Starting phenix.real_space_refine on Tue Aug 26 17:59:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ff7_50352/08_2025/9ff7_50352.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ff7_50352/08_2025/9ff7_50352.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ff7_50352/08_2025/9ff7_50352.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ff7_50352/08_2025/9ff7_50352.map" model { file = "/net/cci-nas-00/data/ceres_data/9ff7_50352/08_2025/9ff7_50352.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ff7_50352/08_2025/9ff7_50352.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.008 sd= 0.047 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 Mg 4 5.21 5 S 216 5.16 5 C 24878 2.51 5 N 7030 2.21 5 O 7424 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 39552 Number of models: 1 Model: "" Number of chains: 19 Chain: "A" Number of atoms: 3289 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3289 Classifications: {'peptide': 418} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 399} Chain: "B" Number of atoms: 3289 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3289 Classifications: {'peptide': 418} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 399} Chain: "C" Number of atoms: 3289 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3289 Classifications: {'peptide': 418} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 399} Chain: "D" Number of atoms: 3289 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3289 Classifications: {'peptide': 418} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 399} Chain: "E" Number of atoms: 3289 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3289 Classifications: {'peptide': 418} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 399} Chain: "F" Number of atoms: 3289 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3289 Classifications: {'peptide': 418} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 399} Chain: "G" Number of atoms: 3289 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3289 Classifications: {'peptide': 418} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 399} Chain: "H" Number of atoms: 3289 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3289 Classifications: {'peptide': 418} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 399} Chain: "I" Number of atoms: 3289 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3289 Classifications: {'peptide': 418} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 399} Chain: "J" Number of atoms: 3289 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3289 Classifications: {'peptide': 418} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 399} Chain: "K" Number of atoms: 3289 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3289 Classifications: {'peptide': 418} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 399} Chain: "L" Number of atoms: 3289 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3289 Classifications: {'peptide': 418} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 399} Chain: "B" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 16 Unusual residues: {'ME7': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 17 Unusual residues: {' MG': 1, 'ME7': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 17 Unusual residues: {' MG': 1, 'ME7': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 16 Unusual residues: {'ME7': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 16 Unusual residues: {'ME7': 1} Classifications: {'undetermined': 1} Time building chain proxies: 8.44, per 1000 atoms: 0.21 Number of scatterers: 39552 At special positions: 0 Unit cell: (174.447, 138.411, 158.067, 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 216 16.00 Mg 4 11.99 O 7424 8.00 N 7030 7.00 C 24878 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.12 Conformation dependent library (CDL) restraints added in 1.5 seconds Enol-peptide restraints added in 715.3 nanoseconds 9984 Ramachandran restraints generated. 4992 Oldfield, 0 Emsley, 4992 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9336 Finding SS restraints... Secondary structure from input PDB file: 223 helices and 44 sheets defined 49.9% alpha, 17.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.27 Creating SS restraints... Processing helix chain 'A' and resid 2 through 9 removed outlier: 3.567A pdb=" N ASN A 8 " --> pdb=" O THR A 4 " (cutoff:3.500A) Processing helix chain 'A' and resid 10 through 22 removed outlier: 3.755A pdb=" N THR A 16 " --> pdb=" O SER A 12 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N MET A 21 " --> pdb=" O LEU A 17 " (cutoff:3.500A) Processing helix chain 'A' and resid 30 through 44 Processing helix chain 'A' and resid 67 through 71 Processing helix chain 'A' and resid 82 through 89 removed outlier: 3.850A pdb=" N ILE A 86 " --> pdb=" O SER A 82 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ARG A 87 " --> pdb=" O PRO A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 128 Processing helix chain 'A' and resid 153 through 166 removed outlier: 3.615A pdb=" N ALA A 159 " --> pdb=" O GLU A 155 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASP A 163 " --> pdb=" O ALA A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 199 removed outlier: 3.679A pdb=" N LEU A 187 " --> pdb=" O GLY A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 223 Processing helix chain 'A' and resid 235 through 256 removed outlier: 3.621A pdb=" N GLU A 248 " --> pdb=" O GLU A 244 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU A 253 " --> pdb=" O LYS A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 278 Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 325 through 335 removed outlier: 4.049A pdb=" N GLU A 329 " --> pdb=" O SER A 325 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL A 330 " --> pdb=" O LYS A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 352 removed outlier: 3.552A pdb=" N LYS A 352 " --> pdb=" O LYS A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 372 removed outlier: 4.260A pdb=" N LEU A 371 " --> pdb=" O LYS A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 388 Processing helix chain 'A' and resid 391 through 406 removed outlier: 3.614A pdb=" N ALA A 395 " --> pdb=" O GLY A 391 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ASN A 401 " --> pdb=" O GLU A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 416 removed outlier: 3.531A pdb=" N GLU A 414 " --> pdb=" O ASP A 410 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N MET A 415 " --> pdb=" O ASP A 411 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N MET A 416 " --> pdb=" O PHE A 412 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 9 Processing helix chain 'B' and resid 10 through 22 removed outlier: 3.562A pdb=" N THR B 16 " --> pdb=" O SER B 12 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N MET B 21 " --> pdb=" O LEU B 17 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 46 removed outlier: 3.540A pdb=" N SER B 45 " --> pdb=" O GLN B 41 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 89 removed outlier: 3.615A pdb=" N ILE B 86 " --> pdb=" O SER B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 128 removed outlier: 3.648A pdb=" N ARG B 128 " --> pdb=" O PRO B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 166 removed outlier: 3.534A pdb=" N LEU B 157 " --> pdb=" O SER B 153 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N THR B 158 " --> pdb=" O THR B 154 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA B 159 " --> pdb=" O GLU B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 199 removed outlier: 3.874A pdb=" N TYR B 197 " --> pdb=" O GLN B 193 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N HIS B 199 " --> pdb=" O ILE B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 221 removed outlier: 3.563A pdb=" N VAL B 216 " --> pdb=" O ARG B 212 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N THR B 217 " --> pdb=" O PRO B 213 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLU B 218 " --> pdb=" O GLU B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 235 through 256 Processing helix chain 'B' and resid 266 through 278 Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 325 through 334 removed outlier: 3.590A pdb=" N TYR B 332 " --> pdb=" O ASP B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 346 through 352 Processing helix chain 'B' and resid 359 through 363 Processing helix chain 'B' and resid 367 through 372 removed outlier: 4.200A pdb=" N LEU B 371 " --> pdb=" O LYS B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 388 removed outlier: 3.697A pdb=" N GLN B 378 " --> pdb=" O GLN B 374 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU B 383 " --> pdb=" O LYS B 379 " (cutoff:3.500A) Processing helix chain 'B' and resid 393 through 405 removed outlier: 3.745A pdb=" N GLU B 397 " --> pdb=" O ILE B 393 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU B 399 " --> pdb=" O ALA B 395 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILE B 400 " --> pdb=" O MET B 396 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LYS B 402 " --> pdb=" O PHE B 398 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 418 removed outlier: 3.959A pdb=" N ARG B 418 " --> pdb=" O GLU B 414 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 9 Processing helix chain 'C' and resid 10 through 21 removed outlier: 3.806A pdb=" N THR C 16 " --> pdb=" O SER C 12 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 46 Processing helix chain 'C' and resid 82 through 89 removed outlier: 3.501A pdb=" N ILE C 86 " --> pdb=" O SER C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 123 through 128 removed outlier: 4.074A pdb=" N ARG C 128 " --> pdb=" O PRO C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 166 removed outlier: 3.828A pdb=" N ALA C 159 " --> pdb=" O GLU C 155 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 199 removed outlier: 3.563A pdb=" N LEU C 187 " --> pdb=" O GLY C 183 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N TYR C 197 " --> pdb=" O GLN C 193 " (cutoff:3.500A) Processing helix chain 'C' and resid 212 through 223 removed outlier: 3.520A pdb=" N VAL C 216 " --> pdb=" O ARG C 212 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N THR C 217 " --> pdb=" O PRO C 213 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLU C 218 " --> pdb=" O GLU C 214 " (cutoff:3.500A) Processing helix chain 'C' and resid 235 through 256 removed outlier: 3.584A pdb=" N HIS C 239 " --> pdb=" O PRO C 235 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ILE C 247 " --> pdb=" O ALA C 243 " (cutoff:3.500A) Processing helix chain 'C' and resid 266 through 278 Processing helix chain 'C' and resid 285 through 289 removed outlier: 3.502A pdb=" N GLY C 288 " --> pdb=" O LEU C 285 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N VAL C 289 " --> pdb=" O THR C 286 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 285 through 289' Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 325 through 337 removed outlier: 3.518A pdb=" N GLU C 329 " --> pdb=" O SER C 325 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N GLY C 337 " --> pdb=" O GLU C 333 " (cutoff:3.500A) Processing helix chain 'C' and resid 346 through 352 Processing helix chain 'C' and resid 367 through 371 Processing helix chain 'C' and resid 373 through 388 Processing helix chain 'C' and resid 393 through 406 removed outlier: 3.744A pdb=" N CYS C 405 " --> pdb=" O ASN C 401 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N THR C 406 " --> pdb=" O LYS C 402 " (cutoff:3.500A) Processing helix chain 'C' and resid 408 through 418 removed outlier: 3.924A pdb=" N ARG C 418 " --> pdb=" O GLU C 414 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 9 Processing helix chain 'D' and resid 10 through 22 removed outlier: 3.536A pdb=" N THR D 16 " --> pdb=" O SER D 12 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N MET D 21 " --> pdb=" O LEU D 17 " (cutoff:3.500A) Processing helix chain 'D' and resid 30 through 46 removed outlier: 3.644A pdb=" N SER D 45 " --> pdb=" O GLN D 41 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 71 Processing helix chain 'D' and resid 84 through 89 Processing helix chain 'D' and resid 123 through 128 removed outlier: 4.172A pdb=" N ARG D 128 " --> pdb=" O PRO D 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 155 through 166 removed outlier: 3.942A pdb=" N ALA D 159 " --> pdb=" O GLU D 155 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 199 removed outlier: 3.710A pdb=" N TYR D 197 " --> pdb=" O GLN D 193 " (cutoff:3.500A) Processing helix chain 'D' and resid 212 through 221 removed outlier: 3.799A pdb=" N THR D 217 " --> pdb=" O PRO D 213 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ARG D 221 " --> pdb=" O THR D 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 235 through 256 removed outlier: 3.507A pdb=" N HIS D 239 " --> pdb=" O PRO D 235 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N VAL D 240 " --> pdb=" O ALA D 236 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N VAL D 246 " --> pdb=" O VAL D 242 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU D 253 " --> pdb=" O LYS D 249 " (cutoff:3.500A) Processing helix chain 'D' and resid 266 through 278 Processing helix chain 'D' and resid 285 through 289 removed outlier: 3.958A pdb=" N VAL D 289 " --> pdb=" O THR D 286 " (cutoff:3.500A) Processing helix chain 'D' and resid 291 through 293 No H-bonds generated for 'chain 'D' and resid 291 through 293' Processing helix chain 'D' and resid 294 through 303 Processing helix chain 'D' and resid 325 through 335 removed outlier: 3.562A pdb=" N TYR D 332 " --> pdb=" O ASP D 328 " (cutoff:3.500A) Processing helix chain 'D' and resid 346 through 352 Processing helix chain 'D' and resid 367 through 372 removed outlier: 4.070A pdb=" N LEU D 371 " --> pdb=" O LYS D 367 " (cutoff:3.500A) Processing helix chain 'D' and resid 373 through 388 Processing helix chain 'D' and resid 391 through 406 removed outlier: 3.854A pdb=" N MET D 396 " --> pdb=" O GLU D 392 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N GLU D 397 " --> pdb=" O ILE D 393 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N THR D 406 " --> pdb=" O LYS D 402 " (cutoff:3.500A) Processing helix chain 'D' and resid 408 through 418 removed outlier: 3.892A pdb=" N ARG D 418 " --> pdb=" O GLU D 414 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 8 Processing helix chain 'E' and resid 10 through 22 removed outlier: 3.710A pdb=" N THR E 16 " --> pdb=" O SER E 12 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N MET E 21 " --> pdb=" O LEU E 17 " (cutoff:3.500A) Processing helix chain 'E' and resid 30 through 46 removed outlier: 3.506A pdb=" N LYS E 44 " --> pdb=" O LYS E 40 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N SER E 45 " --> pdb=" O GLN E 41 " (cutoff:3.500A) Processing helix chain 'E' and resid 67 through 71 Processing helix chain 'E' and resid 82 through 89 removed outlier: 3.566A pdb=" N ILE E 86 " --> pdb=" O SER E 82 " (cutoff:3.500A) Processing helix chain 'E' and resid 123 through 128 Processing helix chain 'E' and resid 153 through 166 Processing helix chain 'E' and resid 183 through 199 removed outlier: 3.524A pdb=" N SER E 194 " --> pdb=" O ASN E 190 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N TYR E 197 " --> pdb=" O GLN E 193 " (cutoff:3.500A) Processing helix chain 'E' and resid 212 through 223 removed outlier: 3.742A pdb=" N GLU E 218 " --> pdb=" O GLU E 214 " (cutoff:3.500A) Processing helix chain 'E' and resid 235 through 256 removed outlier: 3.525A pdb=" N ALA E 243 " --> pdb=" O HIS E 239 " (cutoff:3.500A) Processing helix chain 'E' and resid 266 through 278 Processing helix chain 'E' and resid 285 through 289 removed outlier: 3.825A pdb=" N VAL E 289 " --> pdb=" O THR E 286 " (cutoff:3.500A) Processing helix chain 'E' and resid 294 through 303 Processing helix chain 'E' and resid 325 through 334 removed outlier: 3.584A pdb=" N TYR E 332 " --> pdb=" O ASP E 328 " (cutoff:3.500A) Processing helix chain 'E' and resid 346 through 352 Processing helix chain 'E' and resid 367 through 371 Processing helix chain 'E' and resid 373 through 388 removed outlier: 3.529A pdb=" N ILE E 382 " --> pdb=" O GLN E 378 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N LEU E 383 " --> pdb=" O LYS E 379 " (cutoff:3.500A) Processing helix chain 'E' and resid 391 through 406 removed outlier: 3.534A pdb=" N MET E 396 " --> pdb=" O GLU E 392 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ASN E 401 " --> pdb=" O GLU E 397 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LYS E 402 " --> pdb=" O PHE E 398 " (cutoff:3.500A) Processing helix chain 'E' and resid 408 through 418 Processing helix chain 'F' and resid 2 through 9 removed outlier: 3.719A pdb=" N LEU F 6 " --> pdb=" O ASN F 2 " (cutoff:3.500A) Processing helix chain 'F' and resid 10 through 22 removed outlier: 3.866A pdb=" N MET F 21 " --> pdb=" O LEU F 17 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 46 removed outlier: 3.594A pdb=" N ILE F 35 " --> pdb=" O LYS F 31 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLN F 41 " --> pdb=" O ALA F 37 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N HIS F 42 " --> pdb=" O ILE F 38 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 89 Processing helix chain 'F' and resid 123 through 129 removed outlier: 3.567A pdb=" N ASN F 129 " --> pdb=" O GLU F 125 " (cutoff:3.500A) Processing helix chain 'F' and resid 153 through 166 removed outlier: 3.709A pdb=" N LEU F 162 " --> pdb=" O THR F 158 " (cutoff:3.500A) Processing helix chain 'F' and resid 184 through 199 removed outlier: 3.623A pdb=" N LEU F 188 " --> pdb=" O LYS F 184 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLN F 193 " --> pdb=" O GLN F 189 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N SER F 194 " --> pdb=" O ASN F 190 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA F 196 " --> pdb=" O ALA F 192 " (cutoff:3.500A) Processing helix chain 'F' and resid 212 through 223 removed outlier: 3.745A pdb=" N THR F 217 " --> pdb=" O PRO F 213 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLU F 218 " --> pdb=" O GLU F 214 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU F 222 " --> pdb=" O GLU F 218 " (cutoff:3.500A) Processing helix chain 'F' and resid 235 through 256 removed outlier: 3.563A pdb=" N VAL F 240 " --> pdb=" O ALA F 236 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ALA F 243 " --> pdb=" O HIS F 239 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N MET F 245 " --> pdb=" O GLN F 241 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N VAL F 246 " --> pdb=" O VAL F 242 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLU F 248 " --> pdb=" O GLU F 244 " (cutoff:3.500A) Processing helix chain 'F' and resid 266 through 278 removed outlier: 3.510A pdb=" N ARG F 272 " --> pdb=" O THR F 268 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA F 273 " --> pdb=" O ARG F 269 " (cutoff:3.500A) Processing helix chain 'F' and resid 291 through 293 No H-bonds generated for 'chain 'F' and resid 291 through 293' Processing helix chain 'F' and resid 294 through 302 Processing helix chain 'F' and resid 325 through 335 removed outlier: 3.563A pdb=" N GLU F 329 " --> pdb=" O SER F 325 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILE F 331 " --> pdb=" O MET F 327 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N PHE F 335 " --> pdb=" O ILE F 331 " (cutoff:3.500A) Processing helix chain 'F' and resid 346 through 352 Processing helix chain 'F' and resid 367 through 372 removed outlier: 4.025A pdb=" N LEU F 371 " --> pdb=" O LYS F 367 " (cutoff:3.500A) Processing helix chain 'F' and resid 373 through 388 removed outlier: 3.503A pdb=" N GLN F 378 " --> pdb=" O GLN F 374 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N TRP F 381 " --> pdb=" O LEU F 377 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ILE F 382 " --> pdb=" O GLN F 378 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU F 383 " --> pdb=" O LYS F 379 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ILE F 386 " --> pdb=" O ILE F 382 " (cutoff:3.500A) Processing helix chain 'F' and resid 392 through 406 removed outlier: 3.986A pdb=" N ASN F 401 " --> pdb=" O GLU F 397 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N LYS F 402 " --> pdb=" O PHE F 398 " (cutoff:3.500A) Processing helix chain 'F' and resid 408 through 418 removed outlier: 3.621A pdb=" N ARG F 418 " --> pdb=" O GLU F 414 " (cutoff:3.500A) Processing helix chain 'G' and resid 2 through 8 Processing helix chain 'G' and resid 10 through 21 removed outlier: 3.840A pdb=" N LEU G 14 " --> pdb=" O PRO G 10 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N MET G 21 " --> pdb=" O LEU G 17 " (cutoff:3.500A) Processing helix chain 'G' and resid 30 through 46 removed outlier: 3.535A pdb=" N ILE G 34 " --> pdb=" O ARG G 30 " (cutoff:3.500A) Processing helix chain 'G' and resid 82 through 89 Processing helix chain 'G' and resid 123 through 129 Processing helix chain 'G' and resid 153 through 166 removed outlier: 3.554A pdb=" N VAL G 161 " --> pdb=" O LEU G 157 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LEU G 162 " --> pdb=" O THR G 158 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ASP G 163 " --> pdb=" O ALA G 159 " (cutoff:3.500A) Processing helix chain 'G' and resid 183 through 199 removed outlier: 3.679A pdb=" N ILE G 191 " --> pdb=" O LEU G 187 " (cutoff:3.500A) Processing helix chain 'G' and resid 212 through 223 removed outlier: 3.574A pdb=" N GLN G 220 " --> pdb=" O VAL G 216 " (cutoff:3.500A) Processing helix chain 'G' and resid 235 through 256 removed outlier: 3.570A pdb=" N VAL G 246 " --> pdb=" O VAL G 242 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU G 253 " --> pdb=" O LYS G 249 " (cutoff:3.500A) Processing helix chain 'G' and resid 266 through 278 removed outlier: 3.519A pdb=" N ARG G 272 " --> pdb=" O THR G 268 " (cutoff:3.500A) Processing helix chain 'G' and resid 285 through 289 removed outlier: 3.634A pdb=" N GLY G 288 " --> pdb=" O LEU G 285 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N VAL G 289 " --> pdb=" O THR G 286 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 285 through 289' Processing helix chain 'G' and resid 294 through 303 Processing helix chain 'G' and resid 325 through 335 removed outlier: 3.780A pdb=" N ILE G 331 " --> pdb=" O MET G 327 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N TYR G 332 " --> pdb=" O ASP G 328 " (cutoff:3.500A) Processing helix chain 'G' and resid 346 through 353 Processing helix chain 'G' and resid 367 through 371 removed outlier: 3.668A pdb=" N LEU G 370 " --> pdb=" O LYS G 367 " (cutoff:3.500A) Processing helix chain 'G' and resid 373 through 388 Processing helix chain 'G' and resid 391 through 405 removed outlier: 3.912A pdb=" N ASN G 401 " --> pdb=" O GLU G 397 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LYS G 402 " --> pdb=" O PHE G 398 " (cutoff:3.500A) Processing helix chain 'G' and resid 408 through 418 removed outlier: 3.511A pdb=" N MET G 415 " --> pdb=" O ASP G 411 " (cutoff:3.500A) Processing helix chain 'H' and resid 2 through 9 Processing helix chain 'H' and resid 10 through 22 removed outlier: 3.616A pdb=" N THR H 16 " --> pdb=" O SER H 12 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ASN H 20 " --> pdb=" O THR H 16 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N MET H 21 " --> pdb=" O LEU H 17 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLY H 22 " --> pdb=" O GLY H 18 " (cutoff:3.500A) Processing helix chain 'H' and resid 30 through 46 removed outlier: 3.510A pdb=" N GLN H 41 " --> pdb=" O ALA H 37 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N SER H 45 " --> pdb=" O GLN H 41 " (cutoff:3.500A) Processing helix chain 'H' and resid 67 through 71 Processing helix chain 'H' and resid 84 through 89 Processing helix chain 'H' and resid 123 through 128 removed outlier: 3.646A pdb=" N ARG H 128 " --> pdb=" O PRO H 124 " (cutoff:3.500A) Processing helix chain 'H' and resid 153 through 166 removed outlier: 4.024A pdb=" N THR H 158 " --> pdb=" O THR H 154 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA H 159 " --> pdb=" O GLU H 155 " (cutoff:3.500A) Processing helix chain 'H' and resid 183 through 199 Processing helix chain 'H' and resid 212 through 221 removed outlier: 3.580A pdb=" N THR H 217 " --> pdb=" O PRO H 213 " (cutoff:3.500A) Processing helix chain 'H' and resid 235 through 256 removed outlier: 3.603A pdb=" N ALA H 243 " --> pdb=" O HIS H 239 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU H 253 " --> pdb=" O LYS H 249 " (cutoff:3.500A) Processing helix chain 'H' and resid 266 through 278 Processing helix chain 'H' and resid 285 through 289 removed outlier: 3.574A pdb=" N GLY H 288 " --> pdb=" O LEU H 285 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VAL H 289 " --> pdb=" O THR H 286 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 285 through 289' Processing helix chain 'H' and resid 291 through 293 No H-bonds generated for 'chain 'H' and resid 291 through 293' Processing helix chain 'H' and resid 294 through 303 Processing helix chain 'H' and resid 325 through 334 removed outlier: 3.531A pdb=" N GLU H 329 " --> pdb=" O SER H 325 " (cutoff:3.500A) Processing helix chain 'H' and resid 346 through 352 Processing helix chain 'H' and resid 367 through 371 Processing helix chain 'H' and resid 373 through 388 removed outlier: 3.507A pdb=" N GLN H 378 " --> pdb=" O GLN H 374 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU H 383 " --> pdb=" O LYS H 379 " (cutoff:3.500A) Processing helix chain 'H' and resid 393 through 406 removed outlier: 3.841A pdb=" N THR H 406 " --> pdb=" O LYS H 402 " (cutoff:3.500A) Processing helix chain 'H' and resid 408 through 418 Processing helix chain 'I' and resid 2 through 8 removed outlier: 3.639A pdb=" N ASN I 8 " --> pdb=" O THR I 4 " (cutoff:3.500A) Processing helix chain 'I' and resid 10 through 21 removed outlier: 4.173A pdb=" N THR I 16 " --> pdb=" O SER I 12 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N MET I 21 " --> pdb=" O LEU I 17 " (cutoff:3.500A) Processing helix chain 'I' and resid 30 through 46 removed outlier: 3.520A pdb=" N LYS I 44 " --> pdb=" O LYS I 40 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N SER I 45 " --> pdb=" O GLN I 41 " (cutoff:3.500A) Processing helix chain 'I' and resid 84 through 89 removed outlier: 3.711A pdb=" N PHE I 89 " --> pdb=" O GLN I 85 " (cutoff:3.500A) Processing helix chain 'I' and resid 123 through 128 removed outlier: 3.706A pdb=" N ARG I 128 " --> pdb=" O PRO I 124 " (cutoff:3.500A) Processing helix chain 'I' and resid 156 through 166 removed outlier: 4.031A pdb=" N LEU I 162 " --> pdb=" O THR I 158 " (cutoff:3.500A) Processing helix chain 'I' and resid 183 through 199 Processing helix chain 'I' and resid 212 through 221 removed outlier: 3.660A pdb=" N THR I 217 " --> pdb=" O PRO I 213 " (cutoff:3.500A) Processing helix chain 'I' and resid 235 through 256 removed outlier: 3.657A pdb=" N VAL I 240 " --> pdb=" O ALA I 236 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU I 253 " --> pdb=" O LYS I 249 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N HIS I 256 " --> pdb=" O ARG I 252 " (cutoff:3.500A) Processing helix chain 'I' and resid 266 through 278 Processing helix chain 'I' and resid 285 through 289 removed outlier: 3.686A pdb=" N GLY I 288 " --> pdb=" O LEU I 285 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N VAL I 289 " --> pdb=" O THR I 286 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 285 through 289' Processing helix chain 'I' and resid 294 through 302 Processing helix chain 'I' and resid 325 through 335 removed outlier: 3.687A pdb=" N GLU I 329 " --> pdb=" O SER I 325 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N TYR I 332 " --> pdb=" O ASP I 328 " (cutoff:3.500A) Processing helix chain 'I' and resid 346 through 352 removed outlier: 3.538A pdb=" N ALA I 350 " --> pdb=" O SER I 346 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LYS I 352 " --> pdb=" O LYS I 348 " (cutoff:3.500A) Processing helix chain 'I' and resid 367 through 372 removed outlier: 4.169A pdb=" N LEU I 371 " --> pdb=" O LYS I 367 " (cutoff:3.500A) Processing helix chain 'I' and resid 373 through 388 Processing helix chain 'I' and resid 391 through 406 removed outlier: 4.014A pdb=" N THR I 406 " --> pdb=" O LYS I 402 " (cutoff:3.500A) Processing helix chain 'I' and resid 408 through 418 removed outlier: 3.580A pdb=" N MET I 415 " --> pdb=" O ASP I 411 " (cutoff:3.500A) Processing helix chain 'J' and resid 2 through 8 Processing helix chain 'J' and resid 10 through 22 removed outlier: 4.062A pdb=" N MET J 21 " --> pdb=" O LEU J 17 " (cutoff:3.500A) Processing helix chain 'J' and resid 30 through 46 removed outlier: 3.559A pdb=" N LYS J 44 " --> pdb=" O LYS J 40 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N SER J 45 " --> pdb=" O GLN J 41 " (cutoff:3.500A) Processing helix chain 'J' and resid 67 through 71 Processing helix chain 'J' and resid 84 through 89 removed outlier: 3.787A pdb=" N PHE J 89 " --> pdb=" O GLN J 85 " (cutoff:3.500A) Processing helix chain 'J' and resid 125 through 130 removed outlier: 3.746A pdb=" N ARG J 128 " --> pdb=" O GLU J 125 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LYS J 130 " --> pdb=" O ALA J 127 " (cutoff:3.500A) Processing helix chain 'J' and resid 155 through 166 removed outlier: 3.922A pdb=" N ALA J 159 " --> pdb=" O GLU J 155 " (cutoff:3.500A) Processing helix chain 'J' and resid 183 through 199 Processing helix chain 'J' and resid 212 through 221 removed outlier: 3.924A pdb=" N THR J 217 " --> pdb=" O PRO J 213 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLU J 218 " --> pdb=" O GLU J 214 " (cutoff:3.500A) Processing helix chain 'J' and resid 235 through 256 removed outlier: 3.584A pdb=" N HIS J 239 " --> pdb=" O PRO J 235 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL J 240 " --> pdb=" O ALA J 236 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N VAL J 246 " --> pdb=" O VAL J 242 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N HIS J 256 " --> pdb=" O ARG J 252 " (cutoff:3.500A) Processing helix chain 'J' and resid 266 through 278 Processing helix chain 'J' and resid 285 through 289 removed outlier: 3.872A pdb=" N VAL J 289 " --> pdb=" O THR J 286 " (cutoff:3.500A) Processing helix chain 'J' and resid 294 through 302 Processing helix chain 'J' and resid 325 through 335 Processing helix chain 'J' and resid 346 through 352 Processing helix chain 'J' and resid 367 through 372 removed outlier: 4.122A pdb=" N LEU J 371 " --> pdb=" O LYS J 367 " (cutoff:3.500A) Processing helix chain 'J' and resid 373 through 388 removed outlier: 3.516A pdb=" N ILE J 386 " --> pdb=" O ILE J 382 " (cutoff:3.500A) Processing helix chain 'J' and resid 391 through 406 removed outlier: 3.511A pdb=" N CYS J 405 " --> pdb=" O ASN J 401 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N THR J 406 " --> pdb=" O LYS J 402 " (cutoff:3.500A) Processing helix chain 'J' and resid 408 through 418 removed outlier: 3.874A pdb=" N ARG J 418 " --> pdb=" O GLU J 414 " (cutoff:3.500A) Processing helix chain 'K' and resid 2 through 8 removed outlier: 3.691A pdb=" N ASN K 8 " --> pdb=" O THR K 4 " (cutoff:3.500A) Processing helix chain 'K' and resid 10 through 22 removed outlier: 3.603A pdb=" N THR K 16 " --> pdb=" O SER K 12 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N MET K 21 " --> pdb=" O LEU K 17 " (cutoff:3.500A) Processing helix chain 'K' and resid 30 through 46 removed outlier: 3.680A pdb=" N SER K 45 " --> pdb=" O GLN K 41 " (cutoff:3.500A) Processing helix chain 'K' and resid 84 through 89 Processing helix chain 'K' and resid 123 through 128 removed outlier: 3.783A pdb=" N ARG K 128 " --> pdb=" O PRO K 124 " (cutoff:3.500A) Processing helix chain 'K' and resid 153 through 166 removed outlier: 4.111A pdb=" N THR K 158 " --> pdb=" O THR K 154 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ALA K 159 " --> pdb=" O GLU K 155 " (cutoff:3.500A) Processing helix chain 'K' and resid 183 through 199 Processing helix chain 'K' and resid 212 through 221 removed outlier: 3.716A pdb=" N THR K 217 " --> pdb=" O PRO K 213 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLU K 218 " --> pdb=" O GLU K 214 " (cutoff:3.500A) Processing helix chain 'K' and resid 235 through 256 removed outlier: 3.504A pdb=" N VAL K 240 " --> pdb=" O ALA K 236 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA K 243 " --> pdb=" O HIS K 239 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N VAL K 246 " --> pdb=" O VAL K 242 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU K 253 " --> pdb=" O LYS K 249 " (cutoff:3.500A) Processing helix chain 'K' and resid 266 through 278 Processing helix chain 'K' and resid 285 through 289 removed outlier: 3.678A pdb=" N GLY K 288 " --> pdb=" O LEU K 285 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL K 289 " --> pdb=" O THR K 286 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 285 through 289' Processing helix chain 'K' and resid 294 through 303 Processing helix chain 'K' and resid 325 through 335 Processing helix chain 'K' and resid 346 through 352 Processing helix chain 'K' and resid 359 through 363 removed outlier: 3.621A pdb=" N SER K 363 " --> pdb=" O TYR K 360 " (cutoff:3.500A) Processing helix chain 'K' and resid 367 through 371 Processing helix chain 'K' and resid 373 through 388 removed outlier: 3.541A pdb=" N LEU K 383 " --> pdb=" O LYS K 379 " (cutoff:3.500A) Processing helix chain 'K' and resid 391 through 406 removed outlier: 3.694A pdb=" N MET K 396 " --> pdb=" O GLU K 392 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLU K 397 " --> pdb=" O ILE K 393 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ASN K 401 " --> pdb=" O GLU K 397 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N CYS K 405 " --> pdb=" O ASN K 401 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N THR K 406 " --> pdb=" O LYS K 402 " (cutoff:3.500A) Processing helix chain 'K' and resid 408 through 417 removed outlier: 3.635A pdb=" N LYS K 417 " --> pdb=" O PHE K 413 " (cutoff:3.500A) Processing helix chain 'L' and resid 2 through 9 Processing helix chain 'L' and resid 10 through 22 removed outlier: 3.549A pdb=" N MET L 21 " --> pdb=" O LEU L 17 " (cutoff:3.500A) Processing helix chain 'L' and resid 30 through 46 Processing helix chain 'L' and resid 84 through 89 Processing helix chain 'L' and resid 123 through 128 removed outlier: 3.549A pdb=" N ARG L 128 " --> pdb=" O PRO L 124 " (cutoff:3.500A) Processing helix chain 'L' and resid 155 through 166 removed outlier: 3.580A pdb=" N ALA L 159 " --> pdb=" O GLU L 155 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL L 161 " --> pdb=" O LEU L 157 " (cutoff:3.500A) Processing helix chain 'L' and resid 183 through 199 removed outlier: 3.678A pdb=" N ALA L 196 " --> pdb=" O ALA L 192 " (cutoff:3.500A) Processing helix chain 'L' and resid 212 through 221 removed outlier: 3.847A pdb=" N THR L 217 " --> pdb=" O PRO L 213 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLU L 218 " --> pdb=" O GLU L 214 " (cutoff:3.500A) Processing helix chain 'L' and resid 235 through 256 removed outlier: 4.261A pdb=" N VAL L 246 " --> pdb=" O VAL L 242 " (cutoff:3.500A) Processing helix chain 'L' and resid 266 through 278 Processing helix chain 'L' and resid 285 through 289 removed outlier: 3.976A pdb=" N VAL L 289 " --> pdb=" O THR L 286 " (cutoff:3.500A) Processing helix chain 'L' and resid 294 through 303 Processing helix chain 'L' and resid 325 through 335 removed outlier: 3.633A pdb=" N VAL L 330 " --> pdb=" O LYS L 326 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ILE L 331 " --> pdb=" O MET L 327 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N TYR L 332 " --> pdb=" O ASP L 328 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLU L 333 " --> pdb=" O GLU L 329 " (cutoff:3.500A) Processing helix chain 'L' and resid 346 through 352 removed outlier: 3.624A pdb=" N ALA L 350 " --> pdb=" O SER L 346 " (cutoff:3.500A) Processing helix chain 'L' and resid 367 through 372 removed outlier: 4.275A pdb=" N LEU L 371 " --> pdb=" O LYS L 367 " (cutoff:3.500A) Processing helix chain 'L' and resid 373 through 388 Processing helix chain 'L' and resid 392 through 406 removed outlier: 3.901A pdb=" N GLU L 397 " --> pdb=" O ILE L 393 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASN L 401 " --> pdb=" O GLU L 397 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N CYS L 405 " --> pdb=" O ASN L 401 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N THR L 406 " --> pdb=" O LYS L 402 " (cutoff:3.500A) Processing helix chain 'L' and resid 408 through 418 Processing sheet with id=AA1, first strand: chain 'A' and resid 79 through 81 removed outlier: 3.805A pdb=" N ILE A 79 " --> pdb=" O LEU A 65 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 101 through 102 Processing sheet with id=AA3, first strand: chain 'A' and resid 138 through 139 removed outlier: 3.653A pdb=" N ASN A 306 " --> pdb=" O LEU A 139 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 226 through 231 removed outlier: 6.612A pdb=" N LEU A 204 " --> pdb=" O GLU A 226 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N VAL A 228 " --> pdb=" O LEU A 204 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N VAL A 206 " --> pdb=" O VAL A 228 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N SER A 230 " --> pdb=" O VAL A 206 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N LEU A 208 " --> pdb=" O SER A 230 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ALA A 317 " --> pdb=" O GLY A 174 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 284 through 285 removed outlier: 3.505A pdb=" N VAL A 289 " --> pdb=" O LEU A 285 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 50 through 51 removed outlier: 3.510A pdb=" N GLY B 51 " --> pdb=" O GLY B 99 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 50 through 51 removed outlier: 3.510A pdb=" N GLY B 51 " --> pdb=" O GLY B 99 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 54 through 57 removed outlier: 3.509A pdb=" N PHE B 64 " --> pdb=" O GLU B 56 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ILE B 79 " --> pdb=" O LEU B 65 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 138 through 139 removed outlier: 3.653A pdb=" N ASN B 306 " --> pdb=" O LEU B 139 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 144 through 145 removed outlier: 4.830A pdb=" N ILE B 168 " --> pdb=" O LEU B 145 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 226 through 231 removed outlier: 6.642A pdb=" N LEU B 204 " --> pdb=" O GLU B 226 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N VAL B 228 " --> pdb=" O LEU B 204 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N VAL B 206 " --> pdb=" O VAL B 228 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N SER B 230 " --> pdb=" O VAL B 206 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N LEU B 208 " --> pdb=" O SER B 230 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N VAL B 203 " --> pdb=" O ILE B 261 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N LEU B 263 " --> pdb=" O VAL B 203 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N MET B 205 " --> pdb=" O LEU B 263 " (cutoff:3.500A) removed outlier: 8.308A pdb=" N ASP B 265 " --> pdb=" O MET B 205 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N LEU B 207 " --> pdb=" O ASP B 265 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N VAL B 260 " --> pdb=" O SER B 312 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N GLY B 174 " --> pdb=" O ALA B 317 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N ALA B 319 " --> pdb=" O GLY B 174 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N ILE B 176 " --> pdb=" O ALA B 319 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N MET B 341 " --> pdb=" O ARG B 173 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 284 through 285 Processing sheet with id=AB4, first strand: chain 'C' and resid 118 through 119 removed outlier: 7.775A pdb=" N TYR C 80 " --> pdb=" O LEU C 113 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ILE C 79 " --> pdb=" O LEU C 65 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 138 through 139 removed outlier: 3.658A pdb=" N ASN C 306 " --> pdb=" O LEU C 139 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 226 through 231 removed outlier: 6.510A pdb=" N LEU C 204 " --> pdb=" O GLU C 226 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N VAL C 228 " --> pdb=" O LEU C 204 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N VAL C 206 " --> pdb=" O VAL C 228 " (cutoff:3.500A) removed outlier: 8.194A pdb=" N SER C 230 " --> pdb=" O VAL C 206 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N LEU C 208 " --> pdb=" O SER C 230 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N VAL C 203 " --> pdb=" O ILE C 261 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N LEU C 263 " --> pdb=" O VAL C 203 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N MET C 205 " --> pdb=" O LEU C 263 " (cutoff:3.500A) removed outlier: 8.082A pdb=" N ASP C 265 " --> pdb=" O MET C 205 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N LEU C 207 " --> pdb=" O ASP C 265 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL C 260 " --> pdb=" O SER C 312 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N GLY C 174 " --> pdb=" O ALA C 317 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N ALA C 319 " --> pdb=" O GLY C 174 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N ILE C 176 " --> pdb=" O ALA C 319 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N MET C 341 " --> pdb=" O ARG C 173 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 63 through 66 removed outlier: 3.528A pdb=" N GLY D 51 " --> pdb=" O GLY D 99 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA D 112 " --> pdb=" O ARG D 102 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 63 through 66 removed outlier: 3.528A pdb=" N GLY D 51 " --> pdb=" O GLY D 99 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 226 through 231 removed outlier: 6.898A pdb=" N LEU D 204 " --> pdb=" O GLU D 226 " (cutoff:3.500A) removed outlier: 7.966A pdb=" N VAL D 228 " --> pdb=" O LEU D 204 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N VAL D 206 " --> pdb=" O VAL D 228 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N SER D 230 " --> pdb=" O VAL D 206 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N LEU D 208 " --> pdb=" O SER D 230 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 226 through 231 removed outlier: 6.898A pdb=" N LEU D 204 " --> pdb=" O GLU D 226 " (cutoff:3.500A) removed outlier: 7.966A pdb=" N VAL D 228 " --> pdb=" O LEU D 204 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N VAL D 206 " --> pdb=" O VAL D 228 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N SER D 230 " --> pdb=" O VAL D 206 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N LEU D 208 " --> pdb=" O SER D 230 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N GLY D 174 " --> pdb=" O ALA D 317 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N ALA D 319 " --> pdb=" O GLY D 174 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N ILE D 176 " --> pdb=" O ALA D 319 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 49 through 55 removed outlier: 3.540A pdb=" N ILE E 79 " --> pdb=" O LEU E 65 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N TYR E 80 " --> pdb=" O LEU E 113 " (cutoff:3.500A) removed outlier: 8.947A pdb=" N LYS E 115 " --> pdb=" O TYR E 80 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ALA E 112 " --> pdb=" O ARG E 102 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N LYS E 100 " --> pdb=" O LEU E 114 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N VAL E 116 " --> pdb=" O SER E 98 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N SER E 98 " --> pdb=" O VAL E 116 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N GLU E 118 " --> pdb=" O THR E 96 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N THR E 96 " --> pdb=" O GLU E 118 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLY E 99 " --> pdb=" O GLY E 51 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLY E 51 " --> pdb=" O GLY E 99 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ILE E 49 " --> pdb=" O ILE E 101 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 138 through 139 removed outlier: 3.674A pdb=" N ASN E 306 " --> pdb=" O LEU E 139 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N VAL E 203 " --> pdb=" O ILE E 261 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N LEU E 263 " --> pdb=" O VAL E 203 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N MET E 205 " --> pdb=" O LEU E 263 " (cutoff:3.500A) removed outlier: 8.395A pdb=" N ASP E 265 " --> pdb=" O MET E 205 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N LEU E 207 " --> pdb=" O ASP E 265 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N LEU E 204 " --> pdb=" O GLU E 226 " (cutoff:3.500A) removed outlier: 8.091A pdb=" N VAL E 228 " --> pdb=" O LEU E 204 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N VAL E 206 " --> pdb=" O VAL E 228 " (cutoff:3.500A) removed outlier: 7.873A pdb=" N SER E 230 " --> pdb=" O VAL E 206 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N LEU E 208 " --> pdb=" O SER E 230 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 138 through 139 removed outlier: 3.674A pdb=" N ASN E 306 " --> pdb=" O LEU E 139 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N GLY E 174 " --> pdb=" O ALA E 317 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N ALA E 319 " --> pdb=" O GLY E 174 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N ILE E 176 " --> pdb=" O ALA E 319 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 144 through 145 removed outlier: 4.564A pdb=" N ILE E 168 " --> pdb=" O LEU E 145 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 63 through 66 removed outlier: 4.480A pdb=" N ILE F 49 " --> pdb=" O ILE F 101 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA F 112 " --> pdb=" O ARG F 102 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 63 through 66 removed outlier: 4.480A pdb=" N ILE F 49 " --> pdb=" O ILE F 101 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 138 through 139 removed outlier: 3.765A pdb=" N THR F 318 " --> pdb=" O LEU F 264 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N LEU F 204 " --> pdb=" O GLU F 226 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N VAL F 228 " --> pdb=" O LEU F 204 " (cutoff:3.500A) removed outlier: 5.753A pdb=" N VAL F 206 " --> pdb=" O VAL F 228 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N SER F 230 " --> pdb=" O VAL F 206 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N LEU F 208 " --> pdb=" O SER F 230 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 138 through 139 removed outlier: 6.651A pdb=" N GLY F 174 " --> pdb=" O ALA F 317 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N ALA F 319 " --> pdb=" O GLY F 174 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ILE F 176 " --> pdb=" O ALA F 319 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 50 through 57 removed outlier: 3.607A pdb=" N PHE G 64 " --> pdb=" O GLU G 56 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N TYR G 80 " --> pdb=" O LEU G 113 " (cutoff:3.500A) removed outlier: 8.753A pdb=" N LYS G 115 " --> pdb=" O TYR G 80 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N LYS G 100 " --> pdb=" O LEU G 114 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N VAL G 116 " --> pdb=" O SER G 98 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N SER G 98 " --> pdb=" O VAL G 116 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N GLU G 118 " --> pdb=" O THR G 96 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N THR G 96 " --> pdb=" O GLU G 118 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 144 through 145 removed outlier: 4.780A pdb=" N ILE G 168 " --> pdb=" O LEU G 145 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'G' and resid 226 through 231 removed outlier: 6.283A pdb=" N LEU G 204 " --> pdb=" O GLU G 226 " (cutoff:3.500A) removed outlier: 7.633A pdb=" N VAL G 228 " --> pdb=" O LEU G 204 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N VAL G 206 " --> pdb=" O VAL G 228 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N SER G 230 " --> pdb=" O VAL G 206 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N LEU G 208 " --> pdb=" O SER G 230 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL G 260 " --> pdb=" O SER G 312 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N GLY G 174 " --> pdb=" O ALA G 317 " (cutoff:3.500A) removed outlier: 8.343A pdb=" N ALA G 319 " --> pdb=" O GLY G 174 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ILE G 176 " --> pdb=" O ALA G 319 " (cutoff:3.500A) removed outlier: 10.344A pdb=" N GLU G 342 " --> pdb=" O ASN G 361 " (cutoff:3.500A) removed outlier: 8.720A pdb=" N ASN G 361 " --> pdb=" O GLU G 342 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N HIS G 344 " --> pdb=" O ASP G 359 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 118 through 119 removed outlier: 3.695A pdb=" N ALA H 112 " --> pdb=" O ARG H 102 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N TYR H 80 " --> pdb=" O LEU H 113 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ILE H 79 " --> pdb=" O LEU H 65 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLY H 63 " --> pdb=" O VAL H 81 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N ILE H 49 " --> pdb=" O ILE H 101 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H' and resid 226 through 231 removed outlier: 6.662A pdb=" N LEU H 204 " --> pdb=" O GLU H 226 " (cutoff:3.500A) removed outlier: 8.093A pdb=" N VAL H 228 " --> pdb=" O LEU H 204 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N VAL H 206 " --> pdb=" O VAL H 228 " (cutoff:3.500A) removed outlier: 8.097A pdb=" N SER H 230 " --> pdb=" O VAL H 206 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N LEU H 208 " --> pdb=" O SER H 230 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N VAL H 260 " --> pdb=" O SER H 312 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N GLY H 174 " --> pdb=" O ALA H 317 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N ALA H 319 " --> pdb=" O GLY H 174 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N ILE H 176 " --> pdb=" O ALA H 319 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N MET H 341 " --> pdb=" O ARG H 173 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'I' and resid 118 through 119 removed outlier: 7.726A pdb=" N TYR I 80 " --> pdb=" O LEU I 113 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ILE I 79 " --> pdb=" O LEU I 65 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLY I 63 " --> pdb=" O VAL I 81 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N ILE I 49 " --> pdb=" O ILE I 101 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'I' and resid 138 through 139 Processing sheet with id=AD8, first strand: chain 'I' and resid 226 through 231 removed outlier: 6.668A pdb=" N LEU I 204 " --> pdb=" O GLU I 226 " (cutoff:3.500A) removed outlier: 7.995A pdb=" N VAL I 228 " --> pdb=" O LEU I 204 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N VAL I 206 " --> pdb=" O VAL I 228 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N SER I 230 " --> pdb=" O VAL I 206 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N LEU I 208 " --> pdb=" O SER I 230 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VAL I 260 " --> pdb=" O SER I 312 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N GLY I 174 " --> pdb=" O ALA I 317 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N ALA I 319 " --> pdb=" O GLY I 174 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N ILE I 176 " --> pdb=" O ALA I 319 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'J' and resid 50 through 54 removed outlier: 3.572A pdb=" N GLY J 51 " --> pdb=" O GLY J 99 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N THR J 96 " --> pdb=" O GLU J 118 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N GLU J 118 " --> pdb=" O THR J 96 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N SER J 98 " --> pdb=" O VAL J 116 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N VAL J 116 " --> pdb=" O SER J 98 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N LYS J 100 " --> pdb=" O LEU J 114 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'J' and resid 63 through 65 removed outlier: 3.668A pdb=" N GLY J 63 " --> pdb=" O VAL J 81 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ILE J 79 " --> pdb=" O LEU J 65 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'J' and resid 226 through 231 removed outlier: 3.576A pdb=" N VAL J 260 " --> pdb=" O SER J 312 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N GLY J 174 " --> pdb=" O ALA J 317 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N ALA J 319 " --> pdb=" O GLY J 174 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N ILE J 176 " --> pdb=" O ALA J 319 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N LEU J 175 " --> pdb=" O LEU J 343 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N LEU J 345 " --> pdb=" O LEU J 175 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N VAL J 177 " --> pdb=" O LEU J 345 " (cutoff:3.500A) removed outlier: 10.083A pdb=" N GLU J 342 " --> pdb=" O ASN J 361 " (cutoff:3.500A) removed outlier: 9.051A pdb=" N ASN J 361 " --> pdb=" O GLU J 342 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N HIS J 344 " --> pdb=" O ASP J 359 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'K' and resid 118 through 119 removed outlier: 7.425A pdb=" N TYR K 80 " --> pdb=" O LEU K 113 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ILE K 79 " --> pdb=" O LEU K 65 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'K' and resid 138 through 139 removed outlier: 3.637A pdb=" N ASN K 306 " --> pdb=" O LEU K 139 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'K' and resid 226 through 231 removed outlier: 6.645A pdb=" N LEU K 204 " --> pdb=" O GLU K 226 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N VAL K 228 " --> pdb=" O LEU K 204 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N VAL K 206 " --> pdb=" O VAL K 228 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N SER K 230 " --> pdb=" O VAL K 206 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N LEU K 208 " --> pdb=" O SER K 230 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N VAL K 203 " --> pdb=" O ILE K 261 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N LEU K 263 " --> pdb=" O VAL K 203 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N MET K 205 " --> pdb=" O LEU K 263 " (cutoff:3.500A) removed outlier: 8.213A pdb=" N ASP K 265 " --> pdb=" O MET K 205 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N LEU K 207 " --> pdb=" O ASP K 265 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N VAL K 260 " --> pdb=" O SER K 312 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N GLY K 174 " --> pdb=" O ALA K 317 " (cutoff:3.500A) removed outlier: 8.006A pdb=" N ALA K 319 " --> pdb=" O GLY K 174 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N ILE K 176 " --> pdb=" O ALA K 319 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'L' and resid 118 through 119 removed outlier: 3.666A pdb=" N ALA L 112 " --> pdb=" O ARG L 102 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LEU L 113 " --> pdb=" O TYR L 80 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ILE L 79 " --> pdb=" O LEU L 65 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLY L 63 " --> pdb=" O VAL L 81 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N ILE L 49 " --> pdb=" O ILE L 101 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLY L 51 " --> pdb=" O GLY L 99 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ASP L 95 " --> pdb=" O LEU L 55 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'L' and resid 138 through 139 removed outlier: 3.689A pdb=" N ASN L 306 " --> pdb=" O LEU L 139 " (cutoff:3.500A) removed outlier: 7.867A pdb=" N VAL L 228 " --> pdb=" O LEU L 204 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N VAL L 206 " --> pdb=" O VAL L 228 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N SER L 230 " --> pdb=" O VAL L 206 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N LEU L 208 " --> pdb=" O SER L 230 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'L' and resid 138 through 139 removed outlier: 3.689A pdb=" N ASN L 306 " --> pdb=" O LEU L 139 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N GLY L 174 " --> pdb=" O ALA L 317 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N ALA L 319 " --> pdb=" O GLY L 174 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N ILE L 176 " --> pdb=" O ALA L 319 " (cutoff:3.500A) removed outlier: 10.141A pdb=" N GLU L 342 " --> pdb=" O ASN L 361 " (cutoff:3.500A) removed outlier: 8.868A pdb=" N ASN L 361 " --> pdb=" O GLU L 342 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N HIS L 344 " --> pdb=" O ASP L 359 " (cutoff:3.500A) 1785 hydrogen bonds defined for protein. 5106 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: 8.38 Time building geometry restraints manager: 3.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 7361 1.32 - 1.44: 8877 1.44 - 1.57: 23507 1.57 - 1.69: 0 1.69 - 1.81: 396 Bond restraints: 40141 Sorted by residual: bond pdb=" C HIS L 388 " pdb=" N PRO L 389 " ideal model delta sigma weight residual 1.335 1.352 -0.017 1.30e-02 5.92e+03 1.70e+00 bond pdb=" C HIS D 388 " pdb=" N PRO D 389 " ideal model delta sigma weight residual 1.335 1.350 -0.015 1.30e-02 5.92e+03 1.29e+00 bond pdb=" C ALA L 178 " pdb=" O ALA L 178 " ideal model delta sigma weight residual 1.248 1.237 0.011 1.26e-02 6.30e+03 7.80e-01 bond pdb=" N SER B 166 " pdb=" CA SER B 166 " ideal model delta sigma weight residual 1.463 1.456 0.007 8.80e-03 1.29e+04 6.69e-01 bond pdb=" CA ARG L 296 " pdb=" C ARG L 296 " ideal model delta sigma weight residual 1.520 1.529 -0.009 1.23e-02 6.61e+03 5.45e-01 ... (remaining 40136 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.12: 53288 1.12 - 2.24: 509 2.24 - 3.37: 207 3.37 - 4.49: 32 4.49 - 5.61: 24 Bond angle restraints: 54060 Sorted by residual: angle pdb=" N ILE J 86 " pdb=" CA ILE J 86 " pdb=" C ILE J 86 " ideal model delta sigma weight residual 112.80 108.78 4.02 1.15e+00 7.56e-01 1.22e+01 angle pdb=" C ASP D 265 " pdb=" N SER D 266 " pdb=" CA SER D 266 " ideal model delta sigma weight residual 121.70 125.97 -4.27 1.80e+00 3.09e-01 5.64e+00 angle pdb=" CA GLU D 397 " pdb=" CB GLU D 397 " pdb=" CG GLU D 397 " ideal model delta sigma weight residual 114.10 118.58 -4.48 2.00e+00 2.50e-01 5.01e+00 angle pdb=" C ASP B 265 " pdb=" N SER B 266 " pdb=" CA SER B 266 " ideal model delta sigma weight residual 121.70 125.57 -3.87 1.80e+00 3.09e-01 4.61e+00 angle pdb=" CA GLY B 51 " pdb=" C GLY B 51 " pdb=" N ASP B 52 " ideal model delta sigma weight residual 114.67 117.04 -2.37 1.11e+00 8.12e-01 4.56e+00 ... (remaining 54055 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.57: 24098 27.57 - 55.14: 778 55.14 - 82.71: 12 82.71 - 110.28: 1 110.28 - 137.85: 2 Dihedral angle restraints: 24891 sinusoidal: 10467 harmonic: 14424 Sorted by residual: dihedral pdb=" CAI ME7 E 501 " pdb=" CAJ ME7 E 501 " pdb=" NAP ME7 E 501 " pdb=" CAM ME7 E 501 " ideal model delta sinusoidal sigma weight residual 89.00 -133.15 -137.85 1 3.00e+01 1.11e-03 1.86e+01 dihedral pdb=" CAI ME7 C1002 " pdb=" CAJ ME7 C1002 " pdb=" NAP ME7 C1002 " pdb=" CAM ME7 C1002 " ideal model delta sinusoidal sigma weight residual 89.00 -48.69 137.69 1 3.00e+01 1.11e-03 1.86e+01 dihedral pdb=" CB GLU B 244 " pdb=" CG GLU B 244 " pdb=" CD GLU B 244 " pdb=" OE1 GLU B 244 " ideal model delta sinusoidal sigma weight residual 0.00 -88.00 88.00 1 3.00e+01 1.11e-03 1.03e+01 ... (remaining 24888 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 3468 0.025 - 0.050: 1670 0.050 - 0.074: 535 0.074 - 0.099: 267 0.099 - 0.124: 204 Chirality restraints: 6144 Sorted by residual: chirality pdb=" CA ILE E 316 " pdb=" N ILE E 316 " pdb=" C ILE E 316 " pdb=" CB ILE E 316 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.84e-01 chirality pdb=" CA ILE G 176 " pdb=" N ILE G 176 " pdb=" C ILE G 176 " pdb=" CB ILE G 176 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.52e-01 chirality pdb=" CA ILE L 176 " pdb=" N ILE L 176 " pdb=" C ILE L 176 " pdb=" CB ILE L 176 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.49e-01 ... (remaining 6141 not shown) Planarity restraints: 7054 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CAG ME7 B 501 " -0.169 2.00e-02 2.50e+03 1.55e-01 4.81e+02 pdb=" CAH ME7 B 501 " -0.090 2.00e-02 2.50e+03 pdb=" CAJ ME7 B 501 " -0.225 2.00e-02 2.50e+03 pdb=" CAM ME7 B 501 " 0.033 2.00e-02 2.50e+03 pdb=" CAN ME7 B 501 " 0.053 2.00e-02 2.50e+03 pdb=" NAP ME7 B 501 " -0.047 2.00e-02 2.50e+03 pdb=" OAC ME7 B 501 " 0.238 2.00e-02 2.50e+03 pdb=" OAD ME7 B 501 " 0.206 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CAE ME7 B 501 " -0.033 2.00e-02 2.50e+03 3.53e-02 2.49e+01 pdb=" CAF ME7 B 501 " -0.028 2.00e-02 2.50e+03 pdb=" CAI ME7 B 501 " -0.054 2.00e-02 2.50e+03 pdb=" CAK ME7 B 501 " 0.011 2.00e-02 2.50e+03 pdb=" CAL ME7 B 501 " 0.012 2.00e-02 2.50e+03 pdb=" NAO ME7 B 501 " -0.008 2.00e-02 2.50e+03 pdb=" OAA ME7 B 501 " 0.050 2.00e-02 2.50e+03 pdb=" OAB ME7 B 501 " 0.048 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL C 278 " -0.022 5.00e-02 4.00e+02 3.36e-02 1.80e+00 pdb=" N PRO C 279 " 0.058 5.00e-02 4.00e+02 pdb=" CA PRO C 279 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO C 279 " -0.019 5.00e-02 4.00e+02 ... (remaining 7051 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 307 2.51 - 3.11: 29228 3.11 - 3.71: 64014 3.71 - 4.30: 89254 4.30 - 4.90: 144542 Nonbonded interactions: 327345 Sorted by model distance: nonbonded pdb=" O SER C 346 " pdb="MG MG C1001 " model vdw 1.913 2.170 nonbonded pdb=" N ILE C 349 " pdb="MG MG C1001 " model vdw 1.950 2.250 nonbonded pdb=" O PRO I 180 " pdb="MG MG I1001 " model vdw 1.990 2.170 nonbonded pdb=" O PRO I 179 " pdb="MG MG I1001 " model vdw 2.020 2.170 nonbonded pdb=" N ALA C 350 " pdb="MG MG C1001 " model vdw 2.036 2.250 ... (remaining 327340 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and resid 1 through 418) selection = (chain 'C' and resid 1 through 418) selection = (chain 'D' and resid 1 through 418) selection = (chain 'E' and resid 1 through 418) selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = (chain 'I' and resid 1 through 418) selection = (chain 'J' and resid 1 through 418) selection = chain 'K' selection = (chain 'L' and resid 1 through 418) } 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 individual isotropic 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: 5.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.600 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 33.010 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.100 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: 0.000 Load rotamer database and sin/cos tables:1.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 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 : 0.002 0.166 40142 Z= 0.121 Angle : 0.396 5.610 54060 Z= 0.224 Chirality : 0.038 0.124 6144 Planarity : 0.003 0.155 7054 Dihedral : 12.368 137.849 15555 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Rotamer: Outliers : 0.00 % Allowed : 12.10 % Favored : 87.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.12 (0.12), residues: 4992 helix: 0.32 (0.12), residues: 2064 sheet: 1.37 (0.25), residues: 536 loop : 1.26 (0.13), residues: 2392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 212 TYR 0.008 0.001 TYR J 80 PHE 0.008 0.001 PHE J 232 TRP 0.006 0.000 TRP E 381 HIS 0.008 0.000 HIS B 140 Details of bonding type rmsd covalent geometry : bond 0.00174 (40141) covalent geometry : angle 0.39647 (54060) hydrogen bonds : bond 0.28848 ( 1746) hydrogen bonds : angle 7.90533 ( 5106) Misc. bond : bond 0.16614 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9984 Ramachandran restraints generated. 4992 Oldfield, 0 Emsley, 4992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9984 Ramachandran restraints generated. 4992 Oldfield, 0 Emsley, 4992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 555 residues out of total 4296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 555 time to evaluate : 1.270 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: A 197 TYR cc_start: 0.8957 (t80) cc_final: 0.8371 (t80) REVERT: A 269 ARG cc_start: 0.9413 (mmp80) cc_final: 0.8900 (mmp80) REVERT: A 296 ARG cc_start: 0.9379 (mmm-85) cc_final: 0.9095 (mmm-85) REVERT: A 321 ILE cc_start: 0.8909 (mm) cc_final: 0.8615 (mm) REVERT: A 332 TYR cc_start: 0.8652 (t80) cc_final: 0.7638 (t80) REVERT: A 333 GLU cc_start: 0.9283 (mm-30) cc_final: 0.8944 (mm-30) REVERT: A 341 MET cc_start: 0.8195 (tmm) cc_final: 0.7586 (tmm) REVERT: A 343 LEU cc_start: 0.9337 (mt) cc_final: 0.8983 (mt) REVERT: B 1 MET cc_start: 0.9093 (tpp) cc_final: 0.8429 (tpp) REVERT: B 60 ASP cc_start: 0.8175 (m-30) cc_final: 0.7359 (m-30) REVERT: B 110 TYR cc_start: 0.8128 (m-80) cc_final: 0.7708 (m-80) REVERT: B 189 GLN cc_start: 0.8629 (mm-40) cc_final: 0.8057 (mm-40) REVERT: B 219 MET cc_start: 0.9000 (tpp) cc_final: 0.8598 (tpp) REVERT: B 341 MET cc_start: 0.8009 (tmm) cc_final: 0.7741 (tmm) REVERT: B 415 MET cc_start: 0.9034 (tmm) cc_final: 0.8731 (tmm) REVERT: C 134 GLU cc_start: 0.8262 (pm20) cc_final: 0.7807 (pm20) REVERT: C 415 MET cc_start: 0.8935 (tmm) cc_final: 0.8708 (tmm) REVERT: D 21 MET cc_start: 0.8946 (ppp) cc_final: 0.8534 (ppp) REVERT: D 32 GLN cc_start: 0.8895 (mm110) cc_final: 0.8363 (mm-40) REVERT: D 33 ASP cc_start: 0.9238 (t0) cc_final: 0.8994 (t70) REVERT: D 110 TYR cc_start: 0.8348 (m-80) cc_final: 0.7864 (m-80) REVERT: D 245 MET cc_start: 0.8112 (mmp) cc_final: 0.7714 (mmp) REVERT: D 390 MET cc_start: 0.8493 (pmm) cc_final: 0.8289 (pmm) REVERT: E 110 TYR cc_start: 0.8535 (m-80) cc_final: 0.8175 (m-80) REVERT: E 197 TYR cc_start: 0.8893 (t80) cc_final: 0.8285 (t80) REVERT: E 211 GLU cc_start: 0.7784 (mm-30) cc_final: 0.7535 (mm-30) REVERT: E 241 GLN cc_start: 0.8698 (tm-30) cc_final: 0.8242 (tm-30) REVERT: E 380 MET cc_start: 0.9316 (ptt) cc_final: 0.9090 (ptt) REVERT: F 72 TYR cc_start: 0.9263 (m-10) cc_final: 0.9055 (m-10) REVERT: F 218 GLU cc_start: 0.9331 (tp30) cc_final: 0.9105 (tt0) REVERT: F 274 TYR cc_start: 0.9148 (m-80) cc_final: 0.8774 (m-80) REVERT: F 322 ASP cc_start: 0.8481 (t70) cc_final: 0.8123 (t70) REVERT: F 327 MET cc_start: 0.5528 (tpt) cc_final: 0.5136 (tpt) REVERT: G 269 ARG cc_start: 0.9288 (tpp80) cc_final: 0.8934 (tpp80) REVERT: G 274 TYR cc_start: 0.8791 (m-80) cc_final: 0.8209 (m-80) REVERT: G 326 LYS cc_start: 0.9518 (tppt) cc_final: 0.9258 (tppt) REVERT: G 344 HIS cc_start: 0.8457 (m90) cc_final: 0.8212 (m90) REVERT: H 1 MET cc_start: 0.9024 (tpt) cc_final: 0.8436 (tpp) REVERT: H 39 LEU cc_start: 0.9323 (mt) cc_final: 0.9075 (tp) REVERT: H 210 ASP cc_start: 0.7959 (t0) cc_final: 0.7748 (t0) REVERT: H 326 LYS cc_start: 0.9291 (tppt) cc_final: 0.9051 (tppt) REVERT: H 329 GLU cc_start: 0.8453 (tp30) cc_final: 0.8063 (tp30) REVERT: H 415 MET cc_start: 0.8252 (ppp) cc_final: 0.7462 (tmm) REVERT: I 210 ASP cc_start: 0.7835 (t70) cc_final: 0.7477 (t0) REVERT: I 265 ASP cc_start: 0.7991 (t0) cc_final: 0.7686 (t0) REVERT: J 21 MET cc_start: 0.8500 (tmm) cc_final: 0.8298 (tmm) REVERT: J 197 TYR cc_start: 0.8064 (t80) cc_final: 0.7854 (t80) REVERT: J 396 MET cc_start: 0.9055 (tpp) cc_final: 0.8823 (tpp) REVERT: K 21 MET cc_start: 0.8848 (ttp) cc_final: 0.8642 (ttm) REVERT: K 147 MET cc_start: 0.8583 (mmm) cc_final: 0.8181 (mmm) REVERT: K 360 TYR cc_start: 0.8870 (t80) cc_final: 0.8518 (t80) REVERT: K 415 MET cc_start: 0.9373 (tmm) cc_final: 0.8918 (tmm) REVERT: L 29 MET cc_start: 0.8642 (mtp) cc_final: 0.8230 (mtp) REVERT: L 147 MET cc_start: 0.7297 (tpp) cc_final: 0.6834 (tpp) REVERT: L 189 GLN cc_start: 0.8864 (mt0) cc_final: 0.7910 (tm-30) REVERT: L 197 TYR cc_start: 0.9087 (t80) cc_final: 0.8656 (t80) REVERT: L 272 ARG cc_start: 0.9358 (mtp-110) cc_final: 0.9107 (ptm160) REVERT: L 344 HIS cc_start: 0.8323 (m-70) cc_final: 0.7949 (m170) REVERT: L 390 MET cc_start: 0.5783 (pmm) cc_final: 0.4934 (pmm) outliers start: 0 outliers final: 0 residues processed: 555 average time/residue: 0.2221 time to fit residues: 196.8111 Evaluate side-chains 430 residues out of total 4296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 430 time to evaluate : 1.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 432 optimal weight: 2.9990 chunk 197 optimal weight: 10.0000 chunk 388 optimal weight: 4.9990 chunk 455 optimal weight: 20.0000 chunk 215 optimal weight: 30.0000 chunk 20 optimal weight: 0.0970 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 8.9990 chunk 248 optimal weight: 20.0000 chunk 207 optimal weight: 30.0000 chunk 470 optimal weight: 9.9990 overall best weight: 5.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 ASN B 140 HIS B 344 HIS ** C 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 193 GLN D 32 GLN D 129 ASN ** D 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 90 ASN F 8 ASN ** F 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 42 HIS F 275 ASN F 388 HIS G 85 GLN H 8 ASN ** H 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 241 GLN I 172 GLN J 8 ASN ** J 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 90 ASN J 140 HIS ** J 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 32 GLN K 172 GLN K 292 ASN K 340 ASN ** L 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 85 GLN L 135 ASN ** L 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 295 HIS Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.092960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.062854 restraints weight = 143296.285| |-----------------------------------------------------------------------------| r_work (start): 0.3083 rms_B_bonded: 4.04 r_work: 0.2902 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8654 moved from start: 0.1792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.070 40142 Z= 0.324 Angle : 0.677 9.551 54060 Z= 0.355 Chirality : 0.044 0.163 6144 Planarity : 0.005 0.059 7054 Dihedral : 5.162 143.046 5463 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.72 % Allowed : 13.85 % Favored : 83.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.93 (0.12), residues: 4992 helix: 0.43 (0.11), residues: 2288 sheet: 0.85 (0.22), residues: 592 loop : 1.06 (0.15), residues: 2112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG D 30 TYR 0.023 0.002 TYR H 197 PHE 0.015 0.002 PHE J 232 TRP 0.021 0.001 TRP E 381 HIS 0.009 0.002 HIS K 239 Details of bonding type rmsd covalent geometry : bond 0.00711 (40141) covalent geometry : angle 0.67677 (54060) hydrogen bonds : bond 0.05707 ( 1746) hydrogen bonds : angle 5.67206 ( 5106) Misc. bond : bond 0.00182 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9984 Ramachandran restraints generated. 4992 Oldfield, 0 Emsley, 4992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9984 Ramachandran restraints generated. 4992 Oldfield, 0 Emsley, 4992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 568 residues out of total 4296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 451 time to evaluate : 1.534 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: A 21 MET cc_start: 0.7801 (tmm) cc_final: 0.7576 (tmm) REVERT: A 269 ARG cc_start: 0.9511 (mmp80) cc_final: 0.9022 (mmp80) REVERT: A 318 THR cc_start: 0.8751 (m) cc_final: 0.8535 (t) REVERT: A 341 MET cc_start: 0.8334 (tmm) cc_final: 0.7859 (tmm) REVERT: A 343 LEU cc_start: 0.9243 (mt) cc_final: 0.8978 (mt) REVERT: A 390 MET cc_start: 0.8396 (ppp) cc_final: 0.8172 (ppp) REVERT: B 1 MET cc_start: 0.8865 (tpp) cc_final: 0.8580 (tpp) REVERT: B 59 GLN cc_start: 0.8609 (pm20) cc_final: 0.8138 (pm20) REVERT: B 60 ASP cc_start: 0.8185 (m-30) cc_final: 0.7955 (m-30) REVERT: B 110 TYR cc_start: 0.8203 (m-80) cc_final: 0.7663 (m-80) REVERT: B 211 GLU cc_start: 0.8499 (tp30) cc_final: 0.8270 (tp30) REVERT: B 376 GLU cc_start: 0.9172 (tt0) cc_final: 0.8906 (tt0) REVERT: B 415 MET cc_start: 0.9250 (tmm) cc_final: 0.8974 (tmm) REVERT: C 134 GLU cc_start: 0.8982 (pm20) cc_final: 0.8763 (pm20) REVERT: C 341 MET cc_start: 0.9236 (ppp) cc_final: 0.9031 (ppp) REVERT: D 21 MET cc_start: 0.9101 (ppp) cc_final: 0.8716 (ppp) REVERT: D 29 MET cc_start: 0.8812 (mmm) cc_final: 0.8594 (mmm) REVERT: D 129 ASN cc_start: 0.9208 (OUTLIER) cc_final: 0.8902 (p0) REVERT: D 210 ASP cc_start: 0.8698 (t0) cc_final: 0.8090 (t0) REVERT: D 241 GLN cc_start: 0.8916 (tm-30) cc_final: 0.8649 (tm-30) REVERT: E 197 TYR cc_start: 0.9043 (t80) cc_final: 0.8395 (t80) REVERT: E 211 GLU cc_start: 0.8597 (mm-30) cc_final: 0.7836 (mm-30) REVERT: E 215 GLU cc_start: 0.8828 (tt0) cc_final: 0.8124 (tt0) REVERT: E 241 GLN cc_start: 0.8648 (tm-30) cc_final: 0.8366 (tm-30) REVERT: E 341 MET cc_start: 0.8440 (tmm) cc_final: 0.7492 (tmm) REVERT: E 380 MET cc_start: 0.9476 (ptt) cc_final: 0.9211 (ptt) REVERT: E 413 PHE cc_start: 0.8937 (OUTLIER) cc_final: 0.8663 (m-80) REVERT: E 415 MET cc_start: 0.9014 (mmp) cc_final: 0.8787 (mmp) REVERT: F 29 MET cc_start: 0.9109 (ptm) cc_final: 0.8811 (ptt) REVERT: F 218 GLU cc_start: 0.9350 (tp30) cc_final: 0.9136 (tt0) REVERT: F 322 ASP cc_start: 0.8893 (t70) cc_final: 0.8598 (t70) REVERT: G 269 ARG cc_start: 0.9459 (tpp80) cc_final: 0.9050 (tpp80) REVERT: G 274 TYR cc_start: 0.8858 (m-80) cc_final: 0.8314 (m-80) REVERT: G 326 LYS cc_start: 0.9525 (tppt) cc_final: 0.9182 (tppt) REVERT: G 341 MET cc_start: 0.7710 (tmm) cc_final: 0.7053 (tmm) REVERT: H 33 ASP cc_start: 0.8367 (t0) cc_final: 0.7764 (p0) REVERT: H 85 GLN cc_start: 0.8373 (OUTLIER) cc_final: 0.7949 (mt0) REVERT: H 109 ARG cc_start: 0.8144 (ptt-90) cc_final: 0.7864 (ptt-90) REVERT: H 210 ASP cc_start: 0.8699 (t0) cc_final: 0.8468 (t0) REVERT: H 329 GLU cc_start: 0.8762 (tp30) cc_final: 0.8187 (tp30) REVERT: H 415 MET cc_start: 0.8608 (ppp) cc_final: 0.8145 (tmm) REVERT: H 416 MET cc_start: 0.8274 (mmm) cc_final: 0.8043 (mmm) REVERT: I 59 GLN cc_start: 0.9278 (pm20) cc_final: 0.8931 (pm20) REVERT: I 210 ASP cc_start: 0.8824 (t70) cc_final: 0.8554 (t0) REVERT: I 265 ASP cc_start: 0.8788 (t0) cc_final: 0.8555 (t0) REVERT: J 21 MET cc_start: 0.8851 (tmm) cc_final: 0.8475 (tmm) REVERT: J 58 LEU cc_start: 0.9328 (OUTLIER) cc_final: 0.9109 (mm) REVERT: J 326 LYS cc_start: 0.9199 (mmmt) cc_final: 0.8987 (mtmm) REVERT: J 396 MET cc_start: 0.9539 (tpp) cc_final: 0.9305 (tpp) REVERT: K 1 MET cc_start: 0.7258 (tpt) cc_final: 0.6926 (tpp) REVERT: K 21 MET cc_start: 0.8927 (ttp) cc_final: 0.7776 (tmm) REVERT: K 147 MET cc_start: 0.9028 (mmm) cc_final: 0.8537 (mmm) REVERT: K 341 MET cc_start: 0.9066 (tmm) cc_final: 0.8744 (tmm) REVERT: K 415 MET cc_start: 0.9315 (tmm) cc_final: 0.8754 (tmm) REVERT: K 416 MET cc_start: 0.8956 (ppp) cc_final: 0.8614 (ppp) REVERT: L 29 MET cc_start: 0.8673 (mtp) cc_final: 0.8307 (mtp) REVERT: L 147 MET cc_start: 0.7529 (tpp) cc_final: 0.6815 (tpp) REVERT: L 189 GLN cc_start: 0.8923 (mt0) cc_final: 0.7983 (tm-30) REVERT: L 197 TYR cc_start: 0.9053 (t80) cc_final: 0.8691 (t80) REVERT: L 348 LYS cc_start: 0.9722 (mmmt) cc_final: 0.9463 (tppt) REVERT: L 390 MET cc_start: 0.6398 (pmm) cc_final: 0.5418 (pmm) outliers start: 117 outliers final: 64 residues processed: 542 average time/residue: 0.2012 time to fit residues: 179.8908 Evaluate side-chains 474 residues out of total 4296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 406 time to evaluate : 1.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain B residue 193 GLN Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain C residue 168 ILE Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain D residue 129 ASN Chi-restraints excluded: chain D residue 195 ILE Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain D residue 322 ASP Chi-restraints excluded: chain D residue 363 SER Chi-restraints excluded: chain D residue 381 TRP Chi-restraints excluded: chain E residue 31 LYS Chi-restraints excluded: chain E residue 42 HIS Chi-restraints excluded: chain E residue 157 LEU Chi-restraints excluded: chain E residue 313 LEU Chi-restraints excluded: chain E residue 320 LEU Chi-restraints excluded: chain E residue 365 THR Chi-restraints excluded: chain E residue 413 PHE Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 140 HIS Chi-restraints excluded: chain F residue 157 LEU Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain F residue 190 ASN Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 295 HIS Chi-restraints excluded: chain F residue 412 PHE Chi-restraints excluded: chain G residue 41 GLN Chi-restraints excluded: chain G residue 77 ASP Chi-restraints excluded: chain G residue 121 PHE Chi-restraints excluded: chain G residue 260 VAL Chi-restraints excluded: chain G residue 275 ASN Chi-restraints excluded: chain G residue 308 GLU Chi-restraints excluded: chain G residue 331 ILE Chi-restraints excluded: chain G residue 338 THR Chi-restraints excluded: chain G residue 358 ILE Chi-restraints excluded: chain H residue 85 GLN Chi-restraints excluded: chain H residue 131 ILE Chi-restraints excluded: chain H residue 239 HIS Chi-restraints excluded: chain H residue 260 VAL Chi-restraints excluded: chain I residue 39 LEU Chi-restraints excluded: chain I residue 49 ILE Chi-restraints excluded: chain I residue 158 THR Chi-restraints excluded: chain I residue 228 VAL Chi-restraints excluded: chain I residue 260 VAL Chi-restraints excluded: chain J residue 9 THR Chi-restraints excluded: chain J residue 58 LEU Chi-restraints excluded: chain J residue 84 CYS Chi-restraints excluded: chain J residue 168 ILE Chi-restraints excluded: chain J residue 186 MET Chi-restraints excluded: chain J residue 188 LEU Chi-restraints excluded: chain J residue 228 VAL Chi-restraints excluded: chain J residue 260 VAL Chi-restraints excluded: chain J residue 373 THR Chi-restraints excluded: chain K residue 9 THR Chi-restraints excluded: chain K residue 93 THR Chi-restraints excluded: chain K residue 109 ARG Chi-restraints excluded: chain K residue 214 GLU Chi-restraints excluded: chain K residue 323 THR Chi-restraints excluded: chain L residue 41 GLN Chi-restraints excluded: chain L residue 177 VAL Chi-restraints excluded: chain L residue 228 VAL Chi-restraints excluded: chain L residue 295 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 162 optimal weight: 4.9990 chunk 326 optimal weight: 4.9990 chunk 155 optimal weight: 2.9990 chunk 58 optimal weight: 4.9990 chunk 428 optimal weight: 1.9990 chunk 313 optimal weight: 2.9990 chunk 409 optimal weight: 2.9990 chunk 327 optimal weight: 6.9990 chunk 60 optimal weight: 7.9990 chunk 173 optimal weight: 10.0000 chunk 217 optimal weight: 3.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 25 ASN A 42 HIS B 172 GLN ** C 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 8 ASN ** E 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 275 ASN F 388 HIS H 25 ASN ** H 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 292 ASN ** J 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 41 GLN J 172 GLN ** K 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 189 GLN K 292 ASN K 340 ASN ** L 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 401 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.093598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.063212 restraints weight = 142354.256| |-----------------------------------------------------------------------------| r_work (start): 0.3103 rms_B_bonded: 4.19 r_work: 0.2931 rms_B_bonded: 4.49 restraints_weight: 0.5000 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.1984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 40142 Z= 0.192 Angle : 0.554 9.369 54060 Z= 0.287 Chirality : 0.042 0.168 6144 Planarity : 0.004 0.045 7054 Dihedral : 5.149 147.089 5463 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 2.68 % Allowed : 14.83 % Favored : 82.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.02 (0.12), residues: 4992 helix: 0.60 (0.11), residues: 2290 sheet: 0.69 (0.22), residues: 592 loop : 1.03 (0.15), residues: 2110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 30 TYR 0.022 0.002 TYR H 197 PHE 0.011 0.001 PHE K 36 TRP 0.026 0.001 TRP E 381 HIS 0.005 0.001 HIS H 256 Details of bonding type rmsd covalent geometry : bond 0.00426 (40141) covalent geometry : angle 0.55412 (54060) hydrogen bonds : bond 0.04772 ( 1746) hydrogen bonds : angle 5.17140 ( 5106) Misc. bond : bond 0.00233 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9984 Ramachandran restraints generated. 4992 Oldfield, 0 Emsley, 4992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9984 Ramachandran restraints generated. 4992 Oldfield, 0 Emsley, 4992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 543 residues out of total 4296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 428 time to evaluate : 1.366 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: A 21 MET cc_start: 0.7763 (tmm) cc_final: 0.7522 (tmm) REVERT: A 269 ARG cc_start: 0.9493 (mmp80) cc_final: 0.8988 (mmp80) REVERT: A 322 ASP cc_start: 0.8828 (t0) cc_final: 0.8613 (t0) REVERT: A 336 LYS cc_start: 0.8522 (mmmm) cc_final: 0.8309 (mmmm) REVERT: A 341 MET cc_start: 0.8304 (tmm) cc_final: 0.7829 (tmm) REVERT: A 343 LEU cc_start: 0.9225 (mt) cc_final: 0.8976 (mt) REVERT: A 390 MET cc_start: 0.8455 (ppp) cc_final: 0.8249 (ppp) REVERT: B 1 MET cc_start: 0.8807 (tpp) cc_final: 0.8518 (tpp) REVERT: B 110 TYR cc_start: 0.8200 (m-80) cc_final: 0.7668 (m-80) REVERT: B 193 GLN cc_start: 0.9234 (OUTLIER) cc_final: 0.9030 (mp10) REVERT: B 211 GLU cc_start: 0.8570 (tp30) cc_final: 0.8277 (tp30) REVERT: B 376 GLU cc_start: 0.9187 (tt0) cc_final: 0.8901 (tt0) REVERT: B 415 MET cc_start: 0.9190 (tmm) cc_final: 0.8844 (tmm) REVERT: C 134 GLU cc_start: 0.8990 (OUTLIER) cc_final: 0.8770 (pm20) REVERT: C 245 MET cc_start: 0.9144 (mmt) cc_final: 0.8921 (mmt) REVERT: D 1 MET cc_start: 0.6827 (tpt) cc_final: 0.6464 (tpt) REVERT: D 210 ASP cc_start: 0.8632 (t0) cc_final: 0.8246 (t0) REVERT: D 377 LEU cc_start: 0.9662 (OUTLIER) cc_final: 0.9372 (mt) REVERT: D 390 MET cc_start: 0.8685 (pmm) cc_final: 0.7886 (pmm) REVERT: E 32 GLN cc_start: 0.7202 (tm-30) cc_final: 0.6929 (tm-30) REVERT: E 197 TYR cc_start: 0.9028 (t80) cc_final: 0.8441 (t80) REVERT: E 211 GLU cc_start: 0.8521 (mm-30) cc_final: 0.8133 (mm-30) REVERT: E 241 GLN cc_start: 0.8486 (tm-30) cc_final: 0.8186 (tm-30) REVERT: E 295 HIS cc_start: 0.9101 (t-90) cc_final: 0.8836 (t-90) REVERT: E 327 MET cc_start: 0.8507 (ttm) cc_final: 0.8093 (ttm) REVERT: E 380 MET cc_start: 0.9452 (ptt) cc_final: 0.9199 (ptt) REVERT: F 21 MET cc_start: 0.7250 (mtm) cc_final: 0.6738 (mtp) REVERT: F 29 MET cc_start: 0.9038 (ptm) cc_final: 0.8703 (ptt) REVERT: F 322 ASP cc_start: 0.8866 (t70) cc_final: 0.8563 (t70) REVERT: F 327 MET cc_start: 0.5124 (mmm) cc_final: 0.4850 (tpt) REVERT: G 164 LEU cc_start: 0.9068 (OUTLIER) cc_final: 0.8812 (mt) REVERT: G 269 ARG cc_start: 0.9450 (tpp80) cc_final: 0.9040 (tpp80) REVERT: G 274 TYR cc_start: 0.8789 (m-80) cc_final: 0.8177 (m-80) REVERT: G 326 LYS cc_start: 0.9516 (tppt) cc_final: 0.9176 (tppt) REVERT: G 341 MET cc_start: 0.7679 (tmm) cc_final: 0.7145 (tmm) REVERT: H 33 ASP cc_start: 0.8261 (t0) cc_final: 0.7724 (p0) REVERT: H 52 ASP cc_start: 0.8814 (p0) cc_final: 0.8518 (p0) REVERT: H 210 ASP cc_start: 0.8651 (t0) cc_final: 0.8398 (t0) REVERT: H 244 GLU cc_start: 0.9227 (mm-30) cc_final: 0.8862 (mm-30) REVERT: H 329 GLU cc_start: 0.8754 (tp30) cc_final: 0.8109 (tp30) REVERT: H 415 MET cc_start: 0.8628 (ppp) cc_final: 0.8036 (tmm) REVERT: H 416 MET cc_start: 0.8304 (mmm) cc_final: 0.8046 (mmm) REVERT: I 59 GLN cc_start: 0.9295 (pm20) cc_final: 0.8991 (pm20) REVERT: I 210 ASP cc_start: 0.8745 (t70) cc_final: 0.8461 (t0) REVERT: I 265 ASP cc_start: 0.8762 (t0) cc_final: 0.8540 (t0) REVERT: J 21 MET cc_start: 0.8787 (tmm) cc_final: 0.8503 (tmm) REVERT: J 62 PHE cc_start: 0.8950 (p90) cc_final: 0.8623 (p90) REVERT: K 1 MET cc_start: 0.7223 (tpt) cc_final: 0.6874 (tpp) REVERT: K 21 MET cc_start: 0.8969 (ttp) cc_final: 0.7839 (tmm) REVERT: K 147 MET cc_start: 0.9011 (mmm) cc_final: 0.8534 (mmm) REVERT: K 415 MET cc_start: 0.9311 (tmm) cc_final: 0.8744 (tmm) REVERT: K 416 MET cc_start: 0.9013 (ppp) cc_final: 0.8697 (ppp) REVERT: L 29 MET cc_start: 0.8727 (mtp) cc_final: 0.8332 (mtp) REVERT: L 147 MET cc_start: 0.7660 (tpp) cc_final: 0.6964 (tpp) REVERT: L 189 GLN cc_start: 0.8961 (mt0) cc_final: 0.7976 (tm-30) REVERT: L 197 TYR cc_start: 0.8975 (t80) cc_final: 0.8567 (t80) REVERT: L 234 GLU cc_start: 0.8934 (mt-10) cc_final: 0.8536 (mt-10) REVERT: L 327 MET cc_start: 0.8269 (tpp) cc_final: 0.8067 (tpp) REVERT: L 384 ARG cc_start: 0.7161 (tpt170) cc_final: 0.6942 (tpt170) REVERT: L 390 MET cc_start: 0.6277 (pmm) cc_final: 0.5245 (pmm) outliers start: 115 outliers final: 67 residues processed: 510 average time/residue: 0.1976 time to fit residues: 167.7749 Evaluate side-chains 470 residues out of total 4296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 399 time to evaluate : 1.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain B residue 131 ILE Chi-restraints excluded: chain B residue 193 GLN Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain C residue 134 GLU Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain C residue 205 MET Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 334 GLU Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain D residue 195 ILE Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain D residue 322 ASP Chi-restraints excluded: chain D residue 363 SER Chi-restraints excluded: chain D residue 377 LEU Chi-restraints excluded: chain D residue 411 ASP Chi-restraints excluded: chain E residue 31 LYS Chi-restraints excluded: chain E residue 42 HIS Chi-restraints excluded: chain E residue 110 TYR Chi-restraints excluded: chain E residue 157 LEU Chi-restraints excluded: chain E residue 313 LEU Chi-restraints excluded: chain F residue 140 HIS Chi-restraints excluded: chain F residue 190 ASN Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 286 THR Chi-restraints excluded: chain F residue 295 HIS Chi-restraints excluded: chain F residue 330 VAL Chi-restraints excluded: chain F residue 412 PHE Chi-restraints excluded: chain G residue 41 GLN Chi-restraints excluded: chain G residue 77 ASP Chi-restraints excluded: chain G residue 121 PHE Chi-restraints excluded: chain G residue 164 LEU Chi-restraints excluded: chain G residue 260 VAL Chi-restraints excluded: chain G residue 275 ASN Chi-restraints excluded: chain G residue 308 GLU Chi-restraints excluded: chain G residue 338 THR Chi-restraints excluded: chain G residue 358 ILE Chi-restraints excluded: chain H residue 85 GLN Chi-restraints excluded: chain H residue 131 ILE Chi-restraints excluded: chain H residue 239 HIS Chi-restraints excluded: chain H residue 260 VAL Chi-restraints excluded: chain H residue 286 THR Chi-restraints excluded: chain I residue 39 LEU Chi-restraints excluded: chain I residue 42 HIS Chi-restraints excluded: chain I residue 158 THR Chi-restraints excluded: chain I residue 164 LEU Chi-restraints excluded: chain I residue 259 ASP Chi-restraints excluded: chain J residue 4 THR Chi-restraints excluded: chain J residue 9 THR Chi-restraints excluded: chain J residue 41 GLN Chi-restraints excluded: chain J residue 84 CYS Chi-restraints excluded: chain J residue 154 THR Chi-restraints excluded: chain J residue 168 ILE Chi-restraints excluded: chain J residue 186 MET Chi-restraints excluded: chain J residue 188 LEU Chi-restraints excluded: chain K residue 9 THR Chi-restraints excluded: chain K residue 109 ARG Chi-restraints excluded: chain K residue 214 GLU Chi-restraints excluded: chain K residue 260 VAL Chi-restraints excluded: chain K residue 365 THR Chi-restraints excluded: chain L residue 41 GLN Chi-restraints excluded: chain L residue 158 THR Chi-restraints excluded: chain L residue 275 ASN Chi-restraints excluded: chain L residue 295 HIS Chi-restraints excluded: chain L residue 341 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 313 optimal weight: 2.9990 chunk 249 optimal weight: 1.9990 chunk 431 optimal weight: 3.9990 chunk 120 optimal weight: 3.9990 chunk 221 optimal weight: 40.0000 chunk 320 optimal weight: 2.9990 chunk 61 optimal weight: 4.9990 chunk 114 optimal weight: 0.8980 chunk 250 optimal weight: 8.9990 chunk 377 optimal weight: 2.9990 chunk 121 optimal weight: 0.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 129 ASN ** E 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 388 HIS ** H 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 172 GLN I 292 ASN ** J 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 292 ASN ** L 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 239 HIS L 295 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.094267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.063916 restraints weight = 142603.623| |-----------------------------------------------------------------------------| r_work (start): 0.3119 rms_B_bonded: 4.19 r_work: 0.2950 rms_B_bonded: 4.57 restraints_weight: 0.5000 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 moved from start: 0.2174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 40142 Z= 0.145 Angle : 0.536 9.789 54060 Z= 0.273 Chirality : 0.041 0.253 6144 Planarity : 0.004 0.068 7054 Dihedral : 5.136 148.601 5463 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 2.56 % Allowed : 15.36 % Favored : 82.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.10 (0.12), residues: 4992 helix: 0.76 (0.11), residues: 2288 sheet: 0.61 (0.22), residues: 592 loop : 1.01 (0.14), residues: 2112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG C 30 TYR 0.022 0.001 TYR H 197 PHE 0.017 0.001 PHE H 50 TRP 0.033 0.001 TRP E 381 HIS 0.005 0.001 HIS J 42 Details of bonding type rmsd covalent geometry : bond 0.00324 (40141) covalent geometry : angle 0.53612 (54060) hydrogen bonds : bond 0.04060 ( 1746) hydrogen bonds : angle 4.86183 ( 5106) Misc. bond : bond 0.00126 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9984 Ramachandran restraints generated. 4992 Oldfield, 0 Emsley, 4992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9984 Ramachandran restraints generated. 4992 Oldfield, 0 Emsley, 4992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 548 residues out of total 4296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 438 time to evaluate : 1.030 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: A 269 ARG cc_start: 0.9475 (mmp80) cc_final: 0.8959 (mmp80) REVERT: A 322 ASP cc_start: 0.8937 (t0) cc_final: 0.8664 (t0) REVERT: A 336 LYS cc_start: 0.8587 (mmmm) cc_final: 0.8369 (mmmm) REVERT: A 341 MET cc_start: 0.8347 (tmm) cc_final: 0.7860 (tmm) REVERT: A 343 LEU cc_start: 0.9214 (mt) cc_final: 0.8930 (mt) REVERT: B 1 MET cc_start: 0.8785 (tpp) cc_final: 0.8522 (tpp) REVERT: B 193 GLN cc_start: 0.9278 (OUTLIER) cc_final: 0.9064 (mp10) REVERT: B 322 ASP cc_start: 0.8809 (t0) cc_final: 0.8546 (t0) REVERT: B 376 GLU cc_start: 0.9183 (tt0) cc_final: 0.8882 (tt0) REVERT: B 415 MET cc_start: 0.9230 (tmm) cc_final: 0.8916 (tmm) REVERT: C 134 GLU cc_start: 0.8981 (OUTLIER) cc_final: 0.8767 (pm20) REVERT: C 245 MET cc_start: 0.9060 (mmt) cc_final: 0.8848 (mmt) REVERT: D 1 MET cc_start: 0.6859 (tpt) cc_final: 0.6429 (tpt) REVERT: D 210 ASP cc_start: 0.8612 (t0) cc_final: 0.8383 (t0) REVERT: D 222 LEU cc_start: 0.9318 (OUTLIER) cc_final: 0.9105 (mm) REVERT: D 241 GLN cc_start: 0.8749 (tm-30) cc_final: 0.8514 (tm-30) REVERT: D 334 GLU cc_start: 0.8667 (mm-30) cc_final: 0.8386 (mm-30) REVERT: D 390 MET cc_start: 0.8750 (pmm) cc_final: 0.8054 (pmm) REVERT: E 32 GLN cc_start: 0.7161 (tm-30) cc_final: 0.6911 (tm-30) REVERT: E 197 TYR cc_start: 0.9041 (t80) cc_final: 0.8511 (t80) REVERT: E 211 GLU cc_start: 0.8399 (mm-30) cc_final: 0.8069 (mm-30) REVERT: E 241 GLN cc_start: 0.8485 (tm-30) cc_final: 0.8243 (tm-30) REVERT: E 295 HIS cc_start: 0.9127 (t-90) cc_final: 0.8916 (t-90) REVERT: E 327 MET cc_start: 0.8515 (ttm) cc_final: 0.8220 (ttm) REVERT: E 380 MET cc_start: 0.9422 (ptt) cc_final: 0.9132 (ptt) REVERT: F 29 MET cc_start: 0.9130 (ptm) cc_final: 0.8832 (ptt) REVERT: F 322 ASP cc_start: 0.8924 (t70) cc_final: 0.8636 (t70) REVERT: F 327 MET cc_start: 0.5027 (mmm) cc_final: 0.4789 (tpt) REVERT: G 164 LEU cc_start: 0.9041 (OUTLIER) cc_final: 0.8813 (mt) REVERT: G 269 ARG cc_start: 0.9457 (tpp80) cc_final: 0.9040 (tpp80) REVERT: G 274 TYR cc_start: 0.8730 (m-80) cc_final: 0.8136 (m-80) REVERT: G 326 LYS cc_start: 0.9521 (tppt) cc_final: 0.9204 (tppt) REVERT: G 341 MET cc_start: 0.7704 (tmm) cc_final: 0.7320 (tmm) REVERT: H 1 MET cc_start: 0.8525 (tpt) cc_final: 0.8131 (tpt) REVERT: H 33 ASP cc_start: 0.8343 (t0) cc_final: 0.7716 (p0) REVERT: H 36 PHE cc_start: 0.9262 (t80) cc_final: 0.9034 (t80) REVERT: H 210 ASP cc_start: 0.8604 (t0) cc_final: 0.8306 (t0) REVERT: H 244 GLU cc_start: 0.9167 (mm-30) cc_final: 0.8797 (mm-30) REVERT: H 329 GLU cc_start: 0.8693 (tp30) cc_final: 0.8084 (tp30) REVERT: H 415 MET cc_start: 0.8599 (ppp) cc_final: 0.7959 (tmm) REVERT: H 416 MET cc_start: 0.8351 (mmm) cc_final: 0.8040 (mmm) REVERT: I 210 ASP cc_start: 0.8736 (t70) cc_final: 0.8433 (t0) REVERT: I 265 ASP cc_start: 0.8749 (t0) cc_final: 0.8509 (t0) REVERT: I 374 GLN cc_start: 0.8639 (pm20) cc_final: 0.8424 (pm20) REVERT: J 21 MET cc_start: 0.8707 (tmm) cc_final: 0.8291 (tmm) REVERT: J 58 LEU cc_start: 0.9295 (OUTLIER) cc_final: 0.9093 (mm) REVERT: J 62 PHE cc_start: 0.8975 (p90) cc_final: 0.8625 (p90) REVERT: K 1 MET cc_start: 0.7141 (tpt) cc_final: 0.6784 (tpp) REVERT: K 21 MET cc_start: 0.8960 (ttp) cc_final: 0.7812 (tmm) REVERT: K 147 MET cc_start: 0.9033 (mmm) cc_final: 0.8527 (mmm) REVERT: K 360 TYR cc_start: 0.9213 (t80) cc_final: 0.8999 (t80) REVERT: K 415 MET cc_start: 0.9293 (tmm) cc_final: 0.8739 (tmm) REVERT: K 416 MET cc_start: 0.8981 (ppp) cc_final: 0.8664 (ppp) REVERT: L 29 MET cc_start: 0.8564 (mtp) cc_final: 0.8203 (mtp) REVERT: L 30 ARG cc_start: 0.6987 (tpt170) cc_final: 0.6389 (tpp80) REVERT: L 147 MET cc_start: 0.7725 (tpp) cc_final: 0.7074 (tpp) REVERT: L 189 GLN cc_start: 0.8970 (mt0) cc_final: 0.7990 (tm-30) REVERT: L 197 TYR cc_start: 0.8978 (t80) cc_final: 0.8635 (t80) REVERT: L 348 LYS cc_start: 0.9719 (mmmt) cc_final: 0.9497 (tppt) REVERT: L 380 MET cc_start: 0.9279 (ppp) cc_final: 0.8932 (ptt) REVERT: L 390 MET cc_start: 0.6435 (pmm) cc_final: 0.5446 (pmm) REVERT: L 415 MET cc_start: 0.8325 (ttt) cc_final: 0.8074 (tmm) outliers start: 110 outliers final: 63 residues processed: 524 average time/residue: 0.1961 time to fit residues: 170.1175 Evaluate side-chains 473 residues out of total 4296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 405 time to evaluate : 1.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 398 PHE Chi-restraints excluded: chain B residue 131 ILE Chi-restraints excluded: chain B residue 193 GLN Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain C residue 134 GLU Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain D residue 195 ILE Chi-restraints excluded: chain D residue 222 LEU Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain D residue 322 ASP Chi-restraints excluded: chain D residue 363 SER Chi-restraints excluded: chain D residue 411 ASP Chi-restraints excluded: chain E residue 31 LYS Chi-restraints excluded: chain E residue 42 HIS Chi-restraints excluded: chain E residue 110 TYR Chi-restraints excluded: chain E residue 157 LEU Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 140 HIS Chi-restraints excluded: chain F residue 157 LEU Chi-restraints excluded: chain F residue 190 ASN Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 264 LEU Chi-restraints excluded: chain F residue 286 THR Chi-restraints excluded: chain F residue 295 HIS Chi-restraints excluded: chain F residue 412 PHE Chi-restraints excluded: chain G residue 41 GLN Chi-restraints excluded: chain G residue 77 ASP Chi-restraints excluded: chain G residue 121 PHE Chi-restraints excluded: chain G residue 164 LEU Chi-restraints excluded: chain G residue 260 VAL Chi-restraints excluded: chain G residue 275 ASN Chi-restraints excluded: chain G residue 308 GLU Chi-restraints excluded: chain G residue 338 THR Chi-restraints excluded: chain G residue 358 ILE Chi-restraints excluded: chain H residue 131 ILE Chi-restraints excluded: chain H residue 260 VAL Chi-restraints excluded: chain H residue 286 THR Chi-restraints excluded: chain I residue 29 MET Chi-restraints excluded: chain I residue 39 LEU Chi-restraints excluded: chain I residue 42 HIS Chi-restraints excluded: chain I residue 49 ILE Chi-restraints excluded: chain I residue 158 THR Chi-restraints excluded: chain I residue 164 LEU Chi-restraints excluded: chain I residue 260 VAL Chi-restraints excluded: chain J residue 4 THR Chi-restraints excluded: chain J residue 9 THR Chi-restraints excluded: chain J residue 58 LEU Chi-restraints excluded: chain J residue 84 CYS Chi-restraints excluded: chain J residue 154 THR Chi-restraints excluded: chain J residue 168 ILE Chi-restraints excluded: chain J residue 186 MET Chi-restraints excluded: chain J residue 188 LEU Chi-restraints excluded: chain J residue 205 MET Chi-restraints excluded: chain J residue 373 THR Chi-restraints excluded: chain K residue 9 THR Chi-restraints excluded: chain K residue 93 THR Chi-restraints excluded: chain K residue 284 VAL Chi-restraints excluded: chain K residue 365 THR Chi-restraints excluded: chain L residue 41 GLN Chi-restraints excluded: chain L residue 228 VAL Chi-restraints excluded: chain L residue 275 ASN Chi-restraints excluded: chain L residue 295 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 126 optimal weight: 4.9990 chunk 307 optimal weight: 1.9990 chunk 93 optimal weight: 9.9990 chunk 323 optimal weight: 6.9990 chunk 345 optimal weight: 0.6980 chunk 229 optimal weight: 5.9990 chunk 148 optimal weight: 0.0040 chunk 89 optimal weight: 5.9990 chunk 199 optimal weight: 6.9990 chunk 156 optimal weight: 5.9990 chunk 491 optimal weight: 20.0000 overall best weight: 2.7398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 193 GLN ** F 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 388 HIS ** H 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 85 GLN ** H 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 292 ASN ** L 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.093858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.063457 restraints weight = 142292.732| |-----------------------------------------------------------------------------| r_work (start): 0.3109 rms_B_bonded: 4.11 r_work: 0.2945 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.2302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 40142 Z= 0.176 Angle : 0.554 10.054 54060 Z= 0.279 Chirality : 0.042 0.163 6144 Planarity : 0.003 0.043 7054 Dihedral : 5.143 149.293 5463 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 2.75 % Allowed : 16.04 % Favored : 81.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.12 (0.12), residues: 4992 helix: 0.79 (0.11), residues: 2292 sheet: 0.55 (0.22), residues: 592 loop : 1.02 (0.15), residues: 2108 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG I 109 TYR 0.016 0.001 TYR J 80 PHE 0.012 0.001 PHE G 412 TRP 0.042 0.001 TRP E 381 HIS 0.005 0.001 HIS L 344 Details of bonding type rmsd covalent geometry : bond 0.00396 (40141) covalent geometry : angle 0.55353 (54060) hydrogen bonds : bond 0.03926 ( 1746) hydrogen bonds : angle 4.78936 ( 5106) Misc. bond : bond 0.00110 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9984 Ramachandran restraints generated. 4992 Oldfield, 0 Emsley, 4992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9984 Ramachandran restraints generated. 4992 Oldfield, 0 Emsley, 4992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 549 residues out of total 4296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 431 time to evaluate : 1.546 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: A 93 THR cc_start: 0.8965 (OUTLIER) cc_final: 0.8746 (m) REVERT: A 269 ARG cc_start: 0.9490 (mmp80) cc_final: 0.8979 (mmp80) REVERT: A 322 ASP cc_start: 0.8911 (t0) cc_final: 0.8653 (t0) REVERT: A 336 LYS cc_start: 0.8660 (mmmm) cc_final: 0.8449 (mmmm) REVERT: A 341 MET cc_start: 0.8349 (tmm) cc_final: 0.7828 (tmm) REVERT: B 1 MET cc_start: 0.8851 (tpp) cc_final: 0.8584 (tpp) REVERT: B 193 GLN cc_start: 0.9275 (OUTLIER) cc_final: 0.9048 (mp10) REVERT: B 322 ASP cc_start: 0.8825 (t0) cc_final: 0.8532 (t0) REVERT: B 376 GLU cc_start: 0.9189 (tt0) cc_final: 0.8875 (tt0) REVERT: B 415 MET cc_start: 0.9251 (tmm) cc_final: 0.8953 (tmm) REVERT: C 1 MET cc_start: 0.8014 (tpp) cc_final: 0.7799 (tpp) REVERT: D 1 MET cc_start: 0.6802 (tpt) cc_final: 0.6368 (tpt) REVERT: D 210 ASP cc_start: 0.8585 (t0) cc_final: 0.8347 (t0) REVERT: D 222 LEU cc_start: 0.9315 (OUTLIER) cc_final: 0.9093 (mm) REVERT: D 333 GLU cc_start: 0.8668 (tm-30) cc_final: 0.8195 (tm-30) REVERT: D 334 GLU cc_start: 0.8748 (mm-30) cc_final: 0.8302 (mm-30) REVERT: D 390 MET cc_start: 0.8835 (pmm) cc_final: 0.8334 (pmm) REVERT: E 32 GLN cc_start: 0.7177 (tm-30) cc_final: 0.6904 (tm-30) REVERT: E 197 TYR cc_start: 0.9014 (t80) cc_final: 0.8500 (t80) REVERT: E 211 GLU cc_start: 0.8416 (mm-30) cc_final: 0.8068 (mm-30) REVERT: E 241 GLN cc_start: 0.8449 (tm-30) cc_final: 0.8158 (tm-30) REVERT: E 327 MET cc_start: 0.8516 (ttm) cc_final: 0.8174 (ttm) REVERT: E 380 MET cc_start: 0.9419 (ptt) cc_final: 0.9144 (ptt) REVERT: F 29 MET cc_start: 0.9106 (ptm) cc_final: 0.8759 (ptt) REVERT: F 274 TYR cc_start: 0.9225 (m-80) cc_final: 0.8909 (m-80) REVERT: F 322 ASP cc_start: 0.8837 (t70) cc_final: 0.8530 (t70) REVERT: F 327 MET cc_start: 0.5320 (mmm) cc_final: 0.4950 (tpt) REVERT: G 164 LEU cc_start: 0.9054 (OUTLIER) cc_final: 0.8845 (mt) REVERT: G 269 ARG cc_start: 0.9476 (tpp80) cc_final: 0.9060 (tpp80) REVERT: G 274 TYR cc_start: 0.8728 (m-80) cc_final: 0.8153 (m-80) REVERT: G 326 LYS cc_start: 0.9518 (tppt) cc_final: 0.9200 (tppt) REVERT: G 341 MET cc_start: 0.7843 (tmm) cc_final: 0.7473 (tmm) REVERT: G 390 MET cc_start: 0.8731 (ptm) cc_final: 0.8511 (ptm) REVERT: H 33 ASP cc_start: 0.8324 (t0) cc_final: 0.7651 (p0) REVERT: H 36 PHE cc_start: 0.9265 (t80) cc_final: 0.9026 (t80) REVERT: H 210 ASP cc_start: 0.8635 (t0) cc_final: 0.8339 (t0) REVERT: H 244 GLU cc_start: 0.9165 (mm-30) cc_final: 0.8798 (mm-30) REVERT: H 329 GLU cc_start: 0.8700 (tp30) cc_final: 0.8062 (tp30) REVERT: I 210 ASP cc_start: 0.8743 (t70) cc_final: 0.8445 (t0) REVERT: I 265 ASP cc_start: 0.8770 (t0) cc_final: 0.8533 (t0) REVERT: J 21 MET cc_start: 0.8825 (tmm) cc_final: 0.8442 (tmm) REVERT: J 62 PHE cc_start: 0.8917 (p90) cc_final: 0.8635 (p90) REVERT: K 1 MET cc_start: 0.7199 (tpt) cc_final: 0.6820 (tpp) REVERT: K 21 MET cc_start: 0.8966 (ttp) cc_final: 0.7801 (tmm) REVERT: K 147 MET cc_start: 0.9015 (mmm) cc_final: 0.8497 (mmm) REVERT: K 322 ASP cc_start: 0.8678 (t0) cc_final: 0.8331 (t0) REVERT: K 360 TYR cc_start: 0.9205 (t80) cc_final: 0.8939 (t80) REVERT: K 415 MET cc_start: 0.9364 (tmm) cc_final: 0.8780 (tmm) REVERT: L 29 MET cc_start: 0.8664 (mtp) cc_final: 0.8275 (mtp) REVERT: L 30 ARG cc_start: 0.6997 (tpt170) cc_final: 0.6526 (tpp80) REVERT: L 147 MET cc_start: 0.7851 (tpp) cc_final: 0.7204 (tpp) REVERT: L 189 GLN cc_start: 0.8969 (mt0) cc_final: 0.7988 (tm-30) REVERT: L 197 TYR cc_start: 0.8942 (t80) cc_final: 0.8587 (t80) REVERT: L 380 MET cc_start: 0.9203 (ppp) cc_final: 0.8989 (ppp) REVERT: L 390 MET cc_start: 0.6300 (pmm) cc_final: 0.5282 (pmm) outliers start: 118 outliers final: 81 residues processed: 516 average time/residue: 0.2213 time to fit residues: 190.1163 Evaluate side-chains 489 residues out of total 4296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 404 time to evaluate : 1.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 398 PHE Chi-restraints excluded: chain B residue 131 ILE Chi-restraints excluded: chain B residue 163 ASP Chi-restraints excluded: chain B residue 168 ILE Chi-restraints excluded: chain B residue 193 GLN Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 245 MET Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain C residue 168 ILE Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 334 GLU Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain D residue 101 ILE Chi-restraints excluded: chain D residue 191 ILE Chi-restraints excluded: chain D residue 195 ILE Chi-restraints excluded: chain D residue 222 LEU Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain D residue 322 ASP Chi-restraints excluded: chain D residue 363 SER Chi-restraints excluded: chain D residue 411 ASP Chi-restraints excluded: chain E residue 31 LYS Chi-restraints excluded: chain E residue 42 HIS Chi-restraints excluded: chain E residue 110 TYR Chi-restraints excluded: chain E residue 157 LEU Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 294 LEU Chi-restraints excluded: chain E residue 365 THR Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 49 ILE Chi-restraints excluded: chain F residue 140 HIS Chi-restraints excluded: chain F residue 157 LEU Chi-restraints excluded: chain F residue 190 ASN Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 286 THR Chi-restraints excluded: chain F residue 295 HIS Chi-restraints excluded: chain F residue 412 PHE Chi-restraints excluded: chain G residue 77 ASP Chi-restraints excluded: chain G residue 121 PHE Chi-restraints excluded: chain G residue 164 LEU Chi-restraints excluded: chain G residue 260 VAL Chi-restraints excluded: chain G residue 275 ASN Chi-restraints excluded: chain G residue 308 GLU Chi-restraints excluded: chain G residue 338 THR Chi-restraints excluded: chain G residue 342 GLU Chi-restraints excluded: chain H residue 85 GLN Chi-restraints excluded: chain H residue 131 ILE Chi-restraints excluded: chain H residue 239 HIS Chi-restraints excluded: chain H residue 260 VAL Chi-restraints excluded: chain H residue 286 THR Chi-restraints excluded: chain I residue 39 LEU Chi-restraints excluded: chain I residue 42 HIS Chi-restraints excluded: chain I residue 49 ILE Chi-restraints excluded: chain I residue 101 ILE Chi-restraints excluded: chain I residue 158 THR Chi-restraints excluded: chain I residue 164 LEU Chi-restraints excluded: chain I residue 260 VAL Chi-restraints excluded: chain J residue 4 THR Chi-restraints excluded: chain J residue 9 THR Chi-restraints excluded: chain J residue 84 CYS Chi-restraints excluded: chain J residue 154 THR Chi-restraints excluded: chain J residue 168 ILE Chi-restraints excluded: chain J residue 186 MET Chi-restraints excluded: chain J residue 188 LEU Chi-restraints excluded: chain J residue 228 VAL Chi-restraints excluded: chain J residue 373 THR Chi-restraints excluded: chain K residue 9 THR Chi-restraints excluded: chain K residue 93 THR Chi-restraints excluded: chain K residue 109 ARG Chi-restraints excluded: chain K residue 214 GLU Chi-restraints excluded: chain K residue 260 VAL Chi-restraints excluded: chain K residue 284 VAL Chi-restraints excluded: chain K residue 365 THR Chi-restraints excluded: chain L residue 41 GLN Chi-restraints excluded: chain L residue 158 THR Chi-restraints excluded: chain L residue 228 VAL Chi-restraints excluded: chain L residue 275 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 41 optimal weight: 20.0000 chunk 436 optimal weight: 2.9990 chunk 427 optimal weight: 6.9990 chunk 455 optimal weight: 9.9990 chunk 430 optimal weight: 3.9990 chunk 361 optimal weight: 0.9990 chunk 418 optimal weight: 2.9990 chunk 339 optimal weight: 4.9990 chunk 296 optimal weight: 3.9990 chunk 356 optimal weight: 2.9990 chunk 153 optimal weight: 2.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 120 ASN D 256 HIS ** E 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 193 GLN ** F 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 388 HIS ** H 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 295 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.093918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.063628 restraints weight = 142855.165| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 4.09 r_work: 0.2943 rms_B_bonded: 4.55 restraints_weight: 0.5000 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.2408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 40142 Z= 0.170 Angle : 0.560 11.932 54060 Z= 0.280 Chirality : 0.041 0.171 6144 Planarity : 0.003 0.076 7054 Dihedral : 5.153 149.644 5463 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 2.82 % Allowed : 16.32 % Favored : 80.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.13 (0.12), residues: 4992 helix: 0.85 (0.11), residues: 2292 sheet: 0.42 (0.24), residues: 482 loop : 0.98 (0.14), residues: 2218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG D 30 TYR 0.016 0.001 TYR J 80 PHE 0.012 0.001 PHE G 412 TRP 0.027 0.001 TRP E 381 HIS 0.005 0.001 HIS L 295 Details of bonding type rmsd covalent geometry : bond 0.00384 (40141) covalent geometry : angle 0.55954 (54060) hydrogen bonds : bond 0.03772 ( 1746) hydrogen bonds : angle 4.71436 ( 5106) Misc. bond : bond 0.00097 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9984 Ramachandran restraints generated. 4992 Oldfield, 0 Emsley, 4992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9984 Ramachandran restraints generated. 4992 Oldfield, 0 Emsley, 4992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 546 residues out of total 4296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 425 time to evaluate : 1.247 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: A 93 THR cc_start: 0.8923 (OUTLIER) cc_final: 0.8441 (m) REVERT: A 269 ARG cc_start: 0.9481 (mmp80) cc_final: 0.8976 (mmp80) REVERT: A 322 ASP cc_start: 0.9027 (t0) cc_final: 0.8749 (t0) REVERT: A 336 LYS cc_start: 0.8680 (mmmm) cc_final: 0.8479 (mmmm) REVERT: A 341 MET cc_start: 0.8407 (tmm) cc_final: 0.7858 (tmm) REVERT: B 1 MET cc_start: 0.8765 (tpp) cc_final: 0.8542 (tpp) REVERT: B 59 GLN cc_start: 0.8618 (pm20) cc_final: 0.8135 (pm20) REVERT: B 322 ASP cc_start: 0.8837 (t0) cc_final: 0.8545 (t0) REVERT: B 376 GLU cc_start: 0.9158 (tt0) cc_final: 0.8856 (tt0) REVERT: B 415 MET cc_start: 0.9303 (tmm) cc_final: 0.9010 (tmm) REVERT: D 1 MET cc_start: 0.6784 (tpt) cc_final: 0.6359 (tpt) REVERT: D 210 ASP cc_start: 0.8599 (t0) cc_final: 0.8139 (t0) REVERT: D 222 LEU cc_start: 0.9293 (OUTLIER) cc_final: 0.9055 (mm) REVERT: D 333 GLU cc_start: 0.8686 (tm-30) cc_final: 0.8128 (tm-30) REVERT: D 334 GLU cc_start: 0.8762 (mm-30) cc_final: 0.8278 (mm-30) REVERT: D 390 MET cc_start: 0.8875 (pmm) cc_final: 0.8669 (pmm) REVERT: E 32 GLN cc_start: 0.7071 (tm-30) cc_final: 0.6802 (tm-30) REVERT: E 197 TYR cc_start: 0.9087 (t80) cc_final: 0.8573 (t80) REVERT: E 211 GLU cc_start: 0.8383 (mm-30) cc_final: 0.8023 (mm-30) REVERT: E 241 GLN cc_start: 0.8481 (tm-30) cc_final: 0.8265 (tm-30) REVERT: E 327 MET cc_start: 0.8528 (ttm) cc_final: 0.8123 (ttm) REVERT: E 380 MET cc_start: 0.9406 (ptt) cc_final: 0.9146 (ptt) REVERT: F 29 MET cc_start: 0.9111 (ptm) cc_final: 0.8808 (ptt) REVERT: F 274 TYR cc_start: 0.9294 (m-80) cc_final: 0.8931 (m-80) REVERT: F 322 ASP cc_start: 0.8953 (t70) cc_final: 0.8672 (t70) REVERT: F 327 MET cc_start: 0.5165 (mmm) cc_final: 0.4935 (tpt) REVERT: G 269 ARG cc_start: 0.9468 (tpp80) cc_final: 0.9043 (tpp80) REVERT: G 274 TYR cc_start: 0.8687 (m-80) cc_final: 0.8129 (m-80) REVERT: G 326 LYS cc_start: 0.9521 (tppt) cc_final: 0.9234 (tppt) REVERT: G 341 MET cc_start: 0.7882 (tmm) cc_final: 0.7596 (tmm) REVERT: G 344 HIS cc_start: 0.8795 (m90) cc_final: 0.8544 (m-70) REVERT: H 33 ASP cc_start: 0.8282 (t0) cc_final: 0.7637 (p0) REVERT: H 36 PHE cc_start: 0.9293 (t80) cc_final: 0.9030 (t80) REVERT: H 210 ASP cc_start: 0.8597 (t0) cc_final: 0.8296 (t0) REVERT: H 244 GLU cc_start: 0.9184 (mm-30) cc_final: 0.8811 (mm-30) REVERT: H 292 ASN cc_start: 0.9427 (t0) cc_final: 0.9114 (t0) REVERT: H 329 GLU cc_start: 0.8675 (tp30) cc_final: 0.8083 (tp30) REVERT: I 210 ASP cc_start: 0.8742 (t70) cc_final: 0.8445 (t0) REVERT: I 265 ASP cc_start: 0.8767 (t0) cc_final: 0.8534 (t0) REVERT: J 374 GLN cc_start: 0.8460 (tm-30) cc_final: 0.8225 (tm-30) REVERT: K 1 MET cc_start: 0.7171 (tpt) cc_final: 0.6950 (tpp) REVERT: K 21 MET cc_start: 0.8922 (ttp) cc_final: 0.7746 (tmm) REVERT: K 147 MET cc_start: 0.9043 (mmm) cc_final: 0.8518 (mmm) REVERT: K 322 ASP cc_start: 0.8714 (t0) cc_final: 0.8392 (t0) REVERT: K 415 MET cc_start: 0.9273 (tmm) cc_final: 0.8732 (tmm) REVERT: K 416 MET cc_start: 0.8987 (ppp) cc_final: 0.8661 (ppp) REVERT: L 29 MET cc_start: 0.8601 (mtp) cc_final: 0.8258 (mtp) REVERT: L 30 ARG cc_start: 0.7013 (tpt170) cc_final: 0.6509 (tpp80) REVERT: L 147 MET cc_start: 0.7773 (tpp) cc_final: 0.7103 (tpp) REVERT: L 189 GLN cc_start: 0.8977 (mt0) cc_final: 0.8039 (tm-30) REVERT: L 197 TYR cc_start: 0.8985 (t80) cc_final: 0.8666 (t80) REVERT: L 238 ARG cc_start: 0.7679 (OUTLIER) cc_final: 0.7225 (tpt170) REVERT: L 380 MET cc_start: 0.9277 (ppp) cc_final: 0.9051 (ppp) REVERT: L 390 MET cc_start: 0.6601 (pmm) cc_final: 0.5671 (pmm) outliers start: 121 outliers final: 92 residues processed: 517 average time/residue: 0.1997 time to fit residues: 171.1844 Evaluate side-chains 503 residues out of total 4296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 408 time to evaluate : 1.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 398 PHE Chi-restraints excluded: chain B residue 131 ILE Chi-restraints excluded: chain B residue 168 ILE Chi-restraints excluded: chain B residue 193 GLN Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 245 MET Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain C residue 168 ILE Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 334 GLU Chi-restraints excluded: chain C residue 369 GLU Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain D residue 101 ILE Chi-restraints excluded: chain D residue 120 ASN Chi-restraints excluded: chain D residue 191 ILE Chi-restraints excluded: chain D residue 195 ILE Chi-restraints excluded: chain D residue 222 LEU Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain D residue 322 ASP Chi-restraints excluded: chain D residue 363 SER Chi-restraints excluded: chain D residue 411 ASP Chi-restraints excluded: chain E residue 31 LYS Chi-restraints excluded: chain E residue 42 HIS Chi-restraints excluded: chain E residue 110 TYR Chi-restraints excluded: chain E residue 157 LEU Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 294 LEU Chi-restraints excluded: chain E residue 365 THR Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 49 ILE Chi-restraints excluded: chain F residue 140 HIS Chi-restraints excluded: chain F residue 157 LEU Chi-restraints excluded: chain F residue 190 ASN Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 286 THR Chi-restraints excluded: chain F residue 295 HIS Chi-restraints excluded: chain F residue 412 PHE Chi-restraints excluded: chain G residue 41 GLN Chi-restraints excluded: chain G residue 77 ASP Chi-restraints excluded: chain G residue 101 ILE Chi-restraints excluded: chain G residue 121 PHE Chi-restraints excluded: chain G residue 260 VAL Chi-restraints excluded: chain G residue 275 ASN Chi-restraints excluded: chain G residue 308 GLU Chi-restraints excluded: chain G residue 338 THR Chi-restraints excluded: chain G residue 342 GLU Chi-restraints excluded: chain G residue 358 ILE Chi-restraints excluded: chain H residue 85 GLN Chi-restraints excluded: chain H residue 131 ILE Chi-restraints excluded: chain H residue 205 MET Chi-restraints excluded: chain H residue 239 HIS Chi-restraints excluded: chain H residue 260 VAL Chi-restraints excluded: chain H residue 286 THR Chi-restraints excluded: chain I residue 39 LEU Chi-restraints excluded: chain I residue 42 HIS Chi-restraints excluded: chain I residue 49 ILE Chi-restraints excluded: chain I residue 101 ILE Chi-restraints excluded: chain I residue 158 THR Chi-restraints excluded: chain I residue 164 LEU Chi-restraints excluded: chain I residue 260 VAL Chi-restraints excluded: chain I residue 313 LEU Chi-restraints excluded: chain J residue 4 THR Chi-restraints excluded: chain J residue 9 THR Chi-restraints excluded: chain J residue 84 CYS Chi-restraints excluded: chain J residue 92 ARG Chi-restraints excluded: chain J residue 154 THR Chi-restraints excluded: chain J residue 168 ILE Chi-restraints excluded: chain J residue 186 MET Chi-restraints excluded: chain J residue 188 LEU Chi-restraints excluded: chain J residue 228 VAL Chi-restraints excluded: chain J residue 373 THR Chi-restraints excluded: chain K residue 9 THR Chi-restraints excluded: chain K residue 93 THR Chi-restraints excluded: chain K residue 109 ARG Chi-restraints excluded: chain K residue 214 GLU Chi-restraints excluded: chain K residue 228 VAL Chi-restraints excluded: chain K residue 260 VAL Chi-restraints excluded: chain K residue 284 VAL Chi-restraints excluded: chain K residue 365 THR Chi-restraints excluded: chain L residue 41 GLN Chi-restraints excluded: chain L residue 158 THR Chi-restraints excluded: chain L residue 228 VAL Chi-restraints excluded: chain L residue 238 ARG Chi-restraints excluded: chain L residue 275 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 164 optimal weight: 20.0000 chunk 256 optimal weight: 50.0000 chunk 262 optimal weight: 0.6980 chunk 87 optimal weight: 9.9990 chunk 8 optimal weight: 0.7980 chunk 396 optimal weight: 1.9990 chunk 231 optimal weight: 9.9990 chunk 116 optimal weight: 3.9990 chunk 384 optimal weight: 2.9990 chunk 145 optimal weight: 0.7980 chunk 402 optimal weight: 0.6980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 388 HIS ** H 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.094775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.065119 restraints weight = 138823.493| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 4.18 r_work: 0.2983 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.2497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 40142 Z= 0.112 Angle : 0.550 11.072 54060 Z= 0.273 Chirality : 0.041 0.179 6144 Planarity : 0.003 0.052 7054 Dihedral : 5.108 149.539 5463 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 2.14 % Allowed : 17.25 % Favored : 80.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.23 (0.12), residues: 4992 helix: 0.92 (0.11), residues: 2292 sheet: 0.38 (0.23), residues: 532 loop : 1.07 (0.14), residues: 2168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG D 30 TYR 0.014 0.001 TYR L 110 PHE 0.029 0.001 PHE D 121 TRP 0.021 0.001 TRP E 381 HIS 0.006 0.001 HIS L 295 Details of bonding type rmsd covalent geometry : bond 0.00254 (40141) covalent geometry : angle 0.55040 (54060) hydrogen bonds : bond 0.03484 ( 1746) hydrogen bonds : angle 4.52629 ( 5106) Misc. bond : bond 0.00068 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9984 Ramachandran restraints generated. 4992 Oldfield, 0 Emsley, 4992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9984 Ramachandran restraints generated. 4992 Oldfield, 0 Emsley, 4992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 527 residues out of total 4296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 435 time to evaluate : 1.577 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: A 93 THR cc_start: 0.8860 (OUTLIER) cc_final: 0.8617 (m) REVERT: A 269 ARG cc_start: 0.9472 (mmp80) cc_final: 0.8948 (mmp80) REVERT: A 322 ASP cc_start: 0.8986 (t0) cc_final: 0.8717 (t0) REVERT: A 336 LYS cc_start: 0.8670 (mmmm) cc_final: 0.8427 (mmmm) REVERT: A 341 MET cc_start: 0.8576 (tmm) cc_final: 0.7840 (tmm) REVERT: B 1 MET cc_start: 0.8775 (tpp) cc_final: 0.8466 (tpp) REVERT: B 322 ASP cc_start: 0.8844 (t0) cc_final: 0.8530 (t0) REVERT: B 415 MET cc_start: 0.9280 (tmm) cc_final: 0.9005 (tmm) REVERT: C 1 MET cc_start: 0.8020 (tpp) cc_final: 0.7755 (tpp) REVERT: D 1 MET cc_start: 0.6798 (tpt) cc_final: 0.6393 (tpt) REVERT: D 210 ASP cc_start: 0.8533 (t0) cc_final: 0.8055 (t0) REVERT: D 333 GLU cc_start: 0.8676 (tm-30) cc_final: 0.8469 (tm-30) REVERT: E 197 TYR cc_start: 0.9068 (t80) cc_final: 0.8568 (t80) REVERT: E 211 GLU cc_start: 0.8375 (mm-30) cc_final: 0.7768 (mm-30) REVERT: E 215 GLU cc_start: 0.8741 (tt0) cc_final: 0.7666 (tt0) REVERT: E 241 GLN cc_start: 0.8431 (tm-30) cc_final: 0.8196 (tm-30) REVERT: E 327 MET cc_start: 0.8493 (ttm) cc_final: 0.8088 (ttm) REVERT: E 380 MET cc_start: 0.9425 (ptt) cc_final: 0.9142 (ptt) REVERT: F 29 MET cc_start: 0.9073 (ptm) cc_final: 0.8710 (ptt) REVERT: F 274 TYR cc_start: 0.9282 (m-80) cc_final: 0.8982 (m-80) REVERT: F 322 ASP cc_start: 0.8910 (t70) cc_final: 0.8607 (t70) REVERT: F 327 MET cc_start: 0.5326 (mmm) cc_final: 0.5075 (tpt) REVERT: G 269 ARG cc_start: 0.9451 (tpp80) cc_final: 0.9010 (tpp80) REVERT: G 274 TYR cc_start: 0.8656 (m-80) cc_final: 0.8147 (m-80) REVERT: G 326 LYS cc_start: 0.9502 (tppt) cc_final: 0.9195 (tppt) REVERT: G 341 MET cc_start: 0.7783 (tmm) cc_final: 0.7515 (tmm) REVERT: G 344 HIS cc_start: 0.8702 (m90) cc_final: 0.8313 (m90) REVERT: G 390 MET cc_start: 0.8585 (ptm) cc_final: 0.8116 (ppp) REVERT: H 33 ASP cc_start: 0.8138 (t0) cc_final: 0.7534 (p0) REVERT: H 36 PHE cc_start: 0.9292 (t80) cc_final: 0.9020 (t80) REVERT: H 210 ASP cc_start: 0.8536 (t0) cc_final: 0.8234 (t0) REVERT: H 244 GLU cc_start: 0.9152 (mm-30) cc_final: 0.8783 (mm-30) REVERT: H 292 ASN cc_start: 0.9393 (t0) cc_final: 0.9081 (t0) REVERT: H 329 GLU cc_start: 0.8676 (tp30) cc_final: 0.8110 (tp30) REVERT: H 416 MET cc_start: 0.7869 (mmm) cc_final: 0.7621 (mmm) REVERT: I 110 TYR cc_start: 0.7485 (m-80) cc_final: 0.7241 (m-80) REVERT: I 210 ASP cc_start: 0.8669 (t70) cc_final: 0.8347 (t0) REVERT: I 265 ASP cc_start: 0.8702 (t0) cc_final: 0.8461 (t0) REVERT: J 21 MET cc_start: 0.8768 (tmm) cc_final: 0.8432 (tmm) REVERT: J 374 GLN cc_start: 0.8399 (tm-30) cc_final: 0.8162 (tm-30) REVERT: K 147 MET cc_start: 0.9035 (mmm) cc_final: 0.8484 (mmm) REVERT: K 322 ASP cc_start: 0.8678 (t0) cc_final: 0.8388 (t0) REVERT: K 360 TYR cc_start: 0.9130 (t80) cc_final: 0.8916 (t80) REVERT: K 415 MET cc_start: 0.9299 (tmm) cc_final: 0.8740 (tmm) REVERT: K 416 MET cc_start: 0.9049 (ppp) cc_final: 0.8718 (ppp) REVERT: L 29 MET cc_start: 0.8691 (mtp) cc_final: 0.8330 (mtp) REVERT: L 30 ARG cc_start: 0.7006 (tpt170) cc_final: 0.6499 (tpp80) REVERT: L 147 MET cc_start: 0.7844 (tpp) cc_final: 0.7253 (tpp) REVERT: L 189 GLN cc_start: 0.8981 (mt0) cc_final: 0.8033 (tm-30) REVERT: L 197 TYR cc_start: 0.8942 (t80) cc_final: 0.8585 (t80) REVERT: L 380 MET cc_start: 0.9241 (ppp) cc_final: 0.8990 (ppp) REVERT: L 390 MET cc_start: 0.6423 (pmm) cc_final: 0.5419 (pmm) outliers start: 92 outliers final: 65 residues processed: 503 average time/residue: 0.2130 time to fit residues: 176.5807 Evaluate side-chains 480 residues out of total 4296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 414 time to evaluate : 1.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 GLN Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 398 PHE Chi-restraints excluded: chain B residue 131 ILE Chi-restraints excluded: chain B residue 168 ILE Chi-restraints excluded: chain B residue 193 GLN Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 245 MET Chi-restraints excluded: chain B residue 327 MET Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain C residue 4 THR Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 369 GLU Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain D residue 191 ILE Chi-restraints excluded: chain D residue 195 ILE Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain D residue 322 ASP Chi-restraints excluded: chain D residue 363 SER Chi-restraints excluded: chain E residue 31 LYS Chi-restraints excluded: chain E residue 42 HIS Chi-restraints excluded: chain E residue 110 TYR Chi-restraints excluded: chain E residue 157 LEU Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 365 THR Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 49 ILE Chi-restraints excluded: chain F residue 140 HIS Chi-restraints excluded: chain F residue 157 LEU Chi-restraints excluded: chain F residue 190 ASN Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 286 THR Chi-restraints excluded: chain F residue 295 HIS Chi-restraints excluded: chain F residue 412 PHE Chi-restraints excluded: chain G residue 77 ASP Chi-restraints excluded: chain G residue 275 ASN Chi-restraints excluded: chain G residue 308 GLU Chi-restraints excluded: chain H residue 131 ILE Chi-restraints excluded: chain H residue 239 HIS Chi-restraints excluded: chain H residue 260 VAL Chi-restraints excluded: chain I residue 39 LEU Chi-restraints excluded: chain I residue 42 HIS Chi-restraints excluded: chain I residue 49 ILE Chi-restraints excluded: chain I residue 101 ILE Chi-restraints excluded: chain I residue 158 THR Chi-restraints excluded: chain I residue 164 LEU Chi-restraints excluded: chain J residue 4 THR Chi-restraints excluded: chain J residue 9 THR Chi-restraints excluded: chain J residue 92 ARG Chi-restraints excluded: chain J residue 154 THR Chi-restraints excluded: chain J residue 168 ILE Chi-restraints excluded: chain J residue 186 MET Chi-restraints excluded: chain J residue 188 LEU Chi-restraints excluded: chain J residue 205 MET Chi-restraints excluded: chain K residue 9 THR Chi-restraints excluded: chain K residue 42 HIS Chi-restraints excluded: chain K residue 109 ARG Chi-restraints excluded: chain K residue 284 VAL Chi-restraints excluded: chain K residue 365 THR Chi-restraints excluded: chain L residue 41 GLN Chi-restraints excluded: chain L residue 158 THR Chi-restraints excluded: chain L residue 228 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 321 optimal weight: 5.9990 chunk 423 optimal weight: 0.8980 chunk 469 optimal weight: 4.9990 chunk 311 optimal weight: 0.9980 chunk 254 optimal weight: 8.9990 chunk 26 optimal weight: 10.0000 chunk 47 optimal weight: 5.9990 chunk 37 optimal weight: 20.0000 chunk 369 optimal weight: 10.0000 chunk 78 optimal weight: 1.9990 chunk 39 optimal weight: 10.0000 overall best weight: 2.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 295 HIS D 241 GLN ** E 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 388 HIS ** H 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.093884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.063545 restraints weight = 142249.352| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 4.12 r_work: 0.2949 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8605 moved from start: 0.2577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 40142 Z= 0.188 Angle : 0.587 11.217 54060 Z= 0.291 Chirality : 0.042 0.183 6144 Planarity : 0.003 0.042 7054 Dihedral : 5.148 150.580 5463 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 2.44 % Allowed : 17.39 % Favored : 80.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.22 (0.12), residues: 4992 helix: 0.94 (0.11), residues: 2292 sheet: 0.39 (0.24), residues: 482 loop : 1.02 (0.14), residues: 2218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG L 238 TYR 0.018 0.001 TYR J 80 PHE 0.015 0.001 PHE G 412 TRP 0.022 0.001 TRP E 381 HIS 0.008 0.001 HIS A 295 Details of bonding type rmsd covalent geometry : bond 0.00425 (40141) covalent geometry : angle 0.58691 (54060) hydrogen bonds : bond 0.03632 ( 1746) hydrogen bonds : angle 4.61465 ( 5106) Misc. bond : bond 0.00081 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9984 Ramachandran restraints generated. 4992 Oldfield, 0 Emsley, 4992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9984 Ramachandran restraints generated. 4992 Oldfield, 0 Emsley, 4992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 522 residues out of total 4296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 417 time to evaluate : 1.519 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: A 29 MET cc_start: 0.8125 (mmp) cc_final: 0.7901 (mpp) REVERT: A 93 THR cc_start: 0.8797 (OUTLIER) cc_final: 0.8532 (m) REVERT: A 269 ARG cc_start: 0.9481 (mmp80) cc_final: 0.8974 (mmp80) REVERT: A 322 ASP cc_start: 0.8985 (t0) cc_final: 0.8729 (t0) REVERT: A 336 LYS cc_start: 0.8703 (mmmm) cc_final: 0.8464 (mmmm) REVERT: A 341 MET cc_start: 0.8481 (tmm) cc_final: 0.7985 (tmm) REVERT: A 343 LEU cc_start: 0.9269 (OUTLIER) cc_final: 0.9024 (mm) REVERT: B 1 MET cc_start: 0.8696 (tpp) cc_final: 0.8405 (tpp) REVERT: B 59 GLN cc_start: 0.8571 (pm20) cc_final: 0.8251 (pm20) REVERT: B 322 ASP cc_start: 0.8872 (t0) cc_final: 0.8594 (t0) REVERT: B 415 MET cc_start: 0.9296 (tmm) cc_final: 0.9045 (tmm) REVERT: C 1 MET cc_start: 0.7997 (tpp) cc_final: 0.7753 (tpp) REVERT: C 341 MET cc_start: 0.9217 (ppp) cc_final: 0.8998 (ppp) REVERT: D 1 MET cc_start: 0.6771 (tpt) cc_final: 0.6359 (tpt) REVERT: D 210 ASP cc_start: 0.8553 (t0) cc_final: 0.8064 (t0) REVERT: D 333 GLU cc_start: 0.8686 (tm-30) cc_final: 0.8294 (tm-30) REVERT: D 334 GLU cc_start: 0.8638 (mm-30) cc_final: 0.8239 (mm-30) REVERT: E 197 TYR cc_start: 0.9077 (t80) cc_final: 0.8583 (t80) REVERT: E 210 ASP cc_start: 0.7910 (OUTLIER) cc_final: 0.7648 (t0) REVERT: E 211 GLU cc_start: 0.8395 (mm-30) cc_final: 0.8108 (mm-30) REVERT: E 215 GLU cc_start: 0.8756 (tt0) cc_final: 0.8037 (tt0) REVERT: E 241 GLN cc_start: 0.8447 (tm-30) cc_final: 0.8234 (tm-30) REVERT: E 327 MET cc_start: 0.8486 (ttm) cc_final: 0.8094 (ttm) REVERT: E 380 MET cc_start: 0.9440 (ptt) cc_final: 0.9186 (ptt) REVERT: F 29 MET cc_start: 0.9095 (ptm) cc_final: 0.8744 (ptt) REVERT: F 274 TYR cc_start: 0.9301 (m-80) cc_final: 0.8982 (m-80) REVERT: F 322 ASP cc_start: 0.8923 (t70) cc_final: 0.8613 (t70) REVERT: G 21 MET cc_start: 0.8447 (mtm) cc_final: 0.7779 (mpp) REVERT: G 269 ARG cc_start: 0.9468 (tpp80) cc_final: 0.9032 (tpp80) REVERT: G 274 TYR cc_start: 0.8682 (m-80) cc_final: 0.8161 (m-80) REVERT: G 326 LYS cc_start: 0.9481 (tppt) cc_final: 0.9196 (tppt) REVERT: G 341 MET cc_start: 0.7931 (tmm) cc_final: 0.7608 (tmm) REVERT: G 344 HIS cc_start: 0.8718 (m90) cc_final: 0.8350 (m90) REVERT: G 390 MET cc_start: 0.8566 (ptm) cc_final: 0.8134 (ppp) REVERT: G 396 MET cc_start: 0.9153 (mtt) cc_final: 0.8931 (mtt) REVERT: H 33 ASP cc_start: 0.8182 (t0) cc_final: 0.7514 (p0) REVERT: H 36 PHE cc_start: 0.9329 (t80) cc_final: 0.9068 (t80) REVERT: H 210 ASP cc_start: 0.8621 (t0) cc_final: 0.8320 (t0) REVERT: H 244 GLU cc_start: 0.9149 (mm-30) cc_final: 0.8777 (mm-30) REVERT: H 292 ASN cc_start: 0.9426 (t0) cc_final: 0.9113 (t0) REVERT: H 329 GLU cc_start: 0.8673 (tp30) cc_final: 0.8113 (tp30) REVERT: H 416 MET cc_start: 0.7958 (mmm) cc_final: 0.7733 (mmm) REVERT: I 210 ASP cc_start: 0.8696 (t70) cc_final: 0.8385 (t0) REVERT: I 265 ASP cc_start: 0.8792 (t0) cc_final: 0.8552 (t0) REVERT: J 21 MET cc_start: 0.8787 (tmm) cc_final: 0.8311 (tmm) REVERT: J 374 GLN cc_start: 0.8429 (tm-30) cc_final: 0.8197 (tm-30) REVERT: K 147 MET cc_start: 0.9021 (mmm) cc_final: 0.8506 (mmm) REVERT: K 322 ASP cc_start: 0.8714 (t0) cc_final: 0.8458 (t0) REVERT: K 415 MET cc_start: 0.9286 (tmm) cc_final: 0.8768 (tmm) REVERT: K 416 MET cc_start: 0.9018 (ppp) cc_final: 0.8700 (ppp) REVERT: L 29 MET cc_start: 0.8691 (mtp) cc_final: 0.8325 (mtp) REVERT: L 30 ARG cc_start: 0.7012 (tpt170) cc_final: 0.6520 (tpp80) REVERT: L 147 MET cc_start: 0.7864 (tpp) cc_final: 0.7255 (tpp) REVERT: L 189 GLN cc_start: 0.8979 (mt0) cc_final: 0.8054 (tm-30) REVERT: L 197 TYR cc_start: 0.8933 (t80) cc_final: 0.8600 (t80) REVERT: L 234 GLU cc_start: 0.8650 (mt-10) cc_final: 0.7980 (mt-10) REVERT: L 380 MET cc_start: 0.9265 (ppp) cc_final: 0.8990 (ptt) REVERT: L 390 MET cc_start: 0.6573 (pmm) cc_final: 0.5557 (pmm) outliers start: 105 outliers final: 80 residues processed: 500 average time/residue: 0.2141 time to fit residues: 177.5297 Evaluate side-chains 489 residues out of total 4296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 406 time to evaluate : 1.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 GLN Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 398 PHE Chi-restraints excluded: chain B residue 131 ILE Chi-restraints excluded: chain B residue 193 GLN Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 245 MET Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain C residue 4 THR Chi-restraints excluded: chain C residue 168 ILE Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 369 GLU Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain D residue 101 ILE Chi-restraints excluded: chain D residue 191 ILE Chi-restraints excluded: chain D residue 195 ILE Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain D residue 322 ASP Chi-restraints excluded: chain D residue 363 SER Chi-restraints excluded: chain D residue 411 ASP Chi-restraints excluded: chain E residue 31 LYS Chi-restraints excluded: chain E residue 42 HIS Chi-restraints excluded: chain E residue 60 ASP Chi-restraints excluded: chain E residue 110 TYR Chi-restraints excluded: chain E residue 157 LEU Chi-restraints excluded: chain E residue 210 ASP Chi-restraints excluded: chain E residue 294 LEU Chi-restraints excluded: chain E residue 365 THR Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 49 ILE Chi-restraints excluded: chain F residue 140 HIS Chi-restraints excluded: chain F residue 157 LEU Chi-restraints excluded: chain F residue 190 ASN Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 286 THR Chi-restraints excluded: chain F residue 295 HIS Chi-restraints excluded: chain F residue 412 PHE Chi-restraints excluded: chain G residue 77 ASP Chi-restraints excluded: chain G residue 101 ILE Chi-restraints excluded: chain G residue 260 VAL Chi-restraints excluded: chain G residue 275 ASN Chi-restraints excluded: chain G residue 308 GLU Chi-restraints excluded: chain G residue 338 THR Chi-restraints excluded: chain H residue 49 ILE Chi-restraints excluded: chain H residue 131 ILE Chi-restraints excluded: chain H residue 239 HIS Chi-restraints excluded: chain H residue 260 VAL Chi-restraints excluded: chain H residue 286 THR Chi-restraints excluded: chain I residue 39 LEU Chi-restraints excluded: chain I residue 42 HIS Chi-restraints excluded: chain I residue 49 ILE Chi-restraints excluded: chain I residue 101 ILE Chi-restraints excluded: chain I residue 158 THR Chi-restraints excluded: chain I residue 164 LEU Chi-restraints excluded: chain I residue 260 VAL Chi-restraints excluded: chain J residue 4 THR Chi-restraints excluded: chain J residue 9 THR Chi-restraints excluded: chain J residue 84 CYS Chi-restraints excluded: chain J residue 92 ARG Chi-restraints excluded: chain J residue 154 THR Chi-restraints excluded: chain J residue 168 ILE Chi-restraints excluded: chain J residue 186 MET Chi-restraints excluded: chain J residue 188 LEU Chi-restraints excluded: chain J residue 228 VAL Chi-restraints excluded: chain K residue 9 THR Chi-restraints excluded: chain K residue 29 MET Chi-restraints excluded: chain K residue 109 ARG Chi-restraints excluded: chain K residue 284 VAL Chi-restraints excluded: chain K residue 323 THR Chi-restraints excluded: chain L residue 41 GLN Chi-restraints excluded: chain L residue 228 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 76 optimal weight: 6.9990 chunk 289 optimal weight: 1.9990 chunk 211 optimal weight: 30.0000 chunk 456 optimal weight: 20.0000 chunk 99 optimal weight: 3.9990 chunk 277 optimal weight: 0.8980 chunk 184 optimal weight: 2.9990 chunk 320 optimal weight: 1.9990 chunk 79 optimal weight: 0.8980 chunk 226 optimal weight: 8.9990 chunk 54 optimal weight: 0.8980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 198 ASN B 275 ASN ** E 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 388 HIS ** G 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 42 HIS ** K 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.094925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.064688 restraints weight = 142972.100| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 4.18 r_work: 0.2971 rms_B_bonded: 4.57 restraints_weight: 0.5000 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.2663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 40142 Z= 0.121 Angle : 0.576 16.768 54060 Z= 0.282 Chirality : 0.041 0.188 6144 Planarity : 0.003 0.043 7054 Dihedral : 5.126 150.116 5463 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 1.98 % Allowed : 18.06 % Favored : 79.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.26 (0.12), residues: 4992 helix: 0.98 (0.11), residues: 2294 sheet: 0.45 (0.24), residues: 482 loop : 1.02 (0.14), residues: 2216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 30 TYR 0.035 0.001 TYR L 110 PHE 0.016 0.001 PHE G 412 TRP 0.026 0.001 TRP E 381 HIS 0.008 0.001 HIS I 42 Details of bonding type rmsd covalent geometry : bond 0.00276 (40141) covalent geometry : angle 0.57644 (54060) hydrogen bonds : bond 0.03392 ( 1746) hydrogen bonds : angle 4.48444 ( 5106) Misc. bond : bond 0.00064 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9984 Ramachandran restraints generated. 4992 Oldfield, 0 Emsley, 4992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9984 Ramachandran restraints generated. 4992 Oldfield, 0 Emsley, 4992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 508 residues out of total 4296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 423 time to evaluate : 1.276 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: A 29 MET cc_start: 0.7903 (mmp) cc_final: 0.7701 (mpp) REVERT: A 269 ARG cc_start: 0.9487 (mmp80) cc_final: 0.8988 (mmp80) REVERT: A 322 ASP cc_start: 0.9085 (t0) cc_final: 0.8848 (t0) REVERT: A 336 LYS cc_start: 0.8719 (mmmm) cc_final: 0.8497 (mmmm) REVERT: A 341 MET cc_start: 0.8451 (tmm) cc_final: 0.8096 (tmm) REVERT: A 343 LEU cc_start: 0.9258 (OUTLIER) cc_final: 0.8881 (mm) REVERT: B 1 MET cc_start: 0.8739 (tpp) cc_final: 0.8463 (tpp) REVERT: B 59 GLN cc_start: 0.8701 (pm20) cc_final: 0.8434 (pm20) REVERT: B 322 ASP cc_start: 0.8852 (t0) cc_final: 0.8575 (t0) REVERT: B 415 MET cc_start: 0.9315 (tmm) cc_final: 0.9066 (tmm) REVERT: C 1 MET cc_start: 0.8051 (tpp) cc_final: 0.7762 (tpp) REVERT: D 1 MET cc_start: 0.6854 (tpt) cc_final: 0.6453 (tpt) REVERT: D 210 ASP cc_start: 0.8537 (t0) cc_final: 0.8236 (t0) REVERT: D 333 GLU cc_start: 0.8754 (tm-30) cc_final: 0.8535 (tm-30) REVERT: D 334 GLU cc_start: 0.8592 (mm-30) cc_final: 0.8303 (mm-30) REVERT: D 415 MET cc_start: 0.9434 (tmm) cc_final: 0.8979 (ppp) REVERT: E 197 TYR cc_start: 0.9061 (t80) cc_final: 0.8586 (t80) REVERT: E 210 ASP cc_start: 0.7841 (OUTLIER) cc_final: 0.7532 (m-30) REVERT: E 211 GLU cc_start: 0.8277 (mm-30) cc_final: 0.7748 (mm-30) REVERT: E 215 GLU cc_start: 0.8693 (tt0) cc_final: 0.7531 (tt0) REVERT: E 241 GLN cc_start: 0.8467 (tm-30) cc_final: 0.8259 (tm-30) REVERT: E 327 MET cc_start: 0.8495 (ttm) cc_final: 0.8093 (ttm) REVERT: E 380 MET cc_start: 0.9433 (ptt) cc_final: 0.9104 (ptt) REVERT: F 29 MET cc_start: 0.9098 (ptm) cc_final: 0.8789 (ptt) REVERT: F 322 ASP cc_start: 0.8948 (t70) cc_final: 0.8647 (t70) REVERT: G 21 MET cc_start: 0.8532 (mtm) cc_final: 0.8300 (pmm) REVERT: G 269 ARG cc_start: 0.9471 (tpp80) cc_final: 0.9044 (tpp80) REVERT: G 274 TYR cc_start: 0.8676 (m-80) cc_final: 0.8154 (m-80) REVERT: G 326 LYS cc_start: 0.9516 (tppt) cc_final: 0.9234 (tppt) REVERT: G 341 MET cc_start: 0.7825 (tmm) cc_final: 0.7556 (tmm) REVERT: G 344 HIS cc_start: 0.8646 (m90) cc_final: 0.8292 (m90) REVERT: G 390 MET cc_start: 0.8585 (ptm) cc_final: 0.8162 (ppp) REVERT: G 396 MET cc_start: 0.9179 (mtt) cc_final: 0.8951 (mtt) REVERT: H 33 ASP cc_start: 0.8275 (t0) cc_final: 0.7617 (p0) REVERT: H 36 PHE cc_start: 0.9332 (t80) cc_final: 0.9033 (t80) REVERT: H 210 ASP cc_start: 0.8530 (t0) cc_final: 0.8214 (t0) REVERT: H 244 GLU cc_start: 0.9145 (mm-30) cc_final: 0.8778 (mm-30) REVERT: H 292 ASN cc_start: 0.9418 (t0) cc_final: 0.9100 (t0) REVERT: H 329 GLU cc_start: 0.8682 (tp30) cc_final: 0.8120 (tp30) REVERT: H 416 MET cc_start: 0.7996 (mmm) cc_final: 0.7781 (mmm) REVERT: I 210 ASP cc_start: 0.8633 (t70) cc_final: 0.8315 (t0) REVERT: I 265 ASP cc_start: 0.8724 (t0) cc_final: 0.8486 (t0) REVERT: J 21 MET cc_start: 0.8569 (tmm) cc_final: 0.8252 (tmm) REVERT: J 59 GLN cc_start: 0.8664 (pp30) cc_final: 0.8457 (pp30) REVERT: J 374 GLN cc_start: 0.8429 (tm-30) cc_final: 0.8204 (tm-30) REVERT: K 1 MET cc_start: 0.7605 (tpp) cc_final: 0.7383 (tpp) REVERT: K 147 MET cc_start: 0.9025 (mmm) cc_final: 0.8483 (mmm) REVERT: K 214 GLU cc_start: 0.8748 (OUTLIER) cc_final: 0.8479 (pm20) REVERT: K 322 ASP cc_start: 0.8813 (t0) cc_final: 0.8552 (t0) REVERT: K 415 MET cc_start: 0.9270 (tmm) cc_final: 0.8751 (tmm) REVERT: K 416 MET cc_start: 0.9064 (ppp) cc_final: 0.8742 (ppp) REVERT: L 29 MET cc_start: 0.8550 (mtp) cc_final: 0.8205 (mtp) REVERT: L 30 ARG cc_start: 0.6964 (tpt170) cc_final: 0.6543 (tpp80) REVERT: L 73 LEU cc_start: 0.9245 (tp) cc_final: 0.8849 (pp) REVERT: L 147 MET cc_start: 0.7769 (tpp) cc_final: 0.7150 (tpp) REVERT: L 189 GLN cc_start: 0.8975 (mt0) cc_final: 0.8053 (tm-30) REVERT: L 197 TYR cc_start: 0.8957 (t80) cc_final: 0.8634 (t80) REVERT: L 380 MET cc_start: 0.9240 (ppp) cc_final: 0.8948 (ptt) REVERT: L 390 MET cc_start: 0.6721 (pmm) cc_final: 0.5761 (pmm) outliers start: 85 outliers final: 68 residues processed: 490 average time/residue: 0.1957 time to fit residues: 158.2343 Evaluate side-chains 483 residues out of total 4296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 412 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 GLN Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 398 PHE Chi-restraints excluded: chain B residue 131 ILE Chi-restraints excluded: chain B residue 193 GLN Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 245 MET Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain C residue 4 THR Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 369 GLU Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain D residue 101 ILE Chi-restraints excluded: chain D residue 191 ILE Chi-restraints excluded: chain D residue 195 ILE Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain D residue 322 ASP Chi-restraints excluded: chain D residue 363 SER Chi-restraints excluded: chain E residue 31 LYS Chi-restraints excluded: chain E residue 42 HIS Chi-restraints excluded: chain E residue 60 ASP Chi-restraints excluded: chain E residue 110 TYR Chi-restraints excluded: chain E residue 157 LEU Chi-restraints excluded: chain E residue 210 ASP Chi-restraints excluded: chain E residue 294 LEU Chi-restraints excluded: chain E residue 365 THR Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 49 ILE Chi-restraints excluded: chain F residue 140 HIS Chi-restraints excluded: chain F residue 157 LEU Chi-restraints excluded: chain F residue 190 ASN Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 286 THR Chi-restraints excluded: chain F residue 295 HIS Chi-restraints excluded: chain F residue 412 PHE Chi-restraints excluded: chain G residue 77 ASP Chi-restraints excluded: chain G residue 101 ILE Chi-restraints excluded: chain G residue 275 ASN Chi-restraints excluded: chain G residue 308 GLU Chi-restraints excluded: chain G residue 338 THR Chi-restraints excluded: chain H residue 49 ILE Chi-restraints excluded: chain H residue 131 ILE Chi-restraints excluded: chain H residue 239 HIS Chi-restraints excluded: chain H residue 260 VAL Chi-restraints excluded: chain H residue 286 THR Chi-restraints excluded: chain I residue 42 HIS Chi-restraints excluded: chain I residue 49 ILE Chi-restraints excluded: chain I residue 101 ILE Chi-restraints excluded: chain I residue 158 THR Chi-restraints excluded: chain I residue 164 LEU Chi-restraints excluded: chain I residue 260 VAL Chi-restraints excluded: chain J residue 4 THR Chi-restraints excluded: chain J residue 9 THR Chi-restraints excluded: chain J residue 92 ARG Chi-restraints excluded: chain J residue 154 THR Chi-restraints excluded: chain J residue 168 ILE Chi-restraints excluded: chain J residue 186 MET Chi-restraints excluded: chain J residue 188 LEU Chi-restraints excluded: chain J residue 228 VAL Chi-restraints excluded: chain K residue 9 THR Chi-restraints excluded: chain K residue 109 ARG Chi-restraints excluded: chain K residue 214 GLU Chi-restraints excluded: chain K residue 284 VAL Chi-restraints excluded: chain K residue 323 THR Chi-restraints excluded: chain L residue 228 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 335 optimal weight: 0.8980 chunk 424 optimal weight: 5.9990 chunk 161 optimal weight: 1.9990 chunk 346 optimal weight: 0.9990 chunk 57 optimal weight: 7.9990 chunk 62 optimal weight: 1.9990 chunk 277 optimal weight: 9.9990 chunk 457 optimal weight: 0.9980 chunk 13 optimal weight: 7.9990 chunk 473 optimal weight: 5.9990 chunk 399 optimal weight: 0.6980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 378 GLN ** E 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 189 GLN E 193 GLN ** F 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 388 HIS G 41 GLN G 42 HIS ** H 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 42 HIS ** I 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 189 GLN ** K 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.095144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.065148 restraints weight = 142080.338| |-----------------------------------------------------------------------------| r_work (start): 0.3145 rms_B_bonded: 4.11 r_work: 0.2976 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.2738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 40142 Z= 0.117 Angle : 0.596 15.227 54060 Z= 0.289 Chirality : 0.042 0.270 6144 Planarity : 0.003 0.042 7054 Dihedral : 5.134 151.530 5463 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 1.82 % Allowed : 18.41 % Favored : 79.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.27 (0.12), residues: 4992 helix: 0.97 (0.11), residues: 2294 sheet: 0.51 (0.24), residues: 482 loop : 1.04 (0.14), residues: 2216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 30 TYR 0.028 0.001 TYR L 110 PHE 0.016 0.001 PHE G 412 TRP 0.032 0.001 TRP E 381 HIS 0.018 0.001 HIS I 42 Details of bonding type rmsd covalent geometry : bond 0.00269 (40141) covalent geometry : angle 0.59616 (54060) hydrogen bonds : bond 0.03337 ( 1746) hydrogen bonds : angle 4.43884 ( 5106) Misc. bond : bond 0.00059 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9984 Ramachandran restraints generated. 4992 Oldfield, 0 Emsley, 4992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9984 Ramachandran restraints generated. 4992 Oldfield, 0 Emsley, 4992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 495 residues out of total 4296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 417 time to evaluate : 1.483 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: A 269 ARG cc_start: 0.9488 (mmp80) cc_final: 0.8995 (mmp80) REVERT: A 322 ASP cc_start: 0.9096 (t0) cc_final: 0.8869 (t0) REVERT: A 336 LYS cc_start: 0.8711 (mmmm) cc_final: 0.8476 (mmmm) REVERT: A 341 MET cc_start: 0.8418 (tmm) cc_final: 0.8059 (tmm) REVERT: A 343 LEU cc_start: 0.9241 (OUTLIER) cc_final: 0.8839 (mm) REVERT: A 396 MET cc_start: 0.9380 (tpt) cc_final: 0.9163 (ttm) REVERT: B 1 MET cc_start: 0.8736 (tpp) cc_final: 0.8441 (tpp) REVERT: B 21 MET cc_start: 0.8455 (mmm) cc_final: 0.8142 (mmp) REVERT: B 59 GLN cc_start: 0.8710 (pm20) cc_final: 0.8446 (pm20) REVERT: B 322 ASP cc_start: 0.8848 (t0) cc_final: 0.8566 (t0) REVERT: B 333 GLU cc_start: 0.9282 (mm-30) cc_final: 0.9037 (mm-30) REVERT: B 415 MET cc_start: 0.9364 (tmm) cc_final: 0.9123 (tmm) REVERT: C 1 MET cc_start: 0.8043 (tpp) cc_final: 0.7764 (tpp) REVERT: C 21 MET cc_start: 0.7757 (mmp) cc_final: 0.7043 (ptp) REVERT: D 1 MET cc_start: 0.6906 (tpt) cc_final: 0.6502 (tpt) REVERT: D 210 ASP cc_start: 0.8562 (t0) cc_final: 0.8265 (t0) REVERT: D 415 MET cc_start: 0.9461 (tmm) cc_final: 0.9003 (ppp) REVERT: E 197 TYR cc_start: 0.9092 (t80) cc_final: 0.8600 (t80) REVERT: E 210 ASP cc_start: 0.7852 (OUTLIER) cc_final: 0.7530 (m-30) REVERT: E 211 GLU cc_start: 0.8309 (mm-30) cc_final: 0.7776 (mm-30) REVERT: E 215 GLU cc_start: 0.8680 (tt0) cc_final: 0.7473 (tt0) REVERT: E 241 GLN cc_start: 0.8451 (tm-30) cc_final: 0.8249 (tm-30) REVERT: E 327 MET cc_start: 0.8432 (ttm) cc_final: 0.8034 (ttm) REVERT: E 380 MET cc_start: 0.9435 (ptt) cc_final: 0.9184 (ptt) REVERT: F 29 MET cc_start: 0.9074 (ptm) cc_final: 0.8756 (ptt) REVERT: F 274 TYR cc_start: 0.9311 (m-80) cc_final: 0.9087 (m-80) REVERT: F 322 ASP cc_start: 0.8967 (t70) cc_final: 0.8671 (t70) REVERT: G 269 ARG cc_start: 0.9463 (tpp80) cc_final: 0.9030 (tpp80) REVERT: G 274 TYR cc_start: 0.8624 (m-80) cc_final: 0.8122 (m-80) REVERT: G 326 LYS cc_start: 0.9504 (tppt) cc_final: 0.9232 (tppt) REVERT: G 341 MET cc_start: 0.7834 (tmm) cc_final: 0.7515 (tmm) REVERT: G 344 HIS cc_start: 0.8627 (m90) cc_final: 0.8275 (m90) REVERT: G 390 MET cc_start: 0.8648 (ptm) cc_final: 0.8220 (ppp) REVERT: G 396 MET cc_start: 0.9179 (mtt) cc_final: 0.8944 (mtt) REVERT: H 33 ASP cc_start: 0.8256 (t0) cc_final: 0.7594 (p0) REVERT: H 36 PHE cc_start: 0.9316 (t80) cc_final: 0.9028 (t80) REVERT: H 210 ASP cc_start: 0.8575 (t0) cc_final: 0.8239 (t0) REVERT: H 244 GLU cc_start: 0.9141 (mm-30) cc_final: 0.8770 (mm-30) REVERT: H 292 ASN cc_start: 0.9411 (t0) cc_final: 0.9082 (t0) REVERT: H 329 GLU cc_start: 0.8703 (tp30) cc_final: 0.8128 (tp30) REVERT: H 374 GLN cc_start: 0.8937 (pm20) cc_final: 0.8641 (pp30) REVERT: H 416 MET cc_start: 0.8054 (mmm) cc_final: 0.7839 (mmm) REVERT: I 210 ASP cc_start: 0.8705 (t70) cc_final: 0.8269 (t0) REVERT: I 265 ASP cc_start: 0.8759 (t0) cc_final: 0.8516 (t0) REVERT: J 21 MET cc_start: 0.8635 (tmm) cc_final: 0.8304 (tmm) REVERT: J 374 GLN cc_start: 0.8415 (tm-30) cc_final: 0.8190 (tm-30) REVERT: K 1 MET cc_start: 0.7582 (tpp) cc_final: 0.7355 (tpp) REVERT: K 147 MET cc_start: 0.9042 (mmm) cc_final: 0.8491 (mmm) REVERT: K 214 GLU cc_start: 0.8792 (OUTLIER) cc_final: 0.8513 (pm20) REVERT: K 322 ASP cc_start: 0.8829 (t0) cc_final: 0.8574 (t0) REVERT: K 415 MET cc_start: 0.9213 (tmm) cc_final: 0.8735 (tmm) REVERT: K 416 MET cc_start: 0.9037 (ppp) cc_final: 0.8753 (ppp) REVERT: L 29 MET cc_start: 0.8569 (mtp) cc_final: 0.8226 (mtp) REVERT: L 30 ARG cc_start: 0.6912 (tpt170) cc_final: 0.6504 (tpp80) REVERT: L 73 LEU cc_start: 0.9228 (tp) cc_final: 0.8820 (pp) REVERT: L 147 MET cc_start: 0.7747 (tpp) cc_final: 0.7133 (tpp) REVERT: L 189 GLN cc_start: 0.8968 (mt0) cc_final: 0.8040 (tm-30) REVERT: L 197 TYR cc_start: 0.8964 (t80) cc_final: 0.8643 (t80) REVERT: L 380 MET cc_start: 0.9243 (ppp) cc_final: 0.8955 (ptt) REVERT: L 390 MET cc_start: 0.6686 (pmm) cc_final: 0.5728 (pmm) outliers start: 78 outliers final: 70 residues processed: 477 average time/residue: 0.1952 time to fit residues: 153.5582 Evaluate side-chains 482 residues out of total 4296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 409 time to evaluate : 1.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 GLN Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 398 PHE Chi-restraints excluded: chain B residue 131 ILE Chi-restraints excluded: chain B residue 168 ILE Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 245 MET Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain C residue 4 THR Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 369 GLU Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain D residue 101 ILE Chi-restraints excluded: chain D residue 191 ILE Chi-restraints excluded: chain D residue 195 ILE Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain D residue 322 ASP Chi-restraints excluded: chain D residue 363 SER Chi-restraints excluded: chain E residue 31 LYS Chi-restraints excluded: chain E residue 42 HIS Chi-restraints excluded: chain E residue 110 TYR Chi-restraints excluded: chain E residue 157 LEU Chi-restraints excluded: chain E residue 210 ASP Chi-restraints excluded: chain E residue 294 LEU Chi-restraints excluded: chain E residue 365 THR Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 49 ILE Chi-restraints excluded: chain F residue 140 HIS Chi-restraints excluded: chain F residue 157 LEU Chi-restraints excluded: chain F residue 190 ASN Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 286 THR Chi-restraints excluded: chain F residue 295 HIS Chi-restraints excluded: chain F residue 412 PHE Chi-restraints excluded: chain G residue 41 GLN Chi-restraints excluded: chain G residue 77 ASP Chi-restraints excluded: chain G residue 101 ILE Chi-restraints excluded: chain G residue 275 ASN Chi-restraints excluded: chain G residue 308 GLU Chi-restraints excluded: chain G residue 338 THR Chi-restraints excluded: chain H residue 49 ILE Chi-restraints excluded: chain H residue 131 ILE Chi-restraints excluded: chain H residue 239 HIS Chi-restraints excluded: chain H residue 260 VAL Chi-restraints excluded: chain H residue 286 THR Chi-restraints excluded: chain I residue 39 LEU Chi-restraints excluded: chain I residue 42 HIS Chi-restraints excluded: chain I residue 49 ILE Chi-restraints excluded: chain I residue 101 ILE Chi-restraints excluded: chain I residue 158 THR Chi-restraints excluded: chain I residue 164 LEU Chi-restraints excluded: chain I residue 260 VAL Chi-restraints excluded: chain J residue 4 THR Chi-restraints excluded: chain J residue 9 THR Chi-restraints excluded: chain J residue 92 ARG Chi-restraints excluded: chain J residue 154 THR Chi-restraints excluded: chain J residue 168 ILE Chi-restraints excluded: chain J residue 186 MET Chi-restraints excluded: chain J residue 188 LEU Chi-restraints excluded: chain J residue 228 VAL Chi-restraints excluded: chain K residue 9 THR Chi-restraints excluded: chain K residue 109 ARG Chi-restraints excluded: chain K residue 214 GLU Chi-restraints excluded: chain K residue 284 VAL Chi-restraints excluded: chain L residue 228 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 204 optimal weight: 5.9990 chunk 381 optimal weight: 2.9990 chunk 81 optimal weight: 9.9990 chunk 68 optimal weight: 0.2980 chunk 230 optimal weight: 20.0000 chunk 169 optimal weight: 7.9990 chunk 31 optimal weight: 9.9990 chunk 351 optimal weight: 4.9990 chunk 150 optimal weight: 2.9990 chunk 355 optimal weight: 2.9990 chunk 376 optimal weight: 6.9990 overall best weight: 2.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 193 GLN ** E 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 193 GLN ** F 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 388 HIS ** H 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 42 HIS ** I 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 189 GLN K 2 ASN ** K 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.094193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.063859 restraints weight = 142605.386| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 4.15 r_work: 0.2943 rms_B_bonded: 4.62 restraints_weight: 0.5000 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 moved from start: 0.2767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 40142 Z= 0.182 Angle : 0.613 14.928 54060 Z= 0.301 Chirality : 0.042 0.250 6144 Planarity : 0.003 0.041 7054 Dihedral : 5.172 151.511 5463 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.96 % Allowed : 18.48 % Favored : 79.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.24 (0.12), residues: 4992 helix: 0.93 (0.11), residues: 2304 sheet: 0.44 (0.24), residues: 482 loop : 1.04 (0.14), residues: 2206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 30 TYR 0.026 0.001 TYR L 110 PHE 0.011 0.001 PHE G 412 TRP 0.030 0.002 TRP E 381 HIS 0.007 0.001 HIS I 42 Details of bonding type rmsd covalent geometry : bond 0.00411 (40141) covalent geometry : angle 0.61262 (54060) hydrogen bonds : bond 0.03522 ( 1746) hydrogen bonds : angle 4.54543 ( 5106) Misc. bond : bond 0.00075 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10355.25 seconds wall clock time: 177 minutes 43.88 seconds (10663.88 seconds total)