUTLIER) cc_final: 0.8403 (tt) REVERT: B 432 PHE cc_start: 0.9358 (OUTLIER) cc_final: 0.9116 (t80) REVERT: B 710 MET cc_start: 0.6727 (mmt) cc_final: 0.6047 (tpp) REVERT: B 727 LEU cc_start: 0.7894 (tp) cc_final: 0.7488 (mt) REVERT: B 1020 GLN cc_start: 0.8691 (mm-40) cc_final: 0.8370 (mp10) REVERT: B 1031 ASP cc_start: 0.8228 (m-30) cc_final: 0.7388 (t0) REVERT: B 1246 ARG cc_start: 0.9134 (OUTLIER) cc_final: 0.8401 (mmp80) REVERT: B 1251 ARG cc_start: 0.9221 (OUTLIER) cc_final: 0.8492 (mmt180) REVERT: B 1252 MET cc_start: 0.8900 (ttm) cc_final: 0.8476 (tpp) REVERT: B 1432 PHE cc_start: 0.2989 (OUTLIER) cc_final: 0.2234 (p90) REVERT: B 1536 ILE cc_start: 0.0379 (OUTLIER) cc_final: -0.0020 (pt) REVERT: B 1561 ASP cc_start: 0.6779 (OUTLIER) cc_final: 0.6337 (t0) REVERT: B 1566 LEU cc_start: 0.1664 (OUTLIER) cc_final: 0.1152 (pt) REVERT: C 74 ILE cc_start: 0.9432 (tt) cc_final: 0.9227 (tt) REVERT: C 77 MET cc_start: 0.8697 (mmt) cc_final: 0.8377 (tpt) REVERT: C 78 SER cc_start: 0.9349 (OUTLIER) cc_final: 0.8789 (p) REVERT: C 81 CYS cc_start: 0.7982 (OUTLIER) cc_final: 0.7678 (p) REVERT: C 88 MET cc_start: 0.9005 (OUTLIER) cc_final: 0.8647 (tmm) REVERT: C 92 LEU cc_start: 0.9629 (OUTLIER) cc_final: 0.9409 (tt) REVERT: C 95 PHE cc_start: 0.8870 (t80) cc_final: 0.8659 (t80) REVERT: C 122 LEU cc_start: 0.9255 (OUTLIER) cc_final: 0.9032 (tt) REVERT: C 163 MET cc_start: 0.7894 (ttp) cc_final: 0.7240 (ttt) REVERT: C 182 ILE cc_start: 0.7893 (OUTLIER) cc_final: 0.7690 (pt) REVERT: C 204 ASP cc_start: 0.7975 (OUTLIER) cc_final: 0.7733 (t0) REVERT: C 238 ILE cc_start: 0.7847 (OUTLIER) cc_final: 0.6978 (tt) REVERT: C 286 ILE cc_start: 0.4390 (OUTLIER) cc_final: 0.3740 (tt) REVERT: C 293 THR cc_start: 0.5385 (OUTLIER) cc_final: 0.5156 (t) REVERT: C 332 LYS cc_start: 0.8221 (mtmt) cc_final: 0.7599 (mtmm) REVERT: D 89 ILE cc_start: 0.9121 (mt) cc_final: 0.8785 (mm) REVERT: D 91 GLU cc_start: 0.8440 (mt-10) cc_final: 0.8189 (tm-30) REVERT: D 126 ASN cc_start: 0.8361 (m-40) cc_final: 0.7919 (t0) REVERT: D 135 LEU cc_start: 0.8266 (mt) cc_final: 0.7785 (mt) REVERT: D 175 LEU cc_start: 0.9070 (mt) cc_final: 0.8700 (tt) REVERT: D 233 MET cc_start: 0.9401 (mmm) cc_final: 0.8909 (mmm) REVERT: D 253 LEU cc_start: 0.9142 (OUTLIER) cc_final: 0.8871 (mt) REVERT: D 319 CYS cc_start: 0.9067 (m) cc_final: 0.8750 (p) REVERT: D 327 LEU cc_start: 0.8654 (OUTLIER) cc_final: 0.8413 (tt) REVERT: D 432 PHE cc_start: 0.9360 (OUTLIER) cc_final: 0.9105 (t80) REVERT: D 710 MET cc_start: 0.6732 (mmt) cc_final: 0.6053 (tpp) REVERT: D 727 LEU cc_start: 0.7903 (tp) cc_final: 0.7495 (mt) REVERT: D 1020 GLN cc_start: 0.8687 (mm-40) cc_final: 0.8366 (mp10) REVERT: D 1031 ASP cc_start: 0.8146 (m-30) cc_final: 0.7259 (t0) REVERT: D 1165 LEU cc_start: 0.8538 (tt) cc_final: 0.8297 (tt) REVERT: D 1246 ARG cc_start: 0.9168 (OUTLIER) cc_final: 0.8464 (mmp80) REVERT: D 1251 ARG cc_start: 0.9218 (OUTLIER) cc_final: 0.8488 (mmt180) REVERT: D 1252 MET cc_start: 0.8909 (ttm) cc_final: 0.8342 (tpp) REVERT: D 1432 PHE cc_start: 0.2940 (OUTLIER) cc_final: 0.2146 (p90) REVERT: D 1536 ILE cc_start: 0.0407 (OUTLIER) cc_final: -0.0008 (pt) REVERT: D 1561 ASP cc_start: 0.6790 (OUTLIER) cc_final: 0.6353 (t0) REVERT: D 1566 LEU cc_start: 0.1848 (OUTLIER) cc_final: 0.1189 (pt) REVERT: E 74 ILE cc_start: 0.9437 (tt) cc_final: 0.9236 (tt) REVERT: E 77 MET cc_start: 0.8706 (mmt) cc_final: 0.8376 (tpt) REVERT: E 78 SER cc_start: 0.9353 (OUTLIER) cc_final: 0.8777 (p) REVERT: E 81 CYS cc_start: 0.7958 (OUTLIER) cc_final: 0.7664 (p) REVERT: E 88 MET cc_start: 0.9003 (OUTLIER) cc_final: 0.8658 (tmm) REVERT: E 92 LEU cc_start: 0.9630 (OUTLIER) cc_final: 0.9411 (tt) REVERT: E 95 PHE cc_start: 0.8867 (t80) cc_final: 0.8658 (t80) REVERT: E 122 LEU cc_start: 0.9249 (OUTLIER) cc_final: 0.9034 (tt) REVERT: E 163 MET cc_start: 0.7874 (ttp) cc_final: 0.7375 (ttt) REVERT: E 182 ILE cc_start: 0.7933 (OUTLIER) cc_final: 0.7732 (pt) REVERT: E 204 ASP cc_start: 0.7958 (OUTLIER) cc_final: 0.7727 (t0) REVERT: E 238 ILE cc_start: 0.7842 (OUTLIER) cc_final: 0.6974 (tt) REVERT: E 286 ILE cc_start: 0.4402 (OUTLIER) cc_final: 0.3732 (tt) REVERT: E 293 THR cc_start: 0.5372 (OUTLIER) cc_final: 0.5162 (t) REVERT: E 332 LYS cc_start: 0.8236 (mtmt) cc_final: 0.7877 (mtmm) REVERT: F 89 ILE cc_start: 0.9103 (mt) cc_final: 0.8756 (mm) REVERT: F 91 GLU cc_start: 0.8442 (mt-10) cc_final: 0.8174 (tm-30) REVERT: F 135 LEU cc_start: 0.8271 (mt) cc_final: 0.7838 (mt) REVERT: F 175 LEU cc_start: 0.9077 (mt) cc_final: 0.8695 (tt) REVERT: F 233 MET cc_start: 0.9424 (mmm) cc_final: 0.8967 (mmm) REVERT: F 253 LEU cc_start: 0.9150 (OUTLIER) cc_final: 0.8888 (mt) REVERT: F 319 CYS cc_start: 0.9065 (m) cc_final: 0.8742 (p) REVERT: F 327 LEU cc_start: 0.8659 (OUTLIER) cc_final: 0.8414 (tt) REVERT: F 432 PHE cc_start: 0.9357 (OUTLIER) cc_final: 0.9099 (t80) REVERT: F 710 MET cc_start: 0.6729 (mmt) cc_final: 0.6046 (tpp) REVERT: F 727 LEU cc_start: 0.7888 (tp) cc_final: 0.7480 (mt) REVERT: F 1020 GLN cc_start: 0.8657 (mm-40) cc_final: 0.8330 (mp10) REVERT: F 1031 ASP cc_start: 0.8206 (m-30) cc_final: 0.7377 (t0) REVERT: F 1165 LEU cc_start: 0.8539 (tt) cc_final: 0.8294 (tt) REVERT: F 1246 ARG cc_start: 0.9158 (OUTLIER) cc_final: 0.8455 (mmp80) REVERT: F 1251 ARG cc_start: 0.9225 (OUTLIER) cc_final: 0.8498 (mmt180) REVERT: F 1252 MET cc_start: 0.8901 (ttm) cc_final: 0.8410 (tpp) REVERT: F 1432 PHE cc_start: 0.2928 (OUTLIER) cc_final: 0.2137 (p90) REVERT: F 1536 ILE cc_start: 0.0414 (OUTLIER) cc_final: -0.0004 (pt) REVERT: F 1561 ASP cc_start: 0.6792 (OUTLIER) cc_final: 0.6353 (t0) REVERT: F 1566 LEU cc_start: 0.2135 (OUTLIER) cc_final: 0.1464 (pt) REVERT: G 74 ILE cc_start: 0.9434 (tt) cc_final: 0.9233 (tt) REVERT: G 77 MET cc_start: 0.8714 (mmt) cc_final: 0.8373 (tpt) REVERT: G 78 SER cc_start: 0.9346 (OUTLIER) cc_final: 0.8770 (p) REVERT: G 81 CYS cc_start: 0.7951 (OUTLIER) cc_final: 0.7653 (p) REVERT: G 88 MET cc_start: 0.9000 (OUTLIER) cc_final: 0.8635 (tmm) REVERT: G 92 LEU cc_start: 0.9627 (OUTLIER) cc_final: 0.9406 (tt) REVERT: G 95 PHE cc_start: 0.8861 (t80) cc_final: 0.8643 (t80) REVERT: G 122 LEU cc_start: 0.9242 (OUTLIER) cc_final: 0.9033 (tt) REVERT: G 163 MET cc_start: 0.7807 (ttp) cc_final: 0.7356 (ttt) REVERT: G 182 ILE cc_start: 0.7929 (OUTLIER) cc_final: 0.7726 (pt) REVERT: G 204 ASP cc_start: 0.7964 (OUTLIER) cc_final: 0.7741 (t0) REVERT: G 238 ILE cc_start: 0.7832 (OUTLIER) cc_final: 0.6964 (tt) REVERT: G 286 ILE cc_start: 0.4597 (OUTLIER) cc_final: 0.3908 (tt) REVERT: G 293 THR cc_start: 0.5367 (OUTLIER) cc_final: 0.5159 (t) REVERT: G 332 LYS cc_start: 0.8189 (mtmt) cc_final: 0.7823 (mtmm) REVERT: H 89 ILE cc_start: 0.9171 (mt) cc_final: 0.8956 (mm) REVERT: H 91 GLU cc_start: 0.8459 (mt-10) cc_final: 0.8159 (tm-30) REVERT: H 135 LEU cc_start: 0.8264 (mt) cc_final: 0.7825 (mt) REVERT: H 175 LEU cc_start: 0.9081 (mt) cc_final: 0.8698 (tt) REVERT: H 233 MET cc_start: 0.9402 (mmm) cc_final: 0.8907 (mmm) REVERT: H 253 LEU cc_start: 0.9136 (OUTLIER) cc_final: 0.8889 (mt) REVERT: H 319 CYS cc_start: 0.9056 (m) cc_final: 0.8742 (p) REVERT: H 327 LEU cc_start: 0.8657 (OUTLIER) cc_final: 0.8407 (tt) REVERT: H 710 MET cc_start: 0.6721 (mmt) cc_final: 0.6041 (tpp) REVERT: H 727 LEU cc_start: 0.7899 (tp) cc_final: 0.7488 (mt) REVERT: H 1020 GLN cc_start: 0.8663 (mm-40) cc_final: 0.8341 (mp10) REVERT: H 1031 ASP cc_start: 0.8223 (m-30) cc_final: 0.7388 (t0) REVERT: H 1103 ASN cc_start: 0.8002 (m-40) cc_final: 0.7675 (m-40) REVERT: H 1165 LEU cc_start: 0.8539 (tt) cc_final: 0.8291 (tt) REVERT: H 1246 ARG cc_start: 0.9121 (OUTLIER) cc_final: 0.8387 (mmp80) REVERT: H 1251 ARG cc_start: 0.9228 (OUTLIER) cc_final: 0.8497 (mmt180) REVERT: H 1252 MET cc_start: 0.8892 (ttm) cc_final: 0.8409 (tpp) REVERT: H 1432 PHE cc_start: 0.2922 (OUTLIER) cc_final: 0.2133 (p90) REVERT: H 1536 ILE cc_start: 0.0558 (OUTLIER) cc_final: 0.0166 (pt) REVERT: H 1561 ASP cc_start: 0.6778 (OUTLIER) cc_final: 0.6334 (t0) REVERT: H 1566 LEU cc_start: 0.2070 (OUTLIER) cc_final: 0.1411 (pt) outliers start: 436 outliers final: 58 residues processed: 1493 average time/residue: 0.5979 time to fit residues: 1489.2747 Evaluate side-chains 702 residues out of total 5672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 570 time to evaluate : 6.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 648 random chunks: chunk 547 optimal weight: 10.0000 chunk 491 optimal weight: 8.9990 chunk 272 optimal weight: 6.9990 chunk 167 optimal weight: 7.9990 chunk 331 optimal weight: 9.9990 chunk 262 optimal weight: 40.0000 chunk 507 optimal weight: 7.9990 chunk 196 optimal weight: 6.9990 chunk 308 optimal weight: 10.0000 chunk 378 optimal weight: 10.0000 chunk 588 optimal weight: 0.4980 overall best weight: 6.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: